[1] "ofn"        "-oTCOAD-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/COAD-TP/22506513/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/22596984/transformed.cor.cli.txt"

nPatients in clinical file=458, in cluster file=367, common to both=367
[1] "Reduce the number of clustering variables from 1913 to 1907."
[1] 1907  367
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          295            72 
  APC MUTATED APC WILD-TYPE 
          295            72 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           232            135 
  TP53 MUTATED TP53 WILD-TYPE 
           232            135 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              72              295 
  ARID1A MUTATED ARID1A WILD-TYPE 
              72              295 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             46             321 
  RNF43 MUTATED RNF43 WILD-TYPE 
             46             321 
[1] "SOX9 MUTATION ANALYSIS"
[1] 3
  SOX9 MUTATED SOX9 WILD-TYPE 
            36            331 
  SOX9 MUTATED SOX9 WILD-TYPE 
            36            331 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               50               317 
  FAM123B MUTATED FAM123B WILD-TYPE 
               50               317 
[1] "TXNDC2 MUTATION ANALYSIS"
[1] 3
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              22              345 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              22              345 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              26              341 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              26              341 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           15           352 
  B2M MUTATED B2M WILD-TYPE 
           15           352 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            27            340 
  BCOR MUTATED BCOR WILD-TYPE 
            27            340 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            74            293 
  CDH1 MUTATED CDH1 WILD-TYPE 
            74            293 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
            53            314 
  MLH1 MUTATED MLH1 WILD-TYPE 
            53            314 
[1] "NTAN1 MUTATION ANALYSIS"
[1] 3
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             357 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             357 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               14               353 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               14               353 
[1] "WNT1 MUTATION ANALYSIS"
[1] 3
  WNT1 MUTATED WNT1 WILD-TYPE 
             7            360 
  WNT1 MUTATED WNT1 WILD-TYPE 
             7            360 
[1] "BMPR2 MUTATION ANALYSIS"
[1] 3
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             35             332 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             35             332 
[1] "SELPLG MUTATION ANALYSIS"
[1] 3
  SELPLG MUTATED SELPLG WILD-TYPE 
              16              351 
  SELPLG MUTATED SELPLG WILD-TYPE 
              16              351 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              18              349 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              18              349 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             27             340 
  KDM6A MUTATED KDM6A WILD-TYPE 
             27             340 
[1] "MAPK6 MUTATION ANALYSIS"
[1] 3
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             18             349 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             18             349 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            12            355 
  RHOA MUTATED RHOA WILD-TYPE 
            12            355 
[1] "FMN2 MUTATION ANALYSIS"
[1] 3
  FMN2 MUTATED FMN2 WILD-TYPE 
            49            318 
  FMN2 MUTATED FMN2 WILD-TYPE 
            49            318 
[1] "STARD3NL MUTATION ANALYSIS"
[1] 3
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                13                354 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                13                354 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           62           305 
  NF2 MUTATED NF2 WILD-TYPE 
           62           305 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           89           278 
  NF1 MUTATED NF1 WILD-TYPE 
           89           278 
[1] "OR4D10 MUTATION ANALYSIS"
[1] 3
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              14              353 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              14              353 
[1] "PRKDC MUTATION ANALYSIS"
[1] 3
  PRKDC MUTATED PRKDC WILD-TYPE 
             63             304 
  PRKDC MUTATED PRKDC WILD-TYPE 
             63             304 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           37           330 
  MGA MUTATED MGA WILD-TYPE 
           37           330 
[1] "P2RY13 MUTATION ANALYSIS"
[1] 3
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              15              352 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              15              352 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
           14           353 
  MVK MUTATED MVK WILD-TYPE 
           14           353 
[1] "ATXN3L MUTATION ANALYSIS"
[1] 3
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              17              350 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              17              350 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            103             264 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            103             264 
[1] "DIP2B MUTATION ANALYSIS"
[1] 3
  DIP2B MUTATED DIP2B WILD-TYPE 
             27             340 
  DIP2B MUTATED DIP2B WILD-TYPE 
             27             340 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            18            349 
  RBMX MUTATED RBMX WILD-TYPE 
            18            349 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             16             351 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             16             351 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             40             327 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             40             327 
[1] "ALG12 MUTATION ANALYSIS"
[1] 3
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             360 
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             360 
[1] "NR1H3 MUTATION ANALYSIS"
[1] 3
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             15             352 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             15             352 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              20              347 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              20              347 
[1] "MPHOSPH10 MUTATION ANALYSIS"
[1] 3
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 18                 349 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 18                 349 
[1] "TPRKB MUTATION ANALYSIS"
[1] 3
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             357 
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             357 
[1] "PLAGL2 MUTATION ANALYSIS"
[1] 3
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              361 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              361 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            349 
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            349 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             41             326 
  SETD2 MUTATED SETD2 WILD-TYPE 
             41             326 
[1] "GPATCH8 MUTATION ANALYSIS"
[1] 3
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               353 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               353 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             42             325 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             42             325 
[1] "C11ORF30 MUTATION ANALYSIS"
[1] 3
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                21                346 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                21                346 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            13            354 
  RPTN MUTATED RPTN WILD-TYPE 
            13            354 
[1] "ROS1 MUTATION ANALYSIS"
[1] 3
  ROS1 MUTATED ROS1 WILD-TYPE 
            47            320 
  ROS1 MUTATED ROS1 WILD-TYPE 
            47            320 
[1] "EGR1 MUTATION ANALYSIS"
[1] 3
  EGR1 MUTATED EGR1 WILD-TYPE 
             9            358 
  EGR1 MUTATED EGR1 WILD-TYPE 
             9            358 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
           153            214 
  PTEN MUTATED PTEN WILD-TYPE 
           153            214 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              293 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              293 
[1] "RBM44 MUTATION ANALYSIS"
[1] 3
  RBM44 MUTATED RBM44 WILD-TYPE 
             13             354 
  RBM44 MUTATED RBM44 WILD-TYPE 
             13             354 
[1] "ECT2 MUTATION ANALYSIS"
[1] 3
  ECT2 MUTATED ECT2 WILD-TYPE 
            18            349 
  ECT2 MUTATED ECT2 WILD-TYPE 
            18            349 
[1] "DDX26B MUTATION ANALYSIS"
[1] 3
  DDX26B MUTATED DDX26B WILD-TYPE 
              15              352 
  DDX26B MUTATED DDX26B WILD-TYPE 
              15              352 
[1] "UBQLN2 MUTATION ANALYSIS"
[1] 3
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              10              357 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              10              357 
[1] "THOC7 MUTATION ANALYSIS"
[1] 3
  THOC7 MUTATED THOC7 WILD-TYPE 
             10             357 
  THOC7 MUTATED THOC7 WILD-TYPE 
             10             357 
[1] "TOP2B MUTATION ANALYSIS"
[1] 3
  TOP2B MUTATED TOP2B WILD-TYPE 
             23             344 
  TOP2B MUTATED TOP2B WILD-TYPE 
             23             344 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           88           279 
  RB1 MUTATED RB1 WILD-TYPE 
           88           279 
[1] "ALDH1A3 MUTATION ANALYSIS"
[1] 3
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               18               349 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               18               349 
[1] "GMPS MUTATION ANALYSIS"
[1] 3
  GMPS MUTATED GMPS WILD-TYPE 
            17            350 
  GMPS MUTATED GMPS WILD-TYPE 
            17            350 
[1] "KIAA1586 MUTATION ANALYSIS"
[1] 3
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                11                356 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                11                356 
[1] "L1TD1 MUTATION ANALYSIS"
[1] 3
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             17             350 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             17             350 
[1] "NLRC4 MUTATION ANALYSIS"
[1] 3
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             24             343 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             24             343 
[1] "ZDHHC7 MUTATION ANALYSIS"
[1] 3
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              12              355 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              12              355 
[1] "DCLK2 MUTATION ANALYSIS"
[1] 3
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             14             353 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             14             353 
[1] "C2ORF29 MUTATION ANALYSIS"
[1] 3
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               17               350 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               17               350 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             89             278 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             89             278 
[1] "LINGO4 MUTATION ANALYSIS"
[1] 3
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              357 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              357 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              43              324 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              43              324 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                18                349 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                18                349 
[1] "C14ORF184 MUTATION ANALYSIS"
[1] 3
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  6                 361 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  6                 361 
[1] "ATP6V1B1 MUTATION ANALYSIS"
[1] 3
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                14                353 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                14                353 
[1] "BCL9 MUTATION ANALYSIS"
[1] 3
  BCL9 MUTATED BCL9 WILD-TYPE 
            22            345 
  BCL9 MUTATED BCL9 WILD-TYPE 
            22            345 
[1] "NAA25 MUTATION ANALYSIS"
[1] 3
  NAA25 MUTATED NAA25 WILD-TYPE 
             14             353 
  NAA25 MUTATED NAA25 WILD-TYPE 
             14             353 
[1] "SLC26A8 MUTATION ANALYSIS"
[1] 3
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               16               351 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               16               351 
[1] "IQCD MUTATION ANALYSIS"
[1] 3
  IQCD MUTATED IQCD WILD-TYPE 
            10            357 
  IQCD MUTATED IQCD WILD-TYPE 
            10            357 
[1] "CHD3 MUTATION ANALYSIS"
[1] 3
  CHD3 MUTATED CHD3 WILD-TYPE 
            24            343 
  CHD3 MUTATED CHD3 WILD-TYPE 
            24            343 
[1] "PLEKHF2 MUTATION ANALYSIS"
[1] 3
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               10               357 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               10               357 
[1] "FKBP9 MUTATION ANALYSIS"
[1] 3
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             17             350 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             17             350 
[1] "HPS3 MUTATION ANALYSIS"
[1] 3
  HPS3 MUTATED HPS3 WILD-TYPE 
            20            347 
  HPS3 MUTATED HPS3 WILD-TYPE 
            20            347 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
          132           235 
  ATM MUTATED ATM WILD-TYPE 
          132           235 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
            14            353 
  RLIM MUTATED RLIM WILD-TYPE 
            14            353 
[1] "CYLD MUTATION ANALYSIS"
[1] 3
  CYLD MUTATED CYLD WILD-TYPE 
            22            345 
  CYLD MUTATED CYLD WILD-TYPE 
            22            345 
[1] "GGT1 MUTATION ANALYSIS"
[1] 3
  GGT1 MUTATED GGT1 WILD-TYPE 
             8            359 
  GGT1 MUTATED GGT1 WILD-TYPE 
             8            359 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               15               352 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               15               352 
[1] "ATG5 MUTATION ANALYSIS"
[1] 3
  ATG5 MUTATED ATG5 WILD-TYPE 
             8            359 
  ATG5 MUTATED ATG5 WILD-TYPE 
             8            359 
[1] "MAP4K3 MUTATION ANALYSIS"
[1] 3
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              17              350 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              17              350 
[1] "PRPS1 MUTATION ANALYSIS"
[1] 3
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              8             359 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              8             359 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             17             350 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             17             350 
[1] "PTGDR MUTATION ANALYSIS"
[1] 3
  PTGDR MUTATED PTGDR WILD-TYPE 
              7             360 
  PTGDR MUTATED PTGDR WILD-TYPE 
              7             360 
[1] "BCORL1 MUTATION ANALYSIS"
[1] 3
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              25              342 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              25              342 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            17            350 
  IDH2 MUTATED IDH2 WILD-TYPE 
            17            350 
[1] "TMEM126A MUTATION ANALYSIS"
[1] 3
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                360 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                360 
[1] "GRB2 MUTATION ANALYSIS"
[1] 3
  GRB2 MUTATED GRB2 WILD-TYPE 
             9            358 
  GRB2 MUTATED GRB2 WILD-TYPE 
             9            358 
[1] "PLXNA3 MUTATION ANALYSIS"
[1] 3
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              17              350 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              17              350 
[1] "C15ORF52 MUTATION ANALYSIS"
[1] 3
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                355 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                355 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             10             357 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             10             357 
[1] "SLK MUTATION ANALYSIS"
[1] 3
  SLK MUTATED SLK WILD-TYPE 
           23           344 
  SLK MUTATED SLK WILD-TYPE 
           23           344 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            119             248 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            119             248 
[1] "XYLT2 MUTATION ANALYSIS"
[1] 3
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             353 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             353 
[1] "FAHD2B MUTATION ANALYSIS"
[1] 3
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               6              361 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               6              361 
[1] "RSPH3 MUTATION ANALYSIS"
[1] 3
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             10             357 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             10             357 
[1] "PKD2L1 MUTATION ANALYSIS"
[1] 3
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              23              344 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              23              344 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
             29             338 
  CDK12 MUTATED CDK12 WILD-TYPE 
             29             338 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             350 
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             350 
[1] "KCNK1 MUTATION ANALYSIS"
[1] 3
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             10             357 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             10             357 
[1] "PTK2 MUTATION ANALYSIS"
[1] 3
  PTK2 MUTATED PTK2 WILD-TYPE 
            21            346 
  PTK2 MUTATED PTK2 WILD-TYPE 
            21            346 
[1] "FYN MUTATION ANALYSIS"
[1] 3
  FYN MUTATED FYN WILD-TYPE 
           15           352 
  FYN MUTATED FYN WILD-TYPE 
           15           352 
[1] "CDX2 MUTATION ANALYSIS"
[1] 3
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            361 
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            361 
[1] "KLK10 MUTATION ANALYSIS"
[1] 3
  KLK10 MUTATED KLK10 WILD-TYPE 
              7             360 
  KLK10 MUTATED KLK10 WILD-TYPE 
              7             360 
[1] "TPM4 MUTATION ANALYSIS"
[1] 3
  TPM4 MUTATED TPM4 WILD-TYPE 
             8            359 
  TPM4 MUTATED TPM4 WILD-TYPE 
             8            359 
[1] "UQCRC2 MUTATION ANALYSIS"
[1] 3
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               8              359 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               8              359 
[1] "PIK3IP1 MUTATION ANALYSIS"
[1] 3
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                8               359 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                8               359 
[1] "USP24 MUTATION ANALYSIS"
[1] 3
  USP24 MUTATED USP24 WILD-TYPE 
             30             337 
  USP24 MUTATED USP24 WILD-TYPE 
             30             337 
[1] "OR5V1 MUTATION ANALYSIS"
[1] 3
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             14             353 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             14             353 
[1] "GGTLC2 MUTATION ANALYSIS"
[1] 3
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               7              360 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               7              360 
[1] "ZFYVE26 MUTATION ANALYSIS"
[1] 3
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               28               339 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               28               339 
[1] "MLLT6 MUTATION ANALYSIS"
[1] 3
  MLLT6 MUTATED MLLT6 WILD-TYPE 
             16             351 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
             16             351 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              353 
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              353 
[1] "TNMD MUTATION ANALYSIS"
[1] 3
  TNMD MUTATED TNMD WILD-TYPE 
            11            356 
  TNMD MUTATED TNMD WILD-TYPE 
            11            356 
[1] "GPR174 MUTATION ANALYSIS"
[1] 3
  GPR174 MUTATED GPR174 WILD-TYPE 
               8              359 
  GPR174 MUTATED GPR174 WILD-TYPE 
               8              359 
[1] "CD58 MUTATION ANALYSIS"
[1] 3
  CD58 MUTATED CD58 WILD-TYPE 
            14            353 
  CD58 MUTATED CD58 WILD-TYPE 
            14            353 
[1] "HTR2A MUTATION ANALYSIS"
[1] 3
  HTR2A MUTATED HTR2A WILD-TYPE 
             19             348 
  HTR2A MUTATED HTR2A WILD-TYPE 
             19             348 
[1] "EHBP1 MUTATION ANALYSIS"
[1] 3
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             22             345 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             22             345 
[1] "ZNF583 MUTATION ANALYSIS"
[1] 3
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              15              352 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              15              352 
[1] "ATP11B MUTATION ANALYSIS"
[1] 3
  ATP11B MUTATED ATP11B WILD-TYPE 
              17              350 
  ATP11B MUTATED ATP11B WILD-TYPE 
              17              350 
[1] "NCAPD2 MUTATION ANALYSIS"
[1] 3
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              20              347 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              20              347 
[1] "FNDC7 MUTATION ANALYSIS"
[1] 3
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             358 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             358 
[1] "SVIL MUTATION ANALYSIS"
[1] 3
  SVIL MUTATED SVIL WILD-TYPE 
            32            335 
  SVIL MUTATED SVIL WILD-TYPE 
            32            335 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              29              338 
  LARP4B MUTATED LARP4B WILD-TYPE 
              29              338 
[1] "THOC5 MUTATION ANALYSIS"
[1] 3
  THOC5 MUTATED THOC5 WILD-TYPE 
             14             353 
  THOC5 MUTATED THOC5 WILD-TYPE 
             14             353 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              26              341 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              26              341 
[1] "DNAH12 MUTATION ANALYSIS"
[1] 3
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              23              344 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              23              344 
[1] "ARFGEF1 MUTATION ANALYSIS"
[1] 3
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               34               333 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               34               333 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                361 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                361 
[1] "SENP6 MUTATION ANALYSIS"
[1] 3
  SENP6 MUTATED SENP6 WILD-TYPE 
             15             352 
  SENP6 MUTATED SENP6 WILD-TYPE 
             15             352 
[1] "WDR78 MUTATION ANALYSIS"
[1] 3
  WDR78 MUTATED WDR78 WILD-TYPE 
             12             355 
  WDR78 MUTATED WDR78 WILD-TYPE 
             12             355 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
               9              358 
  CAB39L MUTATED CAB39L WILD-TYPE 
               9              358 
[1] "WEE1 MUTATION ANALYSIS"
[1] 3
  WEE1 MUTATED WEE1 WILD-TYPE 
            12            355 
  WEE1 MUTATED WEE1 WILD-TYPE 
            12            355 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
           13           354 
  ZFX MUTATED ZFX WILD-TYPE 
           13           354 
[1] "ASNSD1 MUTATION ANALYSIS"
[1] 3
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               9              358 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               9              358 
[1] "KLC4 MUTATION ANALYSIS"
[1] 3
  KLC4 MUTATED KLC4 WILD-TYPE 
            16            351 
  KLC4 MUTATED KLC4 WILD-TYPE 
            16            351 
[1] "GLI1 MUTATION ANALYSIS"
[1] 3
  GLI1 MUTATED GLI1 WILD-TYPE 
            18            349 
  GLI1 MUTATED GLI1 WILD-TYPE 
            18            349 
[1] "CRY1 MUTATION ANALYSIS"
[1] 3
  CRY1 MUTATED CRY1 WILD-TYPE 
            13            354 
  CRY1 MUTATED CRY1 WILD-TYPE 
            13            354 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             22             345 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             22             345 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              49              318 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              49              318 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             17             350 
  HLA-A MUTATED HLA-A WILD-TYPE 
             17             350 
[1] "SCAI MUTATION ANALYSIS"
[1] 3
  SCAI MUTATED SCAI WILD-TYPE 
            14            353 
  SCAI MUTATED SCAI WILD-TYPE 
            14            353 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
            24            343 
  MEN1 MUTATED MEN1 WILD-TYPE 
            24            343 
[1] "FAM179A MUTATION ANALYSIS"
[1] 3
  FAM179A MUTATED FAM179A WILD-TYPE 
               27               340 
  FAM179A MUTATED FAM179A WILD-TYPE 
               27               340 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            52            315 
  MLL2 MUTATED MLL2 WILD-TYPE 
            52            315 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             45             322 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             45             322 
[1] "SLC4A10 MUTATION ANALYSIS"
[1] 3
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               27               340 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               27               340 
[1] "RAF1 MUTATION ANALYSIS"
[1] 3
  RAF1 MUTATED RAF1 WILD-TYPE 
            13            354 
  RAF1 MUTATED RAF1 WILD-TYPE 
            13            354 
[1] "KIAA1012 MUTATION ANALYSIS"
[1] 3
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                23                344 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                23                344 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             11             356 
  FAM9A MUTATED FAM9A WILD-TYPE 
             11             356 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
          35          332 
  F8 MUTATED F8 WILD-TYPE 
          35          332 
[1] "TUBE1 MUTATION ANALYSIS"
[1] 3
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             11             356 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             11             356 
[1] "OXSM MUTATION ANALYSIS"
[1] 3
  OXSM MUTATED OXSM WILD-TYPE 
            10            357 
  OXSM MUTATED OXSM WILD-TYPE 
            10            357 
[1] "FHOD3 MUTATION ANALYSIS"
[1] 3
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             27             340 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             27             340 
[1] "MMP8 MUTATION ANALYSIS"
[1] 3
  MMP8 MUTATED MMP8 WILD-TYPE 
            12            355 
  MMP8 MUTATED MMP8 WILD-TYPE 
            12            355 
[1] "SGK269 MUTATION ANALYSIS"
[1] 3
  SGK269 MUTATED SGK269 WILD-TYPE 
              20              347 
  SGK269 MUTATED SGK269 WILD-TYPE 
              20              347 
[1] "CLSPN MUTATION ANALYSIS"
[1] 3
  CLSPN MUTATED CLSPN WILD-TYPE 
             30             337 
  CLSPN MUTATED CLSPN WILD-TYPE 
             30             337 
[1] "LATS1 MUTATION ANALYSIS"
[1] 3
  LATS1 MUTATED LATS1 WILD-TYPE 
             18             349 
  LATS1 MUTATED LATS1 WILD-TYPE 
             18             349 
[1] "SCD5 MUTATION ANALYSIS"
[1] 3
  SCD5 MUTATED SCD5 WILD-TYPE 
             7            360 
  SCD5 MUTATED SCD5 WILD-TYPE 
             7            360 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            358 
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            358 
[1] "TAF7L MUTATION ANALYSIS"
[1] 3
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             356 
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             356 
[1] "ERBB4 MUTATION ANALYSIS"
[1] 3
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             51             316 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             51             316 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              9             358 
  HNF1B MUTATED HNF1B WILD-TYPE 
              9             358 
[1] "OR7C2 MUTATION ANALYSIS"
[1] 3
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             10             357 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             10             357 
[1] "KLHL10 MUTATION ANALYSIS"
[1] 3
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              19              348 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              19              348 
[1] "FBLN5 MUTATION ANALYSIS"
[1] 3
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              8             359 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              8             359 
[1] "GPX6 MUTATION ANALYSIS"
[1] 3
  GPX6 MUTATED GPX6 WILD-TYPE 
             9            358 
  GPX6 MUTATED GPX6 WILD-TYPE 
             9            358 
[1] "PSD MUTATION ANALYSIS"
[1] 3
  PSD MUTATED PSD WILD-TYPE 
           16           351 
  PSD MUTATED PSD WILD-TYPE 
           16           351 
[1] "EP400 MUTATION ANALYSIS"
[1] 3
  EP400 MUTATED EP400 WILD-TYPE 
             36             331 
  EP400 MUTATED EP400 WILD-TYPE 
             36             331 
[1] "DHRS7 MUTATION ANALYSIS"
[1] 3
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             357 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             357 
[1] "ZNF486 MUTATION ANALYSIS"
[1] 3
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              12              355 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              12              355 
[1] "CLEC4F MUTATION ANALYSIS"
[1] 3
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              19              348 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              19              348 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             354 
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             354 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
            14            353 
  KRT2 MUTATED KRT2 WILD-TYPE 
            14            353 
[1] "SLC12A6 MUTATION ANALYSIS"
[1] 3
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               20               347 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               20               347 
[1] "PRKCH MUTATION ANALYSIS"
[1] 3
  PRKCH MUTATED PRKCH WILD-TYPE 
             13             354 
  PRKCH MUTATED PRKCH WILD-TYPE 
             13             354 
[1] "TUBA4A MUTATION ANALYSIS"
[1] 3
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               9              358 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               9              358 
[1] "ZFC3H1 MUTATION ANALYSIS"
[1] 3
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              19              348 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              19              348 
[1] "FRMPD4 MUTATION ANALYSIS"
[1] 3
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              30              337 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              30              337 
[1] "PRRG1 MUTATION ANALYSIS"
[1] 3
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             356 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             356 
[1] "PAQR5 MUTATION ANALYSIS"
[1] 3
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             359 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             359 
[1] "BIRC3 MUTATION ANALYSIS"
[1] 3
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             356 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             356 
[1] "PPP1R12B MUTATION ANALYSIS"
[1] 3
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                12                355 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                12                355 
[1] "TFE3 MUTATION ANALYSIS"
[1] 3
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            356 
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            356 
[1] "ZNF473 MUTATION ANALYSIS"
[1] 3
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              14              353 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              14              353 
[1] "SLAMF7 MUTATION ANALYSIS"
[1] 3
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              356 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              356 
[1] "SNAI2 MUTATION ANALYSIS"
[1] 3
  SNAI2 MUTATED SNAI2 WILD-TYPE 
             10             357 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
             10             357 
[1] "B4GALNT4 MUTATION ANALYSIS"
[1] 3
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                11                356 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                11                356 
[1] "HIPK2 MUTATION ANALYSIS"
[1] 3
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             24             343 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             24             343 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               21               346 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               21               346 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             356 
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             356 
[1] "LHCGR MUTATION ANALYSIS"
[1] 3
  LHCGR MUTATED LHCGR WILD-TYPE 
             24             343 
  LHCGR MUTATED LHCGR WILD-TYPE 
             24             343 
[1] "USP34 MUTATION ANALYSIS"
[1] 3
  USP34 MUTATED USP34 WILD-TYPE 
             42             325 
  USP34 MUTATED USP34 WILD-TYPE 
             42             325 
[1] "ERCC5 MUTATION ANALYSIS"
[1] 3
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             20             347 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             20             347 
[1] "HIST1H1T MUTATION ANALYSIS"
[1] 3
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 9                358 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 9                358 
[1] "RBPJ MUTATION ANALYSIS"
[1] 3
  RBPJ MUTATED RBPJ WILD-TYPE 
            15            352 
  RBPJ MUTATED RBPJ WILD-TYPE 
            15            352 
[1] "ADAM28 MUTATION ANALYSIS"
[1] 3
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              17              350 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              17              350 
[1] "KDM5B MUTATION ANALYSIS"
[1] 3
  KDM5B MUTATED KDM5B WILD-TYPE 
             23             344 
  KDM5B MUTATED KDM5B WILD-TYPE 
             23             344 
[1] "RAG1AP1 MUTATION ANALYSIS"
[1] 3
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                6               361 
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                6               361 
[1] "CNIH4 MUTATION ANALYSIS"
[1] 3
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             361 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             361 
[1] "TRIM13 MUTATION ANALYSIS"
[1] 3
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               7              360 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               7              360 
[1] "SNTN MUTATION ANALYSIS"
[1] 3
  SNTN MUTATED SNTN WILD-TYPE 
             6            361 
  SNTN MUTATED SNTN WILD-TYPE 
             6            361 
[1] "SLC28A2 MUTATION ANALYSIS"
[1] 3
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               13               354 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               13               354 
[1] "OR2M3 MUTATION ANALYSIS"
[1] 3
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             15             352 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             15             352 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            58            309 
  MLL3 MUTATED MLL3 WILD-TYPE 
            58            309 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              16              351 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              16              351 
[1] "COLEC10 MUTATION ANALYSIS"
[1] 3
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                8               359 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                8               359 
[1] "MYEOV MUTATION ANALYSIS"
[1] 3
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             361 
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             361 
[1] "EFHC2 MUTATION ANALYSIS"
[1] 3
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             15             352 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             15             352 
[1] "MYL1 MUTATION ANALYSIS"
[1] 3
  MYL1 MUTATED MYL1 WILD-TYPE 
             8            359 
  MYL1 MUTATED MYL1 WILD-TYPE 
             8            359 
[1] "C12ORF5 MUTATION ANALYSIS"
[1] 3
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               361 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               361 
[1] "ZNF280B MUTATION ANALYSIS"
[1] 3
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               12               355 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               12               355 
[1] "MIER3 MUTATION ANALYSIS"
[1] 3
  MIER3 MUTATED MIER3 WILD-TYPE 
             13             354 
  MIER3 MUTATED MIER3 WILD-TYPE 
             13             354 
[1] "SCLY MUTATION ANALYSIS"
[1] 3
  SCLY MUTATED SCLY WILD-TYPE 
            11            356 
  SCLY MUTATED SCLY WILD-TYPE 
            11            356 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             18             349 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             18             349 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             27             340 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             27             340 
[1] "HM13 MUTATION ANALYSIS"
[1] 3
  HM13 MUTATED HM13 WILD-TYPE 
             5            362 
  HM13 MUTATED HM13 WILD-TYPE 
             5            362 
[1] "RASAL2 MUTATION ANALYSIS"
[1] 3
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              15              352 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              15              352 
[1] "OSBPL2 MUTATION ANALYSIS"
[1] 3
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              11              356 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              11              356 
[1] "OVGP1 MUTATION ANALYSIS"
[1] 3
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             14             353 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             14             353 
[1] "GMCL1 MUTATION ANALYSIS"
[1] 3
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             10             357 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             10             357 
[1] "ZNF789 MUTATION ANALYSIS"
[1] 3
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              360 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              360 
[1] "IVL MUTATION ANALYSIS"
[1] 3
  IVL MUTATED IVL WILD-TYPE 
           17           350 
  IVL MUTATED IVL WILD-TYPE 
           17           350 
[1] "SPR MUTATION ANALYSIS"
[1] 3
  SPR MUTATED SPR WILD-TYPE 
            7           360 
  SPR MUTATED SPR WILD-TYPE 
            7           360 
[1] "C2ORF77 MUTATION ANALYSIS"
[1] 3
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                8               359 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                8               359 
[1] "NT5DC3 MUTATION ANALYSIS"
[1] 3
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              12              355 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              12              355 
[1] "ITPR1 MUTATION ANALYSIS"
[1] 3
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             37             330 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             37             330 
[1] "PDCD5 MUTATION ANALYSIS"
[1] 3
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              8             359 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              8             359 
[1] "AKAP3 MUTATION ANALYSIS"
[1] 3
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             21             346 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             21             346 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               34               333 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               34               333 
[1] "GFI1 MUTATION ANALYSIS"
[1] 3
  GFI1 MUTATED GFI1 WILD-TYPE 
            10            357 
  GFI1 MUTATED GFI1 WILD-TYPE 
            10            357 
[1] "TWISTNB MUTATION ANALYSIS"
[1] 3
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                8               359 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                8               359 
[1] "ASB11 MUTATION ANALYSIS"
[1] 3
  ASB11 MUTATED ASB11 WILD-TYPE 
              8             359 
  ASB11 MUTATED ASB11 WILD-TYPE 
              8             359 
[1] "ETAA1 MUTATION ANALYSIS"
[1] 3
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             16             351 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             16             351 
[1] "NUP188 MUTATION ANALYSIS"
[1] 3
  NUP188 MUTATED NUP188 WILD-TYPE 
              19              348 
  NUP188 MUTATED NUP188 WILD-TYPE 
              19              348 
[1] "GNPAT MUTATION ANALYSIS"
[1] 3
  GNPAT MUTATED GNPAT WILD-TYPE 
             17             350 
  GNPAT MUTATED GNPAT WILD-TYPE 
             17             350 
[1] "TRIM32 MUTATION ANALYSIS"
[1] 3
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              12              355 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              12              355 
[1] "HAS2 MUTATION ANALYSIS"
[1] 3
  HAS2 MUTATED HAS2 WILD-TYPE 
             9            358 
  HAS2 MUTATED HAS2 WILD-TYPE 
             9            358 
[1] "MKL2 MUTATION ANALYSIS"
[1] 3
  MKL2 MUTATED MKL2 WILD-TYPE 
            10            357 
  MKL2 MUTATED MKL2 WILD-TYPE 
            10            357 
[1] "PCSK1 MUTATION ANALYSIS"
[1] 3
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             16             351 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             16             351 
[1] "TIAL1 MUTATION ANALYSIS"
[1] 3
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             12             355 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             12             355 
[1] "NBEA MUTATION ANALYSIS"
[1] 3
  NBEA MUTATED NBEA WILD-TYPE 
            46            321 
  NBEA MUTATED NBEA WILD-TYPE 
            46            321 
[1] "F2RL1 MUTATION ANALYSIS"
[1] 3
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              7             360 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              7             360 
[1] "ALG2 MUTATION ANALYSIS"
[1] 3
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            359 
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            359 
[1] "STBD1 MUTATION ANALYSIS"
[1] 3
  STBD1 MUTATED STBD1 WILD-TYPE 
              6             361 
  STBD1 MUTATED STBD1 WILD-TYPE 
              6             361 
[1] "C12ORF40 MUTATION ANALYSIS"
[1] 3
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                21                346 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                21                346 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
            32            335 
  GNAS MUTATED GNAS WILD-TYPE 
            32            335 
[1] "RBM7 MUTATION ANALYSIS"
[1] 3
  RBM7 MUTATED RBM7 WILD-TYPE 
            10            357 
  RBM7 MUTATED RBM7 WILD-TYPE 
            10            357 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             37             330 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             37             330 
[1] "FAM133B MUTATION ANALYSIS"
[1] 3
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               362 
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               362 
[1] "CARD11 MUTATION ANALYSIS"
[1] 3
  CARD11 MUTATED CARD11 WILD-TYPE 
              41              326 
  CARD11 MUTATED CARD11 WILD-TYPE 
              41              326 
[1] "IFT57 MUTATION ANALYSIS"
[1] 3
  IFT57 MUTATED IFT57 WILD-TYPE 
             10             357 
  IFT57 MUTATED IFT57 WILD-TYPE 
             10             357 
[1] "TNFRSF9 MUTATION ANALYSIS"
[1] 3
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               358 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               358 
[1] "WNT16 MUTATION ANALYSIS"
[1] 3
  WNT16 MUTATED WNT16 WILD-TYPE 
              8             359 
  WNT16 MUTATED WNT16 WILD-TYPE 
              8             359 
[1] "SLC9A10 MUTATION ANALYSIS"
[1] 3
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               18               349 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               18               349 
[1] "VAV2 MUTATION ANALYSIS"
[1] 3
  VAV2 MUTATED VAV2 WILD-TYPE 
            17            350 
  VAV2 MUTATED VAV2 WILD-TYPE 
            17            350 
[1] "HMG20A MUTATION ANALYSIS"
[1] 3
  HMG20A MUTATED HMG20A WILD-TYPE 
              13              354 
  HMG20A MUTATED HMG20A WILD-TYPE 
              13              354 
[1] "ETF1 MUTATION ANALYSIS"
[1] 3
  ETF1 MUTATED ETF1 WILD-TYPE 
            10            357 
  ETF1 MUTATED ETF1 WILD-TYPE 
            10            357 
[1] "CBL MUTATION ANALYSIS"
[1] 3
  CBL MUTATED CBL WILD-TYPE 
           34           333 
  CBL MUTATED CBL WILD-TYPE 
           34           333 
[1] "PRB4 MUTATION ANALYSIS"
[1] 3
  PRB4 MUTATED PRB4 WILD-TYPE 
            10            357 
  PRB4 MUTATED PRB4 WILD-TYPE 
            10            357 
[1] "SOX7 MUTATION ANALYSIS"
[1] 3
  SOX7 MUTATED SOX7 WILD-TYPE 
            11            356 
  SOX7 MUTATED SOX7 WILD-TYPE 
            11            356 
[1] "ARHGAP5 MUTATION ANALYSIS"
[1] 3
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               348 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               348 
[1] "MAGEC1 MUTATION ANALYSIS"
[1] 3
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              28              339 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              28              339 
[1] "RAB28 MUTATION ANALYSIS"
[1] 3
  RAB28 MUTATED RAB28 WILD-TYPE 
              6             361 
  RAB28 MUTATED RAB28 WILD-TYPE 
              6             361 
[1] "UBR4 MUTATION ANALYSIS"
[1] 3
  UBR4 MUTATED UBR4 WILD-TYPE 
            39            328 
  UBR4 MUTATED UBR4 WILD-TYPE 
            39            328 
[1] "OR2T33 MUTATION ANALYSIS"
[1] 3
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              16              351 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              16              351 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              19              348 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              19              348 
[1] "ZBTB7C MUTATION ANALYSIS"
[1] 3
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              353 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              353 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             20             347 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             20             347 
[1] "CENPF MUTATION ANALYSIS"
[1] 3
  CENPF MUTATED CENPF WILD-TYPE 
             41             326 
  CENPF MUTATED CENPF WILD-TYPE 
             41             326 
[1] "MYO3B MUTATION ANALYSIS"
[1] 3
  MYO3B MUTATED MYO3B WILD-TYPE 
             31             336 
  MYO3B MUTATED MYO3B WILD-TYPE 
             31             336 
[1] "G3BP2 MUTATION ANALYSIS"
[1] 3
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              9             358 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              9             358 
[1] "MBD6 MUTATION ANALYSIS"
[1] 3
  MBD6 MUTATED MBD6 WILD-TYPE 
            15            352 
  MBD6 MUTATED MBD6 WILD-TYPE 
            15            352 
[1] "ANAPC4 MUTATION ANALYSIS"
[1] 3
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              10              357 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              10              357 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
             9            358 
  TTF1 MUTATED TTF1 WILD-TYPE 
             9            358 
[1] "FAM134A MUTATION ANALYSIS"
[1] 3
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               359 
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               359 
[1] "ZKSCAN2 MUTATION ANALYSIS"
[1] 3
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               13               354 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               13               354 
[1] "RNF182 MUTATION ANALYSIS"
[1] 3
  RNF182 MUTATED RNF182 WILD-TYPE 
              13              354 
  RNF182 MUTATED RNF182 WILD-TYPE 
              13              354 
[1] "RBBP7 MUTATION ANALYSIS"
[1] 3
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             15             352 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             15             352 
[1] "MAGEA1 MUTATION ANALYSIS"
[1] 3
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              13              354 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              13              354 
[1] "HEPACAM2 MUTATION ANALYSIS"
[1] 3
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                13                354 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                13                354 
[1] "DHX35 MUTATION ANALYSIS"
[1] 3
  DHX35 MUTATED DHX35 WILD-TYPE 
             11             356 
  DHX35 MUTATED DHX35 WILD-TYPE 
             11             356 
[1] "PARP12 MUTATION ANALYSIS"
[1] 3
  PARP12 MUTATED PARP12 WILD-TYPE 
               9              358 
  PARP12 MUTATED PARP12 WILD-TYPE 
               9              358 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             47             320 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             47             320 
[1] "IFIT2 MUTATION ANALYSIS"
[1] 3
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              7             360 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              7             360 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             46             321 
  MUC17 MUTATED MUC17 WILD-TYPE 
             46             321 
[1] "TET3 MUTATION ANALYSIS"
[1] 3
  TET3 MUTATED TET3 WILD-TYPE 
            20            347 
  TET3 MUTATED TET3 WILD-TYPE 
            20            347 
[1] "TOB1 MUTATION ANALYSIS"
[1] 3
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            361 
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            361 
[1] "GOLPH3L MUTATION ANALYSIS"
[1] 3
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                5               362 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                5               362 
[1] "TSHR MUTATION ANALYSIS"
[1] 3
  TSHR MUTATED TSHR WILD-TYPE 
            44            323 
  TSHR MUTATED TSHR WILD-TYPE 
            44            323 
[1] "C14ORF102 MUTATION ANALYSIS"
[1] 3
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 17                 350 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 17                 350 
[1] "EXOC4 MUTATION ANALYSIS"
[1] 3
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             18             349 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             18             349 
[1] "RPS6KA3 MUTATION ANALYSIS"
[1] 3
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               13               354 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               13               354 
[1] "ZNF438 MUTATION ANALYSIS"
[1] 3
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              12              355 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              12              355 
[1] "MST4 MUTATION ANALYSIS"
[1] 3
  MST4 MUTATED MST4 WILD-TYPE 
             7            360 
  MST4 MUTATED MST4 WILD-TYPE 
             7            360 
[1] "RIF1 MUTATION ANALYSIS"
[1] 3
  RIF1 MUTATED RIF1 WILD-TYPE 
            35            332 
  RIF1 MUTATED RIF1 WILD-TYPE 
            35            332 
[1] "INPP1 MUTATION ANALYSIS"
[1] 3
  INPP1 MUTATED INPP1 WILD-TYPE 
              7             360 
  INPP1 MUTATED INPP1 WILD-TYPE 
              7             360 
[1] "SAPS2 MUTATION ANALYSIS"
[1] 3
  SAPS2 MUTATED SAPS2 WILD-TYPE 
             11             356 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
             11             356 
[1] "CEP135 MUTATION ANALYSIS"
[1] 3
  CEP135 MUTATED CEP135 WILD-TYPE 
              21              346 
  CEP135 MUTATED CEP135 WILD-TYPE 
              21              346 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               353 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               353 
[1] "RNF160 MUTATION ANALYSIS"
[1] 3
  RNF160 MUTATED RNF160 WILD-TYPE 
              16              351 
  RNF160 MUTATED RNF160 WILD-TYPE 
              16              351 
[1] "ECM2 MUTATION ANALYSIS"
[1] 3
  ECM2 MUTATED ECM2 WILD-TYPE 
            17            350 
  ECM2 MUTATED ECM2 WILD-TYPE 
            17            350 
[1] "MSH2 MUTATION ANALYSIS"
[1] 3
  MSH2 MUTATED MSH2 WILD-TYPE 
            33            334 
  MSH2 MUTATED MSH2 WILD-TYPE 
            33            334 
[1] "IL1RAPL1 MUTATION ANALYSIS"
[1] 3
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                23                344 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                23                344 
[1] "C6ORF170 MUTATION ANALYSIS"
[1] 3
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                18                349 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                18                349 
[1] "STAB2 MUTATION ANALYSIS"
[1] 3
  STAB2 MUTATED STAB2 WILD-TYPE 
             32             335 
  STAB2 MUTATED STAB2 WILD-TYPE 
             32             335 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             26             341 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             26             341 
[1] "ZNF708 MUTATION ANALYSIS"
[1] 3
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              12              355 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              12              355 
[1] "MBTD1 MUTATION ANALYSIS"
[1] 3
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              9             358 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              9             358 
[1] "ZNF189 MUTATION ANALYSIS"
[1] 3
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              17              350 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              17              350 
[1] "ACP6 MUTATION ANALYSIS"
[1] 3
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            361 
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            361 
[1] "PRKCI MUTATION ANALYSIS"
[1] 3
  PRKCI MUTATED PRKCI WILD-TYPE 
             18             349 
  PRKCI MUTATED PRKCI WILD-TYPE 
             18             349 
[1] "ANKRD50 MUTATION ANALYSIS"
[1] 3
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               15               352 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               15               352 
[1] "IL12RB2 MUTATION ANALYSIS"
[1] 3
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               14               353 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               14               353 
[1] "GPNMB MUTATION ANALYSIS"
[1] 3
  GPNMB MUTATED GPNMB WILD-TYPE 
             13             354 
  GPNMB MUTATED GPNMB WILD-TYPE 
             13             354 
[1] "GLI2 MUTATION ANALYSIS"
[1] 3
  GLI2 MUTATED GLI2 WILD-TYPE 
            20            347 
  GLI2 MUTATED GLI2 WILD-TYPE 
            20            347 
[1] "OR51E1 MUTATION ANALYSIS"
[1] 3
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              13              354 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              13              354 
[1] "AGFG1 MUTATION ANALYSIS"
[1] 3
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             15             352 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             15             352 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            33            334 
  NRAS MUTATED NRAS WILD-TYPE 
            33            334 
[1] "MPO MUTATION ANALYSIS"
[1] 3
  MPO MUTATED MPO WILD-TYPE 
           12           355 
  MPO MUTATED MPO WILD-TYPE 
           12           355 
[1] "TRRAP MUTATION ANALYSIS"
[1] 3
  TRRAP MUTATED TRRAP WILD-TYPE 
             49             318 
  TRRAP MUTATED TRRAP WILD-TYPE 
             49             318 
[1] "OR11G2 MUTATION ANALYSIS"
[1] 3
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               5              362 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               5              362 
[1] "TRIM23 MUTATION ANALYSIS"
[1] 3
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              11              356 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              11              356 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            96            271 
  BRAF MUTATED BRAF WILD-TYPE 
            96            271 
[1] "GTF2B MUTATION ANALYSIS"
[1] 3
  GTF2B MUTATED GTF2B WILD-TYPE 
             11             356 
  GTF2B MUTATED GTF2B WILD-TYPE 
             11             356 
[1] "DDB1 MUTATION ANALYSIS"
[1] 3
  DDB1 MUTATED DDB1 WILD-TYPE 
            13            354 
  DDB1 MUTATED DDB1 WILD-TYPE 
            13            354 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
            44            323 
  EZH2 MUTATED EZH2 WILD-TYPE 
            44            323 
[1] "PRDM1 MUTATION ANALYSIS"
[1] 3
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             20             347 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             20             347 
[1] "USP26 MUTATION ANALYSIS"
[1] 3
  USP26 MUTATED USP26 WILD-TYPE 
             23             344 
  USP26 MUTATED USP26 WILD-TYPE 
             23             344 
[1] "TXNDC15 MUTATION ANALYSIS"
[1] 3
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                6               361 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                6               361 
[1] "OR1I1 MUTATION ANALYSIS"
[1] 3
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             10             357 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             10             357 
[1] "CUL2 MUTATION ANALYSIS"
[1] 3
  CUL2 MUTATED CUL2 WILD-TYPE 
            14            353 
  CUL2 MUTATED CUL2 WILD-TYPE 
            14            353 
[1] "TMEM169 MUTATION ANALYSIS"
[1] 3
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               13               354 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               13               354 
[1] "PIK3C2A MUTATION ANALYSIS"
[1] 3
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               14               353 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               14               353 
[1] "MSH6 MUTATION ANALYSIS"
[1] 3
  MSH6 MUTATED MSH6 WILD-TYPE 
            39            328 
  MSH6 MUTATED MSH6 WILD-TYPE 
            39            328 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           168            199 
  KRAS MUTATED KRAS WILD-TYPE 
           168            199 
[1] "NEXN MUTATION ANALYSIS"
[1] 3
  NEXN MUTATED NEXN WILD-TYPE 
            17            350 
  NEXN MUTATED NEXN WILD-TYPE 
            17            350 
[1] "SP110 MUTATION ANALYSIS"
[1] 3
  SP110 MUTATED SP110 WILD-TYPE 
             10             357 
  SP110 MUTATED SP110 WILD-TYPE 
             10             357 
[1] "MYST4 MUTATION ANALYSIS"
[1] 3
  MYST4 MUTATED MYST4 WILD-TYPE 
             23             344 
  MYST4 MUTATED MYST4 WILD-TYPE 
             23             344 
[1] "PPARGC1A MUTATION ANALYSIS"
[1] 3
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                23                344 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                23                344 
[1] "CLIP4 MUTATION ANALYSIS"
[1] 3
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             14             353 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             14             353 
[1] "PAK3 MUTATION ANALYSIS"
[1] 3
  PAK3 MUTATED PAK3 WILD-TYPE 
            17            350 
  PAK3 MUTATED PAK3 WILD-TYPE 
            17            350 
[1] "KCNS3 MUTATION ANALYSIS"
[1] 3
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             19             348 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             19             348 
[1] "TRPM7 MUTATION ANALYSIS"
[1] 3
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             28             339 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             28             339 
[1] "DSG1 MUTATION ANALYSIS"
[1] 3
  DSG1 MUTATED DSG1 WILD-TYPE 
            18            349 
  DSG1 MUTATED DSG1 WILD-TYPE 
            18            349 
[1] "ZNF585A MUTATION ANALYSIS"
[1] 3
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               16               351 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               16               351 
[1] "KPNA5 MUTATION ANALYSIS"
[1] 3
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             11             356 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             11             356 
[1] "CDC42BPA MUTATION ANALYSIS"
[1] 3
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                29                338 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                29                338 
[1] "KIR2DL3 MUTATION ANALYSIS"
[1] 3
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               19               348 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               19               348 
[1] "C5ORF22 MUTATION ANALYSIS"
[1] 3
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               11               356 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               11               356 
[1] "CSNK1D MUTATION ANALYSIS"
[1] 3
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              14              353 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              14              353 
[1] "IQSEC2 MUTATION ANALYSIS"
[1] 3
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              16              351 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              16              351 
[1] "RAB6C MUTATION ANALYSIS"
[1] 3
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             362 
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             362 
[1] "C9ORF131 MUTATION ANALYSIS"
[1] 3
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                13                354 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                13                354 
[1] "C12ORF10 MUTATION ANALYSIS"
[1] 3
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                363 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                363 
[1] "NUP54 MUTATION ANALYSIS"
[1] 3
  NUP54 MUTATED NUP54 WILD-TYPE 
              8             359 
  NUP54 MUTATED NUP54 WILD-TYPE 
              8             359 
[1] "PLEKHA6 MUTATION ANALYSIS"
[1] 3
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               19               348 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               19               348 
[1] "CYP4X1 MUTATION ANALYSIS"
[1] 3
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               5              362 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               5              362 
[1] "DAXX MUTATION ANALYSIS"
[1] 3
  DAXX MUTATED DAXX WILD-TYPE 
            12            355 
  DAXX MUTATED DAXX WILD-TYPE 
            12            355 
[1] "CDK17 MUTATION ANALYSIS"
[1] 3
  CDK17 MUTATED CDK17 WILD-TYPE 
             11             356 
  CDK17 MUTATED CDK17 WILD-TYPE 
             11             356 
[1] "SYNCRIP MUTATION ANALYSIS"
[1] 3
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               10               357 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               10               357 
[1] "ENPEP MUTATION ANALYSIS"
[1] 3
  ENPEP MUTATED ENPEP WILD-TYPE 
             21             346 
  ENPEP MUTATED ENPEP WILD-TYPE 
             21             346 
[1] "C6ORF89 MUTATION ANALYSIS"
[1] 3
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                6               361 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                6               361 
[1] "USP7 MUTATION ANALYSIS"
[1] 3
  USP7 MUTATED USP7 WILD-TYPE 
            24            343 
  USP7 MUTATED USP7 WILD-TYPE 
            24            343 
[1] "CCAR1 MUTATION ANALYSIS"
[1] 3
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             18             349 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             18             349 
[1] "SLC7A10 MUTATION ANALYSIS"
[1] 3
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                8               359 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                8               359 
[1] "GTF2IRD2 MUTATION ANALYSIS"
[1] 3
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                361 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                361 
[1] "TIFA MUTATION ANALYSIS"
[1] 3
  TIFA MUTATED TIFA WILD-TYPE 
             6            361 
  TIFA MUTATED TIFA WILD-TYPE 
             6            361 
[1] "MFN1 MUTATION ANALYSIS"
[1] 3
  MFN1 MUTATED MFN1 WILD-TYPE 
            13            354 
  MFN1 MUTATED MFN1 WILD-TYPE 
            13            354 
[1] "AMOT MUTATION ANALYSIS"
[1] 3
  AMOT MUTATED AMOT WILD-TYPE 
            13            354 
  AMOT MUTATED AMOT WILD-TYPE 
            13            354 
[1] "ZNF449 MUTATION ANALYSIS"
[1] 3
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              10              357 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              10              357 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               30               337 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               30               337 
[1] "IGFBP7 MUTATION ANALYSIS"
[1] 3
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              363 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              363 
[1] "MARK1 MUTATION ANALYSIS"
[1] 3
  MARK1 MUTATED MARK1 WILD-TYPE 
             25             342 
  MARK1 MUTATED MARK1 WILD-TYPE 
             25             342 
[1] "CCR2 MUTATION ANALYSIS"
[1] 3
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            360 
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            360 
[1] "NUP160 MUTATION ANALYSIS"
[1] 3
  NUP160 MUTATED NUP160 WILD-TYPE 
              11              356 
  NUP160 MUTATED NUP160 WILD-TYPE 
              11              356 
[1] "CYLC1 MUTATION ANALYSIS"
[1] 3
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             27             340 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             27             340 
[1] "PRAMEF12 MUTATION ANALYSIS"
[1] 3
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 5                362 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 5                362 
[1] "C1ORF59 MUTATION ANALYSIS"
[1] 3
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               357 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               357 
[1] "MEPE MUTATION ANALYSIS"
[1] 3
  MEPE MUTATED MEPE WILD-TYPE 
            15            352 
  MEPE MUTATED MEPE WILD-TYPE 
            15            352 
[1] "ZNF384 MUTATION ANALYSIS"
[1] 3
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              358 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              358 
[1] "MOBKL2B MUTATION ANALYSIS"
[1] 3
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                7               360 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                7               360 
[1] "GPR112 MUTATION ANALYSIS"
[1] 3
  GPR112 MUTATED GPR112 WILD-TYPE 
              30              337 
  GPR112 MUTATED GPR112 WILD-TYPE 
              30              337 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           42           325 
  MET MUTATED MET WILD-TYPE 
           42           325 
[1] "FUT10 MUTATION ANALYSIS"
[1] 3
  FUT10 MUTATED FUT10 WILD-TYPE 
              6             361 
  FUT10 MUTATED FUT10 WILD-TYPE 
              6             361 
[1] "BAG4 MUTATION ANALYSIS"
[1] 3
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            359 
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            359 
[1] "GPR87 MUTATION ANALYSIS"
[1] 3
  GPR87 MUTATED GPR87 WILD-TYPE 
             10             357 
  GPR87 MUTATED GPR87 WILD-TYPE 
             10             357 
[1] "RASA2 MUTATION ANALYSIS"
[1] 3
  RASA2 MUTATED RASA2 WILD-TYPE 
             15             352 
  RASA2 MUTATED RASA2 WILD-TYPE 
             15             352 
[1] "TNNI3K MUTATION ANALYSIS"
[1] 3
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              24              343 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              24              343 
[1] "RELN MUTATION ANALYSIS"
[1] 3
  RELN MUTATED RELN WILD-TYPE 
            65            302 
  RELN MUTATED RELN WILD-TYPE 
            65            302 
[1] "USP25 MUTATION ANALYSIS"
[1] 3
  USP25 MUTATED USP25 WILD-TYPE 
             19             348 
  USP25 MUTATED USP25 WILD-TYPE 
             19             348 
[1] "NCOA7 MUTATION ANALYSIS"
[1] 3
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             15             352 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             15             352 
[1] "DDX23 MUTATION ANALYSIS"
[1] 3
  DDX23 MUTATED DDX23 WILD-TYPE 
             18             349 
  DDX23 MUTATED DDX23 WILD-TYPE 
             18             349 
[1] "IGF2R MUTATION ANALYSIS"
[1] 3
  IGF2R MUTATED IGF2R WILD-TYPE 
             37             330 
  IGF2R MUTATED IGF2R WILD-TYPE 
             37             330 
[1] "TMEM92 MUTATION ANALYSIS"
[1] 3
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              364 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              364 
[1] "ODZ1 MUTATION ANALYSIS"
[1] 3
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            61            306 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            61            306 
[1] "FLG2 MUTATION ANALYSIS"
[1] 3
  FLG2 MUTATED FLG2 WILD-TYPE 
            28            339 
  FLG2 MUTATED FLG2 WILD-TYPE 
            28            339 
[1] "TRMT5 MUTATION ANALYSIS"
[1] 3
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              6             361 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              6             361 
[1] "CHML MUTATION ANALYSIS"
[1] 3
  CHML MUTATED CHML WILD-TYPE 
            20            347 
  CHML MUTATED CHML WILD-TYPE 
            20            347 
[1] "AURKA MUTATION ANALYSIS"
[1] 3
  AURKA MUTATED AURKA WILD-TYPE 
              7             360 
  AURKA MUTATED AURKA WILD-TYPE 
              7             360 
[1] "LRRC23 MUTATION ANALYSIS"
[1] 3
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               9              358 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               9              358 
[1] "PHF3 MUTATION ANALYSIS"
[1] 3
  PHF3 MUTATED PHF3 WILD-TYPE 
            23            344 
  PHF3 MUTATED PHF3 WILD-TYPE 
            23            344 
[1] "CNTNAP5 MUTATION ANALYSIS"
[1] 3
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               40               327 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               40               327 
[1] "KRT14 MUTATION ANALYSIS"
[1] 3
  KRT14 MUTATED KRT14 WILD-TYPE 
              8             359 
  KRT14 MUTATED KRT14 WILD-TYPE 
              8             359 
[1] "JAK2 MUTATION ANALYSIS"
[1] 3
  JAK2 MUTATED JAK2 WILD-TYPE 
            40            327 
  JAK2 MUTATED JAK2 WILD-TYPE 
            40            327 
[1] "ANKHD1 MUTATION ANALYSIS"
[1] 3
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              29              338 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              29              338 
[1] "GAB2 MUTATION ANALYSIS"
[1] 3
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            358 
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            358 
[1] "ADAM18 MUTATION ANALYSIS"
[1] 3
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              18              349 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              18              349 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
           96           271 
  KIT MUTATED KIT WILD-TYPE 
           96           271 
[1] "HUWE1 MUTATION ANALYSIS"
[1] 3
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             42             325 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             42             325 
[1] "NTRK3 MUTATION ANALYSIS"
[1] 3
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             25             342 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             25             342 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            75            292 
  EGFR MUTATED EGFR WILD-TYPE 
            75            292 
[1] "GATA3 MUTATION ANALYSIS"
[1] 3
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             351 
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             351 
[1] "ATP13A5 MUTATION ANALYSIS"
[1] 3
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               22               345 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               22               345 
[1] "DKK2 MUTATION ANALYSIS"
[1] 3
  DKK2 MUTATED DKK2 WILD-TYPE 
            23            344 
  DKK2 MUTATED DKK2 WILD-TYPE 
            23            344 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             175              192 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             175              192 
[1] "CLVS2 MUTATION ANALYSIS"
[1] 3
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              9             358 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              9             358 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             36             331 
  EP300 MUTATED EP300 WILD-TYPE 
             36             331 
[1] "ITGAV MUTATION ANALYSIS"
[1] 3
  ITGAV MUTATED ITGAV WILD-TYPE 
             15             352 
  ITGAV MUTATED ITGAV WILD-TYPE 
             15             352 
[1] "PPP1R3A MUTATION ANALYSIS"
[1] 3
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               32               335 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               32               335 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              30              337 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              30              337 
[1] "KIAA1409 MUTATION ANALYSIS"
[1] 3
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                39                328 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                39                328 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             57             310 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             57             310 
[1] "HFE2 MUTATION ANALYSIS"
[1] 3
  HFE2 MUTATED HFE2 WILD-TYPE 
             8            359 
  HFE2 MUTATED HFE2 WILD-TYPE 
             8            359 
[1] "MYH1 MUTATION ANALYSIS"
[1] 3
  MYH1 MUTATED MYH1 WILD-TYPE 
            32            335 
  MYH1 MUTATED MYH1 WILD-TYPE 
            32            335 
[1] "EEA1 MUTATION ANALYSIS"
[1] 3
  EEA1 MUTATED EEA1 WILD-TYPE 
            13            354 
  EEA1 MUTATED EEA1 WILD-TYPE 
            13            354 
[1] "GRM7 MUTATION ANALYSIS"
[1] 3
  GRM7 MUTATED GRM7 WILD-TYPE 
            25            342 
  GRM7 MUTATED GRM7 WILD-TYPE 
            25            342 
[1] "GRM8 MUTATION ANALYSIS"
[1] 3
  GRM8 MUTATED GRM8 WILD-TYPE 
            21            346 
  GRM8 MUTATED GRM8 WILD-TYPE 
            21            346 
[1] "TAF1 MUTATION ANALYSIS"
[1] 3
  TAF1 MUTATED TAF1 WILD-TYPE 
            22            345 
  TAF1 MUTATED TAF1 WILD-TYPE 
            22            345 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                28                339 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                28                339 
[1] "PTPRD MUTATION ANALYSIS"
[1] 3
  PTPRD MUTATED PTPRD WILD-TYPE 
             32             335 
  PTPRD MUTATED PTPRD WILD-TYPE 
             32             335 
[1] "CSMD3 MUTATION ANALYSIS"
[1] 3
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             86             281 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             86             281 
[1] "ZCCHC6 MUTATION ANALYSIS"
[1] 3
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              18              349 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              18              349 
[1] "FUBP3 MUTATION ANALYSIS"
[1] 3
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             358 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             358 
[1] "SYT1 MUTATION ANALYSIS"
[1] 3
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            354 
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            354 
[1] "OSBPL11 MUTATION ANALYSIS"
[1] 3
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               16               351 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               16               351 
[1] "SFRS18 MUTATION ANALYSIS"
[1] 3
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              12              355 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              12              355 
[1] "MAP9 MUTATION ANALYSIS"
[1] 3
  MAP9 MUTATED MAP9 WILD-TYPE 
            16            351 
  MAP9 MUTATED MAP9 WILD-TYPE 
            16            351 
[1] "TNPO1 MUTATION ANALYSIS"
[1] 3
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             16             351 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             16             351 
[1] "CLCNKA MUTATION ANALYSIS"
[1] 3
  CLCNKA MUTATED CLCNKA WILD-TYPE 
              10              357 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
              10              357 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              60              307 
  CREBBP MUTATED CREBBP WILD-TYPE 
              60              307 
[1] "INTS4 MUTATION ANALYSIS"
[1] 3
  INTS4 MUTATED INTS4 WILD-TYPE 
             18             349 
  INTS4 MUTATED INTS4 WILD-TYPE 
             18             349 
[1] "PRKAA2 MUTATION ANALYSIS"
[1] 3
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              12              355 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              12              355 
[1] "LNX2 MUTATION ANALYSIS"
[1] 3
  LNX2 MUTATED LNX2 WILD-TYPE 
            16            351 
  LNX2 MUTATED LNX2 WILD-TYPE 
            16            351 
[1] "ATG2B MUTATION ANALYSIS"
[1] 3
  ATG2B MUTATED ATG2B WILD-TYPE 
             15             352 
  ATG2B MUTATED ATG2B WILD-TYPE 
             15             352 
[1] "CHRM2 MUTATION ANALYSIS"
[1] 3
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             23             344 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             23             344 
[1] "NUDCD1 MUTATION ANALYSIS"
[1] 3
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               9              358 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               9              358 
[1] "INSM2 MUTATION ANALYSIS"
[1] 3
  INSM2 MUTATED INSM2 WILD-TYPE 
             10             357 
  INSM2 MUTATED INSM2 WILD-TYPE 
             10             357 
[1] "GOLGB1 MUTATION ANALYSIS"
[1] 3
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              38              329 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              38              329 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                16                351 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                16                351 
[1] "C10ORF79 MUTATION ANALYSIS"
[1] 3
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                27                340 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                27                340 
[1] "DENND4A MUTATION ANALYSIS"
[1] 3
  DENND4A MUTATED DENND4A WILD-TYPE 
               22               345 
  DENND4A MUTATED DENND4A WILD-TYPE 
               22               345 
[1] "RBL2 MUTATION ANALYSIS"
[1] 3
  RBL2 MUTATED RBL2 WILD-TYPE 
            21            346 
  RBL2 MUTATED RBL2 WILD-TYPE 
            21            346 
[1] "DCAF6 MUTATION ANALYSIS"
[1] 3
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             15             352 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             15             352 
[1] "HIST1H1E MUTATION ANALYSIS"
[1] 3
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                361 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                361 
[1] "ADK MUTATION ANALYSIS"
[1] 3
  ADK MUTATED ADK WILD-TYPE 
            7           360 
  ADK MUTATED ADK WILD-TYPE 
            7           360 
[1] "RPA3 MUTATION ANALYSIS"
[1] 3
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            363 
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            363 
[1] "NFATC3 MUTATION ANALYSIS"
[1] 3
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              12              355 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              12              355 
[1] "C9ORF84 MUTATION ANALYSIS"
[1] 3
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               20               347 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               20               347 
[1] "IKZF4 MUTATION ANALYSIS"
[1] 3
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             13             354 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             13             354 
[1] "MAP7D1 MUTATION ANALYSIS"
[1] 3
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              15              352 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              15              352 
[1] "LRRC39 MUTATION ANALYSIS"
[1] 3
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               8              359 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               8              359 
[1] "RING1 MUTATION ANALYSIS"
[1] 3
  RING1 MUTATED RING1 WILD-TYPE 
             10             357 
  RING1 MUTATED RING1 WILD-TYPE 
             10             357 
[1] "VCX2 MUTATION ANALYSIS"
[1] 3
  VCX2 MUTATED VCX2 WILD-TYPE 
             7            360 
  VCX2 MUTATED VCX2 WILD-TYPE 
             7            360 
[1] "N4BP2 MUTATION ANALYSIS"
[1] 3
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             24             343 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             24             343 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           23           344 
  NRK MUTATED NRK WILD-TYPE 
           23           344 
[1] "PTPRK MUTATION ANALYSIS"
[1] 3
  PTPRK MUTATED PTPRK WILD-TYPE 
             33             334 
  PTPRK MUTATED PTPRK WILD-TYPE 
             33             334 
[1] "HDAC1 MUTATION ANALYSIS"
[1] 3
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             362 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             362 
[1] "E2F7 MUTATION ANALYSIS"
[1] 3
  E2F7 MUTATED E2F7 WILD-TYPE 
            21            346 
  E2F7 MUTATED E2F7 WILD-TYPE 
            21            346 
[1] "SLC11A2 MUTATION ANALYSIS"
[1] 3
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                8               359 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                8               359 
[1] "HIF3A MUTATION ANALYSIS"
[1] 3
  HIF3A MUTATED HIF3A WILD-TYPE 
             15             352 
  HIF3A MUTATED HIF3A WILD-TYPE 
             15             352 
[1] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            362 
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            362 
[1] "WWTR1 MUTATION ANALYSIS"
[1] 3
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              6             361 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              6             361 
[1] "HGS MUTATION ANALYSIS"
[1] 3
  HGS MUTATED HGS WILD-TYPE 
           10           357 
  HGS MUTATED HGS WILD-TYPE 
           10           357 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
           11           356 
  NLK MUTATED NLK WILD-TYPE 
           11           356 
[1] "ATP8B1 MUTATION ANALYSIS"
[1] 3
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              23              344 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              23              344 
[1] "WDR66 MUTATION ANALYSIS"
[1] 3
  WDR66 MUTATED WDR66 WILD-TYPE 
             19             348 
  WDR66 MUTATED WDR66 WILD-TYPE 
             19             348 
[1] "GPR141 MUTATION ANALYSIS"
[1] 3
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              356 
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              356 
[1] "ATP6V1D MUTATION ANALYSIS"
[1] 3
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                6               361 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                6               361 
[1] "LPCAT3 MUTATION ANALYSIS"
[1] 3
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              362 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              362 
[1] "SP4 MUTATION ANALYSIS"
[1] 3
  SP4 MUTATED SP4 WILD-TYPE 
           12           355 
  SP4 MUTATED SP4 WILD-TYPE 
           12           355 
[1] "PLA2G4E MUTATION ANALYSIS"
[1] 3
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               10               357 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               10               357 
[1] "RAB40C MUTATION ANALYSIS"
[1] 3
  RAB40C MUTATED RAB40C WILD-TYPE 
               8              359 
  RAB40C MUTATED RAB40C WILD-TYPE 
               8              359 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              18              349 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              18              349 
[1] "ATAD2B MUTATION ANALYSIS"
[1] 3
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              15              352 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              15              352 
[1] "SLC33A1 MUTATION ANALYSIS"
[1] 3
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                9               358 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                9               358 
[1] "ABCB4 MUTATION ANALYSIS"
[1] 3
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             22             345 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             22             345 
[1] "RUFY1 MUTATION ANALYSIS"
[1] 3
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             13             354 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             13             354 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
            19            348 
  IBTK MUTATED IBTK WILD-TYPE 
            19            348 
[1] "PNP MUTATION ANALYSIS"
[1] 3
  PNP MUTATED PNP WILD-TYPE 
            4           363 
  PNP MUTATED PNP WILD-TYPE 
            4           363 
[1] "ACTL8 MUTATION ANALYSIS"
[1] 3
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              9             358 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              9             358 
[1] "CDK14 MUTATION ANALYSIS"
[1] 3
  CDK14 MUTATED CDK14 WILD-TYPE 
             15             352 
  CDK14 MUTATED CDK14 WILD-TYPE 
             15             352 
[1] "AXIN2 MUTATION ANALYSIS"
[1] 3
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             21             346 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             21             346 
[1] "KCNH7 MUTATION ANALYSIS"
[1] 3
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             32             335 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             32             335 
[1] "SPCS2 MUTATION ANALYSIS"
[1] 3
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             362 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             362 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              18              349 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              18              349 
[1] "OR4E2 MUTATION ANALYSIS"
[1] 3
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              5             362 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              5             362 
[1] "SULT6B1 MUTATION ANALYSIS"
[1] 3
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                9               358 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                9               358 
[1] "LDHA MUTATION ANALYSIS"
[1] 3
  LDHA MUTATED LDHA WILD-TYPE 
            10            357 
  LDHA MUTATED LDHA WILD-TYPE 
            10            357 
[1] "EIF4A2 MUTATION ANALYSIS"
[1] 3
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              10              357 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              10              357 
[1] "RCSD1 MUTATION ANALYSIS"
[1] 3
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             14             353 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             14             353 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
             16             351 
  EIF5B MUTATED EIF5B WILD-TYPE 
             16             351 
[1] "FGFR1 MUTATION ANALYSIS"
[1] 3
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             17             350 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             17             350 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             15             352 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             15             352 
[1] "IRAK3 MUTATION ANALYSIS"
[1] 3
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              8             359 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              8             359 
[1] "KIAA0195 MUTATION ANALYSIS"
[1] 3
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                17                350 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                17                350 
[1] "AGBL2 MUTATION ANALYSIS"
[1] 3
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             14             353 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             14             353 
[1] "OR1J2 MUTATION ANALYSIS"
[1] 3
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             10             357 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             10             357 
[1] "PTPRC MUTATION ANALYSIS"
[1] 3
  PTPRC MUTATED PTPRC WILD-TYPE 
             25             342 
  PTPRC MUTATED PTPRC WILD-TYPE 
             25             342 
[1] "ARMCX5 MUTATION ANALYSIS"
[1] 3
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               8              359 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               8              359 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            12            355 
  PPIG MUTATED PPIG WILD-TYPE 
            12            355 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             32             335 
  NFASC MUTATED NFASC WILD-TYPE 
             32             335 
[1] "PLCH2 MUTATION ANALYSIS"
[1] 3
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             348 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             348 
[1] "MTDH MUTATION ANALYSIS"
[1] 3
  MTDH MUTATED MTDH WILD-TYPE 
            12            355 
  MTDH MUTATED MTDH WILD-TYPE 
            12            355 
[1] "RGS22 MUTATION ANALYSIS"
[1] 3
  RGS22 MUTATED RGS22 WILD-TYPE 
             24             343 
  RGS22 MUTATED RGS22 WILD-TYPE 
             24             343 
[1] "DMRTB1 MUTATION ANALYSIS"
[1] 3
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              361 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              361 
[1] "MAP3K4 MUTATION ANALYSIS"
[1] 3
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              36              331 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              36              331 
[1] "PNPLA8 MUTATION ANALYSIS"
[1] 3
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              18              349 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              18              349 
[1] "ALX4 MUTATION ANALYSIS"
[1] 3
  ALX4 MUTATED ALX4 WILD-TYPE 
            11            356 
  ALX4 MUTATED ALX4 WILD-TYPE 
            11            356 
[1] "ULK1 MUTATION ANALYSIS"
[1] 3
  ULK1 MUTATED ULK1 WILD-TYPE 
            10            357 
  ULK1 MUTATED ULK1 WILD-TYPE 
            10            357 
[1] "POLM MUTATION ANALYSIS"
[1] 3
  POLM MUTATED POLM WILD-TYPE 
            11            356 
  POLM MUTATED POLM WILD-TYPE 
            11            356 
[1] "HIST1H1C MUTATION ANALYSIS"
[1] 3
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 4                363 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 4                363 
[1] "TGFBR1 MUTATION ANALYSIS"
[1] 3
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              14              353 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              14              353 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           23           344 
  CIC MUTATED CIC WILD-TYPE 
           23           344 
[1] "FBXO21 MUTATION ANALYSIS"
[1] 3
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               6              361 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               6              361 
[1] "PI4K2B MUTATION ANALYSIS"
[1] 3
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              10              357 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              10              357 
[1] "OLR1 MUTATION ANALYSIS"
[1] 3
  OLR1 MUTATED OLR1 WILD-TYPE 
             9            358 
  OLR1 MUTATED OLR1 WILD-TYPE 
             9            358 
[1] "CCDC160 MUTATION ANALYSIS"
[1] 3
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               10               357 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               10               357 
[1] "RNF111 MUTATION ANALYSIS"
[1] 3
  RNF111 MUTATED RNF111 WILD-TYPE 
              14              353 
  RNF111 MUTATED RNF111 WILD-TYPE 
              14              353 
[1] "RBM19 MUTATION ANALYSIS"
[1] 3
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             346 
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             346 
[1] "NEUROD1 MUTATION ANALYSIS"
[1] 3
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                8               359 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                8               359 
[1] "SLFN12L MUTATION ANALYSIS"
[1] 3
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                8               359 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                8               359 
[1] "UPF3A MUTATION ANALYSIS"
[1] 3
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             358 
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             358 
[1] "KDM3B MUTATION ANALYSIS"
[1] 3
  KDM3B MUTATED KDM3B WILD-TYPE 
             32             335 
  KDM3B MUTATED KDM3B WILD-TYPE 
             32             335 
[1] "RPGRIP1L MUTATION ANALYSIS"
[1] 3
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                17                350 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                17                350 
[1] "RBM12 MUTATION ANALYSIS"
[1] 3
  RBM12 MUTATED RBM12 WILD-TYPE 
             12             355 
  RBM12 MUTATED RBM12 WILD-TYPE 
             12             355 
[1] "PALB2 MUTATION ANALYSIS"
[1] 3
  PALB2 MUTATED PALB2 WILD-TYPE 
             19             348 
  PALB2 MUTATED PALB2 WILD-TYPE 
             19             348 
[1] "PCDH12 MUTATION ANALYSIS"
[1] 3
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              17              350 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              17              350 
[1] "MIER1 MUTATION ANALYSIS"
[1] 3
  MIER1 MUTATED MIER1 WILD-TYPE 
              6             361 
  MIER1 MUTATED MIER1 WILD-TYPE 
              6             361 
[1] "ICOSLG MUTATION ANALYSIS"
[1] 3
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               4              363 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               4              363 
[1] "ARNT2 MUTATION ANALYSIS"
[1] 3
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             12             355 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             12             355 
[1] "MRE11A MUTATION ANALYSIS"
[1] 3
  MRE11A MUTATED MRE11A WILD-TYPE 
              12              355 
  MRE11A MUTATED MRE11A WILD-TYPE 
              12              355 
[1] "DUSP1 MUTATION ANALYSIS"
[1] 3
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              6             361 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              6             361 
[1] "ERGIC1 MUTATION ANALYSIS"
[1] 3
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               4              363 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               4              363 
[1] "SYNRG MUTATION ANALYSIS"
[1] 3
  SYNRG MUTATED SYNRG WILD-TYPE 
             16             351 
  SYNRG MUTATED SYNRG WILD-TYPE 
             16             351 
[1] "BACE2 MUTATION ANALYSIS"
[1] 3
  BACE2 MUTATED BACE2 WILD-TYPE 
             10             357 
  BACE2 MUTATED BACE2 WILD-TYPE 
             10             357 
[1] "LMTK3 MUTATION ANALYSIS"
[1] 3
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             15             352 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             15             352 
[1] "RTP3 MUTATION ANALYSIS"
[1] 3
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            362 
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            362 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             19             348 
  BCL9L MUTATED BCL9L WILD-TYPE 
             19             348 
[1] "AKAP9 MUTATION ANALYSIS"
[1] 3
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             43             324 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             43             324 
[1] "ZNF547 MUTATION ANALYSIS"
[1] 3
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               8              359 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               8              359 
[1] "MRAS MUTATION ANALYSIS"
[1] 3
  MRAS MUTATED MRAS WILD-TYPE 
             4            363 
  MRAS MUTATED MRAS WILD-TYPE 
             4            363 
[1] "ARFIP1 MUTATION ANALYSIS"
[1] 3
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              355 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              355 
[1] "CNTFR MUTATION ANALYSIS"
[1] 3
  CNTFR MUTATED CNTFR WILD-TYPE 
             10             357 
  CNTFR MUTATED CNTFR WILD-TYPE 
             10             357 
[1] "RANBP17 MUTATION ANALYSIS"
[1] 3
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               10               357 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               10               357 
[1] "ZNF280C MUTATION ANALYSIS"
[1] 3
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                9               358 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                9               358 
[1] "SCN2A MUTATION ANALYSIS"
[1] 3
  SCN2A MUTATED SCN2A WILD-TYPE 
             45             322 
  SCN2A MUTATED SCN2A WILD-TYPE 
             45             322 
[1] "PLEK MUTATION ANALYSIS"
[1] 3
  PLEK MUTATED PLEK WILD-TYPE 
            12            355 
  PLEK MUTATED PLEK WILD-TYPE 
            12            355 
[1] "FAHD2A MUTATION ANALYSIS"
[1] 3
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               6              361 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               6              361 
[1] "SPANXN2 MUTATION ANALYSIS"
[1] 3
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               359 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               359 
[1] "KIF21A MUTATION ANALYSIS"
[1] 3
  KIF21A MUTATED KIF21A WILD-TYPE 
              24              343 
  KIF21A MUTATED KIF21A WILD-TYPE 
              24              343 
[1] "TAOK3 MUTATION ANALYSIS"
[1] 3
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             20             347 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             20             347 
[1] "ANKRD17 MUTATION ANALYSIS"
[1] 3
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               26               341 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               26               341 
[1] "WBP11 MUTATION ANALYSIS"
[1] 3
  WBP11 MUTATED WBP11 WILD-TYPE 
              8             359 
  WBP11 MUTATED WBP11 WILD-TYPE 
              8             359 
[1] "HNRNPH3 MUTATION ANALYSIS"
[1] 3
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                4               363 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                4               363 
[1] "ENTPD4 MUTATION ANALYSIS"
[1] 3
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              17              350 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              17              350 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             357 
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             357 
[1] "MCCC1 MUTATION ANALYSIS"
[1] 3
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             17             350 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             17             350 
[1] "MDH1 MUTATION ANALYSIS"
[1] 3
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            359 
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            359 
[1] "ARHGAP25 MUTATION ANALYSIS"
[1] 3
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                10                357 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                10                357 
[1] "SPEN MUTATION ANALYSIS"
[1] 3
  SPEN MUTATED SPEN WILD-TYPE 
            31            336 
  SPEN MUTATED SPEN WILD-TYPE 
            31            336 
[1] "GPR75 MUTATION ANALYSIS"
[1] 3
  GPR75 MUTATED GPR75 WILD-TYPE 
              8             359 
  GPR75 MUTATED GPR75 WILD-TYPE 
              8             359 
[1] "HERC5 MUTATION ANALYSIS"
[1] 3
  HERC5 MUTATED HERC5 WILD-TYPE 
             18             349 
  HERC5 MUTATED HERC5 WILD-TYPE 
             18             349 
[1] "AKR1C4 MUTATION ANALYSIS"
[1] 3
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               9              358 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               9              358 
[1] "LIG1 MUTATION ANALYSIS"
[1] 3
  LIG1 MUTATED LIG1 WILD-TYPE 
            16            351 
  LIG1 MUTATED LIG1 WILD-TYPE 
            16            351 
[1] "ARHGEF10 MUTATION ANALYSIS"
[1] 3
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                23                344 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                23                344 
[1] "OVCH1 MUTATION ANALYSIS"
[1] 3
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             22             345 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             22             345 
[1] "RRS1 MUTATION ANALYSIS"
[1] 3
  RRS1 MUTATED RRS1 WILD-TYPE 
             4            363 
  RRS1 MUTATED RRS1 WILD-TYPE 
             4            363 
[1] "RFXAP MUTATION ANALYSIS"
[1] 3
  RFXAP MUTATED RFXAP WILD-TYPE 
              6             361 
  RFXAP MUTATED RFXAP WILD-TYPE 
              6             361 
[1] "RBAK MUTATION ANALYSIS"
[1] 3
  RBAK MUTATED RBAK WILD-TYPE 
            17            350 
  RBAK MUTATED RBAK WILD-TYPE 
            17            350 
[1] "ZHX1 MUTATION ANALYSIS"
[1] 3
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             9            358 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             9            358 
[1] "DOCK10 MUTATION ANALYSIS"
[1] 3
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              25              342 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              25              342 
[1] "CHEK2 MUTATION ANALYSIS"
[1] 3
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             357 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             357 
[1] "USP9X MUTATION ANALYSIS"
[1] 3
  USP9X MUTATED USP9X WILD-TYPE 
             31             336 
  USP9X MUTATED USP9X WILD-TYPE 
             31             336 
[1] "OR5B2 MUTATION ANALYSIS"
[1] 3
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             12             355 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             12             355 
[1] "IFNAR1 MUTATION ANALYSIS"
[1] 3
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              360 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              360 
[1] "ALDH2 MUTATION ANALYSIS"
[1] 3
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             11             356 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             11             356 
[1] "ZNF14 MUTATION ANALYSIS"
[1] 3
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             13             354 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             13             354 
[1] "CYP4A22 MUTATION ANALYSIS"
[1] 3
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               13               354 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               13               354 
[1] "AIFM1 MUTATION ANALYSIS"
[1] 3
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             356 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             356 
[1] "ST3GAL6 MUTATION ANALYSIS"
[1] 3
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               10               357 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               10               357 
[1] "NOVA1 MUTATION ANALYSIS"
[1] 3
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             14             353 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             14             353 
[1] "CD244 MUTATION ANALYSIS"
[1] 3
  CD244 MUTATED CD244 WILD-TYPE 
              7             360 
  CD244 MUTATED CD244 WILD-TYPE 
              7             360 
[1] "ARHGEF3 MUTATION ANALYSIS"
[1] 3
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               11               356 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               11               356 
[1] "MRPL13 MUTATION ANALYSIS"
[1] 3
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               6              361 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               6              361 
[1] "STK36 MUTATION ANALYSIS"
[1] 3
  STK36 MUTATED STK36 WILD-TYPE 
             14             353 
  STK36 MUTATED STK36 WILD-TYPE 
             14             353 
[1] "IL13RA2 MUTATION ANALYSIS"
[1] 3
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               14               353 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               14               353 
[1] "FAM26E MUTATION ANALYSIS"
[1] 3
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              362 
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              362 
[1] "ZNF182 MUTATION ANALYSIS"
[1] 3
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              13              354 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              13              354 
[1] "GNA11 MUTATION ANALYSIS"
[1] 3
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             360 
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             360 
[1] "KDM2B MUTATION ANALYSIS"
[1] 3
  KDM2B MUTATED KDM2B WILD-TYPE 
             20             347 
  KDM2B MUTATED KDM2B WILD-TYPE 
             20             347 
[1] "C17ORF47 MUTATION ANALYSIS"
[1] 3
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 5                362 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 5                362 
[1] "KCTD16 MUTATION ANALYSIS"
[1] 3
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              12              355 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              12              355 
[1] "LNPEP MUTATION ANALYSIS"
[1] 3
  LNPEP MUTATED LNPEP WILD-TYPE 
             18             349 
  LNPEP MUTATED LNPEP WILD-TYPE 
             18             349 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
             15             352 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
             15             352 
[1] "FRS3 MUTATION ANALYSIS"
[1] 3
  FRS3 MUTATED FRS3 WILD-TYPE 
            10            357 
  FRS3 MUTATED FRS3 WILD-TYPE 
            10            357 
[1] "POLE MUTATION ANALYSIS"
[1] 3
  POLE MUTATED POLE WILD-TYPE 
            31            336 
  POLE MUTATED POLE WILD-TYPE 
            31            336 
[1] "NIPA2 MUTATION ANALYSIS"
[1] 3
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              7             360 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              7             360 
[1] "CDH10 MUTATION ANALYSIS"
[1] 3
  CDH10 MUTATED CDH10 WILD-TYPE 
             39             328 
  CDH10 MUTATED CDH10 WILD-TYPE 
             39             328 
[1] "CATSPER1 MUTATION ANALYSIS"
[1] 3
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                16                351 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                16                351 
[1] "FOXN3 MUTATION ANALYSIS"
[1] 3
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             356 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             356 
[1] "REXO4 MUTATION ANALYSIS"
[1] 3
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             362 
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             362 
[1] "OTX2 MUTATION ANALYSIS"
[1] 3
  OTX2 MUTATED OTX2 WILD-TYPE 
             6            361 
  OTX2 MUTATED OTX2 WILD-TYPE 
             6            361 
[1] "NGEF MUTATION ANALYSIS"
[1] 3
  NGEF MUTATED NGEF WILD-TYPE 
            16            351 
  NGEF MUTATED NGEF WILD-TYPE 
            16            351 
[1] "GGT5 MUTATION ANALYSIS"
[1] 3
  GGT5 MUTATED GGT5 WILD-TYPE 
            14            353 
  GGT5 MUTATED GGT5 WILD-TYPE 
            14            353 
[1] "CXORF38 MUTATION ANALYSIS"
[1] 3
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                5               362 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                5               362 
[1] "BST2 MUTATION ANALYSIS"
[1] 3
  BST2 MUTATED BST2 WILD-TYPE 
             6            361 
  BST2 MUTATED BST2 WILD-TYPE 
             6            361 
[1] "SFRS15 MUTATION ANALYSIS"
[1] 3
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              19              348 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              19              348 
[1] "EIF2AK4 MUTATION ANALYSIS"
[1] 3
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               18               349 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               18               349 
[1] "LAS1L MUTATION ANALYSIS"
[1] 3
  LAS1L MUTATED LAS1L WILD-TYPE 
              9             358 
  LAS1L MUTATED LAS1L WILD-TYPE 
              9             358 
[1] "CATSPER4 MUTATION ANALYSIS"
[1] 3
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                11                356 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                11                356 
[1] "OR4M2 MUTATION ANALYSIS"
[1] 3
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             14             353 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             14             353 
[1] "HIVEP2 MUTATION ANALYSIS"
[1] 3
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              19              348 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              19              348 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              34              333 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              34              333 
[1] "GPR115 MUTATION ANALYSIS"
[1] 3
  GPR115 MUTATED GPR115 WILD-TYPE 
              18              349 
  GPR115 MUTATED GPR115 WILD-TYPE 
              18              349 
[1] "NCOA6 MUTATION ANALYSIS"
[1] 3
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             24             343 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             24             343 
[1] "LAMC1 MUTATION ANALYSIS"
[1] 3
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             21             346 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             21             346 
[1] "CYP1B1 MUTATION ANALYSIS"
[1] 3
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              11              356 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              11              356 
[1] "AFM MUTATION ANALYSIS"
[1] 3
  AFM MUTATED AFM WILD-TYPE 
           13           354 
  AFM MUTATED AFM WILD-TYPE 
           13           354 
[1] "SLC22A9 MUTATION ANALYSIS"
[1] 3
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                9               358 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                9               358 
[1] "DDX59 MUTATION ANALYSIS"
[1] 3
  DDX59 MUTATED DDX59 WILD-TYPE 
             11             356 
  DDX59 MUTATED DDX59 WILD-TYPE 
             11             356 
[1] "SLC25A13 MUTATION ANALYSIS"
[1] 3
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                14                353 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                14                353 
[1] "EXD2 MUTATION ANALYSIS"
[1] 3
  EXD2 MUTATED EXD2 WILD-TYPE 
            10            357 
  EXD2 MUTATED EXD2 WILD-TYPE 
            10            357 
[1] "ATP8B2 MUTATION ANALYSIS"
[1] 3
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
              17              350 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
              17              350 
[1] "TBL1XR1 MUTATION ANALYSIS"
[1] 3
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               13               354 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               13               354 
[1] "SPANXC MUTATION ANALYSIS"
[1] 3
  SPANXC MUTATED SPANXC WILD-TYPE 
               4              363 
  SPANXC MUTATED SPANXC WILD-TYPE 
               4              363 
[1] "HORMAD1 MUTATION ANALYSIS"
[1] 3
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               13               354 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               13               354 
[1] "TMEM131 MUTATION ANALYSIS"
[1] 3
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               21               346 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               21               346 
[1] "PVRL4 MUTATION ANALYSIS"
[1] 3
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              9             358 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              9             358 
[1] "C12ORF49 MUTATION ANALYSIS"
[1] 3
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                363 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                363 
[1] "CWF19L2 MUTATION ANALYSIS"
[1] 3
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               15               352 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               15               352 
[1] "ATAD5 MUTATION ANALYSIS"
[1] 3
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             21             346 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             21             346 
[1] "PHF21A MUTATION ANALYSIS"
[1] 3
  PHF21A MUTATED PHF21A WILD-TYPE 
              11              356 
  PHF21A MUTATED PHF21A WILD-TYPE 
              11              356 
[1] "BMPR1A MUTATION ANALYSIS"
[1] 3
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              349 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              349 
[1] "C14ORF39 MUTATION ANALYSIS"
[1] 3
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                13                354 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                13                354 
[1] "TAT MUTATION ANALYSIS"
[1] 3
  TAT MUTATED TAT WILD-TYPE 
           14           353 
  TAT MUTATED TAT WILD-TYPE 
           14           353 
[1] "FAS MUTATION ANALYSIS"
[1] 3
  FAS MUTATED FAS WILD-TYPE 
            7           360 
  FAS MUTATED FAS WILD-TYPE 
            7           360 
[1] "TXNDC17 MUTATION ANALYSIS"
[1] 3
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               362 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               362 
[1] "SMTN MUTATION ANALYSIS"
[1] 3
  SMTN MUTATED SMTN WILD-TYPE 
            14            353 
  SMTN MUTATED SMTN WILD-TYPE 
            14            353 
[1] "STRADB MUTATION ANALYSIS"
[1] 3
  STRADB MUTATED STRADB WILD-TYPE 
               5              362 
  STRADB MUTATED STRADB WILD-TYPE 
               5              362 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              17              350 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              17              350 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           26           341 
  WT1 MUTATED WT1 WILD-TYPE 
           26           341 
[1] "EFHC1 MUTATION ANALYSIS"
[1] 3
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             11             356 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             11             356 
[1] "MTMR8 MUTATION ANALYSIS"
[1] 3
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             11             356 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             11             356 
[1] "ACTL6A MUTATION ANALYSIS"
[1] 3
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               6              361 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               6              361 
[1] "FAM163B MUTATION ANALYSIS"
[1] 3
  FAM163B MUTATED FAM163B WILD-TYPE 
                4               363 
  FAM163B MUTATED FAM163B WILD-TYPE 
                4               363 
[1] "GPR22 MUTATION ANALYSIS"
[1] 3
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             358 
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             358 
[1] "MAPK9 MUTATION ANALYSIS"
[1] 3
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             10             357 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             10             357 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            54            313 
  APOB MUTATED APOB WILD-TYPE 
            54            313 
[1] "OR4D2 MUTATION ANALYSIS"
[1] 3
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             363 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             363 
[1] "DSG4 MUTATION ANALYSIS"
[1] 3
  DSG4 MUTATED DSG4 WILD-TYPE 
            21            346 
  DSG4 MUTATED DSG4 WILD-TYPE 
            21            346 
[1] "KIAA0319L MUTATION ANALYSIS"
[1] 3
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 19                 348 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 19                 348 
[1] "TXNDC6 MUTATION ANALYSIS"
[1] 3
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               8              359 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               8              359 
[1] "PFN4 MUTATION ANALYSIS"
[1] 3
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            361 
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            361 
[1] "NOS3 MUTATION ANALYSIS"
[1] 3
  NOS3 MUTATED NOS3 WILD-TYPE 
            18            349 
  NOS3 MUTATED NOS3 WILD-TYPE 
            18            349 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            358 
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            358 
[1] "BCHE MUTATION ANALYSIS"
[1] 3
  BCHE MUTATED BCHE WILD-TYPE 
            25            342 
  BCHE MUTATED BCHE WILD-TYPE 
            25            342 
[1] "SLC27A2 MUTATION ANALYSIS"
[1] 3
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                6               361 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                6               361 
[1] "KRT19 MUTATION ANALYSIS"
[1] 3
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             363 
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             363 
[1] "LASS3 MUTATION ANALYSIS"
[1] 3
  LASS3 MUTATED LASS3 WILD-TYPE 
             14             353 
  LASS3 MUTATED LASS3 WILD-TYPE 
             14             353 
[1] "GAB1 MUTATION ANALYSIS"
[1] 3
  GAB1 MUTATED GAB1 WILD-TYPE 
            15            352 
  GAB1 MUTATED GAB1 WILD-TYPE 
            15            352 
[1] "ZNF518B MUTATION ANALYSIS"
[1] 3
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               10               357 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               10               357 
[1] "C14ORF159 MUTATION ANALYSIS"
[1] 3
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  9                 358 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  9                 358 
[1] "EFEMP1 MUTATION ANALYSIS"
[1] 3
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              347 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              347 
[1] "PDP2 MUTATION ANALYSIS"
[1] 3
  PDP2 MUTATED PDP2 WILD-TYPE 
             5            362 
  PDP2 MUTATED PDP2 WILD-TYPE 
             5            362 
[1] "ENSA MUTATION ANALYSIS"
[1] 3
  ENSA MUTATED ENSA WILD-TYPE 
             5            362 
  ENSA MUTATED ENSA WILD-TYPE 
             5            362 
[1] "C20ORF177 MUTATION ANALYSIS"
[1] 3
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  9                 358 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  9                 358 
[1] "POMGNT1 MUTATION ANALYSIS"
[1] 3
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               359 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               359 
[1] "SMG1 MUTATION ANALYSIS"
[1] 3
  SMG1 MUTATED SMG1 WILD-TYPE 
            25            342 
  SMG1 MUTATED SMG1 WILD-TYPE 
            25            342 
[1] "HMCN1 MUTATION ANALYSIS"
[1] 3
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             72             295 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             72             295 
[1] "CHUK MUTATION ANALYSIS"
[1] 3
  CHUK MUTATED CHUK WILD-TYPE 
            21            346 
  CHUK MUTATED CHUK WILD-TYPE 
            21            346 
[1] "MYH3 MUTATION ANALYSIS"
[1] 3
  MYH3 MUTATED MYH3 WILD-TYPE 
            33            334 
  MYH3 MUTATED MYH3 WILD-TYPE 
            33            334 
[1] "ING2 MUTATION ANALYSIS"
[1] 3
  ING2 MUTATED ING2 WILD-TYPE 
             6            361 
  ING2 MUTATED ING2 WILD-TYPE 
             6            361 
[1] "VAV3 MUTATION ANALYSIS"
[1] 3
  VAV3 MUTATED VAV3 WILD-TYPE 
            24            343 
  VAV3 MUTATED VAV3 WILD-TYPE 
            24            343 
[1] "UIMC1 MUTATION ANALYSIS"
[1] 3
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              6             361 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              6             361 
[1] "LAMB4 MUTATION ANALYSIS"
[1] 3
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             26             341 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             26             341 
[1] "MOV10L1 MUTATION ANALYSIS"
[1] 3
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               15               352 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               15               352 
[1] "CTBP2 MUTATION ANALYSIS"
[1] 3
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              6             361 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              6             361 
[1] "TM9SF2 MUTATION ANALYSIS"
[1] 3
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              10              357 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              10              357 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               30               337 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               30               337 
[1] "ART5 MUTATION ANALYSIS"
[1] 3
  ART5 MUTATED ART5 WILD-TYPE 
             9            358 
  ART5 MUTATED ART5 WILD-TYPE 
             9            358 
[1] "ASPG MUTATION ANALYSIS"
[1] 3
  ASPG MUTATED ASPG WILD-TYPE 
             7            360 
  ASPG MUTATED ASPG WILD-TYPE 
             7            360 
[1] "PLEKHB2 MUTATION ANALYSIS"
[1] 3
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               361 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               361 
[1] "TMTC4 MUTATION ANALYSIS"
[1] 3
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             13             354 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             13             354 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             26             341 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             26             341 
[1] "DNAJC16 MUTATION ANALYSIS"
[1] 3
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                9               358 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                9               358 
[1] "PHF1 MUTATION ANALYSIS"
[1] 3
  PHF1 MUTATED PHF1 WILD-TYPE 
             6            361 
  PHF1 MUTATED PHF1 WILD-TYPE 
             6            361 
[1] "OR2V2 MUTATION ANALYSIS"
[1] 3
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             361 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             361 
[1] "EIF2B5 MUTATION ANALYSIS"
[1] 3
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              15              352 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              15              352 
[1] "SR140 MUTATION ANALYSIS"
[1] 3
  SR140 MUTATED SR140 WILD-TYPE 
             11             356 
  SR140 MUTATED SR140 WILD-TYPE 
             11             356 
[1] "ABI3BP MUTATION ANALYSIS"
[1] 3
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              21              346 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              21              346 
[1] "FBN2 MUTATION ANALYSIS"
[1] 3
  FBN2 MUTATED FBN2 WILD-TYPE 
            43            324 
  FBN2 MUTATED FBN2 WILD-TYPE 
            43            324 
[1] "FAM98B MUTATION ANALYSIS"
[1] 3
  FAM98B MUTATED FAM98B WILD-TYPE 
               4              363 
  FAM98B MUTATED FAM98B WILD-TYPE 
               4              363 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             21             346 
  KDM5C MUTATED KDM5C WILD-TYPE 
             21             346 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             21             346 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             21             346 
[1] "CHRNA3 MUTATION ANALYSIS"
[1] 3
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              10              357 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              10              357 
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            24            343 
  FLT3 MUTATED FLT3 WILD-TYPE 
            24            343 
[1] "STX16 MUTATION ANALYSIS"
[1] 3
  STX16 MUTATED STX16 WILD-TYPE 
              7             360 
  STX16 MUTATED STX16 WILD-TYPE 
              7             360 
[1] "ERBB2IP MUTATION ANALYSIS"
[1] 3
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               15               352 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               15               352 
[1] "RNF145 MUTATION ANALYSIS"
[1] 3
  RNF145 MUTATED RNF145 WILD-TYPE 
              14              353 
  RNF145 MUTATED RNF145 WILD-TYPE 
              14              353 
[1] "KTN1 MUTATION ANALYSIS"
[1] 3
  KTN1 MUTATED KTN1 WILD-TYPE 
            18            349 
  KTN1 MUTATED KTN1 WILD-TYPE 
            18            349 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
             32             335 
  NIPBL MUTATED NIPBL WILD-TYPE 
             32             335 
[1] "DOCK1 MUTATION ANALYSIS"
[1] 3
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             24             343 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             24             343 
[1] "CDH8 MUTATION ANALYSIS"
[1] 3
  CDH8 MUTATED CDH8 WILD-TYPE 
            33            334 
  CDH8 MUTATED CDH8 WILD-TYPE 
            33            334 
[1] "POLDIP3 MUTATION ANALYSIS"
[1] 3
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                5               362 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                5               362 
[1] "KLRC3 MUTATION ANALYSIS"
[1] 3
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              5             362 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              5             362 
[1] "ARMC9 MUTATION ANALYSIS"
[1] 3
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              7             360 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              7             360 
[1] "MAGEB2 MUTATION ANALYSIS"
[1] 3
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              11              356 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              11              356 
[1] "ZNF83 MUTATION ANALYSIS"
[1] 3
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             17             350 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             17             350 
[1] "ADAMTS4 MUTATION ANALYSIS"
[1] 3
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               14               353 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               14               353 
[1] "TMEM50B MUTATION ANALYSIS"
[1] 3
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                6               361 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                6               361 
[1] "CDH22 MUTATION ANALYSIS"
[1] 3
  CDH22 MUTATED CDH22 WILD-TYPE 
             16             351 
  CDH22 MUTATED CDH22 WILD-TYPE 
             16             351 
[1] "LRRC37B MUTATION ANALYSIS"
[1] 3
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                6               361 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                6               361 
[1] "C19ORF66 MUTATION ANALYSIS"
[1] 3
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                363 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                363 
[1] "WWC3 MUTATION ANALYSIS"
[1] 3
  WWC3 MUTATED WWC3 WILD-TYPE 
            22            345 
  WWC3 MUTATED WWC3 WILD-TYPE 
            22            345 
[1] "ZBTB24 MUTATION ANALYSIS"
[1] 3
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               8              359 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               8              359 
[1] "TMEM48 MUTATION ANALYSIS"
[1] 3
  TMEM48 MUTATED TMEM48 WILD-TYPE 
              10              357 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
              10              357 
[1] "EXPH5 MUTATION ANALYSIS"
[1] 3
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             21             346 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             21             346 
[1] "MARVELD2 MUTATION ANALYSIS"
[1] 3
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                10                357 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                10                357 
[1] "GDE1 MUTATION ANALYSIS"
[1] 3
  GDE1 MUTATED GDE1 WILD-TYPE 
             5            362 
  GDE1 MUTATED GDE1 WILD-TYPE 
             5            362 
[1] "ZNF721 MUTATION ANALYSIS"
[1] 3
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              15              352 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              15              352 
[1] "PAX6 MUTATION ANALYSIS"
[1] 3
  PAX6 MUTATED PAX6 WILD-TYPE 
            14            353 
  PAX6 MUTATED PAX6 WILD-TYPE 
            14            353 
[1] "ENPP1 MUTATION ANALYSIS"
[1] 3
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             14             353 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             14             353 
[1] "CHM MUTATION ANALYSIS"
[1] 3
  CHM MUTATED CHM WILD-TYPE 
            4           363 
  CHM MUTATED CHM WILD-TYPE 
            4           363 
[1] "THAP9 MUTATION ANALYSIS"
[1] 3
  THAP9 MUTATED THAP9 WILD-TYPE 
             12             355 
  THAP9 MUTATED THAP9 WILD-TYPE 
             12             355 
[1] "C1QL3 MUTATION ANALYSIS"
[1] 3
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             363 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             363 
[1] "HCRTR2 MUTATION ANALYSIS"
[1] 3
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              360 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              360 
[1] "C9ORF71 MUTATION ANALYSIS"
[1] 3
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               363 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               363 
[1] "RIMBP3 MUTATION ANALYSIS"
[1] 3
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              361 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              361 
[1] "HELQ MUTATION ANALYSIS"
[1] 3
  HELQ MUTATED HELQ WILD-TYPE 
            18            349 
  HELQ MUTATED HELQ WILD-TYPE 
            18            349 
[1] "VPS13B MUTATION ANALYSIS"
[1] 3
  VPS13B MUTATED VPS13B WILD-TYPE 
              52              315 
  VPS13B MUTATED VPS13B WILD-TYPE 
              52              315 
[1] "ZNF620 MUTATION ANALYSIS"
[1] 3
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               8              359 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               8              359 
[1] "ZNF570 MUTATION ANALYSIS"
[1] 3
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               9              358 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               9              358 
[1] "AP1G2 MUTATION ANALYSIS"
[1] 3
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             13             354 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             13             354 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                13                354 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                13                354 
[1] "FER MUTATION ANALYSIS"
[1] 3
  FER MUTATED FER WILD-TYPE 
           15           352 
  FER MUTATED FER WILD-TYPE 
           15           352 
[1] "SCN3A MUTATION ANALYSIS"
[1] 3
  SCN3A MUTATED SCN3A WILD-TYPE 
             42             325 
  SCN3A MUTATED SCN3A WILD-TYPE 
             42             325 
[1] "IQGAP2 MUTATION ANALYSIS"
[1] 3
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              21              346 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              21              346 
[1] "CD3D MUTATION ANALYSIS"
[1] 3
  CD3D MUTATED CD3D WILD-TYPE 
             4            363 
  CD3D MUTATED CD3D WILD-TYPE 
             4            363 
[1] "ADORA3 MUTATION ANALYSIS"
[1] 3
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              14              353 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              14              353 
[1] "ALDOB MUTATION ANALYSIS"
[1] 3
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             352 
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             352 
[1] "ELFN2 MUTATION ANALYSIS"
[1] 3
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             358 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             358 
[1] "AWAT1 MUTATION ANALYSIS"
[1] 3
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              8             359 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              8             359 
[1] "EXT1 MUTATION ANALYSIS"
[1] 3
  EXT1 MUTATED EXT1 WILD-TYPE 
            18            349 
  EXT1 MUTATED EXT1 WILD-TYPE 
            18            349 
[1] "DNAH17 MUTATION ANALYSIS"
[1] 3
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              30              337 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              30              337 
[1] "SYNE1 MUTATION ANALYSIS"
[1] 3
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            118             249 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            118             249 
[1] "C1ORF35 MUTATION ANALYSIS"
[1] 3
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                4               363 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                4               363 
[1] "POLQ MUTATION ANALYSIS"
[1] 3
  POLQ MUTATED POLQ WILD-TYPE 
            30            337 
  POLQ MUTATED POLQ WILD-TYPE 
            30            337 
[1] "BAI3 MUTATION ANALYSIS"
[1] 3
  BAI3 MUTATED BAI3 WILD-TYPE 
            43            324 
  BAI3 MUTATED BAI3 WILD-TYPE 
            43            324 
[1] "WNK3 MUTATION ANALYSIS"
[1] 3
  WNK3 MUTATED WNK3 WILD-TYPE 
            24            343 
  WNK3 MUTATED WNK3 WILD-TYPE 
            24            343 
[1] "CASC1 MUTATION ANALYSIS"
[1] 3
  CASC1 MUTATED CASC1 WILD-TYPE 
             12             355 
  CASC1 MUTATED CASC1 WILD-TYPE 
             12             355 
[1] "IL2RG MUTATION ANALYSIS"
[1] 3
  IL2RG MUTATED IL2RG WILD-TYPE 
              7             360 
  IL2RG MUTATED IL2RG WILD-TYPE 
              7             360 
[1] "ACOT9 MUTATION ANALYSIS"
[1] 3
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              4             363 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              4             363 
[1] "DCTN5 MUTATION ANALYSIS"
[1] 3
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             361 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             361 
[1] "USH2A MUTATION ANALYSIS"
[1] 3
  USH2A MUTATED USH2A WILD-TYPE 
             74             293 
  USH2A MUTATED USH2A WILD-TYPE 
             74             293 
[1] "PARP1 MUTATION ANALYSIS"
[1] 3
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             353 
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             353 
[1] "CCDC141 MUTATION ANALYSIS"
[1] 3
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               21               346 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               21               346 
[1] "OAS1 MUTATION ANALYSIS"
[1] 3
  OAS1 MUTATED OAS1 WILD-TYPE 
             8            359 
  OAS1 MUTATED OAS1 WILD-TYPE 
             8            359 
[1] "KIAA0406 MUTATION ANALYSIS"
[1] 3
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                14                353 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                14                353 
[1] "DNASE1L3 MUTATION ANALYSIS"
[1] 3
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                359 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                359 
[1] "OR8A1 MUTATION ANALYSIS"
[1] 3
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              4             363 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              4             363 
[1] "RANBP1 MUTATION ANALYSIS"
[1] 3
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              361 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              361 
[1] "RBMX2 MUTATION ANALYSIS"
[1] 3
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             11             356 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             11             356 
[1] "SLC35A5 MUTATION ANALYSIS"
[1] 3
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                7               360 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                7               360 
[1] "RAD51AP2 MUTATION ANALYSIS"
[1] 3
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                16                351 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                16                351 
[1] "INADL MUTATION ANALYSIS"
[1] 3
  INADL MUTATED INADL WILD-TYPE 
             13             354 
  INADL MUTATED INADL WILD-TYPE 
             13             354 
[1] "LEF1 MUTATION ANALYSIS"
[1] 3
  LEF1 MUTATED LEF1 WILD-TYPE 
             9            358 
  LEF1 MUTATED LEF1 WILD-TYPE 
             9            358 
[1] "SLC2A3 MUTATION ANALYSIS"
[1] 3
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              356 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              356 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            33            334 
  MLL4 MUTATED MLL4 WILD-TYPE 
            33            334 
[1] "MTA2 MUTATION ANALYSIS"
[1] 3
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            355 
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            355 
[1] "MDN1 MUTATION ANALYSIS"
[1] 3
  MDN1 MUTATED MDN1 WILD-TYPE 
            53            314 
  MDN1 MUTATED MDN1 WILD-TYPE 
            53            314 
[1] "OR10G4 MUTATION ANALYSIS"
[1] 3
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               5              362 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               5              362 
[1] "NEB MUTATION ANALYSIS"
[1] 3
  NEB MUTATED NEB WILD-TYPE 
           57           310 
  NEB MUTATED NEB WILD-TYPE 
           57           310 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              351 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              351 
[1] "OSTM1 MUTATION ANALYSIS"
[1] 3
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             362 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             362 
[1] "UGT1A7 MUTATION ANALYSIS"
[1] 3
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              359 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              359 
[1] "ZNF658 MUTATION ANALYSIS"
[1] 3
  ZNF658 MUTATED ZNF658 WILD-TYPE 
              10              357 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
              10              357 
[1] "ESCO2 MUTATION ANALYSIS"
[1] 3
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             10             357 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             10             357 
[1] "SV2A MUTATION ANALYSIS"
[1] 3
  SV2A MUTATED SV2A WILD-TYPE 
            21            346 
  SV2A MUTATED SV2A WILD-TYPE 
            21            346 
[1] "PSMB8 MUTATION ANALYSIS"
[1] 3
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              4             363 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              4             363 
[1] "CAMSAP1L1 MUTATION ANALYSIS"
[1] 3
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 21                 346 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 21                 346 
[1] "MRPS18B MUTATION ANALYSIS"
[1] 3
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                4               363 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                4               363 
[1] "INSRR MUTATION ANALYSIS"
[1] 3
  INSRR MUTATED INSRR WILD-TYPE 
             26             341 
  INSRR MUTATED INSRR WILD-TYPE 
             26             341 
[1] "PAAF1 MUTATION ANALYSIS"
[1] 3
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              5             362 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              5             362 
[1] "JAK3 MUTATION ANALYSIS"
[1] 3
  JAK3 MUTATED JAK3 WILD-TYPE 
            24            343 
  JAK3 MUTATED JAK3 WILD-TYPE 
            24            343 
[1] "TMEM45A MUTATION ANALYSIS"
[1] 3
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               363 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               363 
[1] "UAP1L1 MUTATION ANALYSIS"
[1] 3
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               7              360 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               7              360 
[1] "OR6A2 MUTATION ANALYSIS"
[1] 3
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             359 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             359 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              17              350 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              17              350 
[1] "OR2Y1 MUTATION ANALYSIS"
[1] 3
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              7             360 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              7             360 
[1] "THOC6 MUTATION ANALYSIS"
[1] 3
  THOC6 MUTATED THOC6 WILD-TYPE 
              8             359 
  THOC6 MUTATED THOC6 WILD-TYPE 
              8             359 
[1] "VASH1 MUTATION ANALYSIS"
[1] 3
  VASH1 MUTATED VASH1 WILD-TYPE 
              5             362 
  VASH1 MUTATED VASH1 WILD-TYPE 
              5             362 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              17              350 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              17              350 
[1] "SGK3 MUTATION ANALYSIS"
[1] 3
  SGK3 MUTATED SGK3 WILD-TYPE 
             8            359 
  SGK3 MUTATED SGK3 WILD-TYPE 
             8            359 
[1] "ARHGAP32 MUTATION ANALYSIS"
[1] 3
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                24                343 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                24                343 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            352 
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            352 
[1] "SLC41A2 MUTATION ANALYSIS"
[1] 3
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                8               359 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                8               359 
[1] "EAPP MUTATION ANALYSIS"
[1] 3
  EAPP MUTATED EAPP WILD-TYPE 
             4            363 
  EAPP MUTATED EAPP WILD-TYPE 
             4            363 
[1] "DNAJC7 MUTATION ANALYSIS"
[1] 3
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               7              360 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               7              360 
[1] "LBP MUTATION ANALYSIS"
[1] 3
  LBP MUTATED LBP WILD-TYPE 
            7           360 
  LBP MUTATED LBP WILD-TYPE 
            7           360 
[1] "ZNF180 MUTATION ANALYSIS"
[1] 3
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              14              353 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              14              353 
[1] "PCDH19 MUTATION ANALYSIS"
[1] 3
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              14              353 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              14              353 
[1] "MACF1 MUTATION ANALYSIS"
[1] 3
  MACF1 MUTATED MACF1 WILD-TYPE 
             58             309 
  MACF1 MUTATED MACF1 WILD-TYPE 
             58             309 
[1] "MYH15 MUTATION ANALYSIS"
[1] 3
  MYH15 MUTATED MYH15 WILD-TYPE 
             25             342 
  MYH15 MUTATED MYH15 WILD-TYPE 
             25             342 
[1] "PLK2 MUTATION ANALYSIS"
[1] 3
  PLK2 MUTATED PLK2 WILD-TYPE 
             6            361 
  PLK2 MUTATED PLK2 WILD-TYPE 
             6            361 
[1] "ZNF619 MUTATION ANALYSIS"
[1] 3
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              11              356 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              11              356 
[1] "WNK1 MUTATION ANALYSIS"
[1] 3
  WNK1 MUTATED WNK1 WILD-TYPE 
            19            348 
  WNK1 MUTATED WNK1 WILD-TYPE 
            19            348 
[1] "TRIM54 MUTATION ANALYSIS"
[1] 3
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               9              358 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               9              358 
[1] "GTF3C3 MUTATION ANALYSIS"
[1] 3
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              15              352 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              15              352 
[1] "OR51A4 MUTATION ANALYSIS"
[1] 3
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               8              359 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               8              359 
[1] "SLC25A17 MUTATION ANALYSIS"
[1] 3
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 7                360 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 7                360 
[1] "GNA14 MUTATION ANALYSIS"
[1] 3
  GNA14 MUTATED GNA14 WILD-TYPE 
             10             357 
  GNA14 MUTATED GNA14 WILD-TYPE 
             10             357 
[1] "PREX2 MUTATION ANALYSIS"
[1] 3
  PREX2 MUTATED PREX2 WILD-TYPE 
             31             336 
  PREX2 MUTATED PREX2 WILD-TYPE 
             31             336 
[1] "MAOA MUTATION ANALYSIS"
[1] 3
  MAOA MUTATED MAOA WILD-TYPE 
             5            362 
  MAOA MUTATED MAOA WILD-TYPE 
             5            362 
[1] "CD55 MUTATION ANALYSIS"
[1] 3
  CD55 MUTATED CD55 WILD-TYPE 
             7            360 
  CD55 MUTATED CD55 WILD-TYPE 
             7            360 
[1] "MATN3 MUTATION ANALYSIS"
[1] 3
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             361 
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             361 
[1] "OR6C75 MUTATION ANALYSIS"
[1] 3
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               7              360 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               7              360 
[1] "NAP1L1 MUTATION ANALYSIS"
[1] 3
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               7              360 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               7              360 
[1] "SLC22A3 MUTATION ANALYSIS"
[1] 3
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               12               355 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               12               355 
[1] "HRSP12 MUTATION ANALYSIS"
[1] 3
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               6              361 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               6              361 
[1] "RYR2 MUTATION ANALYSIS"
[1] 3
  RYR2 MUTATED RYR2 WILD-TYPE 
            84            283 
  RYR2 MUTATED RYR2 WILD-TYPE 
            84            283 
[1] "ZNF605 MUTATION ANALYSIS"
[1] 3
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              359 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              359 
[1] "C1ORF168 MUTATION ANALYSIS"
[1] 3
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                14                353 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                14                353 
[1] "PGAP3 MUTATION ANALYSIS"
[1] 3
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              7             360 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              7             360 
[1] "AGTR2 MUTATION ANALYSIS"
[1] 3
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             15             352 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             15             352 
[1] "RAE1 MUTATION ANALYSIS"
[1] 3
  RAE1 MUTATED RAE1 WILD-TYPE 
             6            361 
  RAE1 MUTATED RAE1 WILD-TYPE 
             6            361 
[1] "PAGE2 MUTATION ANALYSIS"
[1] 3
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              8             359 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              8             359 
[1] "HNMT MUTATION ANALYSIS"
[1] 3
  HNMT MUTATED HNMT WILD-TYPE 
             8            359 
  HNMT MUTATED HNMT WILD-TYPE 
             8            359 
[1] "AHCTF1 MUTATION ANALYSIS"
[1] 3
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              21              346 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              21              346 
[1] "PRPH2 MUTATION ANALYSIS"
[1] 3
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             10             357 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             10             357 
[1] "NOD2 MUTATION ANALYSIS"
[1] 3
  NOD2 MUTATED NOD2 WILD-TYPE 
            16            351 
  NOD2 MUTATED NOD2 WILD-TYPE 
            16            351 
[1] "PTCH2 MUTATION ANALYSIS"
[1] 3
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             17             350 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             17             350 
[1] "GPR126 MUTATION ANALYSIS"
[1] 3
  GPR126 MUTATED GPR126 WILD-TYPE 
              16              351 
  GPR126 MUTATED GPR126 WILD-TYPE 
              16              351 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             359 
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             359 
[1] "TOP2A MUTATION ANALYSIS"
[1] 3
  TOP2A MUTATED TOP2A WILD-TYPE 
             17             350 
  TOP2A MUTATED TOP2A WILD-TYPE 
             17             350 
[1] "CACNG3 MUTATION ANALYSIS"
[1] 3
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              359 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              359 
[1] "CBX3 MUTATION ANALYSIS"
[1] 3
  CBX3 MUTATED CBX3 WILD-TYPE 
             6            361 
  CBX3 MUTATED CBX3 WILD-TYPE 
             6            361 
[1] "DLL3 MUTATION ANALYSIS"
[1] 3
  DLL3 MUTATED DLL3 WILD-TYPE 
             6            361 
  DLL3 MUTATED DLL3 WILD-TYPE 
             6            361 
[1] "KIFAP3 MUTATION ANALYSIS"
[1] 3
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               9              358 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               9              358 
[1] "CRYGA MUTATION ANALYSIS"
[1] 3
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             362 
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             362 
[1] "MCF2 MUTATION ANALYSIS"
[1] 3
  MCF2 MUTATED MCF2 WILD-TYPE 
            28            339 
  MCF2 MUTATED MCF2 WILD-TYPE 
            28            339 
[1] "USP16 MUTATION ANALYSIS"
[1] 3
  USP16 MUTATED USP16 WILD-TYPE 
              8             359 
  USP16 MUTATED USP16 WILD-TYPE 
              8             359 
[1] "ASPM MUTATION ANALYSIS"
[1] 3
  ASPM MUTATED ASPM WILD-TYPE 
            42            325 
  ASPM MUTATED ASPM WILD-TYPE 
            42            325 
[1] "MACC1 MUTATION ANALYSIS"
[1] 3
  MACC1 MUTATED MACC1 WILD-TYPE 
             18             349 
  MACC1 MUTATED MACC1 WILD-TYPE 
             18             349 
[1] "YLPM1 MUTATION ANALYSIS"
[1] 3
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             22             345 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             22             345 
[1] "MIA3 MUTATION ANALYSIS"
[1] 3
  MIA3 MUTATED MIA3 WILD-TYPE 
            19            348 
  MIA3 MUTATED MIA3 WILD-TYPE 
            19            348 
[1] "SLC7A6 MUTATION ANALYSIS"
[1] 3
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               6              361 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               6              361 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              21              346 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              21              346 
[1] "RAB42 MUTATION ANALYSIS"
[1] 3
  RAB42 MUTATED RAB42 WILD-TYPE 
              4             363 
  RAB42 MUTATED RAB42 WILD-TYPE 
              4             363 
[1] "PIK3C3 MUTATION ANALYSIS"
[1] 3
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              23              344 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              23              344 
[1] "FAM189B MUTATION ANALYSIS"
[1] 3
  FAM189B MUTATED FAM189B WILD-TYPE 
               11               356 
  FAM189B MUTATED FAM189B WILD-TYPE 
               11               356 
[1] "SLC24A2 MUTATION ANALYSIS"
[1] 3
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               17               350 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               17               350 
[1] "YES1 MUTATION ANALYSIS"
[1] 3
  YES1 MUTATED YES1 WILD-TYPE 
             9            358 
  YES1 MUTATED YES1 WILD-TYPE 
             9            358 
[1] "KIAA0649 MUTATION ANALYSIS"
[1] 3
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                357 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                357 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              362 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              362 
[1] "PIK3R4 MUTATION ANALYSIS"
[1] 3
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              16              351 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              16              351 
[1] "MTF1 MUTATION ANALYSIS"
[1] 3
  MTF1 MUTATED MTF1 WILD-TYPE 
             9            358 
  MTF1 MUTATED MTF1 WILD-TYPE 
             9            358 
[1] "GAPVD1 MUTATION ANALYSIS"
[1] 3
  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
              22              345 
  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
              22              345 
[1] "CCDC3 MUTATION ANALYSIS"
[1] 3
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              4             363 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              4             363 
[1] "SERPINA9 MUTATION ANALYSIS"
[1] 3
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                10                357 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                10                357 
[1] "ZC3H12C MUTATION ANALYSIS"
[1] 3
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               12               355 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               12               355 
[1] "PRRT2 MUTATION ANALYSIS"
[1] 3
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             361 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             361 
[1] "H2AFJ MUTATION ANALYSIS"
[1] 3
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             364 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             364 
[1] "SLC25A44 MUTATION ANALYSIS"
[1] 3
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                362 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                362 
[1] "CHD1 MUTATION ANALYSIS"
[1] 3
  CHD1 MUTATED CHD1 WILD-TYPE 
            23            344 
  CHD1 MUTATED CHD1 WILD-TYPE 
            23            344 
[1] "ZBTB33 MUTATION ANALYSIS"
[1] 3
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              351 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              351 
[1] "ZNF691 MUTATION ANALYSIS"
[1] 3
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               7              360 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               7              360 
[1] "EFTUD2 MUTATION ANALYSIS"
[1] 3
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              14              353 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              14              353 
[1] "METTL9 MUTATION ANALYSIS"
[1] 3
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              363 
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              363 
[1] "CEL MUTATION ANALYSIS"
[1] 3
  CEL MUTATED CEL WILD-TYPE 
            9           358 
  CEL MUTATED CEL WILD-TYPE 
            9           358 
[1] "OR10J1 MUTATION ANALYSIS"
[1] 3
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              354 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              354 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
             13             354 
  PRKCD MUTATED PRKCD WILD-TYPE 
             13             354 
[1] "SMC1B MUTATION ANALYSIS"
[1] 3
  SMC1B MUTATED SMC1B WILD-TYPE 
             19             348 
  SMC1B MUTATED SMC1B WILD-TYPE 
             19             348 
[1] "AP1M1 MUTATION ANALYSIS"
[1] 3
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             358 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             358 
[1] "CCDC55 MUTATION ANALYSIS"
[1] 3
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              13              354 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              13              354 
[1] "MOV10 MUTATION ANALYSIS"
[1] 3
  MOV10 MUTATED MOV10 WILD-TYPE 
             13             354 
  MOV10 MUTATED MOV10 WILD-TYPE 
             13             354 
[1] "GRINA MUTATION ANALYSIS"
[1] 3
  GRINA MUTATED GRINA WILD-TYPE 
              4             363 
  GRINA MUTATED GRINA WILD-TYPE 
              4             363 
[1] "CAPRIN1 MUTATION ANALYSIS"
[1] 3
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               11               356 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               11               356 
[1] "OR7C1 MUTATION ANALYSIS"
[1] 3
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              9             358 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              9             358 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              5             362 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              5             362 
[1] "SNAPC1 MUTATION ANALYSIS"
[1] 3
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              360 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              360 
[1] "CETN3 MUTATION ANALYSIS"
[1] 3
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             361 
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             361 
[1] "CXXC5 MUTATION ANALYSIS"
[1] 3
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              6             361 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              6             361 
[1] "GMNN MUTATION ANALYSIS"
[1] 3
  GMNN MUTATED GMNN WILD-TYPE 
             3            364 
  GMNN MUTATED GMNN WILD-TYPE 
             3            364 
[1] "POLD3 MUTATION ANALYSIS"
[1] 3
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             356 
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             356 
[1] "FAM155B MUTATION ANALYSIS"
[1] 3
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               359 
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               359 
[1] "CTTN MUTATION ANALYSIS"
[1] 3
  CTTN MUTATED CTTN WILD-TYPE 
             4            363 
  CTTN MUTATED CTTN WILD-TYPE 
             4            363 
[1] "PIGC MUTATION ANALYSIS"
[1] 3
  PIGC MUTATED PIGC WILD-TYPE 
             4            363 
  PIGC MUTATED PIGC WILD-TYPE 
             4            363 
[1] "CSGALNACT1 MUTATION ANALYSIS"
[1] 3
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  359 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  359 
[1] "CACHD1 MUTATION ANALYSIS"
[1] 3
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              21              346 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              21              346 
[1] "DBN1 MUTATION ANALYSIS"
[1] 3
  DBN1 MUTATED DBN1 WILD-TYPE 
             9            358 
  DBN1 MUTATED DBN1 WILD-TYPE 
             9            358 
[1] "CRTC1 MUTATION ANALYSIS"
[1] 3
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             354 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             354 
[1] "RRAGD MUTATION ANALYSIS"
[1] 3
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             360 
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             360 
[1] "CTNNA3 MUTATION ANALYSIS"
[1] 3
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              341 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              341 
[1] "EML4 MUTATION ANALYSIS"
[1] 3
  EML4 MUTATED EML4 WILD-TYPE 
            10            357 
  EML4 MUTATED EML4 WILD-TYPE 
            10            357 
[1] "PLA2G15 MUTATION ANALYSIS"
[1] 3
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                5               362 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                5               362 
[1] "USP29 MUTATION ANALYSIS"
[1] 3
  USP29 MUTATED USP29 WILD-TYPE 
             18             349 
  USP29 MUTATED USP29 WILD-TYPE 
             18             349 
[1] "BAIAP2L1 MUTATION ANALYSIS"
[1] 3
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                12                355 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                12                355 
[1] "ZNF799 MUTATION ANALYSIS"
[1] 3
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               6              361 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               6              361 
[1] "ATIC MUTATION ANALYSIS"
[1] 3
  ATIC MUTATED ATIC WILD-TYPE 
            13            354 
  ATIC MUTATED ATIC WILD-TYPE 
            13            354 
[1] "CPZ MUTATION ANALYSIS"
[1] 3
  CPZ MUTATED CPZ WILD-TYPE 
           15           352 
  CPZ MUTATED CPZ WILD-TYPE 
           15           352 
[1] "GRIA4 MUTATION ANALYSIS"
[1] 3
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             30             337 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             30             337 
[1] "NDUFAF1 MUTATION ANALYSIS"
[1] 3
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               360 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               360 
[1] "SKIL MUTATION ANALYSIS"
[1] 3
  SKIL MUTATED SKIL WILD-TYPE 
             7            360 
  SKIL MUTATED SKIL WILD-TYPE 
             7            360 
[1] "ATP10B MUTATION ANALYSIS"
[1] 3
  ATP10B MUTATED ATP10B WILD-TYPE 
              15              352 
  ATP10B MUTATED ATP10B WILD-TYPE 
              15              352 
[1] "NUP205 MUTATION ANALYSIS"
[1] 3
  NUP205 MUTATED NUP205 WILD-TYPE 
              24              343 
  NUP205 MUTATED NUP205 WILD-TYPE 
              24              343 
[1] "ALK MUTATION ANALYSIS"
[1] 3
  ALK MUTATED ALK WILD-TYPE 
           35           332 
  ALK MUTATED ALK WILD-TYPE 
           35           332 
[1] "GRB14 MUTATION ANALYSIS"
[1] 3
  GRB14 MUTATED GRB14 WILD-TYPE 
              9             358 
  GRB14 MUTATED GRB14 WILD-TYPE 
              9             358 
[1] "NSUN6 MUTATION ANALYSIS"
[1] 3
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              8             359 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              8             359 
[1] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              22              345 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              22              345 
[1] "PPP2R5E MUTATION ANALYSIS"
[1] 3
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               359 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               359 
[1] "LUM MUTATION ANALYSIS"
[1] 3
  LUM MUTATED LUM WILD-TYPE 
           12           355 
  LUM MUTATED LUM WILD-TYPE 
           12           355 
[1] "MTTP MUTATION ANALYSIS"
[1] 3
  MTTP MUTATED MTTP WILD-TYPE 
            23            344 
  MTTP MUTATED MTTP WILD-TYPE 
            23            344 
[1] "GAD2 MUTATION ANALYSIS"
[1] 3
  GAD2 MUTATED GAD2 WILD-TYPE 
            16            351 
  GAD2 MUTATED GAD2 WILD-TYPE 
            16            351 
[1] "UBR2 MUTATION ANALYSIS"
[1] 3
  UBR2 MUTATED UBR2 WILD-TYPE 
            15            352 
  UBR2 MUTATED UBR2 WILD-TYPE 
            15            352 
[1] "SMC2 MUTATION ANALYSIS"
[1] 3
  SMC2 MUTATED SMC2 WILD-TYPE 
            25            342 
  SMC2 MUTATED SMC2 WILD-TYPE 
            25            342 
[1] "PSD3 MUTATION ANALYSIS"
[1] 3
  PSD3 MUTATED PSD3 WILD-TYPE 
            10            357 
  PSD3 MUTATED PSD3 WILD-TYPE 
            10            357 
[1] "PANK1 MUTATION ANALYSIS"
[1] 3
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             360 
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             360 
[1] "C4ORF49 MUTATION ANALYSIS"
[1] 3
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               362 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               362 
[1] "ADM MUTATION ANALYSIS"
[1] 3
  ADM MUTATED ADM WILD-TYPE 
            6           361 
  ADM MUTATED ADM WILD-TYPE 
            6           361 
[1] "DCAF12L2 MUTATION ANALYSIS"
[1] 3
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                17                350 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                17                350 
[1] "DIAPH2 MUTATION ANALYSIS"
[1] 3
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              21              346 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              21              346 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              358 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              358 
[1] "SCN4A MUTATION ANALYSIS"
[1] 3
  SCN4A MUTATED SCN4A WILD-TYPE 
             23             344 
  SCN4A MUTATED SCN4A WILD-TYPE 
             23             344 
[1] "SATB1 MUTATION ANALYSIS"
[1] 3
  SATB1 MUTATED SATB1 WILD-TYPE 
             16             351 
  SATB1 MUTATED SATB1 WILD-TYPE 
             16             351 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              19              348 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              19              348 
[1] "NCAPD3 MUTATION ANALYSIS"
[1] 3
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              25              342 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              25              342 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
            11            356 
  KLF5 MUTATED KLF5 WILD-TYPE 
            11            356 
[1] "DSC2 MUTATION ANALYSIS"
[1] 3
  DSC2 MUTATED DSC2 WILD-TYPE 
            14            353 
  DSC2 MUTATED DSC2 WILD-TYPE 
            14            353 
[1] "NUPL2 MUTATION ANALYSIS"
[1] 3
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             356 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             356 
[1] "ZSWIM3 MUTATION ANALYSIS"
[1] 3
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              12              355 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              12              355 
[1] "C5ORF34 MUTATION ANALYSIS"
[1] 3
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               10               357 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               10               357 
[1] "YSK4 MUTATION ANALYSIS"
[1] 3
  YSK4 MUTATED YSK4 WILD-TYPE 
            26            341 
  YSK4 MUTATED YSK4 WILD-TYPE 
            26            341 
[1] "CBLN3 MUTATION ANALYSIS"
[1] 3
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             361 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             361 
[1] "GGA2 MUTATION ANALYSIS"
[1] 3
  GGA2 MUTATED GGA2 WILD-TYPE 
            12            355 
  GGA2 MUTATED GGA2 WILD-TYPE 
            12            355 
[1] "ING1 MUTATION ANALYSIS"
[1] 3
  ING1 MUTATED ING1 WILD-TYPE 
            10            357 
  ING1 MUTATED ING1 WILD-TYPE 
            10            357 
[1] "LYG1 MUTATION ANALYSIS"
[1] 3
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            361 
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            361 
[1] "PRPF4B MUTATION ANALYSIS"
[1] 3
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              15              352 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              15              352 
[1] "TDRD7 MUTATION ANALYSIS"
[1] 3
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             15             352 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             15             352 
[1] "ADAMTS19 MUTATION ANALYSIS"
[1] 3
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                19                348 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                19                348 
[1] "MALT1 MUTATION ANALYSIS"
[1] 3
  MALT1 MUTATED MALT1 WILD-TYPE 
             11             356 
  MALT1 MUTATED MALT1 WILD-TYPE 
             11             356 
[1] "JMJD6 MUTATION ANALYSIS"
[1] 3
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              8             359 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              8             359 
[1] "THUMPD3 MUTATION ANALYSIS"
[1] 3
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               11               356 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               11               356 
[1] "STAU2 MUTATION ANALYSIS"
[1] 3
  STAU2 MUTATED STAU2 WILD-TYPE 
             10             357 
  STAU2 MUTATED STAU2 WILD-TYPE 
             10             357 
[1] "KIAA1797 MUTATION ANALYSIS"
[1] 3
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                20                347 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                20                347 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
             36             331 
  MKI67 MUTATED MKI67 WILD-TYPE 
             36             331 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             12             355 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             12             355 
[1] "DNAH6 MUTATION ANALYSIS"
[1] 3
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             20             347 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             20             347 
[1] "TRYX3 MUTATION ANALYSIS"
[1] 3
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              6             361 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              6             361 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
            17            350 
  PER3 MUTATED PER3 WILD-TYPE 
            17            350 
[1] "ZNF443 MUTATION ANALYSIS"
[1] 3
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               8              359 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               8              359 
[1] "ACAT2 MUTATION ANALYSIS"
[1] 3
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              8             359 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              8             359 
[1] "TRIM46 MUTATION ANALYSIS"
[1] 3
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              15              352 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              15              352 
[1] "C16ORF45 MUTATION ANALYSIS"
[1] 3
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 5                362 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 5                362 
[1] "APBB1IP MUTATION ANALYSIS"
[1] 3
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               18               349 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               18               349 
[1] "HSD17B11 MUTATION ANALYSIS"
[1] 3
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                363 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                363 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             12             355 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             12             355 
[1] "DCLRE1A MUTATION ANALYSIS"
[1] 3
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               10               357 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               10               357 
[1] "C7ORF50 MUTATION ANALYSIS"
[1] 3
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               362 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               362 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            361 
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            361 
[1] "MAGI1 MUTATION ANALYSIS"
[1] 3
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             23             344 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             23             344 
[1] "PARG MUTATION ANALYSIS"
[1] 3
  PARG MUTATED PARG WILD-TYPE 
            11            356 
  PARG MUTATED PARG WILD-TYPE 
            11            356 
[1] "VPS52 MUTATION ANALYSIS"
[1] 3
  VPS52 MUTATED VPS52 WILD-TYPE 
             11             356 
  VPS52 MUTATED VPS52 WILD-TYPE 
             11             356 
[1] "RRM2B MUTATION ANALYSIS"
[1] 3
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             362 
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             362 
[1] "OR4C15 MUTATION ANALYSIS"
[1] 3
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              13              354 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              13              354 
[1] "MANBA MUTATION ANALYSIS"
[1] 3
  MANBA MUTATED MANBA WILD-TYPE 
             12             355 
  MANBA MUTATED MANBA WILD-TYPE 
             12             355 
[1] "IKBKB MUTATION ANALYSIS"
[1] 3
  IKBKB MUTATED IKBKB WILD-TYPE 
              7             360 
  IKBKB MUTATED IKBKB WILD-TYPE 
              7             360 
[1] "PIK3C2G MUTATION ANALYSIS"
[1] 3
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               20               347 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               20               347 
[1] "RTN4 MUTATION ANALYSIS"
[1] 3
  RTN4 MUTATED RTN4 WILD-TYPE 
            19            348 
  RTN4 MUTATED RTN4 WILD-TYPE 
            19            348 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               21               346 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               21               346 
[1] "WDR75 MUTATION ANALYSIS"
[1] 3
  WDR75 MUTATED WDR75 WILD-TYPE 
              8             359 
  WDR75 MUTATED WDR75 WILD-TYPE 
              8             359 
[1] "FAM20B MUTATION ANALYSIS"
[1] 3
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              357 
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              357 
[1] "CEP164 MUTATION ANALYSIS"
[1] 3
  CEP164 MUTATED CEP164 WILD-TYPE 
              23              344 
  CEP164 MUTATED CEP164 WILD-TYPE 
              23              344 
[1] "SF1 MUTATION ANALYSIS"
[1] 3
  SF1 MUTATED SF1 WILD-TYPE 
           14           353 
  SF1 MUTATED SF1 WILD-TYPE 
           14           353 
[1] "KIF16B MUTATION ANALYSIS"
[1] 3
  KIF16B MUTATED KIF16B WILD-TYPE 
              26              341 
  KIF16B MUTATED KIF16B WILD-TYPE 
              26              341 
[1] "COL6A5 MUTATION ANALYSIS"
[1] 3
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              33              334 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              33              334 
[1] "CYP2C18 MUTATION ANALYSIS"
[1] 3
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                5               362 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                5               362 
[1] "ITGA5 MUTATION ANALYSIS"
[1] 3
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             16             351 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             16             351 
[1] "KRTAP5-3 MUTATION ANALYSIS"
[1] 3
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                363 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                363 
[1] "NOL9 MUTATION ANALYSIS"
[1] 3
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            360 
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            360 
[1] "RAPGEF6 MUTATION ANALYSIS"
[1] 3
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               17               350 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               17               350 
[1] "ERCC3 MUTATION ANALYSIS"
[1] 3
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             19             348 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             19             348 
[1] "GABPA MUTATION ANALYSIS"
[1] 3
  GABPA MUTATED GABPA WILD-TYPE 
             11             356 
  GABPA MUTATED GABPA WILD-TYPE 
             11             356 
[1] "NXF3 MUTATION ANALYSIS"
[1] 3
  NXF3 MUTATED NXF3 WILD-TYPE 
            10            357 
  NXF3 MUTATED NXF3 WILD-TYPE 
            10            357 
[1] "LRIG2 MUTATION ANALYSIS"
[1] 3
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             358 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             358 
[1] "BRSK1 MUTATION ANALYSIS"
[1] 3
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             17             350 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             17             350 
[1] "E2F5 MUTATION ANALYSIS"
[1] 3
  E2F5 MUTATED E2F5 WILD-TYPE 
             7            360 
  E2F5 MUTATED E2F5 WILD-TYPE 
             7            360 
[1] "SEC31A MUTATION ANALYSIS"
[1] 3
  SEC31A MUTATED SEC31A WILD-TYPE 
              13              354 
  SEC31A MUTATED SEC31A WILD-TYPE 
              13              354 
[1] "CTSZ MUTATION ANALYSIS"
[1] 3
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            361 
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            361 
[1] "NUFIP1 MUTATION ANALYSIS"
[1] 3
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               8              359 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               8              359 
[1] "OR5H15 MUTATION ANALYSIS"
[1] 3
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               5              362 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               5              362 
[1] "TPR MUTATION ANALYSIS"
[1] 3
  TPR MUTATED TPR WILD-TYPE 
           24           343 
  TPR MUTATED TPR WILD-TYPE 
           24           343 
[1] "BAZ2B MUTATION ANALYSIS"
[1] 3
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             15             352 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             15             352 
[1] "USP44 MUTATION ANALYSIS"
[1] 3
  USP44 MUTATED USP44 WILD-TYPE 
             16             351 
  USP44 MUTATED USP44 WILD-TYPE 
             16             351 
[1] "EIF4G2 MUTATION ANALYSIS"
[1] 3
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              15              352 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              15              352 
[1] "EYS MUTATION ANALYSIS"
[1] 3
  EYS MUTATED EYS WILD-TYPE 
           38           329 
  EYS MUTATED EYS WILD-TYPE 
           38           329 
[1] "ST8SIA6 MUTATION ANALYSIS"
[1] 3
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               10               357 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               10               357 
[1] "C6ORF222 MUTATION ANALYSIS"
[1] 3
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                361 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                361 
[1] "TPK1 MUTATION ANALYSIS"
[1] 3
  TPK1 MUTATED TPK1 WILD-TYPE 
             5            362 
  TPK1 MUTATED TPK1 WILD-TYPE 
             5            362 
[1] "ZNF555 MUTATION ANALYSIS"
[1] 3
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               8              359 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               8              359 
[1] "CASP1 MUTATION ANALYSIS"
[1] 3
  CASP1 MUTATED CASP1 WILD-TYPE 
              6             361 
  CASP1 MUTATED CASP1 WILD-TYPE 
              6             361 
[1] "IFNA2 MUTATION ANALYSIS"
[1] 3
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              9             358 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              9             358 
[1] "IL1RL1 MUTATION ANALYSIS"
[1] 3
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              14              353 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              14              353 
[1] "UGT1A1 MUTATION ANALYSIS"
[1] 3
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
              11              356 
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
              11              356 
[1] "PTPRR MUTATION ANALYSIS"
[1] 3
  PTPRR MUTATED PTPRR WILD-TYPE 
             10             357 
  PTPRR MUTATED PTPRR WILD-TYPE 
             10             357 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             31             336 
  STK11 MUTATED STK11 WILD-TYPE 
             31             336 
[1] "AGFG2 MUTATION ANALYSIS"
[1] 3
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              9             358 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              9             358 
[1] "MFSD9 MUTATION ANALYSIS"
[1] 3
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             12             355 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             12             355 
[1] "C7ORF66 MUTATION ANALYSIS"
[1] 3
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                7               360 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                7               360 
[1] "MCART1 MUTATION ANALYSIS"
[1] 3
  MCART1 MUTATED MCART1 WILD-TYPE 
              12              355 
  MCART1 MUTATED MCART1 WILD-TYPE 
              12              355 
[1] "P2RX7 MUTATION ANALYSIS"
[1] 3
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             12             355 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             12             355 
[1] "SSX2IP MUTATION ANALYSIS"
[1] 3
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               8              359 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               8              359 
[1] "MRPS5 MUTATION ANALYSIS"
[1] 3
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             11             356 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             11             356 
[1] "DUSP19 MUTATION ANALYSIS"
[1] 3
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               9              358 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               9              358 
[1] "STK35 MUTATION ANALYSIS"
[1] 3
  STK35 MUTATED STK35 WILD-TYPE 
              6             361 
  STK35 MUTATED STK35 WILD-TYPE 
              6             361 
[1] "CCDC110 MUTATION ANALYSIS"
[1] 3
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               13               354 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               13               354 
[1] "RC3H2 MUTATION ANALYSIS"
[1] 3
  RC3H2 MUTATED RC3H2 WILD-TYPE 
              9             358 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
              9             358 
[1] "LEO1 MUTATION ANALYSIS"
[1] 3
  LEO1 MUTATED LEO1 WILD-TYPE 
            10            357 
  LEO1 MUTATED LEO1 WILD-TYPE 
            10            357 
[1] "ANKRD23 MUTATION ANALYSIS"
[1] 3
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               363 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               363 
[1] "FBXL19 MUTATION ANALYSIS"
[1] 3
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               7              360 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               7              360 
[1] "BFSP1 MUTATION ANALYSIS"
[1] 3
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              8             359 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              8             359 
[1] "C18ORF19 MUTATION ANALYSIS"
[1] 3
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 8                359 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 8                359 
[1] "RNF20 MUTATION ANALYSIS"
[1] 3
  RNF20 MUTATED RNF20 WILD-TYPE 
             18             349 
  RNF20 MUTATED RNF20 WILD-TYPE 
             18             349 
[1] "TRIM24 MUTATION ANALYSIS"
[1] 3
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              17              350 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              17              350 
[1] "ODAM MUTATION ANALYSIS"
[1] 3
  ODAM MUTATED ODAM WILD-TYPE 
             5            362 
  ODAM MUTATED ODAM WILD-TYPE 
             5            362 
[1] "CDKL2 MUTATION ANALYSIS"
[1] 3
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             11             356 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             11             356 
[1] "LRP2 MUTATION ANALYSIS"
[1] 3
  LRP2 MUTATED LRP2 WILD-TYPE 
            77            290 
  LRP2 MUTATED LRP2 WILD-TYPE 
            77            290 
[1] "KCNG4 MUTATION ANALYSIS"
[1] 3
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             357 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             357 
[1] "PAK7 MUTATION ANALYSIS"
[1] 3
  PAK7 MUTATED PAK7 WILD-TYPE 
            20            347 
  PAK7 MUTATED PAK7 WILD-TYPE 
            20            347 
[1] "CHD7 MUTATION ANALYSIS"
[1] 3
  CHD7 MUTATED CHD7 WILD-TYPE 
            37            330 
  CHD7 MUTATED CHD7 WILD-TYPE 
            37            330 
[1] "ZNF585B MUTATION ANALYSIS"
[1] 3
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                7               360 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                7               360 
[1] "NSUN2 MUTATION ANALYSIS"
[1] 3
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             11             356 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             11             356 
[1] "CCNH MUTATION ANALYSIS"
[1] 3
  CCNH MUTATED CCNH WILD-TYPE 
             7            360 
  CCNH MUTATED CCNH WILD-TYPE 
             7            360 
[1] "IVD MUTATION ANALYSIS"
[1] 3
  IVD MUTATED IVD WILD-TYPE 
            5           362 
  IVD MUTATED IVD WILD-TYPE 
            5           362 
[1] "PSMA2 MUTATION ANALYSIS"
[1] 3
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             361 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             361 
[1] "TUT1 MUTATION ANALYSIS"
[1] 3
  TUT1 MUTATED TUT1 WILD-TYPE 
             9            358 
  TUT1 MUTATED TUT1 WILD-TYPE 
             9            358 
[1] "AFF1 MUTATION ANALYSIS"
[1] 3
  AFF1 MUTATED AFF1 WILD-TYPE 
            12            355 
  AFF1 MUTATED AFF1 WILD-TYPE 
            12            355 
[1] "KRTAP10-11 MUTATION ANALYSIS"
[1] 3
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   5                  362 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   5                  362 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            17            350 
  CTCF MUTATED CTCF WILD-TYPE 
            17            350 
[1] "STYK1 MUTATION ANALYSIS"
[1] 3
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             360 
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             360 
[1] "BCAP29 MUTATION ANALYSIS"
[1] 3
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               7              360 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               7              360 
[1] "SERPINB7 MUTATION ANALYSIS"
[1] 3
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                359 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                359 
[1] "SPAST MUTATION ANALYSIS"
[1] 3
  SPAST MUTATED SPAST WILD-TYPE 
              9             358 
  SPAST MUTATED SPAST WILD-TYPE 
              9             358 
[1] "NFKBIB MUTATION ANALYSIS"
[1] 3
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              362 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              362 
[1] "ARID5A MUTATION ANALYSIS"
[1] 3
  ARID5A MUTATED ARID5A WILD-TYPE 
               8              359 
  ARID5A MUTATED ARID5A WILD-TYPE 
               8              359 
[1] "CSNK2A2 MUTATION ANALYSIS"
[1] 3
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                7               360 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                7               360 
[1] "AK3L1 MUTATION ANALYSIS"
[1] 3
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              3             364 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              3             364 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               6              361 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               6              361 
[1] "ACTN1 MUTATION ANALYSIS"
[1] 3
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              9             358 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              9             358 
[1] "FAM193A MUTATION ANALYSIS"
[1] 3
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               350 
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               350 
[1] "TAF6 MUTATION ANALYSIS"
[1] 3
  TAF6 MUTATED TAF6 WILD-TYPE 
             9            358 
  TAF6 MUTATED TAF6 WILD-TYPE 
             9            358 
[1] "CYP4F11 MUTATION ANALYSIS"
[1] 3
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               361 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               361 
[1] "MED13 MUTATION ANALYSIS"
[1] 3
  MED13 MUTATED MED13 WILD-TYPE 
             20             347 
  MED13 MUTATED MED13 WILD-TYPE 
             20             347 
[1] "DACT1 MUTATION ANALYSIS"
[1] 3
  DACT1 MUTATED DACT1 WILD-TYPE 
             15             352 
  DACT1 MUTATED DACT1 WILD-TYPE 
             15             352 
[1] "PTTG1IP MUTATION ANALYSIS"
[1] 3
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               360 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               360 
[1] "ATP12A MUTATION ANALYSIS"
[1] 3
  ATP12A MUTATED ATP12A WILD-TYPE 
              26              341 
  ATP12A MUTATED ATP12A WILD-TYPE 
              26              341 
[1] "DHX32 MUTATION ANALYSIS"
[1] 3
  DHX32 MUTATED DHX32 WILD-TYPE 
             10             357 
  DHX32 MUTATED DHX32 WILD-TYPE 
             10             357 
[1] "SLITRK2 MUTATION ANALYSIS"
[1] 3
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               21               346 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               21               346 
[1] "TMC8 MUTATION ANALYSIS"
[1] 3
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            360 
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            360 
[1] "EMR3 MUTATION ANALYSIS"
[1] 3
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            351 
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            351 
[1] "VPS33A MUTATION ANALYSIS"
[1] 3
  VPS33A MUTATED VPS33A WILD-TYPE 
               8              359 
  VPS33A MUTATED VPS33A WILD-TYPE 
               8              359 
[1] "BRE MUTATION ANALYSIS"
[1] 3
  BRE MUTATED BRE WILD-TYPE 
           10           357 
  BRE MUTATED BRE WILD-TYPE 
           10           357 
[1] "NKTR MUTATION ANALYSIS"
[1] 3
  NKTR MUTATED NKTR WILD-TYPE 
            13            354 
  NKTR MUTATED NKTR WILD-TYPE 
            13            354 
[1] "ICA1 MUTATION ANALYSIS"
[1] 3
  ICA1 MUTATED ICA1 WILD-TYPE 
             6            361 
  ICA1 MUTATED ICA1 WILD-TYPE 
             6            361 
[1] "ZFYVE16 MUTATION ANALYSIS"
[1] 3
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               17               350 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               17               350 
[1] "RDBP MUTATION ANALYSIS"
[1] 3
  RDBP MUTATED RDBP WILD-TYPE 
             6            361 
  RDBP MUTATED RDBP WILD-TYPE 
             6            361 
[1] "LMOD1 MUTATION ANALYSIS"
[1] 3
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             12             355 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             12             355 
[1] "AP1G1 MUTATION ANALYSIS"
[1] 3
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             11             356 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             11             356 
[1] "TRPV2 MUTATION ANALYSIS"
[1] 3
  TRPV2 MUTATED TRPV2 WILD-TYPE 
             11             356 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
             11             356 
[1] "ABLIM3 MUTATION ANALYSIS"
[1] 3
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
              16              351 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
              16              351 
[1] "STX7 MUTATION ANALYSIS"
[1] 3
  STX7 MUTATED STX7 WILD-TYPE 
             4            363 
  STX7 MUTATED STX7 WILD-TYPE 
             4            363 
[1] "LEPRE1 MUTATION ANALYSIS"
[1] 3
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              358 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              358 
[1] "KIAA0240 MUTATION ANALYSIS"
[1] 3
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                358 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                358 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             356 
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             356 
[1] "NEK1 MUTATION ANALYSIS"
[1] 3
  NEK1 MUTATED NEK1 WILD-TYPE 
            12            355 
  NEK1 MUTATED NEK1 WILD-TYPE 
            12            355 
[1] "RNASEL MUTATION ANALYSIS"
[1] 3
  RNASEL MUTATED RNASEL WILD-TYPE 
              12              355 
  RNASEL MUTATED RNASEL WILD-TYPE 
              12              355 
[1] "ALCAM MUTATION ANALYSIS"
[1] 3
  ALCAM MUTATED ALCAM WILD-TYPE 
             11             356 
  ALCAM MUTATED ALCAM WILD-TYPE 
             11             356 
[1] "SLC30A8 MUTATION ANALYSIS"
[1] 3
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               14               353 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               14               353 
[1] "CREG2 MUTATION ANALYSIS"
[1] 3
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             362 
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             362 
[1] "MSH4 MUTATION ANALYSIS"
[1] 3
  MSH4 MUTATED MSH4 WILD-TYPE 
            12            355 
  MSH4 MUTATED MSH4 WILD-TYPE 
            12            355 
[1] "PANK3 MUTATION ANALYSIS"
[1] 3
  PANK3 MUTATED PANK3 WILD-TYPE 
              6             361 
  PANK3 MUTATED PANK3 WILD-TYPE 
              6             361 
[1] "DNMT1 MUTATION ANALYSIS"
[1] 3
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             18             349 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             18             349 
[1] "UCHL5 MUTATION ANALYSIS"
[1] 3
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              4             363 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              4             363 
[1] "HERC1 MUTATION ANALYSIS"
[1] 3
  HERC1 MUTATED HERC1 WILD-TYPE 
             31             336 
  HERC1 MUTATED HERC1 WILD-TYPE 
             31             336 
[1] "PROM1 MUTATION ANALYSIS"
[1] 3
  PROM1 MUTATED PROM1 WILD-TYPE 
             12             355 
  PROM1 MUTATED PROM1 WILD-TYPE 
             12             355 
[1] "TMCO6 MUTATION ANALYSIS"
[1] 3
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             360 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             360 
[1] "RAB38 MUTATION ANALYSIS"
[1] 3
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             362 
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             362 
[1] "LRMP MUTATION ANALYSIS"
[1] 3
  LRMP MUTATED LRMP WILD-TYPE 
             5            362 
  LRMP MUTATED LRMP WILD-TYPE 
             5            362 
[1] "NHLRC2 MUTATION ANALYSIS"
[1] 3
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               9              358 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               9              358 
[1] "DCBLD1 MUTATION ANALYSIS"
[1] 3
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               5              362 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               5              362 
[1] "JAK1 MUTATION ANALYSIS"
[1] 3
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            349 
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            349 
[1] "PAK4 MUTATION ANALYSIS"
[1] 3
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            361 
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            361 
[1] "SNX2 MUTATION ANALYSIS"
[1] 3
  SNX2 MUTATED SNX2 WILD-TYPE 
            11            356 
  SNX2 MUTATED SNX2 WILD-TYPE 
            11            356 
[1] "LIMCH1 MUTATION ANALYSIS"
[1] 3
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              13              354 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              13              354 
[1] "CD34 MUTATION ANALYSIS"
[1] 3
  CD34 MUTATED CD34 WILD-TYPE 
             6            361 
  CD34 MUTATED CD34 WILD-TYPE 
             6            361 
[1] "KIAA0564 MUTATION ANALYSIS"
[1] 3
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                22                345 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                22                345 
[1] "CEACAM6 MUTATION ANALYSIS"
[1] 3
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               363 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               363 
[1] "CASP4 MUTATION ANALYSIS"
[1] 3
  CASP4 MUTATED CASP4 WILD-TYPE 
              8             359 
  CASP4 MUTATED CASP4 WILD-TYPE 
              8             359 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              22              345 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              22              345 
[1] "OSMR MUTATION ANALYSIS"
[1] 3
  OSMR MUTATED OSMR WILD-TYPE 
            20            347 
  OSMR MUTATED OSMR WILD-TYPE 
            20            347 
[1] "HDAC5 MUTATION ANALYSIS"
[1] 3
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             11             356 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             11             356 
[1] "NCR3 MUTATION ANALYSIS"
[1] 3
  NCR3 MUTATED NCR3 WILD-TYPE 
             5            362 
  NCR3 MUTATED NCR3 WILD-TYPE 
             5            362 
[1] "ORC4L MUTATION ANALYSIS"
[1] 3
  ORC4L MUTATED ORC4L WILD-TYPE 
              6             361 
  ORC4L MUTATED ORC4L WILD-TYPE 
              6             361 
[1] "SECISBP2 MUTATION ANALYSIS"
[1] 3
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 7                360 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 7                360 
[1] "OR51T1 MUTATION ANALYSIS"
[1] 3
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              11              356 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              11              356 
[1] "SNAPC2 MUTATION ANALYSIS"
[1] 3
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              361 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              361 
[1] "ABHD2 MUTATION ANALYSIS"
[1] 3
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             10             357 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             10             357 
[1] "RNF38 MUTATION ANALYSIS"
[1] 3
  RNF38 MUTATED RNF38 WILD-TYPE 
              5             362 
  RNF38 MUTATED RNF38 WILD-TYPE 
              5             362 
[1] "FGD4 MUTATION ANALYSIS"
[1] 3
  FGD4 MUTATED FGD4 WILD-TYPE 
             5            362 
  FGD4 MUTATED FGD4 WILD-TYPE 
             5            362 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            27            340 
  IRS4 MUTATED IRS4 WILD-TYPE 
            27            340 
[1] "GABRA6 MUTATION ANALYSIS"
[1] 3
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              19              348 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              19              348 
[1] "HECTD2 MUTATION ANALYSIS"
[1] 3
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              10              357 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              10              357 
[1] "ARHGAP11A MUTATION ANALYSIS"
[1] 3
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 14                 353 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 14                 353 
[1] "OR4A16 MUTATION ANALYSIS"
[1] 3
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              14              353 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              14              353 
[1] "TSHZ1 MUTATION ANALYSIS"
[1] 3
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             12             355 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             12             355 
[1] "URGCP MUTATION ANALYSIS"
[1] 3
  URGCP MUTATED URGCP WILD-TYPE 
             15             352 
  URGCP MUTATED URGCP WILD-TYPE 
             15             352 
[1] "FRMD6 MUTATION ANALYSIS"
[1] 3
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             10             357 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             10             357 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            30            337 
  CPS1 MUTATED CPS1 WILD-TYPE 
            30            337 
[1] "TUBB4 MUTATION ANALYSIS"
[1] 3
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              5             362 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              5             362 
[1] "USF1 MUTATION ANALYSIS"
[1] 3
  USF1 MUTATED USF1 WILD-TYPE 
             5            362 
  USF1 MUTATED USF1 WILD-TYPE 
             5            362 
[1] "TM7SF4 MUTATION ANALYSIS"
[1] 3
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              360 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              360 
[1] "PPP1R12A MUTATION ANALYSIS"
[1] 3
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                13                354 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                13                354 
[1] "APOBEC4 MUTATION ANALYSIS"
[1] 3
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                7               360 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                7               360 
[1] "SPOPL MUTATION ANALYSIS"
[1] 3
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             357 
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             357 
[1] "GPR98 MUTATION ANALYSIS"
[1] 3
  GPR98 MUTATED GPR98 WILD-TYPE 
             61             306 
  GPR98 MUTATED GPR98 WILD-TYPE 
             61             306 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               363 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               363 
[1] "RGS3 MUTATION ANALYSIS"
[1] 3
  RGS3 MUTATED RGS3 WILD-TYPE 
            15            352 
  RGS3 MUTATED RGS3 WILD-TYPE 
            15            352 
[1] "FAM119A MUTATION ANALYSIS"
[1] 3
  FAM119A MUTATED FAM119A WILD-TYPE 
                5               362 
  FAM119A MUTATED FAM119A WILD-TYPE 
                5               362 
[1] "TRIM45 MUTATION ANALYSIS"
[1] 3
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              353 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              353 
[1] "MAGEA4 MUTATION ANALYSIS"
[1] 3
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               6              361 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               6              361 
[1] "MANF MUTATION ANALYSIS"
[1] 3
  MANF MUTATED MANF WILD-TYPE 
             4            363 
  MANF MUTATED MANF WILD-TYPE 
             4            363 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                359 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                359 
[1] "DPF3 MUTATION ANALYSIS"
[1] 3
  DPF3 MUTATED DPF3 WILD-TYPE 
             5            362 
  DPF3 MUTATED DPF3 WILD-TYPE 
             5            362 
[1] "DBF4B MUTATION ANALYSIS"
[1] 3
  DBF4B MUTATED DBF4B WILD-TYPE 
              7             360 
  DBF4B MUTATED DBF4B WILD-TYPE 
              7             360 
[1] "AKAP7 MUTATION ANALYSIS"
[1] 3
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              5             362 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              5             362 
[1] "RNF215 MUTATION ANALYSIS"
[1] 3
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              364 
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              364 
[1] "KIRREL2 MUTATION ANALYSIS"
[1] 3
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               12               355 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               12               355 
[1] "METTL5 MUTATION ANALYSIS"
[1] 3
  METTL5 MUTATED METTL5 WILD-TYPE 
               5              362 
  METTL5 MUTATED METTL5 WILD-TYPE 
               5              362 
[1] "CCR8 MUTATION ANALYSIS"
[1] 3
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            360 
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            360 
[1] "OR5AK2 MUTATION ANALYSIS"
[1] 3
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              358 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              358 
[1] "NTRK2 MUTATION ANALYSIS"
[1] 3
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             23             344 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             23             344 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               23               344 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               23               344 
[1] "ERCC6 MUTATION ANALYSIS"
[1] 3
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             28             339 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             28             339 
[1] "RARG MUTATION ANALYSIS"
[1] 3
  RARG MUTATED RARG WILD-TYPE 
            10            357 
  RARG MUTATED RARG WILD-TYPE 
            10            357 
[1] "HEPH MUTATION ANALYSIS"
[1] 3
  HEPH MUTATED HEPH WILD-TYPE 
            15            352 
  HEPH MUTATED HEPH WILD-TYPE 
            15            352 
[1] "RASGRF2 MUTATION ANALYSIS"
[1] 3
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
               17               350 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
               17               350 
[1] "LCN9 MUTATION ANALYSIS"
[1] 3
  LCN9 MUTATED LCN9 WILD-TYPE 
             4            363 
  LCN9 MUTATED LCN9 WILD-TYPE 
             4            363 
[1] "DST MUTATION ANALYSIS"
[1] 3
  DST MUTATED DST WILD-TYPE 
           66           301 
  DST MUTATED DST WILD-TYPE 
           66           301 
[1] "FBXO38 MUTATION ANALYSIS"
[1] 3
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              18              349 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              18              349 
[1] "STAT3 MUTATION ANALYSIS"
[1] 3
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             358 
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             358 
[1] "ATP11C MUTATION ANALYSIS"
[1] 3
  ATP11C MUTATED ATP11C WILD-TYPE 
              25              342 
  ATP11C MUTATED ATP11C WILD-TYPE 
              25              342 
[1] "IRF6 MUTATION ANALYSIS"
[1] 3
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            361 
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            361 
[1] "DNAJC11 MUTATION ANALYSIS"
[1] 3
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                9               358 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                9               358 
[1] "CLDN10 MUTATION ANALYSIS"
[1] 3
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              11              356 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              11              356 
[1] "IGSF5 MUTATION ANALYSIS"
[1] 3
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             14             353 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             14             353 
[1] "PCSK5 MUTATION ANALYSIS"
[1] 3
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             14             353 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             14             353 
[1] "DDHD2 MUTATION ANALYSIS"
[1] 3
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              9             358 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              9             358 
[1] "SPAG7 MUTATION ANALYSIS"
[1] 3
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             364 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             364 
[1] "RARRES3 MUTATION ANALYSIS"
[1] 3
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               362 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               362 
[1] "TRAF3IP1 MUTATION ANALYSIS"
[1] 3
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 6                361 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 6                361 
[1] "C14ORF50 MUTATION ANALYSIS"
[1] 3
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 6                361 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 6                361 
[1] "ALAS1 MUTATION ANALYSIS"
[1] 3
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              9             358 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              9             358 
[1] "FAM151A MUTATION ANALYSIS"
[1] 3
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               361 
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               361 
[1] "SYNGR4 MUTATION ANALYSIS"
[1] 3
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               6              361 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               6              361 
[1] "ADH7 MUTATION ANALYSIS"
[1] 3
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            360 
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            360 
[1] "KLF3 MUTATION ANALYSIS"
[1] 3
  KLF3 MUTATED KLF3 WILD-TYPE 
             7            360 
  KLF3 MUTATED KLF3 WILD-TYPE 
             7            360 
[1] "ARHGAP28 MUTATION ANALYSIS"
[1] 3
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                13                354 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                13                354 
[1] "SLC38A5 MUTATION ANALYSIS"
[1] 3
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                6               361 
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                6               361 
[1] "HIST1H1A MUTATION ANALYSIS"
[1] 3
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                358 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                358 
[1] "OR7D4 MUTATION ANALYSIS"
[1] 3
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              9             358 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              9             358 
[1] "OSR1 MUTATION ANALYSIS"
[1] 3
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            363 
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            363 
[1] "MAP2 MUTATION ANALYSIS"
[1] 3
  MAP2 MUTATED MAP2 WILD-TYPE 
            36            331 
  MAP2 MUTATED MAP2 WILD-TYPE 
            36            331 
[1] "UPF2 MUTATION ANALYSIS"
[1] 3
  UPF2 MUTATED UPF2 WILD-TYPE 
            16            351 
  UPF2 MUTATED UPF2 WILD-TYPE 
            16            351 
[1] "MFSD6 MUTATION ANALYSIS"
[1] 3
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              7             360 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              7             360 
[1] "CACNA1D MUTATION ANALYSIS"
[1] 3
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               22               345 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               22               345 
[1] "OR9Q1 MUTATION ANALYSIS"
[1] 3
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             361 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             361 
[1] "SSRP1 MUTATION ANALYSIS"
[1] 3
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             13             354 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             13             354 
[1] "ST6GALNAC3 MUTATION ANALYSIS"
[1] 3
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  12                  355 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  12                  355 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              23              344 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              23              344 
[1] "PACS2 MUTATION ANALYSIS"
[1] 3
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             362 
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             362 
[1] "STAT5B MUTATION ANALYSIS"
[1] 3
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              355 
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              355 
[1] "ZNF622 MUTATION ANALYSIS"
[1] 3
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               7              360 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               7              360 
[1] "ABCB6 MUTATION ANALYSIS"
[1] 3
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              7             360 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              7             360 
[1] "ZKSCAN1 MUTATION ANALYSIS"
[1] 3
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               360 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               360 
[1] "C10ORF119 MUTATION ANALYSIS"
[1] 3
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  9                 358 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  9                 358 
[1] "CLTCL1 MUTATION ANALYSIS"
[1] 3
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              18              349 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              18              349 
[1] "GFRA4 MUTATION ANALYSIS"
[1] 3
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             364 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             364 
[1] "CYP3A7 MUTATION ANALYSIS"
[1] 3
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              10              357 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              10              357 
[1] "THRAP3 MUTATION ANALYSIS"
[1] 3
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              11              356 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              11              356 
[1] "DNAH8 MUTATION ANALYSIS"
[1] 3
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             59             308 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             59             308 
[1] "PDGFC MUTATION ANALYSIS"
[1] 3
  PDGFC MUTATED PDGFC WILD-TYPE 
              9             358 
  PDGFC MUTATED PDGFC WILD-TYPE 
              9             358 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             354 
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             354 
[1] "CNOT10 MUTATION ANALYSIS"
[1] 3
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               9              358 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               9              358 
[1] "RSPO2 MUTATION ANALYSIS"
[1] 3
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             17             350 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             17             350 
[1] "LPAR6 MUTATION ANALYSIS"
[1] 3
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              7             360 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              7             360 
[1] "FAM175A MUTATION ANALYSIS"
[1] 3
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               359 
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               359 
[1] "SLC8A3 MUTATION ANALYSIS"
[1] 3
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
              12              355 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
              12              355 
[1] "A1CF MUTATION ANALYSIS"
[1] 3
  A1CF MUTATED A1CF WILD-TYPE 
             8            359 
  A1CF MUTATED A1CF WILD-TYPE 
             8            359 
[1] "ARHGEF1 MUTATION ANALYSIS"
[1] 3
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               13               354 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               13               354 
[1] "ZNF559 MUTATION ANALYSIS"
[1] 3
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              15              352 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              15              352 
[1] "EPHA7 MUTATION ANALYSIS"
[1] 3
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             35             332 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             35             332 
[1] "KCTD9 MUTATION ANALYSIS"
[1] 3
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             362 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             362 
[1] "CD47 MUTATION ANALYSIS"
[1] 3
  CD47 MUTATED CD47 WILD-TYPE 
             8            359 
  CD47 MUTATED CD47 WILD-TYPE 
             8            359 
[1] "PTPRB MUTATION ANALYSIS"
[1] 3
  PTPRB MUTATED PTPRB WILD-TYPE 
             17             350 
  PTPRB MUTATED PTPRB WILD-TYPE 
             17             350 
[1] "GPR113 MUTATION ANALYSIS"
[1] 3
  GPR113 MUTATED GPR113 WILD-TYPE 
              14              353 
  GPR113 MUTATED GPR113 WILD-TYPE 
              14              353 
[1] "KIAA1407 MUTATION ANALYSIS"
[1] 3
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                11                356 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                11                356 
[1] "PCDH20 MUTATION ANALYSIS"
[1] 3
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              21              346 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              21              346 
[1] "ADH1B MUTATION ANALYSIS"
[1] 3
  ADH1B MUTATED ADH1B WILD-TYPE 
              7             360 
  ADH1B MUTATED ADH1B WILD-TYPE 
              7             360 
[1] "TGIF1 MUTATION ANALYSIS"
[1] 3
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              9             358 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              9             358 
[1] "IGFBP3 MUTATION ANALYSIS"
[1] 3
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               6              361 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               6              361 
[1] "POPDC3 MUTATION ANALYSIS"
[1] 3
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               6              361 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               6              361 
[1] "SNRNP200 MUTATION ANALYSIS"
[1] 3
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                20                347 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                20                347 
[1] "BEND2 MUTATION ANALYSIS"
[1] 3
  BEND2 MUTATED BEND2 WILD-TYPE 
             23             344 
  BEND2 MUTATED BEND2 WILD-TYPE 
             23             344 
[1] "MAP3K13 MUTATION ANALYSIS"
[1] 3
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
               18               349 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
               18               349 
[1] "ADAMTS16 MUTATION ANALYSIS"
[1] 3
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                30                337 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                30                337 
[1] "MAP3K10 MUTATION ANALYSIS"
[1] 3
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
               10               357 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
               10               357 
[1] "RUNX2 MUTATION ANALYSIS"
[1] 3
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              8             359 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              8             359 
[1] "SMARCA1 MUTATION ANALYSIS"
[1] 3
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               19               348 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               19               348 
[1] "ZNF41 MUTATION ANALYSIS"
[1] 3
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              9             358 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              9             358 
[1] "CD79A MUTATION ANALYSIS"
[1] 3
  CD79A MUTATED CD79A WILD-TYPE 
              6             361 
  CD79A MUTATED CD79A WILD-TYPE 
              6             361 
[1] "TBX4 MUTATION ANALYSIS"
[1] 3
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            356 
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            356 
[1] "EPSTI1 MUTATION ANALYSIS"
[1] 3
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               7              360 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               7              360 
[1] "TSPAN7 MUTATION ANALYSIS"
[1] 3
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               9              358 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               9              358 
[1] "MED14 MUTATION ANALYSIS"
[1] 3
  MED14 MUTATED MED14 WILD-TYPE 
             19             348 
  MED14 MUTATED MED14 WILD-TYPE 
             19             348 
[1] "DOCK7 MUTATION ANALYSIS"
[1] 3
  DOCK7 MUTATED DOCK7 WILD-TYPE 
             17             350 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
             17             350 
[1] "DBF4 MUTATION ANALYSIS"
[1] 3
  DBF4 MUTATED DBF4 WILD-TYPE 
             7            360 
  DBF4 MUTATED DBF4 WILD-TYPE 
             7            360 
[1] "OR13C5 MUTATION ANALYSIS"
[1] 3
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              11              356 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              11              356 
[1] "GOLIM4 MUTATION ANALYSIS"
[1] 3
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               9              358 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               9              358 
[1] "IRGQ MUTATION ANALYSIS"
[1] 3
  IRGQ MUTATED IRGQ WILD-TYPE 
             3            364 
  IRGQ MUTATED IRGQ WILD-TYPE 
             3            364 
[1] "CYP2C9 MUTATION ANALYSIS"
[1] 3
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               8              359 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               8              359 
[1] "IL6R MUTATION ANALYSIS"
[1] 3
  IL6R MUTATED IL6R WILD-TYPE 
             7            360 
  IL6R MUTATED IL6R WILD-TYPE 
             7            360 
[1] "ZNF235 MUTATION ANALYSIS"
[1] 3
  ZNF235 MUTATED ZNF235 WILD-TYPE 
               9              358 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
               9              358 
[1] "C20ORF151 MUTATION ANALYSIS"
[1] 3
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                  9                 358 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                  9                 358 
[1] "CEPT1 MUTATION ANALYSIS"
[1] 3
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              5             362 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              5             362 
[1] "GGNBP2 MUTATION ANALYSIS"
[1] 3
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              356 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              356 
[1] "CTCFL MUTATION ANALYSIS"
[1] 3
  CTCFL MUTATED CTCFL WILD-TYPE 
             15             352 
  CTCFL MUTATED CTCFL WILD-TYPE 
             15             352 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               360 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               360 
[1] "MAP2K4 MUTATION ANALYSIS"
[1] 3
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              30              337 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              30              337 
[1] "DUSP9 MUTATION ANALYSIS"
[1] 3
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             358 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             358 
[1] "BRD2 MUTATION ANALYSIS"
[1] 3
  BRD2 MUTATED BRD2 WILD-TYPE 
            11            356 
  BRD2 MUTATED BRD2 WILD-TYPE 
            11            356 
[1] "AP4B1 MUTATION ANALYSIS"
[1] 3
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             12             355 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             12             355 
[1] "NTNG1 MUTATION ANALYSIS"
[1] 3
  NTNG1 MUTATED NTNG1 WILD-TYPE 
             14             353 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
             14             353 
[1] "LGALS9C MUTATION ANALYSIS"
[1] 3
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                5               362 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                5               362 
[1] "CHMP4C MUTATION ANALYSIS"
[1] 3
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               3              364 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               3              364 
[1] "ZNF630 MUTATION ANALYSIS"
[1] 3
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               7              360 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               7              360 
[1] "PTPDC1 MUTATION ANALYSIS"
[1] 3
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               8              359 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               8              359 
[1] "DMXL2 MUTATION ANALYSIS"
[1] 3
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             33             334 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             33             334 
[1] "DIAPH3 MUTATION ANALYSIS"
[1] 3
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              16              351 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              16              351 
[1] "KLF11 MUTATION ANALYSIS"
[1] 3
  KLF11 MUTATED KLF11 WILD-TYPE 
              7             360 
  KLF11 MUTATED KLF11 WILD-TYPE 
              7             360 
[1] "TAX1BP1 MUTATION ANALYSIS"
[1] 3
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               12               355 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               12               355 
[1] "MCM9 MUTATION ANALYSIS"
[1] 3
  MCM9 MUTATED MCM9 WILD-TYPE 
             7            360 
  MCM9 MUTATED MCM9 WILD-TYPE 
             7            360 
[1] "SBDS MUTATION ANALYSIS"
[1] 3
  SBDS MUTATED SBDS WILD-TYPE 
             3            364 
  SBDS MUTATED SBDS WILD-TYPE 
             3            364 
[1] "ANXA11 MUTATION ANALYSIS"
[1] 3
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               7              360 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               7              360 
[1] "OR2A5 MUTATION ANALYSIS"
[1] 3
  OR2A5 MUTATED OR2A5 WILD-TYPE 
             10             357 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
             10             357 
[1] "SLC45A2 MUTATION ANALYSIS"
[1] 3
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                9               358 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                9               358 
[1] "SYNJ1 MUTATION ANALYSIS"
[1] 3
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             16             351 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             16             351 
[1] "SLC9A2 MUTATION ANALYSIS"
[1] 3
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              10              357 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              10              357 
[1] "DUSP7 MUTATION ANALYSIS"
[1] 3
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              6             361 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              6             361 
[1] "EFCAB4B MUTATION ANALYSIS"
[1] 3
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                5               362 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                5               362 
[1] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
            10            357 
  PAK1 MUTATED PAK1 WILD-TYPE 
            10            357 
[1] "OR4N4 MUTATION ANALYSIS"
[1] 3
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             12             355 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             12             355 
[1] "IFI44 MUTATION ANALYSIS"
[1] 3
  IFI44 MUTATED IFI44 WILD-TYPE 
              8             359 
  IFI44 MUTATED IFI44 WILD-TYPE 
              8             359 
[1] "IPPK MUTATION ANALYSIS"
[1] 3
  IPPK MUTATED IPPK WILD-TYPE 
             9            358 
  IPPK MUTATED IPPK WILD-TYPE 
             9            358 
[1] "SPATA16 MUTATION ANALYSIS"
[1] 3
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               355 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               355 
[1] "ACAN MUTATION ANALYSIS"
[1] 3
  ACAN MUTATED ACAN WILD-TYPE 
            27            340 
  ACAN MUTATED ACAN WILD-TYPE 
            27            340 
[1] "C16ORF88 MUTATION ANALYSIS"
[1] 3
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 7                360 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 7                360 
[1] "ABCG2 MUTATION ANALYSIS"
[1] 3
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             12             355 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             12             355 
[1] "EPC1 MUTATION ANALYSIS"
[1] 3
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            354 
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            354 
[1] "PTPN3 MUTATION ANALYSIS"
[1] 3
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             352 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             352 
[1] "DGKH MUTATION ANALYSIS"
[1] 3
  DGKH MUTATED DGKH WILD-TYPE 
            15            352 
  DGKH MUTATED DGKH WILD-TYPE 
            15            352 
[1] "LEMD1 MUTATION ANALYSIS"
[1] 3
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             364 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             364 
[1] "ABCD4 MUTATION ANALYSIS"
[1] 3
  ABCD4 MUTATED ABCD4 WILD-TYPE 
             10             357 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
             10             357 
[1] "HCLS1 MUTATION ANALYSIS"
[1] 3
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             352 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             352 
[1] "SULT1C4 MUTATION ANALYSIS"
[1] 3
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               364 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               364 
[1] "TRAF2 MUTATION ANALYSIS"
[1] 3
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              7             360 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              7             360 
[1] "ZNF564 MUTATION ANALYSIS"
[1] 3
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              10              357 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              10              357 
[1] "JMJD1C MUTATION ANALYSIS"
[1] 3
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              24              343 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              24              343 
[1] "CCDC111 MUTATION ANALYSIS"
[1] 3
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                7               360 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                7               360 
[1] "PAK2 MUTATION ANALYSIS"
[1] 3
  PAK2 MUTATED PAK2 WILD-TYPE 
            10            357 
  PAK2 MUTATED PAK2 WILD-TYPE 
            10            357 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             12             355 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             12             355 
[1] "HECW2 MUTATION ANALYSIS"
[1] 3
  HECW2 MUTATED HECW2 WILD-TYPE 
             28             339 
  HECW2 MUTATED HECW2 WILD-TYPE 
             28             339 
[1] "BTNL3 MUTATION ANALYSIS"
[1] 3
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              7             360 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              7             360 
[1] "ATF2 MUTATION ANALYSIS"
[1] 3
  ATF2 MUTATED ATF2 WILD-TYPE 
             6            361 
  ATF2 MUTATED ATF2 WILD-TYPE 
             6            361 
[1] "STK38L MUTATION ANALYSIS"
[1] 3
  STK38L MUTATED STK38L WILD-TYPE 
               7              360 
  STK38L MUTATED STK38L WILD-TYPE 
               7              360 
[1] "B4GALT6 MUTATION ANALYSIS"
[1] 3
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               357 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               357 
[1] "MFSD4 MUTATION ANALYSIS"
[1] 3
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             361 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             361 
[1] "LRRC6 MUTATION ANALYSIS"
[1] 3
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              3             364 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              3             364 
[1] "MPP7 MUTATION ANALYSIS"
[1] 3
  MPP7 MUTATED MPP7 WILD-TYPE 
             5            362 
  MPP7 MUTATED MPP7 WILD-TYPE 
             5            362 
[1] "IKBKE MUTATION ANALYSIS"
[1] 3
  IKBKE MUTATED IKBKE WILD-TYPE 
              7             360 
  IKBKE MUTATED IKBKE WILD-TYPE 
              7             360 
[1] "MRPS22 MUTATION ANALYSIS"
[1] 3
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              357 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              357 
[1] "HEATR4 MUTATION ANALYSIS"
[1] 3
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              14              353 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              14              353 
[1] "PSMD11 MUTATION ANALYSIS"
[1] 3
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              359 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              359 
[1] "KRTAP12-3 MUTATION ANALYSIS"
[1] 3
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 364 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 364 
[1] "FLNB MUTATION ANALYSIS"
[1] 3
  FLNB MUTATED FLNB WILD-TYPE 
            28            339 
  FLNB MUTATED FLNB WILD-TYPE 
            28            339 
[1] "PALLD MUTATION ANALYSIS"
[1] 3
  PALLD MUTATED PALLD WILD-TYPE 
              9             358 
  PALLD MUTATED PALLD WILD-TYPE 
              9             358 
[1] "GATA1 MUTATION ANALYSIS"
[1] 3
  GATA1 MUTATED GATA1 WILD-TYPE 
             16             351 
  GATA1 MUTATED GATA1 WILD-TYPE 
             16             351 
[1] "TRIP12 MUTATION ANALYSIS"
[1] 3
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              28              339 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              28              339 
[1] "ZFP91 MUTATION ANALYSIS"
[1] 3
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              7             360 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              7             360 
[1] "OR9Q2 MUTATION ANALYSIS"
[1] 3
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             14             353 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             14             353 
[1] "HIST1H2BC MUTATION ANALYSIS"
[1] 3
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 363 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 363 
[1] "CLK4 MUTATION ANALYSIS"
[1] 3
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            358 
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            358 
[1] "LPGAT1 MUTATION ANALYSIS"
[1] 3
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               3              364 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               3              364 
[1] "C1ORF85 MUTATION ANALYSIS"
[1] 3
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                7               360 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                7               360 
[1] "UGT2A1 MUTATION ANALYSIS"
[1] 3
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
              10              357 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
              10              357 
[1] "TMEM229B MUTATION ANALYSIS"
[1] 3
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                363 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                363 
[1] "FSHR MUTATION ANALYSIS"
[1] 3
  FSHR MUTATED FSHR WILD-TYPE 
            15            352 
  FSHR MUTATED FSHR WILD-TYPE 
            15            352 
[1] "VEPH1 MUTATION ANALYSIS"
[1] 3
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             17             350 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             17             350 
[1] "IFITM5 MUTATION ANALYSIS"
[1] 3
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               3              364 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               3              364 
[1] "SBSN MUTATION ANALYSIS"
[1] 3
  SBSN MUTATED SBSN WILD-TYPE 
            10            357 
  SBSN MUTATED SBSN WILD-TYPE 
            10            357 
[1] "RUSC2 MUTATION ANALYSIS"
[1] 3
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             12             355 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             12             355 
[1] "CLVS1 MUTATION ANALYSIS"
[1] 3
  CLVS1 MUTATED CLVS1 WILD-TYPE 
             10             357 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
             10             357 
[1] "FOXA2 MUTATION ANALYSIS"
[1] 3
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              6             361 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              6             361 
[1] "FAM70A MUTATION ANALYSIS"
[1] 3
  FAM70A MUTATED FAM70A WILD-TYPE 
               7              360 
  FAM70A MUTATED FAM70A WILD-TYPE 
               7              360 
[1] "MAOB MUTATION ANALYSIS"
[1] 3
  MAOB MUTATED MAOB WILD-TYPE 
             6            361 
  MAOB MUTATED MAOB WILD-TYPE 
             6            361 
[1] "CCDC6 MUTATION ANALYSIS"
[1] 3
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             356 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             356 
[1] "WNK4 MUTATION ANALYSIS"
[1] 3
  WNK4 MUTATED WNK4 WILD-TYPE 
            11            356 
  WNK4 MUTATED WNK4 WILD-TYPE 
            11            356 
[1] "METT5D1 MUTATION ANALYSIS"
[1] 3
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                6               361 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                6               361 
[1] "SCYL2 MUTATION ANALYSIS"
[1] 3
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             16             351 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             16             351 
[1] "RBM15B MUTATION ANALYSIS"
[1] 3
  RBM15B MUTATED RBM15B WILD-TYPE 
               8              359 
  RBM15B MUTATED RBM15B WILD-TYPE 
               8              359 
[1] "DHX36 MUTATION ANALYSIS"
[1] 3
  DHX36 MUTATED DHX36 WILD-TYPE 
             12             355 
  DHX36 MUTATED DHX36 WILD-TYPE 
             12             355 
[1] "GFRAL MUTATION ANALYSIS"
[1] 3
  GFRAL MUTATED GFRAL WILD-TYPE 
              4             363 
  GFRAL MUTATED GFRAL WILD-TYPE 
              4             363 
[1] "TAB3 MUTATION ANALYSIS"
[1] 3
  TAB3 MUTATED TAB3 WILD-TYPE 
            10            357 
  TAB3 MUTATED TAB3 WILD-TYPE 
            10            357 
[1] "NXPH1 MUTATION ANALYSIS"
[1] 3
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              8             359 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              8             359 
[1] "KCNN4 MUTATION ANALYSIS"
[1] 3
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              7             360 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              7             360 
[1] "SLC9A9 MUTATION ANALYSIS"
[1] 3
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              21              346 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              21              346 
[1] "ATP6V0A4 MUTATION ANALYSIS"
[1] 3
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                11                356 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                11                356 
[1] "ATG10 MUTATION ANALYSIS"
[1] 3
  ATG10 MUTATED ATG10 WILD-TYPE 
              4             363 
  ATG10 MUTATED ATG10 WILD-TYPE 
              4             363 
[1] "MORC2 MUTATION ANALYSIS"
[1] 3
  MORC2 MUTATED MORC2 WILD-TYPE 
             12             355 
  MORC2 MUTATED MORC2 WILD-TYPE 
             12             355 
[1] "GRIN2B MUTATION ANALYSIS"
[1] 3
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              26              341 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              26              341 
[1] "FSCB MUTATION ANALYSIS"
[1] 3
  FSCB MUTATED FSCB WILD-TYPE 
            20            347 
  FSCB MUTATED FSCB WILD-TYPE 
            20            347 
[1] "DLGAP5 MUTATION ANALYSIS"
[1] 3
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               8              359 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               8              359 
[1] "ACCN5 MUTATION ANALYSIS"
[1] 3
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             13             354 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             13             354 
[1] "DLGAP3 MUTATION ANALYSIS"
[1] 3
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              351 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              351 
[1] "HSPBAP1 MUTATION ANALYSIS"
[1] 3
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                7               360 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                7               360 
[1] "COLEC12 MUTATION ANALYSIS"
[1] 3
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               17               350 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               17               350 
[1] "KIFC2 MUTATION ANALYSIS"
[1] 3
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             361 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             361 
[1] "PPYR1 MUTATION ANALYSIS"
[1] 3
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              5             362 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              5             362 
[1] "CASP10 MUTATION ANALYSIS"
[1] 3
  CASP10 MUTATED CASP10 WILD-TYPE 
               7              360 
  CASP10 MUTATED CASP10 WILD-TYPE 
               7              360 
[1] "STAU1 MUTATION ANALYSIS"
[1] 3
  STAU1 MUTATED STAU1 WILD-TYPE 
              7             360 
  STAU1 MUTATED STAU1 WILD-TYPE 
              7             360 
[1] "EFNB3 MUTATION ANALYSIS"
[1] 3
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              8             359 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              8             359 
[1] "ICAM5 MUTATION ANALYSIS"
[1] 3
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             10             357 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             10             357 
[1] "ZP2 MUTATION ANALYSIS"
[1] 3
  ZP2 MUTATED ZP2 WILD-TYPE 
           12           355 
  ZP2 MUTATED ZP2 WILD-TYPE 
           12           355 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
             8            359 
  RXRA MUTATED RXRA WILD-TYPE 
             8            359 
[1] "CCT5 MUTATION ANALYSIS"
[1] 3
  CCT5 MUTATED CCT5 WILD-TYPE 
             8            359 
  CCT5 MUTATED CCT5 WILD-TYPE 
             8            359 
[1] "DOCK8 MUTATION ANALYSIS"
[1] 3
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             20             347 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             20             347 
[1] "ZNF512 MUTATION ANALYSIS"
[1] 3
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              364 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              364 
[1] "TBCA MUTATION ANALYSIS"
[1] 3
  TBCA MUTATED TBCA WILD-TYPE 
             4            363 
  TBCA MUTATED TBCA WILD-TYPE 
             4            363 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             356 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             356 
[1] "OR6K2 MUTATION ANALYSIS"
[1] 3
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             14             353 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             14             353 
[1] "CTR9 MUTATION ANALYSIS"
[1] 3
  CTR9 MUTATED CTR9 WILD-TYPE 
            17            350 
  CTR9 MUTATED CTR9 WILD-TYPE 
            17            350 
[1] "RWDD4A MUTATION ANALYSIS"
[1] 3
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               5              362 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               5              362 
[1] "STK40 MUTATION ANALYSIS"
[1] 3
  STK40 MUTATED STK40 WILD-TYPE 
              7             360 
  STK40 MUTATED STK40 WILD-TYPE 
              7             360 
[1] "SLC44A1 MUTATION ANALYSIS"
[1] 3
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                9               358 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                9               358 
[1] "LPIN2 MUTATION ANALYSIS"
[1] 3
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              9             358 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              9             358 
[1] "BLM MUTATION ANALYSIS"
[1] 3
  BLM MUTATED BLM WILD-TYPE 
           17           350 
  BLM MUTATED BLM WILD-TYPE 
           17           350 
[1] "C4ORF29 MUTATION ANALYSIS"
[1] 3
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                5               362 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                5               362 
[1] "GPR161 MUTATION ANALYSIS"
[1] 3
  GPR161 MUTATED GPR161 WILD-TYPE 
               9              358 
  GPR161 MUTATED GPR161 WILD-TYPE 
               9              358 
[1] "HAUS1 MUTATION ANALYSIS"
[1] 3
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             361 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             361 
[1] "BTBD3 MUTATION ANALYSIS"
[1] 3
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             13             354 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             13             354 
[1] "KLKB1 MUTATION ANALYSIS"
[1] 3
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             13             354 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             13             354 
[1] "SENP8 MUTATION ANALYSIS"
[1] 3
  SENP8 MUTATED SENP8 WILD-TYPE 
              4             363 
  SENP8 MUTATED SENP8 WILD-TYPE 
              4             363 
[1] "DPP8 MUTATION ANALYSIS"
[1] 3
  DPP8 MUTATED DPP8 WILD-TYPE 
            13            354 
  DPP8 MUTATED DPP8 WILD-TYPE 
            13            354 
[1] "SLC22A10 MUTATION ANALYSIS"
[1] 3
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                15                352 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                15                352 
[1] "FANCD2 MUTATION ANALYSIS"
[1] 3
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              15              352 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              15              352 
[1] "CDS2 MUTATION ANALYSIS"
[1] 3
  CDS2 MUTATED CDS2 WILD-TYPE 
             9            358 
  CDS2 MUTATED CDS2 WILD-TYPE 
             9            358 
[1] "CCDC66 MUTATION ANALYSIS"
[1] 3
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               9              358 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               9              358 
[1] "TTC13 MUTATION ANALYSIS"
[1] 3
  TTC13 MUTATED TTC13 WILD-TYPE 
              9             358 
  TTC13 MUTATED TTC13 WILD-TYPE 
              9             358 
[1] "GLT8D1 MUTATION ANALYSIS"
[1] 3
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              359 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              359 
[1] "UBC MUTATION ANALYSIS"
[1] 3
  UBC MUTATED UBC WILD-TYPE 
            4           363 
  UBC MUTATED UBC WILD-TYPE 
            4           363 
[1] "ZNF594 MUTATION ANALYSIS"
[1] 3
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              14              353 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              14              353 
[1] "BTF3L4 MUTATION ANALYSIS"
[1] 3
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              362 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              362 
[1] "C14ORF105 MUTATION ANALYSIS"
[1] 3
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 364 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 364 
[1] "UBA3 MUTATION ANALYSIS"
[1] 3
  UBA3 MUTATED UBA3 WILD-TYPE 
             6            361 
  UBA3 MUTATED UBA3 WILD-TYPE 
             6            361 
[1] "UBE3C MUTATION ANALYSIS"
[1] 3
  UBE3C MUTATED UBE3C WILD-TYPE 
             18             349 
  UBE3C MUTATED UBE3C WILD-TYPE 
             18             349 
[1] "ZCWPW2 MUTATION ANALYSIS"
[1] 3
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              11              356 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              11              356 
[1] "ZNF711 MUTATION ANALYSIS"
[1] 3
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              10              357 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              10              357 
[1] "PRSS48 MUTATION ANALYSIS"
[1] 3
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               7              360 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               7              360 
[1] "MMP7 MUTATION ANALYSIS"
[1] 3
  MMP7 MUTATED MMP7 WILD-TYPE 
             8            359 
  MMP7 MUTATED MMP7 WILD-TYPE 
             8            359 
[1] "FAM120C MUTATION ANALYSIS"
[1] 3
  FAM120C MUTATED FAM120C WILD-TYPE 
                8               359 
  FAM120C MUTATED FAM120C WILD-TYPE 
                8               359 
[1] "TMSB15B MUTATION ANALYSIS"
[1] 3
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                3               364 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                3               364 
[1] "UHRF1BP1L MUTATION ANALYSIS"
[1] 3
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 20                 347 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 20                 347 
[1] "PLEKHH2 MUTATION ANALYSIS"
[1] 3
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               19               348 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               19               348 
[1] "VPRBP MUTATION ANALYSIS"
[1] 3
  VPRBP MUTATED VPRBP WILD-TYPE 
             12             355 
  VPRBP MUTATED VPRBP WILD-TYPE 
             12             355 
[1] "ZP3 MUTATION ANALYSIS"
[1] 3
  ZP3 MUTATED ZP3 WILD-TYPE 
            6           361 
  ZP3 MUTATED ZP3 WILD-TYPE 
            6           361 
[1] "OR11H12 MUTATION ANALYSIS"
[1] 3
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                3               364 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                3               364 
[1] "MMAA MUTATION ANALYSIS"
[1] 3
  MMAA MUTATED MMAA WILD-TYPE 
             9            358 
  MMAA MUTATED MMAA WILD-TYPE 
             9            358 
[1] "CALCOCO2 MUTATION ANALYSIS"
[1] 3
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 7                360 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 7                360 
[1] "ZNF385B MUTATION ANALYSIS"
[1] 3
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               360 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               360 
[1] "SUPT3H MUTATION ANALYSIS"
[1] 3
  SUPT3H MUTATED SUPT3H WILD-TYPE 
              11              356 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
              11              356 
[1] "FMO5 MUTATION ANALYSIS"
[1] 3
  FMO5 MUTATED FMO5 WILD-TYPE 
            10            357 
  FMO5 MUTATED FMO5 WILD-TYPE 
            10            357 
[1] "CHRM3 MUTATION ANALYSIS"
[1] 3
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             13             354 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             13             354 
[1] "SYT2 MUTATION ANALYSIS"
[1] 3
  SYT2 MUTATED SYT2 WILD-TYPE 
             8            359 
  SYT2 MUTATED SYT2 WILD-TYPE 
             8            359 
[1] "NCL MUTATION ANALYSIS"
[1] 3
  NCL MUTATED NCL WILD-TYPE 
           10           357 
  NCL MUTATED NCL WILD-TYPE 
           10           357 
[1] "ZNF462 MUTATION ANALYSIS"
[1] 3
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              26              341 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              26              341 
[1] "SIX5 MUTATION ANALYSIS"
[1] 3
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            362 
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            362 
[1] "C9ORF125 MUTATION ANALYSIS"
[1] 3
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                355 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                355 
[1] "AMBRA1 MUTATION ANALYSIS"
[1] 3
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              18              349 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              18              349 
[1] "ANAPC16 MUTATION ANALYSIS"
[1] 3
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                3               364 
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                3               364 
[1] "SETX MUTATION ANALYSIS"
[1] 3
  SETX MUTATED SETX WILD-TYPE 
            26            341 
  SETX MUTATED SETX WILD-TYPE 
            26            341 
[1] "PEBP4 MUTATION ANALYSIS"
[1] 3
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              7             360 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              7             360 
[1] "LEPROTL1 MUTATION ANALYSIS"
[1] 3
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 5                362 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 5                362 
[1] "MAP7 MUTATION ANALYSIS"
[1] 3
  MAP7 MUTATED MAP7 WILD-TYPE 
            11            356 
  MAP7 MUTATED MAP7 WILD-TYPE 
            11            356 
[1] "MCF2L2 MUTATION ANALYSIS"
[1] 3
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              19              348 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              19              348 
[1] "ANKRD26 MUTATION ANALYSIS"
[1] 3
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               19               348 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               19               348 
[1] "DNAJC18 MUTATION ANALYSIS"
[1] 3
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                7               360 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                7               360 
[1] "ESRP2 MUTATION ANALYSIS"
[1] 3
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              9             358 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              9             358 
[1] "NLRP13 MUTATION ANALYSIS"
[1] 3
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              27              340 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              27              340 
[1] "LRRN1 MUTATION ANALYSIS"
[1] 3
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             17             350 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             17             350 
[1] "VIM MUTATION ANALYSIS"
[1] 3
  VIM MUTATED VIM WILD-TYPE 
            7           360 
  VIM MUTATED VIM WILD-TYPE 
            7           360 
[1] "WDR45L MUTATION ANALYSIS"
[1] 3
  WDR45L MUTATED WDR45L WILD-TYPE 
               7              360 
  WDR45L MUTATED WDR45L WILD-TYPE 
               7              360 
[1] "PISD MUTATION ANALYSIS"
[1] 3
  PISD MUTATED PISD WILD-TYPE 
             3            364 
  PISD MUTATED PISD WILD-TYPE 
             3            364 
[1] "ST18 MUTATION ANALYSIS"
[1] 3
  ST18 MUTATED ST18 WILD-TYPE 
            23            344 
  ST18 MUTATED ST18 WILD-TYPE 
            23            344 
[1] "MAGOHB MUTATION ANALYSIS"
[1] 3
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              364 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              364 
[1] "DEFB129 MUTATION ANALYSIS"
[1] 3
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               362 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               362 
[1] "OR8K3 MUTATION ANALYSIS"
[1] 3
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             10             357 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             10             357 
[1] "G2E3 MUTATION ANALYSIS"
[1] 3
  G2E3 MUTATED G2E3 WILD-TYPE 
            12            355 
  G2E3 MUTATED G2E3 WILD-TYPE 
            12            355 
[1] "GRK5 MUTATION ANALYSIS"
[1] 3
  GRK5 MUTATED GRK5 WILD-TYPE 
            11            356 
  GRK5 MUTATED GRK5 WILD-TYPE 
            11            356 
[1] "GLDN MUTATION ANALYSIS"
[1] 3
  GLDN MUTATED GLDN WILD-TYPE 
             7            360 
  GLDN MUTATED GLDN WILD-TYPE 
             7            360 
[1] "LAMA3 MUTATION ANALYSIS"
[1] 3
  LAMA3 MUTATED LAMA3 WILD-TYPE 
             34             333 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
             34             333 
[1] "GNG12 MUTATION ANALYSIS"
[1] 3
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             359 
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             359 
[1] "GUCY1A3 MUTATION ANALYSIS"
[1] 3
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               22               345 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               22               345 
[1] "CALB2 MUTATION ANALYSIS"
[1] 3
  CALB2 MUTATED CALB2 WILD-TYPE 
              4             363 
  CALB2 MUTATED CALB2 WILD-TYPE 
              4             363 
[1] "LRRN3 MUTATION ANALYSIS"
[1] 3
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             21             346 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             21             346 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            6           361 
  DEK MUTATED DEK WILD-TYPE 
            6           361 
[1] "PCDH9 MUTATION ANALYSIS"
[1] 3
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             38             329 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             38             329 
[1] "LIX1 MUTATION ANALYSIS"
[1] 3
  LIX1 MUTATED LIX1 WILD-TYPE 
             9            358 
  LIX1 MUTATED LIX1 WILD-TYPE 
             9            358 
[1] "C3ORF63 MUTATION ANALYSIS"
[1] 3
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
               21               346 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
               21               346 
[1] "FAM199X MUTATION ANALYSIS"
[1] 3
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               357 
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               357 
[1] "SKIV2L MUTATION ANALYSIS"
[1] 3
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              12              355 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              12              355 
[1] "TAPBP MUTATION ANALYSIS"
[1] 3
  TAPBP MUTATED TAPBP WILD-TYPE 
              3             364 
  TAPBP MUTATED TAPBP WILD-TYPE 
              3             364 
[1] "CDHR3 MUTATION ANALYSIS"
[1] 3
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             13             354 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             13             354 
[1] "TJP1 MUTATION ANALYSIS"
[1] 3
  TJP1 MUTATED TJP1 WILD-TYPE 
            18            349 
  TJP1 MUTATED TJP1 WILD-TYPE 
            18            349 
[1] "DPPA2 MUTATION ANALYSIS"
[1] 3
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              7             360 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              7             360 
[1] "HIST1H4L MUTATION ANALYSIS"
[1] 3
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 6                361 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 6                361 
[1] "AFF3 MUTATION ANALYSIS"
[1] 3
  AFF3 MUTATED AFF3 WILD-TYPE 
            22            345 
  AFF3 MUTATED AFF3 WILD-TYPE 
            22            345 
[1] "TRAF3IP3 MUTATION ANALYSIS"
[1] 3
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                12                355 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                12                355 
[1] "CDH24 MUTATION ANALYSIS"
[1] 3
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             355 
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             355 
[1] "TYW3 MUTATION ANALYSIS"
[1] 3
  TYW3 MUTATED TYW3 WILD-TYPE 
             6            361 
  TYW3 MUTATED TYW3 WILD-TYPE 
             6            361 
[1] "ZNF197 MUTATION ANALYSIS"
[1] 3
  ZNF197 MUTATED ZNF197 WILD-TYPE 
               9              358 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
               9              358 
[1] "ESCO1 MUTATION ANALYSIS"
[1] 3
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             13             354 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             13             354 
[1] "NT5C3L MUTATION ANALYSIS"
[1] 3
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               5              362 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               5              362 
[1] "KIAA1919 MUTATION ANALYSIS"
[1] 3
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                358 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                358 
[1] "EPB41L4B MUTATION ANALYSIS"
[1] 3
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                12                355 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                12                355 
[1] "SRL MUTATION ANALYSIS"
[1] 3
  SRL MUTATED SRL WILD-TYPE 
           12           355 
  SRL MUTATED SRL WILD-TYPE 
           12           355 
[1] "SKIV2L2 MUTATION ANALYSIS"
[1] 3
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               11               356 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               11               356 
[1] "KBTBD4 MUTATION ANALYSIS"
[1] 3
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               7              360 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               7              360 
[1] "OLFML1 MUTATION ANALYSIS"
[1] 3
  OLFML1 MUTATED OLFML1 WILD-TYPE 
              11              356 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
              11              356 
[1] "C7ORF60 MUTATION ANALYSIS"
[1] 3
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               361 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               361 
[1] "IDE MUTATION ANALYSIS"
[1] 3
  IDE MUTATED IDE WILD-TYPE 
           10           357 
  IDE MUTATED IDE WILD-TYPE 
           10           357 
[1] "C1ORF124 MUTATION ANALYSIS"
[1] 3
  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
                 8                359 
  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
                 8                359 
[1] "PIGK MUTATION ANALYSIS"
[1] 3
  PIGK MUTATED PIGK WILD-TYPE 
            10            357 
  PIGK MUTATED PIGK WILD-TYPE 
            10            357 
[1] "TRIB1 MUTATION ANALYSIS"
[1] 3
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              7             360 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              7             360 
[1] "MYST3 MUTATION ANALYSIS"
[1] 3
  MYST3 MUTATED MYST3 WILD-TYPE 
             24             343 
  MYST3 MUTATED MYST3 WILD-TYPE 
             24             343 
[1] "KLF12 MUTATION ANALYSIS"
[1] 3
  KLF12 MUTATED KLF12 WILD-TYPE 
              3             364 
  KLF12 MUTATED KLF12 WILD-TYPE 
              3             364 
[1] "APLP1 MUTATION ANALYSIS"
[1] 3
  APLP1 MUTATED APLP1 WILD-TYPE 
             16             351 
  APLP1 MUTATED APLP1 WILD-TYPE 
             16             351 
[1] "SPARCL1 MUTATION ANALYSIS"
[1] 3
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               14               353 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               14               353 
[1] "UGT1A9 MUTATION ANALYSIS"
[1] 3
  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
               9              358 
  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
               9              358 
[1] "MBP MUTATION ANALYSIS"
[1] 3
  MBP MUTATED MBP WILD-TYPE 
            6           361 
  MBP MUTATED MBP WILD-TYPE 
            6           361 
[1] "AAMP MUTATION ANALYSIS"
[1] 3
  AAMP MUTATED AAMP WILD-TYPE 
             3            364 
  AAMP MUTATED AAMP WILD-TYPE 
             3            364 
[1] "MGEA5 MUTATION ANALYSIS"
[1] 3
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              8             359 
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              8             359 
[1] "BEX5 MUTATION ANALYSIS"
[1] 3
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            360 
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            360 
[1] "HAUS3 MUTATION ANALYSIS"
[1] 3
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              9             358 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              9             358 
[1] "HYDIN MUTATION ANALYSIS"
[1] 3
  HYDIN MUTATED HYDIN WILD-TYPE 
             80             287 
  HYDIN MUTATED HYDIN WILD-TYPE 
             80             287 
[1] "NUDT16L1 MUTATION ANALYSIS"
[1] 3
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                364 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                364 
[1] "AGBL5 MUTATION ANALYSIS"
[1] 3
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             355 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             355 
[1] "C14ORF104 MUTATION ANALYSIS"
[1] 3
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  4                 363 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  4                 363 
[1] "ZSCAN20 MUTATION ANALYSIS"
[1] 3
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               13               354 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               13               354 
[1] "PLCB2 MUTATION ANALYSIS"
[1] 3
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              9             358 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              9             358 
[1] "SAFB MUTATION ANALYSIS"
[1] 3
  SAFB MUTATED SAFB WILD-TYPE 
            14            353 
  SAFB MUTATED SAFB WILD-TYPE 
            14            353 
[1] "GSK3B MUTATION ANALYSIS"
[1] 3
  GSK3B MUTATED GSK3B WILD-TYPE 
             14             353 
  GSK3B MUTATED GSK3B WILD-TYPE 
             14             353 
[1] "DNAJB11 MUTATION ANALYSIS"
[1] 3
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                9               358 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                9               358 
[1] "SLC46A3 MUTATION ANALYSIS"
[1] 3
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                8               359 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                8               359 
[1] "C9ORF102 MUTATION ANALYSIS"
[1] 3
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 8                359 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 8                359 
[1] "NSF MUTATION ANALYSIS"
[1] 3
  NSF MUTATED NSF WILD-TYPE 
            4           363 
  NSF MUTATED NSF WILD-TYPE 
            4           363 
[1] "MTIF2 MUTATION ANALYSIS"
[1] 3
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              9             358 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              9             358 
[1] "MEGF8 MUTATION ANALYSIS"
[1] 3
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             24             343 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             24             343 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             31             336 
  ARID2 MUTATED ARID2 WILD-TYPE 
             31             336 
[1] "PCDHGA4 MUTATION ANALYSIS"
[1] 3
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               18               349 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               18               349 
[1] "NRAP MUTATION ANALYSIS"
[1] 3
  NRAP MUTATED NRAP WILD-TYPE 
            24            343 
  NRAP MUTATED NRAP WILD-TYPE 
            24            343 
[1] "DDX11 MUTATION ANALYSIS"
[1] 3
  DDX11 MUTATED DDX11 WILD-TYPE 
              7             360 
  DDX11 MUTATED DDX11 WILD-TYPE 
              7             360 
[1] "KIF5B MUTATION ANALYSIS"
[1] 3
  KIF5B MUTATED KIF5B WILD-TYPE 
             14             353 
  KIF5B MUTATED KIF5B WILD-TYPE 
             14             353 
[1] "ZNF418 MUTATION ANALYSIS"
[1] 3
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              14              353 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              14              353 
[1] "TRPC1 MUTATION ANALYSIS"
[1] 3
  TRPC1 MUTATED TRPC1 WILD-TYPE 
             13             354 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
             13             354 
[1] "ZNF124 MUTATION ANALYSIS"
[1] 3
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              359 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              359 
[1] "KLC3 MUTATION ANALYSIS"
[1] 3
  KLC3 MUTATED KLC3 WILD-TYPE 
             6            361 
  KLC3 MUTATED KLC3 WILD-TYPE 
             6            361 
[1] "KIAA0528 MUTATION ANALYSIS"
[1] 3
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                15                352 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                15                352 
[1] "RNF219 MUTATION ANALYSIS"
[1] 3
  RNF219 MUTATED RNF219 WILD-TYPE 
              14              353 
  RNF219 MUTATED RNF219 WILD-TYPE 
              14              353 
[1] "MED12L MUTATION ANALYSIS"
[1] 3
  MED12L MUTATED MED12L WILD-TYPE 
              28              339 
  MED12L MUTATED MED12L WILD-TYPE 
              28              339 
[1] "PIWIL1 MUTATION ANALYSIS"
[1] 3
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
              22              345 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
              22              345 
[1] "ZNF546 MUTATION ANALYSIS"
[1] 3
  ZNF546 MUTATED ZNF546 WILD-TYPE 
              15              352 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
              15              352 
[1] "ZNF643 MUTATION ANALYSIS"
[1] 3
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               9              358 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               9              358 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
            48            319 
  ANK3 MUTATED ANK3 WILD-TYPE 
            48            319 
[1] "KRT25 MUTATION ANALYSIS"
[1] 3
  KRT25 MUTATED KRT25 WILD-TYPE 
             10             357 
  KRT25 MUTATED KRT25 WILD-TYPE 
             10             357 
[1] "ACTA1 MUTATION ANALYSIS"
[1] 3
  ACTA1 MUTATED ACTA1 WILD-TYPE 
             12             355 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
             12             355 
[1] "RNF10 MUTATION ANALYSIS"
[1] 3
  RNF10 MUTATED RNF10 WILD-TYPE 
             13             354 
  RNF10 MUTATED RNF10 WILD-TYPE 
             13             354 
[1] "ZNF577 MUTATION ANALYSIS"
[1] 3
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              12              355 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              12              355 
[1] "SRGAP3 MUTATION ANALYSIS"
[1] 3
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              17              350 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              17              350 
[1] "ZMYND8 MUTATION ANALYSIS"
[1] 3
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              25              342 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              25              342 
[1] "KIAA0319 MUTATION ANALYSIS"
[1] 3
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                15                352 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                15                352 
[1] "PUS7 MUTATION ANALYSIS"
[1] 3
  PUS7 MUTATED PUS7 WILD-TYPE 
            13            354 
  PUS7 MUTATED PUS7 WILD-TYPE 
            13            354 
[1] "DCLRE1C MUTATION ANALYSIS"
[1] 3
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                9               358 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                9               358 
[1] "TEX2 MUTATION ANALYSIS"
[1] 3
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            355 
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            355 
[1] "BRD4 MUTATION ANALYSIS"
[1] 3
  BRD4 MUTATED BRD4 WILD-TYPE 
            20            347 
  BRD4 MUTATED BRD4 WILD-TYPE 
            20            347 
[1] "ZMIZ1 MUTATION ANALYSIS"
[1] 3
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              9             358 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              9             358 
[1] "SLC44A4 MUTATION ANALYSIS"
[1] 3
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               12               355 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               12               355 
[1] "NCF2 MUTATION ANALYSIS"
[1] 3
  NCF2 MUTATED NCF2 WILD-TYPE 
             8            359 
  NCF2 MUTATED NCF2 WILD-TYPE 
             8            359 
[1] "MFRP MUTATION ANALYSIS"
[1] 3
  MFRP MUTATED MFRP WILD-TYPE 
            11            356 
  MFRP MUTATED MFRP WILD-TYPE 
            11            356 
[1] "PKHD1 MUTATION ANALYSIS"
[1] 3
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             57             310 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             57             310 
[1] "TAF4 MUTATION ANALYSIS"
[1] 3
  TAF4 MUTATED TAF4 WILD-TYPE 
             9            358 
  TAF4 MUTATED TAF4 WILD-TYPE 
             9            358 
[1] "USP1 MUTATION ANALYSIS"
[1] 3
  USP1 MUTATED USP1 WILD-TYPE 
             9            358 
  USP1 MUTATED USP1 WILD-TYPE 
             9            358 
[1] "TRHDE MUTATION ANALYSIS"
[1] 3
  TRHDE MUTATED TRHDE WILD-TYPE 
             27             340 
  TRHDE MUTATED TRHDE WILD-TYPE 
             27             340 
[1] "STK3 MUTATION ANALYSIS"
[1] 3
  STK3 MUTATED STK3 WILD-TYPE 
             9            358 
  STK3 MUTATED STK3 WILD-TYPE 
             9            358 
[1] "SEC14L1 MUTATION ANALYSIS"
[1] 3
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
               10               357 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
               10               357 
[1] "IL18R1 MUTATION ANALYSIS"
[1] 3
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              13              354 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              13              354 
[1] "TOX MUTATION ANALYSIS"
[1] 3
  TOX MUTATED TOX WILD-TYPE 
           15           352 
  TOX MUTATED TOX WILD-TYPE 
           15           352 
[1] "ROCK1 MUTATION ANALYSIS"
[1] 3
  ROCK1 MUTATED ROCK1 WILD-TYPE 
             17             350 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
             17             350 
[1] "CCDC158 MUTATION ANALYSIS"
[1] 3
  CCDC158 MUTATED CCDC158 WILD-TYPE 
               16               351 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
               16               351 
[1] "XPO4 MUTATION ANALYSIS"
[1] 3
  XPO4 MUTATED XPO4 WILD-TYPE 
            18            349 
  XPO4 MUTATED XPO4 WILD-TYPE 
            18            349 
[1] "ULK2 MUTATION ANALYSIS"
[1] 3
  ULK2 MUTATED ULK2 WILD-TYPE 
            12            355 
  ULK2 MUTATED ULK2 WILD-TYPE 
            12            355 
[1] "TMEM62 MUTATION ANALYSIS"
[1] 3
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               6              361 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               6              361 
[1] "ATR MUTATION ANALYSIS"
[1] 3
  ATR MUTATED ATR WILD-TYPE 
           28           339 
  ATR MUTATED ATR WILD-TYPE 
           28           339 
[1] "FABP2 MUTATION ANALYSIS"
[1] 3
  FABP2 MUTATED FABP2 WILD-TYPE 
              7             360 
  FABP2 MUTATED FABP2 WILD-TYPE 
              7             360 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              18              349 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              18              349 
[1] "NEDD9 MUTATION ANALYSIS"
[1] 3
  NEDD9 MUTATED NEDD9 WILD-TYPE 
             12             355 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
             12             355 
[1] "HCFC1R1 MUTATION ANALYSIS"
[1] 3
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               362 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               362 
[1] "PRKCQ MUTATION ANALYSIS"
[1] 3
  PRKCQ MUTATED PRKCQ WILD-TYPE 
             15             352 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
             15             352 
[1] "CAMK1 MUTATION ANALYSIS"
[1] 3
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              7             360 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              7             360 
[1] "VCX3A MUTATION ANALYSIS"
[1] 3
  VCX3A MUTATED VCX3A WILD-TYPE 
              5             362 
  VCX3A MUTATED VCX3A WILD-TYPE 
              5             362 
[1] "ATAD1 MUTATION ANALYSIS"
[1] 3
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              8             359 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              8             359 
[1] "C6ORF150 MUTATION ANALYSIS"
[1] 3
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 9                358 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 9                358 
[1] "IGFN1 MUTATION ANALYSIS"
[1] 3
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             16             351 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             16             351 
[1] "CCDC14 MUTATION ANALYSIS"
[1] 3
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              356 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              356 
[1] "ENPP3 MUTATION ANALYSIS"
[1] 3
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              9             358 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              9             358 
[1] "TAB1 MUTATION ANALYSIS"
[1] 3
  TAB1 MUTATED TAB1 WILD-TYPE 
             3            364 
  TAB1 MUTATED TAB1 WILD-TYPE 
             3            364 
[1] "CDK5RAP2 MUTATION ANALYSIS"
[1] 3
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                23                344 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                23                344 
[1] "CASP5 MUTATION ANALYSIS"
[1] 3
  CASP5 MUTATED CASP5 WILD-TYPE 
             13             354 
  CASP5 MUTATED CASP5 WILD-TYPE 
             13             354 
[1] "NONO MUTATION ANALYSIS"
[1] 3
  NONO MUTATED NONO WILD-TYPE 
            11            356 
  NONO MUTATED NONO WILD-TYPE 
            11            356 
[1] "SLC16A5 MUTATION ANALYSIS"
[1] 3
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
               10               357 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
               10               357 
[1] "GUCY2F MUTATION ANALYSIS"
[1] 3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              19              348 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              19              348 
[1] "CXCR7 MUTATION ANALYSIS"
[1] 3
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             19             348 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             19             348 
[1] "RELA MUTATION ANALYSIS"
[1] 3
  RELA MUTATED RELA WILD-TYPE 
             9            358 
  RELA MUTATED RELA WILD-TYPE 
             9            358 
[1] "WDR65 MUTATION ANALYSIS"
[1] 3
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             361 
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             361 
[1] "DTX3L MUTATION ANALYSIS"
[1] 3
  DTX3L MUTATED DTX3L WILD-TYPE 
             10             357 
  DTX3L MUTATED DTX3L WILD-TYPE 
             10             357 
[1] "ARID4B MUTATION ANALYSIS"
[1] 3
  ARID4B MUTATED ARID4B WILD-TYPE 
              11              356 
  ARID4B MUTATED ARID4B WILD-TYPE 
              11              356 
[1] "ZNF295 MUTATION ANALYSIS"
[1] 3
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              10              357 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              10              357 
[1] "FBLIM1 MUTATION ANALYSIS"
[1] 3
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               5              362 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               5              362 
[1] "WFDC10B MUTATION ANALYSIS"
[1] 3
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               362 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               362 
[1] "NAA15 MUTATION ANALYSIS"
[1] 3
  NAA15 MUTATED NAA15 WILD-TYPE 
             15             352 
  NAA15 MUTATED NAA15 WILD-TYPE 
             15             352 
[1] "ACTL7B MUTATION ANALYSIS"
[1] 3
  ACTL7B MUTATED ACTL7B WILD-TYPE 
               4              363 
  ACTL7B MUTATED ACTL7B WILD-TYPE 
               4              363 
[1] "COL4A6 MUTATION ANALYSIS"
[1] 3
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              21              346 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              21              346 
[1] "FGD3 MUTATION ANALYSIS"
[1] 3
  FGD3 MUTATED FGD3 WILD-TYPE 
            13            354 
  FGD3 MUTATED FGD3 WILD-TYPE 
            13            354 
[1] "PHKB MUTATION ANALYSIS"
[1] 3
  PHKB MUTATED PHKB WILD-TYPE 
            12            355 
  PHKB MUTATED PHKB WILD-TYPE 
            12            355 
[1] "CHD5 MUTATION ANALYSIS"
[1] 3
  CHD5 MUTATED CHD5 WILD-TYPE 
            28            339 
  CHD5 MUTATED CHD5 WILD-TYPE 
            28            339 
[1] "GSTA5 MUTATION ANALYSIS"
[1] 3
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              6             361 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              6             361 
[1] "C5ORF42 MUTATION ANALYSIS"
[1] 3
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               32               335 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               32               335 
[1] "ESYT1 MUTATION ANALYSIS"
[1] 3
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              9             358 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              9             358 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               8              359 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               8              359 
[1] "PNPLA5 MUTATION ANALYSIS"
[1] 3
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              10              357 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              10              357 
[1] "TMPRSS5 MUTATION ANALYSIS"
[1] 3
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               360 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               360 
[1] "CSF3R MUTATION ANALYSIS"
[1] 3
  CSF3R MUTATED CSF3R WILD-TYPE 
             14             353 
  CSF3R MUTATED CSF3R WILD-TYPE 
             14             353 
[1] "VANGL1 MUTATION ANALYSIS"
[1] 3
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              10              357 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              10              357 
[1] "MST1R MUTATION ANALYSIS"
[1] 3
  MST1R MUTATED MST1R WILD-TYPE 
             14             353 
  MST1R MUTATED MST1R WILD-TYPE 
             14             353 
[1] "OR5H1 MUTATION ANALYSIS"
[1] 3
  OR5H1 MUTATED OR5H1 WILD-TYPE 
             10             357 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
             10             357 
[1] "VWA5A MUTATION ANALYSIS"
[1] 3
  VWA5A MUTATED VWA5A WILD-TYPE 
             12             355 
  VWA5A MUTATED VWA5A WILD-TYPE 
             12             355 
[1] "ABCF3 MUTATION ANALYSIS"
[1] 3
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             15             352 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             15             352 
[1] "CUBN MUTATION ANALYSIS"
[1] 3
  CUBN MUTATED CUBN WILD-TYPE 
            52            315 
  CUBN MUTATED CUBN WILD-TYPE 
            52            315 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
             9            358 
  LIPH MUTATED LIPH WILD-TYPE 
             9            358 
[1] "SHQ1 MUTATION ANALYSIS"
[1] 3
  SHQ1 MUTATED SHQ1 WILD-TYPE 
             8            359 
  SHQ1 MUTATED SHQ1 WILD-TYPE 
             8            359 
[1] "DAB2 MUTATION ANALYSIS"
[1] 3
  DAB2 MUTATED DAB2 WILD-TYPE 
            13            354 
  DAB2 MUTATED DAB2 WILD-TYPE 
            13            354 
[1] "IFLTD1 MUTATION ANALYSIS"
[1] 3
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              12              355 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              12              355 
[1] "TEX11 MUTATION ANALYSIS"
[1] 3
  TEX11 MUTATED TEX11 WILD-TYPE 
             17             350 
  TEX11 MUTATED TEX11 WILD-TYPE 
             17             350 
[1] "GOLGA1 MUTATION ANALYSIS"
[1] 3
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               7              360 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               7              360 
[1] "ZHX2 MUTATION ANALYSIS"
[1] 3
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            17            350 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            17            350 
[1] "FAM167B MUTATION ANALYSIS"
[1] 3
  FAM167B MUTATED FAM167B WILD-TYPE 
                4               363 
  FAM167B MUTATED FAM167B WILD-TYPE 
                4               363 
[1] "UFSP2 MUTATION ANALYSIS"
[1] 3
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              4             363 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              4             363 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              22              345 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              22              345 
[1] "BFAR MUTATION ANALYSIS"
[1] 3
  BFAR MUTATED BFAR WILD-TYPE 
             8            359 
  BFAR MUTATED BFAR WILD-TYPE 
             8            359 
[1] "SBNO1 MUTATION ANALYSIS"
[1] 3
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             15             352 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             15             352 
[1] "MR1 MUTATION ANALYSIS"
[1] 3
  MR1 MUTATED MR1 WILD-TYPE 
            5           362 
  MR1 MUTATED MR1 WILD-TYPE 
            5           362 
[1] "OR5R1 MUTATION ANALYSIS"
[1] 3
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             14             353 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             14             353 
[1] "RIMS2 MUTATION ANALYSIS"
[1] 3
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             36             331 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             36             331 
[1] "ZNF660 MUTATION ANALYSIS"
[1] 3
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               7              360 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               7              360 
[1] "GSS MUTATION ANALYSIS"
[1] 3
  GSS MUTATED GSS WILD-TYPE 
            8           359 
  GSS MUTATED GSS WILD-TYPE 
            8           359 
[1] "SLC38A9 MUTATION ANALYSIS"
[1] 3
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               11               356 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               11               356 
[1] "VPS72 MUTATION ANALYSIS"
[1] 3
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             359 
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             359 
[1] "LCK MUTATION ANALYSIS"
[1] 3
  LCK MUTATED LCK WILD-TYPE 
            8           359 
  LCK MUTATED LCK WILD-TYPE 
            8           359 
[1] "AGTPBP1 MUTATION ANALYSIS"
[1] 3
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               17               350 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               17               350 
[1] "GRIN2A MUTATION ANALYSIS"
[1] 3
  GRIN2A MUTATED GRIN2A WILD-TYPE 
              41              326 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
              41              326 
[1] "FGD1 MUTATION ANALYSIS"
[1] 3
  FGD1 MUTATED FGD1 WILD-TYPE 
            16            351 
  FGD1 MUTATED FGD1 WILD-TYPE 
            16            351 
[1] "ZNF286A MUTATION ANALYSIS"
[1] 3
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                7               360 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                7               360 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             26             341 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             26             341 
[1] "AOX1 MUTATION ANALYSIS"
[1] 3
  AOX1 MUTATED AOX1 WILD-TYPE 
            12            355 
  AOX1 MUTATED AOX1 WILD-TYPE 
            12            355 
[1] "ZNF323 MUTATION ANALYSIS"
[1] 3
  ZNF323 MUTATED ZNF323 WILD-TYPE 
              10              357 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
              10              357 
[1] "ESR1 MUTATION ANALYSIS"
[1] 3
  ESR1 MUTATED ESR1 WILD-TYPE 
            19            348 
  ESR1 MUTATED ESR1 WILD-TYPE 
            19            348 
[1] "LDLRAD3 MUTATION ANALYSIS"
[1] 3
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                5               362 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                5               362 
[1] "BAZ1B MUTATION ANALYSIS"
[1] 3
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             21             346 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             21             346 
[1] "SLAMF9 MUTATION ANALYSIS"
[1] 3
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               6              361 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               6              361 
[1] "C6ORF203 MUTATION ANALYSIS"
[1] 3
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 4                363 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 4                363 
[1] "CCPG1 MUTATION ANALYSIS"
[1] 3
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             11             356 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             11             356 
[1] "RIC8B MUTATION ANALYSIS"
[1] 3
  RIC8B MUTATED RIC8B WILD-TYPE 
              9             358 
  RIC8B MUTATED RIC8B WILD-TYPE 
              9             358 
[1] "KIAA1429 MUTATION ANALYSIS"
[1] 3
  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
                17                350 
  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
                17                350 
[1] "SPATA6 MUTATION ANALYSIS"
[1] 3
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               6              361 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               6              361 
[1] "PIGN MUTATION ANALYSIS"
[1] 3
  PIGN MUTATED PIGN WILD-TYPE 
             7            360 
  PIGN MUTATED PIGN WILD-TYPE 
             7            360 
[1] "OR4N2 MUTATION ANALYSIS"
[1] 3
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             357 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             357 
[1] "RALA MUTATION ANALYSIS"
[1] 3
  RALA MUTATED RALA WILD-TYPE 
             7            360 
  RALA MUTATED RALA WILD-TYPE 
             7            360 
[1] "MUS81 MUTATION ANALYSIS"
[1] 3
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             360 
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             360 
[1] "CDHR5 MUTATION ANALYSIS"
[1] 3
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             356 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             356 
[1] "ZNF318 MUTATION ANALYSIS"
[1] 3
  ZNF318 MUTATED ZNF318 WILD-TYPE 
              28              339 
  ZNF318 MUTATED ZNF318 WILD-TYPE 
              28              339 
[1] "IL7R MUTATION ANALYSIS"
[1] 3
  IL7R MUTATED IL7R WILD-TYPE 
            11            356 
  IL7R MUTATED IL7R WILD-TYPE 
            11            356 
[1] "LRRTM2 MUTATION ANALYSIS"
[1] 3
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               5              362 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               5              362 
[1] "IGSF1 MUTATION ANALYSIS"
[1] 3
  IGSF1 MUTATED IGSF1 WILD-TYPE 
             21             346 
  IGSF1 MUTATED IGSF1 WILD-TYPE 
             21             346 
[1] "GCC2 MUTATION ANALYSIS"
[1] 3
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            357 
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            357 
[1] "ATRNL1 MUTATION ANALYSIS"
[1] 3
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
              22              345 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
              22              345 
[1] "ERN1 MUTATION ANALYSIS"
[1] 3
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            364 
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            364 
[1] "BTBD7 MUTATION ANALYSIS"
[1] 3
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             12             355 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             12             355 
[1] "COL11A1 MUTATION ANALYSIS"
[1] 3
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               45               322 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               45               322 
[1] "TTLL13 MUTATION ANALYSIS"
[1] 3
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               5              362 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               5              362 
[1] "RPS6KC1 MUTATION ANALYSIS"
[1] 3
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
               15               352 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
               15               352 
[1] "ZNF350 MUTATION ANALYSIS"
[1] 3
  ZNF350 MUTATED ZNF350 WILD-TYPE 
               9              358 
  ZNF350 MUTATED ZNF350 WILD-TYPE 
               9              358 
[1] "ITPRIPL1 MUTATION ANALYSIS"
[1] 3
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 7                360 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 7                360 
[1] "CCDC18 MUTATION ANALYSIS"
[1] 3
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              11              356 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              11              356 
[1] "CUTC MUTATION ANALYSIS"
[1] 3
  CUTC MUTATED CUTC WILD-TYPE 
             5            362 
  CUTC MUTATED CUTC WILD-TYPE 
             5            362 
[1] "GON4L MUTATION ANALYSIS"
[1] 3
  GON4L MUTATED GON4L WILD-TYPE 
             20             347 
  GON4L MUTATED GON4L WILD-TYPE 
             20             347 
[1] "PLCG2 MUTATION ANALYSIS"
[1] 3
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             18             349 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             18             349 
[1] "GLTSCR1 MUTATION ANALYSIS"
[1] 3
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               11               356 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               11               356 
[1] "OR9G4 MUTATION ANALYSIS"
[1] 3
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             359 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             359 
[1] "NFATC2IP MUTATION ANALYSIS"
[1] 3
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
                 3                364 
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
                 3                364 
[1] "C14ORF180 MUTATION ANALYSIS"
[1] 3
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 363 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 363 
[1] "MYLK4 MUTATION ANALYSIS"
[1] 3
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             12             355 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             12             355 
[1] "CENPJ MUTATION ANALYSIS"
[1] 3
  CENPJ MUTATED CENPJ WILD-TYPE 
             21             346 
  CENPJ MUTATED CENPJ WILD-TYPE 
             21             346 
[1] "CHMP4B MUTATION ANALYSIS"
[1] 3
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              364 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              364 
[1] "C20ORF43 MUTATION ANALYSIS"
[1] 3
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                364 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                364 
[1] "CIZ1 MUTATION ANALYSIS"
[1] 3
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            15            352 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            15            352 
[1] "ZNF416 MUTATION ANALYSIS"
[1] 3
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               8              359 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               8              359 
[1] "RBM16 MUTATION ANALYSIS"
[1] 3
  RBM16 MUTATED RBM16 WILD-TYPE 
             15             352 
  RBM16 MUTATED RBM16 WILD-TYPE 
             15             352 
[1] "MORC1 MUTATION ANALYSIS"
[1] 3
  MORC1 MUTATED MORC1 WILD-TYPE 
             13             354 
  MORC1 MUTATED MORC1 WILD-TYPE 
             13             354 
[1] "ROR1 MUTATION ANALYSIS"
[1] 3
  ROR1 MUTATED ROR1 WILD-TYPE 
            20            347 
  ROR1 MUTATED ROR1 WILD-TYPE 
            20            347 
[1] "HSPA4L MUTATION ANALYSIS"
[1] 3
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               8              359 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               8              359 
[1] "GSG2 MUTATION ANALYSIS"
[1] 3
  GSG2 MUTATED GSG2 WILD-TYPE 
             6            361 
  GSG2 MUTATED GSG2 WILD-TYPE 
             6            361 
[1] "MIPEP MUTATION ANALYSIS"
[1] 3
  MIPEP MUTATED MIPEP WILD-TYPE 
              8             359 
  MIPEP MUTATED MIPEP WILD-TYPE 
              8             359 
[1] "CENPA MUTATION ANALYSIS"
[1] 3
  CENPA MUTATED CENPA WILD-TYPE 
              5             362 
  CENPA MUTATED CENPA WILD-TYPE 
              5             362 
[1] "OTUD4 MUTATION ANALYSIS"
[1] 3
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             19             348 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             19             348 
[1] "CASC4 MUTATION ANALYSIS"
[1] 3
  CASC4 MUTATED CASC4 WILD-TYPE 
              5             362 
  CASC4 MUTATED CASC4 WILD-TYPE 
              5             362 
[1] "OR2F2 MUTATION ANALYSIS"
[1] 3
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              7             360 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              7             360 
[1] "MPZL1 MUTATION ANALYSIS"
[1] 3
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             360 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             360 
[1] "VN1R4 MUTATION ANALYSIS"
[1] 3
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              6             361 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              6             361 
[1] "KIF14 MUTATION ANALYSIS"
[1] 3
  KIF14 MUTATED KIF14 WILD-TYPE 
             11             356 
  KIF14 MUTATED KIF14 WILD-TYPE 
             11             356 
[1] "TRIM33 MUTATION ANALYSIS"
[1] 3
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              15              352 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              15              352 
[1] "XRCC6 MUTATION ANALYSIS"
[1] 3
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             360 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             360 
[1] "GTDC1 MUTATION ANALYSIS"
[1] 3
  GTDC1 MUTATED GTDC1 WILD-TYPE 
              9             358 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
              9             358 
[1] "SERPINB10 MUTATION ANALYSIS"
[1] 3
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 10                 357 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 10                 357 
[1] "PCDHGA8 MUTATION ANALYSIS"
[1] 3
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
               14               353 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
               14               353 
[1] "F2R MUTATION ANALYSIS"
[1] 3
  F2R MUTATED F2R WILD-TYPE 
           11           356 
  F2R MUTATED F2R WILD-TYPE 
           11           356 
[1] "C17ORF58 MUTATION ANALYSIS"
[1] 3
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 3                364 
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 3                364 
[1] "TEX13A MUTATION ANALYSIS"
[1] 3
  TEX13A MUTATED TEX13A WILD-TYPE 
              10              357 
  TEX13A MUTATED TEX13A WILD-TYPE 
              10              357 
[1] "LCT MUTATION ANALYSIS"
[1] 3
  LCT MUTATED LCT WILD-TYPE 
           33           334 
  LCT MUTATED LCT WILD-TYPE 
           33           334 
[1] "IDI1 MUTATION ANALYSIS"
[1] 3
  IDI1 MUTATED IDI1 WILD-TYPE 
             4            363 
  IDI1 MUTATED IDI1 WILD-TYPE 
             4            363 
[1] "C6ORF15 MUTATION ANALYSIS"
[1] 3
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                6               361 
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                6               361 
[1] "MYO3A MUTATION ANALYSIS"
[1] 3
  MYO3A MUTATED MYO3A WILD-TYPE 
             37             330 
  MYO3A MUTATED MYO3A WILD-TYPE 
             37             330 
[1] "C5 MUTATION ANALYSIS"
[1] 3
  C5 MUTATED C5 WILD-TYPE 
          17          350 
  C5 MUTATED C5 WILD-TYPE 
          17          350 
[1] "MICAL1 MUTATION ANALYSIS"
[1] 3
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               9              358 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               9              358 
[1] "PTPN13 MUTATION ANALYSIS"
[1] 3
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              22              345 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              22              345 
[1] "TMPRSS15 MUTATION ANALYSIS"
[1] 3
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                22                345 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                22                345 
[1] "C17ORF71 MUTATION ANALYSIS"
[1] 3
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 9                358 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 9                358 
[1] "WDR17 MUTATION ANALYSIS"
[1] 3
  WDR17 MUTATED WDR17 WILD-TYPE 
             23             344 
  WDR17 MUTATED WDR17 WILD-TYPE 
             23             344 
[1] "FBXO40 MUTATION ANALYSIS"
[1] 3
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              16              351 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              16              351 
[1] "PDK1 MUTATION ANALYSIS"
[1] 3
  PDK1 MUTATED PDK1 WILD-TYPE 
             5            362 
  PDK1 MUTATED PDK1 WILD-TYPE 
             5            362 
[1] "FAM81B MUTATION ANALYSIS"
[1] 3
  FAM81B MUTATED FAM81B WILD-TYPE 
               9              358 
  FAM81B MUTATED FAM81B WILD-TYPE 
               9              358 
[1] "HIP1 MUTATION ANALYSIS"
[1] 3
  HIP1 MUTATED HIP1 WILD-TYPE 
            12            355 
  HIP1 MUTATED HIP1 WILD-TYPE 
            12            355 
[1] "PHLDB2 MUTATION ANALYSIS"
[1] 3
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              18              349 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              18              349 
[1] "TATDN2 MUTATION ANALYSIS"
[1] 3
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               9              358 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               9              358 
[1] "SFRP2 MUTATION ANALYSIS"
[1] 3
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              8             359 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              8             359 
[1] "EPRS MUTATION ANALYSIS"
[1] 3
  EPRS MUTATED EPRS WILD-TYPE 
            19            348 
  EPRS MUTATED EPRS WILD-TYPE 
            19            348 
[1] "CELSR1 MUTATION ANALYSIS"
[1] 3
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              22              345 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              22              345 
[1] "PIAS2 MUTATION ANALYSIS"
[1] 3
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              4             363 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              4             363 
[1] "CNGA3 MUTATION ANALYSIS"
[1] 3
  CNGA3 MUTATED CNGA3 WILD-TYPE 
             13             354 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
             13             354 
[1] "OR51E2 MUTATION ANALYSIS"
[1] 3
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               5              362 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               5              362 
[1] "OR6C1 MUTATION ANALYSIS"
[1] 3
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              7             360 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              7             360 
[1] "EVI2A MUTATION ANALYSIS"
[1] 3
  EVI2A MUTATED EVI2A WILD-TYPE 
              7             360 
  EVI2A MUTATED EVI2A WILD-TYPE 
              7             360 
[1] "KIAA0415 MUTATION ANALYSIS"
[1] 3
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                12                355 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                12                355 
[1] "ELANE MUTATION ANALYSIS"
[1] 3
  ELANE MUTATED ELANE WILD-TYPE 
              7             360 
  ELANE MUTATED ELANE WILD-TYPE 
              7             360 
[1] "UGGT1 MUTATION ANALYSIS"
[1] 3
  UGGT1 MUTATED UGGT1 WILD-TYPE 
             18             349 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
             18             349 
[1] "CCDC19 MUTATION ANALYSIS"
[1] 3
  CCDC19 MUTATED CCDC19 WILD-TYPE 
              15              352 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
              15              352 
[1] "C13ORF23 MUTATION ANALYSIS"
[1] 3
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                12                355 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                12                355 
[1] "SMC4 MUTATION ANALYSIS"
[1] 3
  SMC4 MUTATED SMC4 WILD-TYPE 
            18            349 
  SMC4 MUTATED SMC4 WILD-TYPE 
            18            349 
[1] "KIF13A MUTATION ANALYSIS"
[1] 3
  KIF13A MUTATED KIF13A WILD-TYPE 
              21              346 
  KIF13A MUTATED KIF13A WILD-TYPE 
              21              346 
[1] "DONSON MUTATION ANALYSIS"
[1] 3
  DONSON MUTATED DONSON WILD-TYPE 
               4              363 
  DONSON MUTATED DONSON WILD-TYPE 
               4              363 
[1] "SLC26A7 MUTATION ANALYSIS"
[1] 3
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               17               350 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               17               350 
[1] "ACSL3 MUTATION ANALYSIS"
[1] 3
  ACSL3 MUTATED ACSL3 WILD-TYPE 
             10             357 
  ACSL3 MUTATED ACSL3 WILD-TYPE 
             10             357 
[1] "CDC7 MUTATION ANALYSIS"
[1] 3
  CDC7 MUTATED CDC7 WILD-TYPE 
            10            357 
  CDC7 MUTATED CDC7 WILD-TYPE 
            10            357 
[1] "C12ORF51 MUTATION ANALYSIS"
[1] 3
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                31                336 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                31                336 
[1] "LARP7 MUTATION ANALYSIS"
[1] 3
  LARP7 MUTATED LARP7 WILD-TYPE 
              8             359 
  LARP7 MUTATED LARP7 WILD-TYPE 
              8             359 
[1] "TRIP6 MUTATION ANALYSIS"
[1] 3
  TRIP6 MUTATED TRIP6 WILD-TYPE 
             10             357 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
             10             357 
[1] "FOLR3 MUTATION ANALYSIS"
[1] 3
  FOLR3 MUTATED FOLR3 WILD-TYPE 
              6             361 
  FOLR3 MUTATED FOLR3 WILD-TYPE 
              6             361 
[1] "ANKRD40 MUTATION ANALYSIS"
[1] 3
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                8               359 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                8               359 
[1] "MRPL10 MUTATION ANALYSIS"
[1] 3
  MRPL10 MUTATED MRPL10 WILD-TYPE 
               4              363 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
               4              363 
[1] "ACADVL MUTATION ANALYSIS"
[1] 3
  ACADVL MUTATED ACADVL WILD-TYPE 
               6              361 
  ACADVL MUTATED ACADVL WILD-TYPE 
               6              361 
[1] "SLIT3 MUTATION ANALYSIS"
[1] 3
  SLIT3 MUTATED SLIT3 WILD-TYPE 
             25             342 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
             25             342 
[1] "CCL14 MUTATION ANALYSIS"
[1] 3
  CCL14 MUTATED CCL14 WILD-TYPE 
              5             362 
  CCL14 MUTATED CCL14 WILD-TYPE 
              5             362 
[1] "KLK11 MUTATION ANALYSIS"
[1] 3
  KLK11 MUTATED KLK11 WILD-TYPE 
              5             362 
  KLK11 MUTATED KLK11 WILD-TYPE 
              5             362 
[1] "UBR5 MUTATION ANALYSIS"
[1] 3
  UBR5 MUTATED UBR5 WILD-TYPE 
            28            339 
  UBR5 MUTATED UBR5 WILD-TYPE 
            28            339 
[1] "ZNF557 MUTATION ANALYSIS"
[1] 3
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               9              358 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               9              358 
[1] "UVRAG MUTATION ANALYSIS"
[1] 3
  UVRAG MUTATED UVRAG WILD-TYPE 
              7             360 
  UVRAG MUTATED UVRAG WILD-TYPE 
              7             360 
[1] "C14ORF118 MUTATION ANALYSIS"
[1] 3
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  9                 358 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  9                 358 
[1] "XKR3 MUTATION ANALYSIS"
[1] 3
  XKR3 MUTATED XKR3 WILD-TYPE 
            12            355 
  XKR3 MUTATED XKR3 WILD-TYPE 
            12            355 
[1] "EPHA4 MUTATION ANALYSIS"
[1] 3
  EPHA4 MUTATED EPHA4 WILD-TYPE 
             19             348 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
             19             348 
[1] "PARVB MUTATION ANALYSIS"
[1] 3
  PARVB MUTATED PARVB WILD-TYPE 
              9             358 
  PARVB MUTATED PARVB WILD-TYPE 
              9             358 
[1] "TAF2 MUTATION ANALYSIS"
[1] 3
  TAF2 MUTATED TAF2 WILD-TYPE 
            17            350 
  TAF2 MUTATED TAF2 WILD-TYPE 
            17            350 
[1] "KIAA0196 MUTATION ANALYSIS"
[1] 3
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                10                357 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                10                357 
[1] "FRY MUTATION ANALYSIS"
[1] 3
  FRY MUTATED FRY WILD-TYPE 
           38           329 
  FRY MUTATED FRY WILD-TYPE 
           38           329 
[1] "EIF2AK3 MUTATION ANALYSIS"
[1] 3
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               11               356 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               11               356 
[1] "IFI35 MUTATION ANALYSIS"
[1] 3
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             359 
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             359 
[1] "MYPN MUTATION ANALYSIS"
[1] 3
  MYPN MUTATED MYPN WILD-TYPE 
            19            348 
  MYPN MUTATED MYPN WILD-TYPE 
            19            348 
[1] "DTD1 MUTATION ANALYSIS"
[1] 3
  DTD1 MUTATED DTD1 WILD-TYPE 
             5            362 
  DTD1 MUTATED DTD1 WILD-TYPE 
             5            362 
[1] "MGAT5 MUTATION ANALYSIS"
[1] 3
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             13             354 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             13             354 
[1] "GLUD2 MUTATION ANALYSIS"
[1] 3
  GLUD2 MUTATED GLUD2 WILD-TYPE 
             20             347 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
             20             347 
[1] "PTPRZ1 MUTATION ANALYSIS"
[1] 3
  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
              28              339 
  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
              28              339 
[1] "C3ORF27 MUTATION ANALYSIS"
[1] 3
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               364 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               364 
[1] "CCT4 MUTATION ANALYSIS"
[1] 3
  CCT4 MUTATED CCT4 WILD-TYPE 
            12            355 
  CCT4 MUTATED CCT4 WILD-TYPE 
            12            355 
[1] "PON3 MUTATION ANALYSIS"
[1] 3
  PON3 MUTATED PON3 WILD-TYPE 
            10            357 
  PON3 MUTATED PON3 WILD-TYPE 
            10            357 
[1] "TGM1 MUTATION ANALYSIS"
[1] 3
  TGM1 MUTATED TGM1 WILD-TYPE 
            11            356 
  TGM1 MUTATED TGM1 WILD-TYPE 
            11            356 
[1] "NEK3 MUTATION ANALYSIS"
[1] 3
  NEK3 MUTATED NEK3 WILD-TYPE 
            11            356 
  NEK3 MUTATED NEK3 WILD-TYPE 
            11            356 
[1] "GSTM5 MUTATION ANALYSIS"
[1] 3
  GSTM5 MUTATED GSTM5 WILD-TYPE 
              5             362 
  GSTM5 MUTATED GSTM5 WILD-TYPE 
              5             362 
[1] "CLEC1A MUTATION ANALYSIS"
[1] 3
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               8              359 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               8              359 
[1] "CCDC64B MUTATION ANALYSIS"
[1] 3
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                5               362 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                5               362 
[1] "TEK MUTATION ANALYSIS"
[1] 3
  TEK MUTATED TEK WILD-TYPE 
           28           339 
  TEK MUTATED TEK WILD-TYPE 
           28           339 
[1] "IL8 MUTATION ANALYSIS"
[1] 3
  IL8 MUTATED IL8 WILD-TYPE 
            5           362 
  IL8 MUTATED IL8 WILD-TYPE 
            5           362 
[1] "ADCY9 MUTATION ANALYSIS"
[1] 3
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             18             349 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             18             349 
[1] "TNXB MUTATION ANALYSIS"
[1] 3
  TNXB MUTATED TNXB WILD-TYPE 
            39            328 
  TNXB MUTATED TNXB WILD-TYPE 
            39            328 
[1] "MOGAT3 MUTATION ANALYSIS"
[1] 3
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
               6              361 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
               6              361 
[1] "HIST1H3B MUTATION ANALYSIS"
[1] 3
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                363 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                363 
[1] "ERCC6L MUTATION ANALYSIS"
[1] 3
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              12              355 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              12              355 
[1] "SBF1 MUTATION ANALYSIS"
[1] 3
  SBF1 MUTATED SBF1 WILD-TYPE 
            14            353 
  SBF1 MUTATED SBF1 WILD-TYPE 
            14            353 
[1] "ZNF391 MUTATION ANALYSIS"
[1] 3
  ZNF391 MUTATED ZNF391 WILD-TYPE 
               8              359 
  ZNF391 MUTATED ZNF391 WILD-TYPE 
               8              359 
[1] "SORBS1 MUTATION ANALYSIS"
[1] 3
  SORBS1 MUTATED SORBS1 WILD-TYPE 
              10              357 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
              10              357 
[1] "MOGAT1 MUTATION ANALYSIS"
[1] 3
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
               4              363 
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
               4              363 
[1] "GAB3 MUTATION ANALYSIS"
[1] 3
  GAB3 MUTATED GAB3 WILD-TYPE 
            11            356 
  GAB3 MUTATED GAB3 WILD-TYPE 
            11            356 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 8                359 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 8                359 
[1] "GBA2 MUTATION ANALYSIS"
[1] 3
  GBA2 MUTATED GBA2 WILD-TYPE 
            15            352 
  GBA2 MUTATED GBA2 WILD-TYPE 
            15            352 
[1] "RTTN MUTATION ANALYSIS"
[1] 3
  RTTN MUTATED RTTN WILD-TYPE 
            17            350 
  RTTN MUTATED RTTN WILD-TYPE 
            17            350 
[1] "SFRS12IP1 MUTATION ANALYSIS"
[1] 3
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  3                 364 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  3                 364 
[1] "TOMM70A MUTATION ANALYSIS"
[1] 3
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               357 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               357 
[1] "RRP9 MUTATION ANALYSIS"
[1] 3
  RRP9 MUTATED RRP9 WILD-TYPE 
            12            355 
  RRP9 MUTATED RRP9 WILD-TYPE 
            12            355 
[1] "FSTL4 MUTATION ANALYSIS"
[1] 3
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             15             352 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             15             352 
[1] "HIST4H4 MUTATION ANALYSIS"
[1] 3
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               364 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               364 
[1] "C1ORF88 MUTATION ANALYSIS"
[1] 3
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                6               361 
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                6               361 
[1] "SESTD1 MUTATION ANALYSIS"
[1] 3
  SESTD1 MUTATED SESTD1 WILD-TYPE 
              15              352 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
              15              352 
[1] "CAPZA3 MUTATION ANALYSIS"
[1] 3
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               9              358 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               9              358 
[1] "LGALS9 MUTATION ANALYSIS"
[1] 3
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               4              363 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               4              363 
[1] "MC3R MUTATION ANALYSIS"
[1] 3
  MC3R MUTATED MC3R WILD-TYPE 
            13            354 
  MC3R MUTATED MC3R WILD-TYPE 
            13            354 
[1] "ACTL6B MUTATION ANALYSIS"
[1] 3
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               9              358 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               9              358 
[1] "BACH2 MUTATION ANALYSIS"
[1] 3
  BACH2 MUTATED BACH2 WILD-TYPE 
             16             351 
  BACH2 MUTATED BACH2 WILD-TYPE 
             16             351 
[1] "PGM2 MUTATION ANALYSIS"
[1] 3
  PGM2 MUTATED PGM2 WILD-TYPE 
             3            364 
  PGM2 MUTATED PGM2 WILD-TYPE 
             3            364 
[1] "EPHB1 MUTATION ANALYSIS"
[1] 3
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             36             331 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             36             331 
[1] "NFS1 MUTATION ANALYSIS"
[1] 3
  NFS1 MUTATED NFS1 WILD-TYPE 
             5            362 
  NFS1 MUTATED NFS1 WILD-TYPE 
             5            362 
[1] "CLDN17 MUTATION ANALYSIS"
[1] 3
  CLDN17 MUTATED CLDN17 WILD-TYPE 
              13              354 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
              13              354 
[1] "UEVLD MUTATION ANALYSIS"
[1] 3
  UEVLD MUTATED UEVLD WILD-TYPE 
              3             364 
  UEVLD MUTATED UEVLD WILD-TYPE 
              3             364 
[1] "GABRQ MUTATION ANALYSIS"
[1] 3
  GABRQ MUTATED GABRQ WILD-TYPE 
             15             352 
  GABRQ MUTATED GABRQ WILD-TYPE 
             15             352 
[1] "NTSR2 MUTATION ANALYSIS"
[1] 3
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              8             359 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              8             359 
[1] "FRAS1 MUTATION ANALYSIS"
[1] 3
  FRAS1 MUTATED FRAS1 WILD-TYPE 
             37             330 
  FRAS1 MUTATED FRAS1 WILD-TYPE 
             37             330 
[1] "NDUFV2 MUTATION ANALYSIS"
[1] 3
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              364 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              364 
[1] "ATP2B4 MUTATION ANALYSIS"
[1] 3
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              18              349 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              18              349 
[1] "PLEKHA4 MUTATION ANALYSIS"
[1] 3
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
               10               357 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
               10               357 
[1] "AHNAK MUTATION ANALYSIS"
[1] 3
  AHNAK MUTATED AHNAK WILD-TYPE 
             39             328 
  AHNAK MUTATED AHNAK WILD-TYPE 
             39             328 
[1] "TRIM25 MUTATION ANALYSIS"
[1] 3
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               4              363 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               4              363 
[1] "STK10 MUTATION ANALYSIS"
[1] 3
  STK10 MUTATED STK10 WILD-TYPE 
             14             353 
  STK10 MUTATED STK10 WILD-TYPE 
             14             353 
[1] "TLR9 MUTATION ANALYSIS"
[1] 3
  TLR9 MUTATED TLR9 WILD-TYPE 
            11            356 
  TLR9 MUTATED TLR9 WILD-TYPE 
            11            356 
[1] "VWA3A MUTATION ANALYSIS"
[1] 3
  VWA3A MUTATED VWA3A WILD-TYPE 
             11             356 
  VWA3A MUTATED VWA3A WILD-TYPE 
             11             356 
[1] "S1PR1 MUTATION ANALYSIS"
[1] 3
  S1PR1 MUTATED S1PR1 WILD-TYPE 
             11             356 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
             11             356 
[1] "RAPGEF2 MUTATION ANALYSIS"
[1] 3
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               21               346 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               21               346 
[1] "SFRS2IP MUTATION ANALYSIS"
[1] 3
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               26               341 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               26               341 
[1] "LUZP1 MUTATION ANALYSIS"
[1] 3
  LUZP1 MUTATED LUZP1 WILD-TYPE 
             15             352 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
             15             352 
[1] "NDUFB2 MUTATION ANALYSIS"
[1] 3
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               3              364 
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               3              364 
[1] "LRRFIP1 MUTATION ANALYSIS"
[1] 3
  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
               12               355 
  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
               12               355 
[1] "PTPRN MUTATION ANALYSIS"
[1] 3
  PTPRN MUTATED PTPRN WILD-TYPE 
             14             353 
  PTPRN MUTATED PTPRN WILD-TYPE 
             14             353 
[1] "AVPR1A MUTATION ANALYSIS"
[1] 3
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              11              356 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              11              356 
[1] "KCNC4 MUTATION ANALYSIS"
[1] 3
  KCNC4 MUTATED KCNC4 WILD-TYPE 
              8             359 
  KCNC4 MUTATED KCNC4 WILD-TYPE 
              8             359 
[1] "RPAP2 MUTATION ANALYSIS"
[1] 3
  RPAP2 MUTATED RPAP2 WILD-TYPE 
              6             361 
  RPAP2 MUTATED RPAP2 WILD-TYPE 
              6             361 
[1] "DDX24 MUTATION ANALYSIS"
[1] 3
  DDX24 MUTATED DDX24 WILD-TYPE 
             13             354 
  DDX24 MUTATED DDX24 WILD-TYPE 
             13             354 
[1] "CUL1 MUTATION ANALYSIS"
[1] 3
  CUL1 MUTATED CUL1 WILD-TYPE 
            15            352 
  CUL1 MUTATED CUL1 WILD-TYPE 
            15            352 
[1] "FOXF2 MUTATION ANALYSIS"
[1] 3
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              4             363 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              4             363 
[1] "CNKSR3 MUTATION ANALYSIS"
[1] 3
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               9              358 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               9              358 
[1] "C1ORF116 MUTATION ANALYSIS"
[1] 3
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 6                361 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 6                361 
[1] "DENND2C MUTATION ANALYSIS"
[1] 3
  DENND2C MUTATED DENND2C WILD-TYPE 
               18               349 
  DENND2C MUTATED DENND2C WILD-TYPE 
               18               349 
[1] "ITGA9 MUTATION ANALYSIS"
[1] 3
  ITGA9 MUTATED ITGA9 WILD-TYPE 
              9             358 
  ITGA9 MUTATED ITGA9 WILD-TYPE 
              9             358 
[1] "COPB2 MUTATION ANALYSIS"
[1] 3
  COPB2 MUTATED COPB2 WILD-TYPE 
             13             354 
  COPB2 MUTATED COPB2 WILD-TYPE 
             13             354 
[1] "GATAD2A MUTATION ANALYSIS"
[1] 3
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                9               358 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                9               358 
[1] "TAOK1 MUTATION ANALYSIS"
[1] 3
  TAOK1 MUTATED TAOK1 WILD-TYPE 
             16             351 
  TAOK1 MUTATED TAOK1 WILD-TYPE 
             16             351 
[1] "KRT1 MUTATION ANALYSIS"
[1] 3
  KRT1 MUTATED KRT1 WILD-TYPE 
            14            353 
  KRT1 MUTATED KRT1 WILD-TYPE 
            14            353 
[1] "TACC2 MUTATION ANALYSIS"
[1] 3
  TACC2 MUTATED TACC2 WILD-TYPE 
             25             342 
  TACC2 MUTATED TACC2 WILD-TYPE 
             25             342 
[1] "GATA6 MUTATION ANALYSIS"
[1] 3
  GATA6 MUTATED GATA6 WILD-TYPE 
              4             363 
  GATA6 MUTATED GATA6 WILD-TYPE 
              4             363 
[1] "NDC80 MUTATION ANALYSIS"
[1] 3
  NDC80 MUTATED NDC80 WILD-TYPE 
              8             359 
  NDC80 MUTATED NDC80 WILD-TYPE 
              8             359 
[1] "HLA-G MUTATION ANALYSIS"
[1] 3
  HLA-G MUTATED HLA-G WILD-TYPE 
             11             356 
  HLA-G MUTATED HLA-G WILD-TYPE 
             11             356 
[1] "TNNT2 MUTATION ANALYSIS"
[1] 3
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              8             359 
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              8             359 
[1] "PPM1B MUTATION ANALYSIS"
[1] 3
  PPM1B MUTATED PPM1B WILD-TYPE 
              5             362 
  PPM1B MUTATED PPM1B WILD-TYPE 
              5             362 
[1] "ZNF232 MUTATION ANALYSIS"
[1] 3
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              363 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              363 
[1] "HRASLS5 MUTATION ANALYSIS"
[1] 3
  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
                5               362 
  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
                5               362 
[1] "PRSS35 MUTATION ANALYSIS"
[1] 3
  PRSS35 MUTATED PRSS35 WILD-TYPE 
              12              355 
  PRSS35 MUTATED PRSS35 WILD-TYPE 
              12              355 
[1] "SF3B2 MUTATION ANALYSIS"
[1] 3
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             357 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             357 
[1] "OR5L2 MUTATION ANALYSIS"
[1] 3
  OR5L2 MUTATED OR5L2 WILD-TYPE 
             14             353 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
             14             353 
[1] "APAF1 MUTATION ANALYSIS"
[1] 3
  APAF1 MUTATED APAF1 WILD-TYPE 
             18             349 
  APAF1 MUTATED APAF1 WILD-TYPE 
             18             349 
[1] "KRT39 MUTATION ANALYSIS"
[1] 3
  KRT39 MUTATED KRT39 WILD-TYPE 
              7             360 
  KRT39 MUTATED KRT39 WILD-TYPE 
              7             360 
[1] "IL3 MUTATION ANALYSIS"
[1] 3
  IL3 MUTATED IL3 WILD-TYPE 
            6           361 
  IL3 MUTATED IL3 WILD-TYPE 
            6           361 
[1] "UST MUTATION ANALYSIS"
[1] 3
  UST MUTATED UST WILD-TYPE 
            9           358 
  UST MUTATED UST WILD-TYPE 
            9           358 
[1] "CYTSA MUTATION ANALYSIS"
[1] 3
  CYTSA MUTATED CYTSA WILD-TYPE 
             11             356 
  CYTSA MUTATED CYTSA WILD-TYPE 
             11             356 
[1] "PEAR1 MUTATION ANALYSIS"
[1] 3
  PEAR1 MUTATED PEAR1 WILD-TYPE 
             11             356 
  PEAR1 MUTATED PEAR1 WILD-TYPE 
             11             356 
[1] "HIST1H1B MUTATION ANALYSIS"
[1] 3
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                360 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                360 
[1] "SIRT4 MUTATION ANALYSIS"
[1] 3
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              6             361 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              6             361 
[1] "OLFM1 MUTATION ANALYSIS"
[1] 3
  OLFM1 MUTATED OLFM1 WILD-TYPE 
             11             356 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
             11             356 
[1] "DDX55 MUTATION ANALYSIS"
[1] 3
  DDX55 MUTATED DDX55 WILD-TYPE 
             10             357 
  DDX55 MUTATED DDX55 WILD-TYPE 
             10             357 
[1] "CLGN MUTATION ANALYSIS"
[1] 3
  CLGN MUTATED CLGN WILD-TYPE 
            11            356 
  CLGN MUTATED CLGN WILD-TYPE 
            11            356 
[1] "EHBP1L1 MUTATION ANALYSIS"
[1] 3
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                7               360 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                7               360 
[1] "ATP2A2 MUTATION ANALYSIS"
[1] 3
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
              15              352 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
              15              352 
[1] "GRAMD1C MUTATION ANALYSIS"
[1] 3
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
               11               356 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
               11               356 
[1] "TIPARP MUTATION ANALYSIS"
[1] 3
  TIPARP MUTATED TIPARP WILD-TYPE 
               5              362 
  TIPARP MUTATED TIPARP WILD-TYPE 
               5              362 
[1] "POLA1 MUTATION ANALYSIS"
[1] 3
  POLA1 MUTATED POLA1 WILD-TYPE 
              9             358 
  POLA1 MUTATED POLA1 WILD-TYPE 
              9             358 
[1] "SAPS3 MUTATION ANALYSIS"
[1] 3
  SAPS3 MUTATED SAPS3 WILD-TYPE 
             11             356 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
             11             356 
[1] "ZFP1 MUTATION ANALYSIS"
[1] 3
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             4            363 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             4            363 
[1] "MLL MUTATION ANALYSIS"
[1] 3
  MLL MUTATED MLL WILD-TYPE 
           38           329 
  MLL MUTATED MLL WILD-TYPE 
           38           329 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
            15            352 
  TSC2 MUTATED TSC2 WILD-TYPE 
            15            352 
[1] "MAK MUTATION ANALYSIS"
[1] 3
  MAK MUTATED MAK WILD-TYPE 
            9           358 
  MAK MUTATED MAK WILD-TYPE 
            9           358 
[1] "FAAH2 MUTATION ANALYSIS"
[1] 3
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             11             356 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             11             356 
[1] "KIAA0355 MUTATION ANALYSIS"
[1] 3
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 7                360 
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 7                360 
[1] "SLC17A6 MUTATION ANALYSIS"
[1] 3
  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
               13               354 
  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
               13               354 
[1] "HDAC2 MUTATION ANALYSIS"
[1] 3
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              7             360 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              7             360 
[1] "F9 MUTATION ANALYSIS"
[1] 3
  F9 MUTATED F9 WILD-TYPE 
          19          348 
  F9 MUTATED F9 WILD-TYPE 
          19          348 
[1] "ZNF185 MUTATION ANALYSIS"
[1] 3
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              357 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              357 
[1] "NXT1 MUTATION ANALYSIS"
[1] 3
  NXT1 MUTATED NXT1 WILD-TYPE 
             5            362 
  NXT1 MUTATED NXT1 WILD-TYPE 
             5            362 
[1] "CHGB MUTATION ANALYSIS"
[1] 3
  CHGB MUTATED CHGB WILD-TYPE 
            12            355 
  CHGB MUTATED CHGB WILD-TYPE 
            12            355 
[1] "OR14J1 MUTATION ANALYSIS"
[1] 3
  OR14J1 MUTATED OR14J1 WILD-TYPE 
               8              359 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
               8              359 
[1] "LYST MUTATION ANALYSIS"
[1] 3
  LYST MUTATED LYST WILD-TYPE 
            34            333 
  LYST MUTATED LYST WILD-TYPE 
            34            333 
[1] "PPP2R2B MUTATION ANALYSIS"
[1] 3
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
                8               359 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
                8               359 
[1] "ACTBL2 MUTATION ANALYSIS"
[1] 3
  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
              16              351 
  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
              16              351 
[1] "C9ORF41 MUTATION ANALYSIS"
[1] 3
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
               10               357 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
               10               357 
[1] "BATF3 MUTATION ANALYSIS"
[1] 3
  BATF3 MUTATED BATF3 WILD-TYPE 
              4             363 
  BATF3 MUTATED BATF3 WILD-TYPE 
              4             363 
[1] "SEC23IP MUTATION ANALYSIS"
[1] 3
  SEC23IP MUTATED SEC23IP WILD-TYPE 
               16               351 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
               16               351 
[1] "GIMAP5 MUTATION ANALYSIS"
[1] 3
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               6              361 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               6              361 
[1] "FAM91A1 MUTATION ANALYSIS"
[1] 3
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               10               357 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               10               357 
[1] "OSBPL5 MUTATION ANALYSIS"
[1] 3
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
              14              353 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
              14              353 
[1] "TTLL5 MUTATION ANALYSIS"
[1] 3
  TTLL5 MUTATED TTLL5 WILD-TYPE 
             11             356 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
             11             356 
[1] "TMEM171 MUTATION ANALYSIS"
[1] 3
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                5               362 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                5               362 
[1] "GPSM2 MUTATION ANALYSIS"
[1] 3
  GPSM2 MUTATED GPSM2 WILD-TYPE 
             12             355 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
             12             355 
[1] "ANKRD32 MUTATION ANALYSIS"
[1] 3
  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
               13               354 
  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
               13               354 
[1] "HDAC11 MUTATION ANALYSIS"
[1] 3
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               8              359 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               8              359 
[1] "BUB1 MUTATION ANALYSIS"
[1] 3
  BUB1 MUTATED BUB1 WILD-TYPE 
            13            354 
  BUB1 MUTATED BUB1 WILD-TYPE 
            13            354 
[1] "KMO MUTATION ANALYSIS"
[1] 3
  KMO MUTATED KMO WILD-TYPE 
           12           355 
  KMO MUTATED KMO WILD-TYPE 
           12           355 
[1] "COL6A3 MUTATION ANALYSIS"
[1] 3
  COL6A3 MUTATED COL6A3 WILD-TYPE 
              51              316 
  COL6A3 MUTATED COL6A3 WILD-TYPE 
              51              316 
[1] "FKBP5 MUTATION ANALYSIS"
[1] 3
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              6             361 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              6             361 
[1] "ASPN MUTATION ANALYSIS"
[1] 3
  ASPN MUTATED ASPN WILD-TYPE 
             7            360 
  ASPN MUTATED ASPN WILD-TYPE 
             7            360 
[1] "RARS2 MUTATION ANALYSIS"
[1] 3
  RARS2 MUTATED RARS2 WILD-TYPE 
              7             360 
  RARS2 MUTATED RARS2 WILD-TYPE 
              7             360 
[1] "SMPDL3B MUTATION ANALYSIS"
[1] 3
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               358 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               358 
[1] "SEMA3C MUTATION ANALYSIS"
[1] 3
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              12              355 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              12              355 
[1] "GABRG2 MUTATION ANALYSIS"
[1] 3
  GABRG2 MUTATED GABRG2 WILD-TYPE 
              14              353 
  GABRG2 MUTATED GABRG2 WILD-TYPE 
              14              353 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            34            333 
  MTOR MUTATED MTOR WILD-TYPE 
            34            333 
[1] "CD84 MUTATION ANALYSIS"
[1] 3
  CD84 MUTATED CD84 WILD-TYPE 
             9            358 
  CD84 MUTATED CD84 WILD-TYPE 
             9            358 
[1] "PRKD1 MUTATION ANALYSIS"
[1] 3
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             24             343 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             24             343 
[1] "TET1 MUTATION ANALYSIS"
[1] 3
  TET1 MUTATED TET1 WILD-TYPE 
            23            344 
  TET1 MUTATED TET1 WILD-TYPE 
            23            344 
[1] "FLG MUTATION ANALYSIS"
[1] 3
  FLG MUTATED FLG WILD-TYPE 
           64           303 
  FLG MUTATED FLG WILD-TYPE 
           64           303 
[1] "SCNN1G MUTATION ANALYSIS"
[1] 3
  SCNN1G MUTATED SCNN1G WILD-TYPE 
               9              358 
  SCNN1G MUTATED SCNN1G WILD-TYPE 
               9              358 
[1] "SLC19A2 MUTATION ANALYSIS"
[1] 3
  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
                7               360 
  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
                7               360 
[1] "TBC1D25 MUTATION ANALYSIS"
[1] 3
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
               11               356 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
               11               356 
[1] "PCDHGA9 MUTATION ANALYSIS"
[1] 3
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
               12               355 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
               12               355 
[1] "HIF1A MUTATION ANALYSIS"
[1] 3
  HIF1A MUTATED HIF1A WILD-TYPE 
             11             356 
  HIF1A MUTATED HIF1A WILD-TYPE 
             11             356 
[1] "ZNF521 MUTATION ANALYSIS"
[1] 3
  ZNF521 MUTATED ZNF521 WILD-TYPE 
              28              339 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
              28              339 
[1] "TFEC MUTATION ANALYSIS"
[1] 3
  TFEC MUTATED TFEC WILD-TYPE 
            10            357 
  TFEC MUTATED TFEC WILD-TYPE 
            10            357 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            13            354 
  NEFH MUTATED NEFH WILD-TYPE 
            13            354 
[1] "AKAP13 MUTATION ANALYSIS"
[1] 3
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              20              347 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              20              347 
[1] "FAM133A MUTATION ANALYSIS"
[1] 3
  FAM133A MUTATED FAM133A WILD-TYPE 
               11               356 
  FAM133A MUTATED FAM133A WILD-TYPE 
               11               356 
[1] "RAG1 MUTATION ANALYSIS"
[1] 3
  RAG1 MUTATED RAG1 WILD-TYPE 
            14            353 
  RAG1 MUTATED RAG1 WILD-TYPE 
            14            353 
[1] "ZNF615 MUTATION ANALYSIS"
[1] 3
  ZNF615 MUTATED ZNF615 WILD-TYPE 
              17              350 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
              17              350 
[1] "ENGASE MUTATION ANALYSIS"
[1] 3
  ENGASE MUTATED ENGASE WILD-TYPE 
               4              363 
  ENGASE MUTATED ENGASE WILD-TYPE 
               4              363 
[1] "CCDC144A MUTATION ANALYSIS"
[1] 3
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                 9                358 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                 9                358 
[1] "CCDC112 MUTATION ANALYSIS"
[1] 3
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                7               360 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                7               360 
[1] "ZNF286B MUTATION ANALYSIS"
[1] 3
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               362 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               362 
[1] "SFTPB MUTATION ANALYSIS"
[1] 3
  SFTPB MUTATED SFTPB WILD-TYPE 
              9             358 
  SFTPB MUTATED SFTPB WILD-TYPE 
              9             358 
[1] "WNT8A MUTATION ANALYSIS"
[1] 3
  WNT8A MUTATED WNT8A WILD-TYPE 
              5             362 
  WNT8A MUTATED WNT8A WILD-TYPE 
              5             362 
[1] "GPR61 MUTATION ANALYSIS"
[1] 3
  GPR61 MUTATED GPR61 WILD-TYPE 
              9             358 
  GPR61 MUTATED GPR61 WILD-TYPE 
              9             358 
[1] "CACNA1H MUTATION ANALYSIS"
[1] 3
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               27               340 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               27               340 
[1] "G3BP1 MUTATION ANALYSIS"
[1] 3
  G3BP1 MUTATED G3BP1 WILD-TYPE 
             11             356 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
             11             356 
[1] "SULF2 MUTATION ANALYSIS"
[1] 3
  SULF2 MUTATED SULF2 WILD-TYPE 
             22             345 
  SULF2 MUTATED SULF2 WILD-TYPE 
             22             345 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
           28           339 
  KDR MUTATED KDR WILD-TYPE 
           28           339 
[1] "CPB2 MUTATION ANALYSIS"
[1] 3
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            358 
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            358 
[1] "TMEM20 MUTATION ANALYSIS"
[1] 3
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               3              364 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               3              364 
[1] "KCNQ1 MUTATION ANALYSIS"
[1] 3
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              8             359 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              8             359 
[1] "CAMK2G MUTATION ANALYSIS"
[1] 3
  CAMK2G MUTATED CAMK2G WILD-TYPE 
              13              354 
  CAMK2G MUTATED CAMK2G WILD-TYPE 
              13              354 
[1] "SAMD11 MUTATION ANALYSIS"
[1] 3
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               6              361 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               6              361 
[1] "FAM83D MUTATION ANALYSIS"
[1] 3
  FAM83D MUTATED FAM83D WILD-TYPE 
              11              356 
  FAM83D MUTATED FAM83D WILD-TYPE 
              11              356 
[1] "ALG9 MUTATION ANALYSIS"
[1] 3
  ALG9 MUTATED ALG9 WILD-TYPE 
             3            364 
  ALG9 MUTATED ALG9 WILD-TYPE 
             3            364 
[1] "BCL7A MUTATION ANALYSIS"
[1] 3
  BCL7A MUTATED BCL7A WILD-TYPE 
              5             362 
  BCL7A MUTATED BCL7A WILD-TYPE 
              5             362 
[1] "HOXA1 MUTATION ANALYSIS"
[1] 3
  HOXA1 MUTATED HOXA1 WILD-TYPE 
             10             357 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
             10             357 
[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 367 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=67,	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=202,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=8,	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=10,	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=2,	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=19,	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"                "200"                 
freq.contrast "200"              "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 367 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                 
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
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 
  9  67 249  41 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  67 249  41 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  67 249  41 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  67 249  41 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
220  81  66 
[1] "table(vv)"
vv
 N0  N1  N2 
220  81  66 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
220  81  66 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
220  81  66 
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=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=19, 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   224  60
  APC WILD-TYPE  53  18
  APC MUTATED APC WILD-TYPE 
          284            71 
  APC MUTATED APC WILD-TYPE 
           60            18 
$`APC MUTATED`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 
       24.33        24.16         1.02        37.05        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        17.95        23.01        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 
       36.00        85.05        19.04        19.04        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2674 
       63.62        35.80        26.17        91.79        43.76        43.76 
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-A6-6651 
       32.71        27.09        22.52         8.38        25.08        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3538 
       35.01        63.98         6.97         9.07        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       20.98        13.94        61.02        78.08         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-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3837 
       37.05        26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3930 
        0.99        31.07        30.05        53.00        17.03         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       24.00        33.01        21.99        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        38.04        19.00 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00U TCGA-AA-A00W 
       18.05        18.05         4.01        27.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       34.98        15.02        32.02        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02        33.04         1.02        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-A03F TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       18.05        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       21.44        17.82        58.39         5.13        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-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.19        12.69        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 TCGA-F4-6806 TCGA-F4-6807 
        8.61        31.96        35.74        47.87        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       33.67        13.25        47.41        35.31       133.18        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

$`APC WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 
       14.53        13.02        24.03        36.03         8.05         0.99 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3986 TCGA-G4-6321 
       19.99         0.92        14.93        24.03        19.07        22.09 
TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-6648 
       79.69        46.65        42.90        42.28        16.57        25.18 
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       20.12         3.02         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3664 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3819 
        0.00        29.00        54.02         5.03        10.06        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        37.02         0.00         0.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       27.02        18.05        31.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q 
        2.01        16.08        13.94        30.02        34.03        42.02 
TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02Y 
        0.99        10.98        12.00        38.07        26.01        39.98 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AY-4070 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-CA-5255 
       40.96        83.24        16.31         1.41        62.79        12.36 
TCGA-CA-5796 TCGA-CA-6719 TCGA-CM-4747 TCGA-CM-6171 TCGA-D5-6534 TCGA-D5-6930 
       12.39        14.30        25.02        14.04        43.27        13.35 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6299 
        6.18         1.55        34.42         0.53        74.56 

  APC MUTATED APC WILD-TYPE 
            0             0 
  APC MUTATED APC WILD-TYPE 
       148.01         83.24 
  APC MUTATED APC WILD-TYPE 
        22.75         19.07 
[1] "0.0 - 148.0 (22.8)" "0.0 - 83.2 (19.1)" 
[1] "hr=" "1.6"
D1V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APC MUTATED        51        1       20        85         7         1
  APC WILD-TYPE      13        0        6        23         1         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED          11          5         38         25       30        10
  APC WILD-TYPE         7          1          6          8        5         2
               vv
clus            STAGE IVB
  APC MUTATED           1
  APC WILD-TYPE         0
D1V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             51            13
  STAGE IA             1             0
  STAGE II            20             6
  STAGE IIA           85            23
  STAGE IIB            7             1
  STAGE IIC            1             0
  STAGE III           11             7
  STAGE IIIA           5             1
  STAGE IIIB          38             6
  STAGE IIIC          25             8
  STAGE IV            30             5
  STAGE IVA           10             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     7  52 201  34
  APC WILD-TYPE   2  15  48   7
D1V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           7             2
  T2          52            15
  T3         201            48
  T4          34             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   175  68  52
  APC WILD-TYPE  45  13  14
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0         175            45
  N1          68            13
  N2          52            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
               cls
clus              0   1
  APC MUTATED   224  41
  APC WILD-TYPE  61   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    224   41
  APC WILD-TYPE   61    7
   clus
vv  APC MUTATED APC WILD-TYPE
  0         224            61
  1          41             7
[1] 2 2
[1] FALSE
D1V7, binary
               cls
clus              0   1
  APC MUTATED   130 165
  APC WILD-TYPE  40  32
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    130  165
  APC WILD-TYPE   40   32
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE         130            40
  MALE           165            32
[1] 2 2
[1] FALSE
D1V8, binary
               cls
clus              0   1
  APC MUTATED   238   6
  APC WILD-TYPE  62   2
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    238    6
  APC WILD-TYPE   62    2
     clus
vv    APC MUTATED APC WILD-TYPE
  NO          238            62
  YES           6             2
[1] 2 2
[1] FALSE
D1V9, binary
               cls
clus              0   1
  APC MUTATED   255  35
  APC WILD-TYPE  59  13
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    255   35
  APC WILD-TYPE   59   13
                               clus
vv                              APC MUTATED APC WILD-TYPE
  COLON ADENOCARCINOMA                  255            59
  COLON MUCINOUS ADENOCARCINOMA          35            13
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  APC MUTATED   201   2  19  18
  APC WILD-TYPE  58   1   3   3
D1V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0         201            58
  R1           2             1
  R2          19             3
  RX          18             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"
D1V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APC MUTATED                                  0     6
  APC WILD-TYPE                                1     4
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED                          18   157
  APC WILD-TYPE                         1    19
D1V12, multiclass
                                  clus
vv                                 APC MUTATED APC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      6             4
  BLACK OR AFRICAN AMERICAN                 18             1
  WHITE                                    157            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"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   179  50
  TP53 WILD-TYPE  98  28
  TP53 MUTATED TP53 WILD-TYPE 
           229            126 
  TP53 MUTATED TP53 WILD-TYPE 
            50             28 
$`TP53 MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 
       14.53        24.16         1.02        24.03        36.03        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 
       13.02        23.01        19.99         6.05        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       14.93        31.07        24.03        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       38.04        21.37        15.52       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 
       36.53        32.91        30.44        29.19        23.61        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       27.09        22.52        25.08        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       20.28         3.02        63.98         6.97        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       19.07        12.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3842 
       15.02         5.98        37.05        10.06        33.04        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       10.06        33.07         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       27.02        18.05         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       34.03        21.99        34.06        25.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00W 
       13.94        19.00        30.02        34.03        27.02        14.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S 
       34.98        10.98        32.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       33.04        37.02        39.98         2.01         5.03        14.01 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00        40.96        12.16         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20        21.44         1.41         5.13        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-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.19        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 
       17.56       148.01        85.45        15.62        21.99        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       20.02        37.02        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        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       11.08        10.06        54.61        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       25.48        43.27        15.12        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

$`TP53 WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 
       24.33        13.02        37.05         8.05        19.07         0.99 
TCGA-AA-3554 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 
       17.95        19.99         0.92        19.00        36.00        19.04 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A00Z 
       29.98        12.99        24.00         2.01        19.07        21.99 
TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-2672 
       39.06        25.08        10.88        49.08        26.17        46.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 
       33.34        32.75        31.63        33.53        22.09        32.71 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 
        8.38        25.18        24.39        20.12        19.66         7.04 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       35.01         1.02         1.02         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3664 TCGA-AA-3678 
       26.01        14.01        33.99        29.95        54.02        47.01 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       11.01         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        38.99         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 
        0.00         0.00        36.03        32.05        53.00        31.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-3994 
       33.01         2.01        16.08        13.05         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-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       17.03        15.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        1.02        26.01        51.98         0.92        39.98        18.05 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-CA-5254 
       83.24        24.53        17.82        58.39        22.36        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       12.36        12.39        12.59        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-6170 
        2.01       124.27        25.02        22.03        15.02        15.02 
TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 
       12.95        11.01        12.03        45.40        19.59        20.19 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A282 
       17.85         4.80        11.64        10.26       119.70       139.17 
TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6855 TCGA-G4-6309 
       81.37        60.79        35.74         6.18        47.41        85.48 

  TP53 MUTATED TP53 WILD-TYPE 
           0.2            0.0 
  TP53 MUTATED TP53 WILD-TYPE 
        148.01         139.17 
  TP53 MUTATED TP53 WILD-TYPE 
        22.520         20.665 
[1] "0.2 - 148.0 (22.5)" "0.0 - 139.2 (20.7)"
[1] "hr=" "1.2"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TP53 MUTATED        40        1       16        59         4         0
  TP53 WILD-TYPE      24        0       10        49         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED          10          5         30         26       24         8
  TP53 WILD-TYPE         8          1         14          7       11         4
                vv
clus             STAGE IVB
  TP53 MUTATED           1
  TP53 WILD-TYPE         0
D2V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              40             24
  STAGE IA              1              0
  STAGE II             16             10
  STAGE IIA            59             49
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III            10              8
  STAGE IIIA            5              1
  STAGE IIIB           30             14
  STAGE IIIC           26              7
  STAGE IV             24             11
  STAGE IVA             8              4
  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     6  43 158  24
  TP53 WILD-TYPE   3  24  91  17
D2V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            6              3
  T2           43             24
  T3          158             91
  T4           24             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   130  55  47
  TP53 WILD-TYPE  90  26  19
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          130             90
  N1           55             26
  N2           47             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus               0   1
  TP53 MUTATED   178  33
  TP53 WILD-TYPE 107  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    178   33
  TP53 WILD-TYPE  107   15
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          178            107
  1           33             15
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  TP53 MUTATED   104 128
  TP53 WILD-TYPE  66  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    104  128
  TP53 WILD-TYPE   66   69
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          104             66
  MALE            128             69
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  TP53 MUTATED   196   5
  TP53 WILD-TYPE 104   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    196    5
  TP53 WILD-TYPE  104    3
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           196            104
  YES            5              3
[1] 2 2
[1] FALSE
D2V9, binary
                cls
clus               0   1
  TP53 MUTATED   207  20
  TP53 WILD-TYPE 107  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    207   20
  TP53 WILD-TYPE  107   28
                               clus
vv                              TP53 MUTATED TP53 WILD-TYPE
  COLON ADENOCARCINOMA                   207            107
  COLON MUCINOUS ADENOCARCINOMA           20             28
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   160   3  13   8
  TP53 WILD-TYPE  99   0   9  13
D2V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          160             99
  R1            3              0
  R2           13              9
  RX            8             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"
D2V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1     5
  TP53 WILD-TYPE                                0     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          13   132
  TP53 WILD-TYPE                         6    44
D2V12, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       5              5
  BLACK OR AFRICAN AMERICAN                  13              6
  WHITE                                     132             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"

Clustering(3) Variable = ARID1A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    55  14
  ARID1A WILD-TYPE 222  64
  ARID1A MUTATED ARID1A WILD-TYPE 
              69              286 
  ARID1A MUTATED ARID1A WILD-TYPE 
              14               64 
$`ARID1A MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3713 
       14.53         1.02        13.02        17.95         6.05        19.04 
TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-A00L TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       24.03        24.00        38.04        25.08       106.75       100.01 
TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-5665 
       63.62        35.80        26.17        79.69        42.90        22.06 
TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3555 
        8.38        20.12        19.66         3.02         1.02        29.95 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3831 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00E 
       78.08         6.97        17.98        33.01        38.04        30.02 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01R TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       34.98        15.02        35.01         0.20        21.44        58.39 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5797 
        5.13        49.41         6.77        29.56        12.69        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CM-5864 
       12.20        12.76        15.62        51.32        82.95        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       12.00        21.99        14.04        11.01        12.95        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6930 
       10.06        54.61        55.92        16.14         7.53        13.35 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6854 
       24.43        38.20       135.65        31.96         6.18         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6317 
       35.31       133.18        36.00 

$`ARID1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       24.33        24.16        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        19.07        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
       15.52        10.88         1.94        49.08         5.88        22.09 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        43.76        46.65        43.76        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-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       24.39        23.87        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 
       21.01        24.00        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6605 
        1.41        22.36        62.79        88.21        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 
       11.74         3.19        12.36        12.39        12.59        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56       148.01        85.45        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6163 
       15.02         5.03        15.02        17.03        15.02        14.04 
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-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       13.05        11.08        11.01        12.03        45.40        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        25.48        43.27        15.12 
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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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-A1D0 
       13.41        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-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        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        43.04        33.67        13.25 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  ARID1A MUTATED ARID1A WILD-TYPE 
             0.2              0.0 
  ARID1A MUTATED ARID1A WILD-TYPE 
          135.65           148.01 
  ARID1A MUTATED ARID1A WILD-TYPE 
          21.440           22.225 
[1] "0.2 - 135.7 (21.4)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D3V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID1A MUTATED        10        0        6        31         3         0
  ARID1A WILD-TYPE      54        1       20        77         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           4          0          8          5        4
  ARID1A WILD-TYPE        14          6         36         28       31
                  vv
clus               STAGE IVA STAGE IVB
  ARID1A MUTATED           0         0
  ARID1A WILD-TYPE        12         1
D3V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                10               54
  STAGE IA                0                1
  STAGE II                6               20
  STAGE IIA              31               77
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               4               14
  STAGE IIIA              0                6
  STAGE IIIB              8               36
  STAGE IIIC              5               28
  STAGE IV                4               31
  STAGE IVA               0               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
  ARID1A MUTATED     0  11  55   6
  ARID1A WILD-TYPE   9  56 194  35
D3V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              0                9
  T2             11               56
  T3             55              194
  T4              6               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
  ARID1A MUTATED    51  11  10
  ARID1A WILD-TYPE 169  70  56
D3V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             51              169
  N1             11               70
  N2             10               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    57   4
  ARID1A WILD-TYPE 228  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     57    4
  ARID1A WILD-TYPE  228   44
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             57              228
  1              4               44
[1] 2 2
[1] FALSE
D3V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    38  34
  ARID1A WILD-TYPE 132 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     38   34
  ARID1A WILD-TYPE  132  163
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             38              132
  MALE               34              163
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    60   3
  ARID1A WILD-TYPE 240   5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     60    3
  ARID1A WILD-TYPE  240    5
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              60              240
  YES              3                5
[1] 2 2
[1] FALSE
D3V9, binary
                  cls
clus                 0   1
  ARID1A MUTATED    56  14
  ARID1A WILD-TYPE 258  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     56   14
  ARID1A WILD-TYPE  258   34
                               clus
vv                              ARID1A MUTATED ARID1A WILD-TYPE
  COLON ADENOCARCINOMA                      56              258
  COLON MUCINOUS ADENOCARCINOMA             14               34
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    50   0   3   7
  ARID1A WILD-TYPE 209   3  19  14
D3V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             50              209
  R1              0                3
  R2              3               19
  RX              7               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"
D3V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     4
  ARID1A WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           1    45
  ARID1A WILD-TYPE                        18   131
D3V12, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        45              131
[1] 4 2
[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    36   9
  RNF43 WILD-TYPE 241  69
  RNF43 MUTATED RNF43 WILD-TYPE 
             45             310 
  RNF43 MUTATED RNF43 WILD-TYPE 
              9              69 
$`RNF43 MUTATED`
TCGA-A6-6649 TCGA-AA-3672 TCGA-AA-3715 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6586 
       24.16         0.92        19.04        25.08        10.88        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 
       26.17        79.69        43.76        33.53        22.06        24.39 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3710 
       19.66         3.02         1.02        29.95         6.97        26.99 
TCGA-AA-3947 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01P TCGA-AD-5900 
       33.01        18.05        34.98        31.00        38.07        12.16 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-5796 TCGA-CK-5913 TCGA-CK-5916 
       83.24        27.09        49.41        12.39        51.32        21.14 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6171 
       82.95        23.05        37.02        15.02        12.00        14.04 
TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6856 
       12.95        16.14        11.64        13.35         6.18        35.31 
TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6315 
       74.56        85.48        61.91 

$`RNF43 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       63.62        22.09        91.79        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        12.00        31.00         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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.36        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6748 TCGA-CK-6751 
      148.01        85.45        15.62        21.99         2.01       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-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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6307 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        36.00        13.78        46.75 

  RNF43 MUTATED RNF43 WILD-TYPE 
           0.92            0.00 
  RNF43 MUTATED RNF43 WILD-TYPE 
          85.48          148.01 
  RNF43 MUTATED RNF43 WILD-TYPE 
          24.39           21.99 
[1] "0.9 - 85.5 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D4V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF43 MUTATED        10        0        4        18         3         0
  RNF43 WILD-TYPE      54        1       22        90         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF43 MUTATED           2          0          4          2        2         0
  RNF43 WILD-TYPE        16          6         40         31       33        12
                 vv
clus              STAGE IVB
  RNF43 MUTATED           0
  RNF43 WILD-TYPE         1
D4V3, multiclass
            clus
vv           RNF43 MUTATED RNF43 WILD-TYPE
  STAGE I               10              54
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             18              90
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  RNF43 MUTATED     1   9  31   5
  RNF43 WILD-TYPE   8  58 218  36
D4V4, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  T1             1               8
  T2             9              58
  T3            31             218
  T4             5              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
  RNF43 MUTATED    35   8   3
  RNF43 WILD-TYPE 185  73  63
D4V5, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  N0            35             185
  N1             8              73
  N2             3              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"
D4V6, binary
                 cls
clus                0   1
  RNF43 MUTATED    37   2
  RNF43 WILD-TYPE 248  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     37    2
  RNF43 WILD-TYPE  248   46
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0            37             248
  1             2              46
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  RNF43 MUTATED    24  22
  RNF43 WILD-TYPE 146 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     24   22
  RNF43 WILD-TYPE  146  175
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE            24             146
  MALE              22             175
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus                0   1
  RNF43 MUTATED    42   0
  RNF43 WILD-TYPE 258   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     42    0
  RNF43 WILD-TYPE  258    8
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO             42             258
  YES             0               8
[1] 2 2
[1] FALSE
D4V9, binary
                 cls
clus                0   1
  RNF43 MUTATED    36  10
  RNF43 WILD-TYPE 278  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     36   10
  RNF43 WILD-TYPE  278   38
                               clus
vv                              RNF43 MUTATED RNF43 WILD-TYPE
  COLON ADENOCARCINOMA                     36             278
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF43 MUTATED    38   0   0   4
  RNF43 WILD-TYPE 221   3  22  17
D4V10, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0            38             221
  R1             0               3
  R2             0              22
  RX             4              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"
D4V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF43 MUTATED                                  0     2
  RNF43 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF43 MUTATED                           3    29
  RNF43 WILD-TYPE                        16   147
D4V12, multiclass
                                  clus
vv                                 RNF43 MUTATED RNF43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       29             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(5) Variable = SOX9 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  SOX9 MUTATED    26   8
  SOX9 WILD-TYPE 251  70
  SOX9 MUTATED SOX9 WILD-TYPE 
            34            321 
  SOX9 MUTATED SOX9 WILD-TYPE 
             8             70 
$`SOX9 MUTATED`
TCGA-A6-4105 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3939 TCGA-AA-3979 TCGA-AD-6895 
       14.53         0.92        19.04        12.99        24.00        25.08 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3819 
      106.75       100.01         8.38        24.69         3.02        25.02 
TCGA-AA-3831 TCGA-AA-3989 TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 TCGA-AY-6386 
       17.98         7.96        18.05        83.24        24.53        17.82 
TCGA-CA-5255 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 
       12.36        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        12.39        13.41 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-G4-6293 TCGA-G4-6306 
       12.00        24.43       133.18        44.68 

$`SOX9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 
       29.98        24.00         2.01        50.99        26.01        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        15.52        10.88 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        10.06        35.05        33.04         0.99         1.02 
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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       10.06        14.30       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       21.14         2.01        23.05        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-6678 
       15.02        14.04        11.01        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       13.35        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-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 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       74.56        65.85        53.62        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SOX9 MUTATED SOX9 WILD-TYPE 
          0.92           0.00 
  SOX9 MUTATED SOX9 WILD-TYPE 
        133.18         148.01 
  SOX9 MUTATED SOX9 WILD-TYPE 
         19.53          22.09 
[1] "0.9 - 133.2 (19.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D5V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SOX9 MUTATED         3        0        2        17         0         0
  SOX9 WILD-TYPE      61        1       24        91         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX9 MUTATED           3          0          4          1        3         1
  SOX9 WILD-TYPE        15          6         40         32       32        11
                vv
clus             STAGE IVB
  SOX9 MUTATED           0
  SOX9 WILD-TYPE         1
D5V3, multiclass
            clus
vv           SOX9 MUTATED SOX9 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            17             91
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            1             32
  STAGE IV              3             32
  STAGE IVA             1             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
  SOX9 MUTATED     1   4  29   2
  SOX9 WILD-TYPE   8  63 220  39
D5V4, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  T1            1              8
  T2            4             63
  T3           29            220
  T4            2             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
  SOX9 MUTATED    25   7   4
  SOX9 WILD-TYPE 195  74  62
D5V5, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  N0           25            195
  N1            7             74
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                cls
clus               0   1
  SOX9 MUTATED    28   4
  SOX9 WILD-TYPE 257  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     28    4
  SOX9 WILD-TYPE  257   44
   clus
vv  SOX9 MUTATED SOX9 WILD-TYPE
  0           28            257
  1            4             44
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  SOX9 MUTATED    16  20
  SOX9 WILD-TYPE 154 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     16   20
  SOX9 WILD-TYPE  154  177
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  FEMALE           16            154
  MALE             20            177
[1] 2 2
[1] FALSE
D5V8, binary
                cls
clus               0   1
  SOX9 MUTATED    31   2
  SOX9 WILD-TYPE 269   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     31    2
  SOX9 WILD-TYPE  269    6
     clus
vv    SOX9 MUTATED SOX9 WILD-TYPE
  NO            31            269
  YES            2              6
[1] 2 2
[1] FALSE
D5V9, binary
                cls
clus               0   1
  SOX9 MUTATED    33   3
  SOX9 WILD-TYPE 281  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     33    3
  SOX9 WILD-TYPE  281   45
                               clus
vv                              SOX9 MUTATED SOX9 WILD-TYPE
  COLON ADENOCARCINOMA                    33            281
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SOX9 MUTATED    22   1   2   5
  SOX9 WILD-TYPE 237   2  20  16
D5V10, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  R0           22            237
  R1            1              2
  R2            2             20
  RX            5             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"
D5V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOX9 MUTATED                                  0     2
  SOX9 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOX9 MUTATED                           5    18
  SOX9 WILD-TYPE                        14   158
D5V12, multiclass
                                  clus
vv                                 SOX9 MUTATED SOX9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   5             14
  WHITE                                      18            158
[1] 4 2
[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 = FAM123B MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  FAM123B MUTATED    34  13
  FAM123B WILD-TYPE 243  65
  FAM123B MUTATED FAM123B WILD-TYPE 
               47               308 
  FAM123B MUTATED FAM123B WILD-TYPE 
               13                65 
$`FAM123B MUTATED`
TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3939 TCGA-AD-6895 
       14.53        13.02        19.07        17.95        12.99        25.08 
TCGA-A6-3808 TCGA-A6-6137 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3548 TCGA-AA-3655 
       33.34        27.09         3.02         6.97        33.99        61.02 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3680 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 
        6.97         2.01        11.01         1.02         0.00        53.00 
TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01D TCGA-AD-6890 
       27.02        25.02        38.04        34.98        10.98        24.53 
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        10.13        12.59       140.38       117.07 
TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6315 TCGA-G4-6626 
       98.24         6.18        13.25        61.91        46.75 

$`FAM123B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
        8.05        34.03         0.99        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        15.52        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        78.08 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3875 
       32.05         0.99        31.07        30.05        17.03        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        83.24         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       21.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 
      139.17        81.37       119.93        35.97        60.79         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 
       43.04        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-G4-6317 TCGA-G4-6323 
       36.00        13.78 

  FAM123B MUTATED FAM123B WILD-TYPE 
                0                 0 
  FAM123B MUTATED FAM123B WILD-TYPE 
           140.38            148.01 
  FAM123B MUTATED FAM123B WILD-TYPE 
            20.02             22.09 
[1] "0.0 - 140.4 (20.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM123B MUTATED         6        0        6        20         1         0
  FAM123B WILD-TYPE      58        1       20        88         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM123B MUTATED           2          1          3          4        3
  FAM123B WILD-TYPE        16          5         41         29       32
                   vv
clus                STAGE IVA STAGE IVB
  FAM123B MUTATED           1         0
  FAM123B WILD-TYPE        11         1
D6V3, multiclass
            clus
vv           FAM123B MUTATED FAM123B WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 0                 1
  STAGE II                 6                20
  STAGE IIA               20                88
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               1                 5
  STAGE IIIB               3                41
  STAGE IIIC               4                29
  STAGE IV                 3                32
  STAGE IVA                1                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
  FAM123B MUTATED     2   6  37   5
  FAM123B WILD-TYPE   7  61 212  36
D6V4, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  T1               2                 7
  T2               6                61
  T3              37               212
  T4               5                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
  FAM123B MUTATED    34   8   8
  FAM123B WILD-TYPE 186  73  58
D6V5, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0              34               186
  N1               8                73
  N2               8                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"
D6V6, binary
                   cls
clus                  0   1
  FAM123B MUTATED    40   4
  FAM123B WILD-TYPE 245  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     40    4
  FAM123B WILD-TYPE  245   44
   clus
vv  FAM123B MUTATED FAM123B WILD-TYPE
  0              40               245
  1               4                44
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  FAM123B MUTATED    23  27
  FAM123B WILD-TYPE 147 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     23   27
  FAM123B WILD-TYPE  147  170
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE              23               147
  MALE                27               170
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  FAM123B MUTATED    40   0
  FAM123B WILD-TYPE 260   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     40    0
  FAM123B WILD-TYPE  260    8
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  NO               40               260
  YES               0                 8
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  FAM123B MUTATED    45   5
  FAM123B WILD-TYPE 269  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     45    5
  FAM123B WILD-TYPE  269   43
                               clus
vv                              FAM123B MUTATED FAM123B WILD-TYPE
  COLON ADENOCARCINOMA                       45               269
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM123B MUTATED    34   0   2   4
  FAM123B WILD-TYPE 225   3  20  17
D6V10, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0              34               225
  R1               0                 3
  R2               2                20
  RX               4                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"
D6V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM123B MUTATED                                  0     1
  FAM123B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM123B MUTATED                           2    25
  FAM123B WILD-TYPE                        17   151
D6V12, multiclass
                                  clus
vv                                 FAM123B MUTATED FAM123B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         25               151
[1] 4 2
[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 = TXNDC2 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  TXNDC2 MUTATED    19   3
  TXNDC2 WILD-TYPE 258  75
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              22              333 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
               3               75 
$`TXNDC2 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6888 TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-5659 
        0.92        19.04        15.52        22.09        79.69        30.44 
TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3977 TCGA-AD-6901 TCGA-CA-6717 
       25.08        20.12        78.08        25.02        22.42        12.76 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6170 
       82.95         2.01        15.02        14.04        14.99        15.02 
TCGA-CM-6172 TCGA-D5-6533 TCGA-D5-6538 TCGA-DM-A28C 
       11.01        25.48        17.13        81.37 

$`TXNDC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        35.80        26.17        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.99        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        54.61 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
            0.92             0.00 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
           82.95           148.01 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
           19.58            22.09 
[1] "0.9 - 83.0 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D7V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC2 MUTATED         5        0        1         4         0         0
  TXNDC2 WILD-TYPE      59        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC2 MUTATED           2          0          3          1        2
  TXNDC2 WILD-TYPE        16          6         41         32       33
                  vv
clus               STAGE IVA STAGE IVB
  TXNDC2 MUTATED           1         0
  TXNDC2 WILD-TYPE        11         1
D7V3, multiclass
            clus
vv           TXNDC2 MUTATED TXNDC2 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               1               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
  TXNDC2 MUTATED     1   6  14   1
  TXNDC2 WILD-TYPE   8  61 235  40
D7V4, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  T1              1                8
  T2              6               61
  T3             14              235
  T4              1               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
  TXNDC2 MUTATED    14   6   2
  TXNDC2 WILD-TYPE 206  75  64
D7V5, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  N0             14              206
  N1              6               75
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    14   3
  TXNDC2 WILD-TYPE 271  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     14    3
  TXNDC2 WILD-TYPE  271   45
   clus
vv  TXNDC2 MUTATED TXNDC2 WILD-TYPE
  0             14              271
  1              3               45
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    12  10
  TXNDC2 WILD-TYPE 158 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     12   10
  TXNDC2 WILD-TYPE  158  187
        clus
vv       TXNDC2 MUTATED TXNDC2 WILD-TYPE
  FEMALE             12              158
  MALE               10              187
[1] 2 2
[1] FALSE
D7V8, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    20   1
  TXNDC2 WILD-TYPE 280   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     20    1
  TXNDC2 WILD-TYPE  280    7
     clus
vv    TXNDC2 MUTATED TXNDC2 WILD-TYPE
  NO              20              280
  YES              1                7
[1] 2 2
[1] FALSE
D7V9, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    19   3
  TXNDC2 WILD-TYPE 295  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     19    3
  TXNDC2 WILD-TYPE  295   45
                               clus
vv                              TXNDC2 MUTATED TXNDC2 WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TXNDC2 MUTATED    13   0   1   3
  TXNDC2 WILD-TYPE 246   3  21  18
D7V10, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              1               21
  RX              3               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"
D7V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC2 MUTATED                                  0     1
  TXNDC2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TXNDC2 MUTATED                           1    16
  TXNDC2 WILD-TYPE                        18   160
D7V12, multiclass
                                  clus
vv                                 TXNDC2 MUTATED TXNDC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        16              160
[1] 4 2
[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 = ACVR1B MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED    19   5
  ACVR1B WILD-TYPE 258  73
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              24              331 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               5               73 
$`ACVR1B MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-6652 TCGA-AA-3831 
       19.04       100.01        34.65        32.75        24.69        17.98 
TCGA-AA-3833 TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01R 
       15.95        31.00        27.02        18.05        34.98        35.01 
TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A03F TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       51.98         5.03        18.05        12.59        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 

$`ACVR1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.90        42.28        16.57        33.34        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-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
        1.02        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         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        15.02        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-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        37.02        39.98         2.01 
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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            5.03             0.00 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          124.27           148.01 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          21.045           22.060 
[1] "5.0 - 124.3 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D8V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACVR1B MUTATED         4        0        4         8         2         0
  ACVR1B WILD-TYPE      60        1       22       100         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           2          0          3          1        1
  ACVR1B WILD-TYPE        16          6         41         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ACVR1B MUTATED           1         0
  ACVR1B WILD-TYPE        11         1
D8V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               8              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  ACVR1B MUTATED     1   3  18   4
  ACVR1B WILD-TYPE   8  64 231  37
D8V4, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              1                8
  T2              3               64
  T3             18              231
  T4              4               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
  ACVR1B MUTATED    20   3   3
  ACVR1B WILD-TYPE 200  78  63
D8V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0             20              200
  N1              3               78
  N2              3               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"
D8V6, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    22   2
  ACVR1B WILD-TYPE 263  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     22    2
  ACVR1B WILD-TYPE  263   46
   clus
vv  ACVR1B MUTATED ACVR1B WILD-TYPE
  0             22              263
  1              2               46
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    10  16
  ACVR1B WILD-TYPE 160 181
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     10   16
  ACVR1B WILD-TYPE  160  181
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE             10              160
  MALE               16              181
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    22   1
  ACVR1B WILD-TYPE 278   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     22    1
  ACVR1B WILD-TYPE  278    7
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  NO              22              278
  YES              1                7
[1] 2 2
[1] FALSE
D8V9, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    17   9
  ACVR1B WILD-TYPE 297  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     17    9
  ACVR1B WILD-TYPE  297   39
                               clus
vv                              ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              9               39
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED    18   0   1   5
  ACVR1B WILD-TYPE 241   3  21  16
D8V10, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0             18              241
  R1              0                3
  R2              1               21
  RX              5               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"
D8V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACVR1B MUTATED                                  0     3
  ACVR1B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACVR1B MUTATED                           1    10
  ACVR1B WILD-TYPE                        18   166
D8V12, multiclass
                                  clus
vv                                 ACVR1B MUTATED ACVR1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(9) Variable = B2M MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  B2M MUTATED     9   5
  B2M WILD-TYPE 268  73
  B2M MUTATED B2M WILD-TYPE 
           14           341 
  B2M MUTATED B2M WILD-TYPE 
            5            73 
$`B2M MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 
      100.01        79.69        32.75        24.39        20.12        63.98 
TCGA-AA-3845 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-5538 
        0.00        34.98        12.76        10.06        51.32        54.61 
TCGA-DM-A28F TCGA-F4-6703 
       35.97        47.87 

$`B2M WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6781 
       25.08        25.18        21.76        24.69        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  B2M MUTATED B2M WILD-TYPE 
            0             0 
  B2M MUTATED B2M WILD-TYPE 
       100.01        148.01 
  B2M MUTATED B2M WILD-TYPE 
       35.475        21.990 
[1] "0.0 - 100.0 (35.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D9V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  B2M MUTATED         2        0        2         6         3         0
  B2M WILD-TYPE      62        1       24       102         5         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        18          6         42         33       35        12
               vv
clus            STAGE IVB
  B2M MUTATED           0
  B2M WILD-TYPE         1
D9V3, multiclass
            clus
vv           B2M MUTATED B2M WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            6           102
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  B2M MUTATED     0   2  10   3
  B2M WILD-TYPE   9  65 239  38
D9V4, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  T1           0             9
  T2           2            65
  T3          10           239
  T4           3            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
  B2M MUTATED    13   2   0
  B2M WILD-TYPE 207  79  66
D9V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0          13           207
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
               cls
clus              0   1
  B2M MUTATED    12   0
  B2M WILD-TYPE 273  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     12    0
  B2M WILD-TYPE  273   48
   clus
vv  B2M MUTATED B2M WILD-TYPE
  0          12           273
  1           0            48
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  B2M MUTATED     6   9
  B2M WILD-TYPE 164 188
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      6    9
  B2M WILD-TYPE  164  188
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           6           164
  MALE             9           188
[1] 2 2
[1] FALSE
D9V8, binary
               cls
clus              0   1
  B2M MUTATED    12   0
  B2M WILD-TYPE 288   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     12    0
  B2M WILD-TYPE  288    8
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO           12           288
  YES           0             8
[1] 2 2
[1] FALSE
D9V9, binary
               cls
clus              0   1
  B2M MUTATED    12   3
  B2M WILD-TYPE 302  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     12    3
  B2M WILD-TYPE  302   45
                               clus
vv                              B2M MUTATED B2M WILD-TYPE
  COLON ADENOCARCINOMA                   12           302
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  B2M MUTATED     7   0   0   4
  B2M WILD-TYPE 252   3  22  17
D9V10, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  R0           7           252
  R1           0             3
  R2           0            22
  RX           4            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"
D9V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B2M MUTATED                                  0     2
  B2M WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  B2M MUTATED                           0    10
  B2M WILD-TYPE                        19   166
D9V12, multiclass
                                  clus
vv                                 B2M MUTATED B2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                     10           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(10) Variable = BCOR MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    21   4
  BCOR WILD-TYPE 256  74
  BCOR MUTATED BCOR WILD-TYPE 
            25            330 
  BCOR MUTATED BCOR WILD-TYPE 
             4             74 
$`BCOR MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 
        0.92        25.08        26.17        32.75        33.53        20.12 
TCGA-AA-3555 TCGA-AA-3930 TCGA-AA-A010 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 
       29.95         2.01        34.98        33.01         0.20         1.41 
TCGA-AZ-6598 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6169 TCGA-CM-6171 TCGA-D5-6928 
       49.41        22.98        12.00        13.02        14.04        11.64 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A1HA TCGA-F4-6570 TCGA-F4-6805 TCGA-G4-6304 
       13.35        10.26       131.51         6.18        34.42        53.62 
TCGA-G4-6317 
       36.00 

$`BCOR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.13        22.36        62.79        88.21         6.77 
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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        61.91        13.78        46.75 

  BCOR MUTATED BCOR WILD-TYPE 
           0.2            0.0 
  BCOR MUTATED BCOR WILD-TYPE 
        131.51         148.01 
  BCOR MUTATED BCOR WILD-TYPE 
        22.980         22.045 
[1] "0.2 - 131.5 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D10V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCOR MUTATED         3        0        2         9         3         0
  BCOR WILD-TYPE      61        1       24        99         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCOR MUTATED           1          0          3          3        2         1
  BCOR WILD-TYPE        17          6         41         30       33        11
                vv
clus             STAGE IVB
  BCOR MUTATED           0
  BCOR WILD-TYPE         1
D10V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             9             99
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            3             30
  STAGE IV              2             33
  STAGE IVA             1             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
  BCOR MUTATED     0   3  19   5
  BCOR WILD-TYPE   9  64 230  36
D10V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            0              9
  T2            3             64
  T3           19            230
  T4            5             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
  BCOR MUTATED    17   5   5
  BCOR WILD-TYPE 203  76  61
D10V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0           17            203
  N1            5             76
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                cls
clus               0   1
  BCOR MUTATED    19   3
  BCOR WILD-TYPE 266  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     19    3
  BCOR WILD-TYPE  266   45
   clus
vv  BCOR MUTATED BCOR WILD-TYPE
  0           19            266
  1            3             45
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus               0   1
  BCOR MUTATED    16  11
  BCOR WILD-TYPE 154 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     16   11
  BCOR WILD-TYPE  154  186
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE           16            154
  MALE             11            186
[1] 2 2
[1] FALSE
D10V8, binary
                cls
clus               0   1
  BCOR MUTATED    23   0
  BCOR WILD-TYPE 277   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     23    0
  BCOR WILD-TYPE  277    8
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO            23            277
  YES            0              8
[1] 2 2
[1] FALSE
D10V9, binary
                cls
clus               0   1
  BCOR MUTATED    19   8
  BCOR WILD-TYPE 295  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     19    8
  BCOR WILD-TYPE  295   40
                               clus
vv                              BCOR MUTATED BCOR WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    21   0   1   1
  BCOR WILD-TYPE 238   3  21  20
D10V10, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           21            238
  R1            0              3
  R2            1             21
  RX            1             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"
D10V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCOR MUTATED                                  0     0
  BCOR WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BCOR MUTATED                           3    19
  BCOR WILD-TYPE                        16   157
D10V12, multiclass
                                  clus
vv                                 BCOR MUTATED BCOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      19            157
[1] 4 2
[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 = CDH1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    59  14
  CDH1 WILD-TYPE 218  64
  CDH1 MUTATED CDH1 WILD-TYPE 
            73            282 
  CDH1 MUTATED CDH1 WILD-TYPE 
            14             64 
$`CDH1 MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6964 TCGA-CK-5912 TCGA-G4-6310 
        6.05        85.05        19.04        10.88        49.08        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       22.09        35.80        32.75        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3663 
       23.61         8.38        25.18        20.12        35.01         6.97 
TCGA-AA-3821 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-5900 
        1.02         4.01        17.03        35.01        14.01        12.16 
TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 
       83.24        14.50        27.09        21.44        17.82         5.13 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       49.41         6.77        12.10        12.59        12.59        12.76 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4752 
       85.45        15.62        21.99        82.95        23.05        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6170 
       22.03        22.98        30.08        17.03        15.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6535 
       14.04        11.01        11.01        10.06        20.19        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 
       17.85         4.80        12.49        16.14        11.64        13.35 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F 
       11.38        92.75       131.51       139.17       119.93        35.97 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6317 
       31.96         6.18        35.31        53.62        44.68        36.00 
TCGA-G4-6323 
       13.78 

$`CDH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 
       15.52        25.08       106.75       100.01         1.94         5.88 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       32.91        29.19        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       22.52        25.08        21.76        24.69        24.39        23.87 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02         0.99        14.99        34.98        15.02 
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         1.02        26.01        37.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       27.42        26.47        16.31         0.95        33.01         0.20 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 
       58.39         1.41        22.36        62.79        88.21        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        12.36        12.39 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5913 
       12.20        10.06        14.30        17.56       148.01        51.32 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14         2.01       124.27        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       12.99        13.02        12.95        13.05        11.08        11.08 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 
       18.25        25.48        43.27        17.13        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        12.00        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-A1HB TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       44.32       135.65        81.37        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-G4-6293 
       43.04        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6626 
       74.56        65.85        55.04        85.48        61.91        46.75 

  CDH1 MUTATED CDH1 WILD-TYPE 
          1.02           0.00 
  CDH1 MUTATED CDH1 WILD-TYPE 
        139.17         148.01 
  CDH1 MUTATED CDH1 WILD-TYPE 
         19.04          23.44 
[1] "1.0 - 139.2 (19.0)" "0.0 - 148.0 (23.4)"
[1] "hr=" "1.2"
D11V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH1 MUTATED        13        1        3        23         3         0
  CDH1 WILD-TYPE      51        0       23        85         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH1 MUTATED           2          0         14          3        5         4
  CDH1 WILD-TYPE        16          6         30         30       30         8
                vv
clus             STAGE IVB
  CDH1 MUTATED           0
  CDH1 WILD-TYPE         1
D11V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I              13             51
  STAGE IA              1              0
  STAGE II              3             23
  STAGE IIA            23             85
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB           14             30
  STAGE IIIC            3             30
  STAGE IV              5             30
  STAGE IVA             4              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
  CDH1 MUTATED     0  15  48  10
  CDH1 WILD-TYPE   9  52 201  31
D11V4, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            0              9
  T2           15             52
  T3           48            201
  T4           10             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
  CDH1 MUTATED    47  18   9
  CDH1 WILD-TYPE 173  63  57
D11V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0           47            173
  N1           18             63
  N2            9             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                cls
clus               0   1
  CDH1 MUTATED    50   9
  CDH1 WILD-TYPE 235  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     50    9
  CDH1 WILD-TYPE  235   39
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0           50            235
  1            9             39
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  CDH1 MUTATED    30  44
  CDH1 WILD-TYPE 140 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     30   44
  CDH1 WILD-TYPE  140  153
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE           30            140
  MALE             44            153
[1] 2 2
[1] FALSE
D11V8, binary
                cls
clus               0   1
  CDH1 MUTATED    61   3
  CDH1 WILD-TYPE 239   5
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     61    3
  CDH1 WILD-TYPE  239    5
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO            61            239
  YES            3              5
[1] 2 2
[1] FALSE
D11V9, binary
                cls
clus               0   1
  CDH1 MUTATED    61  13
  CDH1 WILD-TYPE 253  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     61   13
  CDH1 WILD-TYPE  253   35
                               clus
vv                              CDH1 MUTATED CDH1 WILD-TYPE
  COLON ADENOCARCINOMA                    61            253
  COLON MUCINOUS ADENOCARCINOMA           13             35
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDH1 MUTATED    48   1   3   8
  CDH1 WILD-TYPE 211   2  19  13
D11V10, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0           48            211
  R1            1              2
  R2            3             19
  RX            8             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"
D11V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH1 MUTATED                                  0     4
  CDH1 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDH1 MUTATED                           8    52
  CDH1 WILD-TYPE                        11   124
D11V12, multiclass
                                  clus
vv                                 CDH1 MUTATED CDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   8             11
  WHITE                                      52            124
[1] 4 2
[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 = MLH1 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  MLH1 MUTATED    38  12
  MLH1 WILD-TYPE 239  66
  MLH1 MUTATED MLH1 WILD-TYPE 
            50            305 
  MLH1 MUTATED MLH1 WILD-TYPE 
            12             66 
$`MLH1 MUTATED`
TCGA-A6-4105 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6310 
       14.53        85.05        19.04        19.04       100.01        63.62 
TCGA-G4-6586 TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-6138 TCGA-A6-6780 TCGA-A6-6781 
       35.80        43.76        32.75        22.52        20.12        19.66 
TCGA-AA-3864 TCGA-AA-A01P TCGA-AA-A02J TCGA-AD-6889 TCGA-AY-5543 TCGA-AY-6196 
       53.00        38.07         5.03        83.24        33.01         0.20 
TCGA-AY-6386 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5916 
       17.82        62.79         6.77        14.30        85.45        21.14 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       23.05        37.02        13.02        22.03        30.08        32.02 
TCGA-CM-5868 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 
       17.03        14.99        14.04        11.01        12.95        11.01 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-F4-6805 
       25.48        43.27        15.12         4.80        16.14        34.42 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6315 
       41.42        13.25        35.31       133.18        44.68        61.91 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

$`MLH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.00        36.00        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        88.21        49.41        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      148.01        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5861 
      124.27        20.02        25.02        29.06        22.98        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        14.04 
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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 
        1.55        43.04        33.67         0.53        47.41        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6626 
       65.85        53.62        55.04        85.48        46.75 

  MLH1 MUTATED MLH1 WILD-TYPE 
           0.2            0.0 
  MLH1 MUTATED MLH1 WILD-TYPE 
        133.18         148.01 
  MLH1 MUTATED MLH1 WILD-TYPE 
        22.785         21.990 
[1] "0.2 - 133.2 (22.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D12V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLH1 MUTATED         9        1        5        12         2         0
  MLH1 WILD-TYPE      55        0       21        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLH1 MUTATED           3          0          7          4        4         4
  MLH1 WILD-TYPE        15          6         37         29       31         8
                vv
clus             STAGE IVB
  MLH1 MUTATED           0
  MLH1 WILD-TYPE         1
D12V3, multiclass
            clus
vv           MLH1 MUTATED MLH1 WILD-TYPE
  STAGE I               9             55
  STAGE IA              1              0
  STAGE II              5             21
  STAGE IIA            12             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            7             37
  STAGE IIIC            4             29
  STAGE IV              4             31
  STAGE IVA             4              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
  MLH1 MUTATED     1   9  36   6
  MLH1 WILD-TYPE   8  58 213  35
D12V4, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  T1            1              8
  T2            9             58
  T3           36            213
  T4            6             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
  MLH1 MUTATED    33  15   5
  MLH1 WILD-TYPE 187  66  61
D12V5, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  N0           33            187
  N1           15             66
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                cls
clus               0   1
  MLH1 MUTATED    34   8
  MLH1 WILD-TYPE 251  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     34    8
  MLH1 WILD-TYPE  251   40
   clus
vv  MLH1 MUTATED MLH1 WILD-TYPE
  0           34            251
  1            8             40
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus               0   1
  MLH1 MUTATED    24  29
  MLH1 WILD-TYPE 146 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     24   29
  MLH1 WILD-TYPE  146  168
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  FEMALE           24            146
  MALE             29            168
[1] 2 2
[1] FALSE
D12V8, binary
                cls
clus               0   1
  MLH1 MUTATED    46   2
  MLH1 WILD-TYPE 254   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     46    2
  MLH1 WILD-TYPE  254    6
     clus
vv    MLH1 MUTATED MLH1 WILD-TYPE
  NO            46            254
  YES            2              6
[1] 2 2
[1] FALSE
D12V9, binary
                cls
clus               0   1
  MLH1 MUTATED    45   8
  MLH1 WILD-TYPE 269  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     45    8
  MLH1 WILD-TYPE  269   40
                               clus
vv                              MLH1 MUTATED MLH1 WILD-TYPE
  COLON ADENOCARCINOMA                    45            269
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLH1 MUTATED    39   1   2   5
  MLH1 WILD-TYPE 220   2  20  16
D12V10, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  R0           39            220
  R1            1              2
  R2            2             20
  RX            5             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"
D12V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLH1 MUTATED                                  0     2
  MLH1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLH1 MUTATED                           7    37
  MLH1 WILD-TYPE                        12   139
D12V12, multiclass
                                  clus
vv                                 MLH1 MUTATED MLH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   7             12
  WHITE                                      37            139
[1] 4 2
[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 = NTAN1 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  NTAN1 MUTATED     8   2
  NTAN1 WILD-TYPE 269  76
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             345 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              2              76 
$`NTAN1 MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-3663 
       19.04        35.80        79.69        22.06        29.95         6.97 
TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-4743 TCGA-D5-6540 
        4.01        12.16        23.05        16.14 

$`NTAN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NTAN1 MUTATED NTAN1 WILD-TYPE 
           4.01            0.00 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          79.69          148.01 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          20.55           22.09 
[1] "4.0 - 79.7 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D13V2, continuous
                 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      61        1       24       104         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  NTAN1 MUTATED           0
  NTAN1 WILD-TYPE         1
D13V3, multiclass
            clus
vv           NTAN1 MUTATED NTAN1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  NTAN1 MUTATED     0   3   6   1
  NTAN1 WILD-TYPE   9  64 243  40
D13V4, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             6             243
  T4             1              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
  NTAN1 MUTATED    10   0   0
  NTAN1 WILD-TYPE 210  81  66
D13V5, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  N0            10             210
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                 cls
clus                0   1
  NTAN1 MUTATED     9   0
  NTAN1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      9    0
  NTAN1 WILD-TYPE  276   48
   clus
vv  NTAN1 MUTATED NTAN1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  NTAN1 MUTATED     3   7
  NTAN1 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      3    7
  NTAN1 WILD-TYPE  167  190
        clus
vv       NTAN1 MUTATED NTAN1 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  NTAN1 MUTATED     9   0
  NTAN1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      9    0
  NTAN1 WILD-TYPE  291    8
     clus
vv    NTAN1 MUTATED NTAN1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D13V9, binary
                 cls
clus                0   1
  NTAN1 MUTATED     6   4
  NTAN1 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      6    4
  NTAN1 WILD-TYPE  308   44
                               clus
vv                              NTAN1 MUTATED NTAN1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NTAN1 MUTATED    10   0   0   0
  NTAN1 WILD-TYPE 249   3  22  21
D13V10, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D13V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTAN1 MUTATED                                  0     0
  NTAN1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTAN1 MUTATED                           0     6
  NTAN1 WILD-TYPE                        19   170
D13V12, multiclass
                                  clus
vv                                 NTAN1 MUTATED NTAN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ZFP36L2 MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED    10   3
  ZFP36L2 WILD-TYPE 267  75
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               13               342 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                3                75 
$`ZFP36L2 MUTATED`
TCGA-AD-6964 TCGA-AZ-4681 TCGA-G4-6588 TCGA-A6-5666 TCGA-AA-3989 TCGA-AZ-6598 
       10.88       106.75        26.17        32.71         7.96        49.41 
TCGA-CA-5797 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D9 
       12.59        14.04        17.85        16.14        11.64       140.38 
TCGA-DM-A1HA 
      131.51 

$`ZFP36L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-6601 
       21.99        39.06        21.37        15.52        25.08       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C 
       12.59         7.50        44.32       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             7.96              0.00 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           140.38            148.01 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           17.850            22.075 
[1] "8.0 - 140.4 (17.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP36L2 MUTATED         2        0        1         6         1         1
  ZFP36L2 WILD-TYPE      62        1       25       102         7         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L2 MUTATED           0          0          0          1        1
  ZFP36L2 WILD-TYPE        18          6         44         32       34
                   vv
clus                STAGE IVA STAGE IVB
  ZFP36L2 MUTATED           0         0
  ZFP36L2 WILD-TYPE        12         1
D14V3, multiclass
            clus
vv           ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                6               102
  STAGE IIB                1                 7
  STAGE IIC                1                 0
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  ZFP36L2 MUTATED     0   2   9   3
  ZFP36L2 WILD-TYPE   9  65 240  38
D14V4, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               9               240
  T4               3                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
  ZFP36L2 MUTATED    11   0   3
  ZFP36L2 WILD-TYPE 209  81  63
D14V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0              11               209
  N1               0                81
  N2               3                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"
D14V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    10   1
  ZFP36L2 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     10    1
  ZFP36L2 WILD-TYPE  275   47
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0              10               275
  1               1                47
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     6   8
  ZFP36L2 WILD-TYPE 164 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      6    8
  ZFP36L2 WILD-TYPE  164  189
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               6               164
  MALE                 8               189
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    11   0
  ZFP36L2 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     11    0
  ZFP36L2 WILD-TYPE  289    8
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    12   2
  ZFP36L2 WILD-TYPE 302  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     12    2
  ZFP36L2 WILD-TYPE  302   46
                               clus
vv                              ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFP36L2 MUTATED     7   0   1   1
  ZFP36L2 WILD-TYPE 252   3  21  20
D14V10, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               1                21
  RX               1                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"
D14V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP36L2 MUTATED                                  0     1
  ZFP36L2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L2 MUTATED                           0    12
  ZFP36L2 WILD-TYPE                        19   164
D14V12, multiclass
                                  clus
vv                                 ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         12               164
[1] 4 2
[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 = WNT1 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  WNT1 MUTATED     3   3
  WNT1 WILD-TYPE 274  75
  WNT1 MUTATED WNT1 WILD-TYPE 
             6            349 
  WNT1 MUTATED WNT1 WILD-TYPE 
             3             75 
$`WNT1 MUTATED`
TCGA-G4-6586 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-5916 TCGA-CM-4743 TCGA-DM-A1HB 
       35.80        83.24        49.41        21.14        23.05       135.65 

$`WNT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         21.990 
[1] "21.1 - 135.7 (42.6)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.2"
D15V2, continuous
                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      63        1       24       105         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  WNT1 MUTATED           0
  WNT1 WILD-TYPE         1
D15V3, multiclass
            clus
vv           WNT1 MUTATED WNT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  WNT1 MUTATED     1   0   5   1
  WNT1 WILD-TYPE   8  67 244  40
D15V4, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  T1            1              8
  T2            0             67
  T3            5            244
  T4            1             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
  WNT1 MUTATED     6   1   0
  WNT1 WILD-TYPE 214  80  66
D15V5, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                cls
clus               0   1
  WNT1 MUTATED     6   0
  WNT1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      6    0
  WNT1 WILD-TYPE  279   48
   clus
vv  WNT1 MUTATED WNT1 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D15V7, binary
                cls
clus               0   1
  WNT1 MUTATED     4   3
  WNT1 WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      4    3
  WNT1 WILD-TYPE  166  194
        clus
vv       WNT1 MUTATED WNT1 WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D15V8, binary
                cls
clus               0   1
  WNT1 MUTATED     5   0
  WNT1 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      5    0
  WNT1 WILD-TYPE  295    8
     clus
vv    WNT1 MUTATED WNT1 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D15V9, binary
                cls
clus               0   1
  WNT1 MUTATED     6   0
  WNT1 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      6    0
  WNT1 WILD-TYPE  308   48
                               clus
vv                              WNT1 MUTATED WNT1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNT1 MUTATED     4   0   0   1
  WNT1 WILD-TYPE 255   3  22  20
D15V10, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            1             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"
D15V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNT1 MUTATED                                  0     1
  WNT1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNT1 MUTATED                           0     5
  WNT1 WILD-TYPE                        19   171
D15V12, multiclass
                                  clus
vv                                 WNT1 MUTATED WNT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = BMPR2 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  BMPR2 MUTATED    27   7
  BMPR2 WILD-TYPE 250  71
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             34             321 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              7              71 
$`BMPR2 MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6895 
       13.02         8.05        17.95         0.92        24.00        25.08 
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 
       35.80        26.17        32.75        33.53        22.06         3.02 
TCGA-AA-3815 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 
       33.04        30.02         4.01        12.16        83.24        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
        0.20        21.44        58.39        88.21        49.41        12.76 
TCGA-CK-4952 TCGA-CK-6747 TCGA-CM-6676 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D6 
       15.62        82.95        11.08        16.14        13.35        49.91 
TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6309 TCGA-G4-6315 
        6.18        33.67        85.48        61.91 

$`BMPR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 
       36.03        19.07        34.03         0.99        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        15.52        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
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-A6-6651 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-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
        0.92        41.00        39.98        18.05        40.96        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.95        33.01        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  BMPR2 MUTATED BMPR2 WILD-TYPE 
            0.2             0.0 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          88.21          148.01 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          24.54           21.99 
[1] "0.2 - 88.2 (24.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D16V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BMPR2 MUTATED         6        0        2        16         3         0
  BMPR2 WILD-TYPE      58        1       24        92         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BMPR2 MUTATED           2          0          3          2        1         0
  BMPR2 WILD-TYPE        16          6         41         31       34        12
                 vv
clus              STAGE IVB
  BMPR2 MUTATED           0
  BMPR2 WILD-TYPE         1
D16V3, multiclass
            clus
vv           BMPR2 MUTATED BMPR2 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             16              92
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  BMPR2 MUTATED     2   4  25   4
  BMPR2 WILD-TYPE   7  63 224  37
D16V4, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  T1             2               7
  T2             4              63
  T3            25             224
  T4             4              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
  BMPR2 MUTATED    27   5   3
  BMPR2 WILD-TYPE 193  76  63
D16V5, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  N0            27             193
  N1             5              76
  N2             3              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"
D16V6, binary
                 cls
clus                0   1
  BMPR2 MUTATED    28   1
  BMPR2 WILD-TYPE 257  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     28    1
  BMPR2 WILD-TYPE  257   47
   clus
vv  BMPR2 MUTATED BMPR2 WILD-TYPE
  0            28             257
  1             1              47
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  BMPR2 MUTATED    20  15
  BMPR2 WILD-TYPE 150 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     20   15
  BMPR2 WILD-TYPE  150  182
        clus
vv       BMPR2 MUTATED BMPR2 WILD-TYPE
  FEMALE            20             150
  MALE              15             182
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus                0   1
  BMPR2 MUTATED    29   0
  BMPR2 WILD-TYPE 271   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     29    0
  BMPR2 WILD-TYPE  271    8
     clus
vv    BMPR2 MUTATED BMPR2 WILD-TYPE
  NO             29             271
  YES             0               8
[1] 2 2
[1] FALSE
D16V9, binary
                 cls
clus                0   1
  BMPR2 MUTATED    24  11
  BMPR2 WILD-TYPE 290  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     24   11
  BMPR2 WILD-TYPE  290   37
                               clus
vv                              BMPR2 MUTATED BMPR2 WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BMPR2 MUTATED    27   0   0   4
  BMPR2 WILD-TYPE 232   3  22  17
D16V10, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  R0            27             232
  R1             0               3
  R2             0              22
  RX             4              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"
D16V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMPR2 MUTATED                                  0     2
  BMPR2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BMPR2 MUTATED                           2    22
  BMPR2 WILD-TYPE                        17   154
D16V12, multiclass
                                  clus
vv                                 BMPR2 MUTATED BMPR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       22             154
[1] 4 2
[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 = SELPLG MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  SELPLG MUTATED    15   1
  SELPLG WILD-TYPE 262  77
  SELPLG MUTATED SELPLG WILD-TYPE 
              16              339 
  SELPLG MUTATED SELPLG WILD-TYPE 
               1               77 
$`SELPLG MUTATED`
TCGA-G4-6625 TCGA-A6-5660 TCGA-A6-5664 TCGA-AA-3864 TCGA-AZ-4315 TCGA-CA-5255 
       91.79        29.19        22.09        53.00        58.39        12.36 
TCGA-CM-4752 TCGA-CM-5864 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 
       13.02        15.02        10.06        25.48        17.85         4.80 
TCGA-D5-6538 TCGA-F4-6855 TCGA-G4-6307 TCGA-G4-6317 
       17.13        47.41        55.04        36.00 

$`SELPLG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       55.92        20.19        18.25        43.27        15.12        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  SELPLG MUTATED SELPLG WILD-TYPE 
             4.8              0.0 
  SELPLG MUTATED SELPLG WILD-TYPE 
           91.79           148.01 
  SELPLG MUTATED SELPLG WILD-TYPE 
          23.785           22.030 
[1] "4.8 - 91.8 (23.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "4.2"
D17V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SELPLG MUTATED         1        0        1         7         0         0
  SELPLG WILD-TYPE      63        1       25       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SELPLG MUTATED           0          0          3          3        0
  SELPLG WILD-TYPE        18          6         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  SELPLG MUTATED           0         0
  SELPLG WILD-TYPE        12         1
D17V3, multiclass
            clus
vv           SELPLG MUTATED SELPLG WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              3               30
  STAGE IV                0               35
  STAGE IVA               0               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
  SELPLG MUTATED     0   1  13   2
  SELPLG WILD-TYPE   9  66 236  39
D17V4, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  T1              0                9
  T2              1               66
  T3             13              236
  T4              2               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
  SELPLG MUTATED    10   2   4
  SELPLG WILD-TYPE 210  79  62
D17V5, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  N0             10              210
  N1              2               79
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                  cls
clus                 0   1
  SELPLG MUTATED    13   0
  SELPLG WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     13    0
  SELPLG WILD-TYPE  272   48
   clus
vv  SELPLG MUTATED SELPLG WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                 0   1
  SELPLG MUTATED     6  10
  SELPLG WILD-TYPE 164 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      6   10
  SELPLG WILD-TYPE  164  187
        clus
vv       SELPLG MUTATED SELPLG WILD-TYPE
  FEMALE              6              164
  MALE               10              187
[1] 2 2
[1] FALSE
D17V8, binary
                  cls
clus                 0   1
  SELPLG MUTATED    15   1
  SELPLG WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     15    1
  SELPLG WILD-TYPE  285    7
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D17V9, binary
                  cls
clus                 0   1
  SELPLG MUTATED    16   0
  SELPLG WILD-TYPE 298  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     16    0
  SELPLG WILD-TYPE  298   48
                               clus
vv                              SELPLG MUTATED SELPLG WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SELPLG MUTATED    13   0   0   1
  SELPLG WILD-TYPE 246   3  22  20
D17V10, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              1               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"
D17V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SELPLG MUTATED                                  0     1
  SELPLG WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SELPLG MUTATED                           3    11
  SELPLG WILD-TYPE                        16   165
D17V12, multiclass
                                  clus
vv                                 SELPLG MUTATED SELPLG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        11              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(18) Variable = CRIPAK MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  CRIPAK MUTATED    11   7
  CRIPAK WILD-TYPE 266  71
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              18              337 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               7               71 
$`CRIPAK MUTATED`
TCGA-AA-3662 TCGA-A6-6142 TCGA-AA-3489 TCGA-AA-3492 TCGA-AY-6196 TCGA-AY-6386 
        6.05        25.08         7.04         3.02         0.20        17.82 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CM-4747 TCGA-CM-6168 TCGA-CM-6172 TCGA-D5-6927 
       49.41        11.74        25.02        12.99        11.01         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6570 
       11.64        13.35        92.75        12.59       140.38         6.18 

$`CRIPAK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        19.66        20.28        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       10.13        12.43        14.30         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32         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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
             0.2              0.0 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          140.38           148.01 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          12.165           22.420 
[1] "0.2 - 140.4 (12.2)" "0.0 - 148.0 (22.4)"
[1] "hr=" "2.1"
D18V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRIPAK MUTATED         0        0        3         7         0         0
  CRIPAK WILD-TYPE      64        1       23       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRIPAK MUTATED           0          0          2          1        2
  CRIPAK WILD-TYPE        18          6         42         32       33
                  vv
clus               STAGE IVA STAGE IVB
  CRIPAK MUTATED           2         0
  CRIPAK WILD-TYPE        10         1
D18V3, multiclass
            clus
vv           CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               2               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
  CRIPAK MUTATED     0   0  15   3
  CRIPAK WILD-TYPE   9  67 234  38
D18V4, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              0                9
  T2              0               67
  T3             15              234
  T4              3               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
  CRIPAK MUTATED    10   5   3
  CRIPAK WILD-TYPE 210  76  63
D18V5, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  N0             10              210
  N1              5               76
  N2              3               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"
D18V6, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    11   4
  CRIPAK WILD-TYPE 274  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     11    4
  CRIPAK WILD-TYPE  274   44
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0             11              274
  1              4               44
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    10   8
  CRIPAK WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     10    8
  CRIPAK WILD-TYPE  160  189
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D18V8, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    14   0
  CRIPAK WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     14    0
  CRIPAK WILD-TYPE  286    8
     clus
vv    CRIPAK MUTATED CRIPAK WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D18V9, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    15   3
  CRIPAK WILD-TYPE 299  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     15    3
  CRIPAK WILD-TYPE  299   45
                               clus
vv                              CRIPAK MUTATED CRIPAK WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CRIPAK MUTATED    11   0   1   0
  CRIPAK WILD-TYPE 248   3  21  21
D18V10, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  R0             11              248
  R1              0                3
  R2              1               21
  RX              0               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"
D18V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRIPAK MUTATED                                  0     0
  CRIPAK WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CRIPAK MUTATED                           2    13
  CRIPAK WILD-TYPE                        17   163
D18V12, multiclass
                                  clus
vv                                 CRIPAK MUTATED CRIPAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        13              163
[1] 4 2
[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 = KDM6A MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    22   5
  KDM6A WILD-TYPE 255  73
  KDM6A MUTATED KDM6A WILD-TYPE 
             27             328 
  KDM6A MUTATED KDM6A WILD-TYPE 
              5              73 
$`KDM6A MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-A010 
       19.04        10.88        35.80        32.75        32.71        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-6164 
       58.39        12.76        21.99        25.02        22.98        29.03 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6540 
       12.99        13.02        11.08        20.19        15.12        16.14 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-DM-A28C 
        9.04        13.41        10.26        38.20       135.65        81.37 
TCGA-DM-A28F TCGA-F4-6805 TCGA-G4-6303 
       35.97        34.42        65.85 

$`KDM6A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       37.02        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 
       12.00        14.04        16.04        21.99        14.99        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       55.92        18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64        13.35        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38       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-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      139.17       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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  KDM6A MUTATED KDM6A WILD-TYPE 
           9.04            0.00 
  KDM6A MUTATED KDM6A WILD-TYPE 
         135.65          148.01 
  KDM6A MUTATED KDM6A WILD-TYPE 
         22.980          22.045 
[1] "9.0 - 135.7 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D19V2, continuous
                 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      61        1       26        99         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM6A MUTATED           0          0          6          1        3         1
  KDM6A WILD-TYPE        18          6         38         32       32        11
                 vv
clus              STAGE IVB
  KDM6A MUTATED           0
  KDM6A WILD-TYPE         1
D19V3, multiclass
            clus
vv           KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              9              99
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              1              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
  KDM6A MUTATED     0   3  18   6
  KDM6A WILD-TYPE   9  64 231  35
D19V4, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             0               9
  T2             3              64
  T3            18             231
  T4             6              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
  KDM6A MUTATED    16   9   2
  KDM6A WILD-TYPE 204  72  64
D19V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0            16             204
  N1             9              72
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                 cls
clus                0   1
  KDM6A MUTATED    20   4
  KDM6A WILD-TYPE 265  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     20    4
  KDM6A WILD-TYPE  265   44
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            20             265
  1             4              44
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  KDM6A MUTATED    11  16
  KDM6A WILD-TYPE 159 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     11   16
  KDM6A WILD-TYPE  159  181
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE            11             159
  MALE              16             181
[1] 2 2
[1] FALSE
D19V8, binary
                 cls
clus                0   1
  KDM6A MUTATED    20   2
  KDM6A WILD-TYPE 280   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     20    2
  KDM6A WILD-TYPE  280    6
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO             20             280
  YES             2               6
[1] 2 2
[1] FALSE
D19V9, binary
                 cls
clus                0   1
  KDM6A MUTATED    21   4
  KDM6A WILD-TYPE 293  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     21    4
  KDM6A WILD-TYPE  293   44
                               clus
vv                              KDM6A MUTATED KDM6A WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED    17   0   1   3
  KDM6A WILD-TYPE 242   3  21  18
D19V10, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0            17             242
  R1             0               3
  R2             1              21
  RX             3              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"
D19V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     1
  KDM6A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           2    22
  KDM6A WILD-TYPE                        17   154
D19V12, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       22             154
[1] 4 2
[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 = MAPK6 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2               0   1
  MAPK6 MUTATED    14   4
  MAPK6 WILD-TYPE 263  74
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             18             337 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
              4              74 
$`MAPK6 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-5661 TCGA-A6-5665 
        0.92       100.01        22.09        91.79        33.53        22.06 
TCGA-A6-6648 TCGA-AA-3510 TCGA-AA-3977 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4950 
       25.18        63.98        25.02        49.41        12.76        85.45 
TCGA-CK-4952 TCGA-CM-4752 TCGA-CM-5344 TCGA-D5-5537 TCGA-F4-6704 TCGA-G4-6303 
       15.62        13.02        22.03        45.40         1.55        65.85 

$`MAPK6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.08        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MAPK6 MUTATED MAPK6 WILD-TYPE 
           0.92            0.00 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
         100.01          148.01 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
          25.10           21.99 
[1] "0.9 - 100.0 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D20V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAPK6 MUTATED         0        0        3         6         0         0
  MAPK6 WILD-TYPE      64        1       23       102         8         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        16          6         42         31       34        11
                 vv
clus              STAGE IVB
  MAPK6 MUTATED           0
  MAPK6 WILD-TYPE         1
D20V3, multiclass
            clus
vv           MAPK6 MUTATED MAPK6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  MAPK6 MUTATED     0   2  15   1
  MAPK6 WILD-TYPE   9  65 234  40
D20V4, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            15             234
  T4             1              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
  MAPK6 MUTATED    10   5   3
  MAPK6 WILD-TYPE 210  76  63
D20V5, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  N0            10             210
  N1             5              76
  N2             3              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"
D20V6, binary
                 cls
clus                0   1
  MAPK6 MUTATED    11   2
  MAPK6 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     11    2
  MAPK6 WILD-TYPE  274   46
   clus
vv  MAPK6 MUTATED MAPK6 WILD-TYPE
  0            11             274
  1             2              46
[1] 2 2
[1] FALSE
D20V7, binary
                 cls
clus                0   1
  MAPK6 MUTATED    10   8
  MAPK6 WILD-TYPE 160 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     10    8
  MAPK6 WILD-TYPE  160  189
        clus
vv       MAPK6 MUTATED MAPK6 WILD-TYPE
  FEMALE            10             160
  MALE               8             189
[1] 2 2
[1] FALSE
D20V8, binary
                 cls
clus                0   1
  MAPK6 MUTATED    16   0
  MAPK6 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     16    0
  MAPK6 WILD-TYPE  284    8
     clus
vv    MAPK6 MUTATED MAPK6 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D20V9, binary
                 cls
clus                0   1
  MAPK6 MUTATED    14   4
  MAPK6 WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     14    4
  MAPK6 WILD-TYPE  300   44
                               clus
vv                              MAPK6 MUTATED MAPK6 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MAPK6 MUTATED    10   1   0   3
  MAPK6 WILD-TYPE 249   2  22  18
D20V10, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  R0            10             249
  R1             1               2
  R2             0              22
  RX             3              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"
D20V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK6 MUTATED                                  1     1
  MAPK6 WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAPK6 MUTATED                           3    10
  MAPK6 WILD-TYPE                        16   166
D20V12, multiclass
                                  clus
vv                                 MAPK6 MUTATED MAPK6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       10             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(21) Variable = RHOA MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     9   3
  RHOA WILD-TYPE 268  75
  RHOA MUTATED RHOA WILD-TYPE 
            12            343 
  RHOA MUTATED RHOA WILD-TYPE 
             3             75 
$`RHOA MUTATED`
TCGA-AA-3972 TCGA-AD-6895 TCGA-G4-6310 TCGA-AA-3845 TCGA-AA-A01P TCGA-AA-A01R 
       50.99        25.08        63.62         0.00        38.07        35.01 
TCGA-AD-6965 TCGA-AZ-6598 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-6678 TCGA-D5-6536 
       26.47        49.41       148.01        85.45        11.01        17.85 

$`RHOA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RHOA MUTATED RHOA WILD-TYPE 
             0              0 
  RHOA MUTATED RHOA WILD-TYPE 
        148.01         140.38 
  RHOA MUTATED RHOA WILD-TYPE 
         36.54          21.99 
[1] "0.0 - 148.0 (36.5)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.3"
D21V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RHOA MUTATED         0        0        1         2         0         0
  RHOA WILD-TYPE      64        1       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHOA MUTATED           3          0          3          1        1         1
  RHOA WILD-TYPE        15          6         41         32       34        11
                vv
clus             STAGE IVB
  RHOA MUTATED           0
  RHOA WILD-TYPE         1
D21V3, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  RHOA MUTATED     0   0  10   2
  RHOA WILD-TYPE   9  67 239  39
D21V4, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            0              9
  T2            0             67
  T3           10            239
  T4            2             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
  RHOA MUTATED     3   7   2
  RHOA WILD-TYPE 217  74  64
D21V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            3            217
  N1            7             74
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                cls
clus               0   1
  RHOA MUTATED     9   2
  RHOA WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      9    2
  RHOA WILD-TYPE  276   46
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0            9            276
  1            2             46
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  RHOA MUTATED     6   6
  RHOA WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      6    6
  RHOA WILD-TYPE  164  191
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus               0   1
  RHOA MUTATED     9   2
  RHOA WILD-TYPE 291   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      9    2
  RHOA WILD-TYPE  291    6
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             9            291
  YES            2              6
[1] 2 2
[1] FALSE
D21V9, binary
                cls
clus               0   1
  RHOA MUTATED    10   2
  RHOA WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     10    2
  RHOA WILD-TYPE  304   46
                               clus
vv                              RHOA MUTATED RHOA WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RHOA MUTATED     8   2   1   0
  RHOA WILD-TYPE 251   1  21  21
D21V10, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  R0            8            251
  R1            2              1
  R2            1             21
  RX            0             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"
D21V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHOA MUTATED                                  0     0
  RHOA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED                           1     7
  RHOA WILD-TYPE                        18   169
D21V12, multiclass
                                  clus
vv                                 RHOA MUTATED RHOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = FMN2 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  FMN2 MUTATED    36  13
  FMN2 WILD-TYPE 241  65
  FMN2 MUTATED FMN2 WILD-TYPE 
            49            306 
  FMN2 MUTATED FMN2 WILD-TYPE 
            13             65 
$`FMN2 MUTATED`
TCGA-AA-3713 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       19.04         1.94         5.88        35.80        26.17        79.69 
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-3861 TCGA-AA-3956 TCGA-AA-3973 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       30.05        34.03        13.05         4.01        34.98        83.24 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-5916 
        6.77        11.74        12.76        10.06        17.56        21.14 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6161 
      124.27        23.05        37.02        15.02         5.03        15.02 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6529 
       13.02        14.04        11.01        10.06        12.03        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-7000 
       18.25        25.48        43.27        16.14         9.44        10.26 
TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6569 
       92.75       135.65       139.17        81.37        31.96        35.74 
TCGA-F4-6570 
        6.18 

$`FMN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 
      100.01        49.08        63.62        22.09        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
        2.01        21.99        16.08        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
       12.39        12.59        12.59        12.20        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       30.08        32.02        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6535 
       45.40        54.61        19.59        56.09        55.92        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41        13.35        12.00        11.38       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-A28E TCGA-DM-A28F TCGA-DM-A28G 
        7.50        44.32       131.51       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
      117.07        98.24         8.61        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  FMN2 MUTATED FMN2 WILD-TYPE 
          1.94           0.00 
  FMN2 MUTATED FMN2 WILD-TYPE 
        139.17         148.01 
  FMN2 MUTATED FMN2 WILD-TYPE 
         21.14          22.09 
[1] "1.9 - 139.2 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D22V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FMN2 MUTATED        11        0        0        21         2         0
  FMN2 WILD-TYPE      53        1       26        87         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMN2 MUTATED           0          1          7          0        4         2
  FMN2 WILD-TYPE        18          5         37         33       31        10
                vv
clus             STAGE IVB
  FMN2 MUTATED           0
  FMN2 WILD-TYPE         1
D22V3, multiclass
            clus
vv           FMN2 MUTATED FMN2 WILD-TYPE
  STAGE I              11             53
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA            21             87
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            7             37
  STAGE IIIC            0             33
  STAGE IV              4             31
  STAGE IVA             2             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
  FMN2 MUTATED     1  11  31   6
  FMN2 WILD-TYPE   8  56 218  35
D22V4, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  T1            1              8
  T2           11             56
  T3           31            218
  T4            6             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
  FMN2 MUTATED    37   9   3
  FMN2 WILD-TYPE 183  72  63
D22V5, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  N0           37            183
  N1            9             72
  N2            3             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"
D22V6, binary
                cls
clus               0   1
  FMN2 MUTATED    41   6
  FMN2 WILD-TYPE 244  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     41    6
  FMN2 WILD-TYPE  244   42
   clus
vv  FMN2 MUTATED FMN2 WILD-TYPE
  0           41            244
  1            6             42
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus               0   1
  FMN2 MUTATED    22  27
  FMN2 WILD-TYPE 148 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     22   27
  FMN2 WILD-TYPE  148  170
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  FEMALE           22            148
  MALE             27            170
[1] 2 2
[1] FALSE
D22V8, binary
                cls
clus               0   1
  FMN2 MUTATED    42   1
  FMN2 WILD-TYPE 258   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     42    1
  FMN2 WILD-TYPE  258    7
     clus
vv    FMN2 MUTATED FMN2 WILD-TYPE
  NO            42            258
  YES            1              7
[1] 2 2
[1] FALSE
D22V9, binary
                cls
clus               0   1
  FMN2 MUTATED    41   7
  FMN2 WILD-TYPE 273  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     41    7
  FMN2 WILD-TYPE  273   41
                               clus
vv                              FMN2 MUTATED FMN2 WILD-TYPE
  COLON ADENOCARCINOMA                    41            273
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FMN2 MUTATED    31   0   2   5
  FMN2 WILD-TYPE 228   3  20  16
D22V10, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  R0           31            228
  R1            0              3
  R2            2             20
  RX            5             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"
D22V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FMN2 MUTATED                                  0     3
  FMN2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FMN2 MUTATED                           5    35
  FMN2 WILD-TYPE                        14   141
D22V12, multiclass
                                  clus
vv                                 FMN2 MUTATED FMN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   5             14
  WHITE                                      35            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(23) Variable = STARD3NL MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  STARD3NL MUTATED    12   1
  STARD3NL WILD-TYPE 265  77
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                13                342 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                 1                 77 
$`STARD3NL MUTATED`
TCGA-AA-3662 TCGA-G4-6588 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A01R 
        6.05        26.17        19.66         6.97        34.98        35.01 
TCGA-AY-6197 TCGA-AZ-6599 TCGA-CK-4950 TCGA-CM-6167 TCGA-D5-5540 TCGA-D5-6536 
       21.44         6.77        85.45        14.99        56.09        17.85 
TCGA-G4-6323 
       13.78 

$`STARD3NL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  STARD3NL MUTATED STARD3NL WILD-TYPE 
              6.05               0.00 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
             85.45             148.01 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
             19.66              22.09 
[1] "6.0 - 85.5 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STARD3NL MUTATED         1        1        1         4         1         0
  STARD3NL WILD-TYPE      63        0       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STARD3NL MUTATED           1          0          1          2        1
  STARD3NL WILD-TYPE        17          6         43         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  STARD3NL MUTATED           0         0
  STARD3NL WILD-TYPE        12         1
D23V3, multiclass
            clus
vv           STARD3NL MUTATED STARD3NL WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  1                  0
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                2                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  STARD3NL MUTATED     0   1   8   3
  STARD3NL WILD-TYPE   9  66 241  38
D23V4, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                8                241
  T4                3                 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
  STARD3NL MUTATED     8   2   3
  STARD3NL WILD-TYPE 212  79  63
D23V5, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  N0                8                212
  N1                2                 79
  N2                3                 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"
D23V6, binary
                    cls
clus                   0   1
  STARD3NL MUTATED     8   1
  STARD3NL WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED      8    1
  STARD3NL WILD-TYPE  277   47
   clus
vv  STARD3NL MUTATED STARD3NL WILD-TYPE
  0                8                277
  1                1                 47
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  STARD3NL MUTATED     5   8
  STARD3NL WILD-TYPE 165 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED      5    8
  STARD3NL WILD-TYPE  165  189
        clus
vv       STARD3NL MUTATED STARD3NL WILD-TYPE
  FEMALE                5                165
  MALE                  8                189
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  STARD3NL MUTATED    12   1
  STARD3NL WILD-TYPE 288   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED     12    1
  STARD3NL WILD-TYPE  288    7
     clus
vv    STARD3NL MUTATED STARD3NL WILD-TYPE
  NO                12                288
  YES                1                  7
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  STARD3NL MUTATED    10   3
  STARD3NL WILD-TYPE 304  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED     10    3
  STARD3NL WILD-TYPE  304   45
                               clus
vv                              STARD3NL MUTATED STARD3NL WILD-TYPE
  COLON ADENOCARCINOMA                        10                304
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  STARD3NL MUTATED    10   1   1   0
  STARD3NL WILD-TYPE 249   2  21  21
D23V10, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  R0               10                249
  R1                1                  2
  R2                1                 21
  RX                0                 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"
D23V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STARD3NL MUTATED                                  0     0
  STARD3NL WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  STARD3NL MUTATED                           3     6
  STARD3NL WILD-TYPE                        16   170
D23V12, multiclass
                                  clus
vv                                 STARD3NL MUTATED STARD3NL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       3                 16
  WHITE                                           6                170
[1] 4 2
[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 = NF2 MUTATION ANALYSIS
D24V1, survival
               sevent
clus2             0   1
  NF2 MUTATED    52   9
  NF2 WILD-TYPE 225  69
  NF2 MUTATED NF2 WILD-TYPE 
           61           294 
  NF2 MUTATED NF2 WILD-TYPE 
            9            69 
$`NF2 MUTATED`
TCGA-AA-3516 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3950 TCGA-CK-5912 TCGA-G4-6310 
       13.02         6.05        19.04        24.00        49.08        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5666 
       22.09        35.80        26.17        31.63        33.53        32.71 
TCGA-A6-6141 TCGA-A6-6142 TCGA-AA-3663 TCGA-AA-3968 TCGA-AA-A01R TCGA-AD-6963 
        8.38        25.08         6.97        21.99        35.01        27.42 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 
       14.50        27.09        17.82        58.39        49.41         6.77 
TCGA-AZ-6603 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4952 TCGA-CM-4743 
       29.56        12.20        12.76        17.56        15.62        23.05 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 
       13.02        22.03        30.08        15.02        15.02        29.03 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        15.02        14.04        11.01        12.95        13.05 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       54.61        55.92        18.25        15.12        17.85        12.49 
TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-DM-A1DB TCGA-F4-6570 
       15.58        10.13         9.04         9.44        44.32         6.18 
TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6323 
       47.87        43.04        35.31        74.56        55.04        13.78 
TCGA-G4-6626 
       46.75 

$`NF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 
       25.08        10.88       106.75       100.01         1.94         5.88 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       27.09        22.52        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        5.79        22.42        26.47        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       88.21        12.10         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.39        12.59        12.59        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
        2.01       124.27        20.02        37.02        25.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       22.98        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00        14.04        16.04        21.99        12.99        13.02 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       19.59        56.09        20.19        25.48        43.27         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14         7.53        12.39        12.43        14.30 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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-F4-6808 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-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 

  NF2 MUTATED NF2 WILD-TYPE 
         6.05          0.00 
  NF2 MUTATED NF2 WILD-TYPE 
        74.56        148.01 
  NF2 MUTATED NF2 WILD-TYPE 
        19.04         22.39 
[1] "6.0 - 74.6 (19.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.5"
D24V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NF2 MUTATED         9        1        2        22         1         1
  NF2 WILD-TYPE      55        0       24        86         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF2 MUTATED           3          1         11          4        2         1
  NF2 WILD-TYPE        15          5         33         29       33        11
               vv
clus            STAGE IVB
  NF2 MUTATED           1
  NF2 WILD-TYPE         0
D24V3, multiclass
            clus
vv           NF2 MUTATED NF2 WILD-TYPE
  STAGE I              9            55
  STAGE IA             1             0
  STAGE II             2            24
  STAGE IIA           22            86
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            3            15
  STAGE IIIA           1             5
  STAGE IIIB          11            33
  STAGE IIIC           4            29
  STAGE IV             2            33
  STAGE IVA            1            11
  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     0  11  44   6
  NF2 WILD-TYPE   9  56 205  35
D24V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           0             9
  T2          11            56
  T3          44           205
  T4           6            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
  NF2 MUTATED    39  15   8
  NF2 WILD-TYPE 181  66  58
D24V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0          39           181
  N1          15            66
  N2           8            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"
D24V6, binary
               cls
clus              0   1
  NF2 MUTATED    49   4
  NF2 WILD-TYPE 236  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     49    4
  NF2 WILD-TYPE  236   44
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0          49           236
  1           4            44
[1] 2 2
[1] FALSE
D24V7, binary
               cls
clus              0   1
  NF2 MUTATED    31  31
  NF2 WILD-TYPE 139 166
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     31   31
  NF2 WILD-TYPE  139  166
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE          31           139
  MALE            31           166
[1] 2 2
[1] FALSE
D24V8, binary
               cls
clus              0   1
  NF2 MUTATED    54   4
  NF2 WILD-TYPE 246   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     54    4
  NF2 WILD-TYPE  246    4
     clus
vv    NF2 MUTATED NF2 WILD-TYPE
  NO           54           246
  YES           4             4
[1] 2 2
[1] FALSE
D24V9, binary
               cls
clus              0   1
  NF2 MUTATED    56   6
  NF2 WILD-TYPE 258  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     56    6
  NF2 WILD-TYPE  258   42
                               clus
vv                              NF2 MUTATED NF2 WILD-TYPE
  COLON ADENOCARCINOMA                   56           258
  COLON MUCINOUS ADENOCARCINOMA           6            42
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NF2 MUTATED    44   0   2   7
  NF2 WILD-TYPE 215   3  20  14
D24V10, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  R0          44           215
  R1           0             3
  R2           2            20
  RX           7            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"
D24V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     2
  NF2 WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           8    45
  NF2 WILD-TYPE                        11   131
D24V12, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  8            11
  WHITE                                     45           131
[1] 4 2
[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 = NF1 MUTATION ANALYSIS
D25V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    68  20
  NF1 WILD-TYPE 209  58
  NF1 MUTATED NF1 WILD-TYPE 
           88           267 
  NF1 MUTATED NF1 WILD-TYPE 
           20            58 
$`NF1 MUTATED`
TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6601 
        1.02         6.05        85.05        19.04        24.00       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        22.09        35.80        91.79        79.69 
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-3555 TCGA-AA-3655 
       32.71        25.08        24.69        19.66        29.95        61.02 
TCGA-AA-3956 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6965 TCGA-AU-3779 
       34.03         4.01        34.98        24.53        26.47        14.50 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 
       27.09        33.01        21.44        17.82        58.39         5.13 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 
       88.21        49.41         6.77        12.10         5.23         3.19 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 
       12.36        12.39        12.59        12.76        14.30        15.62 
TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       51.32       124.27        23.05        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 
        5.03        14.04        29.03        14.99        14.04        11.01 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       12.95        19.59        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.49        16.14        13.41        11.38        24.43       130.65 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28H TCGA-DM-A28K 
       13.32         7.50        44.32       135.65       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6807 TCGA-G4-6293 
        8.61        31.96         6.18         1.55        43.04       133.18 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        36.00        13.78 

$`NF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6588 TCGA-A6-2672 
       10.88       106.75         1.94        63.62        26.17        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6137 
       36.53        32.91        30.44        29.19        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.52         8.38        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AY-4070 TCGA-AY-4071 
       83.24         5.79        22.42        27.42        16.31         0.95 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6606 
        0.20         1.41        22.36        62.79        29.56        11.74 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.69        12.59        12.20        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       85.45        21.99        21.14        82.95         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 
       37.02        25.02        13.02        29.06        22.03        32.02 
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-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       21.99        12.99        13.02        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        43.27 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        38.20        92.75        49.91        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        81.37       119.93        35.97        60.79 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.74        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-G4-6309 TCGA-G4-6315 TCGA-G4-6626 
       85.48        61.91        46.75 

  NF1 MUTATED NF1 WILD-TYPE 
         1.02          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
       135.65        148.01 
  NF1 MUTATED NF1 WILD-TYPE 
       22.535        21.990 
[1] "1.0 - 135.7 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D25V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NF1 MUTATED         9        1        5        29         3         1
  NF1 WILD-TYPE      55        0       21        79         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF1 MUTATED           2          1         13          9        8         5
  NF1 WILD-TYPE        16          5         31         24       27         7
               vv
clus            STAGE IVB
  NF1 MUTATED           0
  NF1 WILD-TYPE         1
D25V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              9            55
  STAGE IA             1             0
  STAGE II             5            21
  STAGE IIA           29            79
  STAGE IIB            3             5
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           1             5
  STAGE IIIB          13            31
  STAGE IIIC           9            24
  STAGE IV             8            27
  STAGE IVA            5             7
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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     3   9  65  11
  NF1 WILD-TYPE   6  58 184  30
D25V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           3             6
  T2           9            58
  T3          65           184
  T4          11            30
[1] 4 2
[1] TRUE
[1] "dimension 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    53  20  16
  NF1 WILD-TYPE 167  61  50
D25V5, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0          53           167
  N1          20            61
  N2          16            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"
D25V6, binary
               cls
clus              0   1
  NF1 MUTATED    62  13
  NF1 WILD-TYPE 223  35
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     62   13
  NF1 WILD-TYPE  223   35
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          62           223
  1          13            35
[1] 2 2
[1] FALSE
D25V7, binary
               cls
clus              0   1
  NF1 MUTATED    44  45
  NF1 WILD-TYPE 126 152
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     44   45
  NF1 WILD-TYPE  126  152
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          44           126
  MALE            45           152
[1] 2 2
[1] FALSE
D25V8, binary
               cls
clus              0   1
  NF1 MUTATED    72   2
  NF1 WILD-TYPE 228   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     72    2
  NF1 WILD-TYPE  228    6
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           72           228
  YES           2             6
[1] 2 2
[1] FALSE
D25V9, binary
               cls
clus              0   1
  NF1 MUTATED    73  14
  NF1 WILD-TYPE 241  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     73   14
  NF1 WILD-TYPE  241   34
                               clus
vv                              NF1 MUTATED NF1 WILD-TYPE
  COLON ADENOCARCINOMA                   73           241
  COLON MUCINOUS ADENOCARCINOMA          14            34
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    55   1   2   9
  NF1 WILD-TYPE 204   2  20  12
D25V10, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          55           204
  R1           1             2
  R2           2            20
  RX           9            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  1     5
  NF1 WILD-TYPE                                0     5
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           8    64
  NF1 WILD-TYPE                        11   112
D25V12, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      5             5
  BLACK OR AFRICAN AMERICAN                  8            11
  WHITE                                     64           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(26) Variable = OR4D10 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  OR4D10 MUTATED     9   5
  OR4D10 WILD-TYPE 268  73
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              14              341 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
               5               73 
$`OR4D10 MUTATED`
TCGA-AZ-6601 TCGA-A6-5657 TCGA-AA-3864 TCGA-AA-A00N TCGA-AD-6899 TCGA-AY-5543 
      100.01        31.63        53.00         4.01         5.79        33.01 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 
       58.39        12.76        10.06        13.02        32.02        15.02 
TCGA-D5-5537 TCGA-D5-6541 
       45.40        15.58 

$`OR4D10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR4D10 MUTATED OR4D10 WILD-TYPE 
            4.01             0.00 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
          100.01           148.01 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
          23.605           22.060 
[1] "4.0 - 100.0 (23.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D26V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4D10 MUTATED         1        0        2         7         1         0
  OR4D10 WILD-TYPE      63        1       24       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4D10 MUTATED           0          0          1          1        0
  OR4D10 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  OR4D10 MUTATED           1         0
  OR4D10 WILD-TYPE        11         1
D26V3, multiclass
            clus
vv           OR4D10 MUTATED OR4D10 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  OR4D10 MUTATED     0   1  11   2
  OR4D10 WILD-TYPE   9  66 238  39
D26V4, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             11              238
  T4              2               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
  OR4D10 MUTATED    10   2   2
  OR4D10 WILD-TYPE 210  79  64
D26V5, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  N0             10              210
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    11   1
  OR4D10 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     11    1
  OR4D10 WILD-TYPE  274   47
   clus
vv  OR4D10 MUTATED OR4D10 WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                 0   1
  OR4D10 MUTATED     2  12
  OR4D10 WILD-TYPE 168 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED      2   12
  OR4D10 WILD-TYPE  168  185
        clus
vv       OR4D10 MUTATED OR4D10 WILD-TYPE
  FEMALE              2              168
  MALE               12              185
[1] 2 2
[1] FALSE
D26V8, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    13   0
  OR4D10 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     13    0
  OR4D10 WILD-TYPE  287    8
     clus
vv    OR4D10 MUTATED OR4D10 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D26V9, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    11   3
  OR4D10 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     11    3
  OR4D10 WILD-TYPE  303   45
                               clus
vv                              OR4D10 MUTATED OR4D10 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR4D10 MUTATED     9   0   0   3
  OR4D10 WILD-TYPE 250   3  22  18
D26V10, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              3               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"
D26V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4D10 MUTATED                                  0     2
  OR4D10 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4D10 MUTATED                           3     7
  OR4D10 WILD-TYPE                        16   169
D26V12, multiclass
                                  clus
vv                                 OR4D10 MUTATED OR4D10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         7              169
[1] 4 2
[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    48  14
  PRKDC WILD-TYPE 229  64
  PRKDC MUTATED PRKDC WILD-TYPE 
             62             293 
  PRKDC MUTATED PRKDC WILD-TYPE 
             14              64 
$`PRKDC MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6586 TCGA-G4-6588 
       19.04        10.88       100.01         1.94        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5665 
       91.79        79.69        32.75        31.63        30.44        22.06 
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 
       32.71         8.38        24.39        20.12        19.66        63.98 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
       61.02         6.97        10.06        53.00        31.00         2.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 
        4.01        34.98        38.07        83.24        14.50        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       21.44        58.39         3.19        12.76        10.06       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6166 
       15.62        51.32        30.08        32.02        15.02        21.99 
TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       11.08        12.03        56.09        18.25        15.12         4.80 
TCGA-D5-6927 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6854 
        9.44       117.07        98.24         6.18        47.87         0.53 
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-G4-6315 TCGA-G4-6317 
       61.91        36.00 

$`PRKDC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-CK-5912 
       39.06        21.37        15.52        25.08       106.75        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        5.88        63.62        22.09        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 
       32.91        29.19        33.53        23.61        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       22.52        25.08        25.18        21.76        24.69        23.87 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        18.05        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       24.53         5.79        22.42        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        54.61        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       55.92        20.19        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      119.93        35.97        60.79         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        43.04        33.67        13.25 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6626 
       47.41        74.56        85.48        13.78        46.75 

  PRKDC MUTATED PRKDC WILD-TYPE 
           0.53            0.00 
  PRKDC MUTATED PRKDC WILD-TYPE 
         148.01          140.38 
  PRKDC MUTATED PRKDC WILD-TYPE 
          30.26           21.76 
[1] "0.5 - 148.0 (30.3)" "0.0 - 140.4 (21.8)"
[1] "hr=" "1.3"
D27V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKDC MUTATED         9        0        6        23         4         1
  PRKDC WILD-TYPE      55        1       20        85         4         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKDC MUTATED           4          1          5          4        4         0
  PRKDC WILD-TYPE        14          5         39         29       31        12
                 vv
clus              STAGE IVB
  PRKDC MUTATED           0
  PRKDC WILD-TYPE         1
D27V3, multiclass
            clus
vv           PRKDC MUTATED PRKDC WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA             23              85
  STAGE IIB              4               4
  STAGE IIC              1               0
  STAGE III              4              14
  STAGE IIIA             1               5
  STAGE IIIB             5              39
  STAGE IIIC             4              29
  STAGE IV               4              31
  STAGE IVA              0              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
  PRKDC MUTATED     1  10  43   9
  PRKDC WILD-TYPE   8  57 206  32
D27V4, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  T1             1               8
  T2            10              57
  T3            43             206
  T4             9              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
  PRKDC MUTATED    44  11   8
  PRKDC WILD-TYPE 176  70  58
D27V5, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  N0            44             176
  N1            11              70
  N2             8              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"
D27V6, binary
                 cls
clus                0   1
  PRKDC MUTATED    51   4
  PRKDC WILD-TYPE 234  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     51    4
  PRKDC WILD-TYPE  234   44
   clus
vv  PRKDC MUTATED PRKDC WILD-TYPE
  0            51             234
  1             4              44
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus                0   1
  PRKDC MUTATED    28  35
  PRKDC WILD-TYPE 142 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     28   35
  PRKDC WILD-TYPE  142  162
        clus
vv       PRKDC MUTATED PRKDC WILD-TYPE
  FEMALE            28             142
  MALE              35             162
[1] 2 2
[1] FALSE
D27V8, binary
                 cls
clus                0   1
  PRKDC MUTATED    57   0
  PRKDC WILD-TYPE 243   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     57    0
  PRKDC WILD-TYPE  243    8
     clus
vv    PRKDC MUTATED PRKDC WILD-TYPE
  NO             57             243
  YES             0               8
[1] 2 2
[1] FALSE
D27V9, binary
                 cls
clus                0   1
  PRKDC MUTATED    54   9
  PRKDC WILD-TYPE 260  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     54    9
  PRKDC WILD-TYPE  260   39
                               clus
vv                              PRKDC MUTATED PRKDC WILD-TYPE
  COLON ADENOCARCINOMA                     54             260
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKDC MUTATED    47   0   1   5
  PRKDC WILD-TYPE 212   3  21  16
D27V10, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  R0            47             212
  R1             0               3
  R2             1              21
  RX             5              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"
D27V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKDC MUTATED                                  0     3
  PRKDC WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKDC MUTATED                           2    46
  PRKDC WILD-TYPE                        17   130
D27V12, multiclass
                                  clus
vv                                 PRKDC MUTATED PRKDC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       46             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(28) Variable = MGA MUTATION ANALYSIS
D28V1, survival
               sevent
clus2             0   1
  MGA MUTATED    29   6
  MGA WILD-TYPE 248  72
  MGA MUTATED MGA WILD-TYPE 
           35           320 
  MGA MUTATED MGA WILD-TYPE 
            6            72 
$`MGA MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-A024 TCGA-AD-6895 TCGA-A6-5661 TCGA-A6-5665 
        0.92        19.04        39.06        25.08        33.53        22.06 
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3660 
       32.71         8.38        19.66         3.02        63.98        78.08 
TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
        6.97        10.06        35.05         4.01        34.98        35.01 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-5913 
       27.09         0.20        21.44        88.21        12.76        51.32 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 
       22.98        15.02        15.02        17.13        16.14        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6306 
        9.44        11.64        13.35        44.32        44.68 

$`MGA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       26.01        24.00        19.07        38.04        21.99        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6137 
       31.63        30.44        29.19        23.61        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 TCGA-AA-3815 
       11.01         5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-5864 
       29.06        22.03        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MGA MUTATED MGA WILD-TYPE 
          0.2           0.0 
  MGA MUTATED MGA WILD-TYPE 
        88.21        148.01 
  MGA MUTATED MGA WILD-TYPE 
       19.660        22.225 
[1] "0.2 - 88.2 (19.7)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D28V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MGA MUTATED         3        0        7        14         2         1
  MGA WILD-TYPE      61        1       19        94         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGA MUTATED           3          0          4          2        0         0
  MGA WILD-TYPE        15          6         40         31       35        12
               vv
clus            STAGE IVB
  MGA MUTATED           0
  MGA WILD-TYPE         1
D28V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             7            19
  STAGE IIA           14            94
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            3            15
  STAGE IIIA           0             6
  STAGE IIIB           4            40
  STAGE IIIC           2            31
  STAGE IV             0            35
  STAGE IVA            0            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
  MGA MUTATED     1   3  28   5
  MGA WILD-TYPE   8  64 221  36
D28V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1           1             8
  T2           3            64
  T3          28           221
  T4           5            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
  MGA MUTATED    28   5   4
  MGA WILD-TYPE 192  76  62
D28V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  N0          28           192
  N1           5            76
  N2           4            62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
               cls
clus              0   1
  MGA MUTATED    33   0
  MGA WILD-TYPE 252  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     33    0
  MGA WILD-TYPE  252   48
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          33           252
  1           0            48
[1] 2 2
[1] FALSE
D28V7, binary
               cls
clus              0   1
  MGA MUTATED    17  20
  MGA WILD-TYPE 153 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     17   20
  MGA WILD-TYPE  153  177
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          17           153
  MALE            20           177
[1] 2 2
[1] FALSE
D28V8, binary
               cls
clus              0   1
  MGA MUTATED    30   1
  MGA WILD-TYPE 270   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     30    1
  MGA WILD-TYPE  270    7
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           30           270
  YES           1             7
[1] 2 2
[1] FALSE
D28V9, binary
               cls
clus              0   1
  MGA MUTATED    27  10
  MGA WILD-TYPE 287  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     27   10
  MGA WILD-TYPE  287   38
                               clus
vv                              MGA MUTATED MGA WILD-TYPE
  COLON ADENOCARCINOMA                   27           287
  COLON MUCINOUS ADENOCARCINOMA          10            38
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    31   0   0   2
  MGA WILD-TYPE 228   3  22  19
D28V10, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          31           228
  R1           0             3
  R2           0            22
  RX           2            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"
D28V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGA MUTATED                                  0     1
  MGA WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MGA MUTATED                           2    20
  MGA WILD-TYPE                        17   156
D28V12, multiclass
                                  clus
vv                                 MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                     20           156
[1] 4 2
[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 = P2RY13 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  P2RY13 MUTATED    11   2
  P2RY13 WILD-TYPE 266  76
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              13              342 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
               2               76 
$`P2RY13 MUTATED`
TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3713 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3977 
        1.02         6.05        19.04        20.12         6.97        25.02 
TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6678 TCGA-D5-6539 TCGA-DM-A28G TCGA-DM-A28H 
       83.24        12.76        11.01        12.49        60.79       117.07 
TCGA-F4-6569 
       35.74 

$`P2RY13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      135.65       139.17        81.37       119.93        35.97        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  P2RY13 MUTATED P2RY13 WILD-TYPE 
            1.02             0.00 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
          117.07           148.01 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
           19.04            22.09 
[1] "1.0 - 117.1 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D29V2, continuous
                  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      63        1       24       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RY13 MUTATED           0          0          0          1        2
  P2RY13 WILD-TYPE        18          6         44         32       33
                  vv
clus               STAGE IVA STAGE IVB
  P2RY13 MUTATED           1         0
  P2RY13 WILD-TYPE        11         1
D29V3, multiclass
            clus
vv           P2RY13 MUTATED P2RY13 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               1               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
  P2RY13 MUTATED     0   2  10   3
  P2RY13 WILD-TYPE   9  65 239  38
D29V4, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              3               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
  P2RY13 MUTATED    12   1   2
  P2RY13 WILD-TYPE 208  80  64
D29V5, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  N0             12              208
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     9   3
  P2RY13 WILD-TYPE 276  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      9    3
  P2RY13 WILD-TYPE  276   45
   clus
vv  P2RY13 MUTATED P2RY13 WILD-TYPE
  0              9              276
  1              3               45
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     6   9
  P2RY13 WILD-TYPE 164 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      6    9
  P2RY13 WILD-TYPE  164  188
        clus
vv       P2RY13 MUTATED P2RY13 WILD-TYPE
  FEMALE              6              164
  MALE                9              188
[1] 2 2
[1] FALSE
D29V8, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     9   1
  P2RY13 WILD-TYPE 291   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      9    1
  P2RY13 WILD-TYPE  291    7
     clus
vv    P2RY13 MUTATED P2RY13 WILD-TYPE
  NO               9              291
  YES              1                7
[1] 2 2
[1] FALSE
D29V9, binary
                  cls
clus                 0   1
  P2RY13 MUTATED    13   2
  P2RY13 WILD-TYPE 301  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED     13    2
  P2RY13 WILD-TYPE  301   46
                               clus
vv                              P2RY13 MUTATED P2RY13 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  P2RY13 MUTATED     7   0   2   2
  P2RY13 WILD-TYPE 252   3  20  19
D29V10, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              2               20
  RX              2               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"
D29V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  P2RY13 MUTATED                                  0     2
  P2RY13 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  P2RY13 MUTATED                           0     7
  P2RY13 WILD-TYPE                        19   169
D29V12, multiclass
                                  clus
vv                                 P2RY13 MUTATED P2RY13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = MVK MUTATION ANALYSIS
D30V1, survival
               sevent
clus2             0   1
  MVK MUTATED    10   2
  MVK WILD-TYPE 267  76
  MVK MUTATED MVK WILD-TYPE 
           12           343 
  MVK MUTATED MVK WILD-TYPE 
            2            76 
$`MVK MUTATED`
TCGA-AA-3950 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6781 TCGA-AD-5900 TCGA-AD-6889 
       24.00        26.17        22.06        19.66        12.16        83.24 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6540 
       12.76        21.14        37.02        12.00        12.95        16.14 

$`MVK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MVK MUTATED MVK WILD-TYPE 
           12             0 
  MVK MUTATED MVK WILD-TYPE 
        83.24        148.01 
  MVK MUTATED MVK WILD-TYPE 
        20.40         22.09 
[1] "12.0 - 83.2 (20.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D30V2, continuous
               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      60        1       25       102         7         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        18          6         43         32       35        12
               vv
clus            STAGE IVB
  MVK MUTATED           0
  MVK WILD-TYPE         1
D30V3, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              4            60
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            6           102
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  MVK MUTATED     1   3   7   3
  MVK WILD-TYPE   8  64 242  38
D30V4, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  T1           1             8
  T2           3            64
  T3           7           242
  T4           3            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
  MVK MUTATED    12   2   0
  MVK WILD-TYPE 208  79  66
D30V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0          12           208
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
               cls
clus              0   1
  MVK MUTATED    11   0
  MVK WILD-TYPE 274  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     11    0
  MVK WILD-TYPE  274   48
   clus
vv  MVK MUTATED MVK WILD-TYPE
  0          11           274
  1           0            48
[1] 2 2
[1] FALSE
D30V7, binary
               cls
clus              0   1
  MVK MUTATED     7   7
  MVK WILD-TYPE 163 190
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      7    7
  MVK WILD-TYPE  163  190
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           7           163
  MALE             7           190
[1] 2 2
[1] FALSE
D30V8, binary
               cls
clus              0   1
  MVK MUTATED    12   0
  MVK WILD-TYPE 288   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     12    0
  MVK WILD-TYPE  288    8
     clus
vv    MVK MUTATED MVK WILD-TYPE
  NO           12           288
  YES           0             8
[1] 2 2
[1] FALSE
D30V9, binary
               cls
clus              0   1
  MVK MUTATED     8   6
  MVK WILD-TYPE 306  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      8    6
  MVK WILD-TYPE  306   42
                               clus
vv                              MVK MUTATED MVK WILD-TYPE
  COLON ADENOCARCINOMA                    8           306
  COLON MUCINOUS ADENOCARCINOMA           6            42
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MVK MUTATED    11   0   0   3
  MVK WILD-TYPE 248   3  22  18
D30V10, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  R0          11           248
  R1           0             3
  R2           0            22
  RX           3            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"
D30V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MVK MUTATED                                  0     2
  MVK WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MVK MUTATED                           1     9
  MVK WILD-TYPE                        18   167
D30V12, multiclass
                                  clus
vv                                 MVK MUTATED MVK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      9           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(31) Variable = ATXN3L MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  ATXN3L MUTATED    13   4
  ATXN3L WILD-TYPE 264  74
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              17              338 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
               4               74 
$`ATXN3L MUTATED`
TCGA-AA-3713 TCGA-G4-6310 TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3818 
       19.04        63.62        43.76        33.53        23.61         0.99 
TCGA-AA-3947 TCGA-AA-A00N TCGA-AY-6196 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6166 
       33.01         4.01         0.20        22.98        15.02        21.99 
TCGA-D5-6536 TCGA-D5-6930 TCGA-DM-A1HA TCGA-F4-6809 TCGA-G4-6293 
       17.85        13.35       131.51        13.25       133.18 

$`ATXN3L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05        33.04        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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        43.04 
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-G4-6304 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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ATXN3L MUTATED ATXN3L WILD-TYPE 
             0.2              0.0 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
          133.18           148.01 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
          21.990           22.075 
[1] "0.2 - 133.2 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATXN3L MUTATED         1        0        0         5         2         0
  ATXN3L WILD-TYPE      63        1       26       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN3L MUTATED           1          0          2          2        2
  ATXN3L WILD-TYPE        17          6         42         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ATXN3L MUTATED           2         0
  ATXN3L WILD-TYPE        10         1
D31V3, multiclass
            clus
vv           ATXN3L MUTATED ATXN3L WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                2               33
  STAGE IVA               2               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
  ATXN3L MUTATED     0   1  14   2
  ATXN3L WILD-TYPE   9  66 235  39
D31V4, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  T1              0                9
  T2              1               66
  T3             14              235
  T4              2               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
  ATXN3L MUTATED     9   4   4
  ATXN3L WILD-TYPE 211  77  62
D31V5, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  N0              9              211
  N1              4               77
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    12   4
  ATXN3L WILD-TYPE 273  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     12    4
  ATXN3L WILD-TYPE  273   44
   clus
vv  ATXN3L MUTATED ATXN3L WILD-TYPE
  0             12              273
  1              4               44
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  ATXN3L MUTATED     7  10
  ATXN3L WILD-TYPE 163 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED      7   10
  ATXN3L WILD-TYPE  163  187
        clus
vv       ATXN3L MUTATED ATXN3L WILD-TYPE
  FEMALE              7              163
  MALE               10              187
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    11   2
  ATXN3L WILD-TYPE 289   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     11    2
  ATXN3L WILD-TYPE  289    6
     clus
vv    ATXN3L MUTATED ATXN3L WILD-TYPE
  NO              11              289
  YES              2                6
[1] 2 2
[1] FALSE
D31V9, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    13   4
  ATXN3L WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     13    4
  ATXN3L WILD-TYPE  301   44
                               clus
vv                              ATXN3L MUTATED ATXN3L WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATXN3L MUTATED    14   0   1   0
  ATXN3L WILD-TYPE 245   3  21  21
D31V10, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  R0             14              245
  R1              0                3
  R2              1               21
  RX              0               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"
D31V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATXN3L MUTATED                                  0     0
  ATXN3L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATXN3L MUTATED                           1    12
  ATXN3L WILD-TYPE                        18   164
D31V12, multiclass
                                  clus
vv                                 ATXN3L MUTATED ATXN3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = FBXW7 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    75  25
  FBXW7 WILD-TYPE 202  53
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            100             255 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             25              53 
$`FBXW7 MUTATED`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3672 
       24.33        13.02        36.03         0.99        19.99         0.92 
TCGA-AA-3713 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       19.04        39.06        21.37        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-2676 
        1.94        49.08        22.09        26.17        46.65        42.90 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       34.65        32.75        32.91        31.63        30.44        33.53 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6651 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3681 
       27.09        25.08        21.76         1.02        61.02         5.98 
TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 
       33.04        17.98        15.95        38.99         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3949 TCGA-AA-3982 TCGA-AA-A01K TCGA-AA-A01Q 
        0.00         0.00        26.01        27.02        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 
       35.01        37.02        18.05        12.16        83.24         5.79 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
       27.09        17.82        62.79        88.21        49.41        12.76 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 
       10.06       148.01        85.45        15.62        51.32        82.95 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
        2.01        20.02        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6171 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6532 
        5.03        15.02        14.04        11.08        11.08        18.25 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58         7.53        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 
       13.35        12.00        10.26        24.43       130.65        49.91 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28G TCGA-DM-A28H 
        7.50        44.32       135.65       139.17        60.79       117.07 
TCGA-F4-6703 TCGA-F4-6704 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.87         1.55       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       55.04        85.48        61.91        36.00 

$`FBXW7 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        24.16         1.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       19.07        34.03        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        6.05        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AD-6888 TCGA-AD-6895 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 
       15.52        25.08         5.88        63.62        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 
       79.69        43.76        43.76        42.28        16.57        33.34 
TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       36.53        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       22.52         8.38        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3842 
       10.06        35.05         0.99        25.02         1.02        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        38.07         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
        1.02        26.01        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-6890 
       14.01         0.92        41.00        39.98        40.96        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 
       12.20        14.30        17.56        21.99        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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 
       25.48        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        12.39        10.13        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28K 
      140.38       131.51        81.37       119.93        35.97        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 
        8.61        31.96        35.74         6.18        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6323 TCGA-G4-6626 
       74.56        13.78        46.75 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
              0               0 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         148.01          140.38 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         24.755          21.990 
[1] "0.0 - 148.0 (24.8)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D32V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXW7 MUTATED        15        0        9        32         4         0
  FBXW7 WILD-TYPE      49        1       17        76         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED           8          1         13         12        5         2
  FBXW7 WILD-TYPE        10          5         31         21       30        10
                 vv
clus              STAGE IVB
  FBXW7 MUTATED           0
  FBXW7 WILD-TYPE         1
D32V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               15              49
  STAGE IA               0               1
  STAGE II               9              17
  STAGE IIA             32              76
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              8              10
  STAGE IIIA             1               5
  STAGE IIIB            13              31
  STAGE IIIC            12              21
  STAGE IV               5              30
  STAGE IVA              2              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
  FBXW7 MUTATED     1  17  76   9
  FBXW7 WILD-TYPE   8  50 173  32
D32V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             1               8
  T2            17              50
  T3            76             173
  T4             9              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
  FBXW7 MUTATED    62  25  16
  FBXW7 WILD-TYPE 158  56  50
D32V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            62             158
  N1            25              56
  N2            16              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"
D32V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    83   7
  FBXW7 WILD-TYPE 202  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     83    7
  FBXW7 WILD-TYPE  202   41
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            83             202
  1             7              41
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    56  47
  FBXW7 WILD-TYPE 114 150
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     56   47
  FBXW7 WILD-TYPE  114  150
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            56             114
  MALE              47             150
[1] 2 2
[1] FALSE
D32V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    81   2
  FBXW7 WILD-TYPE 219   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     81    2
  FBXW7 WILD-TYPE  219    6
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             81             219
  YES             2               6
[1] 2 2
[1] FALSE
D32V9, binary
                 cls
clus                0   1
  FBXW7 MUTATED    82  20
  FBXW7 WILD-TYPE 232  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     82   20
  FBXW7 WILD-TYPE  232   28
                               clus
vv                              FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON ADENOCARCINOMA                     82             232
  COLON MUCINOUS ADENOCARCINOMA            20              28
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    71   1   1   8
  FBXW7 WILD-TYPE 188   2  21  13
D32V10, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            71             188
  R1             1               2
  R2             1              21
  RX             8              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"
D32V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  1     3
  FBXW7 WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED                           5    67
  FBXW7 WILD-TYPE                        14   109
D32V12, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       67             109
[1] 4 2
[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 = DIP2B MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  DIP2B MUTATED    22   3
  DIP2B WILD-TYPE 255  75
  DIP2B MUTATED DIP2B WILD-TYPE 
             25             330 
  DIP2B MUTATED DIP2B WILD-TYPE 
              3              75 
$`DIP2B MUTATED`
TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3672 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-5661 
        1.02         6.05         0.92        26.17        46.65        33.53 
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3517 TCGA-AA-3973 TCGA-AA-A00J TCGA-AA-A00N 
       22.06        20.12        38.99        13.05        18.05         4.01 
TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5254 TCGA-CK-4952 
       34.98        33.01        58.39        88.21        12.69        15.62 
TCGA-D5-6926 TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6323 
        9.04         6.18        33.67        55.04        61.91        13.78 
TCGA-G4-6626 
       46.75 

$`DIP2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        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-A6-5662 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6317 
       74.56        65.85        53.62        44.68        85.48        36.00 

  DIP2B MUTATED DIP2B WILD-TYPE 
           0.92            0.00 
  DIP2B MUTATED DIP2B WILD-TYPE 
          88.21          148.01 
  DIP2B MUTATED DIP2B WILD-TYPE 
          22.06           22.06 
[1] "0.9 - 88.2 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D33V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIP2B MUTATED         2        1        1        10         2         0
  DIP2B WILD-TYPE      62        0       25        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DIP2B MUTATED           1          0          4          1        4         1
  DIP2B WILD-TYPE        17          6         40         32       31        11
                 vv
clus              STAGE IVB
  DIP2B MUTATED           0
  DIP2B WILD-TYPE         1
D33V3, multiclass
            clus
vv           DIP2B MUTATED DIP2B WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               4              31
  STAGE IVA              1              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
  DIP2B MUTATED     2   0  16   8
  DIP2B WILD-TYPE   7  67 233  33
D33V4, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  T1             2               7
  T2             0              67
  T3            16             233
  T4             8              33
[1] 4 2
[1] TRUE
[1] "dimension 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    16   8   3
  DIP2B WILD-TYPE 204  73  63
D33V5, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  N0            16             204
  N1             8              73
  N2             3              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"
D33V6, binary
                 cls
clus                0   1
  DIP2B MUTATED    20   5
  DIP2B WILD-TYPE 265  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     20    5
  DIP2B WILD-TYPE  265   43
   clus
vv  DIP2B MUTATED DIP2B WILD-TYPE
  0            20             265
  1             5              43
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  DIP2B MUTATED    17  10
  DIP2B WILD-TYPE 153 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     17   10
  DIP2B WILD-TYPE  153  187
        clus
vv       DIP2B MUTATED DIP2B WILD-TYPE
  FEMALE            17             153
  MALE              10             187
[1] 2 2
[1] FALSE
D33V8, binary
                 cls
clus                0   1
  DIP2B MUTATED    21   1
  DIP2B WILD-TYPE 279   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     21    1
  DIP2B WILD-TYPE  279    7
     clus
vv    DIP2B MUTATED DIP2B WILD-TYPE
  NO             21             279
  YES             1               7
[1] 2 2
[1] FALSE
D33V9, binary
                 cls
clus                0   1
  DIP2B MUTATED    22   5
  DIP2B WILD-TYPE 292  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     22    5
  DIP2B WILD-TYPE  292   43
                               clus
vv                              DIP2B MUTATED DIP2B WILD-TYPE
  COLON ADENOCARCINOMA                     22             292
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DIP2B MUTATED    20   0   3   2
  DIP2B WILD-TYPE 239   3  19  19
D33V10, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  R0            20             239
  R1             0               3
  R2             3              19
  RX             2              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"
D33V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIP2B MUTATED                                  0     1
  DIP2B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DIP2B MUTATED                           3    13
  DIP2B WILD-TYPE                        16   163
D33V12, multiclass
                                  clus
vv                                 DIP2B MUTATED DIP2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       13             163
[1] 4 2
[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 = RBMX MUTATION ANALYSIS
D34V1, survival
                sevent
clus2              0   1
  RBMX MUTATED    17   0
  RBMX WILD-TYPE 260  78
  RBMX MUTATED RBMX WILD-TYPE 
            17            338 
  RBMX MUTATED RBMX WILD-TYPE 
             0             78 
$`RBMX MUTATED`
TCGA-G4-6628 TCGA-A6-5656 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6780 TCGA-A6-6781 
       79.69        32.91        22.09        25.08        20.12        19.66 
TCGA-AA-3549 TCGA-AD-5900 TCGA-CA-6717 TCGA-D5-6898 TCGA-D5-7000 TCGA-DM-A1HB 
       21.01        12.16        12.76         7.53        10.26       135.65 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6855 TCGA-F4-6856 
      117.07        98.24        47.87        47.41        35.31 

$`RBMX WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        33.99        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
       12.39        10.13        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        13.41        13.35        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-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RBMX MUTATED RBMX WILD-TYPE 
          7.53           0.00 
  RBMX MUTATED RBMX WILD-TYPE 
        135.65         148.01 
  RBMX MUTATED RBMX WILD-TYPE 
         25.08          22.01 
[1] "7.5 - 135.7 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.8e+07"
D34V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBMX MUTATED         7        0        0         5         1         0
  RBMX WILD-TYPE      57        1       26       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBMX MUTATED           0          0          1          3        0         1
  RBMX WILD-TYPE        18          6         43         30       35        11
                vv
clus             STAGE IVB
  RBMX MUTATED           0
  RBMX WILD-TYPE         1
D34V3, multiclass
            clus
vv           RBMX MUTATED RBMX WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            3             30
  STAGE IV              0             35
  STAGE IVA             1             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
  RBMX MUTATED     0   7   8   3
  RBMX WILD-TYPE   9  60 241  38
D34V4, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  T1            0              9
  T2            7             60
  T3            8            241
  T4            3             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
  RBMX MUTATED    13   3   2
  RBMX WILD-TYPE 207  78  64
D34V5, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  N0           13            207
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                cls
clus               0   1
  RBMX MUTATED    12   1
  RBMX WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     12    1
  RBMX WILD-TYPE  273   47
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D34V7, binary
                cls
clus               0   1
  RBMX MUTATED     5  13
  RBMX WILD-TYPE 165 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      5   13
  RBMX WILD-TYPE  165  184
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            5            165
  MALE             13            184
[1] 2 2
[1] FALSE
D34V8, binary
                cls
clus               0   1
  RBMX MUTATED    13   1
  RBMX WILD-TYPE 287   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     13    1
  RBMX WILD-TYPE  287    7
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO            13            287
  YES            1              7
[1] 2 2
[1] FALSE
D34V9, binary
                cls
clus               0   1
  RBMX MUTATED    10   7
  RBMX WILD-TYPE 304  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     10    7
  RBMX WILD-TYPE  304   41
                               clus
vv                              RBMX MUTATED RBMX WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBMX MUTATED     9   0   0   2
  RBMX WILD-TYPE 250   3  22  19
D34V10, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            2             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"
D34V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBMX MUTATED                                  0     1
  RBMX WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED                           1    15
  RBMX WILD-TYPE                        18   161
D34V12, multiclass
                                  clus
vv                                 RBMX MUTATED RBMX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      15            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(35) Variable = SMAD2 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED    11   4
  SMAD2 WILD-TYPE 266  74
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             340 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              4              74 
$`SMAD2 MUTATED`
TCGA-AA-3520 TCGA-AA-A024 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3696 
       24.03        39.06        20.12        63.98         6.97         5.03 
TCGA-AA-3842 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A029 
       37.02        53.00        25.02         4.01         1.02        51.98 
TCGA-AZ-6600 TCGA-CM-6168 TCGA-CM-6169 
       12.10        12.99        13.02 

$`SMAD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3710 
       47.01        15.02        11.01         5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A02F 
       35.01         1.02        33.04        26.01        37.02        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           1.02            0.00 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          63.98          148.01 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
         20.120          22.075 
[1] "1.0 - 64.0 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D35V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAD2 MUTATED         1        0        6         3         1         0
  SMAD2 WILD-TYPE      63        1       20       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED           0          1          0          0        3         0
  SMAD2 WILD-TYPE        18          5         44         33       32        12
                 vv
clus              STAGE IVB
  SMAD2 MUTATED           0
  SMAD2 WILD-TYPE         1
D35V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              0              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
  SMAD2 MUTATED     0   3  10   3
  SMAD2 WILD-TYPE   9  64 239  38
D35V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             3              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
  SMAD2 MUTATED    12   3   1
  SMAD2 WILD-TYPE 208  78  65
D35V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0            12             208
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                 cls
clus                0   1
  SMAD2 MUTATED    11   3
  SMAD2 WILD-TYPE 274  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     11    3
  SMAD2 WILD-TYPE  274   45
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0            11             274
  1             3              45
[1] 2 2
[1] FALSE
D35V7, binary
                 cls
clus                0   1
  SMAD2 MUTATED     4  12
  SMAD2 WILD-TYPE 166 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      4   12
  SMAD2 WILD-TYPE  166  185
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             4             166
  MALE              12             185
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED    13   0
  SMAD2 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     13    0
  SMAD2 WILD-TYPE  287    8
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D35V9, binary
                 cls
clus                0   1
  SMAD2 MUTATED    12   4
  SMAD2 WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     12    4
  SMAD2 WILD-TYPE  302   44
                               clus
vv                              SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED    11   0   2   0
  SMAD2 WILD-TYPE 248   3  20  21
D35V10, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             2              20
  RX             0              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"
D35V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD2 MUTATED                                  0     0
  SMAD2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD2 MUTATED                           3     1
  SMAD2 WILD-TYPE                        16   175
D35V12, multiclass
                                  clus
vv                                 SMAD2 MUTATED SMAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        1             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(36) Variable = ASXL1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED    27  12
  ASXL1 WILD-TYPE 250  66
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             39             316 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             12              66 
$`ASXL1 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-5657 
        0.92        19.04        10.88       100.01        79.69        31.63 
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3561 TCGA-AA-3680 
       29.19        22.06        63.98        12.99        13.94        11.01 
TCGA-AA-3864 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6901 TCGA-AU-6004 
       53.00        30.02        34.98        12.16        22.42        27.09 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6718 TCGA-CA-6719 
       58.39         1.41        88.21         6.77        10.06        14.30 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5540 
       32.02        15.02        29.03        15.02        11.01        56.09 
TCGA-D5-6535 TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6809 
       15.12       139.17        35.97         6.18        41.42        13.25 
TCGA-G4-6304 TCGA-G4-6323 TCGA-G4-6626 
       53.62        13.78        46.75 

$`ASXL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5656 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        32.91        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        20.98        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-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       24.53         5.79        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 
        0.95        33.01         0.20        21.44        17.82         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        12.76        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5862 TCGA-CM-5863 
       29.06        22.03        22.98        30.08         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        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       21.99        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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        54.61        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        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-A28G TCGA-DM-A28H TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 
       55.04        85.48        61.91        36.00 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           0.92            0.00 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         139.17          148.01 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          22.42           22.01 
[1] "0.9 - 139.2 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D36V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASXL1 MUTATED         8        1        4        13         2         0
  ASXL1 WILD-TYPE      56        0       22        95         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASXL1 MUTATED           1          0          4          2        2         1
  ASXL1 WILD-TYPE        17          6         40         31       33        11
                 vv
clus              STAGE IVB
  ASXL1 MUTATED           0
  ASXL1 WILD-TYPE         1
D36V3, multiclass
            clus
vv           ASXL1 MUTATED ASXL1 WILD-TYPE
  STAGE I                8              56
  STAGE IA               1               0
  STAGE II               4              22
  STAGE IIA             13              95
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              1              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
  ASXL1 MUTATED     1   7  26   5
  ASXL1 WILD-TYPE   8  60 223  36
D36V4, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  T1             1               8
  T2             7              60
  T3            26             223
  T4             5              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
  ASXL1 MUTATED    29   6   5
  ASXL1 WILD-TYPE 191  75  61
D36V5, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  N0            29             191
  N1             6              75
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                 cls
clus                0   1
  ASXL1 MUTATED    30   3
  ASXL1 WILD-TYPE 255  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     30    3
  ASXL1 WILD-TYPE  255   45
   clus
vv  ASXL1 MUTATED ASXL1 WILD-TYPE
  0            30             255
  1             3              45
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus                0   1
  ASXL1 MUTATED    16  24
  ASXL1 WILD-TYPE 154 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     16   24
  ASXL1 WILD-TYPE  154  173
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE            16             154
  MALE              24             173
[1] 2 2
[1] FALSE
D36V8, binary
                 cls
clus                0   1
  ASXL1 MUTATED    36   0
  ASXL1 WILD-TYPE 264   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     36    0
  ASXL1 WILD-TYPE  264    8
     clus
vv    ASXL1 MUTATED ASXL1 WILD-TYPE
  NO             36             264
  YES             0               8
[1] 2 2
[1] FALSE
D36V9, binary
                 cls
clus                0   1
  ASXL1 MUTATED    39   1
  ASXL1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     39    1
  ASXL1 WILD-TYPE  275   47
                               clus
vv                              ASXL1 MUTATED ASXL1 WILD-TYPE
  COLON ADENOCARCINOMA                     39             275
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASXL1 MUTATED    26   0   1   4
  ASXL1 WILD-TYPE 233   3  21  17
D36V10, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  R0            26             233
  R1             0               3
  R2             1              21
  RX             4              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"
D36V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL1 MUTATED                                  0     2
  ASXL1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED                           3    26
  ASXL1 WILD-TYPE                        16   150
D36V12, multiclass
                                  clus
vv                                 ASXL1 MUTATED ASXL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       26             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(37) Variable = ALG12 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  ALG12 MUTATED     5   2
  ALG12 WILD-TYPE 272  76
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             348 
  ALG12 MUTATED ALG12 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.075 
[1] "8.0 - 135.7 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D37V2, continuous
                 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      63        1       25       107         8         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        18          6         42         33       33        12
                 vv
clus              STAGE IVB
  ALG12 MUTATED           0
  ALG12 WILD-TYPE         1
D37V3, multiclass
            clus
vv           ALG12 MUTATED ALG12 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  ALG12 MUTATED     0   1   5   1
  ALG12 WILD-TYPE   9  66 244  40
D37V4, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             1              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
  ALG12 MUTATED     4   2   1
  ALG12 WILD-TYPE 216  79  65
D37V5, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                 cls
clus                0   1
  ALG12 MUTATED     4   2
  ALG12 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      4    2
  ALG12 WILD-TYPE  281   46
   clus
vv  ALG12 MUTATED ALG12 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D37V7, binary
                 cls
clus                0   1
  ALG12 MUTATED     2   5
  ALG12 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      2    5
  ALG12 WILD-TYPE  168  192
        clus
vv       ALG12 MUTATED ALG12 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D37V8, binary
                 cls
clus                0   1
  ALG12 MUTATED     5   1
  ALG12 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      5    1
  ALG12 WILD-TYPE  295    7
     clus
vv    ALG12 MUTATED ALG12 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D37V9, binary
                 cls
clus                0   1
  ALG12 MUTATED     5   1
  ALG12 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      5    1
  ALG12 WILD-TYPE  309   47
                               clus
vv                              ALG12 MUTATED ALG12 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALG12 MUTATED     3   0   2   0
  ALG12 WILD-TYPE 256   3  20  21
D37V10, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             2              20
  RX             0              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"
D37V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG12 MUTATED                                  0     0
  ALG12 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALG12 MUTATED                           1     3
  ALG12 WILD-TYPE                        18   173
D37V12, multiclass
                                  clus
vv                                 ALG12 MUTATED ALG12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = NR1H3 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  NR1H3 MUTATED    12   2
  NR1H3 WILD-TYPE 265  76
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             14             341 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              2              76 
$`NR1H3 MUTATED`
TCGA-G4-6628 TCGA-A6-6648 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00R 
       79.69        25.18        78.08        53.00        18.05         0.99 
TCGA-AA-A02J TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6674 
        5.03        51.32        21.14        14.04        14.04        12.95 
TCGA-D5-6536 TCGA-G4-6309 
       17.85        85.48 

$`NR1H3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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-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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  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          22.090 
[1] "1.0 - 85.5 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D38V2, continuous
                 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      58        1       24       105         8         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        18          6         42         33       34        11
                 vv
clus              STAGE IVB
  NR1H3 MUTATED           0
  NR1H3 WILD-TYPE         1
D38V3, multiclass
            clus
vv           NR1H3 MUTATED NR1H3 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  NR1H3 MUTATED     2   4   8   1
  NR1H3 WILD-TYPE   7  63 241  40
D38V4, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  T1             2               7
  T2             4              63
  T3             8             241
  T4             1              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
  NR1H3 MUTATED    13   2   0
  NR1H3 WILD-TYPE 207  79  66
D38V5, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  N0            13             207
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                 cls
clus                0   1
  NR1H3 MUTATED    11   2
  NR1H3 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     11    2
  NR1H3 WILD-TYPE  274   46
   clus
vv  NR1H3 MUTATED NR1H3 WILD-TYPE
  0            11             274
  1             2              46
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus                0   1
  NR1H3 MUTATED     7   8
  NR1H3 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED      7    8
  NR1H3 WILD-TYPE  163  189
        clus
vv       NR1H3 MUTATED NR1H3 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D38V8, binary
                 cls
clus                0   1
  NR1H3 MUTATED    12   0
  NR1H3 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     12    0
  NR1H3 WILD-TYPE  288    8
     clus
vv    NR1H3 MUTATED NR1H3 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D38V9, binary
                 cls
clus                0   1
  NR1H3 MUTATED    14   1
  NR1H3 WILD-TYPE 300  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     14    1
  NR1H3 WILD-TYPE  300   47
                               clus
vv                              NR1H3 MUTATED NR1H3 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NR1H3 MUTATED    10   0   1   3
  NR1H3 WILD-TYPE 249   3  21  18
D38V10, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             1              21
  RX             3              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"
D38V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR1H3 MUTATED                                  0     0
  NR1H3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR1H3 MUTATED                           1     9
  NR1H3 WILD-TYPE                        18   167
D38V12, multiclass
                                  clus
vv                                 NR1H3 MUTATED NR1H3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(39) Variable = ZBTB20 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    15   4
  ZBTB20 WILD-TYPE 262  74
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              19              336 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               4               74 
$`ZBTB20 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6653 
        0.92        24.00        10.88        26.17        33.53        24.39 
TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3966 TCGA-AY-6197 
       20.12         6.97        33.04         0.00         2.01        21.44 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6922 TCGA-F4-6570 
       51.32        21.14        14.04        17.13        10.13         6.18 
TCGA-F4-6856 
       35.31 

$`ZBTB20 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       15.62        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               0                0 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           51.32           148.01 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          20.120           22.225 
[1] "0.0 - 51.3 (20.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.4"
D39V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB20 MUTATED         4        0        1        10         1         0
  ZBTB20 WILD-TYPE      60        1       25        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           1          1          1          0        0
  ZBTB20 WILD-TYPE        17          5         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB20 MUTATED           0         0
  ZBTB20 WILD-TYPE        12         1
D39V3, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              10               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZBTB20 MUTATED     1   3  14   2
  ZBTB20 WILD-TYPE   8  64 235  39
D39V4, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             14              235
  T4              2               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
  ZBTB20 MUTATED    16   2   2
  ZBTB20 WILD-TYPE 204  79  64
D39V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0             16              204
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    15   0
  ZBTB20 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     15    0
  ZBTB20 WILD-TYPE  270   48
   clus
vv  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  0             15              270
  1              0               48
[1] 2 2
[1] FALSE
D39V7, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    13   7
  ZBTB20 WILD-TYPE 157 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     13    7
  ZBTB20 WILD-TYPE  157  190
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE             13              157
  MALE                7              190
[1] 2 2
[1] FALSE
D39V8, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    17   0
  ZBTB20 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     17    0
  ZBTB20 WILD-TYPE  283    8
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D39V9, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    16   4
  ZBTB20 WILD-TYPE 298  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     16    4
  ZBTB20 WILD-TYPE  298   44
                               clus
vv                              ZBTB20 MUTATED ZBTB20 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB20 MUTATED    13   0   0   3
  ZBTB20 WILD-TYPE 246   3  22  18
D39V10, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              3               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"
D39V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB20 MUTATED                                  0     0
  ZBTB20 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB20 MUTATED                           1    13
  ZBTB20 WILD-TYPE                        18   163
D39V12, multiclass
                                  clus
vv                                 ZBTB20 MUTATED ZBTB20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        13              163
[1] 4 2
[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 = MPHOSPH10 MUTATION ANALYSIS
D40V1, survival
                     sevent
clus2                   0   1
  MPHOSPH10 MUTATED    12   5
  MPHOSPH10 WILD-TYPE 265  73
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 17                 338 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                  5                  73 
$`MPHOSPH10 MUTATED`
TCGA-AD-6895 TCGA-AD-6964 TCGA-DM-A285 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6781 
       25.08        10.88         5.88        21.76        20.12        19.66 
TCGA-AA-A00K TCGA-AD-6901 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 
       18.05        22.42        27.09        21.44        58.39        49.41 
TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5344 TCGA-D5-6927 
       10.06       124.27        23.05        22.03         9.44 

$`MPHOSPH10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        21.37        15.52       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       51.32        21.99        21.14        82.95         2.01        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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
               5.88                0.00 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
             124.27              148.01 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
              21.76               22.09 
[1] "5.9 - 124.3 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D40V2, continuous
                     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      62        1       25       100         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MPHOSPH10 MUTATED           0          0          3          1        1
  MPHOSPH10 WILD-TYPE        18          6         41         32       34
                     vv
clus                  STAGE IVA STAGE IVB
  MPHOSPH10 MUTATED           0         0
  MPHOSPH10 WILD-TYPE        12         1
D40V3, multiclass
            clus
vv           MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  8                 100
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 3                  41
  STAGE IIIC                 1                  32
  STAGE IV                   1                  34
  STAGE IVA                  0                  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
  MPHOSPH10 MUTATED     0   2  14   2
  MPHOSPH10 WILD-TYPE   9  65 235  39
D40V4, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  T1                 0                   9
  T2                 2                  65
  T3                14                 235
  T4                 2                  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
  MPHOSPH10 MUTATED    12   4   2
  MPHOSPH10 WILD-TYPE 208  77  64
D40V5, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  N0                12                 208
  N1                 4                  77
  N2                 2                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED     9   1
  MPHOSPH10 WILD-TYPE 276  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED      9    1
  MPHOSPH10 WILD-TYPE  276   47
   clus
vv  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  0                 9                 276
  1                 1                  47
[1] 2 2
[1] FALSE
D40V7, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED     7  11
  MPHOSPH10 WILD-TYPE 163 186
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED      7   11
  MPHOSPH10 WILD-TYPE  163  186
        clus
vv       MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  FEMALE                 7                 163
  MALE                  11                 186
[1] 2 2
[1] FALSE
D40V8, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED    14   0
  MPHOSPH10 WILD-TYPE 286   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED     14    0
  MPHOSPH10 WILD-TYPE  286    8
     clus
vv    MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  NO                 14                 286
  YES                 0                   8
[1] 2 2
[1] FALSE
D40V9, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED    14   4
  MPHOSPH10 WILD-TYPE 300  44
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED     14    4
  MPHOSPH10 WILD-TYPE  300   44
                               clus
vv                              MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  COLON ADENOCARCINOMA                         14                 300
  COLON MUCINOUS ADENOCARCINOMA                 4                  44
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  MPHOSPH10 MUTATED    10   0   0   2
  MPHOSPH10 WILD-TYPE 249   3  22  19
D40V10, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  R0                10                 249
  R1                 0                   3
  R2                 0                  22
  RX                 2                  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"
D40V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPHOSPH10 MUTATED                                  0     1
  MPHOSPH10 WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  MPHOSPH10 MUTATED                           0    15
  MPHOSPH10 WILD-TYPE                        19   161
D40V12, multiclass
                                  clus
vv                                 MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                   9
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                           15                 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(41) Variable = TPRKB MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  TPRKB MUTATED     8   2
  TPRKB WILD-TYPE 269  76
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             345 
  TPRKB MUTATED TPRKB WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.090 
[1] "10.3 - 100.0 (16.4)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.3"
D41V2, continuous
                 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      63        1       25       104         8         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        18          5         42         32       35        12
                 vv
clus              STAGE IVB
  TPRKB MUTATED           0
  TPRKB WILD-TYPE         1
D41V3, multiclass
            clus
vv           TPRKB MUTATED TPRKB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TPRKB MUTATED     0   1   8   1
  TPRKB WILD-TYPE   9  66 241  40
D41V4, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             1              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
  TPRKB MUTATED     6   2   2
  TPRKB WILD-TYPE 214  79  64
D41V5, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  N0             6             214
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                 cls
clus                0   1
  TPRKB MUTATED    10   0
  TPRKB WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED     10    0
  TPRKB WILD-TYPE  275   48
   clus
vv  TPRKB MUTATED TPRKB WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  TPRKB MUTATED     4   6
  TPRKB WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED      4    6
  TPRKB WILD-TYPE  166  191
        clus
vv       TPRKB MUTATED TPRKB WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D41V8, binary
                 cls
clus                0   1
  TPRKB MUTATED     8   0
  TPRKB WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED      8    0
  TPRKB WILD-TYPE  292    8
     clus
vv    TPRKB MUTATED TPRKB WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D41V9, binary
                 cls
clus                0   1
  TPRKB MUTATED     5   5
  TPRKB WILD-TYPE 309  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED      5    5
  TPRKB WILD-TYPE  309   43
                               clus
vv                              TPRKB MUTATED TPRKB WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TPRKB MUTATED     6   0   0   2
  TPRKB WILD-TYPE 253   3  22  19
D41V10, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D41V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPRKB MUTATED                                  0     1
  TPRKB WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TPRKB MUTATED                           0     9
  TPRKB WILD-TYPE                        19   167
D41V12, multiclass
                                  clus
vv                                 TPRKB MUTATED TPRKB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(42) Variable = PLAGL2 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2                0   1
  PLAGL2 MUTATED     5   1
  PLAGL2 WILD-TYPE 272  77
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              349 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               1               77 
$`PLAGL2 MUTATED`
TCGA-AA-3713 TCGA-G4-6586 TCGA-A6-5665 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-4743 
       19.04        35.80        22.06        21.44        49.41        23.05 

$`PLAGL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.030 
[1] "19.0 - 49.4 (22.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D42V2, continuous
                  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      64        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAGL2 MUTATED           0          0          0          0        1
  PLAGL2 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PLAGL2 MUTATED           0         0
  PLAGL2 WILD-TYPE        12         1
D42V3, multiclass
            clus
vv           PLAGL2 MUTATED PLAGL2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  PLAGL2 MUTATED     0   0   6   0
  PLAGL2 WILD-TYPE   9  67 243  41
D42V4, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              0               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
  PLAGL2 MUTATED     6   0   0
  PLAGL2 WILD-TYPE 214  81  66
D42V5, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     3   1
  PLAGL2 WILD-TYPE 282  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      3    1
  PLAGL2 WILD-TYPE  282   47
   clus
vv  PLAGL2 MUTATED PLAGL2 WILD-TYPE
  0              3              282
  1              1               47
[1] 2 2
[1] FALSE
D42V7, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     3   3
  PLAGL2 WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      3    3
  PLAGL2 WILD-TYPE  167  194
        clus
vv       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D42V8, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     5   1
  PLAGL2 WILD-TYPE 295   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      5    1
  PLAGL2 WILD-TYPE  295    7
     clus
vv    PLAGL2 MUTATED PLAGL2 WILD-TYPE
  NO               5              295
  YES              1                7
[1] 2 2
[1] FALSE
D42V9, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     6   0
  PLAGL2 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      6    0
  PLAGL2 WILD-TYPE  308   48
                               clus
vv                              PLAGL2 MUTATED PLAGL2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PLAGL2 MUTATED     4   0   1   0
  PLAGL2 WILD-TYPE 255   3  21  21
D42V10, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              1               21
  RX              0               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"
D42V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLAGL2 MUTATED                                  0     0
  PLAGL2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLAGL2 MUTATED                           0     5
  PLAGL2 WILD-TYPE                        19   171
D42V12, multiclass
                                  clus
vv                                 PLAGL2 MUTATED PLAGL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = IDH1 MUTATION ANALYSIS
D43V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED    14   4
  IDH1 WILD-TYPE 263  74
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            337 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             74 
$`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        12.16        83.24        17.82 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6168 
       49.41        12.10        12.39         2.01        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        10.13       139.17        31.96 

$`IDH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00         2.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
        0.92        41.00        39.98        18.05        40.96        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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        12.36 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
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        14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        56.09        18.25        25.48        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 
        7.53        12.39        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  IDH1 MUTATED IDH1 WILD-TYPE 
          2.01           0.00 
  IDH1 MUTATED IDH1 WILD-TYPE 
        139.17         148.01 
  IDH1 MUTATED IDH1 WILD-TYPE 
         21.62          22.06 
[1] "2.0 - 139.2 (21.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D43V2, continuous
                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      63        1       25       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDH1 MUTATED           0          1          4          0        2         0
  IDH1 WILD-TYPE        18          5         40         33       33        12
                vv
clus             STAGE IVB
  IDH1 MUTATED           0
  IDH1 WILD-TYPE         1
D43V3, multiclass
            clus
vv           IDH1 MUTATED IDH1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  IDH1 MUTATED     0   1  15   2
  IDH1 WILD-TYPE   9  66 234  39
D43V4, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           15            234
  T4            2             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
  IDH1 MUTATED    11   7   0
  IDH1 WILD-TYPE 209  74  66
D43V5, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  N0           11            209
  N1            7             74
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                cls
clus               0   1
  IDH1 MUTATED    14   2
  IDH1 WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     14    2
  IDH1 WILD-TYPE  271   46
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0           14            271
  1            2             46
[1] 2 2
[1] FALSE
D43V7, binary
                cls
clus               0   1
  IDH1 MUTATED    11   7
  IDH1 WILD-TYPE 159 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     11    7
  IDH1 WILD-TYPE  159  190
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE           11            159
  MALE              7            190
[1] 2 2
[1] FALSE
D43V8, binary
                cls
clus               0   1
  IDH1 MUTATED    17   0
  IDH1 WILD-TYPE 283   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     17    0
  IDH1 WILD-TYPE  283    8
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO            17            283
  YES            0              8
[1] 2 2
[1] FALSE
D43V9, binary
                cls
clus               0   1
  IDH1 MUTATED    12   6
  IDH1 WILD-TYPE 302  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     12    6
  IDH1 WILD-TYPE  302   42
                               clus
vv                              IDH1 MUTATED IDH1 WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED    14   0   0   1
  IDH1 WILD-TYPE 245   3  22  20
D43V10, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            0             22
  RX            1             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"
D43V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH1 MUTATED                                  0     2
  IDH1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED                           3    10
  IDH1 WILD-TYPE                        16   166
D43V12, multiclass
                                  clus
vv                                 IDH1 MUTATED IDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      10            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(44) Variable = SETD2 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    32   8
  SETD2 WILD-TYPE 245  70
  SETD2 MUTATED SETD2 WILD-TYPE 
             40             315 
  SETD2 MUTATED SETD2 WILD-TYPE 
              8              70 
$`SETD2 MUTATED`
TCGA-AA-3525 TCGA-AA-3543 TCGA-AD-6548 TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5664 
        8.05         0.99        21.37        46.65        30.44        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3851 
       22.06         8.38         6.97        11.01        26.99        33.07 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       30.02         4.01        83.24        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        14.04 
TCGA-CM-6171 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6540 
       14.04        12.03        54.61        56.09        18.25        16.14 
TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 
       35.97         6.18        34.42        13.25 

$`SETD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       37.05        36.03        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        79.69        43.76        43.76        42.90        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-A6-5666 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 
       14.50        16.31         0.95        33.01         0.20         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       17.56       148.01        21.99        21.14        82.95         2.01 
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-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-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-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-D5-5537 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.01        10.06        45.40        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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-F4-6806 TCGA-F4-6807 
       31.96        35.74        47.87         1.55        41.42        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.99            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
         124.27          148.01 
  SETD2 MUTATED SETD2 WILD-TYPE 
         21.735          22.360 
[1] "1.0 - 124.3 (21.7)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D44V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETD2 MUTATED         9        0        1        18         1         0
  SETD2 WILD-TYPE      55        1       25        90         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD2 MUTATED           0          0          8          2        1         1
  SETD2 WILD-TYPE        18          6         36         31       34        11
                 vv
clus              STAGE IVB
  SETD2 MUTATED           0
  SETD2 WILD-TYPE         1
D44V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             18              90
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             8              36
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  SETD2 MUTATED     1   8  28   4
  SETD2 WILD-TYPE   8  59 221  37
D44V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             1               8
  T2             8              59
  T3            28             221
  T4             4              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
  SETD2 MUTATED    29   8   4
  SETD2 WILD-TYPE 191  73  62
D44V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            29             191
  N1             8              73
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    34   2
  SETD2 WILD-TYPE 251  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     34    2
  SETD2 WILD-TYPE  251   46
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            34             251
  1             2              46
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    20  21
  SETD2 WILD-TYPE 150 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     20   21
  SETD2 WILD-TYPE  150  176
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            20             150
  MALE              21             176
[1] 2 2
[1] FALSE
D44V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    36   0
  SETD2 WILD-TYPE 264   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     36    0
  SETD2 WILD-TYPE  264    8
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO             36             264
  YES             0               8
[1] 2 2
[1] FALSE
D44V9, binary
                 cls
clus                0   1
  SETD2 MUTATED    34   7
  SETD2 WILD-TYPE 280  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     34    7
  SETD2 WILD-TYPE  280   41
                               clus
vv                              SETD2 MUTATED SETD2 WILD-TYPE
  COLON ADENOCARCINOMA                     34             280
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    31   1   1   4
  SETD2 WILD-TYPE 228   2  21  17
D44V10, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            31             228
  R1             1               2
  R2             1              21
  RX             4              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"
D44V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     2
  SETD2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           4    26
  SETD2 WILD-TYPE                        15   150
D44V12, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       26             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(45) Variable = GPATCH8 MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  GPATCH8 MUTATED    12   2
  GPATCH8 WILD-TYPE 265  76
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               341 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
                2                76 
$`GPATCH8 MUTATED`
TCGA-AA-3713 TCGA-G4-6321 TCGA-G4-6586 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3811 
       19.04        22.09        35.80        24.39        19.66        10.06 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 
       33.01        25.02        12.16        27.09        58.39        49.41 
TCGA-CA-6717 TCGA-CM-5860 
       12.76        32.02 

$`GPATCH8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6588 
      100.01         1.94        49.08         5.88        63.62        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            10.06              0.00 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            58.39            148.01 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
           24.705            21.990 
[1] "10.1 - 58.4 (24.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPATCH8 MUTATED         3        0        1         4         1         0
  GPATCH8 WILD-TYPE      61        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH8 MUTATED           2          0          0          1        1
  GPATCH8 WILD-TYPE        16          6         44         32       34
                   vv
clus                STAGE IVA STAGE IVB
  GPATCH8 MUTATED           0         0
  GPATCH8 WILD-TYPE        12         1
D45V3, multiclass
            clus
vv           GPATCH8 MUTATED GPATCH8 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  GPATCH8 MUTATED     0   5   7   2
  GPATCH8 WILD-TYPE   9  62 242  39
D45V4, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3               7               242
  T4               2                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
  GPATCH8 MUTATED    11   2   1
  GPATCH8 WILD-TYPE 209  79  65
D45V5, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  N0              11               209
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     8   1
  GPATCH8 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      8    1
  GPATCH8 WILD-TYPE  277   47
   clus
vv  GPATCH8 MUTATED GPATCH8 WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     6   8
  GPATCH8 WILD-TYPE 164 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      6    8
  GPATCH8 WILD-TYPE  164  189
        clus
vv       GPATCH8 MUTATED GPATCH8 WILD-TYPE
  FEMALE               6               164
  MALE                 8               189
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    12   1
  GPATCH8 WILD-TYPE 288   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     12    1
  GPATCH8 WILD-TYPE  288    7
     clus
vv    GPATCH8 MUTATED GPATCH8 WILD-TYPE
  NO               12               288
  YES               1                 7
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    10   4
  GPATCH8 WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     10    4
  GPATCH8 WILD-TYPE  304   44
                               clus
vv                              GPATCH8 MUTATED GPATCH8 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GPATCH8 MUTATED     9   0   1   1
  GPATCH8 WILD-TYPE 250   3  21  20
D45V10, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               1                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"
D45V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPATCH8 MUTATED                                  0     1
  GPATCH8 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GPATCH8 MUTATED                           0     9
  GPATCH8 WILD-TYPE                        19   167
D45V12, multiclass
                                  clus
vv                                 GPATCH8 MUTATED GPATCH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(46) Variable = ALPK2 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    34   7
  ALPK2 WILD-TYPE 243  71
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             41             314 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              7              71 
$`ALPK2 MUTATED`
TCGA-AA-3525 TCGA-AA-3697 TCGA-AA-3844 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-5666 
        8.05        85.05        14.93        26.17        33.53        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 
       27.09         8.38        25.18        20.12        19.66         3.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       78.08         6.97         1.02        25.02         4.01        34.98 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 
       12.16        27.09        21.44        49.41         6.77        12.36 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 
       12.76        10.06        15.62        23.05        20.02        13.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       15.02        12.00        12.99        15.02        14.04        11.01 
TCGA-D5-5540 TCGA-D5-6540 TCGA-DM-A28G TCGA-F4-6809 TCGA-G4-6309 
       56.09        16.14        60.79        13.25        85.48 

$`ALPK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        19.04        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       22.52        25.08        21.76        24.69        24.39        23.87 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 
       24.00        29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        12.10        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        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-4747 
       21.14        82.95         2.01       124.27        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-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6675 
       16.04        21.99        14.99        13.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-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 
       54.61        19.59        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           1.02            0.00 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          85.48          148.01 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          15.62           22.75 
[1] "1.0 - 85.5 (15.6)"  "0.0 - 148.0 (22.8)"
[1] "hr=" "1.2"
D46V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALPK2 MUTATED         8        0        5        15         2         1
  ALPK2 WILD-TYPE      56        1       21        93         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALPK2 MUTATED           0          0          5          3        0         2
  ALPK2 WILD-TYPE        18          6         39         30       35        10
                 vv
clus              STAGE IVB
  ALPK2 MUTATED           0
  ALPK2 WILD-TYPE         1
D46V3, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  STAGE I                8              56
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             15              93
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              2              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
  ALPK2 MUTATED     0   9  28   5
  ALPK2 WILD-TYPE   9  58 221  36
D46V4, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  T1             0               9
  T2             9              58
  T3            28             221
  T4             5              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
  ALPK2 MUTATED    33   7   2
  ALPK2 WILD-TYPE 187  74  64
D46V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0            33             187
  N1             7              74
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                 cls
clus                0   1
  ALPK2 MUTATED    33   2
  ALPK2 WILD-TYPE 252  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     33    2
  ALPK2 WILD-TYPE  252   46
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            33             252
  1             2              46
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED    19  23
  ALPK2 WILD-TYPE 151 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     19   23
  ALPK2 WILD-TYPE  151  174
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  FEMALE            19             151
  MALE              23             174
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus                0   1
  ALPK2 MUTATED    35   2
  ALPK2 WILD-TYPE 265   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     35    2
  ALPK2 WILD-TYPE  265    6
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             35             265
  YES             2               6
[1] 2 2
[1] FALSE
D46V9, binary
                 cls
clus                0   1
  ALPK2 MUTATED    33   9
  ALPK2 WILD-TYPE 281  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     33    9
  ALPK2 WILD-TYPE  281   39
                               clus
vv                              ALPK2 MUTATED ALPK2 WILD-TYPE
  COLON ADENOCARCINOMA                     33             281
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALPK2 MUTATED    29   0   0   4
  ALPK2 WILD-TYPE 230   3  22  17
D46V10, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            29             230
  R1             0               3
  R2             0              22
  RX             4              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"
D46V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALPK2 MUTATED                                  0     3
  ALPK2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALPK2 MUTATED                           5    23
  ALPK2 WILD-TYPE                        14   153
D46V12, multiclass
                                  clus
vv                                 ALPK2 MUTATED ALPK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       23             153
[1] 4 2
[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 = C11ORF30 MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                  0   1
  C11ORF30 MUTATED    16   4
  C11ORF30 WILD-TYPE 261  74
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                20                335 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                 4                 74 
$`C11ORF30 MUTATED`
TCGA-AA-3554 TCGA-AA-3672 TCGA-AD-6895 TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6780 
       17.95         0.92        25.08        35.80        22.06        20.12 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 
       33.01        26.01        25.02         4.01        83.24        58.39 
TCGA-AZ-6599 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6161 TCGA-D5-6541 TCGA-D5-6927 
        6.77        12.59        12.76        15.02        15.58         9.44 
TCGA-DM-A0XD TCGA-F4-6807 
       24.43        43.04 

$`C11ORF30 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.39        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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-F4-6808 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
              0.92               0.00 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
             83.24             148.01 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
             21.09              22.09 
[1] "0.9 - 83.2 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D47V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C11ORF30 MUTATED         2        0        0        11         2         0
  C11ORF30 WILD-TYPE      62        1       26        97         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF30 MUTATED           1          0          3          1        0
  C11ORF30 WILD-TYPE        17          6         41         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C11ORF30 MUTATED           0         0
  C11ORF30 WILD-TYPE        12         1
D47V3, multiclass
            clus
vv           C11ORF30 MUTATED C11ORF30 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                11                 97
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C11ORF30 MUTATED     0   3  16   2
  C11ORF30 WILD-TYPE   9  64 233  39
D47V4, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3               16                233
  T4                2                 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
  C11ORF30 MUTATED    16   4   1
  C11ORF30 WILD-TYPE 204  77  65
D47V5, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  N0               16                204
  N1                4                 77
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    18   0
  C11ORF30 WILD-TYPE 267  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     18    0
  C11ORF30 WILD-TYPE  267   48
   clus
vv  C11ORF30 MUTATED C11ORF30 WILD-TYPE
  0               18                267
  1                0                 48
[1] 2 2
[1] FALSE
D47V7, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED     9  12
  C11ORF30 WILD-TYPE 161 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED      9   12
  C11ORF30 WILD-TYPE  161  185
        clus
vv       C11ORF30 MUTATED C11ORF30 WILD-TYPE
  FEMALE                9                161
  MALE                 12                185
[1] 2 2
[1] FALSE
D47V8, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    18   0
  C11ORF30 WILD-TYPE 282   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     18    0
  C11ORF30 WILD-TYPE  282    8
     clus
vv    C11ORF30 MUTATED C11ORF30 WILD-TYPE
  NO                18                282
  YES                0                  8
[1] 2 2
[1] FALSE
D47V9, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    16   5
  C11ORF30 WILD-TYPE 298  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     16    5
  C11ORF30 WILD-TYPE  298   43
                               clus
vv                              C11ORF30 MUTATED C11ORF30 WILD-TYPE
  COLON ADENOCARCINOMA                        16                298
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C11ORF30 MUTATED    15   0   0   2
  C11ORF30 WILD-TYPE 244   3  22  19
D47V10, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  R0               15                244
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D47V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C11ORF30 MUTATED                                  0     3
  C11ORF30 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C11ORF30 MUTATED                           0    11
  C11ORF30 WILD-TYPE                        19   165
D47V12, multiclass
                                  clus
vv                                 C11ORF30 MUTATED C11ORF30 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          11                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(48) Variable = RPTN MUTATION ANALYSIS
D48V1, survival
                sevent
clus2              0   1
  RPTN MUTATED    12   1
  RPTN WILD-TYPE 265  77
  RPTN MUTATED RPTN WILD-TYPE 
            13            342 
  RPTN MUTATED RPTN WILD-TYPE 
             1             77 
$`RPTN MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6628 TCGA-AA-3663 TCGA-CA-6716 TCGA-CA-6717 
       19.04       100.01        79.69         6.97        12.20        12.76 
TCGA-CM-5344 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6679 TCGA-D5-6932 TCGA-F4-6704 
       22.03        21.99        14.04        10.06        11.38         1.55 
TCGA-G4-6323 
       13.78 

$`RPTN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
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-6172 TCGA-CM-6674 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  RPTN MUTATED RPTN WILD-TYPE 
          1.55           0.00 
  RPTN MUTATED RPTN WILD-TYPE 
        100.01         148.01 
  RPTN MUTATED RPTN WILD-TYPE 
         13.78          22.47 
[1] "1.6 - 100.0 (13.8)" "0.0 - 148.0 (22.5)"
[1] "hr=" "2.8"
D48V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPTN MUTATED         3        1        2         4         0         0
  RPTN WILD-TYPE      61        0       24       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPTN MUTATED           0          0          1          1        1         0
  RPTN WILD-TYPE        18          6         43         32       34        12
                vv
clus             STAGE IVB
  RPTN MUTATED           0
  RPTN WILD-TYPE         1
D48V3, multiclass
            clus
vv           RPTN MUTATED RPTN WILD-TYPE
  STAGE I               3             61
  STAGE IA              1              0
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  RPTN MUTATED     0   3   9   0
  RPTN WILD-TYPE   9  64 240  41
D48V4, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  T1            0              9
  T2            3             64
  T3            9            240
  T4            0             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
  RPTN MUTATED    11   1   1
  RPTN WILD-TYPE 209  80  65
D48V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0           11            209
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                cls
clus               0   1
  RPTN MUTATED    10   1
  RPTN WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     10    1
  RPTN WILD-TYPE  275   47
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D48V7, binary
                cls
clus               0   1
  RPTN MUTATED     3  10
  RPTN WILD-TYPE 167 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      3   10
  RPTN WILD-TYPE  167  187
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE            3            167
  MALE             10            187
[1] 2 2
[1] FALSE
D48V8, binary
                cls
clus               0   1
  RPTN MUTATED    11   1
  RPTN WILD-TYPE 289   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     11    1
  RPTN WILD-TYPE  289    7
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO            11            289
  YES            1              7
[1] 2 2
[1] FALSE
D48V9, binary
                cls
clus               0   1
  RPTN MUTATED    11   2
  RPTN WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     11    2
  RPTN WILD-TYPE  303   46
                               clus
vv                              RPTN MUTATED RPTN WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RPTN MUTATED     9   0   1   2
  RPTN WILD-TYPE 250   3  21  19
D48V10, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0            9            250
  R1            0              3
  R2            1             21
  RX            2             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"
D48V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPTN MUTATED                                  1     2
  RPTN WILD-TYPE                                0     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED                           1     7
  RPTN WILD-TYPE                        18   169
D48V12, multiclass
                                  clus
vv                                 RPTN MUTATED RPTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = ROS1 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  ROS1 MUTATED    36   8
  ROS1 WILD-TYPE 241  70
  ROS1 MUTATED ROS1 WILD-TYPE 
            44            311 
  ROS1 MUTATED ROS1 WILD-TYPE 
             8             70 
$`ROS1 MUTATED`
TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 
        1.02         6.05         0.92        24.00        25.08        10.88 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3510 
       22.09        35.80        26.17        31.63        19.66        63.98 
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3977 
       29.95         6.97         1.02        53.00        18.05        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 
        4.01        34.98        26.47        14.50        27.09         0.20 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 
       58.39        88.21        49.41        12.10         3.19        12.76 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6165 
       10.06        15.62        21.14        23.05        22.03        16.04 
TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6541 TCGA-F4-6570 
       14.04        25.48        15.12        17.13        15.58         6.18 
TCGA-F4-6856 TCGA-G4-6317 
       35.31        36.00 

$`ROS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       24.00        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
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-6599 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        22.36        62.79         6.77        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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       12.20        14.30        17.56       148.01        85.45        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99        82.95         2.01       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-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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        54.61 
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-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        12.49        16.14         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        13.78        46.75 

  ROS1 MUTATED ROS1 WILD-TYPE 
           0.2            0.0 
  ROS1 MUTATED ROS1 WILD-TYPE 
         88.21         148.01 
  ROS1 MUTATED ROS1 WILD-TYPE 
         20.40          22.36 
[1] "0.2 - 88.2 (20.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1"  
D49V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ROS1 MUTATED         7        0        6        13         2         0
  ROS1 WILD-TYPE      57        1       20        95         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ROS1 MUTATED           3          0          5          5        3         0
  ROS1 WILD-TYPE        15          6         39         28       32        12
                vv
clus             STAGE IVB
  ROS1 MUTATED           0
  ROS1 WILD-TYPE         1
D49V3, multiclass
            clus
vv           ROS1 MUTATED ROS1 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA            13             95
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            5             39
  STAGE IIIC            5             28
  STAGE IV              3             32
  STAGE IVA             0             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
  ROS1 MUTATED     3   6  27  11
  ROS1 WILD-TYPE   6  61 222  30
D49V4, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  T1            3              6
  T2            6             61
  T3           27            222
  T4           11             30
[1] 4 2
[1] TRUE
[1] "dimension 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    30   8   9
  ROS1 WILD-TYPE 190  73  57
D49V5, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  N0           30            190
  N1            8             73
  N2            9             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                cls
clus               0   1
  ROS1 MUTATED    36   3
  ROS1 WILD-TYPE 249  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     36    3
  ROS1 WILD-TYPE  249   45
   clus
vv  ROS1 MUTATED ROS1 WILD-TYPE
  0           36            249
  1            3             45
[1] 2 2
[1] FALSE
D49V7, binary
                cls
clus               0   1
  ROS1 MUTATED    26  21
  ROS1 WILD-TYPE 144 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     26   21
  ROS1 WILD-TYPE  144  176
        clus
vv       ROS1 MUTATED ROS1 WILD-TYPE
  FEMALE           26            144
  MALE             21            176
[1] 2 2
[1] FALSE
D49V8, binary
                cls
clus               0   1
  ROS1 MUTATED    39   0
  ROS1 WILD-TYPE 261   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     39    0
  ROS1 WILD-TYPE  261    8
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  NO            39            261
  YES            0              8
[1] 2 2
[1] FALSE
D49V9, binary
                cls
clus               0   1
  ROS1 MUTATED    38   9
  ROS1 WILD-TYPE 276  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     38    9
  ROS1 WILD-TYPE  276   39
                               clus
vv                              ROS1 MUTATED ROS1 WILD-TYPE
  COLON ADENOCARCINOMA                    38            276
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ROS1 MUTATED    34   1   1   5
  ROS1 WILD-TYPE 225   2  21  16
D49V10, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  R0           34            225
  R1            1              2
  R2            1             21
  RX            5             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"
D49V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ROS1 MUTATED                                  0     2
  ROS1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ROS1 MUTATED                           2    27
  ROS1 WILD-TYPE                        17   149
D49V12, multiclass
                                  clus
vv                                 ROS1 MUTATED ROS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      27            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(50) Variable = EGR1 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  EGR1 MUTATED     8   1
  EGR1 WILD-TYPE 269  77
  EGR1 MUTATED EGR1 WILD-TYPE 
             9            346 
  EGR1 MUTATED EGR1 WILD-TYPE 
             1             77 
$`EGR1 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3877 
       26.17        79.69        22.06        20.12         6.97        31.00 
TCGA-AA-3994 TCGA-AZ-6598 TCGA-CM-4743 
       27.02        49.41        23.05 

$`EGR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  EGR1 MUTATED EGR1 WILD-TYPE 
          6.97           0.00 
  EGR1 MUTATED EGR1 WILD-TYPE 
         79.69         148.01 
  EGR1 MUTATED EGR1 WILD-TYPE 
         26.17          21.99 
[1] "7.0 - 79.7 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D50V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EGR1 MUTATED         2        0        2         4         0         0
  EGR1 WILD-TYPE      62        1       24       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EGR1 MUTATED           0          0          1          0        0         0
  EGR1 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  EGR1 MUTATED           0
  EGR1 WILD-TYPE         1
D50V3, multiclass
            clus
vv           EGR1 MUTATED EGR1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  EGR1 MUTATED     1   1   7   0
  EGR1 WILD-TYPE   8  66 242  41
D50V4, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            7            242
  T4            0             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
  EGR1 MUTATED     8   1   0
  EGR1 WILD-TYPE 212  80  66
D50V5, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                cls
clus               0   1
  EGR1 MUTATED     7   0
  EGR1 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      7    0
  EGR1 WILD-TYPE  278   48
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D50V7, binary
                cls
clus               0   1
  EGR1 MUTATED     4   5
  EGR1 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      4    5
  EGR1 WILD-TYPE  166  192
        clus
vv       EGR1 MUTATED EGR1 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D50V8, binary
                cls
clus               0   1
  EGR1 MUTATED     9   0
  EGR1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      9    0
  EGR1 WILD-TYPE  291    8
     clus
vv    EGR1 MUTATED EGR1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D50V9, binary
                cls
clus               0   1
  EGR1 MUTATED     6   3
  EGR1 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      6    3
  EGR1 WILD-TYPE  308   45
                               clus
vv                              EGR1 MUTATED EGR1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EGR1 MUTATED     7   0   0   0
  EGR1 WILD-TYPE 252   3  22  21
D50V10, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            0             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"
D50V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGR1 MUTATED                                  0     0
  EGR1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGR1 MUTATED                           0     6
  EGR1 WILD-TYPE                        19   170
D50V12, multiclass
                                  clus
vv                                 EGR1 MUTATED EGR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = PTEN MUTATION ANALYSIS
D51V1, survival
                sevent
clus2              0   1
  PTEN MUTATED   119  31
  PTEN WILD-TYPE 158  47
  PTEN MUTATED PTEN WILD-TYPE 
           150            205 
  PTEN MUTATED PTEN WILD-TYPE 
            31             47 
$`PTEN MUTATED`
TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6888 
       24.16         1.02        36.00        19.04        24.00        15.52 
TCGA-AD-6895 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6586 TCGA-G4-6588 
       25.08       100.01         1.94        49.08        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       91.79        79.69        43.76        32.75        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3655 
       25.18        21.76        24.69        19.66        35.01        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3968 TCGA-AA-3977 
       78.08         6.97        33.04        53.00        21.99        25.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-6004 
       34.98        12.16        83.24        22.42        26.47        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 
       33.01        21.44        17.82        58.39        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 
       12.69        12.36        12.39        12.20        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 
        2.01        23.05        37.02        25.02        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-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-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       11.08        11.01        12.03        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        25.48        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         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.44        11.64        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA 
      119.70        24.43        38.20        49.91        12.59         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-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       35.97        60.79        98.24        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

$`PTEN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-4681 
       38.04        21.99        39.06        21.37        10.88       106.75 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.88        63.62        22.09        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5665 
       42.28        16.57        34.65        33.34        36.53        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6653 TCGA-A6-6654 
       27.09        22.52         8.38        25.08        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       20.12        20.28         7.04         3.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       33.01        26.01        20.98        34.03         2.01        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-4070 
       40.96        24.53         5.79        27.42        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6607 
        0.95         0.20         1.41         5.13        12.10         3.19 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6751 
       12.59        12.59        12.76        14.30        21.14       124.27 
TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 
       20.02        13.02        29.06        15.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6541 
       12.95        10.06        45.40        54.61        56.09        15.58 
TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.39         9.04        13.35        12.00       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       13.32       140.38       117.07         8.61        31.96         1.55 
TCGA-G4-6304 
       53.62 

  PTEN MUTATED PTEN WILD-TYPE 
          0.53           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
        148.01         140.38 
  PTEN MUTATED PTEN WILD-TYPE 
         24.56          20.02 
[1] "0.5 - 148.0 (24.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D51V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTEN MUTATED        25        1        8        48         3         1
  PTEN WILD-TYPE      39        0       18        60         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTEN MUTATED           3          3         23         12        8        10
  PTEN WILD-TYPE        15          3         21         21       27         2
                vv
clus             STAGE IVB
  PTEN MUTATED           1
  PTEN WILD-TYPE         0
D51V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I              25             39
  STAGE IA              1              0
  STAGE II              8             18
  STAGE IIA            48             60
  STAGE IIB             3              5
  STAGE IIC             1              0
  STAGE III             3             15
  STAGE IIIA            3              3
  STAGE IIIB           23             21
  STAGE IIIC           12             21
  STAGE IV              8             27
  STAGE IVA            10              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
  PTEN MUTATED     2  27 108  15
  PTEN WILD-TYPE   7  40 141  26
D51V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            2              7
  T2           27             40
  T3          108            141
  T4           15             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
  PTEN MUTATED    95  39  19
  PTEN WILD-TYPE 125  42  47
D51V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           95            125
  N1           39             42
  N2           19             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                cls
clus               0   1
  PTEN MUTATED   112  19
  PTEN WILD-TYPE 173  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    112   19
  PTEN WILD-TYPE  173   29
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0          112            173
  1           19             29
[1] 2 2
[1] FALSE
D51V7, binary
                cls
clus               0   1
  PTEN MUTATED    72  81
  PTEN WILD-TYPE  98 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     72   81
  PTEN WILD-TYPE   98  116
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           72             98
  MALE             81            116
[1] 2 2
[1] FALSE
D51V8, binary
                cls
clus               0   1
  PTEN MUTATED   128   3
  PTEN WILD-TYPE 172   5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    128    3
  PTEN WILD-TYPE  172    5
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO           128            172
  YES            3              5
[1] 2 2
[1] FALSE
D51V9, binary
                cls
clus               0   1
  PTEN MUTATED   133  18
  PTEN WILD-TYPE 181  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    133   18
  PTEN WILD-TYPE  181   30
                               clus
vv                              PTEN MUTATED PTEN WILD-TYPE
  COLON ADENOCARCINOMA                   133            181
  COLON MUCINOUS ADENOCARCINOMA           18             30
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED   100   2   2  14
  PTEN WILD-TYPE 159   1  20   7
D51V10, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0          100            159
  R1            2              1
  R2            2             20
  RX           14              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"
D51V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     6
  PTEN WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                          15   118
  PTEN WILD-TYPE                         4    58
D51V12, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       6              4
  BLACK OR AFRICAN AMERICAN                  15              4
  WHITE                                     118             58
[1] 4 2
[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 = CTNNB1 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    52  19
  CTNNB1 WILD-TYPE 225  59
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              71              284 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19               59 
$`CTNNB1 MUTATED`
TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 
        1.02         6.05        85.05        10.88       100.01         1.94 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2678 TCGA-A6-5660 
       35.80        26.17        91.79        79.69        42.28        29.19 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3655 
       33.53        22.06        20.12        63.98        29.00        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3831 TCGA-AA-A00N TCGA-AA-A00U 
       78.08         6.97         5.03        17.98         4.01        17.03 
TCGA-AA-A01K TCGA-AD-6901 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
       31.00        22.42        14.50        58.39        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5916 
        6.77         5.23        12.76        10.06        15.62        21.14 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 
       23.05        20.02        25.02        13.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       32.02        14.04        29.03        14.99        12.99        14.04 
TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       13.05        56.09        25.48        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       17.13        16.14        15.58        38.20        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6854 TCGA-F4-6855 
       13.32        44.32        35.74        47.87         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       35.31        65.85        61.91        13.78        46.75 

$`CTNNB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       15.52        25.08       106.75        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 
       22.09        43.76        46.65        43.76        42.90        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-A6-5662 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 
       21.01        24.00        29.95        20.98        13.94        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-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        27.09        16.31         0.95        33.01         0.20 
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-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
      124.27        37.02        29.06        22.98        15.02         5.03 
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-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       21.99        13.02        15.02        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        54.61 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6539 
       19.59        55.92        20.19        18.25        43.27        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1D9 
       10.26       119.70        24.43       130.65        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       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-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       13.25       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6317 
       85.48        36.00 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.53             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          100.01           148.01 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           22.42            21.99 
[1] "0.5 - 100.0 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D52V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTNNB1 MUTATED        11        1        8        29         2         0
  CTNNB1 WILD-TYPE      53        0       18        79         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNB1 MUTATED           1          1          7          5        4
  CTNNB1 WILD-TYPE        17          5         37         28       31
                  vv
clus               STAGE IVA STAGE IVB
  CTNNB1 MUTATED           1         1
  CTNNB1 WILD-TYPE        11         0
D52V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                11               53
  STAGE IA                1                0
  STAGE II                8               18
  STAGE IIA              29               79
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              7               37
  STAGE IIIC              5               28
  STAGE IV                4               31
  STAGE IVA               1               11
  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     3   9  53   8
  CTNNB1 WILD-TYPE   6  58 196  33
D52V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              3                6
  T2              9               58
  T3             53              196
  T4              8               33
[1] 4 2
[1] TRUE
[1] "dimension 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    53  11  10
  CTNNB1 WILD-TYPE 167  70  56
D52V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0             53              167
  N1             11               70
  N2             10               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    58   6
  CTNNB1 WILD-TYPE 227  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     58    6
  CTNNB1 WILD-TYPE  227   42
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             58              227
  1              6               42
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    32  42
  CTNNB1 WILD-TYPE 138 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     32   42
  CTNNB1 WILD-TYPE  138  155
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             32              138
  MALE               42              155
[1] 2 2
[1] FALSE
D52V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    63   0
  CTNNB1 WILD-TYPE 237   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     63    0
  CTNNB1 WILD-TYPE  237    8
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              63              237
  YES              0                8
[1] 2 2
[1] FALSE
D52V9, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    65   7
  CTNNB1 WILD-TYPE 249  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     65    7
  CTNNB1 WILD-TYPE  249   41
                               clus
vv                              CTNNB1 MUTATED CTNNB1 WILD-TYPE
  COLON ADENOCARCINOMA                      65              249
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    50   0   2   7
  CTNNB1 WILD-TYPE 209   3  20  14
D52V10, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             50              209
  R1              0                3
  R2              2               20
  RX              7               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"
D52V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  0     2
  CTNNB1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           7    51
  CTNNB1 WILD-TYPE                        12   125
D52V12, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     7               12
  WHITE                                        51              125
[1] 4 2
[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 = RBM44 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  RBM44 MUTATED    10   2
  RBM44 WILD-TYPE 267  76
  RBM44 MUTATED RBM44 WILD-TYPE 
             12             343 
  RBM44 MUTATED RBM44 WILD-TYPE 
              2              76 
$`RBM44 MUTATED`
TCGA-AA-3672 TCGA-G4-6588 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 
        0.92        26.17         8.38        24.39        19.66        63.98 
TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-4746 TCGA-F4-6703 
       10.06         4.01        34.98        12.76        37.02        47.87 

$`RBM44 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RBM44 MUTATED RBM44 WILD-TYPE 
           0.92            0.00 
  RBM44 MUTATED RBM44 WILD-TYPE 
          63.98          148.01 
  RBM44 MUTATED RBM44 WILD-TYPE 
         22.025          22.060 
[1] "0.9 - 64.0 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D53V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM44 MUTATED         2        0        1         5         2         0
  RBM44 WILD-TYPE      62        1       25       103         6         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        16          6         44         32       35        12
                 vv
clus              STAGE IVB
  RBM44 MUTATED           0
  RBM44 WILD-TYPE         1
D53V3, multiclass
            clus
vv           RBM44 MUTATED RBM44 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RBM44 MUTATED     0   2   8   3
  RBM44 WILD-TYPE   9  65 241  38
D53V4, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             3              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
  RBM44 MUTATED    10   2   1
  RBM44 WILD-TYPE 210  79  65
D53V5, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                 cls
clus                0   1
  RBM44 MUTATED    12   0
  RBM44 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     12    0
  RBM44 WILD-TYPE  273   48
   clus
vv  RBM44 MUTATED RBM44 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D53V7, binary
                 cls
clus                0   1
  RBM44 MUTATED     5   8
  RBM44 WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED      5    8
  RBM44 WILD-TYPE  165  189
        clus
vv       RBM44 MUTATED RBM44 WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D53V8, binary
                 cls
clus                0   1
  RBM44 MUTATED    11   0
  RBM44 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     11    0
  RBM44 WILD-TYPE  289    8
     clus
vv    RBM44 MUTATED RBM44 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D53V9, binary
                 cls
clus                0   1
  RBM44 MUTATED    10   3
  RBM44 WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     10    3
  RBM44 WILD-TYPE  304   45
                               clus
vv                              RBM44 MUTATED RBM44 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBM44 MUTATED    10   0   0   1
  RBM44 WILD-TYPE 249   3  22  20
D53V10, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             1              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"
D53V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM44 MUTATED                                  0     1
  RBM44 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM44 MUTATED                           2     4
  RBM44 WILD-TYPE                        17   172
D53V12, multiclass
                                  clus
vv                                 RBM44 MUTATED RBM44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = ECT2 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  ECT2 MUTATED    13   5
  ECT2 WILD-TYPE 264  73
  ECT2 MUTATED ECT2 WILD-TYPE 
            18            337 
  ECT2 MUTATED ECT2 WILD-TYPE 
             5             73 
$`ECT2 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6608 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-2672 
       19.04        24.00         1.94        35.80        79.69        46.65 
TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-A00D TCGA-AA-A00N TCGA-AZ-5403 TCGA-CK-5913 
       42.90        19.66        19.00         4.01        62.79        51.32 
TCGA-CM-5861 TCGA-CM-6170 TCGA-D5-6926 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       15.02        15.02         9.04        65.85        53.62        85.48 

$`ECT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       74.56        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ECT2 MUTATED ECT2 WILD-TYPE 
          1.94           0.00 
  ECT2 MUTATED ECT2 WILD-TYPE 
         85.48         148.01 
  ECT2 MUTATED ECT2 WILD-TYPE 
         29.90          22.03 
[1] "1.9 - 85.5 (29.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D54V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ECT2 MUTATED         3        0        1         4         3         0
  ECT2 WILD-TYPE      61        1       25       104         5         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        18          5         41         32       33        12
                vv
clus             STAGE IVB
  ECT2 MUTATED           0
  ECT2 WILD-TYPE         1
D54V3, multiclass
            clus
vv           ECT2 MUTATED ECT2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  ECT2 MUTATED     0   4   9   5
  ECT2 WILD-TYPE   9  63 240  36
D54V4, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  T1            0              9
  T2            4             63
  T3            9            240
  T4            5             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
  ECT2 MUTATED    12   6   0
  ECT2 WILD-TYPE 208  75  66
D54V5, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  N0           12            208
  N1            6             75
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                cls
clus               0   1
  ECT2 MUTATED    13   2
  ECT2 WILD-TYPE 272  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     13    2
  ECT2 WILD-TYPE  272   46
   clus
vv  ECT2 MUTATED ECT2 WILD-TYPE
  0           13            272
  1            2             46
[1] 2 2
[1] FALSE
D54V7, binary
                cls
clus               0   1
  ECT2 MUTATED    11   7
  ECT2 WILD-TYPE 159 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     11    7
  ECT2 WILD-TYPE  159  190
        clus
vv       ECT2 MUTATED ECT2 WILD-TYPE
  FEMALE           11            159
  MALE              7            190
[1] 2 2
[1] FALSE
D54V8, binary
                cls
clus               0   1
  ECT2 MUTATED    15   2
  ECT2 WILD-TYPE 285   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     15    2
  ECT2 WILD-TYPE  285    6
     clus
vv    ECT2 MUTATED ECT2 WILD-TYPE
  NO            15            285
  YES            2              6
[1] 2 2
[1] FALSE
D54V9, binary
                cls
clus               0   1
  ECT2 MUTATED    15   3
  ECT2 WILD-TYPE 299  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     15    3
  ECT2 WILD-TYPE  299   45
                               clus
vv                              ECT2 MUTATED ECT2 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ECT2 MUTATED    14   0   1   1
  ECT2 WILD-TYPE 245   3  21  20
D54V10, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            1             21
  RX            1             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"
D54V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ECT2 MUTATED                                  0     0
  ECT2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ECT2 MUTATED                           1    13
  ECT2 WILD-TYPE                        18   163
D54V12, multiclass
                                  clus
vv                                 ECT2 MUTATED ECT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      13            163
[1] 4 2
[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 = DDX26B MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  DDX26B MUTATED    12   2
  DDX26B WILD-TYPE 265  76
  DDX26B MUTATED DDX26B WILD-TYPE 
              14              341 
  DDX26B MUTATED DDX26B WILD-TYPE 
               2               76 
$`DDX26B MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 
       19.04        24.00        35.80        33.53        22.06        20.12 
TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6162 TCGA-CM-6674 
       27.09        12.76        51.32        21.14        12.00        12.95 
TCGA-D5-6536 TCGA-F4-6570 
       17.85         6.18 

$`DDX26B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DDX26B MUTATED DDX26B WILD-TYPE 
            6.18             0.00 
  DDX26B MUTATED DDX26B WILD-TYPE 
           51.32           148.01 
  DDX26B MUTATED DDX26B WILD-TYPE 
           20.63            22.09 
[1] "6.2 - 51.3 (20.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D55V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX26B MUTATED         2        0        0        10         1         0
  DDX26B WILD-TYPE      62        1       26        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX26B MUTATED           0          0          1          0        1
  DDX26B WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  DDX26B MUTATED           0         0
  DDX26B WILD-TYPE        12         1
D55V3, multiclass
            clus
vv           DDX26B MUTATED DDX26B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA              10               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  DDX26B MUTATED     1   1  12   1
  DDX26B WILD-TYPE   8  66 237  40
D55V4, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  T1              1                8
  T2              1               66
  T3             12              237
  T4              1               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
  DDX26B MUTATED    14   1   0
  DDX26B WILD-TYPE 206  80  66
D55V5, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  N0             14              206
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                  cls
clus                 0   1
  DDX26B MUTATED    11   1
  DDX26B WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     11    1
  DDX26B WILD-TYPE  274   47
   clus
vv  DDX26B MUTATED DDX26B WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  DDX26B MUTATED    10   5
  DDX26B WILD-TYPE 160 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     10    5
  DDX26B WILD-TYPE  160  192
        clus
vv       DDX26B MUTATED DDX26B WILD-TYPE
  FEMALE             10              160
  MALE                5              192
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                 0   1
  DDX26B MUTATED    12   1
  DDX26B WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     12    1
  DDX26B WILD-TYPE  288    7
     clus
vv    DDX26B MUTATED DDX26B WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D55V9, binary
                  cls
clus                 0   1
  DDX26B MUTATED    11   4
  DDX26B WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     11    4
  DDX26B WILD-TYPE  303   44
                               clus
vv                              DDX26B MUTATED DDX26B WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DDX26B MUTATED     9   0   1   4
  DDX26B WILD-TYPE 250   3  21  17
D55V10, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              4               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"
D55V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX26B MUTATED                                  0     1
  DDX26B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DDX26B MUTATED                           1    11
  DDX26B WILD-TYPE                        18   165
D55V12, multiclass
                                  clus
vv                                 DDX26B MUTATED DDX26B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(56) Variable = UBQLN2 MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  UBQLN2 MUTATED     9   0
  UBQLN2 WILD-TYPE 268  78
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               9              346 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               0               78 
$`UBQLN2 MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-A01Q 
        0.92        35.80        26.17        24.39        19.66         1.02 
TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-6920 
       15.02        12.99        12.39 

$`UBQLN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
            0.92             0.00 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           35.80           148.01 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           15.02            22.09 
[1] "0.9 - 35.8 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D56V2, continuous
                  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      63        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBQLN2 MUTATED           1          0          0          1        0
  UBQLN2 WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  UBQLN2 MUTATED           0         0
  UBQLN2 WILD-TYPE        12         1
D56V3, multiclass
            clus
vv           UBQLN2 MUTATED UBQLN2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  UBQLN2 MUTATED     0   1   7   2
  UBQLN2 WILD-TYPE   9  66 242  39
D56V4, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              2               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
  UBQLN2 MUTATED     8   2   0
  UBQLN2 WILD-TYPE 212  79  66
D56V5, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  N0              8              212
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     8   0
  UBQLN2 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      8    0
  UBQLN2 WILD-TYPE  277   48
   clus
vv  UBQLN2 MUTATED UBQLN2 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D56V7, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     8   2
  UBQLN2 WILD-TYPE 162 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      8    2
  UBQLN2 WILD-TYPE  162  195
        clus
vv       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  FEMALE              8              162
  MALE                2              195
[1] 2 2
[1] FALSE
D56V8, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     8   0
  UBQLN2 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      8    0
  UBQLN2 WILD-TYPE  292    8
     clus
vv    UBQLN2 MUTATED UBQLN2 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D56V9, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     9   1
  UBQLN2 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      9    1
  UBQLN2 WILD-TYPE  305   47
                               clus
vv                              UBQLN2 MUTATED UBQLN2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UBQLN2 MUTATED     8   0   0   1
  UBQLN2 WILD-TYPE 251   3  22  20
D56V10, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              1               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"
D56V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBQLN2 MUTATED                                  0     0
  UBQLN2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UBQLN2 MUTATED                           1     7
  UBQLN2 WILD-TYPE                        18   169
D56V12, multiclass
                                  clus
vv                                 UBQLN2 MUTATED UBQLN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = THOC7 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  THOC7 MUTATED     8   2
  THOC7 WILD-TYPE 269  76
  THOC7 MUTATED THOC7 WILD-TYPE 
             10             345 
  THOC7 MUTATED THOC7 WILD-TYPE 
              2              76 
$`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 
       43.27        17.13        33.67        13.25 

$`THOC7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       26.47        14.50        27.09        16.31         0.95         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       43.04         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  THOC7 MUTATED THOC7 WILD-TYPE 
           1.02            0.00 
  THOC7 MUTATED THOC7 WILD-TYPE 
          43.27          148.01 
  THOC7 MUTATED THOC7 WILD-TYPE 
          20.50           22.06 
[1] "1.0 - 43.3 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D57V2, continuous
                 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      61        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THOC7 MUTATED           0          0          3          0        0         2
  THOC7 WILD-TYPE        18          6         41         33       35        10
                 vv
clus              STAGE IVB
  THOC7 MUTATED           0
  THOC7 WILD-TYPE         1
D57V3, multiclass
            clus
vv           THOC7 MUTATED THOC7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              2              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
  THOC7 MUTATED     1   2   6   1
  THOC7 WILD-TYPE   8  65 243  40
D57V4, multiclass
    clus
vv   THOC7 MUTATED THOC7 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             6             243
  T4             1              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
  THOC7 MUTATED     5   4   1
  THOC7 WILD-TYPE 215  77  65
D57V5, multiclass
    clus
vv   THOC7 MUTATED THOC7 WILD-TYPE
  N0             5             215
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                 cls
clus                0   1
  THOC7 MUTATED     8   2
  THOC7 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED      8    2
  THOC7 WILD-TYPE  277   46
   clus
vv  THOC7 MUTATED THOC7 WILD-TYPE
  0             8             277
  1             2              46
[1] 2 2
[1] FALSE
D57V7, binary
                 cls
clus                0   1
  THOC7 MUTATED     7   3
  THOC7 WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED      7    3
  THOC7 WILD-TYPE  163  194
        clus
vv       THOC7 MUTATED THOC7 WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D57V8, binary
                 cls
clus                0   1
  THOC7 MUTATED     9   0
  THOC7 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED      9    0
  THOC7 WILD-TYPE  291    8
     clus
vv    THOC7 MUTATED THOC7 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D57V9, binary
                 cls
clus                0   1
  THOC7 MUTATED     9   1
  THOC7 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED      9    1
  THOC7 WILD-TYPE  305   47
                               clus
vv                              THOC7 MUTATED THOC7 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  THOC7 MUTATED     8   0   0   0
  THOC7 WILD-TYPE 251   3  22  21
D57V10, multiclass
    clus
vv   THOC7 MUTATED THOC7 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D57V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THOC7 MUTATED                                  0     0
  THOC7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THOC7 MUTATED                           2     7
  THOC7 WILD-TYPE                        17   169
D57V12, multiclass
                                  clus
vv                                 THOC7 MUTATED THOC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        7             169
[1] 4 2
[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 = TOP2B MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  TOP2B MUTATED    18   4
  TOP2B WILD-TYPE 259  74
  TOP2B MUTATED TOP2B WILD-TYPE 
             22             333 
  TOP2B MUTATED TOP2B WILD-TYPE 
              4              74 
$`TOP2B MUTATED`
TCGA-CK-5912 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 
       49.08        35.80        79.69        33.53        22.06        63.98 
TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 
       33.04        32.05        53.00        34.98        35.01        83.24 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6165 
       58.39        49.41        23.05        15.02        15.02        16.04 
TCGA-D5-6536 TCGA-DM-A0XD TCGA-F4-6856 TCGA-G4-6315 
       17.85        24.43        35.31        61.91 

$`TOP2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-G4-6293 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TOP2B MUTATED TOP2B WILD-TYPE 
          15.02            0.00 
  TOP2B MUTATED TOP2B WILD-TYPE 
          83.24          148.01 
  TOP2B MUTATED TOP2B WILD-TYPE 
         34.995          21.440 
[1] "15.0 - 83.2 (35.0)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.7"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOP2B MUTATED         5        0        4        11         1         0
  TOP2B WILD-TYPE      59        1       22        97         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOP2B MUTATED           1          0          0          0        1         0
  TOP2B WILD-TYPE        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  TOP2B MUTATED           0
  TOP2B WILD-TYPE         1
D58V3, multiclass
            clus
vv           TOP2B MUTATED TOP2B WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             11              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TOP2B MUTATED     0   5  16   2
  TOP2B WILD-TYPE   9  62 233  39
D58V4, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  T1             0               9
  T2             5              62
  T3            16             233
  T4             2              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
  TOP2B MUTATED    21   1   1
  TOP2B WILD-TYPE 199  80  65
D58V5, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  N0            21             199
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                 cls
clus                0   1
  TOP2B MUTATED    20   1
  TOP2B WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     20    1
  TOP2B WILD-TYPE  265   47
   clus
vv  TOP2B MUTATED TOP2B WILD-TYPE
  0            20             265
  1             1              47
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  TOP2B MUTATED     9  14
  TOP2B WILD-TYPE 161 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED      9   14
  TOP2B WILD-TYPE  161  183
        clus
vv       TOP2B MUTATED TOP2B WILD-TYPE
  FEMALE             9             161
  MALE              14             183
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus                0   1
  TOP2B MUTATED    20   1
  TOP2B WILD-TYPE 280   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     20    1
  TOP2B WILD-TYPE  280    7
     clus
vv    TOP2B MUTATED TOP2B WILD-TYPE
  NO             20             280
  YES             1               7
[1] 2 2
[1] FALSE
D58V9, binary
                 cls
clus                0   1
  TOP2B MUTATED    21   2
  TOP2B WILD-TYPE 293  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     21    2
  TOP2B WILD-TYPE  293   46
                               clus
vv                              TOP2B MUTATED TOP2B WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TOP2B MUTATED    20   0   0   1
  TOP2B WILD-TYPE 239   3  22  20
D58V10, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  R0            20             239
  R1             0               3
  R2             0              22
  RX             1              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"
D58V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOP2B MUTATED                                  0     1
  TOP2B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TOP2B MUTATED                           1    14
  TOP2B WILD-TYPE                        18   162
D58V12, multiclass
                                  clus
vv                                 TOP2B MUTATED TOP2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       14             162
[1] 4 2
[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 = RB1 MUTATION ANALYSIS
D59V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    70  18
  RB1 WILD-TYPE 207  60
  RB1 MUTATED RB1 WILD-TYPE 
           88           267 
  RB1 MUTATED RB1 WILD-TYPE 
           18            60 
$`RB1 MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 
       14.53        24.16         1.02         6.05        85.05        19.04 
TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       19.04        25.08       100.01        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       91.79        33.53        23.61        22.06        32.71         8.38 
TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3655 
       25.08        24.69        20.12        35.01        63.98        61.02 
TCGA-AA-3811 TCGA-AA-3968 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6901 TCGA-AU-3779 
       10.06        21.99        34.98        83.24        22.42        14.50 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       27.09        21.44         1.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-4952 
       29.56        12.59        12.76        14.30        85.45        15.62 
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-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6169 
       30.08        32.02        15.02        12.00        16.04        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 
       14.04        11.01        12.95        11.01        54.61        19.59 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6540 
       18.25        25.48        43.27        15.12        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6932 TCGA-D5-7000 
        7.53        12.39        12.43         9.44        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
       24.43        92.75       135.65        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
      117.07         6.18        41.42       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        61.91        36.00        13.78 

$`RB1 WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       24.33        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 
       19.99        19.99         0.92        19.00        36.00        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       49.08         5.88        63.62        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       22.09        27.09        22.52        25.18        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 
       23.87        19.66        20.28         7.04         3.02         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
       24.53         5.79        27.42        26.47        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82        58.39         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       62.79        88.21         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 
       12.36        12.39        12.59        12.20        10.06        17.56 
TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
      124.27        20.02        37.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       12.99        15.02        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6536 
       12.03        45.40        56.09        55.92        20.19        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
        4.80        17.13        15.58        10.13        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A0XF 
       11.64        13.41        13.35        12.00       119.70        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-A282 TCGA-DM-A28E TCGA-DM-A28K TCGA-F4-6459 
       44.32       131.51       139.17       119.93        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       31.96        35.74        47.87         1.55        34.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 
       33.67        13.25         0.53        47.41        35.31        65.85 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6626 
       55.04        85.48        46.75 

  RB1 MUTATED RB1 WILD-TYPE 
         1.02          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       135.65        148.01 
  RB1 MUTATED RB1 WILD-TYPE 
        22.70         21.99 
[1] "1.0 - 135.7 (22.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D59V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RB1 MUTATED        11        1        7        31         2         1
  RB1 WILD-TYPE      53        0       19        77         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RB1 MUTATED           3          2         11          4        5         5
  RB1 WILD-TYPE        15          4         33         29       30         7
               vv
clus            STAGE IVB
  RB1 MUTATED           0
  RB1 WILD-TYPE         1
D59V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I             11            53
  STAGE IA             1             0
  STAGE II             7            19
  STAGE IIA           31            77
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            3            15
  STAGE IIIA           2             4
  STAGE IIIB          11            33
  STAGE IIIC           4            29
  STAGE IV             5            30
  STAGE IVA            5             7
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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     0  15  62  10
  RB1 WILD-TYPE   9  52 187  31
D59V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           0             9
  T2          15            52
  T3          62           187
  T4          10            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
  RB1 MUTATED    59  21   8
  RB1 WILD-TYPE 161  60  58
D59V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0          59           161
  N1          21            60
  N2           8            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"
D59V6, binary
               cls
clus              0   1
  RB1 MUTATED    68  10
  RB1 WILD-TYPE 217  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     68   10
  RB1 WILD-TYPE  217   38
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          68           217
  1          10            38
[1] 2 2
[1] FALSE
D59V7, binary
               cls
clus              0   1
  RB1 MUTATED    39  49
  RB1 WILD-TYPE 131 148
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     39   49
  RB1 WILD-TYPE  131  148
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          39           131
  MALE            49           148
[1] 2 2
[1] FALSE
D59V8, binary
               cls
clus              0   1
  RB1 MUTATED    77   1
  RB1 WILD-TYPE 223   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     77    1
  RB1 WILD-TYPE  223    7
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           77           223
  YES           1             7
[1] 2 2
[1] FALSE
D59V9, binary
               cls
clus              0   1
  RB1 MUTATED    78   9
  RB1 WILD-TYPE 236  39
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     78    9
  RB1 WILD-TYPE  236   39
                               clus
vv                              RB1 MUTATED RB1 WILD-TYPE
  COLON ADENOCARCINOMA                   78           236
  COLON MUCINOUS ADENOCARCINOMA           9            39
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    59   1   2   4
  RB1 WILD-TYPE 200   2  20  17
D59V10, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          59           200
  R1           1             2
  R2           2            20
  RX           4            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"
D59V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     4
  RB1 WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           8    65
  RB1 WILD-TYPE                        11   111
D59V12, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      4             6
  BLACK OR AFRICAN AMERICAN                  8            11
  WHITE                                     65           111
[1] 4 2
[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 = ALDH1A3 MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                 0   1
  ALDH1A3 MUTATED    12   4
  ALDH1A3 WILD-TYPE 265  74
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               16               339 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
                4                74 
$`ALDH1A3 MUTATED`
TCGA-AA-3950 TCGA-AD-6964 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3558 
       24.00        10.88        23.87        63.98        29.95        20.98 
TCGA-AA-3655 TCGA-AA-3977 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5916 TCGA-D5-6539 
       61.02        25.02        49.41        15.62        21.14        12.49 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-G4-6304 TCGA-G4-6309 
       13.35        49.91        53.62        85.48 

$`ALDH1A3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 
       33.99        21.01        24.00        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        85.45        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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 
       43.04        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-G4-6315 
      133.18        74.56        65.85        44.68        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
            10.88              0.00 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
            85.48            148.01 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
            24.51             21.99 
[1] "10.9 - 85.5 (24.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D60V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALDH1A3 MUTATED         2        0        3         5         2         0
  ALDH1A3 WILD-TYPE      62        1       23       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH1A3 MUTATED           0          0          2          1        0
  ALDH1A3 WILD-TYPE        18          6         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ALDH1A3 MUTATED           0         0
  ALDH1A3 WILD-TYPE        12         1
D60V3, multiclass
            clus
vv           ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                5               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  ALDH1A3 MUTATED     1   2  11   4
  ALDH1A3 WILD-TYPE   8  65 238  37
D60V4, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3              11               238
  T4               4                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
  ALDH1A3 MUTATED    14   2   2
  ALDH1A3 WILD-TYPE 206  79  64
D60V5, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  N0              14               206
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    14   0
  ALDH1A3 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     14    0
  ALDH1A3 WILD-TYPE  271   48
   clus
vv  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  0              14               271
  1               0                48
[1] 2 2
[1] FALSE
D60V7, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    11   7
  ALDH1A3 WILD-TYPE 159 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     11    7
  ALDH1A3 WILD-TYPE  159  190
        clus
vv       ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  FEMALE              11               159
  MALE                 7               190
[1] 2 2
[1] FALSE
D60V8, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    14   0
  ALDH1A3 WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     14    0
  ALDH1A3 WILD-TYPE  286    8
     clus
vv    ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D60V9, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    13   5
  ALDH1A3 WILD-TYPE 301  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     13    5
  ALDH1A3 WILD-TYPE  301   43
                               clus
vv                              ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ALDH1A3 MUTATED     9   0   1   3
  ALDH1A3 WILD-TYPE 250   3  21  18
D60V10, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               3                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"
D60V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDH1A3 MUTATED                                  0     0
  ALDH1A3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ALDH1A3 MUTATED                           1    10
  ALDH1A3 WILD-TYPE                        18   166
D60V12, multiclass
                                  clus
vv                                 ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         10               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(61) Variable = GMPS MUTATION ANALYSIS
D61V1, survival
                sevent
clus2              0   1
  GMPS MUTATED    15   1
  GMPS WILD-TYPE 262  77
  GMPS MUTATED GMPS WILD-TYPE 
            16            339 
  GMPS MUTATED GMPS WILD-TYPE 
             1             77 
$`GMPS MUTATED`
TCGA-G4-6588 TCGA-A6-3809 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01I 
       26.17        32.75        26.99        25.02        34.98        31.00 
TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5864 
       24.53        58.39        12.10        12.76        13.02        15.02 
TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6930 TCGA-F4-6569 
       16.14        10.13        13.35        35.74 

$`GMPS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        83.24         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        12.39        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 
       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GMPS MUTATED GMPS WILD-TYPE 
         10.13           0.00 
  GMPS MUTATED GMPS WILD-TYPE 
         58.39         148.01 
  GMPS MUTATED GMPS WILD-TYPE 
        24.775         22.030 
[1] "10.1 - 58.4 (24.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.1"
D61V2, continuous
                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      60        1       26       101         6         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        18          5         44         33       34        12
                vv
clus             STAGE IVB
  GMPS MUTATED           0
  GMPS WILD-TYPE         1
D61V3, multiclass
            clus
vv           GMPS MUTATED GMPS WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  GMPS MUTATED     1   5   8   3
  GMPS WILD-TYPE   8  62 241  38
D61V4, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  T1            1              8
  T2            5             62
  T3            8            241
  T4            3             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
  GMPS MUTATED    15   2   0
  GMPS WILD-TYPE 205  79  66
D61V5, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  N0           15            205
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                cls
clus               0   1
  GMPS MUTATED    14   1
  GMPS WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     14    1
  GMPS WILD-TYPE  271   47
   clus
vv  GMPS MUTATED GMPS WILD-TYPE
  0           14            271
  1            1             47
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus               0   1
  GMPS MUTATED     5  12
  GMPS WILD-TYPE 165 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED      5   12
  GMPS WILD-TYPE  165  185
        clus
vv       GMPS MUTATED GMPS WILD-TYPE
  FEMALE            5            165
  MALE             12            185
[1] 2 2
[1] FALSE
D61V8, binary
                cls
clus               0   1
  GMPS MUTATED    16   0
  GMPS WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     16    0
  GMPS WILD-TYPE  284    8
     clus
vv    GMPS MUTATED GMPS WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D61V9, binary
                cls
clus               0   1
  GMPS MUTATED    13   4
  GMPS WILD-TYPE 301  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     13    4
  GMPS WILD-TYPE  301   44
                               clus
vv                              GMPS MUTATED GMPS WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GMPS MUTATED    13   0   0   1
  GMPS WILD-TYPE 246   3  22  20
D61V10, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            1             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"
D61V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GMPS MUTATED                                  0     1
  GMPS WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GMPS MUTATED                           2     9
  GMPS WILD-TYPE                        17   167
D61V12, multiclass
                                  clus
vv                                 GMPS MUTATED GMPS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       9            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(62) Variable = KIAA1586 MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  KIAA1586 MUTATED     6   3
  KIAA1586 WILD-TYPE 271  75
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                 9                346 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                 3                 75 
$`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 
        2.01        13.32         6.18 

$`KIAA1586 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        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-5860 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
              2.01               0.00 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
             63.98             148.01 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
            13.320             22.075 
[1] "2.0 - 64.0 (13.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1586 MUTATED         0        0        1         7         1         0
  KIAA1586 WILD-TYPE      64        1       25       101         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1586 MUTATED           0          0          0          0        1
  KIAA1586 WILD-TYPE        18          6         44         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1586 MUTATED           0         0
  KIAA1586 WILD-TYPE        12         1
D62V3, multiclass
            clus
vv           KIAA1586 MUTATED KIAA1586 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 7                101
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  KIAA1586 MUTATED     0   1   9   1
  KIAA1586 WILD-TYPE   9  66 240  40
D62V4, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                9                240
  T4                1                 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
  KIAA1586 MUTATED    10   1   0
  KIAA1586 WILD-TYPE 210  80  66
D62V5, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  N0               10                210
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     8   1
  KIAA1586 WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      8    1
  KIAA1586 WILD-TYPE  277   47
   clus
vv  KIAA1586 MUTATED KIAA1586 WILD-TYPE
  0                8                277
  1                1                 47
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     5   6
  KIAA1586 WILD-TYPE 165 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      5    6
  KIAA1586 WILD-TYPE  165  191
        clus
vv       KIAA1586 MUTATED KIAA1586 WILD-TYPE
  FEMALE                5                165
  MALE                  6                191
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     8   0
  KIAA1586 WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      8    0
  KIAA1586 WILD-TYPE  292    8
     clus
vv    KIAA1586 MUTATED KIAA1586 WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     8   2
  KIAA1586 WILD-TYPE 306  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      8    2
  KIAA1586 WILD-TYPE  306   46
                               clus
vv                              KIAA1586 MUTATED KIAA1586 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1586 MUTATED     5   0   0   4
  KIAA1586 WILD-TYPE 254   3  22  17
D62V10, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                4                 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"
D62V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1586 MUTATED                                  0     2
  KIAA1586 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1586 MUTATED                           0     5
  KIAA1586 WILD-TYPE                        19   171
D62V12, multiclass
                                  clus
vv                                 KIAA1586 MUTATED KIAA1586 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = L1TD1 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  L1TD1 MUTATED    14   2
  L1TD1 WILD-TYPE 263  76
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             339 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
              2              76 
$`L1TD1 MUTATED`
TCGA-AA-3525 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 
        8.05        26.17        32.75        23.87        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5254 
       63.98         6.97        18.05         4.01        34.98        12.69 
TCGA-CA-6717 TCGA-CM-6166 TCGA-D5-6929 TCGA-G4-6309 
       12.76        21.99        13.41        85.48 

$`L1TD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6780 
       25.08        25.18        21.76        24.69        24.39        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  L1TD1 MUTATED L1TD1 WILD-TYPE 
           3.02            0.00 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
          85.48          148.01 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
         18.855          22.090 
[1] "3.0 - 85.5 (18.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D63V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  L1TD1 MUTATED         1        0        3         4         3         0
  L1TD1 WILD-TYPE      63        1       23       104         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  L1TD1 MUTATED           0          0          4          1        1         0
  L1TD1 WILD-TYPE        18          6         40         32       34        12
                 vv
clus              STAGE IVB
  L1TD1 MUTATED           0
  L1TD1 WILD-TYPE         1
D63V3, multiclass
            clus
vv           L1TD1 MUTATED L1TD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  L1TD1 MUTATED     0   1  11   5
  L1TD1 WILD-TYPE   9  66 238  36
D63V4, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             5              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
  L1TD1 MUTATED    11   6   0
  L1TD1 WILD-TYPE 209  75  66
D63V5, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  N0            11             209
  N1             6              75
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                 cls
clus                0   1
  L1TD1 MUTATED    15   1
  L1TD1 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     15    1
  L1TD1 WILD-TYPE  270   47
   clus
vv  L1TD1 MUTATED L1TD1 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus                0   1
  L1TD1 MUTATED    10   7
  L1TD1 WILD-TYPE 160 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     10    7
  L1TD1 WILD-TYPE  160  190
        clus
vv       L1TD1 MUTATED L1TD1 WILD-TYPE
  FEMALE            10             160
  MALE               7             190
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus                0   1
  L1TD1 MUTATED    15   0
  L1TD1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     15    0
  L1TD1 WILD-TYPE  285    8
     clus
vv    L1TD1 MUTATED L1TD1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D63V9, binary
                 cls
clus                0   1
  L1TD1 MUTATED    12   5
  L1TD1 WILD-TYPE 302  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     12    5
  L1TD1 WILD-TYPE  302   43
                               clus
vv                              L1TD1 MUTATED L1TD1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  L1TD1 MUTATED    14   0   0   2
  L1TD1 WILD-TYPE 245   3  22  19
D63V10, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D63V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  L1TD1 MUTATED                                  0     2
  L1TD1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  L1TD1 MUTATED                           1     6
  L1TD1 WILD-TYPE                        18   170
D63V12, multiclass
                                  clus
vv                                 L1TD1 MUTATED L1TD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = NLRC4 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  NLRC4 MUTATED    20   4
  NLRC4 WILD-TYPE 257  74
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             24             331 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
              4              74 
$`NLRC4 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-6141 
       85.05        19.04        19.04        25.08        26.17         8.38 
TCGA-A6-6781 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6901 TCGA-AU-3779 
       19.66         2.01        25.02        34.98        22.42        14.50 
TCGA-AY-6196 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5344 
        0.20        12.39        12.76        21.14        13.02        22.03 
TCGA-CM-5349 TCGA-D5-6536 TCGA-D5-6928 TCGA-DM-A1DA TCGA-G4-6293 TCGA-G4-6317 
       30.08        17.85        11.64         7.50       133.18        36.00 

$`NLRC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
        0.92        19.00        36.00        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       24.53         5.79        27.42        26.47        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.59        12.59        12.20        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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        43.04        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  NLRC4 MUTATED NLRC4 WILD-TYPE 
            0.2             0.0 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
         133.18          148.01 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
          19.35           22.36 
[1] "0.2 - 133.2 (19.4)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D64V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRC4 MUTATED         1        0        2        10         1         0
  NLRC4 WILD-TYPE      63        1       24        98         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLRC4 MUTATED           1          0          2          4        1         0
  NLRC4 WILD-TYPE        17          6         42         29       34        12
                 vv
clus              STAGE IVB
  NLRC4 MUTATED           0
  NLRC4 WILD-TYPE         1
D64V3, multiclass
            clus
vv           NLRC4 MUTATED NLRC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             10              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             4              29
  STAGE IV               1              34
  STAGE IVA              0              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
  NLRC4 MUTATED     1   1  20   2
  NLRC4 WILD-TYPE   8  66 229  39
D64V4, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            20             229
  T4             2              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
  NLRC4 MUTATED    17   4   3
  NLRC4 WILD-TYPE 203  77  63
D64V5, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  N0            17             203
  N1             4              77
  N2             3              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"
D64V6, binary
                 cls
clus                0   1
  NLRC4 MUTATED    18   1
  NLRC4 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     18    1
  NLRC4 WILD-TYPE  267   47
   clus
vv  NLRC4 MUTATED NLRC4 WILD-TYPE
  0            18             267
  1             1              47
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus                0   1
  NLRC4 MUTATED    11  13
  NLRC4 WILD-TYPE 159 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     11   13
  NLRC4 WILD-TYPE  159  184
        clus
vv       NLRC4 MUTATED NLRC4 WILD-TYPE
  FEMALE            11             159
  MALE              13             184
[1] 2 2
[1] FALSE
D64V8, binary
                 cls
clus                0   1
  NLRC4 MUTATED    20   1
  NLRC4 WILD-TYPE 280   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     20    1
  NLRC4 WILD-TYPE  280    7
     clus
vv    NLRC4 MUTATED NLRC4 WILD-TYPE
  NO             20             280
  YES             1               7
[1] 2 2
[1] FALSE
D64V9, binary
                 cls
clus                0   1
  NLRC4 MUTATED    18   6
  NLRC4 WILD-TYPE 296  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     18    6
  NLRC4 WILD-TYPE  296   42
                               clus
vv                              NLRC4 MUTATED NLRC4 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NLRC4 MUTATED    16   0   1   2
  NLRC4 WILD-TYPE 243   3  21  19
D64V10, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             1              21
  RX             2              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"
D64V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRC4 MUTATED                                  0     2
  NLRC4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLRC4 MUTATED                           2    14
  NLRC4 WILD-TYPE                        17   162
D64V12, multiclass
                                  clus
vv                                 NLRC4 MUTATED NLRC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       14             162
[1] 4 2
[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 = ZDHHC7 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  ZDHHC7 MUTATED     9   2
  ZDHHC7 WILD-TYPE 268  76
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              11              344 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               2               76 
$`ZDHHC7 MUTATED`
TCGA-AA-3662 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3949 
        6.05        79.69        24.39        10.06        33.01        26.01 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-D5-6930 TCGA-DM-A28F TCGA-G4-6304 
       27.09        58.39        13.35        35.97        53.62 

$`ZDHHC7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
            6.05             0.00 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           79.69           148.01 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           27.09            21.99 
[1] "6.0 - 79.7 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D65V2, continuous
                  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      61        1       26       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC7 MUTATED           1          0          2          0        1
  ZDHHC7 WILD-TYPE        17          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZDHHC7 MUTATED           0         0
  ZDHHC7 WILD-TYPE        12         1
D65V3, multiclass
            clus
vv           ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZDHHC7 MUTATED     0   3   6   3
  ZDHHC7 WILD-TYPE   9  64 243  38
D65V4, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              6              243
  T4              3               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
  ZDHHC7 MUTATED     8   2   2
  ZDHHC7 WILD-TYPE 212  79  64
D65V5, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  N0              8              212
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED    11   1
  ZDHHC7 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED     11    1
  ZDHHC7 WILD-TYPE  274   47
   clus
vv  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D65V7, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     7   5
  ZDHHC7 WILD-TYPE 163 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      7    5
  ZDHHC7 WILD-TYPE  163  192
        clus
vv       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  FEMALE              7              163
  MALE                5              192
[1] 2 2
[1] FALSE
D65V8, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     9   0
  ZDHHC7 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      9    0
  ZDHHC7 WILD-TYPE  291    8
     clus
vv    ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D65V9, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     9   3
  ZDHHC7 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      9    3
  ZDHHC7 WILD-TYPE  305   45
                               clus
vv                              ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZDHHC7 MUTATED     9   0   1   0
  ZDHHC7 WILD-TYPE 250   3  21  21
D65V10, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              0               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"
D65V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZDHHC7 MUTATED                                  0     0
  ZDHHC7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC7 MUTATED                           0     7
  ZDHHC7 WILD-TYPE                        19   169
D65V12, multiclass
                                  clus
vv                                 ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = DCLK2 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  DCLK2 MUTATED    13   0
  DCLK2 WILD-TYPE 264  78
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             13             342 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
              0              78 
$`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        25.48        12.49        11.64        47.87 
TCGA-G4-6306 
       44.68 

$`DCLK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
       17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-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        54.61        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-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DCLK2 MUTATED DCLK2 WILD-TYPE 
           1.02            0.00 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
          88.21          148.01 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
         25.480          22.045 
[1] "1.0 - 88.2 (25.5)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D66V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLK2 MUTATED         2        0        1         6         1         0
  DCLK2 WILD-TYPE      62        1       25       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCLK2 MUTATED           0          0          0          0        0         1
  DCLK2 WILD-TYPE        18          6         44         33       35        11
                 vv
clus              STAGE IVB
  DCLK2 MUTATED           0
  DCLK2 WILD-TYPE         1
D66V3, multiclass
            clus
vv           DCLK2 MUTATED DCLK2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  DCLK2 MUTATED     1   2   8   3
  DCLK2 WILD-TYPE   8  65 241  38
D66V4, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             8             241
  T4             3              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
  DCLK2 MUTATED    13   1   0
  DCLK2 WILD-TYPE 207  80  66
D66V5, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  N0            13             207
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                 cls
clus                0   1
  DCLK2 MUTATED    13   1
  DCLK2 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     13    1
  DCLK2 WILD-TYPE  272   47
   clus
vv  DCLK2 MUTATED DCLK2 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  DCLK2 MUTATED     8   6
  DCLK2 WILD-TYPE 162 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED      8    6
  DCLK2 WILD-TYPE  162  191
        clus
vv       DCLK2 MUTATED DCLK2 WILD-TYPE
  FEMALE             8             162
  MALE               6             191
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  DCLK2 MUTATED    13   0
  DCLK2 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     13    0
  DCLK2 WILD-TYPE  287    8
     clus
vv    DCLK2 MUTATED DCLK2 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D66V9, binary
                 cls
clus                0   1
  DCLK2 MUTATED    11   3
  DCLK2 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     11    3
  DCLK2 WILD-TYPE  303   45
                               clus
vv                              DCLK2 MUTATED DCLK2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DCLK2 MUTATED    13   0   0   0
  DCLK2 WILD-TYPE 246   3  22  21
D66V10, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             0              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"
D66V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCLK2 MUTATED                                  0     0
  DCLK2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCLK2 MUTATED                           0     9
  DCLK2 WILD-TYPE                        19   167
D66V12, multiclass
                                  clus
vv                                 DCLK2 MUTATED DCLK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(67) Variable = C2ORF29 MUTATION ANALYSIS
D67V1, survival
                   sevent
clus2                 0   1
  C2ORF29 MUTATED    14   3
  C2ORF29 WILD-TYPE 263  75
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               17               338 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
                3                75 
$`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        12.36        15.62        22.98 
TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-6529 TCGA-D5-6540 
       14.04        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 
       13.41       131.51        31.96       133.18        85.48 

$`C2ORF29 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-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-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        54.61        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        25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50        44.32       135.65       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       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        43.04 
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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
             6.77              0.00 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
           133.18            148.01 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
           15.620            22.225 
[1] "6.8 - 133.2 (15.6)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.5"
D67V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2ORF29 MUTATED         4        0        0         5         1         0
  C2ORF29 WILD-TYPE      60        1       26       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF29 MUTATED           1          0          3          2        1
  C2ORF29 WILD-TYPE        17          6         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF29 MUTATED           0         0
  C2ORF29 WILD-TYPE        12         1
D67V3, multiclass
            clus
vv           C2ORF29 MUTATED C2ORF29 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  C2ORF29 MUTATED     1   3  11   2
  C2ORF29 WILD-TYPE   8  64 238  39
D67V4, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  T1               1                 8
  T2               3                64
  T3              11               238
  T4               2                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
  C2ORF29 MUTATED    10   5   2
  C2ORF29 WILD-TYPE 210  76  64
D67V5, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  N0              10               210
  N1               5                76
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    15   1
  C2ORF29 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     15    1
  C2ORF29 WILD-TYPE  270   47
   clus
vv  C2ORF29 MUTATED C2ORF29 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D67V7, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED     9   8
  C2ORF29 WILD-TYPE 161 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED      9    8
  C2ORF29 WILD-TYPE  161  189
        clus
vv       C2ORF29 MUTATED C2ORF29 WILD-TYPE
  FEMALE               9               161
  MALE                 8               189
[1] 2 2
[1] FALSE
D67V8, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    14   1
  C2ORF29 WILD-TYPE 286   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     14    1
  C2ORF29 WILD-TYPE  286    7
     clus
vv    C2ORF29 MUTATED C2ORF29 WILD-TYPE
  NO               14               286
  YES               1                 7
[1] 2 2
[1] FALSE
D67V9, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    15   2
  C2ORF29 WILD-TYPE 299  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     15    2
  C2ORF29 WILD-TYPE  299   46
                               clus
vv                              C2ORF29 MUTATED C2ORF29 WILD-TYPE
  COLON ADENOCARCINOMA                       15               299
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C2ORF29 MUTATED    12   0   0   2
  C2ORF29 WILD-TYPE 247   3  22  19
D67V10, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               2                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"
D67V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2ORF29 MUTATED                                  0     1
  C2ORF29 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C2ORF29 MUTATED                           2    13
  C2ORF29 WILD-TYPE                        17   163
D67V12, multiclass
                                  clus
vv                                 C2ORF29 MUTATED C2ORF29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         13               163
[1] 4 2
[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 = PTCH1 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED    67  21
  PTCH1 WILD-TYPE 210  57
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             88             267 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             21              57 
$`PTCH1 MUTATED`
TCGA-A6-6649 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       24.16         0.99        17.95        85.05        19.04        19.04 
TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
       24.00        10.88       100.01        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       35.80        26.17        32.75        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3660 TCGA-AA-3861 
       22.06        24.69        23.87        19.66        78.08        30.05 
TCGA-AA-3864 TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02K 
       53.00         0.99        34.98        38.07        35.01        14.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AU-3779 TCGA-AU-6004 
       12.16        83.24        24.53        22.42        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 
       33.01         0.20        21.44        58.39        88.21         6.77 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 
      148.01        15.62        21.99        23.05        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6168 
       22.98        30.08        32.02        15.02        29.03        12.99 
TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6532 
       11.01        11.08        45.40        54.61        19.59        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       16.14        15.58        14.30         9.44        13.41        13.35 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        24.43        92.75        12.59         7.50        44.32 
TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       35.97        98.24         6.18        53.62        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

$`PTCH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       36.03         8.05        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-G4-6310 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       63.62        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 
       32.91        31.63        30.44        33.53        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        21.76        24.39 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       32.05         0.99        31.07        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
        4.01        27.02        42.02        17.03        14.99        15.02 
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-A029 
        1.02        33.04         1.02        26.01        37.02        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-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       18.05        40.96         5.79        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.95        17.82         1.41         5.13        22.36        62.79 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5913 
       12.76        10.06        14.30        17.56        85.45        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       25.02        29.06         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        14.04        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       11.01        10.06        12.03        56.09        55.92        20.19 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.12         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D0 
       11.64        12.00        11.38        10.26        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       49.91        13.32       140.38       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        60.79       117.07         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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       74.56        65.85        44.68 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
            0.2             0.0 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
         148.01          140.38 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          23.33           21.14 
[1] "0.2 - 148.0 (23.3)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.1"
D68V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTCH1 MUTATED         9        1        5        32         4         0
  PTCH1 WILD-TYPE      55        0       21        76         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH1 MUTATED           4          1         12          7        5         3
  PTCH1 WILD-TYPE        14          5         32         26       30         9
                 vv
clus              STAGE IVB
  PTCH1 MUTATED           0
  PTCH1 WILD-TYPE         1
D68V3, multiclass
            clus
vv           PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I                9              55
  STAGE IA               1               0
  STAGE II               5              21
  STAGE IIA             32              76
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              4              14
  STAGE IIIA             1               5
  STAGE IIIB            12              32
  STAGE IIIC             7              26
  STAGE IV               5              30
  STAGE IVA              3               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
  PTCH1 MUTATED     2   9  67  10
  PTCH1 WILD-TYPE   7  58 182  31
D68V4, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  T1             2               7
  T2             9              58
  T3            67             182
  T4            10              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
  PTCH1 MUTATED    56  20  13
  PTCH1 WILD-TYPE 164  61  53
D68V5, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  N0            56             164
  N1            20              61
  N2            13              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED    63   8
  PTCH1 WILD-TYPE 222  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     63    8
  PTCH1 WILD-TYPE  222   40
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0            63             222
  1             8              40
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED    40  49
  PTCH1 WILD-TYPE 130 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     40   49
  PTCH1 WILD-TYPE  130  148
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE            40             130
  MALE              49             148
[1] 2 2
[1] FALSE
D68V8, binary
                 cls
clus                0   1
  PTCH1 MUTATED    72   2
  PTCH1 WILD-TYPE 228   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     72    2
  PTCH1 WILD-TYPE  228    6
     clus
vv    PTCH1 MUTATED PTCH1 WILD-TYPE
  NO             72             228
  YES             2               6
[1] 2 2
[1] FALSE
D68V9, binary
                 cls
clus                0   1
  PTCH1 MUTATED    75  14
  PTCH1 WILD-TYPE 239  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     75   14
  PTCH1 WILD-TYPE  239   34
                               clus
vv                              PTCH1 MUTATED PTCH1 WILD-TYPE
  COLON ADENOCARCINOMA                     75             239
  COLON MUCINOUS ADENOCARCINOMA            14              34
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTCH1 MUTATED    61   0   2   5
  PTCH1 WILD-TYPE 198   3  20  16
D68V10, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  R0            61             198
  R1             0               3
  R2             2              20
  RX             5              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"
D68V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTCH1 MUTATED                                  0     1
  PTCH1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTCH1 MUTATED                           8    66
  PTCH1 WILD-TYPE                        11   110
D68V12, multiclass
                                  clus
vv                                 PTCH1 MUTATED PTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    8              11
  WHITE                                       66             110
[1] 4 2
[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 = LINGO4 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  LINGO4 MUTATED     5   4
  LINGO4 WILD-TYPE 272  74
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               9              346 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               4               74 
$`LINGO4 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-A6-2671 TCGA-AA-3864 TCGA-AA-A00N TCGA-AZ-6598 
        0.92        24.00        43.76        53.00         4.01        49.41 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6930 
       14.04         4.80        13.35 

$`LINGO4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.075 
[1] "0.9 - 53.0 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D69V2, continuous
                  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      63        1       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LINGO4 MUTATED           1          0          1          0        1
  LINGO4 WILD-TYPE        17          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  LINGO4 MUTATED           0         0
  LINGO4 WILD-TYPE        12         1
D69V3, multiclass
            clus
vv           LINGO4 MUTATED LINGO4 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  LINGO4 MUTATED     0   1   7   2
  LINGO4 WILD-TYPE   9  66 242  39
D69V4, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              2               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
  LINGO4 MUTATED     7   2   1
  LINGO4 WILD-TYPE 213  79  65
D69V5, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   1
  LINGO4 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    1
  LINGO4 WILD-TYPE  278   47
   clus
vv  LINGO4 MUTATED LINGO4 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D69V7, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     5   5
  LINGO4 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      5    5
  LINGO4 WILD-TYPE  165  192
        clus
vv       LINGO4 MUTATED LINGO4 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D69V8, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     8   0
  LINGO4 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      8    0
  LINGO4 WILD-TYPE  292    8
     clus
vv    LINGO4 MUTATED LINGO4 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D69V9, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   3
  LINGO4 WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    3
  LINGO4 WILD-TYPE  307   45
                               clus
vv                              LINGO4 MUTATED LINGO4 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LINGO4 MUTATED     9   0   0   0
  LINGO4 WILD-TYPE 250   3  22  21
D69V10, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D69V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LINGO4 MUTATED                                  0     0
  LINGO4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LINGO4 MUTATED                           0     5
  LINGO4 WILD-TYPE                        19   171
D69V12, multiclass
                                  clus
vv                                 LINGO4 MUTATED LINGO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = PIK3R1 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    34   8
  PIK3R1 WILD-TYPE 243  70
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              42              313 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               8               70 
$`PIK3R1 MUTATED`
TCGA-AA-3552 TCGA-AA-3662 TCGA-AA-3697 TCGA-AD-6895 TCGA-AZ-6608 TCGA-A6-5660 
       13.02         6.05        85.05        25.08         1.94        29.19 
TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3511 TCGA-AA-3664 TCGA-AA-3833 
       22.06        20.12        19.66         6.97        54.02        15.95 
TCGA-AA-A010 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CA-5255 
       34.98        14.50        27.09        33.01        58.39        12.36 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5862 
       12.76        85.45        21.99        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        10.13         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 

$`PIK3R1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       15.52        10.88       106.75       100.01        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.39        23.87        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       27.42        26.47        16.31         0.95         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        15.02        17.03        12.00        14.04 
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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        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-D5-6533 
       45.40        54.61        19.59        56.09        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        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         7.53        12.39        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        13.41        13.35        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-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C 
       13.32        12.59         7.50       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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6317 
      133.18        74.56        65.85        53.62        44.68        36.00 
TCGA-G4-6323 
       13.78 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            1.94             0.00 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          140.38           148.01 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          22.025           22.090 
[1] "1.9 - 140.4 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D70V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3R1 MUTATED         4        0        3        17         1         0
  PIK3R1 WILD-TYPE      60        1       23        91         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R1 MUTATED           0          2          8          4        2
  PIK3R1 WILD-TYPE        18          4         36         29       33
                  vv
clus               STAGE IVA STAGE IVB
  PIK3R1 MUTATED           2         0
  PIK3R1 WILD-TYPE        10         1
D70V3, multiclass
            clus
vv           PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              17               91
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              2                4
  STAGE IIIB              8               36
  STAGE IIIC              4               29
  STAGE IV                2               33
  STAGE IVA               2               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
  PIK3R1 MUTATED     1   4  34   4
  PIK3R1 WILD-TYPE   8  63 215  37
D70V4, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T1              1                8
  T2              4               63
  T3             34              215
  T4              4               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
  PIK3R1 MUTATED    25  14   4
  PIK3R1 WILD-TYPE 195  67  62
D70V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0             25              195
  N1             14               67
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    36   4
  PIK3R1 WILD-TYPE 249  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     36    4
  PIK3R1 WILD-TYPE  249   44
   clus
vv  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  0             36              249
  1              4               44
[1] 2 2
[1] FALSE
D70V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    20  23
  PIK3R1 WILD-TYPE 150 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     20   23
  PIK3R1 WILD-TYPE  150  174
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE             20              150
  MALE               23              174
[1] 2 2
[1] FALSE
D70V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    35   1
  PIK3R1 WILD-TYPE 265   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     35    1
  PIK3R1 WILD-TYPE  265    7
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO              35              265
  YES              1                7
[1] 2 2
[1] FALSE
D70V9, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    38   4
  PIK3R1 WILD-TYPE 276  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     38    4
  PIK3R1 WILD-TYPE  276   44
                               clus
vv                              PIK3R1 MUTATED PIK3R1 WILD-TYPE
  COLON ADENOCARCINOMA                      38              276
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R1 MUTATED    30   1   1   4
  PIK3R1 WILD-TYPE 229   2  21  17
D70V10, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  R0             30              229
  R1              1                2
  R2              1               21
  RX              4               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"
D70V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R1 MUTATED                                  0     2
  PIK3R1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED                           6    27
  PIK3R1 WILD-TYPE                        13   149
D70V12, multiclass
                                  clus
vv                                 PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     6               13
  WHITE                                        27              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(71) Variable = C14ORF43 MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  C14ORF43 MUTATED    14   4
  C14ORF43 WILD-TYPE 263  74
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                18                337 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 4                 74 
$`C14ORF43 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-3809 TCGA-AA-3518 
       19.04       100.01        26.17        91.79        32.75         1.02 
TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3864 TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-6598 
        6.97        26.99        53.00        12.16        83.24        49.41 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6930 TCGA-G4-6309 
       12.76        21.14        15.02        14.04        13.35        85.48 

$`C14ORF43 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5665 
       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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
        0.92        41.00        39.98        18.05        40.96        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
              1.02               0.00 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
            100.01             148.01 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
            23.655             22.060 
[1] "1.0 - 100.0 (23.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF43 MUTATED         4        0        4         7         1         0
  C14ORF43 WILD-TYPE      60        1       22       101         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF43 MUTATED           0          0          1          0        1
  C14ORF43 WILD-TYPE        18          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF43 MUTATED           0         0
  C14ORF43 WILD-TYPE        12         1
D71V3, multiclass
            clus
vv           C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                 7                101
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  C14ORF43 MUTATED     1   3  13   1
  C14ORF43 WILD-TYPE   8  64 236  40
D71V4, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T1                1                  8
  T2                3                 64
  T3               13                236
  T4                1                 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
  C14ORF43 MUTATED    17   1   0
  C14ORF43 WILD-TYPE 203  80  66
D71V5, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  N0               17                203
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    15   1
  C14ORF43 WILD-TYPE 270  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     15    1
  C14ORF43 WILD-TYPE  270   47
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0               15                270
  1                1                 47
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    10   8
  C14ORF43 WILD-TYPE 160 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     10    8
  C14ORF43 WILD-TYPE  160  189
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  FEMALE               10                160
  MALE                  8                189
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    16   1
  C14ORF43 WILD-TYPE 284   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     16    1
  C14ORF43 WILD-TYPE  284    7
     clus
vv    C14ORF43 MUTATED C14ORF43 WILD-TYPE
  NO                16                284
  YES                1                  7
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    14   4
  C14ORF43 WILD-TYPE 300  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     14    4
  C14ORF43 WILD-TYPE  300   44
                               clus
vv                              C14ORF43 MUTATED C14ORF43 WILD-TYPE
  COLON ADENOCARCINOMA                        14                300
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C14ORF43 MUTATED    13   0   1   2
  C14ORF43 WILD-TYPE 246   3  21  19
D71V10, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  R0               13                246
  R1                0                  3
  R2                1                 21
  RX                2                 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"
D71V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF43 MUTATED                                  0     2
  C14ORF43 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF43 MUTATED                           1    10
  C14ORF43 WILD-TYPE                        18   166
D71V12, multiclass
                                  clus
vv                                 C14ORF43 MUTATED C14ORF43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          10                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(72) Variable = C14ORF184 MUTATION ANALYSIS
D72V1, survival
                     sevent
clus2                   0   1
  C14ORF184 MUTATED     4   2
  C14ORF184 WILD-TYPE 273  76
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  6                 349 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  2                  76 
$`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 

$`C14ORF184 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                7.5                 0.0 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
              61.02              148.01 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
              23.11               22.06 
[1] "7.5 - 61.0 (23.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D72V2, continuous
                     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      63        1       25       107         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF184 MUTATED           0          0          1          1        1
  C14ORF184 WILD-TYPE        18          6         43         32       34
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF184 MUTATED           0         0
  C14ORF184 WILD-TYPE        12         1
D72V3, multiclass
            clus
vv           C14ORF184 MUTATED C14ORF184 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  1                 107
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 1                  43
  STAGE IIIC                 1                  32
  STAGE IV                   1                  34
  STAGE IVA                  0                  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
  C14ORF184 MUTATED     0   1   4   1
  C14ORF184 WILD-TYPE   9  66 245  40
D72V4, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 4                 245
  T4                 1                  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
  C14ORF184 MUTATED     3   2   1
  C14ORF184 WILD-TYPE 217  79  65
D72V5, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  N0                 3                 217
  N1                 2                  79
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   1
  C14ORF184 WILD-TYPE 280  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    1
  C14ORF184 WILD-TYPE  280   47
   clus
vv  C14ORF184 MUTATED C14ORF184 WILD-TYPE
  0                 5                 280
  1                 1                  47
[1] 2 2
[1] FALSE
D72V7, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     3   3
  C14ORF184 WILD-TYPE 167 194
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      3    3
  C14ORF184 WILD-TYPE  167  194
        clus
vv       C14ORF184 MUTATED C14ORF184 WILD-TYPE
  FEMALE                 3                 167
  MALE                   3                 194
[1] 2 2
[1] FALSE
D72V8, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   0
  C14ORF184 WILD-TYPE 295   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    0
  C14ORF184 WILD-TYPE  295    8
     clus
vv    C14ORF184 MUTATED C14ORF184 WILD-TYPE
  NO                  5                 295
  YES                 0                   8
[1] 2 2
[1] FALSE
D72V9, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   1
  C14ORF184 WILD-TYPE 309  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    1
  C14ORF184 WILD-TYPE  309   47
                               clus
vv                              C14ORF184 MUTATED C14ORF184 WILD-TYPE
  COLON ADENOCARCINOMA                          5                 309
  COLON MUCINOUS ADENOCARCINOMA                 1                  47
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF184 MUTATED     4   0   0   0
  C14ORF184 WILD-TYPE 255   3  22  21
D72V10, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  R0                 4                 255
  R1                 0                   3
  R2                 0                  22
  RX                 0                  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"
D72V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF184 MUTATED                                  0     0
  C14ORF184 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF184 MUTATED                           1     4
  C14ORF184 WILD-TYPE                        18   172
D72V12, multiclass
                                  clus
vv                                 C14ORF184 MUTATED C14ORF184 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        1                  18
  WHITE                                            4                 172
[1] 4 2
[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 = ATP6V1B1 MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  ATP6V1B1 MUTATED    12   1
  ATP6V1B1 WILD-TYPE 265  77
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                13                342 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                 1                 77 
$`ATP6V1B1 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6548 TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3664 
       19.04        24.00        21.37        32.75        19.66        54.02 
TCGA-AA-3877 TCGA-AA-3966 TCGA-AD-5900 TCGA-CA-6716 TCGA-CK-5916 TCGA-CM-5861 
       31.00         2.01        12.16        12.20        21.14        15.02 
TCGA-G4-6309 
       85.48 

$`ATP6V1B1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
              2.01               0.00 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             85.48             148.01 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             21.14              22.09 
[1] "2.0 - 85.5 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.9"
D73V2, continuous
                    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      60        1       25       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1B1 MUTATED           0          0          1          1        1
  ATP6V1B1 WILD-TYPE        18          6         43         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  ATP6V1B1 MUTATED           0         0
  ATP6V1B1 WILD-TYPE        12         1
D73V3, multiclass
            clus
vv           ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  ATP6V1B1 MUTATED     2   2   8   2
  ATP6V1B1 WILD-TYPE   7  65 241  39
D73V4, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  T1                2                  7
  T2                2                 65
  T3                8                241
  T4                2                 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
  ATP6V1B1 MUTATED    12   2   0
  ATP6V1B1 WILD-TYPE 208  79  66
D73V5, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  N0               12                208
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   1
  ATP6V1B1 WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    1
  ATP6V1B1 WILD-TYPE  274   47
   clus
vv  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  0               11                274
  1                1                 47
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    10   4
  ATP6V1B1 WILD-TYPE 160 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     10    4
  ATP6V1B1 WILD-TYPE  160  193
        clus
vv       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  FEMALE               10                160
  MALE                  4                193
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   1
  ATP6V1B1 WILD-TYPE 289   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    1
  ATP6V1B1 WILD-TYPE  289    7
     clus
vv    ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  NO                11                289
  YES                1                  7
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED     8   6
  ATP6V1B1 WILD-TYPE 306  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED      8    6
  ATP6V1B1 WILD-TYPE  306   42
                               clus
vv                              ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                6                 42
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ATP6V1B1 MUTATED    10   0   1   2
  ATP6V1B1 WILD-TYPE 249   3  21  19
D73V10, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  R0               10                249
  R1                0                  3
  R2                1                 21
  RX                2                 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"
D73V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V1B1 MUTATED                                  0     1
  ATP6V1B1 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1B1 MUTATED                           1     6
  ATP6V1B1 WILD-TYPE                        18   170
D73V12, multiclass
                                  clus
vv                                 ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           6                170
[1] 4 2
[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 = BCL9 MUTATION ANALYSIS
D74V1, survival
                sevent
clus2              0   1
  BCL9 MUTATED    15   7
  BCL9 WILD-TYPE 262  71
  BCL9 MUTATED BCL9 WILD-TYPE 
            22            333 
  BCL9 MUTATED BCL9 WILD-TYPE 
             7             71 
$`BCL9 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6586 
       19.04        24.00        10.88       100.01         5.88        35.80 
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3947 
       33.53        19.66        29.95         6.97        33.04        33.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-6718 TCGA-CM-6678 
       25.02         4.01        34.98        35.01        10.06        11.01 
TCGA-DM-A0X9 TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6854 
      119.70       139.17         6.18         0.53 

$`BCL9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       106.75         1.94        49.08 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       63.62        22.09        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  BCL9 MUTATED BCL9 WILD-TYPE 
          0.53           0.00 
  BCL9 MUTATED BCL9 WILD-TYPE 
        139.17         148.01 
  BCL9 MUTATED BCL9 WILD-TYPE 
         24.51          22.03 
[1] "0.5 - 139.2 (24.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D74V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCL9 MUTATED         0        0        3        10         3         0
  BCL9 WILD-TYPE      64        1       23        98         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9 MUTATED           1          0          0          1        1         1
  BCL9 WILD-TYPE        17          6         44         32       34        11
                vv
clus             STAGE IVB
  BCL9 MUTATED           0
  BCL9 WILD-TYPE         1
D74V3, multiclass
            clus
vv           BCL9 MUTATED BCL9 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            10             98
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  BCL9 MUTATED     0   1  15   6
  BCL9 WILD-TYPE   9  66 234  35
D74V4, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           15            234
  T4            6             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
  BCL9 MUTATED    17   2   3
  BCL9 WILD-TYPE 203  79  63
D74V5, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  N0           17            203
  N1            2             79
  N2            3             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"
D74V6, binary
                cls
clus               0   1
  BCL9 MUTATED    17   2
  BCL9 WILD-TYPE 268  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     17    2
  BCL9 WILD-TYPE  268   46
   clus
vv  BCL9 MUTATED BCL9 WILD-TYPE
  0           17            268
  1            2             46
[1] 2 2
[1] FALSE
D74V7, binary
                cls
clus               0   1
  BCL9 MUTATED    13   9
  BCL9 WILD-TYPE 157 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     13    9
  BCL9 WILD-TYPE  157  188
        clus
vv       BCL9 MUTATED BCL9 WILD-TYPE
  FEMALE           13            157
  MALE              9            188
[1] 2 2
[1] FALSE
D74V8, binary
                cls
clus               0   1
  BCL9 MUTATED    17   1
  BCL9 WILD-TYPE 283   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     17    1
  BCL9 WILD-TYPE  283    7
     clus
vv    BCL9 MUTATED BCL9 WILD-TYPE
  NO            17            283
  YES            1              7
[1] 2 2
[1] FALSE
D74V9, binary
                cls
clus               0   1
  BCL9 MUTATED    15   7
  BCL9 WILD-TYPE 299  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     15    7
  BCL9 WILD-TYPE  299   41
                               clus
vv                              BCL9 MUTATED BCL9 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCL9 MUTATED    15   0   0   1
  BCL9 WILD-TYPE 244   3  22  20
D74V10, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  R0           15            244
  R1            0              3
  R2            0             22
  RX            1             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"
D74V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL9 MUTATED                                  0     1
  BCL9 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BCL9 MUTATED                           1    10
  BCL9 WILD-TYPE                        18   166
D74V12, multiclass
                                  clus
vv                                 BCL9 MUTATED BCL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(75) Variable = NAA25 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  NAA25 MUTATED    11   2
  NAA25 WILD-TYPE 266  76
  NAA25 MUTATED NAA25 WILD-TYPE 
             13             342 
  NAA25 MUTATED NAA25 WILD-TYPE 
              2              76 
$`NAA25 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-6780 
       19.04        24.00        32.75        33.53        22.09        20.12 
TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-CM-6678 
       29.95        26.99        53.00         4.01        34.98        11.01 
TCGA-F4-6808 
       33.67 

$`NAA25 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NAA25 MUTATED NAA25 WILD-TYPE 
           4.01            0.00 
  NAA25 MUTATED NAA25 WILD-TYPE 
          53.00          148.01 
  NAA25 MUTATED NAA25 WILD-TYPE 
          26.99           21.99 
[1] "4.0 - 53.0 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D75V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAA25 MUTATED         1        0        2         6         3         0
  NAA25 WILD-TYPE      63        1       24       102         5         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        18          6         44         32       35        11
                 vv
clus              STAGE IVB
  NAA25 MUTATED           0
  NAA25 WILD-TYPE         1
D75V3, multiclass
            clus
vv           NAA25 MUTATED NAA25 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  NAA25 MUTATED     1   0   8   5
  NAA25 WILD-TYPE   8  67 241  36
D75V4, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             8             241
  T4             5              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
  NAA25 MUTATED    12   1   1
  NAA25 WILD-TYPE 208  80  65
D75V5, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                 cls
clus                0   1
  NAA25 MUTATED    11   1
  NAA25 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     11    1
  NAA25 WILD-TYPE  274   47
   clus
vv  NAA25 MUTATED NAA25 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D75V7, binary
                 cls
clus                0   1
  NAA25 MUTATED     9   5
  NAA25 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      9    5
  NAA25 WILD-TYPE  161  192
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D75V8, binary
                 cls
clus                0   1
  NAA25 MUTATED    12   0
  NAA25 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     12    0
  NAA25 WILD-TYPE  288    8
     clus
vv    NAA25 MUTATED NAA25 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D75V9, binary
                 cls
clus                0   1
  NAA25 MUTATED     9   5
  NAA25 WILD-TYPE 305  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      9    5
  NAA25 WILD-TYPE  305   43
                               clus
vv                              NAA25 MUTATED NAA25 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NAA25 MUTATED    12   0   0   0
  NAA25 WILD-TYPE 247   3  22  21
D75V10, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             0              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"
D75V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAA25 MUTATED                                  0     0
  NAA25 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NAA25 MUTATED                           2     4
  NAA25 WILD-TYPE                        17   172
D75V12, multiclass
                                  clus
vv                                 NAA25 MUTATED NAA25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = SLC26A8 MUTATION ANALYSIS
D76V1, survival
                   sevent
clus2                 0   1
  SLC26A8 MUTATED    11   4
  SLC26A8 WILD-TYPE 266  74
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               15               340 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
                4                74 
$`SLC26A8 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 
       26.17        79.69        22.06        19.66         3.02        63.98 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AA-A01D TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6537 
       30.02        34.98        10.98        12.76        23.05         4.80 
TCGA-D5-6924 TCGA-DM-A1HB TCGA-DM-A28F 
       14.30       135.65        35.97 

$`SLC26A8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.12        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
             3.02              0.00 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           135.65            148.01 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
            23.05             22.01 
[1] "3.0 - 135.7 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D76V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC26A8 MUTATED         1        0        2         7         1         0
  SLC26A8 WILD-TYPE      63        1       24       101         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A8 MUTATED           0          0          3          2        0
  SLC26A8 WILD-TYPE        18          6         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC26A8 MUTATED           0         0
  SLC26A8 WILD-TYPE        12         1
D76V3, multiclass
            clus
vv           SLC26A8 MUTATED SLC26A8 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                7               101
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC26A8 MUTATED     0   1  13   2
  SLC26A8 WILD-TYPE   9  66 236  39
D76V4, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              13               236
  T4               2                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
  SLC26A8 MUTATED    11   4   1
  SLC26A8 WILD-TYPE 209  77  65
D76V5, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  N0              11               209
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    14   0
  SLC26A8 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     14    0
  SLC26A8 WILD-TYPE  271   48
   clus
vv  SLC26A8 MUTATED SLC26A8 WILD-TYPE
  0              14               271
  1               0                48
[1] 2 2
[1] FALSE
D76V7, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     6  10
  SLC26A8 WILD-TYPE 164 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      6   10
  SLC26A8 WILD-TYPE  164  187
        clus
vv       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  FEMALE               6               164
  MALE                10               187
[1] 2 2
[1] FALSE
D76V8, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    13   0
  SLC26A8 WILD-TYPE 287   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     13    0
  SLC26A8 WILD-TYPE  287    8
     clus
vv    SLC26A8 MUTATED SLC26A8 WILD-TYPE
  NO               13               287
  YES               0                 8
[1] 2 2
[1] FALSE
D76V9, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    12   3
  SLC26A8 WILD-TYPE 302  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     12    3
  SLC26A8 WILD-TYPE  302   45
                               clus
vv                              SLC26A8 MUTATED SLC26A8 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC26A8 MUTATED    13   0   0   1
  SLC26A8 WILD-TYPE 246   3  22  20
D76V10, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               1                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"
D76V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A8 MUTATED                                  0     1
  SLC26A8 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC26A8 MUTATED                           0     9
  SLC26A8 WILD-TYPE                        19   167
D76V12, multiclass
                                  clus
vv                                 SLC26A8 MUTATED SLC26A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(77) Variable = IQCD MUTATION ANALYSIS
D77V1, survival
                sevent
clus2              0   1
  IQCD MUTATED     9   1
  IQCD WILD-TYPE 268  77
  IQCD MUTATED IQCD WILD-TYPE 
            10            345 
  IQCD MUTATED IQCD WILD-TYPE 
             1             77 
$`IQCD MUTATED`
TCGA-AA-3672 TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3538 TCGA-AY-6196 TCGA-AZ-6599 
        0.92         8.38        23.87        26.01         0.20         6.77 
TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6171 TCGA-G4-6317 
       20.02        15.02        14.04        36.00 

$`IQCD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  IQCD MUTATED IQCD WILD-TYPE 
           0.2            0.0 
  IQCD MUTATED IQCD WILD-TYPE 
         36.00         148.01 
  IQCD MUTATED IQCD WILD-TYPE 
         14.53          22.09 
[1] "0.2 - 36.0 (14.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D77V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQCD MUTATED         4        0        0         2         0         0
  IQCD WILD-TYPE      60        1       26       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IQCD MUTATED           1          0          1          2        0         0
  IQCD WILD-TYPE        17          6         43         31       35        12
                vv
clus             STAGE IVB
  IQCD MUTATED           0
  IQCD WILD-TYPE         1
D77V3, multiclass
            clus
vv           IQCD MUTATED IQCD WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  IQCD MUTATED     0   4   6   0
  IQCD WILD-TYPE   9  63 243  41
D77V4, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  T1            0              9
  T2            4             63
  T3            6            243
  T4            0             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
  IQCD MUTATED     6   2   2
  IQCD WILD-TYPE 214  79  64
D77V5, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  N0            6            214
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                cls
clus               0   1
  IQCD MUTATED     7   0
  IQCD WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      7    0
  IQCD WILD-TYPE  278   48
   clus
vv  IQCD MUTATED IQCD WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D77V7, binary
                cls
clus               0   1
  IQCD MUTATED     6   4
  IQCD WILD-TYPE 164 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      6    4
  IQCD WILD-TYPE  164  193
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  FEMALE            6            164
  MALE              4            193
[1] 2 2
[1] FALSE
D77V8, binary
                cls
clus               0   1
  IQCD MUTATED     9   0
  IQCD WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      9    0
  IQCD WILD-TYPE  291    8
     clus
vv    IQCD MUTATED IQCD WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D77V9, binary
                cls
clus               0   1
  IQCD MUTATED     9   1
  IQCD WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      9    1
  IQCD WILD-TYPE  305   47
                               clus
vv                              IQCD MUTATED IQCD WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IQCD MUTATED     7   0   0   0
  IQCD WILD-TYPE 252   3  22  21
D77V10, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            0             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"
D77V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQCD MUTATED                                  0     0
  IQCD WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IQCD MUTATED                           1     7
  IQCD WILD-TYPE                        18   169
D77V12, multiclass
                                  clus
vv                                 IQCD MUTATED IQCD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = CHD3 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  CHD3 MUTATED    17   6
  CHD3 WILD-TYPE 260  72
  CHD3 MUTATED CHD3 WILD-TYPE 
            23            332 
  CHD3 MUTATED CHD3 WILD-TYPE 
             6             72 
$`CHD3 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-2676 
       19.04        19.04        25.08       100.01        26.17        42.90 
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3845 
       33.53        24.39        19.66         3.02        26.99         0.00 
TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-6197 
       53.00        18.05         4.01        34.98         1.02        21.44 
TCGA-AZ-4315 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6854 TCGA-G4-6309 
       58.39         9.44       135.65         0.53        85.48 

$`CHD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CHD3 MUTATED CHD3 WILD-TYPE 
             0              0 
  CHD3 MUTATED CHD3 WILD-TYPE 
        135.65         148.01 
  CHD3 MUTATED CHD3 WILD-TYPE 
        24.390         22.045 
[1] "0.0 - 135.7 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D78V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD3 MUTATED         1        0        5         8         4         0
  CHD3 WILD-TYPE      63        1       21       100         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD3 MUTATED           0          0          4          1        1         0
  CHD3 WILD-TYPE        18          6         40         32       34        12
                vv
clus             STAGE IVB
  CHD3 MUTATED           0
  CHD3 WILD-TYPE         1
D78V3, multiclass
            clus
vv           CHD3 MUTATED CHD3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA             8            100
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  CHD3 MUTATED     0   1  17   6
  CHD3 WILD-TYPE   9  66 232  35
D78V4, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           17            232
  T4            6             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
  CHD3 MUTATED    19   5   0
  CHD3 WILD-TYPE 201  76  66
D78V5, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  N0           19            201
  N1            5             76
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                cls
clus               0   1
  CHD3 MUTATED    20   1
  CHD3 WILD-TYPE 265  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     20    1
  CHD3 WILD-TYPE  265   47
   clus
vv  CHD3 MUTATED CHD3 WILD-TYPE
  0           20            265
  1            1             47
[1] 2 2
[1] FALSE
D78V7, binary
                cls
clus               0   1
  CHD3 MUTATED    11  13
  CHD3 WILD-TYPE 159 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     11   13
  CHD3 WILD-TYPE  159  184
        clus
vv       CHD3 MUTATED CHD3 WILD-TYPE
  FEMALE           11            159
  MALE             13            184
[1] 2 2
[1] FALSE
D78V8, binary
                cls
clus               0   1
  CHD3 MUTATED    18   1
  CHD3 WILD-TYPE 282   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     18    1
  CHD3 WILD-TYPE  282    7
     clus
vv    CHD3 MUTATED CHD3 WILD-TYPE
  NO            18            282
  YES            1              7
[1] 2 2
[1] FALSE
D78V9, binary
                cls
clus               0   1
  CHD3 MUTATED    20   3
  CHD3 WILD-TYPE 294  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     20    3
  CHD3 WILD-TYPE  294   45
                               clus
vv                              CHD3 MUTATED CHD3 WILD-TYPE
  COLON ADENOCARCINOMA                    20            294
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD3 MUTATED    19   0   1   1
  CHD3 WILD-TYPE 240   3  21  20
D78V10, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  R0           19            240
  R1            0              3
  R2            1             21
  RX            1             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"
D78V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD3 MUTATED                                  0     0
  CHD3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD3 MUTATED                           2    12
  CHD3 WILD-TYPE                        17   164
D78V12, multiclass
                                  clus
vv                                 CHD3 MUTATED CHD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      12            164
[1] 4 2
[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 = PLEKHF2 MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  PLEKHF2 MUTATED     7   2
  PLEKHF2 WILD-TYPE 270  76
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
                9               346 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
                2                76 
$`PLEKHF2 MUTATED`
TCGA-AA-3713 TCGA-A6-5665 TCGA-AA-3977 TCGA-D5-6533 TCGA-D5-6541 TCGA-G4-6303 
       19.04        22.06        25.02        25.48        15.58        65.85 
TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6626 
       85.48        13.78        46.75 

$`PLEKHF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 
       44.68        55.04        61.91        36.00 

  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
            13.78              0.00 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
            85.48            148.01 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
            25.02             22.01 
[1] "13.8 - 85.5 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D79V2, continuous
                   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      63        0       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHF2 MUTATED           0          0          1          0        2
  PLEKHF2 WILD-TYPE        18          6         43         33       33
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHF2 MUTATED           0         0
  PLEKHF2 WILD-TYPE        12         1
D79V3, multiclass
            clus
vv           PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 1                 0
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  PLEKHF2 MUTATED     0   2   6   1
  PLEKHF2 WILD-TYPE   9  65 243  40
D79V4, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               6               243
  T4               1                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
  PLEKHF2 MUTATED     8   2   0
  PLEKHF2 WILD-TYPE 212  79  66
D79V5, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  N0               8               212
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     5   2
  PLEKHF2 WILD-TYPE 280  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      5    2
  PLEKHF2 WILD-TYPE  280   46
   clus
vv  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  0               5               280
  1               2                46
[1] 2 2
[1] FALSE
D79V7, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     4   6
  PLEKHF2 WILD-TYPE 166 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      4    6
  PLEKHF2 WILD-TYPE  166  191
        clus
vv       PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  FEMALE               4               166
  MALE                 6               191
[1] 2 2
[1] FALSE
D79V8, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     8   1
  PLEKHF2 WILD-TYPE 292   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      8    1
  PLEKHF2 WILD-TYPE  292    7
     clus
vv    PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  NO                8               292
  YES               1                 7
[1] 2 2
[1] FALSE
D79V9, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED    10   0
  PLEKHF2 WILD-TYPE 304  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED     10    0
  PLEKHF2 WILD-TYPE  304   48
                               clus
vv                              PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHF2 MUTATED     7   0   1   1
  PLEKHF2 WILD-TYPE 252   3  21  20
D79V10, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               1                21
  RX               1                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"
D79V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHF2 MUTATED                                  0     0
  PLEKHF2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHF2 MUTATED                           2     6
  PLEKHF2 WILD-TYPE                        17   170
D79V12, multiclass
                                  clus
vv                                 PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = FKBP9 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  FKBP9 MUTATED    14   3
  FKBP9 WILD-TYPE 263  75
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             17             338 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              3              75 
$`FKBP9 MUTATED`
TCGA-AA-3697 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6780 TCGA-AA-3977 
       85.05       100.01        26.17        79.69        20.12        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-5913 
        4.01        34.98         1.02        83.24        58.39        51.32 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6678 TCGA-D5-6930 TCGA-DM-A28H 
       22.98        15.02        11.01        13.35       117.07 

$`FKBP9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FKBP9 MUTATED FKBP9 WILD-TYPE 
           1.02            0.00 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
         117.07          148.01 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
          26.17           21.99 
[1] "1.0 - 117.1 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D80V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKBP9 MUTATED         1        0        3         7         2         0
  FKBP9 WILD-TYPE      63        1       23       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FKBP9 MUTATED           0          0          1          1        0         1
  FKBP9 WILD-TYPE        18          6         43         32       35        11
                 vv
clus              STAGE IVB
  FKBP9 MUTATED           0
  FKBP9 WILD-TYPE         1
D80V3, multiclass
            clus
vv           FKBP9 MUTATED FKBP9 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  FKBP9 MUTATED     0   2  12   3
  FKBP9 WILD-TYPE   9  65 237  38
D80V4, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            12             237
  T4             3              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
  FKBP9 MUTATED    14   2   1
  FKBP9 WILD-TYPE 206  79  65
D80V5, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  N0            14             206
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                 cls
clus                0   1
  FKBP9 MUTATED    13   1
  FKBP9 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     13    1
  FKBP9 WILD-TYPE  272   47
   clus
vv  FKBP9 MUTATED FKBP9 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D80V7, binary
                 cls
clus                0   1
  FKBP9 MUTATED     6  11
  FKBP9 WILD-TYPE 164 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED      6   11
  FKBP9 WILD-TYPE  164  186
        clus
vv       FKBP9 MUTATED FKBP9 WILD-TYPE
  FEMALE             6             164
  MALE              11             186
[1] 2 2
[1] FALSE
D80V8, binary
                 cls
clus                0   1
  FKBP9 MUTATED    14   0
  FKBP9 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     14    0
  FKBP9 WILD-TYPE  286    8
     clus
vv    FKBP9 MUTATED FKBP9 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D80V9, binary
                 cls
clus                0   1
  FKBP9 MUTATED    14   3
  FKBP9 WILD-TYPE 300  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     14    3
  FKBP9 WILD-TYPE  300   45
                               clus
vv                              FKBP9 MUTATED FKBP9 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FKBP9 MUTATED    12   0   0   1
  FKBP9 WILD-TYPE 247   3  22  20
D80V10, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D80V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKBP9 MUTATED                                  0     1
  FKBP9 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FKBP9 MUTATED                           0    11
  FKBP9 WILD-TYPE                        19   165
D80V12, multiclass
                                  clus
vv                                 FKBP9 MUTATED FKBP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(81) Variable = HPS3 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  HPS3 MUTATED    16   4
  HPS3 WILD-TYPE 261  74
  HPS3 MUTATED HPS3 WILD-TYPE 
            20            335 
  HPS3 MUTATED HPS3 WILD-TYPE 
             4             74 
$`HPS3 MUTATED`
TCGA-AA-3697 TCGA-AA-3950 TCGA-AD-6548 TCGA-AD-6895 TCGA-G4-6321 TCGA-G4-6588 
       85.05        24.00        21.37        25.08        22.09        26.17 
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01Q 
       30.44        63.98        78.08        25.02         4.01         1.02 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5797 TCGA-CK-4950 
       58.39        22.36        49.41         6.77        12.59        85.45 
TCGA-CM-6172 TCGA-G4-6307 
       11.01        55.04 

$`HPS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        63.62        35.80        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        62.79        88.21        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  HPS3 MUTATED HPS3 WILD-TYPE 
          1.02           0.00 
  HPS3 MUTATED HPS3 WILD-TYPE 
         85.45         148.01 
  HPS3 MUTATED HPS3 WILD-TYPE 
         25.05          21.99 
[1] "1.0 - 85.5 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D81V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HPS3 MUTATED         3        0        5         4         1         0
  HPS3 WILD-TYPE      61        1       21       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HPS3 MUTATED           1          0          4          0        0         1
  HPS3 WILD-TYPE        17          6         40         33       35        11
                vv
clus             STAGE IVB
  HPS3 MUTATED           0
  HPS3 WILD-TYPE         1
D81V3, multiclass
            clus
vv           HPS3 MUTATED HPS3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  HPS3 MUTATED     0   5  14   1
  HPS3 WILD-TYPE   9  62 235  40
D81V4, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           14            235
  T4            1             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
  HPS3 MUTATED    15   5   0
  HPS3 WILD-TYPE 205  76  66
D81V5, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  N0           15            205
  N1            5             76
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                cls
clus               0   1
  HPS3 MUTATED    15   1
  HPS3 WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     15    1
  HPS3 WILD-TYPE  270   47
   clus
vv  HPS3 MUTATED HPS3 WILD-TYPE
  0           15            270
  1            1             47
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus               0   1
  HPS3 MUTATED    10  10
  HPS3 WILD-TYPE 160 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     10   10
  HPS3 WILD-TYPE  160  187
        clus
vv       HPS3 MUTATED HPS3 WILD-TYPE
  FEMALE           10            160
  MALE             10            187
[1] 2 2
[1] FALSE
D81V8, binary
                cls
clus               0   1
  HPS3 MUTATED    18   0
  HPS3 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     18    0
  HPS3 WILD-TYPE  282    8
     clus
vv    HPS3 MUTATED HPS3 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D81V9, binary
                cls
clus               0   1
  HPS3 MUTATED    17   3
  HPS3 WILD-TYPE 297  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     17    3
  HPS3 WILD-TYPE  297   45
                               clus
vv                              HPS3 MUTATED HPS3 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HPS3 MUTATED    16   1   0   0
  HPS3 WILD-TYPE 243   2  22  21
D81V10, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  R0           16            243
  R1            1              2
  R2            0             22
  RX            0             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"
D81V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HPS3 MUTATED                                  0     1
  HPS3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HPS3 MUTATED                           1    11
  HPS3 WILD-TYPE                        18   165
D81V12, multiclass
                                  clus
vv                                 HPS3 MUTATED HPS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(82) Variable = ATM MUTATION ANALYSIS
D82V1, survival
               sevent
clus2             0   1
  ATM MUTATED   101  27
  ATM WILD-TYPE 176  51
  ATM MUTATED ATM WILD-TYPE 
          128           227 
  ATM MUTATED ATM WILD-TYPE 
           27            51 
$`ATM MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3662 
       14.53         1.02        13.02        37.05        19.07         6.05 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3950 TCGA-AD-6548 TCGA-AZ-6601 
       85.05        19.04        31.07        24.00        21.37       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
        1.94        49.08        22.09        35.80        26.17        79.69 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       29.19        33.53        22.09        22.06         8.38        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 
       20.12        19.66         3.02        35.01        63.98         1.02 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 
       29.95        61.02        78.08         6.97        54.02        47.01 
TCGA-AA-3679 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3861 TCGA-AA-3966 
       15.02        26.99        10.06        25.02        30.05         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02Y TCGA-AD-6889 
       25.02         4.01        34.98        35.01        39.98        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        14.50        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20        21.44        58.39        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       49.41         6.77        29.56        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 
       14.30        17.56        15.62        51.32        21.99         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
      124.27        23.05        13.02        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6171 
       15.02         5.03        15.02        17.03        29.03        14.04 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       11.08        10.06        12.03        54.61        19.59        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        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         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 
       14.30        11.64        13.41        10.26        38.20        92.75 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       44.32       135.65        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
      117.07        98.24         6.18        43.04        33.67         0.53 
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-G4-6315 TCGA-G4-6317 
       61.91        36.00 

$`ATM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 
       24.33        24.16        24.03        36.03         8.05        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 
        0.92        19.00        36.00        19.04        14.93        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 
       19.07        38.04        21.99        39.06        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 TCGA-A6-2671 
       10.88       106.75         5.88        63.62        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3511 
       21.76        24.69        23.87        20.28         7.04         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       24.00        20.98        13.94         2.01        14.01        50.04 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3815 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6965 TCGA-AY-4070 
       41.00        18.05        40.96        12.16        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6600 
        0.95        33.01        17.82         1.41         5.13        12.10 
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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5916 TCGA-CK-6747 
       12.59        12.20       148.01        85.45        21.14        82.95 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 
       20.02        37.02        25.02        29.06        22.03        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        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-D5-5537 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6534 
       11.08        11.01        45.40        56.09        55.92        43.27 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       10.13         9.04         9.44        13.35        12.00        11.38 
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-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-F4-6459 TCGA-F4-6460 
      140.38         7.50       131.51       139.17         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
       35.74        47.87         1.55        34.42        41.42        13.25 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6323 TCGA-G4-6626 
       47.41        74.56        65.85        13.78        46.75 

  ATM MUTATED ATM WILD-TYPE 
          0.2           0.0 
  ATM MUTATED ATM WILD-TYPE 
       135.65        148.01 
  ATM MUTATED ATM WILD-TYPE 
        22.70         21.76 
[1] "0.2 - 135.7 (22.7)" "0.0 - 148.0 (21.8)"
[1] "hr=" "1.3"
D82V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATM MUTATED        19        0       12        48         4         0
  ATM WILD-TYPE      45        1       14        60         4         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATM MUTATED           6          2         14         10        6         3
  ATM WILD-TYPE        12          4         30         23       29         9
               vv
clus            STAGE IVB
  ATM MUTATED           0
  ATM WILD-TYPE         1
D82V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I             19            45
  STAGE IA             0             1
  STAGE II            12            14
  STAGE IIA           48            60
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            6            12
  STAGE IIIA           2             4
  STAGE IIIB          14            30
  STAGE IIIC          10            23
  STAGE IV             6            29
  STAGE IVA            3             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
  ATM MUTATED     3  23  93  13
  ATM WILD-TYPE   6  44 156  28
D82V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           3             6
  T2          23            44
  T3          93           156
  T4          13            28
[1] 4 2
[1] TRUE
[1] "dimension 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    92  24  16
  ATM WILD-TYPE 128  57  50
D82V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          92           128
  N1          24            57
  N2          16            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"
D82V6, binary
               cls
clus              0   1
  ATM MUTATED   100   9
  ATM WILD-TYPE 185  39
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    100    9
  ATM WILD-TYPE  185   39
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0         100           185
  1           9            39
[1] 2 2
[1] FALSE
D82V7, binary
               cls
clus              0   1
  ATM MUTATED    64  68
  ATM WILD-TYPE 106 129
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     64   68
  ATM WILD-TYPE  106  129
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          64           106
  MALE            68           129
[1] 2 2
[1] FALSE
D82V8, binary
               cls
clus              0   1
  ATM MUTATED   108   2
  ATM WILD-TYPE 192   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    108    2
  ATM WILD-TYPE  192    6
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO          108           192
  YES           2             6
[1] 2 2
[1] FALSE
D82V9, binary
               cls
clus              0   1
  ATM MUTATED   110  20
  ATM WILD-TYPE 204  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    110   20
  ATM WILD-TYPE  204   28
                               clus
vv                              ATM MUTATED ATM WILD-TYPE
  COLON ADENOCARCINOMA                  110           204
  COLON MUCINOUS ADENOCARCINOMA          20            28
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    86   0   3  13
  ATM WILD-TYPE 173   3  19   8
D82V10, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          86           173
  R1           0             3
  R2           3            19
  RX          13             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"
D82V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     5
  ATM WILD-TYPE                                1     5
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           6    88
  ATM WILD-TYPE                        13    88
D82V12, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      5             5
  BLACK OR AFRICAN AMERICAN                  6            13
  WHITE                                     88            88
[1] 4 2
[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 = RLIM MUTATION ANALYSIS
D83V1, survival
                sevent
clus2              0   1
  RLIM MUTATED    12   2
  RLIM WILD-TYPE 265  76
  RLIM MUTATED RLIM WILD-TYPE 
            14            341 
  RLIM MUTATED RLIM WILD-TYPE 
             2             76 
$`RLIM MUTATED`
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-6651 TCGA-AA-3678 TCGA-AA-3947 
       22.09        35.80        91.79        21.76        47.01        33.01 
TCGA-AZ-5407 TCGA-CK-4952 TCGA-CM-4752 TCGA-D5-5540 TCGA-F4-6570 TCGA-F4-6855 
       88.21        15.62        13.02        56.09         6.18        47.41 
TCGA-G4-6293 TCGA-G4-6303 
      133.18        65.85 

$`RLIM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        0.53        35.31        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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         21.990 
[1] "6.2 - 133.2 (41.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D83V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RLIM MUTATED         1        0        0         6         1         0
  RLIM WILD-TYPE      63        1       26       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RLIM MUTATED           3          0          1          1        1         0
  RLIM WILD-TYPE        15          6         43         32       34        12
                vv
clus             STAGE IVB
  RLIM MUTATED           0
  RLIM WILD-TYPE         1
D83V3, multiclass
            clus
vv           RLIM MUTATED RLIM WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  RLIM MUTATED     1   2   9   2
  RLIM WILD-TYPE   8  65 240  39
D83V4, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  T1            1              8
  T2            2             65
  T3            9            240
  T4            2             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
  RLIM MUTATED     8   5   1
  RLIM WILD-TYPE 212  76  65
D83V5, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  N0            8            212
  N1            5             76
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                cls
clus               0   1
  RLIM MUTATED    11   1
  RLIM WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     11    1
  RLIM WILD-TYPE  274   47
   clus
vv  RLIM MUTATED RLIM WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D83V7, binary
                cls
clus               0   1
  RLIM MUTATED    12   2
  RLIM WILD-TYPE 158 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     12    2
  RLIM WILD-TYPE  158  195
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  FEMALE           12            158
  MALE              2            195
[1] 2 2
[1] FALSE
D83V8, binary
                cls
clus               0   1
  RLIM MUTATED    13   0
  RLIM WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     13    0
  RLIM WILD-TYPE  287    8
     clus
vv    RLIM MUTATED RLIM WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D83V9, binary
                cls
clus               0   1
  RLIM MUTATED    12   2
  RLIM WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     12    2
  RLIM WILD-TYPE  302   46
                               clus
vv                              RLIM MUTATED RLIM WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RLIM MUTATED    11   0   0   1
  RLIM WILD-TYPE 248   3  22  20
D83V10, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            1             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"
D83V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RLIM MUTATED                                  0     0
  RLIM WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RLIM MUTATED                           1    11
  RLIM WILD-TYPE                        18   165
D83V12, multiclass
                                  clus
vv                                 RLIM MUTATED RLIM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(84) Variable = CYLD MUTATION ANALYSIS
D84V1, survival
                sevent
clus2              0   1
  CYLD MUTATED    18   4
  CYLD WILD-TYPE 259  74
  CYLD MUTATED CYLD WILD-TYPE 
            22            333 
  CYLD MUTATED CYLD WILD-TYPE 
             4             74 
$`CYLD MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3815 
        1.02        19.04        31.63        63.98        78.08        33.04 
TCGA-AA-3973 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 
       13.05        34.98        83.24        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 
       12.49        33.67        65.85        46.75 

$`CYLD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-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        14.04        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-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       61.91        36.00        13.78 

  CYLD MUTATED CYLD WILD-TYPE 
          1.02           0.00 
  CYLD MUTATED CYLD WILD-TYPE 
         88.21         148.01 
  CYLD MUTATED CYLD WILD-TYPE 
        31.825         21.990 
[1] "1.0 - 88.2 (31.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D84V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYLD MUTATED         3        0        4         7         1         0
  CYLD WILD-TYPE      61        1       22       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYLD MUTATED           0          1          2          1        2         0
  CYLD WILD-TYPE        18          5         42         32       33        12
                vv
clus             STAGE IVB
  CYLD MUTATED           0
  CYLD WILD-TYPE         1
D84V3, multiclass
            clus
vv           CYLD MUTATED CYLD WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  CYLD MUTATED     2   1  16   3
  CYLD WILD-TYPE   7  66 233  38
D84V4, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  T1            2              7
  T2            1             66
  T3           16            233
  T4            3             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
  CYLD MUTATED    16   5   1
  CYLD WILD-TYPE 204  76  65
D84V5, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  N0           16            204
  N1            5             76
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
                cls
clus               0   1
  CYLD MUTATED    20   2
  CYLD WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     20    2
  CYLD WILD-TYPE  265   46
   clus
vv  CYLD MUTATED CYLD WILD-TYPE
  0           20            265
  1            2             46
[1] 2 2
[1] FALSE
D84V7, binary
                cls
clus               0   1
  CYLD MUTATED    11  11
  CYLD WILD-TYPE 159 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     11   11
  CYLD WILD-TYPE  159  186
        clus
vv       CYLD MUTATED CYLD WILD-TYPE
  FEMALE           11            159
  MALE             11            186
[1] 2 2
[1] FALSE
D84V8, binary
                cls
clus               0   1
  CYLD MUTATED    20   0
  CYLD WILD-TYPE 280   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     20    0
  CYLD WILD-TYPE  280    8
     clus
vv    CYLD MUTATED CYLD WILD-TYPE
  NO            20            280
  YES            0              8
[1] 2 2
[1] FALSE
D84V9, binary
                cls
clus               0   1
  CYLD MUTATED    19   3
  CYLD WILD-TYPE 295  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     19    3
  CYLD WILD-TYPE  295   45
                               clus
vv                              CYLD MUTATED CYLD WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CYLD MUTATED    18   0   1   2
  CYLD WILD-TYPE 241   3  21  19
D84V10, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  R0           18            241
  R1            0              3
  R2            1             21
  RX            2             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"
D84V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYLD MUTATED                                  0     2
  CYLD WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CYLD MUTATED                           1    12
  CYLD WILD-TYPE                        18   164
D84V12, multiclass
                                  clus
vv                                 CYLD MUTATED CYLD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      12            164
[1] 4 2
[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 = GGT1 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  GGT1 MUTATED     6   2
  GGT1 WILD-TYPE 271  76
  GGT1 MUTATED GGT1 WILD-TYPE 
             8            347 
  GGT1 MUTATED GGT1 WILD-TYPE 
             2             76 
$`GGT1 MUTATED`
TCGA-A6-5662 TCGA-CK-6748 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6537 TCGA-D5-6538 
       23.61         2.01         5.03        15.02         4.80        17.13 
TCGA-DM-A1D0 TCGA-G4-6306 
      130.65        44.68 

$`GGT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6751 TCGA-CM-4743 
       51.32        21.99        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-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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GGT1 MUTATED GGT1 WILD-TYPE 
          2.01           0.00 
  GGT1 MUTATED GGT1 WILD-TYPE 
        130.65         148.01 
  GGT1 MUTATED GGT1 WILD-TYPE 
        16.075         22.090 
[1] "2.0 - 130.7 (16.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D85V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGT1 MUTATED         1        0        0         1         0         0
  GGT1 WILD-TYPE      63        1       26       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GGT1 MUTATED           0          0          2          0        1         2
  GGT1 WILD-TYPE        18          6         42         33       34        10
                vv
clus             STAGE IVB
  GGT1 MUTATED           0
  GGT1 WILD-TYPE         1
D85V3, multiclass
            clus
vv           GGT1 MUTATED GGT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             2             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
  GGT1 MUTATED     0   2   6   0
  GGT1 WILD-TYPE   9  65 243  41
D85V4, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            0             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
  GGT1 MUTATED     3   3   2
  GGT1 WILD-TYPE 217  78  64
D85V5, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  N0            3            217
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
                cls
clus               0   1
  GGT1 MUTATED     4   3
  GGT1 WILD-TYPE 281  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      4    3
  GGT1 WILD-TYPE  281   45
   clus
vv  GGT1 MUTATED GGT1 WILD-TYPE
  0            4            281
  1            3             45
[1] 2 2
[1] FALSE
D85V7, binary
                cls
clus               0   1
  GGT1 MUTATED     4   4
  GGT1 WILD-TYPE 166 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      4    4
  GGT1 WILD-TYPE  166  193
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  FEMALE            4            166
  MALE              4            193
[1] 2 2
[1] FALSE
D85V8, binary
                cls
clus               0   1
  GGT1 MUTATED     7   0
  GGT1 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      7    0
  GGT1 WILD-TYPE  293    8
     clus
vv    GGT1 MUTATED GGT1 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D85V9, binary
                cls
clus               0   1
  GGT1 MUTATED     7   1
  GGT1 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      7    1
  GGT1 WILD-TYPE  307   47
                               clus
vv                              GGT1 MUTATED GGT1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GGT1 MUTATED     5   0   0   1
  GGT1 WILD-TYPE 254   3  22  20
D85V10, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D85V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGT1 MUTATED                                  0     0
  GGT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GGT1 MUTATED                           0     8
  GGT1 WILD-TYPE                        19   168
D85V12, multiclass
                                  clus
vv                                 GGT1 MUTATED GGT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = CYSLTR2 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                 0   1
  CYSLTR2 MUTATED    13   2
  CYSLTR2 WILD-TYPE 264  76
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               15               340 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                2                76 
$`CYSLTR2 MUTATED`
TCGA-AA-3496 TCGA-AA-3525 TCGA-AD-6548 TCGA-G4-6310 TCGA-A6-2671 TCGA-A6-6781 
        1.02         8.05        21.37        63.62        43.76        19.66 
TCGA-AA-A00J TCGA-AA-A00O TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-6676 
       18.05        27.02        12.76        10.06        13.02        11.08 
TCGA-CM-6680 TCGA-D5-5539 TCGA-DM-A28K 
       12.03        19.59        98.24 

$`CYSLTR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        46.65        43.76        42.90        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-A6-6648 
       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-A6-6782 
       21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        10.06        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
             1.02              0.00 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            98.24            148.01 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            18.05             22.39 
[1] "1.0 - 98.2 (18.1)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D86V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYSLTR2 MUTATED         2        0        1         4         0         0
  CYSLTR2 WILD-TYPE      62        1       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYSLTR2 MUTATED           0          1          4          2        1
  CYSLTR2 WILD-TYPE        18          5         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  CYSLTR2 MUTATED           0         0
  CYSLTR2 WILD-TYPE        12         1
D86V3, multiclass
            clus
vv           CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               4                40
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  CYSLTR2 MUTATED     0   2  11   2
  CYSLTR2 WILD-TYPE   9  65 238  39
D86V4, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              11               238
  T4               2                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
  CYSLTR2 MUTATED     7   5   3
  CYSLTR2 WILD-TYPE 213  76  63
D86V5, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  N0               7               213
  N1               5                76
  N2               3                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"
D86V6, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    13   1
  CYSLTR2 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     13    1
  CYSLTR2 WILD-TYPE  272   47
   clus
vv  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  0              13               272
  1               1                47
[1] 2 2
[1] FALSE
D86V7, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED     4  11
  CYSLTR2 WILD-TYPE 166 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      4   11
  CYSLTR2 WILD-TYPE  166  186
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  FEMALE               4               166
  MALE                11               186
[1] 2 2
[1] FALSE
D86V8, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    12   1
  CYSLTR2 WILD-TYPE 288   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     12    1
  CYSLTR2 WILD-TYPE  288    7
     clus
vv    CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  NO               12               288
  YES               1                 7
[1] 2 2
[1] FALSE
D86V9, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    10   5
  CYSLTR2 WILD-TYPE 304  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     10    5
  CYSLTR2 WILD-TYPE  304   43
                               clus
vv                              CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYSLTR2 MUTATED    12   0   0   2
  CYSLTR2 WILD-TYPE 247   3  22  19
D86V10, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               2                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"
D86V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYSLTR2 MUTATED                                  0     2
  CYSLTR2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYSLTR2 MUTATED                           1     8
  CYSLTR2 WILD-TYPE                        18   168
D86V12, multiclass
                                  clus
vv                                 CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          8               168
[1] 4 2
[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 = ATG5 MUTATION ANALYSIS
D87V1, survival
                sevent
clus2              0   1
  ATG5 MUTATED     7   0
  ATG5 WILD-TYPE 270  78
  ATG5 MUTATED ATG5 WILD-TYPE 
             7            348 
  ATG5 MUTATED ATG5 WILD-TYPE 
             0             78 
$`ATG5 MUTATED`
TCGA-AA-3977 TCGA-AA-A017 TCGA-AY-6197 TCGA-CM-4744 TCGA-D5-6532 TCGA-D5-6540 
       25.02        15.02        21.44        20.02        18.25        16.14 
TCGA-D5-6929 
       13.41 

$`ATG5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ATG5 MUTATED ATG5 WILD-TYPE 
         13.41           0.00 
  ATG5 MUTATED ATG5 WILD-TYPE 
         25.02         148.01 
  ATG5 MUTATED ATG5 WILD-TYPE 
        18.250         22.225 
[1] "13.4 - 25.0 (18.2)" "0.0 - 148.0 (22.2)"
[1] "hr="     "9200000"
D87V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG5 MUTATED         2        0        0         3         1         0
  ATG5 WILD-TYPE      62        1       26       105         7         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        18          6         44         33       34        12
                vv
clus             STAGE IVB
  ATG5 MUTATED           0
  ATG5 WILD-TYPE         1
D87V3, multiclass
            clus
vv           ATG5 MUTATED ATG5 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  ATG5 MUTATED     0   3   4   1
  ATG5 WILD-TYPE   9  64 245  40
D87V4, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            4            245
  T4            1             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
  ATG5 MUTATED     7   1   0
  ATG5 WILD-TYPE 213  80  66
D87V5, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                cls
clus               0   1
  ATG5 MUTATED     4   1
  ATG5 WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      4    1
  ATG5 WILD-TYPE  281   47
   clus
vv  ATG5 MUTATED ATG5 WILD-TYPE
  0            4            281
  1            1             47
[1] 2 2
[1] FALSE
D87V7, binary
                cls
clus               0   1
  ATG5 MUTATED     3   5
  ATG5 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      3    5
  ATG5 WILD-TYPE  167  192
        clus
vv       ATG5 MUTATED ATG5 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D87V8, binary
                cls
clus               0   1
  ATG5 MUTATED     7   0
  ATG5 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      7    0
  ATG5 WILD-TYPE  293    8
     clus
vv    ATG5 MUTATED ATG5 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D87V9, binary
                cls
clus               0   1
  ATG5 MUTATED     7   1
  ATG5 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      7    1
  ATG5 WILD-TYPE  307   47
                               clus
vv                              ATG5 MUTATED ATG5 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ATG5 MUTATED     6   0   0   1
  ATG5 WILD-TYPE 253   3  22  20
D87V10, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D87V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG5 MUTATED                                  0     0
  ATG5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATG5 MUTATED                           0     6
  ATG5 WILD-TYPE                        19   170
D87V12, multiclass
                                  clus
vv                                 ATG5 MUTATED ATG5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = MAP4K3 MUTATION ANALYSIS
D88V1, survival
                  sevent
clus2                0   1
  MAP4K3 MUTATED    11   5
  MAP4K3 WILD-TYPE 266  73
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              16              339 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               5               73 
$`MAP4K3 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-3489 TCGA-AA-3663 TCGA-AA-3947 
       26.17        79.69        33.53         7.04         6.97        33.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-6169 
        4.01        34.98        83.24         5.23        12.76        13.02 
TCGA-CM-6679 TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6569 
       10.06        60.79       117.07        35.74 

$`MAP4K3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
      119.93        35.97        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
            4.01             0.00 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
          117.07           148.01 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
           29.59            22.03 
[1] "4.0 - 117.1 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D88V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP4K3 MUTATED         2        0        2         7         4         0
  MAP4K3 WILD-TYPE      62        1       24       101         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP4K3 MUTATED           0          0          1          1        0
  MAP4K3 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  MAP4K3 MUTATED           0         0
  MAP4K3 WILD-TYPE        12         1
D88V3, multiclass
            clus
vv           MAP4K3 MUTATED MAP4K3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  MAP4K3 MUTATED     0   2  10   5
  MAP4K3 WILD-TYPE   9  65 239  36
D88V4, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              5               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
  MAP4K3 MUTATED    15   1   1
  MAP4K3 WILD-TYPE 205  80  65
D88V5, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  N0             15              205
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V6, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    16   0
  MAP4K3 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     16    0
  MAP4K3 WILD-TYPE  269   48
   clus
vv  MAP4K3 MUTATED MAP4K3 WILD-TYPE
  0             16              269
  1              0               48
[1] 2 2
[1] FALSE
D88V7, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED     5  12
  MAP4K3 WILD-TYPE 165 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED      5   12
  MAP4K3 WILD-TYPE  165  185
        clus
vv       MAP4K3 MUTATED MAP4K3 WILD-TYPE
  FEMALE              5              165
  MALE               12              185
[1] 2 2
[1] FALSE
D88V8, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    13   0
  MAP4K3 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     13    0
  MAP4K3 WILD-TYPE  287    8
     clus
vv    MAP4K3 MUTATED MAP4K3 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D88V9, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    14   3
  MAP4K3 WILD-TYPE 300  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     14    3
  MAP4K3 WILD-TYPE  300   45
                               clus
vv                              MAP4K3 MUTATED MAP4K3 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP4K3 MUTATED    12   0   0   2
  MAP4K3 WILD-TYPE 247   3  22  19
D88V10, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              2               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"
D88V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP4K3 MUTATED                                  0     2
  MAP4K3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP4K3 MUTATED                           2     8
  MAP4K3 WILD-TYPE                        17   168
D88V12, multiclass
                                  clus
vv                                 MAP4K3 MUTATED MAP4K3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         8              168
[1] 4 2
[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 = PRPS1 MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  PRPS1 MUTATED     7   1
  PRPS1 WILD-TYPE 270  77
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              8             347 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              1              77 
$`PRPS1 MUTATED`
TCGA-AA-3713 TCGA-A6-5660 TCGA-A6-6781 TCGA-AZ-6598 TCGA-CM-4752 TCGA-CM-5348 
       19.04        29.19        19.66        49.41        13.02        22.98 
TCGA-D5-6539 TCGA-DM-A1HB 
       12.49       135.65 

$`PRPS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PRPS1 MUTATED PRPS1 WILD-TYPE 
          12.49            0.00 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
         135.65          148.01 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
          21.32           22.06 
[1] "12.5 - 135.7 (21.3)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "2.2"
D89V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPS1 MUTATED         0        0        1         1         0         0
  PRPS1 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRPS1 MUTATED           0          0          2          2        1         0
  PRPS1 WILD-TYPE        18          6         42         31       34        12
                 vv
clus              STAGE IVB
  PRPS1 MUTATED           0
  PRPS1 WILD-TYPE         1
D89V3, multiclass
            clus
vv           PRPS1 MUTATED PRPS1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  PRPS1 MUTATED     0   0   7   1
  PRPS1 WILD-TYPE   9  67 242  40
D89V4, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  PRPS1 MUTATED     4   3   1
  PRPS1 WILD-TYPE 216  78  65
D89V5, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  N0             4             216
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V6, binary
                 cls
clus                0   1
  PRPS1 MUTATED     5   1
  PRPS1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      5    1
  PRPS1 WILD-TYPE  280   47
   clus
vv  PRPS1 MUTATED PRPS1 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D89V7, binary
                 cls
clus                0   1
  PRPS1 MUTATED     2   6
  PRPS1 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      2    6
  PRPS1 WILD-TYPE  168  191
        clus
vv       PRPS1 MUTATED PRPS1 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D89V8, binary
                 cls
clus                0   1
  PRPS1 MUTATED     6   1
  PRPS1 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      6    1
  PRPS1 WILD-TYPE  294    7
     clus
vv    PRPS1 MUTATED PRPS1 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D89V9, binary
                 cls
clus                0   1
  PRPS1 MUTATED     6   1
  PRPS1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      6    1
  PRPS1 WILD-TYPE  308   47
                               clus
vv                              PRPS1 MUTATED PRPS1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRPS1 MUTATED     4   0   1   0
  PRPS1 WILD-TYPE 255   3  21  21
D89V10, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D89V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRPS1 MUTATED                                  0     0
  PRPS1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRPS1 MUTATED                           2     5
  PRPS1 WILD-TYPE                        17   171
D89V12, multiclass
                                  clus
vv                                 PRPS1 MUTATED PRPS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = KCTD3 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  KCTD3 MUTATED    11   5
  KCTD3 WILD-TYPE 266  73
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             16             339 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              5              73 
$`KCTD3 MUTATED`
TCGA-A6-6649 TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5664 
       24.16        10.88        35.80        26.17        79.69        22.09 
TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4682 TCGA-CA-6718 
       24.39         4.01        34.98        12.16        22.36        10.06 
TCGA-CM-4743 TCGA-CM-6171 TCGA-F4-6570 TCGA-G4-6309 
       23.05        14.04         6.18        85.48 

$`KCTD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-5656 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-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.06        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
           4.01            0.00 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          85.48          148.01 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
         22.705          21.990 
[1] "4.0 - 85.5 (22.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D90V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCTD3 MUTATED         4        0        1         5         2         0
  KCTD3 WILD-TYPE      60        1       25       103         6         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        18          6         42         32       35        11
                 vv
clus              STAGE IVB
  KCTD3 MUTATED           0
  KCTD3 WILD-TYPE         1
D90V3, multiclass
            clus
vv           KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  KCTD3 MUTATED     0   4   8   5
  KCTD3 WILD-TYPE   9  63 241  36
D90V4, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             8             241
  T4             5              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
  KCTD3 MUTATED    13   2   2
  KCTD3 WILD-TYPE 207  79  64
D90V5, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  N0            13             207
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V6, binary
                 cls
clus                0   1
  KCTD3 MUTATED    13   1
  KCTD3 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     13    1
  KCTD3 WILD-TYPE  272   47
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D90V7, binary
                 cls
clus                0   1
  KCTD3 MUTATED     7  10
  KCTD3 WILD-TYPE 163 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      7   10
  KCTD3 WILD-TYPE  163  187
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             7             163
  MALE              10             187
[1] 2 2
[1] FALSE
D90V8, binary
                 cls
clus                0   1
  KCTD3 MUTATED    15   0
  KCTD3 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     15    0
  KCTD3 WILD-TYPE  285    8
     clus
vv    KCTD3 MUTATED KCTD3 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D90V9, binary
                 cls
clus                0   1
  KCTD3 MUTATED    15   2
  KCTD3 WILD-TYPE 299  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     15    2
  KCTD3 WILD-TYPE  299   46
                               clus
vv                              KCTD3 MUTATED KCTD3 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCTD3 MUTATED    12   0   0   1
  KCTD3 WILD-TYPE 247   3  22  20
D90V10, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D90V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD3 MUTATED                                  0     1
  KCTD3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCTD3 MUTATED                           2    11
  KCTD3 WILD-TYPE                        17   165
D90V12, multiclass
                                  clus
vv                                 KCTD3 MUTATED KCTD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       11             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(91) Variable = PTGDR MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2               0   1
  PTGDR MUTATED     6   0
  PTGDR WILD-TYPE 271  78
  PTGDR MUTATED PTGDR WILD-TYPE 
              6             349 
  PTGDR MUTATED PTGDR WILD-TYPE 
              0              78 
$`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        13.35 

$`PTGDR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        43.27        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PTGDR MUTATED PTGDR WILD-TYPE 
          13.02            0.00 
  PTGDR MUTATED PTGDR WILD-TYPE 
          63.98          148.01 
  PTGDR MUTATED PTGDR WILD-TYPE 
         16.125          22.090 
[1] "13.0 - 64.0 (16.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D91V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTGDR MUTATED         0        0        1         3         0         0
  PTGDR WILD-TYPE      64        1       25       105         8         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        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  PTGDR MUTATED           0
  PTGDR WILD-TYPE         1
D91V3, multiclass
            clus
vv           PTGDR MUTATED PTGDR WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PTGDR MUTATED     0   0   7   0
  PTGDR WILD-TYPE   9  67 242  41
D91V4, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             0              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
  PTGDR MUTATED     4   1   2
  PTGDR WILD-TYPE 216  80  64
D91V5, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  N0             4             216
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V6, binary
                 cls
clus                0   1
  PTGDR MUTATED     5   0
  PTGDR WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      5    0
  PTGDR WILD-TYPE  280   48
   clus
vv  PTGDR MUTATED PTGDR WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D91V7, binary
                 cls
clus                0   1
  PTGDR MUTATED     2   5
  PTGDR WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      2    5
  PTGDR WILD-TYPE  168  192
        clus
vv       PTGDR MUTATED PTGDR WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D91V8, binary
                 cls
clus                0   1
  PTGDR MUTATED     6   0
  PTGDR WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      6    0
  PTGDR WILD-TYPE  294    8
     clus
vv    PTGDR MUTATED PTGDR WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D91V9, binary
                 cls
clus                0   1
  PTGDR MUTATED     6   1
  PTGDR WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      6    1
  PTGDR WILD-TYPE  308   47
                               clus
vv                              PTGDR MUTATED PTGDR WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTGDR MUTATED     6   0   0   1
  PTGDR WILD-TYPE 253   3  22  20
D91V10, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D91V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTGDR MUTATED                                  0     0
  PTGDR WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTGDR MUTATED                           1     4
  PTGDR WILD-TYPE                        18   172
D91V12, multiclass
                                  clus
vv                                 PTGDR MUTATED PTGDR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = BCORL1 MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2                0   1
  BCORL1 MUTATED    17   7
  BCORL1 WILD-TYPE 260  71
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              24              331 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               7               71 
$`BCORL1 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-2676 
       19.04        25.08       106.75         1.94        26.17        42.90 
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3861 TCGA-AA-A010 
       22.06        19.66        63.98        10.06        30.05        34.98 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4323 TCGA-CK-5916 TCGA-CM-5861 
       83.24        27.09        21.44         1.41        21.14        15.02 
TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6538 TCGA-DM-A1DA TCGA-DM-A28H 
       12.00        12.95        25.48        17.13         7.50       117.07 

$`BCORL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 TCGA-CK-5912 
       39.06        21.37        15.52        10.88       100.01        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82        58.39         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  BCORL1 MUTATED BCORL1 WILD-TYPE 
            1.41             0.00 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          117.07           148.01 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
           21.75            22.09 
[1] "1.4 - 117.1 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D92V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCORL1 MUTATED         2        0        1         8         3         0
  BCORL1 WILD-TYPE      62        1       25       100         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCORL1 MUTATED           1          1          3          3        2
  BCORL1 WILD-TYPE        17          5         41         30       33
                  vv
clus               STAGE IVA STAGE IVB
  BCORL1 MUTATED           0         0
  BCORL1 WILD-TYPE        12         1
D92V3, multiclass
            clus
vv           BCORL1 MUTATED BCORL1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              3               41
  STAGE IIIC              3               30
  STAGE IV                2               33
  STAGE IVA               0               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
  BCORL1 MUTATED     1   2  16   6
  BCORL1 WILD-TYPE   8  65 233  35
D92V4, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             16              233
  T4              6               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
  BCORL1 MUTATED    16   4   5
  BCORL1 WILD-TYPE 204  77  61
D92V5, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  N0             16              204
  N1              4               77
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V6, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    20   2
  BCORL1 WILD-TYPE 265  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     20    2
  BCORL1 WILD-TYPE  265   46
   clus
vv  BCORL1 MUTATED BCORL1 WILD-TYPE
  0             20              265
  1              2               46
[1] 2 2
[1] FALSE
D92V7, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    15  10
  BCORL1 WILD-TYPE 155 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     15   10
  BCORL1 WILD-TYPE  155  187
        clus
vv       BCORL1 MUTATED BCORL1 WILD-TYPE
  FEMALE             15              155
  MALE               10              187
[1] 2 2
[1] FALSE
D92V8, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    20   1
  BCORL1 WILD-TYPE 280   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     20    1
  BCORL1 WILD-TYPE  280    7
     clus
vv    BCORL1 MUTATED BCORL1 WILD-TYPE
  NO              20              280
  YES              1                7
[1] 2 2
[1] FALSE
D92V9, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    23   2
  BCORL1 WILD-TYPE 291  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     23    2
  BCORL1 WILD-TYPE  291   46
                               clus
vv                              BCORL1 MUTATED BCORL1 WILD-TYPE
  COLON ADENOCARCINOMA                      23              291
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BCORL1 MUTATED    18   0   1   2
  BCORL1 WILD-TYPE 241   3  21  19
D92V10, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  R0             18              241
  R1              0                3
  R2              1               21
  RX              2               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"
D92V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCORL1 MUTATED                                  0     1
  BCORL1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCORL1 MUTATED                           0    19
  BCORL1 WILD-TYPE                        19   157
D92V12, multiclass
                                  clus
vv                                 BCORL1 MUTATED BCORL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        19              157
[1] 4 2
[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 = IDH2 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED    12   2
  IDH2 WILD-TYPE 265  76
  IDH2 MUTATED IDH2 WILD-TYPE 
            14            341 
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             76 
$`IDH2 MUTATED`
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3715 TCGA-A6-5661 TCGA-AA-3833 TCGA-AA-3864 
       23.01         0.92        19.04        33.53        15.95        53.00 
TCGA-AA-A01Z TCGA-AD-6889 TCGA-AY-6196 TCGA-CK-4948 TCGA-CM-6164 TCGA-CM-6170 
       37.02        83.24         0.20       148.01        29.03        15.02 
TCGA-D5-6535 TCGA-G4-6307 
       15.12        55.04 

$`IDH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        17.95        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02         1.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  IDH2 MUTATED IDH2 WILD-TYPE 
           0.2            0.0 
  IDH2 MUTATED IDH2 WILD-TYPE 
        148.01         140.38 
  IDH2 MUTATED IDH2 WILD-TYPE 
         26.02          22.03 
[1] "0.2 - 148.0 (26.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "2"  
D93V2, continuous
                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      62        1       22       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDH2 MUTATED           2          0          2          1        1         0
  IDH2 WILD-TYPE        16          6         42         32       34        12
                vv
clus             STAGE IVB
  IDH2 MUTATED           0
  IDH2 WILD-TYPE         1
D93V3, multiclass
            clus
vv           IDH2 MUTATED IDH2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  IDH2 MUTATED     0   2  12   3
  IDH2 WILD-TYPE   9  65 237  38
D93V4, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           12            237
  T4            3             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
  IDH2 MUTATED    11   5   1
  IDH2 WILD-TYPE 209  76  65
D93V5, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  N0           11            209
  N1            5             76
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V6, binary
                cls
clus               0   1
  IDH2 MUTATED    13   1
  IDH2 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     13    1
  IDH2 WILD-TYPE  272   47
   clus
vv  IDH2 MUTATED IDH2 WILD-TYPE
  0           13            272
  1            1             47
[1] 2 2
[1] FALSE
D93V7, binary
                cls
clus               0   1
  IDH2 MUTATED    11   6
  IDH2 WILD-TYPE 159 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     11    6
  IDH2 WILD-TYPE  159  191
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE           11            159
  MALE              6            191
[1] 2 2
[1] FALSE
D93V8, binary
                cls
clus               0   1
  IDH2 MUTATED    13   0
  IDH2 WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     13    0
  IDH2 WILD-TYPE  287    8
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D93V9, binary
                cls
clus               0   1
  IDH2 MUTATED    15   1
  IDH2 WILD-TYPE 299  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     15    1
  IDH2 WILD-TYPE  299   47
                               clus
vv                              IDH2 MUTATED IDH2 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH2 MUTATED    14   0   1   2
  IDH2 WILD-TYPE 245   3  21  19
D93V10, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            1             21
  RX            2             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"
D93V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH2 MUTATED                                  0     1
  IDH2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH2 MUTATED                           1     7
  IDH2 WILD-TYPE                        18   169
D93V12, multiclass
                                  clus
vv                                 IDH2 MUTATED IDH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = TMEM126A MUTATION ANALYSIS
D94V1, survival
                    sevent
clus2                  0   1
  TMEM126A MUTATED     4   3
  TMEM126A WILD-TYPE 273  75
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                348 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 3                 75 
$`TMEM126A MUTATED`
TCGA-AA-3662 TCGA-AD-6895 TCGA-AZ-6608 TCGA-AZ-6603 TCGA-DM-A1HA TCGA-DM-A28G 
        6.05        25.08         1.94        29.56       131.51        60.79 
TCGA-DM-A28K 
       98.24 

$`TMEM126A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6605 
       62.79        88.21        49.41         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6459 
      139.17        81.37       119.93        35.97       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TMEM126A MUTATED TMEM126A WILD-TYPE 
              1.94               0.00 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
            131.51             148.01 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
             29.56              22.01 
[1] "1.9 - 131.5 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D94V2, continuous
                    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      64        1       26       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM126A MUTATED           0          1          1          1        1
  TMEM126A WILD-TYPE        18          5         43         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  TMEM126A MUTATED           0         0
  TMEM126A WILD-TYPE        12         1
D94V3, multiclass
            clus
vv           TMEM126A MUTATED TMEM126A WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  TMEM126A MUTATED     0   2   4   1
  TMEM126A WILD-TYPE   9  65 245  40
D94V4, multiclass
    clus
vv   TMEM126A MUTATED TMEM126A WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                4                245
  T4                1                 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
  TMEM126A MUTATED     2   3   2
  TMEM126A WILD-TYPE 218  78  64
D94V5, multiclass
    clus
vv   TMEM126A MUTATED TMEM126A WILD-TYPE
  N0                2                218
  N1                3                 78
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V6, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     5   1
  TMEM126A WILD-TYPE 280  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      5    1
  TMEM126A WILD-TYPE  280   47
   clus
vv  TMEM126A MUTATED TMEM126A WILD-TYPE
  0                5                280
  1                1                 47
[1] 2 2
[1] FALSE
D94V7, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     3   4
  TMEM126A WILD-TYPE 167 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      3    4
  TMEM126A WILD-TYPE  167  193
        clus
vv       TMEM126A MUTATED TMEM126A WILD-TYPE
  FEMALE                3                167
  MALE                  4                193
[1] 2 2
[1] FALSE
D94V8, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     4   0
  TMEM126A WILD-TYPE 296   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      4    0
  TMEM126A WILD-TYPE  296    8
     clus
vv    TMEM126A MUTATED TMEM126A WILD-TYPE
  NO                 4                296
  YES                0                  8
[1] 2 2
[1] FALSE
D94V9, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     6   1
  TMEM126A WILD-TYPE 308  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      6    1
  TMEM126A WILD-TYPE  308   47
                               clus
vv                              TMEM126A MUTATED TMEM126A WILD-TYPE
  COLON ADENOCARCINOMA                         6                308
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TMEM126A MUTATED     1   0   1   0
  TMEM126A WILD-TYPE 258   3  21  21
D94V10, multiclass
[1] "Remove cluster labels:" "TMEM126A MUTATED"      
clus
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 2                303 
        TCGA-A6-2677         TCGA-AA-3496         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-3527         TCGA-AA-3530 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3672         TCGA-AA-3688 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3697         TCGA-AA-3713 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3814         TCGA-AA-3844 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3867         TCGA-AA-3870 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3950         TCGA-AA-3952 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3976         TCGA-AA-3979 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-A00L         TCGA-AA-A00Z 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A024         TCGA-AD-6548         TCGA-AD-6888 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AZ-4681         TCGA-CK-5912         TCGA-G4-6310 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6586         TCGA-G4-6588 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6628         TCGA-A6-2671 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-2672         TCGA-A6-2674         TCGA-A6-2676 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2683         TCGA-A6-3807 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-3808         TCGA-A6-3809         TCGA-A6-3810 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-5657         TCGA-A6-5659         TCGA-A6-5661 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-5665         TCGA-A6-6781         TCGA-AA-3489 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3492         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-3526 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3532         TCGA-AA-3534 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3544 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3553 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3558         TCGA-AA-3561 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3655         TCGA-AA-3660         TCGA-AA-3663 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3666         TCGA-AA-3667 
"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-3693         TCGA-AA-3695 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3712 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         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-3845         TCGA-AA-3846 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3861 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3869 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3941         TCGA-AA-3947 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3955         TCGA-AA-3956 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3973 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3984         TCGA-AA-3989 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         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-A010 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01D         TCGA-AA-A01F 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01R 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01S         TCGA-AA-A01T         TCGA-AA-A01V 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01X         TCGA-AA-A01Z         TCGA-AA-A022 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02F         TCGA-AA-A02H 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02K         TCGA-AA-A02O 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AD-5900         TCGA-AD-6889 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AD-6965         TCGA-AU-3779         TCGA-AU-6004 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AZ-4315         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-5913         TCGA-CK-5914         TCGA-CK-5915 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-F4-6459 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6315 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
D94V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM126A MUTATED                                  0     0
  TMEM126A WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMEM126A MUTATED                           0     6
  TMEM126A WILD-TYPE                        19   170
D94V12, multiclass
                                  clus
vv                                 TMEM126A MUTATED TMEM126A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = GRB2 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2              0   1
  GRB2 MUTATED     5   3
  GRB2 WILD-TYPE 272  75
  GRB2 MUTATED GRB2 WILD-TYPE 
             8            347 
  GRB2 MUTATED GRB2 WILD-TYPE 
             3             75 
$`GRB2 MUTATED`
TCGA-AA-3543 TCGA-AD-6964 TCGA-G4-6625 TCGA-A6-5661 TCGA-AA-A00N TCGA-AY-6197 
        0.99        10.88        91.79        33.53         4.01        21.44 
TCGA-D5-6538 TCGA-DM-A1DA 
       17.13         7.50 

$`GRB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GRB2 MUTATED GRB2 WILD-TYPE 
          0.99           0.00 
  GRB2 MUTATED GRB2 WILD-TYPE 
         91.79         148.01 
  GRB2 MUTATED GRB2 WILD-TYPE 
        14.005         22.090 
[1] "1.0 - 91.8 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D95V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRB2 MUTATED         1        0        0         3         1         0
  GRB2 WILD-TYPE      63        1       26       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRB2 MUTATED           1          0          1          1        0         0
  GRB2 WILD-TYPE        17          6         43         32       35        12
                vv
clus             STAGE IVB
  GRB2 MUTATED           0
  GRB2 WILD-TYPE         1
D95V3, multiclass
            clus
vv           GRB2 MUTATED GRB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  GRB2 MUTATED     0   1   6   2
  GRB2 WILD-TYPE   9  66 243  39
D95V4, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            2             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
  GRB2 MUTATED     5   0   4
  GRB2 WILD-TYPE 215  81  62
D95V5, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V6, binary
                cls
clus               0   1
  GRB2 MUTATED     7   0
  GRB2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      7    0
  GRB2 WILD-TYPE  278   48
   clus
vv  GRB2 MUTATED GRB2 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D95V7, binary
                cls
clus               0   1
  GRB2 MUTATED     4   5
  GRB2 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      4    5
  GRB2 WILD-TYPE  166  192
        clus
vv       GRB2 MUTATED GRB2 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D95V8, binary
                cls
clus               0   1
  GRB2 MUTATED     6   0
  GRB2 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      6    0
  GRB2 WILD-TYPE  294    8
     clus
vv    GRB2 MUTATED GRB2 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D95V9, binary
                cls
clus               0   1
  GRB2 MUTATED     7   2
  GRB2 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      7    2
  GRB2 WILD-TYPE  307   46
                               clus
vv                              GRB2 MUTATED GRB2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GRB2 MUTATED     7   0   0   0
  GRB2 WILD-TYPE 252   3  22  21
D95V10, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            0             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"
D95V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRB2 MUTATED                                  0     0
  GRB2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRB2 MUTATED                           1     5
  GRB2 WILD-TYPE                        18   171
D95V12, multiclass
                                  clus
vv                                 GRB2 MUTATED GRB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = PLXNA3 MUTATION ANALYSIS
D96V1, survival
                  sevent
clus2                0   1
  PLXNA3 MUTATED    15   2
  PLXNA3 WILD-TYPE 262  76
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              17              338 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               2               76 
$`PLXNA3 MUTATED`
TCGA-AA-3713 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3947 
       19.04        79.69        33.53        22.06         6.97        33.01 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-CA-5797 TCGA-CK-5916 
       12.16        27.09        21.44        17.82        12.59        21.14 
TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6171 TCGA-F4-6460 TCGA-G4-6309 
       37.02        15.02        14.04        31.96        85.48 

$`PLXNA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
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-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
            6.97             0.00 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
           85.48           148.01 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
           21.44            22.09 
[1] "7.0 - 85.5 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D96V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLXNA3 MUTATED         6        0        1         5         1         0
  PLXNA3 WILD-TYPE      58        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNA3 MUTATED           0          0          3          0        1
  PLXNA3 WILD-TYPE        18          6         41         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PLXNA3 MUTATED           0         0
  PLXNA3 WILD-TYPE        12         1
D96V3, multiclass
            clus
vv           PLXNA3 MUTATED PLXNA3 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  PLXNA3 MUTATED     1   5  10   1
  PLXNA3 WILD-TYPE   8  62 239  40
D96V4, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  T1              1                8
  T2              5               62
  T3             10              239
  T4              1               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
  PLXNA3 MUTATED    14   3   0
  PLXNA3 WILD-TYPE 206  78  66
D96V5, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  N0             14              206
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V6, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    14   1
  PLXNA3 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     14    1
  PLXNA3 WILD-TYPE  271   47
   clus
vv  PLXNA3 MUTATED PLXNA3 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D96V7, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    10   7
  PLXNA3 WILD-TYPE 160 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     10    7
  PLXNA3 WILD-TYPE  160  190
        clus
vv       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  FEMALE             10              160
  MALE                7              190
[1] 2 2
[1] FALSE
D96V8, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    15   1
  PLXNA3 WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     15    1
  PLXNA3 WILD-TYPE  285    7
     clus
vv    PLXNA3 MUTATED PLXNA3 WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D96V9, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    15   2
  PLXNA3 WILD-TYPE 299  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     15    2
  PLXNA3 WILD-TYPE  299   46
                               clus
vv                              PLXNA3 MUTATED PLXNA3 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PLXNA3 MUTATED    15   0   1   1
  PLXNA3 WILD-TYPE 244   3  21  20
D96V10, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              1               21
  RX              1               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"
D96V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLXNA3 MUTATED                                  0     1
  PLXNA3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLXNA3 MUTATED                           4     9
  PLXNA3 WILD-TYPE                        15   167
D96V12, multiclass
                                  clus
vv                                 PLXNA3 MUTATED PLXNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                         9              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(97) Variable = C15ORF52 MUTATION ANALYSIS
D97V1, survival
                    sevent
clus2                  0   1
  C15ORF52 MUTATED     7   5
  C15ORF52 WILD-TYPE 270  73
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                343 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 5                 73 
$`C15ORF52 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6964 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
        0.92        24.00        10.88        22.06         8.38        24.39 
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3845 TCGA-AD-6889 TCGA-CK-5913 TCGA-DM-A28G 
        3.02         6.97         0.00        83.24        51.32        60.79 

$`C15ORF52 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 0                  0 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             83.24             148.01 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             16.47              22.09 
[1] "0.0 - 83.2 (16.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D97V2, continuous
                    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      63        1       24       101         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF52 MUTATED           1          0          0          0        0
  C15ORF52 WILD-TYPE        17          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C15ORF52 MUTATED           0         0
  C15ORF52 WILD-TYPE        12         1
D97V3, multiclass
            clus
vv           C15ORF52 MUTATED C15ORF52 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 7                101
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C15ORF52 MUTATED     0   1  10   1
  C15ORF52 WILD-TYPE   9  66 239  40
D97V4, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3               10                239
  T4                1                 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
  C15ORF52 MUTATED    10   1   1
  C15ORF52 WILD-TYPE 210  80  65
D97V5, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  N0               10                210
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V6, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    10   0
  C15ORF52 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     10    0
  C15ORF52 WILD-TYPE  275   48
   clus
vv  C15ORF52 MUTATED C15ORF52 WILD-TYPE
  0               10                275
  1                0                 48
[1] 2 2
[1] FALSE
D97V7, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     6   6
  C15ORF52 WILD-TYPE 164 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      6    6
  C15ORF52 WILD-TYPE  164  191
        clus
vv       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  FEMALE                6                164
  MALE                  6                191
[1] 2 2
[1] FALSE
D97V8, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    10   0
  C15ORF52 WILD-TYPE 290   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     10    0
  C15ORF52 WILD-TYPE  290    8
     clus
vv    C15ORF52 MUTATED C15ORF52 WILD-TYPE
  NO                10                290
  YES                0                  8
[1] 2 2
[1] FALSE
D97V9, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    11   1
  C15ORF52 WILD-TYPE 303  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     11    1
  C15ORF52 WILD-TYPE  303   47
                               clus
vv                              C15ORF52 MUTATED C15ORF52 WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C15ORF52 MUTATED     7   0   0   1
  C15ORF52 WILD-TYPE 252   3  22  20
D97V10, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D97V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C15ORF52 MUTATED                                  0     1
  C15ORF52 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C15ORF52 MUTATED                           1     5
  C15ORF52 WILD-TYPE                        18   171
D97V12, multiclass
                                  clus
vv                                 C15ORF52 MUTATED C15ORF52 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           5                171
[1] 4 2
[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 = PCBP1 MUTATION ANALYSIS
D98V1, survival
                 sevent
clus2               0   1
  PCBP1 MUTATED     8   1
  PCBP1 WILD-TYPE 269  77
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              9             346 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              1              77 
$`PCBP1 MUTATED`
TCGA-AA-3979 TCGA-AA-3941 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 
      124.27        12.03        20.19 

$`PCBP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.59        12.20        12.76        14.30       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
          10.06            0.00 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
         124.27          148.01 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
         24.000          22.045 
[1] "10.1 - 124.3 (24.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.6"
D98V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCBP1 MUTATED         2        0        0         4         0         0
  PCBP1 WILD-TYPE      62        1       26       104         8         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        18          6         41         33       35        11
                 vv
clus              STAGE IVB
  PCBP1 MUTATED           0
  PCBP1 WILD-TYPE         1
D98V3, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  PCBP1 MUTATED     0   2   6   2
  PCBP1 WILD-TYPE   9  65 243  39
D98V4, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  PCBP1 MUTATED     6   3   1
  PCBP1 WILD-TYPE 214  78  65
D98V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V6, binary
                 cls
clus                0   1
  PCBP1 MUTATED     8   1
  PCBP1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      8    1
  PCBP1 WILD-TYPE  277   47
   clus
vv  PCBP1 MUTATED PCBP1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D98V7, binary
                 cls
clus                0   1
  PCBP1 MUTATED     6   4
  PCBP1 WILD-TYPE 164 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      6    4
  PCBP1 WILD-TYPE  164  193
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             6             164
  MALE               4             193
[1] 2 2
[1] FALSE
D98V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     9   0
  PCBP1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      9    0
  PCBP1 WILD-TYPE  291    8
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D98V9, binary
                 cls
clus                0   1
  PCBP1 MUTATED     8   2
  PCBP1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      8    2
  PCBP1 WILD-TYPE  306   46
                               clus
vv                              PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCBP1 MUTATED     6   1   0   3
  PCBP1 WILD-TYPE 253   2  22  18
D98V10, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             6             253
  R1             1               2
  R2             0              22
  RX             3              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"
D98V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCBP1 MUTATED                                  0     1
  PCBP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCBP1 MUTATED                           1     4
  PCBP1 WILD-TYPE                        18   172
D98V12, multiclass
                                  clus
vv                                 PCBP1 MUTATED PCBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = SLK MUTATION ANALYSIS
D99V1, survival
               sevent
clus2             0   1
  SLK MUTATED    18   3
  SLK WILD-TYPE 259  75
  SLK MUTATED SLK WILD-TYPE 
           21           334 
  SLK MUTATED SLK WILD-TYPE 
            3            75 
$`SLK MUTATED`
TCGA-G4-6321 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3510 
       22.09        22.06        32.71        21.76        20.28        63.98 
TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6889 
        6.97        26.99        31.00        34.98        31.00        83.24 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CM-6172 TCGA-D5-6533 
       27.09        58.39        29.56        12.76        11.01        25.48 
TCGA-D5-6924 TCGA-D5-7000 TCGA-G4-6303 
       14.30        10.26        65.85 

$`SLK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        23.61        22.09        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       19.66         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        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         7.53        12.39        10.13 
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        13.41        13.35 
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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SLK MUTATED SLK WILD-TYPE 
         6.97          0.00 
  SLK MUTATED SLK WILD-TYPE 
        83.24        148.01 
  SLK MUTATED SLK WILD-TYPE 
        26.99         21.99 
[1] "7.0 - 83.2 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D99V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLK MUTATED         5        0        3         6         2         1
  SLK WILD-TYPE      59        1       23       102         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLK MUTATED           1          0          2          0        1         0
  SLK WILD-TYPE        17          6         42         33       34        12
               vv
clus            STAGE IVB
  SLK MUTATED           0
  SLK WILD-TYPE         1
D99V3, multiclass
            clus
vv           SLK MUTATED SLK WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            6           102
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  SLK MUTATED     1   6  11   5
  SLK WILD-TYPE   8  61 238  36
D99V4, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  T1           1             8
  T2           6            61
  T3          11           238
  T4           5            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
  SLK MUTATED    18   5   0
  SLK WILD-TYPE 202  76  66
D99V5, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  N0          18           202
  N1           5            76
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V6, binary
               cls
clus              0   1
  SLK MUTATED    17   1
  SLK WILD-TYPE 268  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     17    1
  SLK WILD-TYPE  268   47
   clus
vv  SLK MUTATED SLK WILD-TYPE
  0          17           268
  1           1            47
[1] 2 2
[1] FALSE
D99V7, binary
               cls
clus              0   1
  SLK MUTATED    13  10
  SLK WILD-TYPE 157 187
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     13   10
  SLK WILD-TYPE  157  187
        clus
vv       SLK MUTATED SLK WILD-TYPE
  FEMALE          13           157
  MALE            10           187
[1] 2 2
[1] FALSE
D99V8, binary
               cls
clus              0   1
  SLK MUTATED    20   0
  SLK WILD-TYPE 280   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     20    0
  SLK WILD-TYPE  280    8
     clus
vv    SLK MUTATED SLK WILD-TYPE
  NO           20           280
  YES           0             8
[1] 2 2
[1] FALSE
D99V9, binary
               cls
clus              0   1
  SLK MUTATED    20   3
  SLK WILD-TYPE 294  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     20    3
  SLK WILD-TYPE  294   45
                               clus
vv                              SLK MUTATED SLK WILD-TYPE
  COLON ADENOCARCINOMA                   20           294
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SLK MUTATED    17   0   0   2
  SLK WILD-TYPE 242   3  22  19
D99V10, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  R0          17           242
  R1           0             3
  R2           0            22
  RX           2            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"
D99V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLK MUTATED                                  0     2
  SLK WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SLK MUTATED                           0    14
  SLK WILD-TYPE                        19   162
D99V12, multiclass
                                  clus
vv                                 SLK MUTATED SLK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                     14           162
[1] 4 2
[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 = SMAD4 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    87  29
  SMAD4 WILD-TYPE 190  49
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            116             239 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             29              49 
$`SMAD4 MUTATED`
TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3662 TCGA-AA-3692 
        1.02        24.03        37.05        19.07         6.05        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       85.05        19.04        24.00        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
      100.01         5.88        63.62        35.80        91.79        79.69 
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-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3811 TCGA-AA-3821 
       29.95        20.98        78.08         2.01        10.06         1.02 
TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-A00K 
        0.00        30.05        53.00        21.99        13.05        18.05 
TCGA-AA-A01D TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       10.98         0.92         5.79        27.42        14.50        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6598 
        0.20        21.44        17.82         5.13        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5796 
        6.77        12.10        29.56         5.23         3.19        12.39 
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        21.99 
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        14.04        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        54.61        19.59        56.09 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6898 
       18.25        25.48        43.27        17.85        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       12.39        14.30         9.44        11.64        13.35        10.26 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A28H 
       38.20        92.75        12.59       140.38        44.32       117.07 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 
       31.96        35.74         6.18        34.42        43.04        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 
      133.18        74.56        65.85        53.62        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

$`SMAD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3524 TCGA-AA-3525 
       24.33        14.53        24.16        13.02        36.03         8.05 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.99         0.92        19.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6895 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-2671 
       25.08         1.94        49.08        22.09        26.17        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       46.65        43.76        16.57        34.65        33.34        36.53 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       31.63        33.53        23.61        22.06        32.71         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       25.08        25.18        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       24.00        13.94        61.02         6.97        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 
       12.16        83.24        24.53        22.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5407 
        0.95        33.01        58.39         1.41        22.36        88.21 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 
       11.74        12.69        12.36        12.59        12.59        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        15.62        51.32        21.14        82.95         2.01 
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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 
        5.03        15.02        15.02        12.00        29.03        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       12.99        13.02        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6535 
       11.01        10.06        45.40        55.92        20.19        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6923 
        4.80        17.13        12.49        16.14        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.04        13.41        12.00        11.38       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
      130.65        49.91        13.32         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
        8.61        47.87         1.55        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 
        0.53        35.31        44.68        55.04        61.91 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
              0               0 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         140.38          148.01 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          21.99           22.36 
[1] "0.0 - 140.4 (22.0)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D100V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAD4 MUTATED        19        1        9        39         4         0
  SMAD4 WILD-TYPE      45        0       17        69         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED           3          1         17         10        9         2
  SMAD4 WILD-TYPE        15          5         27         23       26        10
                 vv
clus              STAGE IVB
  SMAD4 MUTATED           0
  SMAD4 WILD-TYPE         1
D100V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               19              45
  STAGE IA               1               0
  STAGE II               9              17
  STAGE IIA             39              69
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             1               5
  STAGE IIIB            17              27
  STAGE IIIC            10              23
  STAGE IV               9              26
  STAGE IVA              2              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
  SMAD4 MUTATED     1  19  84  14
  SMAD4 WILD-TYPE   8  48 165  27
D100V4, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             1               8
  T2            19              48
  T3            84             165
  T4            14              27
[1] 4 2
[1] TRUE
[1] "dimension 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    76  25  18
  SMAD4 WILD-TYPE 144  56  48
D100V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0            76             144
  N1            25              56
  N2            18              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED    91  11
  SMAD4 WILD-TYPE 194  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     91   11
  SMAD4 WILD-TYPE  194   37
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            91             194
  1            11              37
[1] 2 2
[1] FALSE
D100V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED    60  59
  SMAD4 WILD-TYPE 110 138
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     60   59
  SMAD4 WILD-TYPE  110  138
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            60             110
  MALE              59             138
[1] 2 2
[1] FALSE
D100V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED    98   3
  SMAD4 WILD-TYPE 202   5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     98    3
  SMAD4 WILD-TYPE  202    5
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO             98             202
  YES             3               5
[1] 2 2
[1] FALSE
D100V9, binary
                 cls
clus                0   1
  SMAD4 MUTATED   101  17
  SMAD4 WILD-TYPE 213  31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED    101   17
  SMAD4 WILD-TYPE  213   31
                               clus
vv                              SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON ADENOCARCINOMA                    101             213
  COLON MUCINOUS ADENOCARCINOMA            17              31
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    79   1   5   7
  SMAD4 WILD-TYPE 180   2  17  14
D100V10, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            79             180
  R1             1               2
  R2             5              17
  RX             7              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"
D100V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD4 MUTATED                                  0     5
  SMAD4 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED                           9    81
  SMAD4 WILD-TYPE                        10    95
D100V12, multiclass
                                  clus
vv                                 SMAD4 MUTATED SMAD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        5               5
  BLACK OR AFRICAN AMERICAN                    9              10
  WHITE                                       81              95
[1] 4 2
[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 = XYLT2 MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2               0   1
  XYLT2 MUTATED    12   2
  XYLT2 WILD-TYPE 265  76
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             341 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
              2              76 
$`XYLT2 MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 
        0.92        35.80        26.17        33.53        22.06        19.66 
TCGA-AA-3663 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-5861 
        6.97        12.16        58.39        49.41        37.02        15.02 
TCGA-D5-6923 TCGA-F4-6570 
       12.43         6.18 

$`XYLT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  XYLT2 MUTATED XYLT2 WILD-TYPE 
           0.92            0.00 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          58.39          148.01 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          20.86           22.09 
[1] "0.9 - 58.4 (20.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D101V2, continuous
                 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      61        1       24       101         8         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        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  XYLT2 MUTATED           0
  XYLT2 WILD-TYPE         1
D101V3, multiclass
            clus
vv           XYLT2 MUTATED XYLT2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  XYLT2 MUTATED     0   3  10   1
  XYLT2 WILD-TYPE   9  64 239  40
D101V4, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             1              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
  XYLT2 MUTATED    12   2   0
  XYLT2 WILD-TYPE 208  79  66
D101V5, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V6, binary
                 cls
clus                0   1
  XYLT2 MUTATED    11   0
  XYLT2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     11    0
  XYLT2 WILD-TYPE  274   48
   clus
vv  XYLT2 MUTATED XYLT2 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D101V7, binary
                 cls
clus                0   1
  XYLT2 MUTATED     8   6
  XYLT2 WILD-TYPE 162 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED      8    6
  XYLT2 WILD-TYPE  162  191
        clus
vv       XYLT2 MUTATED XYLT2 WILD-TYPE
  FEMALE             8             162
  MALE               6             191
[1] 2 2
[1] FALSE
D101V8, binary
                 cls
clus                0   1
  XYLT2 MUTATED    14   0
  XYLT2 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     14    0
  XYLT2 WILD-TYPE  286    8
     clus
vv    XYLT2 MUTATED XYLT2 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D101V9, binary
                 cls
clus                0   1
  XYLT2 MUTATED    12   2
  XYLT2 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     12    2
  XYLT2 WILD-TYPE  302   46
                               clus
vv                              XYLT2 MUTATED XYLT2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  XYLT2 MUTATED    13   0   0   0
  XYLT2 WILD-TYPE 246   3  22  21
D101V10, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             0              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"
D101V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XYLT2 MUTATED                                  0     0
  XYLT2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  XYLT2 MUTATED                           2    10
  XYLT2 WILD-TYPE                        17   166
D101V12, multiclass
                                  clus
vv                                 XYLT2 MUTATED XYLT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       10             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(102) Variable = FAHD2B MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  FAHD2B MUTATED     5   0
  FAHD2B WILD-TYPE 272  78
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              350 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               0               78 
$`FAHD2B MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AD-5900 TCGA-AU-6004 TCGA-CM-5861 
       22.06        20.12        12.16        27.09        15.02 

$`FAHD2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FAHD2B MUTATED FAHD2B WILD-TYPE 
           12.16             0.00 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           27.09           148.01 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           20.12            22.09 
[1] "12.2 - 27.1 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D102V2, continuous
                  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      62        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2B MUTATED           0          0          0          0        0
  FAHD2B WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FAHD2B MUTATED           0         0
  FAHD2B WILD-TYPE        12         1
D102V3, multiclass
            clus
vv           FAHD2B MUTATED FAHD2B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  FAHD2B MUTATED     0   2   3   1
  FAHD2B WILD-TYPE   9  65 246  40
D102V4, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  T1              0                9
  T2              2               65
  T3              3              246
  T4              1               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
  FAHD2B MUTATED     6   0   0
  FAHD2B WILD-TYPE 214  81  66
D102V5, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  N0              6              214
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V6, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     3   0
  FAHD2B WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      3    0
  FAHD2B WILD-TYPE  282   48
   clus
vv  FAHD2B MUTATED FAHD2B WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D102V7, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     4   2
  FAHD2B WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      4    2
  FAHD2B WILD-TYPE  166  195
        clus
vv       FAHD2B MUTATED FAHD2B WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D102V8, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     4   0
  FAHD2B WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      4    0
  FAHD2B WILD-TYPE  296    8
     clus
vv    FAHD2B MUTATED FAHD2B WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D102V9, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     4   2
  FAHD2B WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      4    2
  FAHD2B WILD-TYPE  310   46
                               clus
vv                              FAHD2B MUTATED FAHD2B WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAHD2B MUTATED     4   0   0   1
  FAHD2B WILD-TYPE 255   3  22  20
D102V10, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D102V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAHD2B MUTATED                                  0     0
  FAHD2B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAHD2B MUTATED                           0     6
  FAHD2B WILD-TYPE                        19   170
D102V12, multiclass
                                  clus
vv                                 FAHD2B MUTATED FAHD2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = RSPH3 MUTATION ANALYSIS
D103V1, survival
                 sevent
clus2               0   1
  RSPH3 MUTATED     7   3
  RSPH3 WILD-TYPE 270  75
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             10             345 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
              3              75 
$`RSPH3 MUTATED`
TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-6652 TCGA-A6-6653 TCGA-AA-A010 TCGA-AD-6965 
       25.08       100.01        24.69        24.39        34.98        26.47 
TCGA-AZ-6599 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6309 
        6.77         7.50       117.07        85.48 

$`RSPH3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6780 
        8.38        25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RSPH3 MUTATED RSPH3 WILD-TYPE 
           6.77            0.00 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
         117.07          148.01 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
         25.775          21.990 
[1] "6.8 - 117.1 (25.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D103V2, continuous
                 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      62        1       25       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RSPH3 MUTATED           0          0          2          3        0         1
  RSPH3 WILD-TYPE        18          6         42         30       35        11
                 vv
clus              STAGE IVB
  RSPH3 MUTATED           0
  RSPH3 WILD-TYPE         1
D103V3, multiclass
            clus
vv           RSPH3 MUTATED RSPH3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              1              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
  RSPH3 MUTATED     0   2   6   2
  RSPH3 WILD-TYPE   9  65 243  39
D103V4, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  RSPH3 MUTATED     5   2   3
  RSPH3 WILD-TYPE 215  79  63
D103V5, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             3              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"
D103V6, binary
                 cls
clus                0   1
  RSPH3 MUTATED     8   1
  RSPH3 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      8    1
  RSPH3 WILD-TYPE  277   47
   clus
vv  RSPH3 MUTATED RSPH3 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D103V7, binary
                 cls
clus                0   1
  RSPH3 MUTATED     3   7
  RSPH3 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      3    7
  RSPH3 WILD-TYPE  167  190
        clus
vv       RSPH3 MUTATED RSPH3 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D103V8, binary
                 cls
clus                0   1
  RSPH3 MUTATED     8   0
  RSPH3 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      8    0
  RSPH3 WILD-TYPE  292    8
     clus
vv    RSPH3 MUTATED RSPH3 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D103V9, binary
                 cls
clus                0   1
  RSPH3 MUTATED    10   0
  RSPH3 WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED     10    0
  RSPH3 WILD-TYPE  304   48
                               clus
vv                              RSPH3 MUTATED RSPH3 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RSPH3 MUTATED     3   1   0   0
  RSPH3 WILD-TYPE 256   2  22  21
D103V10, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  R0             3             256
  R1             1               2
  R2             0              22
  RX             0              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"
D103V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RSPH3 MUTATED                                  0     0
  RSPH3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RSPH3 MUTATED                           2     7
  RSPH3 WILD-TYPE                        17   169
D103V12, multiclass
                                  clus
vv                                 RSPH3 MUTATED RSPH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        7             169
[1] 4 2
[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 = PKD2L1 MUTATION ANALYSIS
D104V1, survival
                  sevent
clus2                0   1
  PKD2L1 MUTATED    18   4
  PKD2L1 WILD-TYPE 259  74
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              22              333 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
               4               74 
$`PKD2L1 MUTATED`
TCGA-AA-3552 TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 
       13.02        19.04        19.04        30.44         8.38        19.66 
TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 
       33.99        29.95        34.98        35.01        12.16        83.24 
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 
       14.04        15.12        16.14       133.18 

$`PKD2L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        21.01        24.00 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
            8.38             0.00 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
          133.18           148.01 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
           20.55            22.09 
[1] "8.4 - 133.2 (20.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D104V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKD2L1 MUTATED         4        0        2         8         1         0
  PKD2L1 WILD-TYPE      60        1       24       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKD2L1 MUTATED           2          0          1          4        1
  PKD2L1 WILD-TYPE        16          6         43         29       34
                  vv
clus               STAGE IVA STAGE IVB
  PKD2L1 MUTATED           0         0
  PKD2L1 WILD-TYPE        12         1
D104V3, multiclass
            clus
vv           PKD2L1 MUTATED PKD2L1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              4               29
  STAGE IV                1               34
  STAGE IVA               0               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
  PKD2L1 MUTATED     0   4  16   3
  PKD2L1 WILD-TYPE   9  63 233  38
D104V4, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             16              233
  T4              3               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
  PKD2L1 MUTATED    16   3   4
  PKD2L1 WILD-TYPE 204  78  62
D104V5, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  N0             16              204
  N1              3               78
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V6, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    17   1
  PKD2L1 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     17    1
  PKD2L1 WILD-TYPE  268   47
   clus
vv  PKD2L1 MUTATED PKD2L1 WILD-TYPE
  0             17              268
  1              1               47
[1] 2 2
[1] FALSE
D104V7, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED     9  14
  PKD2L1 WILD-TYPE 161 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED      9   14
  PKD2L1 WILD-TYPE  161  183
        clus
vv       PKD2L1 MUTATED PKD2L1 WILD-TYPE
  FEMALE              9              161
  MALE               14              183
[1] 2 2
[1] FALSE
D104V8, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    19   2
  PKD2L1 WILD-TYPE 281   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     19    2
  PKD2L1 WILD-TYPE  281    6
     clus
vv    PKD2L1 MUTATED PKD2L1 WILD-TYPE
  NO              19              281
  YES              2                6
[1] 2 2
[1] FALSE
D104V9, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    17   6
  PKD2L1 WILD-TYPE 297  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     17    6
  PKD2L1 WILD-TYPE  297   42
                               clus
vv                              PKD2L1 MUTATED PKD2L1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PKD2L1 MUTATED    17   0   1   3
  PKD2L1 WILD-TYPE 242   3  21  18
D104V10, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              1               21
  RX              3               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"
D104V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKD2L1 MUTATED                                  0     2
  PKD2L1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PKD2L1 MUTATED                           1    12
  PKD2L1 WILD-TYPE                        18   164
D104V12, multiclass
                                  clus
vv                                 PKD2L1 MUTATED PKD2L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = CDK12 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED    22   5
  CDK12 WILD-TYPE 255  73
  CDK12 MUTATED CDK12 WILD-TYPE 
             27             328 
  CDK12 MUTATED CDK12 WILD-TYPE 
              5              73 
$`CDK12 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5659 
       85.05        19.04        35.80        26.17        79.69        30.44 
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 
       22.06        20.12         3.02        78.08         6.97        33.04 
TCGA-AA-3864 TCGA-AA-3989 TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-5543 
       53.00         7.96         0.99        34.98        38.07        33.01 
TCGA-AZ-4315 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-5861 TCGA-D5-6928 
       58.39       148.01        85.45        37.02        15.02        11.64 
TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6309 
        8.61         6.18        85.48 

$`CDK12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        19.66        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02        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-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       27.02        42.02        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       10.06        14.30        17.56        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6460 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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           21.99 
[1] "1.0 - 148.0 (33.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.6"
D105V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK12 MUTATED         4        0        5        10         1         0
  CDK12 WILD-TYPE      60        1       21        98         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK12 MUTATED           2          0          3          0        3         1
  CDK12 WILD-TYPE        16          6         41         33       32        11
                 vv
clus              STAGE IVB
  CDK12 MUTATED           0
  CDK12 WILD-TYPE         1
D105V3, multiclass
            clus
vv           CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             10              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              1              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
  CDK12 MUTATED     0   4  23   2
  CDK12 WILD-TYPE   9  63 226  39
D105V4, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            23             226
  T4             2              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
  CDK12 MUTATED    21   6   2
  CDK12 WILD-TYPE 199  75  64
D105V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  N0            21             199
  N1             6              75
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V6, binary
                 cls
clus                0   1
  CDK12 MUTATED    24   4
  CDK12 WILD-TYPE 261  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     24    4
  CDK12 WILD-TYPE  261   44
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0            24             261
  1             4              44
[1] 2 2
[1] FALSE
D105V7, binary
                 cls
clus                0   1
  CDK12 MUTATED    18  11
  CDK12 WILD-TYPE 152 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     18   11
  CDK12 WILD-TYPE  152  186
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE            18             152
  MALE              11             186
[1] 2 2
[1] FALSE
D105V8, binary
                 cls
clus                0   1
  CDK12 MUTATED    25   1
  CDK12 WILD-TYPE 275   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     25    1
  CDK12 WILD-TYPE  275    7
     clus
vv    CDK12 MUTATED CDK12 WILD-TYPE
  NO             25             275
  YES             1               7
[1] 2 2
[1] FALSE
D105V9, binary
                 cls
clus                0   1
  CDK12 MUTATED    26   3
  CDK12 WILD-TYPE 288  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     26    3
  CDK12 WILD-TYPE  288   45
                               clus
vv                              CDK12 MUTATED CDK12 WILD-TYPE
  COLON ADENOCARCINOMA                     26             288
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED    24   1   3   0
  CDK12 WILD-TYPE 235   2  19  21
D105V10, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0            24             235
  R1             1               2
  R2             3              19
  RX             0              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"
D105V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK12 MUTATED                                  0     0
  CDK12 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED                           4    12
  CDK12 WILD-TYPE                        15   164
D105V12, multiclass
                                  clus
vv                                 CDK12 MUTATED CDK12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       12             164
[1] 4 2
[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 = CASP8 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    12   4
  CASP8 WILD-TYPE 265  74
  CASP8 MUTATED CASP8 WILD-TYPE 
             16             339 
  CASP8 MUTATED CASP8 WILD-TYPE 
              4              74 
$`CASP8 MUTATED`
TCGA-AA-3543 TCGA-AA-3715 TCGA-AD-6895 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3518 
        0.99        19.04        25.08         7.04         3.02         1.02 
TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00R 
       26.99        53.00        33.01        38.04        18.05         0.99 
TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-4746 TCGA-DM-A28F 
       21.44        12.76        37.02        35.97 

$`CASP8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.12        19.66        20.28        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.99            0.00 
  CASP8 MUTATED CASP8 WILD-TYPE 
          53.00          148.01 
  CASP8 MUTATED CASP8 WILD-TYPE 
          20.24           22.09 
[1] "1.0 - 53.0 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D106V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP8 MUTATED         3        0        5         5         1         0
  CASP8 WILD-TYPE      61        1       21       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP8 MUTATED           0          0          3          0        0         0
  CASP8 WILD-TYPE        18          6         41         33       35        12
                 vv
clus              STAGE IVB
  CASP8 MUTATED           0
  CASP8 WILD-TYPE         1
D106V3, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CASP8 MUTATED     0   3  11   3
  CASP8 WILD-TYPE   9  64 238  38
D106V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            11             238
  T4             3              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
  CASP8 MUTATED    14   3   0
  CASP8 WILD-TYPE 206  78  66
D106V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            14             206
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    16   0
  CASP8 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     16    0
  CASP8 WILD-TYPE  269   48
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            16             269
  1             0              48
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus                0   1
  CASP8 MUTATED     6  11
  CASP8 WILD-TYPE 164 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      6   11
  CASP8 WILD-TYPE  164  186
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             6             164
  MALE              11             186
[1] 2 2
[1] FALSE
D106V8, binary
                 cls
clus                0   1
  CASP8 MUTATED    13   0
  CASP8 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     13    0
  CASP8 WILD-TYPE  287    8
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D106V9, binary
                 cls
clus                0   1
  CASP8 MUTATED    13   4
  CASP8 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     13    4
  CASP8 WILD-TYPE  301   44
                               clus
vv                              CASP8 MUTATED CASP8 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    15   0   0   1
  CASP8 WILD-TYPE 244   3  22  20
D106V10, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             1              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"
D106V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     1
  CASP8 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED                           1     3
  CASP8 WILD-TYPE                        18   173
D106V12, multiclass
                                  clus
vv                                 CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = KCNK1 MUTATION ANALYSIS
D107V1, survival
                 sevent
clus2               0   1
  KCNK1 MUTATED     8   2
  KCNK1 WILD-TYPE 269  76
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             10             345 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
              2              76 
$`KCNK1 MUTATED`
TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3845 TCGA-CM-4747 TCGA-CM-5344 
       10.88        26.17        33.53         0.00        25.02        22.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6679 TCGA-G4-6315 
       15.02        14.04        10.06        61.91 

$`KCNK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
        5.03        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KCNK1 MUTATED KCNK1 WILD-TYPE 
              0               0 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
          61.91          148.01 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
         18.525          22.090 
[1] "0.0 - 61.9 (18.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D107V2, continuous
                 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      62        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNK1 MUTATED           0          0          1          0        1         1
  KCNK1 WILD-TYPE        18          6         43         33       34        11
                 vv
clus              STAGE IVB
  KCNK1 MUTATED           0
  KCNK1 WILD-TYPE         1
D107V3, multiclass
            clus
vv           KCNK1 MUTATED KCNK1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  KCNK1 MUTATED     1   1   6   2
  KCNK1 WILD-TYPE   8  66 243  39
D107V4, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             6             243
  T4             2              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
  KCNK1 MUTATED     6   3   1
  KCNK1 WILD-TYPE 214  78  65
D107V5, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V6, binary
                 cls
clus                0   1
  KCNK1 MUTATED     7   2
  KCNK1 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED      7    2
  KCNK1 WILD-TYPE  278   46
   clus
vv  KCNK1 MUTATED KCNK1 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D107V7, binary
                 cls
clus                0   1
  KCNK1 MUTATED     4   6
  KCNK1 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED      4    6
  KCNK1 WILD-TYPE  166  191
        clus
vv       KCNK1 MUTATED KCNK1 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D107V8, binary
                 cls
clus                0   1
  KCNK1 MUTATED     9   0
  KCNK1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED      9    0
  KCNK1 WILD-TYPE  291    8
     clus
vv    KCNK1 MUTATED KCNK1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D107V9, binary
                 cls
clus                0   1
  KCNK1 MUTATED    10   0
  KCNK1 WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED     10    0
  KCNK1 WILD-TYPE  304   48
                               clus
vv                              KCNK1 MUTATED KCNK1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNK1 MUTATED     9   0   0   0
  KCNK1 WILD-TYPE 250   3  22  21
D107V10, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D107V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNK1 MUTATED                                  0     0
  KCNK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNK1 MUTATED                           1     8
  KCNK1 WILD-TYPE                        18   168
D107V12, multiclass
                                  clus
vv                                 KCNK1 MUTATED KCNK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = PTK2 MUTATION ANALYSIS
D108V1, survival
                sevent
clus2              0   1
  PTK2 MUTATED    15   6
  PTK2 WILD-TYPE 262  72
  PTK2 MUTATED PTK2 WILD-TYPE 
            21            334 
  PTK2 MUTATED PTK2 WILD-TYPE 
             6             72 
$`PTK2 MUTATED`
TCGA-AZ-6601 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3526 TCGA-AA-3821 
      100.01        22.06        20.12        63.98        19.07         1.02 
TCGA-AA-3877 TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6718 
       31.00        34.98        33.01        88.21         6.77        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        54.61        12.39        12.00 
TCGA-DM-A0XF TCGA-G4-6299 TCGA-G4-6303 
       38.20        74.56        65.85 

$`PTK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 
        6.97         1.02        38.99         1.02         9.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       26.47        14.50        27.09        16.31         0.95         0.20 
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-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PTK2 MUTATED PTK2 WILD-TYPE 
          1.02           0.00 
  PTK2 MUTATED PTK2 WILD-TYPE 
        100.01         148.01 
  PTK2 MUTATED PTK2 WILD-TYPE 
         31.00          22.01 
[1] "1.0 - 100.0 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D108V2, continuous
                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      58        1       24       102         7         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        18          6         43         30       34        11
                vv
clus             STAGE IVB
  PTK2 MUTATED           0
  PTK2 WILD-TYPE         1
D108V3, multiclass
            clus
vv           PTK2 MUTATED PTK2 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            3             30
  STAGE IV              1             34
  STAGE IVA             1             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
  PTK2 MUTATED     2   4  13   2
  PTK2 WILD-TYPE   7  63 236  39
D108V4, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  T1            2              7
  T2            4             63
  T3           13            236
  T4            2             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
  PTK2 MUTATED    15   3   3
  PTK2 WILD-TYPE 205  78  63
D108V5, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  N0           15            205
  N1            3             78
  N2            3             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"
D108V6, binary
                cls
clus               0   1
  PTK2 MUTATED    16   2
  PTK2 WILD-TYPE 269  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     16    2
  PTK2 WILD-TYPE  269   46
   clus
vv  PTK2 MUTATED PTK2 WILD-TYPE
  0           16            269
  1            2             46
[1] 2 2
[1] FALSE
D108V7, binary
                cls
clus               0   1
  PTK2 MUTATED    13   8
  PTK2 WILD-TYPE 157 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     13    8
  PTK2 WILD-TYPE  157  189
        clus
vv       PTK2 MUTATED PTK2 WILD-TYPE
  FEMALE           13            157
  MALE              8            189
[1] 2 2
[1] FALSE
D108V8, binary
                cls
clus               0   1
  PTK2 MUTATED    20   0
  PTK2 WILD-TYPE 280   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     20    0
  PTK2 WILD-TYPE  280    8
     clus
vv    PTK2 MUTATED PTK2 WILD-TYPE
  NO            20            280
  YES            0              8
[1] 2 2
[1] FALSE
D108V9, binary
                cls
clus               0   1
  PTK2 MUTATED    17   3
  PTK2 WILD-TYPE 297  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     17    3
  PTK2 WILD-TYPE  297   45
                               clus
vv                              PTK2 MUTATED PTK2 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTK2 MUTATED    14   0   0   2
  PTK2 WILD-TYPE 245   3  22  19
D108V10, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            0             22
  RX            2             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"
D108V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTK2 MUTATED                                  0     1
  PTK2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTK2 MUTATED                           1    14
  PTK2 WILD-TYPE                        18   162
D108V12, multiclass
                                  clus
vv                                 PTK2 MUTATED PTK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      14            162
[1] 4 2
[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 = FYN MUTATION ANALYSIS
D109V1, survival
               sevent
clus2             0   1
  FYN MUTATED    12   2
  FYN WILD-TYPE 265  76
  FYN MUTATED FYN WILD-TYPE 
           14           341 
  FYN MUTATED FYN WILD-TYPE 
            2            76 
$`FYN MUTATED`
TCGA-AA-3713 TCGA-A6-2671 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3815 
       19.04        43.76        32.71         8.38        24.39        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 
      133.18        13.78 

$`FYN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        22.06        27.09        22.52        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  FYN MUTATED FYN WILD-TYPE 
         8.38          0.00 
  FYN MUTATED FYN WILD-TYPE 
       133.18        148.01 
  FYN MUTATED FYN WILD-TYPE 
       30.885        21.990 
[1] "8.4 - 133.2 (30.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D109V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FYN MUTATED         1        1        0         4         1         1
  FYN WILD-TYPE      63        0       26       104         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FYN MUTATED           2          1          2          0        2         0
  FYN WILD-TYPE        16          5         42         33       33        12
               vv
clus            STAGE IVB
  FYN MUTATED           0
  FYN WILD-TYPE         1
D109V3, multiclass
            clus
vv           FYN MUTATED FYN WILD-TYPE
  STAGE I              1            63
  STAGE IA             1             0
  STAGE II             0            26
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           1             5
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             2            33
  STAGE IVA            0            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
  FYN MUTATED     0   2  10   2
  FYN WILD-TYPE   9  65 239  39
D109V4, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  T1           0             9
  T2           2            65
  T3          10           239
  T4           2            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
  FYN MUTATED     9   5   1
  FYN WILD-TYPE 211  76  65
D109V5, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  N0           9           211
  N1           5            76
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V6, binary
               cls
clus              0   1
  FYN MUTATED    12   2
  FYN WILD-TYPE 273  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     12    2
  FYN WILD-TYPE  273   46
   clus
vv  FYN MUTATED FYN WILD-TYPE
  0          12           273
  1           2            46
[1] 2 2
[1] FALSE
D109V7, binary
               cls
clus              0   1
  FYN MUTATED     7   8
  FYN WILD-TYPE 163 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED      7    8
  FYN WILD-TYPE  163  189
        clus
vv       FYN MUTATED FYN WILD-TYPE
  FEMALE           7           163
  MALE             8           189
[1] 2 2
[1] FALSE
D109V8, binary
               cls
clus              0   1
  FYN MUTATED    13   1
  FYN WILD-TYPE 287   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     13    1
  FYN WILD-TYPE  287    7
     clus
vv    FYN MUTATED FYN WILD-TYPE
  NO           13           287
  YES           1             7
[1] 2 2
[1] FALSE
D109V9, binary
               cls
clus              0   1
  FYN MUTATED    13   2
  FYN WILD-TYPE 301  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     13    2
  FYN WILD-TYPE  301   46
                               clus
vv                              FYN MUTATED FYN WILD-TYPE
  COLON ADENOCARCINOMA                   13           301
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FYN MUTATED    11   0   1   0
  FYN WILD-TYPE 248   3  21  21
D109V10, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  R0          11           248
  R1           0             3
  R2           1            21
  RX           0            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"
D109V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FYN MUTATED                                  0     0
  FYN WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FYN MUTATED                           2     7
  FYN WILD-TYPE                        17   169
D109V12, multiclass
                                  clus
vv                                 FYN MUTATED FYN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                      7           169
[1] 4 2
[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 = CDX2 MUTATION ANALYSIS
D110V1, survival
                sevent
clus2              0   1
  CDX2 MUTATED     4   2
  CDX2 WILD-TYPE 273  76
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            349 
  CDX2 MUTATED CDX2 WILD-TYPE 
             2             76 
$`CDX2 MUTATED`
TCGA-AA-3713 TCGA-G4-6586 TCGA-A6-2672 TCGA-AD-6889 TCGA-AZ-6598 TCGA-D5-6927 
       19.04        35.80        46.65        83.24        49.41         9.44 

$`CDX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CDX2 MUTATED CDX2 WILD-TYPE 
          9.44           0.00 
  CDX2 MUTATED CDX2 WILD-TYPE 
         83.24         148.01 
  CDX2 MUTATED CDX2 WILD-TYPE 
        41.225         22.030 
[1] "9.4 - 83.2 (41.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D110V2, continuous
                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      64        1       25       105         8         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  CDX2 MUTATED           0
  CDX2 WILD-TYPE         1
D110V3, multiclass
            clus
vv           CDX2 MUTATED CDX2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  CDX2 MUTATED     0   0   6   0
  CDX2 WILD-TYPE   9  67 243  41
D110V4, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            0             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
  CDX2 MUTATED     5   1   0
  CDX2 WILD-TYPE 215  80  66
D110V5, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V6, binary
                cls
clus               0   1
  CDX2 MUTATED     4   1
  CDX2 WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      4    1
  CDX2 WILD-TYPE  281   47
   clus
vv  CDX2 MUTATED CDX2 WILD-TYPE
  0            4            281
  1            1             47
[1] 2 2
[1] FALSE
D110V7, binary
                cls
clus               0   1
  CDX2 MUTATED     3   3
  CDX2 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      3    3
  CDX2 WILD-TYPE  167  194
        clus
vv       CDX2 MUTATED CDX2 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D110V8, binary
                cls
clus               0   1
  CDX2 MUTATED     5   1
  CDX2 WILD-TYPE 295   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      5    1
  CDX2 WILD-TYPE  295    7
     clus
vv    CDX2 MUTATED CDX2 WILD-TYPE
  NO             5            295
  YES            1              7
[1] 2 2
[1] FALSE
D110V9, binary
                cls
clus               0   1
  CDX2 MUTATED     6   0
  CDX2 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      6    0
  CDX2 WILD-TYPE  308   48
                               clus
vv                              CDX2 MUTATED CDX2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDX2 MUTATED     4   0   1   0
  CDX2 WILD-TYPE 255   3  21  21
D110V10, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            1             21
  RX            0             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"
D110V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDX2 MUTATED                                  0     1
  CDX2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDX2 MUTATED                           0     4
  CDX2 WILD-TYPE                        19   172
D110V12, multiclass
                                  clus
vv                                 CDX2 MUTATED CDX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = KLK10 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2               0   1
  KLK10 MUTATED     4   2
  KLK10 WILD-TYPE 273  76
  KLK10 MUTATED KLK10 WILD-TYPE 
              6             349 
  KLK10 MUTATED KLK10 WILD-TYPE 
              2              76 
$`KLK10 MUTATED`
TCGA-AZ-6601 TCGA-A6-6651 TCGA-AA-3815 TCGA-D5-6540 TCGA-DM-A1DA TCGA-DM-A1HB 
      100.01        21.76        33.04        16.14         7.50       135.65 

$`KLK10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KLK10 MUTATED KLK10 WILD-TYPE 
            7.5             0.0 
  KLK10 MUTATED KLK10 WILD-TYPE 
         135.65          148.01 
  KLK10 MUTATED KLK10 WILD-TYPE 
          27.40           22.06 
[1] "7.5 - 135.7 (27.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D111V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLK10 MUTATED         2        0        1         1         0         0
  KLK10 WILD-TYPE      62        1       25       107         8         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        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  KLK10 MUTATED           0
  KLK10 WILD-TYPE         1
D111V3, multiclass
            clus
vv           KLK10 MUTATED KLK10 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  KLK10 MUTATED     0   2   5   0
  KLK10 WILD-TYPE   9  65 244  41
D111V4, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             0              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
  KLK10 MUTATED     4   2   1
  KLK10 WILD-TYPE 216  79  65
D111V5, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V6, binary
                 cls
clus                0   1
  KLK10 MUTATED     5   0
  KLK10 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      5    0
  KLK10 WILD-TYPE  280   48
   clus
vv  KLK10 MUTATED KLK10 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D111V7, binary
                 cls
clus                0   1
  KLK10 MUTATED     3   4
  KLK10 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      3    4
  KLK10 WILD-TYPE  167  193
        clus
vv       KLK10 MUTATED KLK10 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D111V8, binary
                 cls
clus                0   1
  KLK10 MUTATED     4   0
  KLK10 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      4    0
  KLK10 WILD-TYPE  296    8
     clus
vv    KLK10 MUTATED KLK10 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D111V9, binary
                 cls
clus                0   1
  KLK10 MUTATED     5   1
  KLK10 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      5    1
  KLK10 WILD-TYPE  309   47
                               clus
vv                              KLK10 MUTATED KLK10 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLK10 MUTATED     2   0   0   1
  KLK10 WILD-TYPE 257   3  22  20
D111V10, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             1              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"
D111V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLK10 MUTATED                                  0     0
  KLK10 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLK10 MUTATED                           0     6
  KLK10 WILD-TYPE                        19   170
D111V12, multiclass
                                  clus
vv                                 KLK10 MUTATED KLK10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = TPM4 MUTATION ANALYSIS
D112V1, survival
                sevent
clus2              0   1
  TPM4 MUTATED     8   0
  TPM4 WILD-TYPE 269  78
  TPM4 MUTATED TPM4 WILD-TYPE 
             8            347 
  TPM4 MUTATED TPM4 WILD-TYPE 
             0             78 
$`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 
       12.59        15.62 

$`TPM4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6716 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TPM4 MUTATED TPM4 WILD-TYPE 
          1.02           0.00 
  TPM4 MUTATED TPM4 WILD-TYPE 
         63.98         148.01 
  TPM4 MUTATED TPM4 WILD-TYPE 
        24.705         22.030 
[1] "1.0 - 64.0 (24.7)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D112V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPM4 MUTATED         3        0        2         0         0         0
  TPM4 WILD-TYPE      61        1       24       108         8         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  TPM4 MUTATED           0
  TPM4 WILD-TYPE         1
D112V3, multiclass
            clus
vv           TPM4 MUTATED TPM4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TPM4 MUTATED     0   4   3   1
  TPM4 WILD-TYPE   9  63 246  40
D112V4, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  T1            0              9
  T2            4             63
  T3            3            246
  T4            1             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
  TPM4 MUTATED     6   1   1
  TPM4 WILD-TYPE 214  80  65
D112V5, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V6, binary
                cls
clus               0   1
  TPM4 MUTATED     7   0
  TPM4 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      7    0
  TPM4 WILD-TYPE  278   48
   clus
vv  TPM4 MUTATED TPM4 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D112V7, binary
                cls
clus               0   1
  TPM4 MUTATED     3   5
  TPM4 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      3    5
  TPM4 WILD-TYPE  167  192
        clus
vv       TPM4 MUTATED TPM4 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D112V8, binary
                cls
clus               0   1
  TPM4 MUTATED     6   0
  TPM4 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      6    0
  TPM4 WILD-TYPE  294    8
     clus
vv    TPM4 MUTATED TPM4 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D112V9, binary
                cls
clus               0   1
  TPM4 MUTATED     6   2
  TPM4 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      6    2
  TPM4 WILD-TYPE  308   46
                               clus
vv                              TPM4 MUTATED TPM4 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TPM4 MUTATED     4   0   0   2
  TPM4 WILD-TYPE 255   3  22  19
D112V10, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            2             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"
D112V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPM4 MUTATED                                  0     1
  TPM4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPM4 MUTATED                           0     3
  TPM4 WILD-TYPE                        19   173
D112V12, multiclass
                                  clus
vv                                 TPM4 MUTATED TPM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = UQCRC2 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  UQCRC2 MUTATED     5   3
  UQCRC2 WILD-TYPE 272  75
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               8              347 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               3               75 
$`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 
       98.24        65.85 

$`UQCRC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        79.69        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
            5.03             0.00 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
           98.24           148.01 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
          29.685           22.030 
[1] "5.0 - 98.2 (29.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D113V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UQCRC2 MUTATED         1        0        0         1         1         0
  UQCRC2 WILD-TYPE      63        1       26       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UQCRC2 MUTATED           0          0          2          0        2
  UQCRC2 WILD-TYPE        18          6         42         33       33
                  vv
clus               STAGE IVA STAGE IVB
  UQCRC2 MUTATED           1         0
  UQCRC2 WILD-TYPE        11         1
D113V3, multiclass
            clus
vv           UQCRC2 MUTATED UQCRC2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               1               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
  UQCRC2 MUTATED     0   1   5   2
  UQCRC2 WILD-TYPE   9  66 244  39
D113V4, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              2               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
  UQCRC2 MUTATED     3   4   1
  UQCRC2 WILD-TYPE 217  77  65
D113V5, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  N0              3              217
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V6, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     4   3
  UQCRC2 WILD-TYPE 281  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      4    3
  UQCRC2 WILD-TYPE  281   45
   clus
vv  UQCRC2 MUTATED UQCRC2 WILD-TYPE
  0              4              281
  1              3               45
[1] 2 2
[1] FALSE
D113V7, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     4   4
  UQCRC2 WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      4    4
  UQCRC2 WILD-TYPE  166  193
        clus
vv       UQCRC2 MUTATED UQCRC2 WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D113V8, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     7   0
  UQCRC2 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      7    0
  UQCRC2 WILD-TYPE  293    8
     clus
vv    UQCRC2 MUTATED UQCRC2 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D113V9, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     7   1
  UQCRC2 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      7    1
  UQCRC2 WILD-TYPE  307   47
                               clus
vv                              UQCRC2 MUTATED UQCRC2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UQCRC2 MUTATED     4   0   0   2
  UQCRC2 WILD-TYPE 255   3  22  19
D113V10, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              2               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"
D113V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UQCRC2 MUTATED                                  0     0
  UQCRC2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UQCRC2 MUTATED                           0     7
  UQCRC2 WILD-TYPE                        19   169
D113V12, multiclass
                                  clus
vv                                 UQCRC2 MUTATED UQCRC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = PIK3IP1 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                 0   1
  PIK3IP1 MUTATED     7   1
  PIK3IP1 WILD-TYPE 270  77
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                8               347 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                1                77 
$`PIK3IP1 MUTATED`
TCGA-A6-3807 TCGA-AA-3663 TCGA-AY-6196 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 
       34.65         6.97         0.20        14.04        17.85        16.14 
TCGA-DM-A1D6 TCGA-G4-6293 
       49.91       133.18 

$`PIK3IP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 
       46.65        43.76        42.90        42.28        16.57        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        43.27        15.12         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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
              0.2               0.0 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
           133.18            148.01 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
           16.995            22.090 
[1] "0.2 - 133.2 (17.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D114V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3IP1 MUTATED         2        0        1         2         0         0
  PIK3IP1 WILD-TYPE      62        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3IP1 MUTATED           1          0          0          2        0
  PIK3IP1 WILD-TYPE        17          6         44         31       35
                   vv
clus                STAGE IVA STAGE IVB
  PIK3IP1 MUTATED           0         0
  PIK3IP1 WILD-TYPE        12         1
D114V3, multiclass
            clus
vv           PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  PIK3IP1 MUTATED     0   2   6   0
  PIK3IP1 WILD-TYPE   9  65 243  41
D114V4, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               6               243
  T4               0                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
  PIK3IP1 MUTATED     5   1   2
  PIK3IP1 WILD-TYPE 215  80  64
D114V5, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  N0               5               215
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V6, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     7   0
  PIK3IP1 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      7    0
  PIK3IP1 WILD-TYPE  278   48
   clus
vv  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D114V7, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     3   5
  PIK3IP1 WILD-TYPE 167 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      3    5
  PIK3IP1 WILD-TYPE  167  192
        clus
vv       PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  FEMALE               3               167
  MALE                 5               192
[1] 2 2
[1] FALSE
D114V8, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     6   0
  PIK3IP1 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      6    0
  PIK3IP1 WILD-TYPE  294    8
     clus
vv    PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D114V9, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     5   3
  PIK3IP1 WILD-TYPE 309  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      5    3
  PIK3IP1 WILD-TYPE  309   45
                               clus
vv                              PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PIK3IP1 MUTATED     7   0   0   0
  PIK3IP1 WILD-TYPE 252   3  22  21
D114V10, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D114V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3IP1 MUTATED                                  0     0
  PIK3IP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3IP1 MUTATED                           0     7
  PIK3IP1 WILD-TYPE                        19   169
D114V12, multiclass
                                  clus
vv                                 PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = USP24 MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2               0   1
  USP24 MUTATED    22   7
  USP24 WILD-TYPE 255  71
  USP24 MUTATED USP24 WILD-TYPE 
             29             326 
  USP24 MUTATED USP24 WILD-TYPE 
              7              71 
$`USP24 MUTATED`
TCGA-AD-6964 TCGA-G4-6586 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 
       10.88        35.80        33.53        24.39        19.66        63.98 
TCGA-AA-3511 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-A00N 
        6.97         6.97        33.04        37.02         0.00         4.01 
TCGA-AA-A010 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-5797 TCGA-CK-4950 
       34.98        88.21        49.41        11.74        12.59        85.45 
TCGA-CM-6167 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       14.99        12.03        56.09        15.12        17.13        12.49 
TCGA-D5-6540 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A282 TCGA-G4-6323 
       16.14        49.91        12.59       139.17        13.78 

$`USP24 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04         3.02        35.01         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        5.23         3.19        12.69        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        54.61        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        25.48        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
        4.80        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6626 
       36.00        46.75 

  USP24 MUTATED USP24 WILD-TYPE 
              0               0 
  USP24 MUTATED USP24 WILD-TYPE 
         139.17          148.01 
  USP24 MUTATED USP24 WILD-TYPE 
          17.13           22.09 
[1] "0.0 - 139.2 (17.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D115V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP24 MUTATED         3        1        4         8         3         0
  USP24 WILD-TYPE      61        0       22       100         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP24 MUTATED           0          1          4          2        1         0
  USP24 WILD-TYPE        18          5         40         31       34        12
                 vv
clus              STAGE IVB
  USP24 MUTATED           0
  USP24 WILD-TYPE         1
D115V3, multiclass
            clus
vv           USP24 MUTATED USP24 WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               4              22
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  USP24 MUTATED     1   3  18   7
  USP24 WILD-TYPE   8  64 231  34
D115V4, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            18             231
  T4             7              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
  USP24 MUTATED    20   5   5
  USP24 WILD-TYPE 200  76  61
D115V5, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  N0            20             200
  N1             5              76
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V6, binary
                 cls
clus                0   1
  USP24 MUTATED    22   1
  USP24 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     22    1
  USP24 WILD-TYPE  263   47
   clus
vv  USP24 MUTATED USP24 WILD-TYPE
  0            22             263
  1             1              47
[1] 2 2
[1] FALSE
D115V7, binary
                 cls
clus                0   1
  USP24 MUTATED    16  14
  USP24 WILD-TYPE 154 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     16   14
  USP24 WILD-TYPE  154  183
        clus
vv       USP24 MUTATED USP24 WILD-TYPE
  FEMALE            16             154
  MALE              14             183
[1] 2 2
[1] FALSE
D115V8, binary
                 cls
clus                0   1
  USP24 MUTATED    24   0
  USP24 WILD-TYPE 276   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     24    0
  USP24 WILD-TYPE  276    8
     clus
vv    USP24 MUTATED USP24 WILD-TYPE
  NO             24             276
  YES             0               8
[1] 2 2
[1] FALSE
D115V9, binary
                 cls
clus                0   1
  USP24 MUTATED    25   5
  USP24 WILD-TYPE 289  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     25    5
  USP24 WILD-TYPE  289   43
                               clus
vv                              USP24 MUTATED USP24 WILD-TYPE
  COLON ADENOCARCINOMA                     25             289
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP24 MUTATED    19   1   0   2
  USP24 WILD-TYPE 240   2  22  19
D115V10, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  R0            19             240
  R1             1               2
  R2             0              22
  RX             2              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"
D115V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP24 MUTATED                                  0     1
  USP24 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP24 MUTATED                           4    17
  USP24 WILD-TYPE                        15   159
D115V12, multiclass
                                  clus
vv                                 USP24 MUTATED USP24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       17             159
[1] 4 2
[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 = OR5V1 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  OR5V1 MUTATED    13   1
  OR5V1 WILD-TYPE 264  77
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             14             341 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
              1              77 
$`OR5V1 MUTATED`
TCGA-CK-5912 TCGA-G4-6321 TCGA-AA-3866 TCGA-AA-3977 TCGA-AU-3779 TCGA-CA-6717 
       49.08        22.09        17.03        25.02        14.50        12.76 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-6164 TCGA-CM-6676 TCGA-D5-6535 
       14.30        85.45        15.62        29.03        11.08        15.12 
TCGA-D5-6928 TCGA-DM-A1HB 
       11.64       135.65 

$`OR5V1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      106.75       100.01         1.94         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 
       12.20        10.06        17.56       148.01        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR5V1 MUTATED OR5V1 WILD-TYPE 
          11.08            0.00 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
         135.65          148.01 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
         16.325          22.090 
[1] "11.1 - 135.7 (16.3)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "3.6"
D116V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5V1 MUTATED         3        0        0         5         0         0
  OR5V1 WILD-TYPE      61        1       26       103         8         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        17          6         41         32       35        12
                 vv
clus              STAGE IVB
  OR5V1 MUTATED           0
  OR5V1 WILD-TYPE         1
D116V3, multiclass
            clus
vv           OR5V1 MUTATED OR5V1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OR5V1 MUTATED     0   5   8   1
  OR5V1 WILD-TYPE   9  62 241  40
D116V4, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             8             241
  T4             1              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
  OR5V1 MUTATED     9   4   1
  OR5V1 WILD-TYPE 211  77  65
D116V5, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  N0             9             211
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V6, binary
                 cls
clus                0   1
  OR5V1 MUTATED    10   0
  OR5V1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     10    0
  OR5V1 WILD-TYPE  275   48
   clus
vv  OR5V1 MUTATED OR5V1 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D116V7, binary
                 cls
clus                0   1
  OR5V1 MUTATED     7   7
  OR5V1 WILD-TYPE 163 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED      7    7
  OR5V1 WILD-TYPE  163  190
        clus
vv       OR5V1 MUTATED OR5V1 WILD-TYPE
  FEMALE             7             163
  MALE               7             190
[1] 2 2
[1] FALSE
D116V8, binary
                 cls
clus                0   1
  OR5V1 MUTATED    12   0
  OR5V1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     12    0
  OR5V1 WILD-TYPE  288    8
     clus
vv    OR5V1 MUTATED OR5V1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D116V9, binary
                 cls
clus                0   1
  OR5V1 MUTATED     9   4
  OR5V1 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED      9    4
  OR5V1 WILD-TYPE  305   44
                               clus
vv                              OR5V1 MUTATED OR5V1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5V1 MUTATED     6   1   0   5
  OR5V1 WILD-TYPE 253   2  22  16
D116V10, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  R0             6             253
  R1             1               2
  R2             0              22
  RX             5              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"
D116V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5V1 MUTATED                                  0     2
  OR5V1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5V1 MUTATED                           1     9
  OR5V1 WILD-TYPE                        18   167
D116V12, multiclass
                                  clus
vv                                 OR5V1 MUTATED OR5V1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(117) Variable = GGTLC2 MUTATION ANALYSIS
D117V1, survival
                  sevent
clus2                0   1
  GGTLC2 MUTATED     6   0
  GGTLC2 WILD-TYPE 271  78
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               6              349 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               0               78 
$`GGTLC2 MUTATED`
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-AU-3779 TCGA-D5-6535 TCGA-G4-6306 
       22.09        35.80        26.17        14.50        15.12        44.68 

$`GGTLC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.03 
[1] "14.5 - 44.7 (24.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D117V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGTLC2 MUTATED         0        0        0         3         1         0
  GGTLC2 WILD-TYPE      64        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GGTLC2 MUTATED           1          0          1          0        0
  GGTLC2 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  GGTLC2 MUTATED           0         0
  GGTLC2 WILD-TYPE        12         1
D117V3, multiclass
            clus
vv           GGTLC2 MUTATED GGTLC2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  GGTLC2 MUTATED     0   2   4   1
  GGTLC2 WILD-TYPE   9  65 245  40
D117V4, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              1               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
  GGTLC2 MUTATED     5   2   0
  GGTLC2 WILD-TYPE 215  79  66
D117V5, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  N0              5              215
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V6, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     4   0
  GGTLC2 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      4    0
  GGTLC2 WILD-TYPE  281   48
   clus
vv  GGTLC2 MUTATED GGTLC2 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D117V7, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     6   1
  GGTLC2 WILD-TYPE 164 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      6    1
  GGTLC2 WILD-TYPE  164  196
        clus
vv       GGTLC2 MUTATED GGTLC2 WILD-TYPE
  FEMALE              6              164
  MALE                1              196
[1] 2 2
[1] FALSE
D117V8, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     6   0
  GGTLC2 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      6    0
  GGTLC2 WILD-TYPE  294    8
     clus
vv    GGTLC2 MUTATED GGTLC2 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D117V9, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     7   0
  GGTLC2 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      7    0
  GGTLC2 WILD-TYPE  307   48
                               clus
vv                              GGTLC2 MUTATED GGTLC2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GGTLC2 MUTATED     5   0   0   2
  GGTLC2 WILD-TYPE 254   3  22  19
D117V10, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D117V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGTLC2 MUTATED                                  0     0
  GGTLC2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GGTLC2 MUTATED                           0     7
  GGTLC2 WILD-TYPE                        19   169
D117V12, multiclass
                                  clus
vv                                 GGTLC2 MUTATED GGTLC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = ZFYVE26 MUTATION ANALYSIS
D118V1, survival
                   sevent
clus2                 0   1
  ZFYVE26 MUTATED    20   7
  ZFYVE26 WILD-TYPE 257  71
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               27               328 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                7                71 
$`ZFYVE26 MUTATED`
TCGA-AZ-6608 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-6137 TCGA-A6-6651 
        1.94        26.17        79.69        32.75        27.09        21.76 
TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N 
       24.39        29.95        53.00        33.01        25.02         4.01 
TCGA-AD-6889 TCGA-AU-3779 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 
       83.24        14.50        21.44        17.82        58.39        49.41 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CK-4952 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6538 
       12.10         5.23        15.62        15.02        14.04        17.13 
TCGA-D5-6928 TCGA-DM-A28H TCGA-F4-6570 
       11.64       117.07         6.18 

$`ZFYVE26 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20         1.41         5.13        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        6.77        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
             1.94              0.00 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
           117.07            148.01 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
           21.760            22.075 
[1] "1.9 - 117.1 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D118V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFYVE26 MUTATED         3        0        2        10         3         0
  ZFYVE26 WILD-TYPE      61        1       24        98         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFYVE26 MUTATED           0          1          5          2        1
  ZFYVE26 WILD-TYPE        18          5         39         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ZFYVE26 MUTATED           0         0
  ZFYVE26 WILD-TYPE        12         1
D118V3, multiclass
            clus
vv           ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA               10                98
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               5                39
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  ZFYVE26 MUTATED     0   5  17   6
  ZFYVE26 WILD-TYPE   9  62 232  35
D118V4, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3              17               232
  T4               6                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
  ZFYVE26 MUTATED    19   6   3
  ZFYVE26 WILD-TYPE 201  75  63
D118V5, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  N0              19               201
  N1               6                75
  N2               3                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"
D118V6, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    23   1
  ZFYVE26 WILD-TYPE 262  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     23    1
  ZFYVE26 WILD-TYPE  262   47
   clus
vv  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  0              23               262
  1               1                47
[1] 2 2
[1] FALSE
D118V7, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    15  13
  ZFYVE26 WILD-TYPE 155 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     15   13
  ZFYVE26 WILD-TYPE  155  184
        clus
vv       ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  FEMALE              15               155
  MALE                13               184
[1] 2 2
[1] FALSE
D118V8, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    24   0
  ZFYVE26 WILD-TYPE 276   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     24    0
  ZFYVE26 WILD-TYPE  276    8
     clus
vv    ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  NO               24               276
  YES               0                 8
[1] 2 2
[1] FALSE
D118V9, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    22   6
  ZFYVE26 WILD-TYPE 292  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     22    6
  ZFYVE26 WILD-TYPE  292   42
                               clus
vv                              ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  COLON ADENOCARCINOMA                       22               292
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFYVE26 MUTATED    18   0   0   1
  ZFYVE26 WILD-TYPE 241   3  22  20
D118V10, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               0                22
  RX               1                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"
D118V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFYVE26 MUTATED                                  0     1
  ZFYVE26 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFYVE26 MUTATED                           2    19
  ZFYVE26 WILD-TYPE                        17   157
D118V12, multiclass
                                  clus
vv                                 ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         19               157
[1] 4 2
[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 = MLLT6 MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2               0   1
  MLLT6 MUTATED    11   5
  MLLT6 WILD-TYPE 266  73
  MLLT6 MUTATED MLLT6 WILD-TYPE 
             16             339 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
              5              73 
$`MLLT6 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6652 
        0.92        19.04       100.01        26.17        22.06        24.69 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-A01K TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CM-6162 
       19.66         3.02        31.00         6.77        29.56        12.00 
TCGA-CM-6170 TCGA-CM-6674 TCGA-D5-6927 TCGA-DM-A28H 
       15.02        12.95         9.44       117.07 

$`MLLT6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.39        23.87        20.12        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        49.41        12.10         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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MLLT6 MUTATED MLLT6 WILD-TYPE 
           0.92            0.00 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
         117.07          148.01 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
          19.35           22.09 
[1] "0.9 - 117.1 (19.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D119V2, continuous
                 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      62        1       23       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLLT6 MUTATED           1          0          1          3        0         1
  MLLT6 WILD-TYPE        17          6         43         30       35        11
                 vv
clus              STAGE IVB
  MLLT6 MUTATED           0
  MLLT6 WILD-TYPE         1
D119V3, multiclass
            clus
vv           MLLT6 MUTATED MLLT6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              1              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
  MLLT6 MUTATED     0   3  12   1
  MLLT6 WILD-TYPE   9  64 237  40
D119V4, multiclass
    clus
vv   MLLT6 MUTATED MLLT6 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             1              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
  MLLT6 MUTATED    10   4   2
  MLLT6 WILD-TYPE 210  77  64
D119V5, multiclass
    clus
vv   MLLT6 MUTATED MLLT6 WILD-TYPE
  N0            10             210
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V6, binary
                 cls
clus                0   1
  MLLT6 MUTATED    12   1
  MLLT6 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED     12    1
  MLLT6 WILD-TYPE  273   47
   clus
vv  MLLT6 MUTATED MLLT6 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D119V7, binary
                 cls
clus                0   1
  MLLT6 MUTATED     8   8
  MLLT6 WILD-TYPE 162 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED      8    8
  MLLT6 WILD-TYPE  162  189
        clus
vv       MLLT6 MUTATED MLLT6 WILD-TYPE
  FEMALE             8             162
  MALE               8             189
[1] 2 2
[1] FALSE
D119V8, binary
                 cls
clus                0   1
  MLLT6 MUTATED    15   0
  MLLT6 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED     15    0
  MLLT6 WILD-TYPE  285    8
     clus
vv    MLLT6 MUTATED MLLT6 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D119V9, binary
                 cls
clus                0   1
  MLLT6 MUTATED    14   2
  MLLT6 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED     14    2
  MLLT6 WILD-TYPE  300   46
                               clus
vv                              MLLT6 MUTATED MLLT6 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MLLT6 MUTATED    11   0   0   0
  MLLT6 WILD-TYPE 248   3  22  21
D119V10, multiclass
    clus
vv   MLLT6 MUTATED MLLT6 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D119V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLLT6 MUTATED                                  0     0
  MLLT6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MLLT6 MUTATED                           1    11
  MLLT6 WILD-TYPE                        18   165
D119V12, multiclass
                                  clus
vv                                 MLLT6 MUTATED MLLT6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(120) Variable = RNF128 MUTATION ANALYSIS
D120V1, survival
                  sevent
clus2                0   1
  RNF128 MUTATED    11   2
  RNF128 WILD-TYPE 266  76
  RNF128 MUTATED RNF128 WILD-TYPE 
              13              342 
  RNF128 MUTATED RNF128 WILD-TYPE 
               2               76 
$`RNF128 MUTATED`
TCGA-AA-3697 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6588 
       85.05        21.37        25.08        10.88        35.80        26.17 
TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3492 TCGA-AZ-4315 TCGA-CM-4746 TCGA-D5-6928 
       79.69        22.06         3.02        58.39        37.02        11.64 
TCGA-DM-A0X9 
      119.70 

$`RNF128 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       39.06        15.52       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
        5.88        63.62        22.09        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RNF128 MUTATED RNF128 WILD-TYPE 
            3.02             0.00 
  RNF128 MUTATED RNF128 WILD-TYPE 
          119.70           148.01 
  RNF128 MUTATED RNF128 WILD-TYPE 
           26.17            21.99 
[1] "3.0 - 119.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D120V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF128 MUTATED         3        0        2         6         1         0
  RNF128 WILD-TYPE      61        1       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF128 MUTATED           0          0          1          0        0
  RNF128 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF128 MUTATED           0         0
  RNF128 WILD-TYPE        12         1
D120V3, multiclass
            clus
vv           RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  RNF128 MUTATED     0   3   9   2
  RNF128 WILD-TYPE   9  64 240  39
D120V4, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              9              240
  T4              2               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
  RNF128 MUTATED    12   1   1
  RNF128 WILD-TYPE 208  80  65
D120V5, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  N0             12              208
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V6, binary
                  cls
clus                 0   1
  RNF128 MUTATED    12   0
  RNF128 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     12    0
  RNF128 WILD-TYPE  273   48
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D120V7, binary
                  cls
clus                 0   1
  RNF128 MUTATED     7   7
  RNF128 WILD-TYPE 163 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      7    7
  RNF128 WILD-TYPE  163  190
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  FEMALE              7              163
  MALE                7              190
[1] 2 2
[1] FALSE
D120V8, binary
                  cls
clus                 0   1
  RNF128 MUTATED    12   0
  RNF128 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     12    0
  RNF128 WILD-TYPE  288    8
     clus
vv    RNF128 MUTATED RNF128 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D120V9, binary
                  cls
clus                 0   1
  RNF128 MUTATED    13   1
  RNF128 WILD-TYPE 301  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     13    1
  RNF128 WILD-TYPE  301   47
                               clus
vv                              RNF128 MUTATED RNF128 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF128 MUTATED    11   0   0   1
  RNF128 WILD-TYPE 248   3  22  20
D120V10, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              1               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"
D120V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF128 MUTATED                                  0     0
  RNF128 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF128 MUTATED                           1    11
  RNF128 WILD-TYPE                        18   165
D120V12, multiclass
                                  clus
vv                                 RNF128 MUTATED RNF128 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(121) Variable = TNMD MUTATION ANALYSIS
D121V1, survival
                sevent
clus2              0   1
  TNMD MUTATED     9   2
  TNMD WILD-TYPE 268  76
  TNMD MUTATED TNMD WILD-TYPE 
            11            344 
  TNMD MUTATED TNMD WILD-TYPE 
             2             76 
$`TNMD MUTATED`
TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3502 TCGA-AA-3542 TCGA-AA-3815 
       35.80        22.06         8.38        35.01        12.99        33.04 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AZ-6598 TCGA-CK-5916 TCGA-D5-6930 
       53.00        25.02        49.41        21.14        13.35 

$`TNMD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TNMD MUTATED TNMD WILD-TYPE 
          8.38           0.00 
  TNMD MUTATED TNMD WILD-TYPE 
         53.00         148.01 
  TNMD MUTATED TNMD WILD-TYPE 
         25.02          22.01 
[1] "8.4 - 53.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D121V2, continuous
                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      62        1       24       103         8         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        18          6         44         32       35        12
                vv
clus             STAGE IVB
  TNMD MUTATED           0
  TNMD WILD-TYPE         1
D121V3, multiclass
            clus
vv           TNMD MUTATED TNMD WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TNMD MUTATED     1   2   8   0
  TNMD WILD-TYPE   8  65 241  41
D121V4, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  T1            1              8
  T2            2             65
  T3            8            241
  T4            0             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
  TNMD MUTATED    10   0   1
  TNMD WILD-TYPE 210  81  65
D121V5, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  N0           10            210
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V6, binary
                cls
clus               0   1
  TNMD MUTATED     9   0
  TNMD WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED      9    0
  TNMD WILD-TYPE  276   48
   clus
vv  TNMD MUTATED TNMD WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D121V7, binary
                cls
clus               0   1
  TNMD MUTATED     5   6
  TNMD WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED      5    6
  TNMD WILD-TYPE  165  191
        clus
vv       TNMD MUTATED TNMD WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D121V8, binary
                cls
clus               0   1
  TNMD MUTATED    11   0
  TNMD WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED     11    0
  TNMD WILD-TYPE  289    8
     clus
vv    TNMD MUTATED TNMD WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D121V9, binary
                cls
clus               0   1
  TNMD MUTATED    10   1
  TNMD WILD-TYPE 304  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED     10    1
  TNMD WILD-TYPE  304   47
                               clus
vv                              TNMD MUTATED TNMD WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TNMD MUTATED     7   0   0   1
  TNMD WILD-TYPE 252   3  22  20
D121V10, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D121V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNMD MUTATED                                  0     0
  TNMD WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TNMD MUTATED                           1     5
  TNMD WILD-TYPE                        18   171
D121V12, multiclass
                                  clus
vv                                 TNMD MUTATED TNMD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = GPR174 MUTATION ANALYSIS
D122V1, survival
                  sevent
clus2                0   1
  GPR174 MUTATED     6   2
  GPR174 WILD-TYPE 271  76
  GPR174 MUTATED GPR174 WILD-TYPE 
               8              347 
  GPR174 MUTATED GPR174 WILD-TYPE 
               2               76 
$`GPR174 MUTATED`
TCGA-AA-3543 TCGA-G4-6625 TCGA-A6-5659 TCGA-AA-3955 TCGA-CA-6718 TCGA-CM-6679 
        0.99        91.79        30.44        20.98        10.06        10.06 
TCGA-D5-5538 TCGA-D5-6539 
       54.61        12.49 

$`GPR174 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        26.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPR174 MUTATED GPR174 WILD-TYPE 
            0.99             0.00 
  GPR174 MUTATED GPR174 WILD-TYPE 
           91.79           148.01 
  GPR174 MUTATED GPR174 WILD-TYPE 
          16.735           22.090 
[1] "1.0 - 91.8 (16.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D122V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR174 MUTATED         2        0        0         3         0         0
  GPR174 WILD-TYPE      62        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR174 MUTATED           0          0          2          0        0
  GPR174 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR174 MUTATED           0         0
  GPR174 WILD-TYPE        12         1
D122V3, multiclass
            clus
vv           GPR174 MUTATED GPR174 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  GPR174 MUTATED     0   3   5   0
  GPR174 WILD-TYPE   9  64 244  41
D122V4, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              0               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
  GPR174 MUTATED     6   1   1
  GPR174 WILD-TYPE 214  80  65
D122V5, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V6, binary
                  cls
clus                 0   1
  GPR174 MUTATED     8   0
  GPR174 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      8    0
  GPR174 WILD-TYPE  277   48
   clus
vv  GPR174 MUTATED GPR174 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D122V7, binary
                  cls
clus                 0   1
  GPR174 MUTATED     3   5
  GPR174 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      3    5
  GPR174 WILD-TYPE  167  192
        clus
vv       GPR174 MUTATED GPR174 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D122V8, binary
                  cls
clus                 0   1
  GPR174 MUTATED     8   0
  GPR174 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      8    0
  GPR174 WILD-TYPE  292    8
     clus
vv    GPR174 MUTATED GPR174 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D122V9, binary
                  cls
clus                 0   1
  GPR174 MUTATED     7   1
  GPR174 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      7    1
  GPR174 WILD-TYPE  307   47
                               clus
vv                              GPR174 MUTATED GPR174 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR174 MUTATED     7   0   0   1
  GPR174 WILD-TYPE 252   3  22  20
D122V10, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D122V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR174 MUTATED                                  0     1
  GPR174 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR174 MUTATED                           0     5
  GPR174 WILD-TYPE                        19   171
D122V12, multiclass
                                  clus
vv                                 GPR174 MUTATED GPR174 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = CD58 MUTATION ANALYSIS
D123V1, survival
                sevent
clus2              0   1
  CD58 MUTATED    10   4
  CD58 WILD-TYPE 267  74
  CD58 MUTATED CD58 WILD-TYPE 
            14            341 
  CD58 MUTATED CD58 WILD-TYPE 
             4             74 
$`CD58 MUTATED`
TCGA-AD-6895 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A010 
       25.08        91.79        79.69        22.06         6.97        34.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       12.16        83.24        58.39        49.41        12.76        21.14 
TCGA-CM-5861 TCGA-F4-6570 
       15.02         6.18 

$`CD58 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        26.17        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       18.05        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CD58 MUTATED CD58 WILD-TYPE 
          6.18           0.00 
  CD58 MUTATED CD58 WILD-TYPE 
         91.79         148.01 
  CD58 MUTATED CD58 WILD-TYPE 
         23.57          22.03 
[1] "6.2 - 91.8 (23.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D123V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD58 MUTATED         3        0        2         7         1         0
  CD58 WILD-TYPE      61        1       24       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD58 MUTATED           0          0          1          0        0         0
  CD58 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  CD58 MUTATED           0
  CD58 WILD-TYPE         1
D123V3, multiclass
            clus
vv           CD58 MUTATED CD58 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CD58 MUTATED     1   2  10   1
  CD58 WILD-TYPE   8  65 239  40
D123V4, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  T1            1              8
  T2            2             65
  T3           10            239
  T4            1             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
  CD58 MUTATED    13   1   0
  CD58 WILD-TYPE 207  80  66
D123V5, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  N0           13            207
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V6, binary
                cls
clus               0   1
  CD58 MUTATED    12   0
  CD58 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     12    0
  CD58 WILD-TYPE  273   48
   clus
vv  CD58 MUTATED CD58 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D123V7, binary
                cls
clus               0   1
  CD58 MUTATED     7   7
  CD58 WILD-TYPE 163 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      7    7
  CD58 WILD-TYPE  163  190
        clus
vv       CD58 MUTATED CD58 WILD-TYPE
  FEMALE            7            163
  MALE              7            190
[1] 2 2
[1] FALSE
D123V8, binary
                cls
clus               0   1
  CD58 MUTATED    14   0
  CD58 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     14    0
  CD58 WILD-TYPE  286    8
     clus
vv    CD58 MUTATED CD58 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D123V9, binary
                cls
clus               0   1
  CD58 MUTATED    12   2
  CD58 WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     12    2
  CD58 WILD-TYPE  302   46
                               clus
vv                              CD58 MUTATED CD58 WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD58 MUTATED    11   0   0   2
  CD58 WILD-TYPE 248   3  22  19
D123V10, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            2             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"
D123V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD58 MUTATED                                  0     2
  CD58 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD58 MUTATED                           0    10
  CD58 WILD-TYPE                        19   166
D123V12, multiclass
                                  clus
vv                                 CD58 MUTATED CD58 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(124) Variable = HTR2A MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2               0   1
  HTR2A MUTATED    14   5
  HTR2A WILD-TYPE 263  73
  HTR2A MUTATED HTR2A WILD-TYPE 
             19             336 
  HTR2A MUTATED HTR2A WILD-TYPE 
              5              73 
$`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        12.36 
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 
       74.56 

$`HTR2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02        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        14.04        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        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       25.48        43.27        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      135.65       139.17       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HTR2A MUTATED HTR2A WILD-TYPE 
           4.01            0.00 
  HTR2A MUTATED HTR2A WILD-TYPE 
         131.51          148.01 
  HTR2A MUTATED HTR2A WILD-TYPE 
         19.590          22.225 
[1] "4.0 - 131.5 (19.6)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D124V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HTR2A MUTATED         1        0        0         6         2         0
  HTR2A WILD-TYPE      63        1       26       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HTR2A MUTATED           0          1          3          4        0         1
  HTR2A WILD-TYPE        18          5         41         29       35        11
                 vv
clus              STAGE IVB
  HTR2A MUTATED           0
  HTR2A WILD-TYPE         1
D124V3, multiclass
            clus
vv           HTR2A MUTATED HTR2A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             4              29
  STAGE IV               0              35
  STAGE IVA              1              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
  HTR2A MUTATED     0   1  15   3
  HTR2A WILD-TYPE   9  66 234  38
D124V4, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  T1             0               9
  T2             1              66
  T3            15             234
  T4             3              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
  HTR2A MUTATED    10   5   4
  HTR2A WILD-TYPE 210  76  62
D124V5, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  N0            10             210
  N1             5              76
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V6, binary
                 cls
clus                0   1
  HTR2A MUTATED    16   1
  HTR2A WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     16    1
  HTR2A WILD-TYPE  269   47
   clus
vv  HTR2A MUTATED HTR2A WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D124V7, binary
                 cls
clus                0   1
  HTR2A MUTATED     7  12
  HTR2A WILD-TYPE 163 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED      7   12
  HTR2A WILD-TYPE  163  185
        clus
vv       HTR2A MUTATED HTR2A WILD-TYPE
  FEMALE             7             163
  MALE              12             185
[1] 2 2
[1] FALSE
D124V8, binary
                 cls
clus                0   1
  HTR2A MUTATED    12   1
  HTR2A WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     12    1
  HTR2A WILD-TYPE  288    7
     clus
vv    HTR2A MUTATED HTR2A WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D124V9, binary
                 cls
clus                0   1
  HTR2A MUTATED    14   4
  HTR2A WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     14    4
  HTR2A WILD-TYPE  300   44
                               clus
vv                              HTR2A MUTATED HTR2A WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HTR2A MUTATED     9   0   0   4
  HTR2A WILD-TYPE 250   3  22  17
D124V10, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             4              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"
D124V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTR2A MUTATED                                  0     2
  HTR2A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTR2A MUTATED                           1    14
  HTR2A WILD-TYPE                        18   162
D124V12, multiclass
                                  clus
vv                                 HTR2A MUTATED HTR2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       14             162
[1] 4 2
[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 = EHBP1 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2               0   1
  EHBP1 MUTATED    16   5
  EHBP1 WILD-TYPE 261  73
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             21             334 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
              5              73 
$`EHBP1 MUTATED`
TCGA-AA-3496 TCGA-G4-6310 TCGA-G4-6588 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3845 
        1.02        63.62        26.17        32.71        35.01         0.00 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5913 TCGA-CK-5914 
       53.00        25.02        83.24        27.09        51.32        21.99 
TCGA-CM-6167 TCGA-D5-5538 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1D7 
       14.99        54.61        18.25        15.12        16.14        13.32 
TCGA-DM-A28H TCGA-F4-6570 TCGA-G4-6307 
      117.07         6.18        55.04 

$`EHBP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-3510 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  EHBP1 MUTATED EHBP1 WILD-TYPE 
              0               0 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
         117.07          148.01 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
          26.17           22.01 
[1] "0.0 - 117.1 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D125V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EHBP1 MUTATED         3        0        2         8         0         1
  EHBP1 WILD-TYPE      61        1       24       100         8         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        18          6         39         31       35        12
                 vv
clus              STAGE IVB
  EHBP1 MUTATED           0
  EHBP1 WILD-TYPE         1
D125V3, multiclass
            clus
vv           EHBP1 MUTATED EHBP1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  EHBP1 MUTATED     0   4  17   1
  EHBP1 WILD-TYPE   9  63 232  40
D125V4, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            17             232
  T4             1              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
  EHBP1 MUTATED    15   5   2
  EHBP1 WILD-TYPE 205  76  64
D125V5, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  N0            15             205
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V6, binary
                 cls
clus                0   1
  EHBP1 MUTATED    18   0
  EHBP1 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     18    0
  EHBP1 WILD-TYPE  267   48
   clus
vv  EHBP1 MUTATED EHBP1 WILD-TYPE
  0            18             267
  1             0              48
[1] 2 2
[1] FALSE
D125V7, binary
                 cls
clus                0   1
  EHBP1 MUTATED    11  11
  EHBP1 WILD-TYPE 159 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     11   11
  EHBP1 WILD-TYPE  159  186
        clus
vv       EHBP1 MUTATED EHBP1 WILD-TYPE
  FEMALE            11             159
  MALE              11             186
[1] 2 2
[1] FALSE
D125V8, binary
                 cls
clus                0   1
  EHBP1 MUTATED    14   1
  EHBP1 WILD-TYPE 286   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     14    1
  EHBP1 WILD-TYPE  286    7
     clus
vv    EHBP1 MUTATED EHBP1 WILD-TYPE
  NO             14             286
  YES             1               7
[1] 2 2
[1] FALSE
D125V9, binary
                 cls
clus                0   1
  EHBP1 MUTATED    20   1
  EHBP1 WILD-TYPE 294  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     20    1
  EHBP1 WILD-TYPE  294   47
                               clus
vv                              EHBP1 MUTATED EHBP1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EHBP1 MUTATED    15   0   0   3
  EHBP1 WILD-TYPE 244   3  22  18
D125V10, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             3              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"
D125V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EHBP1 MUTATED                                  0     1
  EHBP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EHBP1 MUTATED                           1    14
  EHBP1 WILD-TYPE                        18   162
D125V12, multiclass
                                  clus
vv                                 EHBP1 MUTATED EHBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       14             162
[1] 4 2
[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 = ZNF583 MUTATION ANALYSIS
D126V1, survival
                  sevent
clus2                0   1
  ZNF583 MUTATED    13   2
  ZNF583 WILD-TYPE 264  76
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              15              340 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
               2               76 
$`ZNF583 MUTATED`
TCGA-AA-3939 TCGA-AD-6895 TCGA-AD-6964 TCGA-A6-6138 TCGA-AA-3977 TCGA-AA-A00O 
       12.99        25.08        10.88        22.52        25.02        27.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 
       34.98        12.16        58.39        12.76        15.62        51.32 
TCGA-CM-5862 TCGA-CM-5868 TCGA-DM-A1HB 
        5.03        17.03       135.65 

$`ZNF583 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF583 MUTATED ZNF583 WILD-TYPE 
            5.03             0.00 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
          135.65           148.01 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
          22.520           22.045 
[1] "5.0 - 135.7 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D126V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF583 MUTATED         2        0        0         4         1         0
  ZNF583 WILD-TYPE      62        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF583 MUTATED           0          0          2          2        0
  ZNF583 WILD-TYPE        18          6         42         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF583 MUTATED           2         0
  ZNF583 WILD-TYPE        10         1
D126V3, multiclass
            clus
vv           ZNF583 MUTATED ZNF583 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               2               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
  ZNF583 MUTATED     0   3   8   4
  ZNF583 WILD-TYPE   9  64 241  37
D126V4, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              8              241
  T4              4               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
  ZNF583 MUTATED     8   4   3
  ZNF583 WILD-TYPE 212  77  63
D126V5, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  N0              8              212
  N1              4               77
  N2              3               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"
D126V6, binary
                  cls
clus                 0   1
  ZNF583 MUTATED     9   2
  ZNF583 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED      9    2
  ZNF583 WILD-TYPE  276   46
   clus
vv  ZNF583 MUTATED ZNF583 WILD-TYPE
  0              9              276
  1              2               46
[1] 2 2
[1] FALSE
D126V7, binary
                  cls
clus                 0   1
  ZNF583 MUTATED     5  10
  ZNF583 WILD-TYPE 165 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED      5   10
  ZNF583 WILD-TYPE  165  187
        clus
vv       ZNF583 MUTATED ZNF583 WILD-TYPE
  FEMALE              5              165
  MALE               10              187
[1] 2 2
[1] FALSE
D126V8, binary
                  cls
clus                 0   1
  ZNF583 MUTATED    13   0
  ZNF583 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED     13    0
  ZNF583 WILD-TYPE  287    8
     clus
vv    ZNF583 MUTATED ZNF583 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D126V9, binary
                  cls
clus                 0   1
  ZNF583 MUTATED    11   3
  ZNF583 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED     11    3
  ZNF583 WILD-TYPE  303   45
                               clus
vv                              ZNF583 MUTATED ZNF583 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF583 MUTATED     8   0   0   3
  ZNF583 WILD-TYPE 251   3  22  18
D126V10, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              3               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"
D126V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF583 MUTATED                                  0     1
  ZNF583 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF583 MUTATED                           0    10
  ZNF583 WILD-TYPE                        19   166
D126V12, multiclass
                                  clus
vv                                 ZNF583 MUTATED ZNF583 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(127) Variable = ATP11B MUTATION ANALYSIS
D127V1, survival
                  sevent
clus2                0   1
  ATP11B MUTATED    13   3
  ATP11B WILD-TYPE 264  75
  ATP11B MUTATED ATP11B WILD-TYPE 
              16              339 
  ATP11B MUTATED ATP11B WILD-TYPE 
               3               75 
$`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        25.48        24.43 
TCGA-F4-6569 TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6315 
       35.74        33.67        53.62        61.91 

$`ATP11B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        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        54.61        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ATP11B MUTATED ATP11B WILD-TYPE 
            0.92             0.00 
  ATP11B MUTATED ATP11B WILD-TYPE 
           61.91           148.01 
  ATP11B MUTATED ATP11B WILD-TYPE 
           23.74            22.03 
[1] "0.9 - 61.9 (23.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D127V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP11B MUTATED         4        0        0         7         1         0
  ATP11B WILD-TYPE      60        1       26       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11B MUTATED           2          0          0          0        2
  ATP11B WILD-TYPE        16          6         44         33       33
                  vv
clus               STAGE IVA STAGE IVB
  ATP11B MUTATED           0         0
  ATP11B WILD-TYPE        12         1
D127V3, multiclass
            clus
vv           ATP11B MUTATED ATP11B WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  ATP11B MUTATED     1   3  11   2
  ATP11B WILD-TYPE   8  64 238  39
D127V4, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  T1              1                8
  T2              3               64
  T3             11              238
  T4              2               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
  ATP11B MUTATED    14   2   1
  ATP11B WILD-TYPE 206  79  65
D127V5, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  N0             14              206
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V6, binary
                  cls
clus                 0   1
  ATP11B MUTATED    15   2
  ATP11B WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     15    2
  ATP11B WILD-TYPE  270   46
   clus
vv  ATP11B MUTATED ATP11B WILD-TYPE
  0             15              270
  1              2               46
[1] 2 2
[1] FALSE
D127V7, binary
                  cls
clus                 0   1
  ATP11B MUTATED     8   9
  ATP11B WILD-TYPE 162 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      8    9
  ATP11B WILD-TYPE  162  188
        clus
vv       ATP11B MUTATED ATP11B WILD-TYPE
  FEMALE              8              162
  MALE                9              188
[1] 2 2
[1] FALSE
D127V8, binary
                  cls
clus                 0   1
  ATP11B MUTATED    14   1
  ATP11B WILD-TYPE 286   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     14    1
  ATP11B WILD-TYPE  286    7
     clus
vv    ATP11B MUTATED ATP11B WILD-TYPE
  NO              14              286
  YES              1                7
[1] 2 2
[1] FALSE
D127V9, binary
                  cls
clus                 0   1
  ATP11B MUTATED    15   2
  ATP11B WILD-TYPE 299  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     15    2
  ATP11B WILD-TYPE  299   46
                               clus
vv                              ATP11B MUTATED ATP11B WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP11B MUTATED    12   0   1   2
  ATP11B WILD-TYPE 247   3  21  19
D127V10, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  R0             12              247
  R1              0                3
  R2              1               21
  RX              2               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"
D127V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP11B MUTATED                                  0     2
  ATP11B WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP11B MUTATED                           1    10
  ATP11B WILD-TYPE                        18   166
D127V12, multiclass
                                  clus
vv                                 ATP11B MUTATED ATP11B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(128) Variable = NCAPD2 MUTATION ANALYSIS
D128V1, survival
                  sevent
clus2                0   1
  NCAPD2 MUTATED    17   1
  NCAPD2 WILD-TYPE 260  77
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              18              337 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
               1               77 
$`NCAPD2 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 
       24.00       100.01        79.69        24.39        19.66        63.98 
TCGA-AA-3663 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CM-4743 
        6.97        18.05        34.98         1.02        58.39        23.05 
TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A28K TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 
       12.00        13.35        98.24       133.18        53.62        44.68 

$`NCAPD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       65.85        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
            1.02             0.00 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
          133.18           148.01 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
          29.685           21.990 
[1] "1.0 - 133.2 (29.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "6.7"
D128V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCAPD2 MUTATED         2        0        4         7         3         0
  NCAPD2 WILD-TYPE      62        1       22       101         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD2 MUTATED           1          0          1          1        0
  NCAPD2 WILD-TYPE        17          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  NCAPD2 MUTATED           0         0
  NCAPD2 WILD-TYPE        12         1
D128V3, multiclass
            clus
vv           NCAPD2 MUTATED NCAPD2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               7              101
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  NCAPD2 MUTATED     0   3  13   4
  NCAPD2 WILD-TYPE   9  64 236  37
D128V4, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             13              236
  T4              4               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
  NCAPD2 MUTATED    17   3   0
  NCAPD2 WILD-TYPE 203  78  66
D128V5, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  N0             17              203
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V6, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    18   0
  NCAPD2 WILD-TYPE 267  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     18    0
  NCAPD2 WILD-TYPE  267   48
   clus
vv  NCAPD2 MUTATED NCAPD2 WILD-TYPE
  0             18              267
  1              0               48
[1] 2 2
[1] FALSE
D128V7, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED     8  12
  NCAPD2 WILD-TYPE 162 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED      8   12
  NCAPD2 WILD-TYPE  162  185
        clus
vv       NCAPD2 MUTATED NCAPD2 WILD-TYPE
  FEMALE              8              162
  MALE               12              185
[1] 2 2
[1] FALSE
D128V8, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    15   0
  NCAPD2 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     15    0
  NCAPD2 WILD-TYPE  285    8
     clus
vv    NCAPD2 MUTATED NCAPD2 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D128V9, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    15   5
  NCAPD2 WILD-TYPE 299  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     15    5
  NCAPD2 WILD-TYPE  299   43
                               clus
vv                              NCAPD2 MUTATED NCAPD2 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NCAPD2 MUTATED    16   0   0   1
  NCAPD2 WILD-TYPE 243   3  22  20
D128V10, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  R0             16              243
  R1              0                3
  R2              0               22
  RX              1               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"
D128V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCAPD2 MUTATED                                  0     0
  NCAPD2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NCAPD2 MUTATED                           0    13
  NCAPD2 WILD-TYPE                        19   163
D128V12, multiclass
                                  clus
vv                                 NCAPD2 MUTATED NCAPD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        13              163
[1] 4 2
[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 = FNDC7 MUTATION ANALYSIS
D129V1, survival
                 sevent
clus2               0   1
  FNDC7 MUTATED     8   1
  FNDC7 WILD-TYPE 269  77
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             346 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              1              77 
$`FNDC7 MUTATED`
TCGA-AD-6895 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3947 TCGA-AZ-4315 
       25.08        29.19        22.06         6.97        33.01        58.39 
TCGA-AZ-6599 TCGA-CM-6162 TCGA-CM-6164 
        6.77        12.00        29.03 

$`FNDC7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FNDC7 MUTATED FNDC7 WILD-TYPE 
           6.77            0.00 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          58.39          148.01 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          25.08           22.01 
[1] "6.8 - 58.4 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D129V2, continuous
                 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      63        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FNDC7 MUTATED           0          0          2          1        0         0
  FNDC7 WILD-TYPE        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  FNDC7 MUTATED           0
  FNDC7 WILD-TYPE         1
D129V3, multiclass
            clus
vv           FNDC7 MUTATED FNDC7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  FNDC7 MUTATED     0   1   7   1
  FNDC7 WILD-TYPE   9  66 242  40
D129V4, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             1              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
  FNDC7 MUTATED     6   2   1
  FNDC7 WILD-TYPE 214  79  65
D129V5, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V6, binary
                 cls
clus                0   1
  FNDC7 MUTATED     8   0
  FNDC7 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      8    0
  FNDC7 WILD-TYPE  277   48
   clus
vv  FNDC7 MUTATED FNDC7 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D129V7, binary
                 cls
clus                0   1
  FNDC7 MUTATED     4   5
  FNDC7 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      4    5
  FNDC7 WILD-TYPE  166  192
        clus
vv       FNDC7 MUTATED FNDC7 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D129V8, binary
                 cls
clus                0   1
  FNDC7 MUTATED     9   0
  FNDC7 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      9    0
  FNDC7 WILD-TYPE  291    8
     clus
vv    FNDC7 MUTATED FNDC7 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D129V9, binary
                 cls
clus                0   1
  FNDC7 MUTATED     7   2
  FNDC7 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      7    2
  FNDC7 WILD-TYPE  307   46
                               clus
vv                              FNDC7 MUTATED FNDC7 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FNDC7 MUTATED     7   0   0   0
  FNDC7 WILD-TYPE 252   3  22  21
D129V10, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D129V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FNDC7 MUTATED                                  0     0
  FNDC7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FNDC7 MUTATED                           1     6
  FNDC7 WILD-TYPE                        18   170
D129V12, multiclass
                                  clus
vv                                 FNDC7 MUTATED FNDC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = SVIL MUTATION ANALYSIS
D130V1, survival
                sevent
clus2              0   1
  SVIL MUTATED    20  10
  SVIL WILD-TYPE 257  68
  SVIL MUTATED SVIL WILD-TYPE 
            30            325 
  SVIL MUTATED SVIL WILD-TYPE 
            10             68 
$`SVIL MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-3809 
       19.04        10.88       100.01        26.17        79.69        32.75 
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3696 
       22.06        24.39        20.12        19.66         1.02         5.03 
TCGA-AA-3845 TCGA-AA-3864 TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
        0.00        53.00        12.16        83.24        21.44        58.39 
TCGA-AZ-6598 TCGA-CK-5916 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6537 
       49.41        21.14        15.02        12.00        14.04         4.80 
TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6307 
       16.14        15.58       135.65         8.61         6.18        55.04 

$`SVIL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
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-A6-3810 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-A6-5666 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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3710 
       47.01        15.02        11.01         5.98        37.05        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-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-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 
       12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SVIL MUTATED SVIL WILD-TYPE 
             0              0 
  SVIL MUTATED SVIL WILD-TYPE 
        135.65         148.01 
  SVIL MUTATED SVIL WILD-TYPE 
         19.89          22.42 
[1] "0.0 - 135.7 (19.9)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D130V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SVIL MUTATED         6        0        4        12         1         0
  SVIL WILD-TYPE      58        1       22        96         7         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        18          6         39         32       33        12
                vv
clus             STAGE IVB
  SVIL MUTATED           0
  SVIL WILD-TYPE         1
D130V3, multiclass
            clus
vv           SVIL MUTATED SVIL WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            12             96
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            5             39
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  SVIL MUTATED     1   5  22   4
  SVIL WILD-TYPE   8  62 227  37
D130V4, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  T1            1              8
  T2            5             62
  T3           22            227
  T4            4             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
  SVIL MUTATED    24   6   2
  SVIL WILD-TYPE 196  75  64
D130V5, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  N0           24            196
  N1            6             75
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V6, binary
                cls
clus               0   1
  SVIL MUTATED    23   2
  SVIL WILD-TYPE 262  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     23    2
  SVIL WILD-TYPE  262   46
   clus
vv  SVIL MUTATED SVIL WILD-TYPE
  0           23            262
  1            2             46
[1] 2 2
[1] FALSE
D130V7, binary
                cls
clus               0   1
  SVIL MUTATED    16  16
  SVIL WILD-TYPE 154 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     16   16
  SVIL WILD-TYPE  154  181
        clus
vv       SVIL MUTATED SVIL WILD-TYPE
  FEMALE           16            154
  MALE             16            181
[1] 2 2
[1] FALSE
D130V8, binary
                cls
clus               0   1
  SVIL MUTATED    26   1
  SVIL WILD-TYPE 274   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     26    1
  SVIL WILD-TYPE  274    7
     clus
vv    SVIL MUTATED SVIL WILD-TYPE
  NO            26            274
  YES            1              7
[1] 2 2
[1] FALSE
D130V9, binary
                cls
clus               0   1
  SVIL MUTATED    25   6
  SVIL WILD-TYPE 289  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     25    6
  SVIL WILD-TYPE  289   42
                               clus
vv                              SVIL MUTATED SVIL WILD-TYPE
  COLON ADENOCARCINOMA                    25            289
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SVIL MUTATED    23   0   2   1
  SVIL WILD-TYPE 236   3  20  20
D130V10, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  R0           23            236
  R1            0              3
  R2            2             20
  RX            1             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"
D130V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SVIL MUTATED                                  0     1
  SVIL WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SVIL MUTATED                           0    24
  SVIL WILD-TYPE                        19   152
D130V12, multiclass
                                  clus
vv                                 SVIL MUTATED SVIL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      24            152
[1] 4 2
[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 = LARP4B MUTATION ANALYSIS
D131V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED    25   3
  LARP4B WILD-TYPE 252  75
  LARP4B MUTATED LARP4B WILD-TYPE 
              28              327 
  LARP4B MUTATED LARP4B WILD-TYPE 
               3               75 
$`LARP4B MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5666 
        0.92        19.04       100.01        35.80        26.17        32.71 
TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3949 
        6.97        33.04         1.02         0.00        31.00        26.01 
TCGA-AA-3977 TCGA-AA-A01Q TCGA-AA-A02O TCGA-AY-5543 TCGA-AZ-6598 TCGA-CA-6717 
       25.02         1.02         0.92        33.01        49.41        12.76 
TCGA-CK-4950 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6540 
       85.45        23.05        13.02        15.02        12.00        16.14 
TCGA-D5-6930 TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6309 
       13.35       135.65        35.31        85.48 

$`LARP4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        63.62        22.09        91.79        79.69 
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-A6-5656 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LARP4B MUTATED LARP4B WILD-TYPE 
               0                0 
  LARP4B MUTATED LARP4B WILD-TYPE 
          135.65           148.01 
  LARP4B MUTATED LARP4B WILD-TYPE 
          24.035           22.030 
[1] "0.0 - 135.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D131V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LARP4B MUTATED         4        0        5        10         0         1
  LARP4B WILD-TYPE      60        1       21        98         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           1          0          5          0        1
  LARP4B WILD-TYPE        17          6         39         33       34
                  vv
clus               STAGE IVA STAGE IVB
  LARP4B MUTATED           1         0
  LARP4B WILD-TYPE        11         1
D131V3, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA              10               98
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              5               39
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  LARP4B MUTATED     1   4  23   1
  LARP4B WILD-TYPE   8  63 226  40
D131V4, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  T1              1                8
  T2              4               63
  T3             23              226
  T4              1               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
  LARP4B MUTATED    22   7   0
  LARP4B WILD-TYPE 198  74  66
D131V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0             22              198
  N1              7               74
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V6, binary
                  cls
clus                 0   1
  LARP4B MUTATED    25   2
  LARP4B WILD-TYPE 260  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     25    2
  LARP4B WILD-TYPE  260   46
   clus
vv  LARP4B MUTATED LARP4B WILD-TYPE
  0             25              260
  1              2               46
[1] 2 2
[1] FALSE
D131V7, binary
                  cls
clus                 0   1
  LARP4B MUTATED    16  13
  LARP4B WILD-TYPE 154 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     16   13
  LARP4B WILD-TYPE  154  184
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  FEMALE             16              154
  MALE               13              184
[1] 2 2
[1] FALSE
D131V8, binary
                  cls
clus                 0   1
  LARP4B MUTATED    23   1
  LARP4B WILD-TYPE 277   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     23    1
  LARP4B WILD-TYPE  277    7
     clus
vv    LARP4B MUTATED LARP4B WILD-TYPE
  NO              23              277
  YES              1                7
[1] 2 2
[1] FALSE
D131V9, binary
                  cls
clus                 0   1
  LARP4B MUTATED    19   9
  LARP4B WILD-TYPE 295  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     19    9
  LARP4B WILD-TYPE  295   39
                               clus
vv                              LARP4B MUTATED LARP4B WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              9               39
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LARP4B MUTATED    21   1   1   1
  LARP4B WILD-TYPE 238   2  21  20
D131V10, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  R0             21              238
  R1              1                2
  R2              1               21
  RX              1               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"
D131V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LARP4B MUTATED                                  0     1
  LARP4B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LARP4B MUTATED                           4    12
  LARP4B WILD-TYPE                        15   164
D131V12, multiclass
                                  clus
vv                                 LARP4B MUTATED LARP4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                        12              164
[1] 4 2
[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 = THOC5 MUTATION ANALYSIS
D132V1, survival
                 sevent
clus2               0   1
  THOC5 MUTATED     9   5
  THOC5 WILD-TYPE 268  73
  THOC5 MUTATED THOC5 WILD-TYPE 
             14             341 
  THOC5 MUTATED THOC5 WILD-TYPE 
              5              73 
$`THOC5 MUTATED`
TCGA-AZ-4681 TCGA-DM-A285 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-A00N 
      106.75         5.88         3.02         1.02         6.97         4.01 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-6747 
       34.98        21.44        12.10        10.06        85.45        82.95 
TCGA-CM-6171 TCGA-G4-6309 
       14.04        85.48 

$`THOC5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        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        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  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           22.09 
[1] "1.0 - 106.8 (13.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D132V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THOC5 MUTATED         1        0        2         5         2         0
  THOC5 WILD-TYPE      63        1       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THOC5 MUTATED           0          0          2          0        2         0
  THOC5 WILD-TYPE        18          6         42         33       33        12
                 vv
clus              STAGE IVB
  THOC5 MUTATED           0
  THOC5 WILD-TYPE         1
D132V3, multiclass
            clus
vv           THOC5 MUTATED THOC5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  THOC5 MUTATED     0   1  10   3
  THOC5 WILD-TYPE   9  66 239  38
D132V4, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             3              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
  THOC5 MUTATED    10   3   1
  THOC5 WILD-TYPE 210  78  65
D132V5, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  N0            10             210
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V6, binary
                 cls
clus                0   1
  THOC5 MUTATED    10   2
  THOC5 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     10    2
  THOC5 WILD-TYPE  275   46
   clus
vv  THOC5 MUTATED THOC5 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D132V7, binary
                 cls
clus                0   1
  THOC5 MUTATED     9   5
  THOC5 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED      9    5
  THOC5 WILD-TYPE  161  192
        clus
vv       THOC5 MUTATED THOC5 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D132V8, binary
                 cls
clus                0   1
  THOC5 MUTATED    11   0
  THOC5 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     11    0
  THOC5 WILD-TYPE  289    8
     clus
vv    THOC5 MUTATED THOC5 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D132V9, binary
                 cls
clus                0   1
  THOC5 MUTATED    11   3
  THOC5 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     11    3
  THOC5 WILD-TYPE  303   45
                               clus
vv                              THOC5 MUTATED THOC5 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  THOC5 MUTATED     9   1   0   2
  THOC5 WILD-TYPE 250   2  22  19
D132V10, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  R0             9             250
  R1             1               2
  R2             0              22
  RX             2              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"
D132V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THOC5 MUTATED                                  0     1
  THOC5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THOC5 MUTATED                           3     5
  THOC5 WILD-TYPE                        16   171
D132V12, multiclass
                                  clus
vv                                 THOC5 MUTATED THOC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        5             171
[1] 4 2
[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 = GIGYF2 MUTATION ANALYSIS
D133V1, survival
                  sevent
clus2                0   1
  GIGYF2 MUTATED    21   4
  GIGYF2 WILD-TYPE 256  74
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              25              330 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4               74 
$`GIGYF2 MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 
        0.92        25.08       100.01        79.69        33.53        22.06 
TCGA-AA-3492 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A010 TCGA-AY-6196 
        3.02        31.00        26.01        18.05        34.98         0.20 
TCGA-AY-6197 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6163 
       21.44        62.79        49.41        23.05        15.02        14.04 
TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28H 
       11.01        17.85        12.39        11.64        13.41       117.07 
TCGA-F4-6856 
       35.31 

$`GIGYF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        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-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        88.21         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        10.13        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        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
             0.2              0.0 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          117.07           148.01 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
           22.06            22.06 
[1] "0.2 - 117.1 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D133V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GIGYF2 MUTATED         4        0        4         8         1         0
  GIGYF2 WILD-TYPE      60        1       22       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIGYF2 MUTATED           1          0          5          2        1
  GIGYF2 WILD-TYPE        17          6         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  GIGYF2 MUTATED           0         0
  GIGYF2 WILD-TYPE        12         1
D133V3, multiclass
            clus
vv           GIGYF2 MUTATED GIGYF2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              5               39
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  GIGYF2 MUTATED     2   2  20   2
  GIGYF2 WILD-TYPE   7  65 229  39
D133V4, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  T1              2                7
  T2              2               65
  T3             20              229
  T4              2               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
  GIGYF2 MUTATED    17   7   2
  GIGYF2 WILD-TYPE 203  74  64
D133V5, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  N0             17              203
  N1              7               74
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V6, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    21   1
  GIGYF2 WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     21    1
  GIGYF2 WILD-TYPE  264   47
   clus
vv  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  0             21              264
  1              1               47
[1] 2 2
[1] FALSE
D133V7, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    13  13
  GIGYF2 WILD-TYPE 157 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     13   13
  GIGYF2 WILD-TYPE  157  184
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  FEMALE             13              157
  MALE               13              184
[1] 2 2
[1] FALSE
D133V8, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    23   0
  GIGYF2 WILD-TYPE 277   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     23    0
  GIGYF2 WILD-TYPE  277    8
     clus
vv    GIGYF2 MUTATED GIGYF2 WILD-TYPE
  NO              23              277
  YES              0                8
[1] 2 2
[1] FALSE
D133V9, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    19   7
  GIGYF2 WILD-TYPE 295  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     19    7
  GIGYF2 WILD-TYPE  295   41
                               clus
vv                              GIGYF2 MUTATED GIGYF2 WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GIGYF2 MUTATED    22   0   0   0
  GIGYF2 WILD-TYPE 237   3  22  21
D133V10, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  R0             22              237
  R1              0                3
  R2              0               22
  RX              0               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"
D133V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GIGYF2 MUTATED                                  0     0
  GIGYF2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GIGYF2 MUTATED                           1    18
  GIGYF2 WILD-TYPE                        18   158
D133V12, multiclass
                                  clus
vv                                 GIGYF2 MUTATED GIGYF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        18              158
[1] 4 2
[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 = DNAH12 MUTATION ANALYSIS
D134V1, survival
                  sevent
clus2                0   1
  DNAH12 MUTATED    19   4
  DNAH12 WILD-TYPE 258  74
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              23              332 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
               4               74 
$`DNAH12 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6141 
       19.04        24.00        25.08        32.75        22.06         8.38 
TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3815 
       20.12         7.04        35.01        63.98        10.06        33.04 
TCGA-AA-3877 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       31.00        34.98        21.44        58.39        12.76        10.06 
TCGA-CM-5341 TCGA-D5-6923 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6570 
       29.06        12.43         9.44       135.65         6.18 

$`DNAH12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       24.69        24.39        23.87        19.66        20.28         3.02 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DNAH12 MUTATED DNAH12 WILD-TYPE 
            6.18             0.00 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
          135.65           148.01 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
           22.06            22.06 
[1] "6.2 - 135.7 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D134V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH12 MUTATED         3        0        2        11         2         0
  DNAH12 WILD-TYPE      61        1       24        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH12 MUTATED           1          1          2          0        1
  DNAH12 WILD-TYPE        17          5         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  DNAH12 MUTATED           0         0
  DNAH12 WILD-TYPE        12         1
D134V3, multiclass
            clus
vv           DNAH12 MUTATED DNAH12 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              11               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  DNAH12 MUTATED     1   3  17   2
  DNAH12 WILD-TYPE   8  64 232  39
D134V4, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             17              232
  T4              2               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
  DNAH12 MUTATED    19   3   1
  DNAH12 WILD-TYPE 201  78  65
D134V5, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  N0             19              201
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V6, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    20   1
  DNAH12 WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     20    1
  DNAH12 WILD-TYPE  265   47
   clus
vv  DNAH12 MUTATED DNAH12 WILD-TYPE
  0             20              265
  1              1               47
[1] 2 2
[1] FALSE
D134V7, binary
                  cls
clus                 0   1
  DNAH12 MUTATED     9  14
  DNAH12 WILD-TYPE 161 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED      9   14
  DNAH12 WILD-TYPE  161  183
        clus
vv       DNAH12 MUTATED DNAH12 WILD-TYPE
  FEMALE              9              161
  MALE               14              183
[1] 2 2
[1] FALSE
D134V8, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    21   1
  DNAH12 WILD-TYPE 279   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     21    1
  DNAH12 WILD-TYPE  279    7
     clus
vv    DNAH12 MUTATED DNAH12 WILD-TYPE
  NO              21              279
  YES              1                7
[1] 2 2
[1] FALSE
D134V9, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    17   5
  DNAH12 WILD-TYPE 297  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     17    5
  DNAH12 WILD-TYPE  297   43
                               clus
vv                              DNAH12 MUTATED DNAH12 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAH12 MUTATED    17   0   1   2
  DNAH12 WILD-TYPE 242   3  21  19
D134V10, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              1               21
  RX              2               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"
D134V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH12 MUTATED                                  0     2
  DNAH12 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAH12 MUTATED                           1    11
  DNAH12 WILD-TYPE                        18   165
D134V12, multiclass
                                  clus
vv                                 DNAH12 MUTATED DNAH12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(135) Variable = ARFGEF1 MUTATION ANALYSIS
D135V1, survival
                   sevent
clus2                 0   1
  ARFGEF1 MUTATED    23   9
  ARFGEF1 WILD-TYPE 254  69
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               32               323 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                9                69 
$`ARFGEF1 MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AZ-4681 TCGA-CK-5912 TCGA-G4-6586 
        6.05        85.05        19.04       106.75        49.08        35.80 
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3852 
       22.06         3.02        19.07        29.95        78.08         0.00 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-5403 TCGA-AZ-6598 
       53.00        25.02         4.01        34.98        62.79        49.41 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-5344 
       12.59        12.76        10.06        82.95        23.05        22.03 
TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A0X9 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28K 
       14.04        13.35       119.70       139.17        81.37        98.24 
TCGA-F4-6460 TCGA-F4-6704 
       31.96         1.55 

$`ARFGEF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 
       15.52        25.08        10.88       100.01         1.94         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       63.62        22.09        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-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-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        9.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14         2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      131.51       135.65       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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                0                 0 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
           139.17            148.01 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
           27.485            21.990 
[1] "0.0 - 139.2 (27.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D135V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARFGEF1 MUTATED         3        0        6        16         2         0
  ARFGEF1 WILD-TYPE      61        1       20        92         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFGEF1 MUTATED           1          0          2          1        2
  ARFGEF1 WILD-TYPE        17          6         42         32       33
                   vv
clus                STAGE IVA STAGE IVB
  ARFGEF1 MUTATED           0         0
  ARFGEF1 WILD-TYPE        12         1
D135V3, multiclass
            clus
vv           ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 6                20
  STAGE IIA               16                92
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 2                33
  STAGE IVA                0                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
  ARFGEF1 MUTATED     0   4  27   3
  ARFGEF1 WILD-TYPE   9  63 222  38
D135V4, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3              27               222
  T4               3                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
  ARFGEF1 MUTATED    29   2   3
  ARFGEF1 WILD-TYPE 191  79  63
D135V5, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  N0              29               191
  N1               2                79
  N2               3                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"
D135V6, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    26   2
  ARFGEF1 WILD-TYPE 259  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     26    2
  ARFGEF1 WILD-TYPE  259   46
   clus
vv  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  0              26               259
  1               2                46
[1] 2 2
[1] FALSE
D135V7, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    16  18
  ARFGEF1 WILD-TYPE 154 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     16   18
  ARFGEF1 WILD-TYPE  154  179
        clus
vv       ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  FEMALE              16               154
  MALE                18               179
[1] 2 2
[1] FALSE
D135V8, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    24   1
  ARFGEF1 WILD-TYPE 276   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     24    1
  ARFGEF1 WILD-TYPE  276    7
     clus
vv    ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  NO               24               276
  YES               1                 7
[1] 2 2
[1] FALSE
D135V9, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    27   7
  ARFGEF1 WILD-TYPE 287  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     27    7
  ARFGEF1 WILD-TYPE  287   41
                               clus
vv                              ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  COLON ADENOCARCINOMA                       27               287
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARFGEF1 MUTATED    21   0   2   4
  ARFGEF1 WILD-TYPE 238   3  20  17
D135V10, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  R0              21               238
  R1               0                 3
  R2               2                20
  RX               4                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"
D135V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARFGEF1 MUTATED                                  1     3
  ARFGEF1 WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARFGEF1 MUTATED                           0    16
  ARFGEF1 WILD-TYPE                        19   160
D135V12, multiclass
                                  clus
vv                                 ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         16               160
[1] 4 2
[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 = NOTCH2NL MUTATION ANALYSIS
D136V1, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     5   1
  NOTCH2NL WILD-TYPE 272  77
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                349 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 1                 77 
$`NOTCH2NL MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-G4-6588 TCGA-AA-A00N TCGA-AZ-4315 TCGA-D5-6923 
       24.16        24.03        26.17         4.01        58.39        12.43 

$`NOTCH2NL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53         1.02        13.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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             22.030 
[1] "4.0 - 58.4 (24.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D136V2, continuous
                    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      63        1       25       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOTCH2NL MUTATED           0          0          1          0        0
  NOTCH2NL WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  NOTCH2NL MUTATED           0         0
  NOTCH2NL WILD-TYPE        12         1
D136V3, multiclass
            clus
vv           NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 2                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  NOTCH2NL MUTATED     0   1   4   1
  NOTCH2NL WILD-TYPE   9  66 245  40
D136V4, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                4                245
  T4                1                 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
  NOTCH2NL MUTATED     5   1   0
  NOTCH2NL WILD-TYPE 215  80  66
D136V5, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  N0                5                215
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V6, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     6   0
  NOTCH2NL WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      6    0
  NOTCH2NL WILD-TYPE  279   48
   clus
vv  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D136V7, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     2   4
  NOTCH2NL WILD-TYPE 168 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      2    4
  NOTCH2NL WILD-TYPE  168  193
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  FEMALE                2                168
  MALE                  4                193
[1] 2 2
[1] FALSE
D136V8, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     5   0
  NOTCH2NL WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      5    0
  NOTCH2NL WILD-TYPE  295    8
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D136V9, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     5   1
  NOTCH2NL WILD-TYPE 309  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      5    1
  NOTCH2NL WILD-TYPE  309   47
                               clus
vv                              NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  NOTCH2NL MUTATED     5   0   0   0
  NOTCH2NL WILD-TYPE 254   3  22  21
D136V10, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D136V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH2NL MUTATED                                  0     0
  NOTCH2NL WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2NL MUTATED                           0     4
  NOTCH2NL WILD-TYPE                        19   172
D136V12, multiclass
                                  clus
vv                                 NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = SENP6 MUTATION ANALYSIS
D137V1, survival
                 sevent
clus2               0   1
  SENP6 MUTATED    11   3
  SENP6 WILD-TYPE 266  75
  SENP6 MUTATED SENP6 WILD-TYPE 
             14             341 
  SENP6 MUTATED SENP6 WILD-TYPE 
              3              75 
$`SENP6 MUTATED`
TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-A00N 
       49.08        26.17        22.06        19.66         6.97         4.01 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5348 TCGA-D5-5539 
       27.09        21.44        49.41        12.76        22.98        19.59 
TCGA-D5-5540 TCGA-DM-A1HB 
       56.09       135.65 

$`SENP6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       45.40        54.61        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SENP6 MUTATED SENP6 WILD-TYPE 
           4.01            0.00 
  SENP6 MUTATED SENP6 WILD-TYPE 
         135.65          148.01 
  SENP6 MUTATED SENP6 WILD-TYPE 
          22.52           22.03 
[1] "4.0 - 135.7 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D137V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SENP6 MUTATED         2        0        2         5         2         0
  SENP6 WILD-TYPE      62        1       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SENP6 MUTATED           0          1          2          1        0         0
  SENP6 WILD-TYPE        18          5         42         32       35        12
                 vv
clus              STAGE IVB
  SENP6 MUTATED           0
  SENP6 WILD-TYPE         1
D137V3, multiclass
            clus
vv           SENP6 MUTATED SENP6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  SENP6 MUTATED     0   2  10   3
  SENP6 WILD-TYPE   9  65 239  38
D137V4, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             3              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
  SENP6 MUTATED    11   4   0
  SENP6 WILD-TYPE 209  77  66
D137V5, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  N0            11             209
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V6, binary
                 cls
clus                0   1
  SENP6 MUTATED    10   0
  SENP6 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     10    0
  SENP6 WILD-TYPE  275   48
   clus
vv  SENP6 MUTATED SENP6 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D137V7, binary
                 cls
clus                0   1
  SENP6 MUTATED     5  10
  SENP6 WILD-TYPE 165 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED      5   10
  SENP6 WILD-TYPE  165  187
        clus
vv       SENP6 MUTATED SENP6 WILD-TYPE
  FEMALE             5             165
  MALE              10             187
[1] 2 2
[1] FALSE
D137V8, binary
                 cls
clus                0   1
  SENP6 MUTATED    11   0
  SENP6 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     11    0
  SENP6 WILD-TYPE  289    8
     clus
vv    SENP6 MUTATED SENP6 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D137V9, binary
                 cls
clus                0   1
  SENP6 MUTATED    10   4
  SENP6 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     10    4
  SENP6 WILD-TYPE  304   44
                               clus
vv                              SENP6 MUTATED SENP6 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SENP6 MUTATED    10   0   0   3
  SENP6 WILD-TYPE 249   3  22  18
D137V10, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             3              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"
D137V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SENP6 MUTATED                                  0     1
  SENP6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SENP6 MUTATED                           0    12
  SENP6 WILD-TYPE                        19   164
D137V12, multiclass
                                  clus
vv                                 SENP6 MUTATED SENP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = WDR78 MUTATION ANALYSIS
D138V1, survival
                 sevent
clus2               0   1
  WDR78 MUTATED    10   2
  WDR78 WILD-TYPE 267  76
  WDR78 MUTATED WDR78 WILD-TYPE 
             12             343 
  WDR78 MUTATED WDR78 WILD-TYPE 
              2              76 
$`WDR78 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3680 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-6717 
        0.92        19.04        11.01        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 

$`WDR78 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        55.92        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       65.85        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  WDR78 MUTATED WDR78 WILD-TYPE 
           0.92            0.00 
  WDR78 MUTATED WDR78 WILD-TYPE 
          58.39          148.01 
  WDR78 MUTATED WDR78 WILD-TYPE 
         19.615          22.090 
[1] "0.9 - 58.4 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D138V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR78 MUTATED         1        0        0         5         1         0
  WDR78 WILD-TYPE      63        1       26       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR78 MUTATED           1          0          1          0        2         0
  WDR78 WILD-TYPE        17          6         43         33       33        12
                 vv
clus              STAGE IVB
  WDR78 MUTATED           0
  WDR78 WILD-TYPE         1
D138V3, multiclass
            clus
vv           WDR78 MUTATED WDR78 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  WDR78 MUTATED     0   2   8   2
  WDR78 WILD-TYPE   9  65 241  39
D138V4, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             2              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
  WDR78 MUTATED     9   2   1
  WDR78 WILD-TYPE 211  79  65
D138V5, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V6, binary
                 cls
clus                0   1
  WDR78 MUTATED     9   2
  WDR78 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED      9    2
  WDR78 WILD-TYPE  276   46
   clus
vv  WDR78 MUTATED WDR78 WILD-TYPE
  0             9             276
  1             2              46
[1] 2 2
[1] FALSE
D138V7, binary
                 cls
clus                0   1
  WDR78 MUTATED     4   8
  WDR78 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED      4    8
  WDR78 WILD-TYPE  166  189
        clus
vv       WDR78 MUTATED WDR78 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D138V8, binary
                 cls
clus                0   1
  WDR78 MUTATED    11   1
  WDR78 WILD-TYPE 289   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED     11    1
  WDR78 WILD-TYPE  289    7
     clus
vv    WDR78 MUTATED WDR78 WILD-TYPE
  NO             11             289
  YES             1               7
[1] 2 2
[1] FALSE
D138V9, binary
                 cls
clus                0   1
  WDR78 MUTATED    11   1
  WDR78 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED     11    1
  WDR78 WILD-TYPE  303   47
                               clus
vv                              WDR78 MUTATED WDR78 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR78 MUTATED     7   0   2   2
  WDR78 WILD-TYPE 252   3  20  19
D138V10, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             2              20
  RX             2              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"
D138V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR78 MUTATED                                  0     2
  WDR78 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR78 MUTATED                           0     6
  WDR78 WILD-TYPE                        19   170
D138V12, multiclass
                                  clus
vv                                 WDR78 MUTATED WDR78 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = CAB39L MUTATION ANALYSIS
D139V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     8   1
  CAB39L WILD-TYPE 269  77
  CAB39L MUTATED CAB39L WILD-TYPE 
               9              346 
  CAB39L MUTATED CAB39L WILD-TYPE 
               1               77 
$`CAB39L MUTATED`
TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-A010 TCGA-AD-5900 
       26.17        33.53        24.39        20.12        34.98        12.16 
TCGA-AY-6197 TCGA-CK-5916 TCGA-F4-6856 
       21.44        21.14        35.31 

$`CAB39L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CAB39L MUTATED CAB39L WILD-TYPE 
           12.16             0.00 
  CAB39L MUTATED CAB39L WILD-TYPE 
           35.31           148.01 
  CAB39L MUTATED CAB39L WILD-TYPE 
          24.390           22.045 
[1] "12.2 - 35.3 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D139V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAB39L MUTATED         4        0        0         4         1         0
  CAB39L WILD-TYPE      60        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAB39L MUTATED           0          0          0          0        0
  CAB39L WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CAB39L MUTATED           0         0
  CAB39L WILD-TYPE        12         1
D139V3, multiclass
            clus
vv           CAB39L MUTATED CAB39L WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CAB39L MUTATED     1   3   4   1
  CAB39L WILD-TYPE   8  64 245  40
D139V4, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  T1              1                8
  T2              3               64
  T3              4              245
  T4              1               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
  CAB39L MUTATED     9   0   0
  CAB39L WILD-TYPE 211  81  66
D139V5, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  N0              9              211
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V6, binary
                  cls
clus                 0   1
  CAB39L MUTATED     6   0
  CAB39L WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      6    0
  CAB39L WILD-TYPE  279   48
   clus
vv  CAB39L MUTATED CAB39L WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D139V7, binary
                  cls
clus                 0   1
  CAB39L MUTATED     4   5
  CAB39L WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      4    5
  CAB39L WILD-TYPE  166  192
        clus
vv       CAB39L MUTATED CAB39L WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D139V8, binary
                  cls
clus                 0   1
  CAB39L MUTATED     9   0
  CAB39L WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      9    0
  CAB39L WILD-TYPE  291    8
     clus
vv    CAB39L MUTATED CAB39L WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D139V9, binary
                  cls
clus                 0   1
  CAB39L MUTATED     6   3
  CAB39L WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      6    3
  CAB39L WILD-TYPE  308   45
                               clus
vv                              CAB39L MUTATED CAB39L WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CAB39L MUTATED     6   0   0   1
  CAB39L WILD-TYPE 253   3  22  20
D139V10, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D139V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAB39L MUTATED                                  0     0
  CAB39L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CAB39L MUTATED                           1     7
  CAB39L WILD-TYPE                        18   169
D139V12, multiclass
                                  clus
vv                                 CAB39L MUTATED CAB39L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = WEE1 MUTATION ANALYSIS
D140V1, survival
                sevent
clus2              0   1
  WEE1 MUTATED     8   3
  WEE1 WILD-TYPE 269  75
  WEE1 MUTATED WEE1 WILD-TYPE 
            11            344 
  WEE1 MUTATED WEE1 WILD-TYPE 
             3             75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        12.10        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  WEE1 MUTATED WEE1 WILD-TYPE 
          1.02           0.00 
  WEE1 MUTATED WEE1 WILD-TYPE 
        133.18         148.01 
  WEE1 MUTATED WEE1 WILD-TYPE 
         27.09          22.01 
[1] "1.0 - 133.2 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D140V2, continuous
                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      61        1       23       104         8         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        17          6         43         33       35        12
                vv
clus             STAGE IVB
  WEE1 MUTATED           0
  WEE1 WILD-TYPE         1
D140V3, multiclass
            clus
vv           WEE1 MUTATED WEE1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  WEE1 MUTATED     0   3   8   1
  WEE1 WILD-TYPE   9  64 241  40
D140V4, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            8            241
  T4            1             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
  WEE1 MUTATED    10   2   0
  WEE1 WILD-TYPE 210  79  66
D140V5, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  N0           10            210
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V6, binary
                cls
clus               0   1
  WEE1 MUTATED    10   0
  WEE1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED     10    0
  WEE1 WILD-TYPE  275   48
   clus
vv  WEE1 MUTATED WEE1 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D140V7, binary
                cls
clus               0   1
  WEE1 MUTATED     7   5
  WEE1 WILD-TYPE 163 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      7    5
  WEE1 WILD-TYPE  163  192
        clus
vv       WEE1 MUTATED WEE1 WILD-TYPE
  FEMALE            7            163
  MALE              5            192
[1] 2 2
[1] FALSE
D140V8, binary
                cls
clus               0   1
  WEE1 MUTATED     9   0
  WEE1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      9    0
  WEE1 WILD-TYPE  291    8
     clus
vv    WEE1 MUTATED WEE1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D140V9, binary
                cls
clus               0   1
  WEE1 MUTATED    11   1
  WEE1 WILD-TYPE 303  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED     11    1
  WEE1 WILD-TYPE  303   47
                               clus
vv                              WEE1 MUTATED WEE1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WEE1 MUTATED     8   0   0   1
  WEE1 WILD-TYPE 251   3  22  20
D140V10, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D140V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WEE1 MUTATED                                  0     1
  WEE1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WEE1 MUTATED                           0     8
  WEE1 WILD-TYPE                        19   168
D140V12, multiclass
                                  clus
vv                                 WEE1 MUTATED WEE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = ZFX MUTATION ANALYSIS
D141V1, survival
               sevent
clus2             0   1
  ZFX MUTATED     8   5
  ZFX WILD-TYPE 269  73
  ZFX MUTATED ZFX WILD-TYPE 
           13           342 
  ZFX MUTATED ZFX WILD-TYPE 
            5            73 
$`ZFX MUTATED`
TCGA-AA-3516 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5656 TCGA-A6-5662 TCGA-AA-3492 
       13.02        26.17        42.90        32.91        23.61         3.02 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6196 TCGA-AZ-6599 
       26.01         2.01        34.98        83.24         0.20         6.77 
TCGA-CM-5860 
       32.02 

$`ZFX WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6780 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-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZFX MUTATED ZFX WILD-TYPE 
          0.2           0.0 
  ZFX MUTATED ZFX WILD-TYPE 
        83.24        148.01 
  ZFX MUTATED ZFX WILD-TYPE 
        26.01         22.01 
[1] "0.2 - 83.2 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D141V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFX MUTATED         2        0        1         4         2         0
  ZFX WILD-TYPE      62        1       25       104         6         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        17          6         43         32       35        11
               vv
clus            STAGE IVB
  ZFX MUTATED           0
  ZFX WILD-TYPE         1
D141V3, multiclass
            clus
vv           ZFX MUTATED ZFX WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            4           104
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            1            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
  ZFX MUTATED     0   2   9   2
  ZFX WILD-TYPE   9  65 240  39
D141V4, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  T1           0             9
  T2           2            65
  T3           9           240
  T4           2            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
  ZFX MUTATED     9   1   3
  ZFX WILD-TYPE 211  80  63
D141V5, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  N0           9           211
  N1           1            80
  N2           3            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"
D141V6, binary
               cls
clus              0   1
  ZFX MUTATED    10   1
  ZFX WILD-TYPE 275  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     10    1
  ZFX WILD-TYPE  275   47
   clus
vv  ZFX MUTATED ZFX WILD-TYPE
  0          10           275
  1           1            47
[1] 2 2
[1] FALSE
D141V7, binary
               cls
clus              0   1
  ZFX MUTATED     7   6
  ZFX WILD-TYPE 163 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      7    6
  ZFX WILD-TYPE  163  191
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  FEMALE           7           163
  MALE             6           191
[1] 2 2
[1] FALSE
D141V8, binary
               cls
clus              0   1
  ZFX MUTATED    11   0
  ZFX WILD-TYPE 289   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     11    0
  ZFX WILD-TYPE  289    8
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO           11           289
  YES           0             8
[1] 2 2
[1] FALSE
D141V9, binary
               cls
clus              0   1
  ZFX MUTATED     9   4
  ZFX WILD-TYPE 305  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      9    4
  ZFX WILD-TYPE  305   44
                               clus
vv                              ZFX MUTATED ZFX WILD-TYPE
  COLON ADENOCARCINOMA                    9           305
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ZFX MUTATED     8   0   0   0
  ZFX WILD-TYPE 251   3  22  21
D141V10, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  R0           8           251
  R1           0             3
  R2           0            22
  RX           0            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"
D141V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFX MUTATED                                  0     1
  ZFX WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZFX MUTATED                           0     7
  ZFX WILD-TYPE                        19   169
D141V12, multiclass
                                  clus
vv                                 ZFX MUTATED ZFX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      7           169
[1] 4 2
[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 = ASNSD1 MUTATION ANALYSIS
D142V1, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     6   2
  ASNSD1 WILD-TYPE 271  76
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               8              347 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2               76 
$`ASNSD1 MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3947 
       19.04        10.88        20.12        63.98        53.00        33.01 
TCGA-AY-6196 TCGA-CA-6717 
        0.20        12.76 

$`ASNSD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
             0.2              0.0 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           63.98           148.01 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           19.58            22.09 
[1] "0.2 - 64.0 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D142V2, continuous
                  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      64        1       23       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASNSD1 MUTATED           0          0          0          1        0
  ASNSD1 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ASNSD1 MUTATED           0         0
  ASNSD1 WILD-TYPE        12         1
D142V3, multiclass
            clus
vv           ASNSD1 MUTATED ASNSD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ASNSD1 MUTATED     0   0   7   2
  ASNSD1 WILD-TYPE   9  67 242  39
D142V4, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              2               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
  ASNSD1 MUTATED     7   0   2
  ASNSD1 WILD-TYPE 213  81  64
D142V5, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V6, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     6   0
  ASNSD1 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      6    0
  ASNSD1 WILD-TYPE  279   48
   clus
vv  ASNSD1 MUTATED ASNSD1 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D142V7, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     2   7
  ASNSD1 WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      2    7
  ASNSD1 WILD-TYPE  168  190
        clus
vv       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D142V8, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     7   0
  ASNSD1 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      7    0
  ASNSD1 WILD-TYPE  293    8
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D142V9, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     5   4
  ASNSD1 WILD-TYPE 309  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      5    4
  ASNSD1 WILD-TYPE  309   44
                               clus
vv                              ASNSD1 MUTATED ASNSD1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ASNSD1 MUTATED     6   0   0   1
  ASNSD1 WILD-TYPE 253   3  22  20
D142V10, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D142V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASNSD1 MUTATED                                  0     1
  ASNSD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ASNSD1 MUTATED                           0     3
  ASNSD1 WILD-TYPE                        19   173
D142V12, multiclass
                                  clus
vv                                 ASNSD1 MUTATED ASNSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = KLC4 MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  KLC4 MUTATED    10   4
  KLC4 WILD-TYPE 267  74
  KLC4 MUTATED KLC4 WILD-TYPE 
            14            341 
  KLC4 MUTATED KLC4 WILD-TYPE 
             4             74 
$`KLC4 MUTATED`
TCGA-AA-3713 TCGA-AA-3860 TCGA-A6-2676 TCGA-AA-3518 TCGA-AA-3845 TCGA-AA-3864 
       19.04        31.07        42.90         1.02         0.00        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 
       19.59        31.96 

$`KLC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14        82.95         2.01       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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        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        14.04        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-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KLC4 MUTATED KLC4 WILD-TYPE 
             0              0 
  KLC4 MUTATED KLC4 WILD-TYPE 
         53.00         148.01 
  KLC4 MUTATED KLC4 WILD-TYPE 
         22.52          22.06 
[1] "0.0 - 53.0 (22.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D143V2, continuous
                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      61        1       25       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLC4 MUTATED           0          1          2          0        2         0
  KLC4 WILD-TYPE        18          5         42         33       33        12
                vv
clus             STAGE IVB
  KLC4 MUTATED           0
  KLC4 WILD-TYPE         1
D143V3, multiclass
            clus
vv           KLC4 MUTATED KLC4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  KLC4 MUTATED     0   3  12   1
  KLC4 WILD-TYPE   9  64 237  40
D143V4, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           12            237
  T4            1             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
  KLC4 MUTATED    12   3   1
  KLC4 WILD-TYPE 208  78  65
D143V5, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  N0           12            208
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V6, binary
                cls
clus               0   1
  KLC4 MUTATED    12   2
  KLC4 WILD-TYPE 273  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     12    2
  KLC4 WILD-TYPE  273   46
   clus
vv  KLC4 MUTATED KLC4 WILD-TYPE
  0           12            273
  1            2             46
[1] 2 2
[1] FALSE
D143V7, binary
                cls
clus               0   1
  KLC4 MUTATED     9   7
  KLC4 WILD-TYPE 161 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED      9    7
  KLC4 WILD-TYPE  161  190
        clus
vv       KLC4 MUTATED KLC4 WILD-TYPE
  FEMALE            9            161
  MALE              7            190
[1] 2 2
[1] FALSE
D143V8, binary
                cls
clus               0   1
  KLC4 MUTATED    11   1
  KLC4 WILD-TYPE 289   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     11    1
  KLC4 WILD-TYPE  289    7
     clus
vv    KLC4 MUTATED KLC4 WILD-TYPE
  NO            11            289
  YES            1              7
[1] 2 2
[1] FALSE
D143V9, binary
                cls
clus               0   1
  KLC4 MUTATED    15   1
  KLC4 WILD-TYPE 299  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     15    1
  KLC4 WILD-TYPE  299   47
                               clus
vv                              KLC4 MUTATED KLC4 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLC4 MUTATED    11   0   2   3
  KLC4 WILD-TYPE 248   3  20  18
D143V10, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            2             20
  RX            3             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"
D143V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLC4 MUTATED                                  0     1
  KLC4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLC4 MUTATED                           1     8
  KLC4 WILD-TYPE                        18   168
D143V12, multiclass
                                  clus
vv                                 KLC4 MUTATED KLC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = GLI1 MUTATION ANALYSIS
D144V1, survival
                sevent
clus2              0   1
  GLI1 MUTATED    13   5
  GLI1 WILD-TYPE 264  73
  GLI1 MUTATED GLI1 WILD-TYPE 
            18            337 
  GLI1 MUTATED GLI1 WILD-TYPE 
             5             73 
$`GLI1 MUTATED`
TCGA-A6-4105 TCGA-G4-6628 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 
       14.53        79.69        29.95         4.01        34.98        27.09 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       58.39        12.10        10.06        15.62        51.32        21.14 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6171 TCGA-F4-6856 TCGA-G4-6293 
       29.06        32.02        15.02        14.04        35.31       133.18 

$`GLI1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       17.56       148.01        85.45        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-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-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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GLI1 MUTATED GLI1 WILD-TYPE 
          4.01           0.00 
  GLI1 MUTATED GLI1 WILD-TYPE 
        133.18         148.01 
  GLI1 MUTATED GLI1 WILD-TYPE 
        28.075         22.030 
[1] "4.0 - 133.2 (28.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D144V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLI1 MUTATED         6        0        0         6         2         0
  GLI1 WILD-TYPE      58        1       26       102         6         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        17          5         44         32       34        12
                vv
clus             STAGE IVB
  GLI1 MUTATED           0
  GLI1 WILD-TYPE         1
D144V3, multiclass
            clus
vv           GLI1 MUTATED GLI1 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  GLI1 MUTATED     1   6   7   4
  GLI1 WILD-TYPE   8  61 242  37
D144V4, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  T1            1              8
  T2            6             61
  T3            7            242
  T4            4             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
  GLI1 MUTATED    14   3   1
  GLI1 WILD-TYPE 206  78  65
D144V5, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  N0           14            206
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V6, binary
                cls
clus               0   1
  GLI1 MUTATED    16   1
  GLI1 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     16    1
  GLI1 WILD-TYPE  269   47
   clus
vv  GLI1 MUTATED GLI1 WILD-TYPE
  0           16            269
  1            1             47
[1] 2 2
[1] FALSE
D144V7, binary
                cls
clus               0   1
  GLI1 MUTATED    10   8
  GLI1 WILD-TYPE 160 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     10    8
  GLI1 WILD-TYPE  160  189
        clus
vv       GLI1 MUTATED GLI1 WILD-TYPE
  FEMALE           10            160
  MALE              8            189
[1] 2 2
[1] FALSE
D144V8, binary
                cls
clus               0   1
  GLI1 MUTATED    15   0
  GLI1 WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     15    0
  GLI1 WILD-TYPE  285    8
     clus
vv    GLI1 MUTATED GLI1 WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D144V9, binary
                cls
clus               0   1
  GLI1 MUTATED    14   4
  GLI1 WILD-TYPE 300  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     14    4
  GLI1 WILD-TYPE  300   44
                               clus
vv                              GLI1 MUTATED GLI1 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GLI1 MUTATED    12   0   0   4
  GLI1 WILD-TYPE 247   3  22  17
D144V10, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            4             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"
D144V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLI1 MUTATED                                  0     1
  GLI1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLI1 MUTATED                           1    13
  GLI1 WILD-TYPE                        18   163
D144V12, multiclass
                                  clus
vv                                 GLI1 MUTATED GLI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      13            163
[1] 4 2
[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 = CRY1 MUTATION ANALYSIS
D145V1, survival
                sevent
clus2              0   1
  CRY1 MUTATED     9   4
  CRY1 WILD-TYPE 268  74
  CRY1 MUTATED CRY1 WILD-TYPE 
            13            342 
  CRY1 MUTATED CRY1 WILD-TYPE 
             4             74 
$`CRY1 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6895 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3511 
        0.92        19.04        25.08        21.76         3.02         6.97 
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 
       46.75 

$`CRY1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3514 
       19.66        20.28         7.04        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 

  CRY1 MUTATED CRY1 WILD-TYPE 
          0.92           0.00 
  CRY1 MUTATED CRY1 WILD-TYPE 
        135.65         148.01 
  CRY1 MUTATED CRY1 WILD-TYPE 
         19.04          22.09 
[1] "0.9 - 135.7 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D145V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRY1 MUTATED         0        0        2         5         0         0
  CRY1 WILD-TYPE      64        1       24       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRY1 MUTATED           1          0          3          1        1         0
  CRY1 WILD-TYPE        17          6         41         32       34        12
                vv
clus             STAGE IVB
  CRY1 MUTATED           0
  CRY1 WILD-TYPE         1
D145V3, multiclass
            clus
vv           CRY1 MUTATED CRY1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  CRY1 MUTATED     0   0  12   1
  CRY1 WILD-TYPE   9  67 237  40
D145V4, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3           12            237
  T4            1             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
  CRY1 MUTATED     7   4   2
  CRY1 WILD-TYPE 213  77  64
D145V5, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  N0            7            213
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V6, binary
                cls
clus               0   1
  CRY1 MUTATED     9   1
  CRY1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED      9    1
  CRY1 WILD-TYPE  276   47
   clus
vv  CRY1 MUTATED CRY1 WILD-TYPE
  0            9            276
  1            1             47
[1] 2 2
[1] FALSE
D145V7, binary
                cls
clus               0   1
  CRY1 MUTATED     6   7
  CRY1 WILD-TYPE 164 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED      6    7
  CRY1 WILD-TYPE  164  190
        clus
vv       CRY1 MUTATED CRY1 WILD-TYPE
  FEMALE            6            164
  MALE              7            190
[1] 2 2
[1] FALSE
D145V8, binary
                cls
clus               0   1
  CRY1 MUTATED    11   1
  CRY1 WILD-TYPE 289   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED     11    1
  CRY1 WILD-TYPE  289    7
     clus
vv    CRY1 MUTATED CRY1 WILD-TYPE
  NO            11            289
  YES            1              7
[1] 2 2
[1] FALSE
D145V9, binary
                cls
clus               0   1
  CRY1 MUTATED    11   1
  CRY1 WILD-TYPE 303  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED     11    1
  CRY1 WILD-TYPE  303   47
                               clus
vv                              CRY1 MUTATED CRY1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CRY1 MUTATED     8   0   1   2
  CRY1 WILD-TYPE 251   3  21  19
D145V10, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            2             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"
D145V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRY1 MUTATED                                  0     1
  CRY1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CRY1 MUTATED                           1     7
  CRY1 WILD-TYPE                        18   169
D145V12, multiclass
                                  clus
vv                                 CRY1 MUTATED CRY1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = FGFR3 MUTATION ANALYSIS
D146V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED    17   5
  FGFR3 WILD-TYPE 260  73
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             22             333 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              5              73 
$`FGFR3 MUTATED`
TCGA-AA-3939 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6310 TCGA-A6-5665 TCGA-AA-A01R 
       12.99        25.08        10.88        63.62        22.06        35.01 
TCGA-AD-6889 TCGA-AD-6963 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6719 
       83.24        27.42        58.39        49.41         6.77        14.30 
TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6167 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6541 
       32.02        12.00        14.99        43.27        16.14        15.58 
TCGA-DM-A1D7 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 
       13.32        47.87        35.31       133.18 

$`FGFR3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6704 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
           6.77            0.00 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         133.18          148.01 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          26.25           21.99 
[1] "6.8 - 133.2 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D146V2, continuous
                 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      61        1       25        98         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR3 MUTATED           2          0          3          1        0         0
  FGFR3 WILD-TYPE        16          6         41         32       35        12
                 vv
clus              STAGE IVB
  FGFR3 MUTATED           0
  FGFR3 WILD-TYPE         1
D146V3, multiclass
            clus
vv           FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  FGFR3 MUTATED     0   3  18   1
  FGFR3 WILD-TYPE   9  64 231  40
D146V4, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            18             231
  T4             1              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
  FGFR3 MUTATED    15   4   3
  FGFR3 WILD-TYPE 205  77  63
D146V5, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  N0            15             205
  N1             4              77
  N2             3              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"
D146V6, binary
                 cls
clus                0   1
  FGFR3 MUTATED    18   0
  FGFR3 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     18    0
  FGFR3 WILD-TYPE  267   48
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0            18             267
  1             0              48
[1] 2 2
[1] FALSE
D146V7, binary
                 cls
clus                0   1
  FGFR3 MUTATED     6  16
  FGFR3 WILD-TYPE 164 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      6   16
  FGFR3 WILD-TYPE  164  181
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             6             164
  MALE              16             181
[1] 2 2
[1] FALSE
D146V8, binary
                 cls
clus                0   1
  FGFR3 MUTATED    19   2
  FGFR3 WILD-TYPE 281   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     19    2
  FGFR3 WILD-TYPE  281    6
     clus
vv    FGFR3 MUTATED FGFR3 WILD-TYPE
  NO             19             281
  YES             2               6
[1] 2 2
[1] FALSE
D146V9, binary
                 cls
clus                0   1
  FGFR3 MUTATED    16   5
  FGFR3 WILD-TYPE 298  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     16    5
  FGFR3 WILD-TYPE  298   43
                               clus
vv                              FGFR3 MUTATED FGFR3 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR3 MUTATED    16   0   0   1
  FGFR3 WILD-TYPE 243   3  22  20
D146V10, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             1              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"
D146V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR3 MUTATED                                  0     2
  FGFR3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED                           1    17
  FGFR3 WILD-TYPE                        18   159
D146V12, multiclass
                                  clus
vv                                 FGFR3 MUTATED FGFR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       17             159
[1] 4 2
[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 = PDGFRA MUTATION ANALYSIS
D147V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED    37  11
  PDGFRA WILD-TYPE 240  67
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              48              307 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11               67 
$`PDGFRA MUTATED`
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3952 TCGA-AD-6895 TCGA-G4-6310 TCGA-G4-6586 
        6.05         0.92         2.01        25.08        63.62        35.80 
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-3666 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
        2.01        53.00        33.01         4.01        34.98        35.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 
        0.20        21.44        17.82        58.39         1.41        88.21 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5344 TCGA-CM-5349 
       12.59        12.20        12.76        85.45        22.03        30.08 
TCGA-CM-5868 TCGA-CM-6172 TCGA-CM-6675 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6923 
       17.03        11.01        13.05        12.49        10.13        12.43 
TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 
       11.64        10.26        38.20        92.75        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
        7.50       135.65       139.17         8.61        31.96         6.18 

$`PDGFRA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       13.02        17.95        23.01        19.99        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99        24.00        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        22.09        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       33.34        32.75        36.53        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       23.61        22.09        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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        0.95        33.01         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6718 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.39        14.30         9.04         9.44        13.41        13.35 
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-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       12.59        44.32       131.51        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       60.79       117.07        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PDGFRA MUTATED PDGFRA WILD-TYPE 
             0.2              0.0 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          140.38           148.01 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          21.735           22.090 
[1] "0.2 - 140.4 (21.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D147V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDGFRA MUTATED         4        0        3        14         3         1
  PDGFRA WILD-TYPE      60        1       23        94         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PDGFRA MUTATED           3          1         10          5        2
  PDGFRA WILD-TYPE        15          5         34         28       33
                  vv
clus               STAGE IVA STAGE IVB
  PDGFRA MUTATED           1         1
  PDGFRA WILD-TYPE        11         0
D147V3, multiclass
            clus
vv           PDGFRA MUTATED PDGFRA WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              14               94
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               3               15
  STAGE IIIA              1                5
  STAGE IIIB             10               34
  STAGE IIIC              5               28
  STAGE IV                2               33
  STAGE IVA               1               11
  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     1   3  38   7
  PDGFRA WILD-TYPE   8  64 211  34
D147V4, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  T1              1                8
  T2              3               64
  T3             38              211
  T4              7               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
  PDGFRA MUTATED    26  13  10
  PDGFRA WILD-TYPE 194  68  56
D147V5, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  N0             26              194
  N1             13               68
  N2             10               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V6, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    43   4
  PDGFRA WILD-TYPE 242  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     43    4
  PDGFRA WILD-TYPE  242   44
   clus
vv  PDGFRA MUTATED PDGFRA WILD-TYPE
  0             43              242
  1              4               44
[1] 2 2
[1] FALSE
D147V7, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    24  25
  PDGFRA WILD-TYPE 146 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     24   25
  PDGFRA WILD-TYPE  146  172
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  FEMALE             24              146
  MALE               25              172
[1] 2 2
[1] FALSE
D147V8, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    35   2
  PDGFRA WILD-TYPE 265   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     35    2
  PDGFRA WILD-TYPE  265    6
     clus
vv    PDGFRA MUTATED PDGFRA WILD-TYPE
  NO              35              265
  YES              2                6
[1] 2 2
[1] FALSE
D147V9, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    38   8
  PDGFRA WILD-TYPE 276  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     38    8
  PDGFRA WILD-TYPE  276   40
                               clus
vv                              PDGFRA MUTATED PDGFRA WILD-TYPE
  COLON ADENOCARCINOMA                      38              276
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PDGFRA MUTATED    33   1   1   3
  PDGFRA WILD-TYPE 226   2  21  18
D147V10, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  R0             33              226
  R1              1                2
  R2              1               21
  RX              3               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"
D147V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDGFRA MUTATED                                  0     3
  PDGFRA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PDGFRA MUTATED                           4    30
  PDGFRA WILD-TYPE                        15   146
D147V12, multiclass
                                  clus
vv                                 PDGFRA MUTATED PDGFRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                        30              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(148) Variable = HLA-A MUTATION ANALYSIS
D148V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    14   3
  HLA-A WILD-TYPE 263  75
  HLA-A MUTATED HLA-A WILD-TYPE 
             17             338 
  HLA-A MUTATED HLA-A WILD-TYPE 
              3              75 
$`HLA-A MUTATED`
TCGA-AA-3662 TCGA-AA-3713 TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 
        6.05        19.04        35.80        22.06        19.66         3.02 
TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6718 
       33.04        30.05        25.02        83.24        58.39        10.06 
TCGA-CK-5913 TCGA-CM-4743 TCGA-D5-6541 TCGA-D5-6931 TCGA-G4-6304 
       51.32        23.05        15.58        12.00        53.62 

$`HLA-A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  HLA-A MUTATED HLA-A WILD-TYPE 
           3.02            0.00 
  HLA-A MUTATED HLA-A WILD-TYPE 
          83.24          148.01 
  HLA-A MUTATED HLA-A WILD-TYPE 
          23.05           22.01 
[1] "3.0 - 83.2 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D148V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HLA-A MUTATED         0        0        1        10         1         0
  HLA-A WILD-TYPE      64        1       25        98         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-A MUTATED           0          0          0          2        2         0
  HLA-A WILD-TYPE        18          6         44         31       33        12
                 vv
clus              STAGE IVB
  HLA-A MUTATED           0
  HLA-A WILD-TYPE         1
D148V3, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  HLA-A MUTATED     0   1  12   4
  HLA-A WILD-TYPE   9  66 237  37
D148V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0               9
  T2             1              66
  T3            12             237
  T4             4              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
  HLA-A MUTATED    14   1   2
  HLA-A WILD-TYPE 206  80  64
D148V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0            14             206
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V6, binary
                 cls
clus                0   1
  HLA-A MUTATED    12   2
  HLA-A WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     12    2
  HLA-A WILD-TYPE  273   46
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            12             273
  1             2              46
[1] 2 2
[1] FALSE
D148V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     7  10
  HLA-A WILD-TYPE 163 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      7   10
  HLA-A WILD-TYPE  163  187
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             7             163
  MALE              10             187
[1] 2 2
[1] FALSE
D148V8, binary
                 cls
clus                0   1
  HLA-A MUTATED    16   1
  HLA-A WILD-TYPE 284   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     16    1
  HLA-A WILD-TYPE  284    7
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO             16             284
  YES             1               7
[1] 2 2
[1] FALSE
D148V9, binary
                 cls
clus                0   1
  HLA-A MUTATED    16   1
  HLA-A WILD-TYPE 298  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     16    1
  HLA-A WILD-TYPE  298   47
                               clus
vv                              HLA-A MUTATED HLA-A WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-A MUTATED    12   0   2   2
  HLA-A WILD-TYPE 247   3  20  19
D148V10, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  R0            12             247
  R1             0               3
  R2             2              20
  RX             2              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"
D148V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-A MUTATED                                  0     2
  HLA-A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED                           0     9
  HLA-A WILD-TYPE                        19   167
D148V12, multiclass
                                  clus
vv                                 HLA-A MUTATED HLA-A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(149) Variable = SCAI MUTATION ANALYSIS
D149V1, survival
                sevent
clus2              0   1
  SCAI MUTATED    10   3
  SCAI WILD-TYPE 267  75
  SCAI MUTATED SCAI WILD-TYPE 
            13            342 
  SCAI MUTATED SCAI WILD-TYPE 
             3             75 
$`SCAI MUTATED`
TCGA-AA-3950 TCGA-AD-6888 TCGA-AD-6895 TCGA-DM-A285 TCGA-AA-A01R TCGA-AZ-5403 
       24.00        15.52        25.08         5.88        35.01        62.79 
TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6541 TCGA-D5-6927 TCGA-DM-A1HB TCGA-DM-A28H 
       12.76        51.32        15.58         9.44       135.65       117.07 
TCGA-DM-A28K 
       98.24 

$`SCAI WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 
      139.17        81.37       119.93        35.97        60.79         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SCAI MUTATED SCAI WILD-TYPE 
          5.88           0.00 
  SCAI MUTATED SCAI WILD-TYPE 
        135.65         148.01 
  SCAI MUTATED SCAI WILD-TYPE 
         25.08          22.01 
[1] "5.9 - 135.7 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D149V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCAI MUTATED         0        0        1         7         0         0
  SCAI WILD-TYPE      64        1       25       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCAI MUTATED           1          0          3          1        1         0
  SCAI WILD-TYPE        17          6         41         32       34        12
                vv
clus             STAGE IVB
  SCAI MUTATED           0
  SCAI WILD-TYPE         1
D149V3, multiclass
            clus
vv           SCAI MUTATED SCAI WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  SCAI MUTATED     0   0  14   0
  SCAI WILD-TYPE   9  67 235  41
D149V4, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  T1            0              9
  T2            0             67
  T3           14            235
  T4            0             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
  SCAI MUTATED     8   3   3
  SCAI WILD-TYPE 212  78  63
D149V5, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  N0            8            212
  N1            3             78
  N2            3             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"
D149V6, binary
                cls
clus               0   1
  SCAI MUTATED    11   1
  SCAI WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED     11    1
  SCAI WILD-TYPE  274   47
   clus
vv  SCAI MUTATED SCAI WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D149V7, binary
                cls
clus               0   1
  SCAI MUTATED     4  10
  SCAI WILD-TYPE 166 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED      4   10
  SCAI WILD-TYPE  166  187
        clus
vv       SCAI MUTATED SCAI WILD-TYPE
  FEMALE            4            166
  MALE             10            187
[1] 2 2
[1] FALSE
D149V8, binary
                cls
clus               0   1
  SCAI MUTATED     8   1
  SCAI WILD-TYPE 292   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED      8    1
  SCAI WILD-TYPE  292    7
     clus
vv    SCAI MUTATED SCAI WILD-TYPE
  NO             8            292
  YES            1              7
[1] 2 2
[1] FALSE
D149V9, binary
                cls
clus               0   1
  SCAI MUTATED     8   5
  SCAI WILD-TYPE 306  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED      8    5
  SCAI WILD-TYPE  306   43
                               clus
vv                              SCAI MUTATED SCAI WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SCAI MUTATED     7   0   0   2
  SCAI WILD-TYPE 252   3  22  19
D149V10, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            2             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"
D149V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCAI MUTATED                                  0     1
  SCAI WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SCAI MUTATED                           0    10
  SCAI WILD-TYPE                        19   166
D149V12, multiclass
                                  clus
vv                                 SCAI MUTATED SCAI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(150) Variable = MEN1 MUTATION ANALYSIS
D150V1, survival
                sevent
clus2              0   1
  MEN1 MUTATED    15   8
  MEN1 WILD-TYPE 262  70
  MEN1 MUTATED MEN1 WILD-TYPE 
            23            332 
  MEN1 MUTATED MEN1 WILD-TYPE 
             8             70 
$`MEN1 MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       14.53         6.05       100.01        22.09        35.80        26.17 
TCGA-A6-2676 TCGA-A6-6137 TCGA-AA-3492 TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-4948 
       42.90        27.09         3.02        33.01        49.41       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6540 
       85.45        15.62        12.99        45.40        25.48        16.14 
TCGA-D5-6922 TCGA-DM-A1D6 TCGA-F4-6460 TCGA-F4-6856 TCGA-G4-6293 
       10.13        49.91        31.96        35.31       133.18 

$`MEN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       49.08         5.88        63.62        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5913 
       12.20        12.76        10.06        14.30        17.56        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        54.61        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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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-F4-6569 
       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MEN1 MUTATED MEN1 WILD-TYPE 
          3.02           0.00 
  MEN1 MUTATED MEN1 WILD-TYPE 
        148.01         140.38 
  MEN1 MUTATED MEN1 WILD-TYPE 
         31.96          21.99 
[1] "3.0 - 148.0 (32.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D150V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEN1 MUTATED         2        0        3         6         1         0
  MEN1 WILD-TYPE      62        1       23       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEN1 MUTATED           4          1          3          1        1         1
  MEN1 WILD-TYPE        14          5         41         32       34        11
                vv
clus             STAGE IVB
  MEN1 MUTATED           0
  MEN1 WILD-TYPE         1
D150V3, multiclass
            clus
vv           MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             4             14
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  MEN1 MUTATED     0   3  17   4
  MEN1 WILD-TYPE   9  64 232  37
D150V4, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           17            232
  T4            4             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
  MEN1 MUTATED    12   8   4
  MEN1 WILD-TYPE 208  73  62
D150V5, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  N0           12            208
  N1            8             73
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V6, binary
                cls
clus               0   1
  MEN1 MUTATED    19   2
  MEN1 WILD-TYPE 266  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     19    2
  MEN1 WILD-TYPE  266   46
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0           19            266
  1            2             46
[1] 2 2
[1] FALSE
D150V7, binary
                cls
clus               0   1
  MEN1 MUTATED    15   9
  MEN1 WILD-TYPE 155 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     15    9
  MEN1 WILD-TYPE  155  188
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  FEMALE           15            155
  MALE              9            188
[1] 2 2
[1] FALSE
D150V8, binary
                cls
clus               0   1
  MEN1 MUTATED    21   0
  MEN1 WILD-TYPE 279   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     21    0
  MEN1 WILD-TYPE  279    8
     clus
vv    MEN1 MUTATED MEN1 WILD-TYPE
  NO            21            279
  YES            0              8
[1] 2 2
[1] FALSE
D150V9, binary
                cls
clus               0   1
  MEN1 MUTATED    19   5
  MEN1 WILD-TYPE 295  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     19    5
  MEN1 WILD-TYPE  295   43
                               clus
vv                              MEN1 MUTATED MEN1 WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MEN1 MUTATED    15   1   1   2
  MEN1 WILD-TYPE 244   2  21  19
D150V10, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  R0           15            244
  R1            1              2
  R2            1             21
  RX            2             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"
D150V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEN1 MUTATED                                  0     0
  MEN1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MEN1 MUTATED                           3    18
  MEN1 WILD-TYPE                        16   158
D150V12, multiclass
                                  clus
vv                                 MEN1 MUTATED MEN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      18            158
[1] 4 2
[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 = FAM179A MUTATION ANALYSIS
D151V1, survival
                   sevent
clus2                 0   1
  FAM179A MUTATED    20   7
  FAM179A WILD-TYPE 257  71
  FAM179A MUTATED FAM179A WILD-TYPE 
               27               328 
  FAM179A MUTATED FAM179A WILD-TYPE 
                7                71 
$`FAM179A MUTATED`
TCGA-AA-3950 TCGA-A6-3809 TCGA-A6-6137 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3949 
       24.00        32.75        27.09        19.66        63.98        26.01 
TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
       25.02        35.01        12.16        83.24        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 
        6.18        43.04        53.62 

$`FAM179A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 
       12.10        29.56         5.23        11.74        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        51.32        21.99        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
      139.17        81.37       119.93        35.97       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-F4-6808 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-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  FAM179A MUTATED FAM179A WILD-TYPE 
             3.19              0.00 
  FAM179A MUTATED FAM179A WILD-TYPE 
           130.65            148.01 
  FAM179A MUTATED FAM179A WILD-TYPE 
            24.00             22.01 
[1] "3.2 - 130.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D151V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM179A MUTATED         3        0        2        11         2         0
  FAM179A WILD-TYPE      61        1       24        97         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM179A MUTATED           1          0          2          4        1
  FAM179A WILD-TYPE        17          6         42         29       34
                   vv
clus                STAGE IVA STAGE IVB
  FAM179A MUTATED           0         0
  FAM179A WILD-TYPE        12         1
D151V3, multiclass
            clus
vv           FAM179A MUTATED FAM179A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA               11                97
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               4                29
  STAGE IV                 1                34
  STAGE IVA                0                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
  FAM179A MUTATED     1   3  18   5
  FAM179A WILD-TYPE   8  64 231  36
D151V4, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  T1               1                 8
  T2               3                64
  T3              18               231
  T4               5                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
  FAM179A MUTATED    19   3   5
  FAM179A WILD-TYPE 201  78  61
D151V5, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  N0              19               201
  N1               3                78
  N2               5                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V6, binary
                   cls
clus                  0   1
  FAM179A MUTATED    21   1
  FAM179A WILD-TYPE 264  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     21    1
  FAM179A WILD-TYPE  264   47
   clus
vv  FAM179A MUTATED FAM179A WILD-TYPE
  0              21               264
  1               1                47
[1] 2 2
[1] FALSE
D151V7, binary
                   cls
clus                  0   1
  FAM179A MUTATED    13  14
  FAM179A WILD-TYPE 157 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     13   14
  FAM179A WILD-TYPE  157  183
        clus
vv       FAM179A MUTATED FAM179A WILD-TYPE
  FEMALE              13               157
  MALE                14               183
[1] 2 2
[1] FALSE
D151V8, binary
                   cls
clus                  0   1
  FAM179A MUTATED    22   1
  FAM179A WILD-TYPE 278   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     22    1
  FAM179A WILD-TYPE  278    7
     clus
vv    FAM179A MUTATED FAM179A WILD-TYPE
  NO               22               278
  YES               1                 7
[1] 2 2
[1] FALSE
D151V9, binary
                   cls
clus                  0   1
  FAM179A MUTATED    19   8
  FAM179A WILD-TYPE 295  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     19    8
  FAM179A WILD-TYPE  295   40
                               clus
vv                              FAM179A MUTATED FAM179A WILD-TYPE
  COLON ADENOCARCINOMA                       19               295
  COLON MUCINOUS ADENOCARCINOMA               8                40
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM179A MUTATED    16   0   0   4
  FAM179A WILD-TYPE 243   3  22  17
D151V10, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  R0              16               243
  R1               0                 3
  R2               0                22
  RX               4                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"
D151V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM179A MUTATED                                  0     3
  FAM179A WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM179A MUTATED                           0    19
  FAM179A WILD-TYPE                        19   157
D151V12, multiclass
                                  clus
vv                                 FAM179A MUTATED FAM179A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         19               157
[1] 4 2
[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 = MLL2 MUTATION ANALYSIS
D152V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    39  12
  MLL2 WILD-TYPE 238  66
  MLL2 MUTATED MLL2 WILD-TYPE 
            51            304 
  MLL2 MUTATED MLL2 WILD-TYPE 
            12             66 
$`MLL2 MUTATED`
TCGA-A6-6649 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AD-6964 TCGA-AZ-6601 
       24.16         0.92        85.05        19.04        10.88       100.01 
TCGA-DM-A285 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-5665 
        5.88        35.80        79.69        33.34        33.53        22.06 
TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 
       25.18        24.69        24.39        20.12        19.66        63.98 
TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3833 TCGA-AA-A00N 
        6.97         5.98        26.99        10.06        15.95         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 
       34.98        35.01        12.16        21.44        58.39        49.41 
TCGA-AZ-6600 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 
       12.10        12.59        12.76        10.06        21.14       124.27 
TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       23.05        25.02        13.02        14.99        12.99        14.04 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6540 TCGA-DM-A1D6 
       18.25        25.48        15.12        17.13        16.14        49.91 
TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 
        6.18        47.87        61.91 

$`MLL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
       25.08       106.75         1.94        49.08        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3685 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       11.01        37.05         5.03        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02         1.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.36        12.39        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        2.01        20.02        37.02        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       21.99        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-D5-6534 
       54.61        19.59        56.09        55.92        20.19        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.92           0.00 
  MLL2 MUTATED MLL2 WILD-TYPE 
        124.27         148.01 
  MLL2 MUTATED MLL2 WILD-TYPE 
        21.140         22.225 
[1] "0.9 - 124.3 (21.1)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1"  
D152V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL2 MUTATED         7        0        6        18         3         0
  MLL2 WILD-TYPE      57        1       20        90         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL2 MUTATED           4          0          4          2        3         3
  MLL2 WILD-TYPE        14          6         40         31       32         9
                vv
clus             STAGE IVB
  MLL2 MUTATED           0
  MLL2 WILD-TYPE         1
D152V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA            18             90
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             4             14
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            2             31
  STAGE IV              3             32
  STAGE IVA             3              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
  MLL2 MUTATED     1   6  37   8
  MLL2 WILD-TYPE   8  61 212  33
D152V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            1              8
  T2            6             61
  T3           37            212
  T4            8             33
[1] 4 2
[1] TRUE
[1] "dimension 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    37   9   6
  MLL2 WILD-TYPE 183  72  60
D152V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           37            183
  N1            9             72
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V6, binary
                cls
clus               0   1
  MLL2 MUTATED    37   6
  MLL2 WILD-TYPE 248  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     37    6
  MLL2 WILD-TYPE  248   42
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           37            248
  1            6             42
[1] 2 2
[1] FALSE
D152V7, binary
                cls
clus               0   1
  MLL2 MUTATED    21  31
  MLL2 WILD-TYPE 149 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     21   31
  MLL2 WILD-TYPE  149  166
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           21            149
  MALE             31            166
[1] 2 2
[1] FALSE
D152V8, binary
                cls
clus               0   1
  MLL2 MUTATED    47   1
  MLL2 WILD-TYPE 253   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     47    1
  MLL2 WILD-TYPE  253    7
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            47            253
  YES            1              7
[1] 2 2
[1] FALSE
D152V9, binary
                cls
clus               0   1
  MLL2 MUTATED    42  10
  MLL2 WILD-TYPE 272  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     42   10
  MLL2 WILD-TYPE  272   38
                               clus
vv                              MLL2 MUTATED MLL2 WILD-TYPE
  COLON ADENOCARCINOMA                    42            272
  COLON MUCINOUS ADENOCARCINOMA           10             38
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    34   0   0   7
  MLL2 WILD-TYPE 225   3  22  14
D152V10, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           34            225
  R1            0              3
  R2            0             22
  RX            7             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"
D152V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  0     3
  MLL2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED                           6    31
  MLL2 WILD-TYPE                        13   145
D152V12, multiclass
                                  clus
vv                                 MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   6             13
  WHITE                                      31            145
[1] 4 2
[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 = FGFR2 MUTATION ANALYSIS
D153V1, survival
                 sevent
clus2               0   1
  FGFR2 MUTATED    30  15
  FGFR2 WILD-TYPE 247  63
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             45             310 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             15              63 
$`FGFR2 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-5660 
       19.04       100.01        26.17        91.79        79.69        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6142 TCGA-AA-3489 TCGA-AA-3510 
       23.61        32.71        22.52        25.08         7.04        63.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3710 TCGA-AD-6889 TCGA-AD-6901 TCGA-AY-6196 
       78.08         6.97        26.99        83.24        22.42         0.20 
TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4950 
       17.82        49.41         6.77        12.10        12.76        85.45 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6168 
       15.62        23.05        13.02        22.98         5.03        12.99 
TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       20.19        15.12         4.80        12.49        16.14         7.53 
TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6570 
       38.20        49.91        44.32        35.97        60.79         6.18 
TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 
       53.62        36.00        13.78 

$`FGFR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 
       30.44        33.53        22.09        22.06        27.09         8.38 
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-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 
       24.00        29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        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-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        22.36        62.79        88.21        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
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-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        14.04        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-D5-6532 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       43.27        17.85        17.13        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
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-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H 
      131.51       135.65       139.17        81.37       119.93       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        43.04        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-G4-6315 TCGA-G4-6626 
       55.04        85.48        61.91        46.75 

  FGFR2 MUTATED FGFR2 WILD-TYPE 
            0.2             0.0 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
         100.01          148.01 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          22.98           21.99 
[1] "0.2 - 100.0 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D153V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGFR2 MUTATED         5        1        6        13         1         1
  FGFR2 WILD-TYPE      59        0       20        95         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR2 MUTATED           0          0          6          5        2         3
  FGFR2 WILD-TYPE        18          6         38         28       33         9
                 vv
clus              STAGE IVB
  FGFR2 MUTATED           0
  FGFR2 WILD-TYPE         1
D153V3, multiclass
            clus
vv           FGFR2 MUTATED FGFR2 WILD-TYPE
  STAGE I                5              59
  STAGE IA               1               0
  STAGE II               6              20
  STAGE IIA             13              95
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             5              28
  STAGE IV               2              33
  STAGE IVA              3               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
  FGFR2 MUTATED     0   5  35   4
  FGFR2 WILD-TYPE   9  62 214  37
D153V4, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            35             214
  T4             4              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
  FGFR2 MUTATED    30   9   6
  FGFR2 WILD-TYPE 190  72  60
D153V5, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  N0            30             190
  N1             9              72
  N2             6              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V6, binary
                 cls
clus                0   1
  FGFR2 MUTATED    32   5
  FGFR2 WILD-TYPE 253  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     32    5
  FGFR2 WILD-TYPE  253   43
   clus
vv  FGFR2 MUTATED FGFR2 WILD-TYPE
  0            32             253
  1             5              43
[1] 2 2
[1] FALSE
D153V7, binary
                 cls
clus                0   1
  FGFR2 MUTATED    17  28
  FGFR2 WILD-TYPE 153 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     17   28
  FGFR2 WILD-TYPE  153  169
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  FEMALE            17             153
  MALE              28             169
[1] 2 2
[1] FALSE
D153V8, binary
                 cls
clus                0   1
  FGFR2 MUTATED    37   1
  FGFR2 WILD-TYPE 263   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     37    1
  FGFR2 WILD-TYPE  263    7
     clus
vv    FGFR2 MUTATED FGFR2 WILD-TYPE
  NO             37             263
  YES             1               7
[1] 2 2
[1] FALSE
D153V9, binary
                 cls
clus                0   1
  FGFR2 MUTATED    38   6
  FGFR2 WILD-TYPE 276  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     38    6
  FGFR2 WILD-TYPE  276   42
                               clus
vv                              FGFR2 MUTATED FGFR2 WILD-TYPE
  COLON ADENOCARCINOMA                     38             276
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR2 MUTATED    25   1   1   3
  FGFR2 WILD-TYPE 234   2  21  18
D153V10, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  R0            25             234
  R1             1               2
  R2             1              21
  RX             3              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"
D153V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR2 MUTATED                                  0     2
  FGFR2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FGFR2 MUTATED                           7    30
  FGFR2 WILD-TYPE                        12   146
D153V12, multiclass
                                  clus
vv                                 FGFR2 MUTATED FGFR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    7              12
  WHITE                                       30             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(154) Variable = SLC4A10 MUTATION ANALYSIS
D154V1, survival
                   sevent
clus2                 0   1
  SLC4A10 MUTATED    20   6
  SLC4A10 WILD-TYPE 257  72
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               26               329 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
                6                72 
$`SLC4A10 MUTATED`
TCGA-AZ-4681 TCGA-DM-A285 TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-6141 TCGA-AA-A010 
      106.75         5.88        32.75        30.44         8.38        34.98 
TCGA-AA-A01R TCGA-AD-6901 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CK-6747 
       35.01        22.42        17.82        58.39        11.74        82.95 
TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6162 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 
       32.02        15.02        12.00        17.85        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6570 
       14.30        13.35        49.91        60.79        98.24         6.18 
TCGA-F4-6856 TCGA-G4-6293 
       35.31       133.18 

$`SLC4A10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44         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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       12.39         9.04         9.44        11.64        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
             5.88              0.00 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
           133.18            148.01 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
            26.43             22.03 
[1] "5.9 - 133.2 (26.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D154V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC4A10 MUTATED         4        0        0        12         2         0
  SLC4A10 WILD-TYPE      60        1       26        96         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC4A10 MUTATED           2          1          2          0        3
  SLC4A10 WILD-TYPE        16          5         42         33       32
                   vv
clus                STAGE IVA STAGE IVB
  SLC4A10 MUTATED           0         0
  SLC4A10 WILD-TYPE        12         1
D154V3, multiclass
            clus
vv           SLC4A10 MUTATED SLC4A10 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA               12                96
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 3                32
  STAGE IVA                0                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
  SLC4A10 MUTATED     0   4  20   3
  SLC4A10 WILD-TYPE   9  63 229  38
D154V4, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3              20               229
  T4               3                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
  SLC4A10 MUTATED    19   4   4
  SLC4A10 WILD-TYPE 201  77  62
D154V5, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  N0              19               201
  N1               4                77
  N2               4                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V6, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    22   3
  SLC4A10 WILD-TYPE 263  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     22    3
  SLC4A10 WILD-TYPE  263   45
   clus
vv  SLC4A10 MUTATED SLC4A10 WILD-TYPE
  0              22               263
  1               3                45
[1] 2 2
[1] FALSE
D154V7, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    10  17
  SLC4A10 WILD-TYPE 160 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     10   17
  SLC4A10 WILD-TYPE  160  180
        clus
vv       SLC4A10 MUTATED SLC4A10 WILD-TYPE
  FEMALE              10               160
  MALE                17               180
[1] 2 2
[1] FALSE
D154V8, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    21   1
  SLC4A10 WILD-TYPE 279   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     21    1
  SLC4A10 WILD-TYPE  279    7
     clus
vv    SLC4A10 MUTATED SLC4A10 WILD-TYPE
  NO               21               279
  YES               1                 7
[1] 2 2
[1] FALSE
D154V9, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    19   8
  SLC4A10 WILD-TYPE 295  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     19    8
  SLC4A10 WILD-TYPE  295   40
                               clus
vv                              SLC4A10 MUTATED SLC4A10 WILD-TYPE
  COLON ADENOCARCINOMA                       19               295
  COLON MUCINOUS ADENOCARCINOMA               8                40
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC4A10 MUTATED    18   0   1   1
  SLC4A10 WILD-TYPE 241   3  21  20
D154V10, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               1                21
  RX               1                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"
D154V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC4A10 MUTATED                                  0     0
  SLC4A10 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC4A10 MUTATED                           2    22
  SLC4A10 WILD-TYPE                        17   154
D154V12, multiclass
                                  clus
vv                                 SLC4A10 MUTATED SLC4A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         22               154
[1] 4 2
[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 = RAF1 MUTATION ANALYSIS
D155V1, survival
                sevent
clus2              0   1
  RAF1 MUTATED    11   2
  RAF1 WILD-TYPE 266  76
  RAF1 MUTATED RAF1 WILD-TYPE 
            13            342 
  RAF1 MUTATED RAF1 WILD-TYPE 
             2             76 
$`RAF1 MUTATED`
TCGA-AA-3516 TCGA-AA-3562 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A01V TCGA-AZ-4315 
       13.02        19.99        63.98         4.01         1.02        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 
       44.68 

$`RAF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A029 
       35.01         1.02        33.04        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RAF1 MUTATED RAF1 WILD-TYPE 
          1.02           0.00 
  RAF1 MUTATED RAF1 WILD-TYPE 
        117.07         148.01 
  RAF1 MUTATED RAF1 WILD-TYPE 
        35.310         22.045 
[1] "1.0 - 117.1 (35.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D155V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAF1 MUTATED         4        0        1         2         1         0
  RAF1 WILD-TYPE      60        1       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAF1 MUTATED           1          0          1          2        0         0
  RAF1 WILD-TYPE        17          6         43         31       35        12
                vv
clus             STAGE IVB
  RAF1 MUTATED           0
  RAF1 WILD-TYPE         1
D155V3, multiclass
            clus
vv           RAF1 MUTATED RAF1 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  RAF1 MUTATED     1   4   7   1
  RAF1 WILD-TYPE   8  63 242  40
D155V4, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  T1            1              8
  T2            4             63
  T3            7            242
  T4            1             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
  RAF1 MUTATED     9   1   3
  RAF1 WILD-TYPE 211  80  63
D155V5, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  N0            9            211
  N1            1             80
  N2            3             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"
D155V6, binary
                cls
clus               0   1
  RAF1 MUTATED    13   0
  RAF1 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED     13    0
  RAF1 WILD-TYPE  272   48
   clus
vv  RAF1 MUTATED RAF1 WILD-TYPE
  0           13            272
  1            0             48
[1] 2 2
[1] FALSE
D155V7, binary
                cls
clus               0   1
  RAF1 MUTATED     3  10
  RAF1 WILD-TYPE 167 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      3   10
  RAF1 WILD-TYPE  167  187
        clus
vv       RAF1 MUTATED RAF1 WILD-TYPE
  FEMALE            3            167
  MALE             10            187
[1] 2 2
[1] FALSE
D155V8, binary
                cls
clus               0   1
  RAF1 MUTATED    10   0
  RAF1 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED     10    0
  RAF1 WILD-TYPE  290    8
     clus
vv    RAF1 MUTATED RAF1 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D155V9, binary
                cls
clus               0   1
  RAF1 MUTATED     8   5
  RAF1 WILD-TYPE 306  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      8    5
  RAF1 WILD-TYPE  306   43
                               clus
vv                              RAF1 MUTATED RAF1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RAF1 MUTATED     9   0   0   1
  RAF1 WILD-TYPE 250   3  22  20
D155V10, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            1             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"
D155V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAF1 MUTATED                                  0     1
  RAF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAF1 MUTATED                           1     6
  RAF1 WILD-TYPE                        18   170
D155V12, multiclass
                                  clus
vv                                 RAF1 MUTATED RAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = KIAA1012 MUTATION ANALYSIS
D156V1, survival
                    sevent
clus2                  0   1
  KIAA1012 MUTATED    17   5
  KIAA1012 WILD-TYPE 260  73
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                22                333 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                 5                 73 
$`KIAA1012 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-G4-6588 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3811 
        0.92        19.04        26.17        19.66         6.97        10.06 
TCGA-AA-3815 TCGA-AA-3989 TCGA-AA-A010 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4315 
       33.04         7.96        34.98        14.50         0.20        58.39 
TCGA-AZ-4682 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 
       22.36        12.76        51.32        22.03        32.02        15.02 
TCGA-CM-6162 TCGA-D5-5539 TCGA-D5-6536 TCGA-G4-6626 
       12.00        19.59        17.85        46.75 

$`KIAA1012 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02        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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        62.79        88.21        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
               0.2                0.0 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
             58.39             148.01 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
            19.315             22.420 
[1] "0.2 - 58.4 (19.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.3"
D156V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1012 MUTATED         1        0        2        10         1         0
  KIAA1012 WILD-TYPE      63        1       24        98         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1012 MUTATED           2          1          2          2        1
  KIAA1012 WILD-TYPE        16          5         42         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1012 MUTATED           1         0
  KIAA1012 WILD-TYPE        11         1
D156V3, multiclass
            clus
vv           KIAA1012 MUTATED KIAA1012 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                10                 98
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                1                  5
  STAGE IIIB                2                 42
  STAGE IIIC                2                 31
  STAGE IV                  1                 34
  STAGE IVA                 1                 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
  KIAA1012 MUTATED     0   1  20   2
  KIAA1012 WILD-TYPE   9  66 229  39
D156V4, multiclass
    clus
vv   KIAA1012 MUTATED KIAA1012 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3               20                229
  T4                2                 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
  KIAA1012 MUTATED    15   5   3
  KIAA1012 WILD-TYPE 205  76  63
D156V5, multiclass
    clus
vv   KIAA1012 MUTATED KIAA1012 WILD-TYPE
  N0               15                205
  N1                5                 76
  N2                3                 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"
D156V6, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    17   2
  KIAA1012 WILD-TYPE 268  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     17    2
  KIAA1012 WILD-TYPE  268   46
   clus
vv  KIAA1012 MUTATED KIAA1012 WILD-TYPE
  0               17                268
  1                2                 46
[1] 2 2
[1] FALSE
D156V7, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    10  13
  KIAA1012 WILD-TYPE 160 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     10   13
  KIAA1012 WILD-TYPE  160  184
        clus
vv       KIAA1012 MUTATED KIAA1012 WILD-TYPE
  FEMALE               10                160
  MALE                 13                184
[1] 2 2
[1] FALSE
D156V8, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    21   0
  KIAA1012 WILD-TYPE 279   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     21    0
  KIAA1012 WILD-TYPE  279    8
     clus
vv    KIAA1012 MUTATED KIAA1012 WILD-TYPE
  NO                21                279
  YES                0                  8
[1] 2 2
[1] FALSE
D156V9, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    18   5
  KIAA1012 WILD-TYPE 296  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     18    5
  KIAA1012 WILD-TYPE  296   43
                               clus
vv                              KIAA1012 MUTATED KIAA1012 WILD-TYPE
  COLON ADENOCARCINOMA                        18                296
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1012 MUTATED    19   0   1   3
  KIAA1012 WILD-TYPE 240   3  21  18
D156V10, multiclass
    clus
vv   KIAA1012 MUTATED KIAA1012 WILD-TYPE
  R0               19                240
  R1                0                  3
  R2                1                 21
  RX                3                 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"
D156V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1012 MUTATED                                  0     1
  KIAA1012 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1012 MUTATED                           0    15
  KIAA1012 WILD-TYPE                        19   161
D156V12, multiclass
                                  clus
vv                                 KIAA1012 MUTATED KIAA1012 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          15                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(157) Variable = FAM9A MUTATION ANALYSIS
D157V1, survival
                 sevent
clus2               0   1
  FAM9A MUTATED     5   5
  FAM9A WILD-TYPE 272  73
  FAM9A MUTATED FAM9A WILD-TYPE 
             10             345 
  FAM9A MUTATED FAM9A WILD-TYPE 
              5              73 
$`FAM9A MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3815 
       10.88       100.01        26.17        20.12        19.66        33.04 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CK-5913 TCGA-F4-6570 
       49.41        29.56        51.32         6.18 

$`FAM9A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FAM9A MUTATED FAM9A WILD-TYPE 
           6.18            0.00 
  FAM9A MUTATED FAM9A WILD-TYPE 
         100.01          148.01 
  FAM9A MUTATED FAM9A WILD-TYPE 
         27.865          22.030 
[1] "6.2 - 100.0 (27.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D157V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM9A MUTATED         0        0        2         6         0         0
  FAM9A WILD-TYPE      64        1       24       102         8         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  FAM9A MUTATED           0
  FAM9A WILD-TYPE         1
D157V3, multiclass
            clus
vv           FAM9A MUTATED FAM9A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  FAM9A MUTATED     0   1   8   2
  FAM9A WILD-TYPE   9  66 241  39
D157V4, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             2              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
  FAM9A MUTATED     8   2   1
  FAM9A WILD-TYPE 212  79  65
D157V5, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  N0             8             212
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V6, binary
                 cls
clus                0   1
  FAM9A MUTATED     5   0
  FAM9A WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      5    0
  FAM9A WILD-TYPE  280   48
   clus
vv  FAM9A MUTATED FAM9A WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D157V7, binary
                 cls
clus                0   1
  FAM9A MUTATED     7   4
  FAM9A WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      7    4
  FAM9A WILD-TYPE  163  193
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D157V8, binary
                 cls
clus                0   1
  FAM9A MUTATED    10   0
  FAM9A WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED     10    0
  FAM9A WILD-TYPE  290    8
     clus
vv    FAM9A MUTATED FAM9A WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D157V9, binary
                 cls
clus                0   1
  FAM9A MUTATED     9   2
  FAM9A WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      9    2
  FAM9A WILD-TYPE  305   46
                               clus
vv                              FAM9A MUTATED FAM9A WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FAM9A MUTATED     5   0   0   1
  FAM9A WILD-TYPE 254   3  22  20
D157V10, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D157V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM9A MUTATED                                  0     0
  FAM9A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FAM9A MUTATED                           0     9
  FAM9A WILD-TYPE                        19   167
D157V12, multiclass
                                  clus
vv                                 FAM9A MUTATED FAM9A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(158) Variable = F8 MUTATION ANALYSIS
D158V1, survival
              sevent
clus2            0   1
  F8 MUTATED    25   8
  F8 WILD-TYPE 252  70
  F8 MUTATED F8 WILD-TYPE 
          33          322 
  F8 MUTATED F8 WILD-TYPE 
           8           70 
$`F8 MUTATED`
TCGA-AA-3950 TCGA-AA-3952 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6586 
       24.00         2.01        25.08        10.88       100.01        35.80 
TCGA-G4-6588 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3492 
       26.17        32.91        29.19        25.08        19.66         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-3977 
       35.01        63.98        29.95        26.99        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-5796 
        4.01        34.98        83.24        21.44        49.41        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6172 
       12.59        12.59        12.76        23.05        22.03        11.01 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-G4-6309 
       13.35        49.91        85.48 

$`F8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 
       14.93        31.07        24.03        29.98        12.99        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       21.37        15.52       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       63.62        22.09        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       32.75        36.53        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       20.28         7.04         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.19        12.69        12.36        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  F8 MUTATED F8 WILD-TYPE 
        2.01         0.00 
  F8 MUTATED F8 WILD-TYPE 
      100.01       148.01 
  F8 MUTATED F8 WILD-TYPE 
       25.08        21.99 
[1] "2.0 - 100.0 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D158V2, continuous
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F8 MUTATED         2        0        4        14         4         0
  F8 WILD-TYPE      62        1       22        94         4         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F8 MUTATED           0          0          5          3        0         1
  F8 WILD-TYPE        18          6         39         30       35        11
              vv
clus           STAGE IVB
  F8 MUTATED           0
  F8 WILD-TYPE         1
D158V3, multiclass
            clus
vv           F8 MUTATED F8 WILD-TYPE
  STAGE I             2           62
  STAGE IA            0            1
  STAGE II            4           22
  STAGE IIA          14           94
  STAGE IIB           4            4
  STAGE IIC           0            1
  STAGE III           0           18
  STAGE IIIA          0            6
  STAGE IIIB          5           39
  STAGE IIIC          3           30
  STAGE IV            0           35
  STAGE IVA           1           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
  F8 MUTATED     0   3  26   6
  F8 WILD-TYPE   9  64 223  35
D158V4, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  T1          0            9
  T2          3           64
  T3         26          223
  T4          6           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
  F8 MUTATED    25   7   3
  F8 WILD-TYPE 195  74  63
D158V5, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  N0         25          195
  N1          7           74
  N2          3           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"
D158V6, binary
              cls
clus             0   1
  F8 MUTATED    28   1
  F8 WILD-TYPE 257  47
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     28    1
  F8 WILD-TYPE  257   47
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0         28          257
  1          1           47
[1] 2 2
[1] FALSE
D158V7, binary
              cls
clus             0   1
  F8 MUTATED    16  19
  F8 WILD-TYPE 154 178
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     16   19
  F8 WILD-TYPE  154  178
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE         16          154
  MALE           19          178
[1] 2 2
[1] FALSE
D158V8, binary
              cls
clus             0   1
  F8 MUTATED    30   0
  F8 WILD-TYPE 270   8
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     30    0
  F8 WILD-TYPE  270    8
     clus
vv    F8 MUTATED F8 WILD-TYPE
  NO          30          270
  YES          0            8
[1] 2 2
[1] FALSE
D158V9, binary
              cls
clus             0   1
  F8 MUTATED    26   9
  F8 WILD-TYPE 288  39
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     26    9
  F8 WILD-TYPE  288   39
                               clus
vv                              F8 MUTATED F8 WILD-TYPE
  COLON ADENOCARCINOMA                  26          288
  COLON MUCINOUS ADENOCARCINOMA          9           39
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  F8 MUTATED    24   0   0   3
  F8 WILD-TYPE 235   3  22  18
D158V10, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  R0         24          235
  R1          0            3
  R2          0           22
  RX          3           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"
D158V11, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F8 MUTATED                                  0     5                         2
  F8 WILD-TYPE                                1     5                        17
              vv
clus           WHITE
  F8 MUTATED      16
  F8 WILD-TYPE   160
D158V12, multiclass
                                  clus
vv                                 F8 MUTATED F8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     5            5
  BLACK OR AFRICAN AMERICAN                 2           17
  WHITE                                    16          160
[1] 4 2
[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 = TUBE1 MUTATION ANALYSIS
D159V1, survival
                 sevent
clus2               0   1
  TUBE1 MUTATED     8   3
  TUBE1 WILD-TYPE 269  75
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             11             344 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              3              75 
$`TUBE1 MUTATED`
TCGA-A6-2677 TCGA-AA-3516 TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-A010 TCGA-CA-6717 
       24.33        13.02        33.53         6.97        34.98        12.76 
TCGA-CK-4950 TCGA-CM-6162 TCGA-CM-6171 TCGA-DM-A1HB TCGA-DM-A28G 
       85.45        12.00        14.04       135.65        60.79 

$`TUBE1 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       14.53        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      131.51       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TUBE1 MUTATED TUBE1 WILD-TYPE 
           6.97            0.00 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         135.65          148.01 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         24.330          22.045 
[1] "7.0 - 135.7 (24.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D159V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUBE1 MUTATED         1        0        1         3         1         0
  TUBE1 WILD-TYPE      63        1       25       105         7         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        17          6         41         32       35        12
                 vv
clus              STAGE IVB
  TUBE1 MUTATED           0
  TUBE1 WILD-TYPE         1
D159V3, multiclass
            clus
vv           TUBE1 MUTATED TUBE1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TUBE1 MUTATED     0   1   9   1
  TUBE1 WILD-TYPE   9  66 240  40
D159V4, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             1              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
  TUBE1 MUTATED     6   3   2
  TUBE1 WILD-TYPE 214  78  64
D159V5, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V6, binary
                 cls
clus                0   1
  TUBE1 MUTATED    11   0
  TUBE1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED     11    0
  TUBE1 WILD-TYPE  274   48
   clus
vv  TUBE1 MUTATED TUBE1 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D159V7, binary
                 cls
clus                0   1
  TUBE1 MUTATED     7   4
  TUBE1 WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      7    4
  TUBE1 WILD-TYPE  163  193
        clus
vv       TUBE1 MUTATED TUBE1 WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D159V8, binary
                 cls
clus                0   1
  TUBE1 MUTATED     9   0
  TUBE1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      9    0
  TUBE1 WILD-TYPE  291    8
     clus
vv    TUBE1 MUTATED TUBE1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D159V9, binary
                 cls
clus                0   1
  TUBE1 MUTATED     6   4
  TUBE1 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      6    4
  TUBE1 WILD-TYPE  308   44
                               clus
vv                              TUBE1 MUTATED TUBE1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TUBE1 MUTATED     6   1   0   1
  TUBE1 WILD-TYPE 253   2  22  20
D159V10, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  R0             6             253
  R1             1               2
  R2             0              22
  RX             1              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"
D159V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBE1 MUTATED                                  0     1
  TUBE1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TUBE1 MUTATED                           2     5
  TUBE1 WILD-TYPE                        17   171
D159V12, multiclass
                                  clus
vv                                 TUBE1 MUTATED TUBE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = OXSM MUTATION ANALYSIS
D160V1, survival
                sevent
clus2              0   1
  OXSM MUTATED     9   1
  OXSM WILD-TYPE 268  77
  OXSM MUTATED OXSM WILD-TYPE 
            10            345 
  OXSM MUTATED OXSM WILD-TYPE 
             1             77 
$`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        12.16        20.02 
TCGA-CM-4746 TCGA-D5-6923 TCGA-DM-A1D9 TCGA-G4-6304 
       37.02        12.43       140.38        53.62 

$`OXSM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        2.01       124.27        23.05        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  OXSM MUTATED OXSM WILD-TYPE 
          4.01           0.00 
  OXSM MUTATED OXSM WILD-TYPE 
        140.38         148.01 
  OXSM MUTATED OXSM WILD-TYPE 
        26.005         22.030 
[1] "4.0 - 140.4 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D160V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OXSM MUTATED         4        0        0         3         2         0
  OXSM WILD-TYPE      60        1       26       105         6         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  OXSM MUTATED           0
  OXSM WILD-TYPE         1
D160V3, multiclass
            clus
vv           OXSM MUTATED OXSM WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  OXSM MUTATED     0   5   3   2
  OXSM WILD-TYPE   9  62 246  39
D160V4, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  T1            0              9
  T2            5             62
  T3            3            246
  T4            2             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
  OXSM MUTATED    10   0   0
  OXSM WILD-TYPE 210  81  66
D160V5, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  N0           10            210
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V6, binary
                cls
clus               0   1
  OXSM MUTATED     8   0
  OXSM WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      8    0
  OXSM WILD-TYPE  277   48
   clus
vv  OXSM MUTATED OXSM WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D160V7, binary
                cls
clus               0   1
  OXSM MUTATED     3   7
  OXSM WILD-TYPE 167 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      3    7
  OXSM WILD-TYPE  167  190
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  FEMALE            3            167
  MALE              7            190
[1] 2 2
[1] FALSE
D160V8, binary
                cls
clus               0   1
  OXSM MUTATED     8   0
  OXSM WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      8    0
  OXSM WILD-TYPE  292    8
     clus
vv    OXSM MUTATED OXSM WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D160V9, binary
                cls
clus               0   1
  OXSM MUTATED     8   2
  OXSM WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      8    2
  OXSM WILD-TYPE  306   46
                               clus
vv                              OXSM MUTATED OXSM WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OXSM MUTATED     8   0   0   0
  OXSM WILD-TYPE 251   3  22  21
D160V10, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D160V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OXSM MUTATED                                  0     0
  OXSM WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OXSM MUTATED                           1     5
  OXSM WILD-TYPE                        18   171
D160V12, multiclass
                                  clus
vv                                 OXSM MUTATED OXSM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = FHOD3 MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2               0   1
  FHOD3 MUTATED    18   7
  FHOD3 WILD-TYPE 259  71
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             25             330 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              7              71 
$`FHOD3 MUTATED`
TCGA-AA-3525 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 
        8.05        26.17        79.69        33.53        19.66         3.02 
TCGA-AA-3502 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N 
       35.01         2.01        33.01         2.01        38.04         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       34.98         1.02        21.44        49.41        12.76        10.06 
TCGA-CM-4743 TCGA-CM-6162 TCGA-D5-6536 TCGA-D5-6927 TCGA-DM-A28C TCGA-F4-6570 
       23.05        12.00        17.85         9.44        81.37         6.18 
TCGA-G4-6309 
       85.48 

$`FHOD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       31.00        24.00        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  FHOD3 MUTATED FHOD3 WILD-TYPE 
           1.02            0.00 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          85.48          148.01 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          19.66           22.09 
[1] "1.0 - 85.5 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D161V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FHOD3 MUTATED         3        0        3        13         3         0
  FHOD3 WILD-TYPE      61        1       23        95         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FHOD3 MUTATED           0          0          3          1        1         0
  FHOD3 WILD-TYPE        18          6         41         32       34        12
                 vv
clus              STAGE IVB
  FHOD3 MUTATED           0
  FHOD3 WILD-TYPE         1
D161V3, multiclass
            clus
vv           FHOD3 MUTATED FHOD3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             13              95
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  FHOD3 MUTATED     0   3  20   4
  FHOD3 WILD-TYPE   9  64 229  37
D161V4, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            20             229
  T4             4              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
  FHOD3 MUTATED    22   4   1
  FHOD3 WILD-TYPE 198  77  65
D161V5, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  N0            22             198
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V6, binary
                 cls
clus                0   1
  FHOD3 MUTATED    22   1
  FHOD3 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     22    1
  FHOD3 WILD-TYPE  263   47
   clus
vv  FHOD3 MUTATED FHOD3 WILD-TYPE
  0            22             263
  1             1              47
[1] 2 2
[1] FALSE
D161V7, binary
                 cls
clus                0   1
  FHOD3 MUTATED    12  15
  FHOD3 WILD-TYPE 158 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     12   15
  FHOD3 WILD-TYPE  158  182
        clus
vv       FHOD3 MUTATED FHOD3 WILD-TYPE
  FEMALE            12             158
  MALE              15             182
[1] 2 2
[1] FALSE
D161V8, binary
                 cls
clus                0   1
  FHOD3 MUTATED    21   0
  FHOD3 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     21    0
  FHOD3 WILD-TYPE  279    8
     clus
vv    FHOD3 MUTATED FHOD3 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D161V9, binary
                 cls
clus                0   1
  FHOD3 MUTATED    21   6
  FHOD3 WILD-TYPE 293  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     21    6
  FHOD3 WILD-TYPE  293   42
                               clus
vv                              FHOD3 MUTATED FHOD3 WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FHOD3 MUTATED    20   0   1   3
  FHOD3 WILD-TYPE 239   3  21  18
D161V10, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  R0            20             239
  R1             0               3
  R2             1              21
  RX             3              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"
D161V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FHOD3 MUTATED                                  0     2
  FHOD3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FHOD3 MUTATED                           2    12
  FHOD3 WILD-TYPE                        17   164
D161V12, multiclass
                                  clus
vv                                 FHOD3 MUTATED FHOD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       12             164
[1] 4 2
[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 = MMP8 MUTATION ANALYSIS
D162V1, survival
                sevent
clus2              0   1
  MMP8 MUTATED     9   3
  MMP8 WILD-TYPE 268  75
  MMP8 MUTATED MMP8 WILD-TYPE 
            12            343 
  MMP8 MUTATED MMP8 WILD-TYPE 
             3             75 
$`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        21.99        37.02        12.99         6.18 

$`MMP8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        23.61        22.06        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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MMP8 MUTATED MMP8 WILD-TYPE 
          6.18           0.00 
  MMP8 MUTATED MMP8 WILD-TYPE 
         63.98         148.01 
  MMP8 MUTATED MMP8 WILD-TYPE 
        28.535         22.030 
[1] "6.2 - 64.0 (28.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D162V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP8 MUTATED         1        0        3         5         1         0
  MMP8 WILD-TYPE      63        1       23       103         7         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  MMP8 MUTATED           0
  MMP8 WILD-TYPE         1
D162V3, multiclass
            clus
vv           MMP8 MUTATED MMP8 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  MMP8 MUTATED     0   1   9   2
  MMP8 WILD-TYPE   9  66 240  39
D162V4, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            9            240
  T4            2             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
  MMP8 MUTATED    10   1   1
  MMP8 WILD-TYPE 210  80  65
D162V5, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V6, binary
                cls
clus               0   1
  MMP8 MUTATED     6   0
  MMP8 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED      6    0
  MMP8 WILD-TYPE  279   48
   clus
vv  MMP8 MUTATED MMP8 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D162V7, binary
                cls
clus               0   1
  MMP8 MUTATED     6   6
  MMP8 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED      6    6
  MMP8 WILD-TYPE  164  191
        clus
vv       MMP8 MUTATED MMP8 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D162V8, binary
                cls
clus               0   1
  MMP8 MUTATED    11   0
  MMP8 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED     11    0
  MMP8 WILD-TYPE  289    8
     clus
vv    MMP8 MUTATED MMP8 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D162V9, binary
                cls
clus               0   1
  MMP8 MUTATED    11   1
  MMP8 WILD-TYPE 303  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED     11    1
  MMP8 WILD-TYPE  303   47
                               clus
vv                              MMP8 MUTATED MMP8 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MMP8 MUTATED     5   0   0   3
  MMP8 WILD-TYPE 254   3  22  18
D162V10, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            3             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"
D162V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP8 MUTATED                                  0     1
  MMP8 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MMP8 MUTATED                           3     6
  MMP8 WILD-TYPE                        16   170
D162V12, multiclass
                                  clus
vv                                 MMP8 MUTATED MMP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                       6            170
[1] 4 2
[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 = SGK269 MUTATION ANALYSIS
D163V1, survival
                  sevent
clus2                0   1
  SGK269 MUTATED    16   4
  SGK269 WILD-TYPE 261  74
  SGK269 MUTATED SGK269 WILD-TYPE 
              20              335 
  SGK269 MUTATED SGK269 WILD-TYPE 
               4               74 
$`SGK269 MUTATED`
TCGA-A6-4105 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
       14.53        35.80        79.69        33.53        22.06         8.38 
TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3864 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6386 
       20.12         6.97        53.00        83.24        27.09        17.82 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6930 
       12.20        12.76        14.04        25.48         9.44        13.35 
TCGA-F4-6570 TCGA-G4-6303 
        6.18        65.85 

$`SGK269 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 
       32.71        27.09        22.52        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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-6718 
       12.69        12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SGK269 MUTATED SGK269 WILD-TYPE 
            6.18             0.00 
  SGK269 MUTATED SGK269 WILD-TYPE 
           83.24           148.01 
  SGK269 MUTATED SGK269 WILD-TYPE 
           18.97            22.09 
[1] "6.2 - 83.2 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D163V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGK269 MUTATED         3        0        2        12         0         0
  SGK269 WILD-TYPE      61        1       24        96         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGK269 MUTATED           0          0          1          0        1
  SGK269 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  SGK269 MUTATED           0         0
  SGK269 WILD-TYPE        12         1
D163V3, multiclass
            clus
vv           SGK269 MUTATED SGK269 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              12               96
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  SGK269 MUTATED     0   3  16   1
  SGK269 WILD-TYPE   9  64 233  40
D163V4, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             16              233
  T4              1               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
  SGK269 MUTATED    18   2   0
  SGK269 WILD-TYPE 202  79  66
D163V5, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  N0             18              202
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V6, binary
                  cls
clus                 0   1
  SGK269 MUTATED    18   1
  SGK269 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     18    1
  SGK269 WILD-TYPE  267   47
   clus
vv  SGK269 MUTATED SGK269 WILD-TYPE
  0             18              267
  1              1               47
[1] 2 2
[1] FALSE
D163V7, binary
                  cls
clus                 0   1
  SGK269 MUTATED     9  11
  SGK269 WILD-TYPE 161 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED      9   11
  SGK269 WILD-TYPE  161  186
        clus
vv       SGK269 MUTATED SGK269 WILD-TYPE
  FEMALE              9              161
  MALE               11              186
[1] 2 2
[1] FALSE
D163V8, binary
                  cls
clus                 0   1
  SGK269 MUTATED    19   0
  SGK269 WILD-TYPE 281   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     19    0
  SGK269 WILD-TYPE  281    8
     clus
vv    SGK269 MUTATED SGK269 WILD-TYPE
  NO              19              281
  YES              0                8
[1] 2 2
[1] FALSE
D163V9, binary
                  cls
clus                 0   1
  SGK269 MUTATED    17   3
  SGK269 WILD-TYPE 297  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     17    3
  SGK269 WILD-TYPE  297   45
                               clus
vv                              SGK269 MUTATED SGK269 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SGK269 MUTATED    15   0   0   2
  SGK269 WILD-TYPE 244   3  22  19
D163V10, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              2               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"
D163V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGK269 MUTATED                                  0     3
  SGK269 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SGK269 MUTATED                           3    12
  SGK269 WILD-TYPE                        16   164
D163V12, multiclass
                                  clus
vv                                 SGK269 MUTATED SGK269 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        12              164
[1] 4 2
[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 = CLSPN MUTATION ANALYSIS
D164V1, survival
                 sevent
clus2               0   1
  CLSPN MUTATED    23   6
  CLSPN WILD-TYPE 254  72
  CLSPN MUTATED CLSPN WILD-TYPE 
             29             326 
  CLSPN MUTATED CLSPN WILD-TYPE 
              6              72 
$`CLSPN MUTATED`
TCGA-AA-3496 TCGA-G4-6586 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6782 
        1.02        35.80         8.38        25.08        21.76        20.28 
TCGA-AA-3664 TCGA-AA-A00A TCGA-AA-A02J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 
       54.02        38.04         5.03        58.39        49.41        12.10 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-CM-6166 
       12.59        12.20        12.76       148.01        22.98        21.99 
TCGA-CM-6678 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A282 
       11.01        17.13        16.14        12.00       119.70       139.17 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6809 TCGA-G4-6626 
       31.96        35.74        47.87        13.25        46.75 

$`CLSPN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21         6.77        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6167 TCGA-CM-6168 
       12.00        14.04        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 
       43.27        15.12        17.85         4.80        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-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        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

  CLSPN MUTATED CLSPN WILD-TYPE 
           1.02            0.00 
  CLSPN MUTATED CLSPN WILD-TYPE 
         148.01          140.38 
  CLSPN MUTATED CLSPN WILD-TYPE 
         21.990          22.075 
[1] "1.0 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.3"
D164V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLSPN MUTATED         3        0        3        12         1         0
  CLSPN WILD-TYPE      61        1       23        96         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLSPN MUTATED           1          0          4          1        2         3
  CLSPN WILD-TYPE        17          6         40         32       33         9
                 vv
clus              STAGE IVB
  CLSPN MUTATED           0
  CLSPN WILD-TYPE         1
D164V3, multiclass
            clus
vv           CLSPN MUTATED CLSPN WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             12              96
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              3               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
  CLSPN MUTATED     0   3  23   4
  CLSPN WILD-TYPE   9  64 226  37
D164V4, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  T1             0               9
  T2             3              64
  T3            23             226
  T4             4              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
  CLSPN MUTATED    20   8   2
  CLSPN WILD-TYPE 200  73  64
D164V5, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  N0            20             200
  N1             8              73
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V6, binary
                 cls
clus                0   1
  CLSPN MUTATED    22   5
  CLSPN WILD-TYPE 263  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     22    5
  CLSPN WILD-TYPE  263   43
   clus
vv  CLSPN MUTATED CLSPN WILD-TYPE
  0            22             263
  1             5              43
[1] 2 2
[1] FALSE
D164V7, binary
                 cls
clus                0   1
  CLSPN MUTATED    16  14
  CLSPN WILD-TYPE 154 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     16   14
  CLSPN WILD-TYPE  154  183
        clus
vv       CLSPN MUTATED CLSPN WILD-TYPE
  FEMALE            16             154
  MALE              14             183
[1] 2 2
[1] FALSE
D164V8, binary
                 cls
clus                0   1
  CLSPN MUTATED    25   0
  CLSPN WILD-TYPE 275   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     25    0
  CLSPN WILD-TYPE  275    8
     clus
vv    CLSPN MUTATED CLSPN WILD-TYPE
  NO             25             275
  YES             0               8
[1] 2 2
[1] FALSE
D164V9, binary
                 cls
clus                0   1
  CLSPN MUTATED    28   2
  CLSPN WILD-TYPE 286  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     28    2
  CLSPN WILD-TYPE  286   46
                               clus
vv                              CLSPN MUTATED CLSPN WILD-TYPE
  COLON ADENOCARCINOMA                     28             286
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLSPN MUTATED    19   0   1   2
  CLSPN WILD-TYPE 240   3  21  19
D164V10, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  R0            19             240
  R1             0               3
  R2             1              21
  RX             2              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"
D164V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLSPN MUTATED                                  0     3
  CLSPN WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLSPN MUTATED                           2    20
  CLSPN WILD-TYPE                        17   156
D164V12, multiclass
                                  clus
vv                                 CLSPN MUTATED CLSPN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       20             156
[1] 4 2
[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 = LATS1 MUTATION ANALYSIS
D165V1, survival
                 sevent
clus2               0   1
  LATS1 MUTATED     7  10
  LATS1 WILD-TYPE 270  68
  LATS1 MUTATED LATS1 WILD-TYPE 
             17             338 
  LATS1 MUTATED LATS1 WILD-TYPE 
             10              68 
$`LATS1 MUTATED`
TCGA-AA-3516 TCGA-AD-6964 TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-2676 TCGA-AA-3492 
       13.02        10.88        22.09        26.17        42.90         3.02 
TCGA-AA-3681 TCGA-AA-A00N TCGA-AA-A02H TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-4950 
        5.98         4.01         2.01        83.24        49.41        85.45 
TCGA-CK-5916 TCGA-CM-6168 TCGA-D5-6536 TCGA-DM-A1HB TCGA-F4-6570 
       21.14        12.99        17.85       135.65         6.18 

$`LATS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LATS1 MUTATED LATS1 WILD-TYPE 
           2.01            0.00 
  LATS1 MUTATED LATS1 WILD-TYPE 
         135.65          148.01 
  LATS1 MUTATED LATS1 WILD-TYPE 
         17.850          22.225 
[1] "2.0 - 135.7 (17.9)" "0.0 - 148.0 (22.2)"
[1] "hr=" "2.7"
D165V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LATS1 MUTATED         1        0        2         6         2         0
  LATS1 WILD-TYPE      63        1       24       102         6         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        15          6         42         33       34        12
                 vv
clus              STAGE IVB
  LATS1 MUTATED           0
  LATS1 WILD-TYPE         1
D165V3, multiclass
            clus
vv           LATS1 MUTATED LATS1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  LATS1 MUTATED     1   1  13   3
  LATS1 WILD-TYPE   8  66 236  38
D165V4, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            13             236
  T4             3              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
  LATS1 MUTATED    11   4   3
  LATS1 WILD-TYPE 209  77  63
D165V5, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  N0            11             209
  N1             4              77
  N2             3              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"
D165V6, binary
                 cls
clus                0   1
  LATS1 MUTATED    14   1
  LATS1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     14    1
  LATS1 WILD-TYPE  271   47
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D165V7, binary
                 cls
clus                0   1
  LATS1 MUTATED    13   5
  LATS1 WILD-TYPE 157 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     13    5
  LATS1 WILD-TYPE  157  192
        clus
vv       LATS1 MUTATED LATS1 WILD-TYPE
  FEMALE            13             157
  MALE               5             192
[1] 2 2
[1] FALSE
D165V8, binary
                 cls
clus                0   1
  LATS1 MUTATED    14   0
  LATS1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     14    0
  LATS1 WILD-TYPE  286    8
     clus
vv    LATS1 MUTATED LATS1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D165V9, binary
                 cls
clus                0   1
  LATS1 MUTATED    14   3
  LATS1 WILD-TYPE 300  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     14    3
  LATS1 WILD-TYPE  300   45
                               clus
vv                              LATS1 MUTATED LATS1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LATS1 MUTATED    11   1   1   1
  LATS1 WILD-TYPE 248   2  21  20
D165V10, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  R0            11             248
  R1             1               2
  R2             1              21
  RX             1              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"
D165V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LATS1 MUTATED                                  0     1
  LATS1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LATS1 MUTATED                           2     9
  LATS1 WILD-TYPE                        17   167
D165V12, multiclass
                                  clus
vv                                 LATS1 MUTATED LATS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(166) Variable = SCD5 MUTATION ANALYSIS
D166V1, survival
                sevent
clus2              0   1
  SCD5 MUTATED     4   3
  SCD5 WILD-TYPE 273  75
  SCD5 MUTATED SCD5 WILD-TYPE 
             7            348 
  SCD5 MUTATED SCD5 WILD-TYPE 
             3             75 
$`SCD5 MUTATED`
TCGA-AD-6964 TCGA-G4-6586 TCGA-AA-3696 TCGA-AA-3710 TCGA-CM-6162 TCGA-DM-A28K 
       10.88        35.80         5.03        26.99        12.00        98.24 
TCGA-G4-6626 
       46.75 

$`SCD5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  SCD5 MUTATED SCD5 WILD-TYPE 
          5.03           0.00 
  SCD5 MUTATED SCD5 WILD-TYPE 
         98.24         148.01 
  SCD5 MUTATED SCD5 WILD-TYPE 
        26.990         22.045 
[1] "5.0 - 98.2 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D166V2, continuous
                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      64        1       26       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCD5 MUTATED           0          0          1          0        1         0
  SCD5 WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  SCD5 MUTATED           0
  SCD5 WILD-TYPE         1
D166V3, multiclass
            clus
vv           SCD5 MUTATED SCD5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  SCD5 MUTATED     0   0   6   1
  SCD5 WILD-TYPE   9  67 243  40
D166V4, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            1             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
  SCD5 MUTATED     4   2   1
  SCD5 WILD-TYPE 216  79  65
D166V5, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  N0            4            216
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V6, binary
                cls
clus               0   1
  SCD5 MUTATED     5   1
  SCD5 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      5    1
  SCD5 WILD-TYPE  280   47
   clus
vv  SCD5 MUTATED SCD5 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D166V7, binary
                cls
clus               0   1
  SCD5 MUTATED     4   3
  SCD5 WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      4    3
  SCD5 WILD-TYPE  166  194
        clus
vv       SCD5 MUTATED SCD5 WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D166V8, binary
                cls
clus               0   1
  SCD5 MUTATED     6   0
  SCD5 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      6    0
  SCD5 WILD-TYPE  294    8
     clus
vv    SCD5 MUTATED SCD5 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D166V9, binary
                cls
clus               0   1
  SCD5 MUTATED     5   2
  SCD5 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      5    2
  SCD5 WILD-TYPE  309   46
                               clus
vv                              SCD5 MUTATED SCD5 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SCD5 MUTATED     4   0   1   0
  SCD5 WILD-TYPE 255   3  21  21
D166V10, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            1             21
  RX            0             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"
D166V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCD5 MUTATED                                  0     0
  SCD5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SCD5 MUTATED                           0     5
  SCD5 WILD-TYPE                        19   171
D166V12, multiclass
                                  clus
vv                                 SCD5 MUTATED SCD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = DDX5 MUTATION ANALYSIS
D167V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     8   1
  DDX5 WILD-TYPE 269  77
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            346 
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             77 
$`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 
       25.48        53.62        13.78 

$`DDX5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       85.48        61.91        36.00        46.75 

  DDX5 MUTATED DDX5 WILD-TYPE 
          2.01           0.00 
  DDX5 MUTATED DDX5 WILD-TYPE 
         53.62         148.01 
  DDX5 MUTATED DDX5 WILD-TYPE 
        13.780         22.225 
[1] "2.0 - 53.6 (13.8)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.4"
D167V2, continuous
                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      63        0       26       106         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX5 MUTATED           0          0          0          0        2         0
  DDX5 WILD-TYPE        18          6         44         33       33        12
                vv
clus             STAGE IVB
  DDX5 MUTATED           0
  DDX5 WILD-TYPE         1
D167V3, multiclass
            clus
vv           DDX5 MUTATED DDX5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  DDX5 MUTATED     0   1   3   4
  DDX5 WILD-TYPE   9  66 246  37
D167V4, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            4             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
  DDX5 MUTATED     8   0   1
  DDX5 WILD-TYPE 212  81  65
D167V5, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V6, binary
                cls
clus               0   1
  DDX5 MUTATED     6   2
  DDX5 WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      6    2
  DDX5 WILD-TYPE  279   46
   clus
vv  DDX5 MUTATED DDX5 WILD-TYPE
  0            6            279
  1            2             46
[1] 2 2
[1] FALSE
D167V7, binary
                cls
clus               0   1
  DDX5 MUTATED     4   5
  DDX5 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      4    5
  DDX5 WILD-TYPE  166  192
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D167V8, binary
                cls
clus               0   1
  DDX5 MUTATED     6   1
  DDX5 WILD-TYPE 294   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      6    1
  DDX5 WILD-TYPE  294    7
     clus
vv    DDX5 MUTATED DDX5 WILD-TYPE
  NO             6            294
  YES            1              7
[1] 2 2
[1] FALSE
D167V9, binary
                cls
clus               0   1
  DDX5 MUTATED     6   3
  DDX5 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      6    3
  DDX5 WILD-TYPE  308   45
                               clus
vv                              DDX5 MUTATED DDX5 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DDX5 MUTATED     5   0   2   1
  DDX5 WILD-TYPE 254   3  20  20
D167V10, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            2             20
  RX            1             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"
D167V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX5 MUTATED                                  0     1
  DDX5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DDX5 MUTATED                           1     3
  DDX5 WILD-TYPE                        18   173
D167V12, multiclass
                                  clus
vv                                 DDX5 MUTATED DDX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = TAF7L MUTATION ANALYSIS
D168V1, survival
                 sevent
clus2               0   1
  TAF7L MUTATED     8   3
  TAF7L WILD-TYPE 269  75
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             344 
  TAF7L MUTATED TAF7L WILD-TYPE 
              3              75 
$`TAF7L MUTATED`
TCGA-A6-4105 TCGA-G4-6321 TCGA-A6-5665 TCGA-AA-3875 TCGA-AA-A010 TCGA-CM-4743 
       14.53        22.09        22.06        18.05        34.98        23.05 
TCGA-D5-6929 TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 
       13.41         6.18        65.85        44.68        85.48 

$`TAF7L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
      133.18        74.56        53.62        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TAF7L MUTATED TAF7L WILD-TYPE 
           6.18            0.00 
  TAF7L MUTATED TAF7L WILD-TYPE 
          85.48          148.01 
  TAF7L MUTATED TAF7L WILD-TYPE 
          22.09           22.01 
[1] "6.2 - 85.5 (22.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D168V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF7L MUTATED         1        0        0         4         1         0
  TAF7L WILD-TYPE      63        1       26       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF7L MUTATED           1          0          1          0        2         0
  TAF7L WILD-TYPE        17          6         43         33       33        12
                 vv
clus              STAGE IVB
  TAF7L MUTATED           0
  TAF7L WILD-TYPE         1
D168V3, multiclass
            clus
vv           TAF7L MUTATED TAF7L WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  TAF7L MUTATED     1   2   7   1
  TAF7L WILD-TYPE   8  65 242  40
D168V4, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             1              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
  TAF7L MUTATED     7   4   0
  TAF7L WILD-TYPE 213  77  66
D168V5, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  N0             7             213
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V6, binary
                 cls
clus                0   1
  TAF7L MUTATED     8   2
  TAF7L WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      8    2
  TAF7L WILD-TYPE  277   46
   clus
vv  TAF7L MUTATED TAF7L WILD-TYPE
  0             8             277
  1             2              46
[1] 2 2
[1] FALSE
D168V7, binary
                 cls
clus                0   1
  TAF7L MUTATED     8   3
  TAF7L WILD-TYPE 162 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      8    3
  TAF7L WILD-TYPE  162  194
        clus
vv       TAF7L MUTATED TAF7L WILD-TYPE
  FEMALE             8             162
  MALE               3             194
[1] 2 2
[1] FALSE
D168V8, binary
                 cls
clus                0   1
  TAF7L MUTATED    11   0
  TAF7L WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     11    0
  TAF7L WILD-TYPE  289    8
     clus
vv    TAF7L MUTATED TAF7L WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D168V9, binary
                 cls
clus                0   1
  TAF7L MUTATED    11   0
  TAF7L WILD-TYPE 303  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     11    0
  TAF7L WILD-TYPE  303   48
                               clus
vv                              TAF7L MUTATED TAF7L WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAF7L MUTATED    10   0   0   0
  TAF7L WILD-TYPE 249   3  22  21
D168V10, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D168V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF7L MUTATED                                  0     0
  TAF7L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAF7L MUTATED                           1     8
  TAF7L WILD-TYPE                        18   168
D168V12, multiclass
                                  clus
vv                                 TAF7L MUTATED TAF7L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = ERBB4 MUTATION ANALYSIS
D169V1, survival
                 sevent
clus2               0   1
  ERBB4 MUTATED    35  13
  ERBB4 WILD-TYPE 242  65
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             48             307 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             13              65 
$`ERBB4 MUTATED`
TCGA-A6-6649 TCGA-AA-3713 TCGA-AA-3870 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AZ-6608 
       24.16        19.04        29.98        25.08       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6137 
        5.88        26.17        46.65        30.44        22.06        27.09 
TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3850 TCGA-AA-3861 TCGA-AA-3864 
       63.98        33.04         0.99         0.00        30.05        53.00 
TCGA-AA-3875 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 
       18.05        33.01         2.01        27.02         4.01        34.98 
TCGA-AA-A01Q TCGA-AD-6899 TCGA-AY-4071 TCGA-AZ-4616 TCGA-CA-6717 TCGA-CK-4948 
        1.02         5.79         0.95         5.13        12.76       148.01 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       23.05        15.02        14.04        14.99        12.99        15.02 
TCGA-CM-6172 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6928 
       11.01        54.61        56.09        15.58         7.53        11.64 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6703 
       11.38         7.50        44.32       117.07         8.61        47.87 

$`ERBB4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
       15.52        10.88       106.75        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        22.52         8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        17.03        10.06        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09        16.31        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82        58.39         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.20        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        25.48        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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ERBB4 MUTATED ERBB4 WILD-TYPE 
              0               0 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
         148.01          140.38 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
         18.545          22.090 
[1] "0.0 - 148.0 (18.5)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.3"
D169V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB4 MUTATED         7        0        4        18         4         0
  ERBB4 WILD-TYPE      57        1       22        90         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB4 MUTATED           1          1          8          4        4         0
  ERBB4 WILD-TYPE        17          5         36         29       31        12
                 vv
clus              STAGE IVB
  ERBB4 MUTATED           0
  ERBB4 WILD-TYPE         1
D169V3, multiclass
            clus
vv           ERBB4 MUTATED ERBB4 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             18              90
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             8              36
  STAGE IIIC             4              29
  STAGE IV               4              31
  STAGE IVA              0              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
  ERBB4 MUTATED     3   5  38   5
  ERBB4 WILD-TYPE   6  62 211  36
D169V4, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  T1             3               6
  T2             5              62
  T3            38             211
  T4             5              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
  ERBB4 MUTATED    34   9   8
  ERBB4 WILD-TYPE 186  72  58
D169V5, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  N0            34             186
  N1             9              72
  N2             8              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"
D169V6, binary
                 cls
clus                0   1
  ERBB4 MUTATED    44   4
  ERBB4 WILD-TYPE 241  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     44    4
  ERBB4 WILD-TYPE  241   44
   clus
vv  ERBB4 MUTATED ERBB4 WILD-TYPE
  0            44             241
  1             4              44
[1] 2 2
[1] FALSE
D169V7, binary
                 cls
clus                0   1
  ERBB4 MUTATED    28  23
  ERBB4 WILD-TYPE 142 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     28   23
  ERBB4 WILD-TYPE  142  174
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  FEMALE            28             142
  MALE              23             174
[1] 2 2
[1] FALSE
D169V8, binary
                 cls
clus                0   1
  ERBB4 MUTATED    37   1
  ERBB4 WILD-TYPE 263   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     37    1
  ERBB4 WILD-TYPE  263    7
     clus
vv    ERBB4 MUTATED ERBB4 WILD-TYPE
  NO             37             263
  YES             1               7
[1] 2 2
[1] FALSE
D169V9, binary
                 cls
clus                0   1
  ERBB4 MUTATED    43   7
  ERBB4 WILD-TYPE 271  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     43    7
  ERBB4 WILD-TYPE  271   41
                               clus
vv                              ERBB4 MUTATED ERBB4 WILD-TYPE
  COLON ADENOCARCINOMA                     43             271
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB4 MUTATED    36   0   1   2
  ERBB4 WILD-TYPE 223   3  21  19
D169V10, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  R0            36             223
  R1             0               3
  R2             1              21
  RX             2              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"
D169V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB4 MUTATED                                  0     1
  ERBB4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB4 MUTATED                           2    31
  ERBB4 WILD-TYPE                        17   145
D169V12, multiclass
                                  clus
vv                                 ERBB4 MUTATED ERBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       31             145
[1] 4 2
[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 = HNF1B MUTATION ANALYSIS
D170V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     6   3
  HNF1B WILD-TYPE 271  75
  HNF1B MUTATED HNF1B WILD-TYPE 
              9             346 
  HNF1B MUTATED HNF1B WILD-TYPE 
              3              75 
$`HNF1B MUTATED`
TCGA-A6-4105 TCGA-G4-6586 TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3819 TCGA-AD-6889 
       14.53        35.80        32.91         8.38        25.02        83.24 
TCGA-AD-6899 TCGA-AD-6965 TCGA-D5-6540 
        5.79        26.47        16.14 

$`HNF1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        31.63        30.44        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6901 
       39.98        18.05        40.96        12.16        24.53        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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  HNF1B MUTATED HNF1B WILD-TYPE 
           5.79            0.00 
  HNF1B MUTATED HNF1B WILD-TYPE 
          83.24          148.01 
  HNF1B MUTATED HNF1B WILD-TYPE 
         25.020          22.045 
[1] "5.8 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D170V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HNF1B MUTATED         2        0        0         5         0         0
  HNF1B WILD-TYPE      62        1       26       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HNF1B MUTATED           0          0          0          2        0         0
  HNF1B WILD-TYPE        18          6         44         31       35        12
                 vv
clus              STAGE IVB
  HNF1B MUTATED           0
  HNF1B WILD-TYPE         1
D170V3, multiclass
            clus
vv           HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  HNF1B MUTATED     0   2   5   2
  HNF1B WILD-TYPE   9  65 244  39
D170V4, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             2              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
  HNF1B MUTATED     7   0   2
  HNF1B WILD-TYPE 213  81  64
D170V5, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  N0             7             213
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     8   0
  HNF1B WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      8    0
  HNF1B WILD-TYPE  277   48
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D170V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     2   7
  HNF1B WILD-TYPE 168 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      2    7
  HNF1B WILD-TYPE  168  190
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             2             168
  MALE               7             190
[1] 2 2
[1] FALSE
D170V8, binary
                 cls
clus                0   1
  HNF1B MUTATED     9   0
  HNF1B WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      9    0
  HNF1B WILD-TYPE  291    8
     clus
vv    HNF1B MUTATED HNF1B WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D170V9, binary
                 cls
clus                0   1
  HNF1B MUTATED     7   2
  HNF1B WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      7    2
  HNF1B WILD-TYPE  307   46
                               clus
vv                              HNF1B MUTATED HNF1B WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HNF1B MUTATED     4   1   0   0
  HNF1B WILD-TYPE 255   2  22  21
D170V10, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  R0             4             255
  R1             1               2
  R2             0              22
  RX             0              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"
D170V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1B MUTATED                                  0     1
  HNF1B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1B MUTATED                           1     6
  HNF1B WILD-TYPE                        18   170
D170V12, multiclass
                                  clus
vv                                 HNF1B MUTATED HNF1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = OR7C2 MUTATION ANALYSIS
D171V1, survival
                 sevent
clus2               0   1
  OR7C2 MUTATED     9   1
  OR7C2 WILD-TYPE 268  77
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             10             345 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
              1              77 
$`OR7C2 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6781 TCGA-AA-A010 TCGA-AU-3779 
       24.00       100.01        26.17        19.66        34.98        14.50 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-5540 TCGA-D5-6926 
       88.21        12.76        56.09         9.04 

$`OR7C2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  OR7C2 MUTATED OR7C2 WILD-TYPE 
           9.04            0.00 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
         100.01          148.01 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
         25.085          22.030 
[1] "9.0 - 100.0 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.1"
D171V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR7C2 MUTATED         1        0        1         5         1         0
  OR7C2 WILD-TYPE      63        1       25       103         7         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  OR7C2 MUTATED           0
  OR7C2 WILD-TYPE         1
D171V3, multiclass
            clus
vv           OR7C2 MUTATED OR7C2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OR7C2 MUTATED     1   0   6   3
  OR7C2 WILD-TYPE   8  67 243  38
D171V4, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             6             243
  T4             3              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
  OR7C2 MUTATED     8   2   0
  OR7C2 WILD-TYPE 212  79  66
D171V5, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V6, binary
                 cls
clus                0   1
  OR7C2 MUTATED     9   0
  OR7C2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      9    0
  OR7C2 WILD-TYPE  276   48
   clus
vv  OR7C2 MUTATED OR7C2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D171V7, binary
                 cls
clus                0   1
  OR7C2 MUTATED     5   5
  OR7C2 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      5    5
  OR7C2 WILD-TYPE  165  192
        clus
vv       OR7C2 MUTATED OR7C2 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D171V8, binary
                 cls
clus                0   1
  OR7C2 MUTATED     9   1
  OR7C2 WILD-TYPE 291   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      9    1
  OR7C2 WILD-TYPE  291    7
     clus
vv    OR7C2 MUTATED OR7C2 WILD-TYPE
  NO              9             291
  YES             1               7
[1] 2 2
[1] FALSE
D171V9, binary
                 cls
clus                0   1
  OR7C2 MUTATED     7   3
  OR7C2 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      7    3
  OR7C2 WILD-TYPE  307   45
                               clus
vv                              OR7C2 MUTATED OR7C2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR7C2 MUTATED     7   0   0   1
  OR7C2 WILD-TYPE 252   3  22  20
D171V10, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D171V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR7C2 MUTATED                                  0     1
  OR7C2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR7C2 MUTATED                           0     7
  OR7C2 WILD-TYPE                        19   169
D171V12, multiclass
                                  clus
vv                                 OR7C2 MUTATED OR7C2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = KLHL10 MUTATION ANALYSIS
D172V1, survival
                  sevent
clus2                0   1
  KLHL10 MUTATED    12   6
  KLHL10 WILD-TYPE 265  72
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              18              337 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
               6               72 
$`KLHL10 MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-5659 TCGA-A6-5660 
       10.88       100.01         1.94        26.17        30.44        29.19 
TCGA-AA-3663 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-CA-6718 TCGA-CM-4743 
        6.97        27.09         0.20        21.44        10.06        23.05 
TCGA-CM-5868 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6928 TCGA-DM-A1D4 TCGA-G4-6626 
       17.03        25.48        15.12        11.64        92.75        46.75 

$`KLHL10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5661 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  KLHL10 MUTATED KLHL10 WILD-TYPE 
             0.2              0.0 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
          100.01           148.01 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
          22.245           22.060 
[1] "0.2 - 100.0 (22.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D172V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLHL10 MUTATED         2        0        2         7         0         0
  KLHL10 WILD-TYPE      62        1       24       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL10 MUTATED           0          1          1          2        1
  KLHL10 WILD-TYPE        18          5         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  KLHL10 MUTATED           1         0
  KLHL10 WILD-TYPE        11         1
D172V3, multiclass
            clus
vv           KLHL10 MUTATED KLHL10 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               1               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
  KLHL10 MUTATED     0   3  13   3
  KLHL10 WILD-TYPE   9  64 236  38
D172V4, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             13              236
  T4              3               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
  KLHL10 MUTATED    12   3   4
  KLHL10 WILD-TYPE 208  78  62
D172V5, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  N0             12              208
  N1              3               78
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V6, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    13   2
  KLHL10 WILD-TYPE 272  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     13    2
  KLHL10 WILD-TYPE  272   46
   clus
vv  KLHL10 MUTATED KLHL10 WILD-TYPE
  0             13              272
  1              2               46
[1] 2 2
[1] FALSE
D172V7, binary
                  cls
clus                 0   1
  KLHL10 MUTATED     7  12
  KLHL10 WILD-TYPE 163 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED      7   12
  KLHL10 WILD-TYPE  163  185
        clus
vv       KLHL10 MUTATED KLHL10 WILD-TYPE
  FEMALE              7              163
  MALE               12              185
[1] 2 2
[1] FALSE
D172V8, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    15   0
  KLHL10 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     15    0
  KLHL10 WILD-TYPE  285    8
     clus
vv    KLHL10 MUTATED KLHL10 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D172V9, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    17   2
  KLHL10 WILD-TYPE 297  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     17    2
  KLHL10 WILD-TYPE  297   46
                               clus
vv                              KLHL10 MUTATED KLHL10 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KLHL10 MUTATED    11   0   1   2
  KLHL10 WILD-TYPE 248   3  21  19
D172V10, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              1               21
  RX              2               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"
D172V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHL10 MUTATED                                  0     1
  KLHL10 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KLHL10 MUTATED                           1    15
  KLHL10 WILD-TYPE                        18   161
D172V12, multiclass
                                  clus
vv                                 KLHL10 MUTATED KLHL10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        15              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(173) Variable = FBLN5 MUTATION ANALYSIS
D173V1, survival
                 sevent
clus2               0   1
  FBLN5 MUTATED     4   4
  FBLN5 WILD-TYPE 273  74
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              8             347 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              4              74 
$`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 
       44.32        46.75 

$`FBLN5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
      140.38         7.50       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        43.04        33.67        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 
       55.04        85.48        61.91        36.00        13.78 

  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           21.99 
[1] "12.8 - 88.2 (41.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D173V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBLN5 MUTATED         1        0        1         3         0         0
  FBLN5 WILD-TYPE      63        1       25       105         8         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        18          6         44         31       35        11
                 vv
clus              STAGE IVB
  FBLN5 MUTATED           0
  FBLN5 WILD-TYPE         1
D173V3, multiclass
            clus
vv           FBLN5 MUTATED FBLN5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              1              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
  FBLN5 MUTATED     1   0   6   1
  FBLN5 WILD-TYPE   8  67 243  40
D173V4, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             6             243
  T4             1              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
  FBLN5 MUTATED     5   1   2
  FBLN5 WILD-TYPE 215  80  64
D173V5, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V6, binary
                 cls
clus                0   1
  FBLN5 MUTATED     6   1
  FBLN5 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      6    1
  FBLN5 WILD-TYPE  279   47
   clus
vv  FBLN5 MUTATED FBLN5 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D173V7, binary
                 cls
clus                0   1
  FBLN5 MUTATED     5   3
  FBLN5 WILD-TYPE 165 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      5    3
  FBLN5 WILD-TYPE  165  194
        clus
vv       FBLN5 MUTATED FBLN5 WILD-TYPE
  FEMALE             5             165
  MALE               3             194
[1] 2 2
[1] FALSE
D173V8, binary
                 cls
clus                0   1
  FBLN5 MUTATED     5   0
  FBLN5 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      5    0
  FBLN5 WILD-TYPE  295    8
     clus
vv    FBLN5 MUTATED FBLN5 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D173V9, binary
                 cls
clus                0   1
  FBLN5 MUTATED     5   2
  FBLN5 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      5    2
  FBLN5 WILD-TYPE  309   46
                               clus
vv                              FBLN5 MUTATED FBLN5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBLN5 MUTATED     2   0   0   2
  FBLN5 WILD-TYPE 257   3  22  19
D173V10, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             2              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"
D173V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBLN5 MUTATED                                  0     1
  FBLN5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBLN5 MUTATED                           1     6
  FBLN5 WILD-TYPE                        18   170
D173V12, multiclass
                                  clus
vv                                 FBLN5 MUTATED FBLN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = GPX6 MUTATION ANALYSIS
D174V1, survival
                sevent
clus2              0   1
  GPX6 MUTATED     5   3
  GPX6 WILD-TYPE 272  75
  GPX6 MUTATED GPX6 WILD-TYPE 
             8            347 
  GPX6 MUTATED GPX6 WILD-TYPE 
             3             75 
$`GPX6 MUTATED`
TCGA-A6-6649 TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-A010 TCGA-CK-5914 
       24.16        79.69        63.98         0.00        34.98        21.99 
TCGA-DM-A1DB TCGA-G4-6303 
       44.32        65.85 

$`GPX6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPX6 MUTATED GPX6 WILD-TYPE 
             0              0 
  GPX6 MUTATED GPX6 WILD-TYPE 
         79.69         148.01 
  GPX6 MUTATED GPX6 WILD-TYPE 
         39.65          21.99 
[1] "0.0 - 79.7 (39.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D174V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPX6 MUTATED         1        0        1         2         2         0
  GPX6 WILD-TYPE      63        1       25       106         6         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        18          6         42         33       34        12
                vv
clus             STAGE IVB
  GPX6 MUTATED           0
  GPX6 WILD-TYPE         1
D174V3, multiclass
            clus
vv           GPX6 MUTATED GPX6 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  GPX6 MUTATED     0   1   6   2
  GPX6 WILD-TYPE   9  66 243  39
D174V4, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            2             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
  GPX6 MUTATED     6   3   0
  GPX6 WILD-TYPE 214  78  66
D174V5, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  N0            6            214
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V6, binary
                cls
clus               0   1
  GPX6 MUTATED     6   1
  GPX6 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      6    1
  GPX6 WILD-TYPE  279   47
   clus
vv  GPX6 MUTATED GPX6 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D174V7, binary
                cls
clus               0   1
  GPX6 MUTATED     4   5
  GPX6 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      4    5
  GPX6 WILD-TYPE  166  192
        clus
vv       GPX6 MUTATED GPX6 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D174V8, binary
                cls
clus               0   1
  GPX6 MUTATED     5   0
  GPX6 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      5    0
  GPX6 WILD-TYPE  295    8
     clus
vv    GPX6 MUTATED GPX6 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D174V9, binary
                cls
clus               0   1
  GPX6 MUTATED     9   0
  GPX6 WILD-TYPE 305  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      9    0
  GPX6 WILD-TYPE  305   48
                               clus
vv                              GPX6 MUTATED GPX6 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GPX6 MUTATED     5   0   0   2
  GPX6 WILD-TYPE 254   3  22  19
D174V10, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            2             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"
D174V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPX6 MUTATED                                  0     0
  GPX6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GPX6 MUTATED                           0     6
  GPX6 WILD-TYPE                        19   170
D174V12, multiclass
                                  clus
vv                                 GPX6 MUTATED GPX6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = PSD MUTATION ANALYSIS
D175V1, survival
               sevent
clus2             0   1
  PSD MUTATED    11   4
  PSD WILD-TYPE 266  74
  PSD MUTATED PSD WILD-TYPE 
           15           340 
  PSD MUTATED PSD WILD-TYPE 
            4            74 
$`PSD MUTATED`
TCGA-AA-3516 TCGA-AZ-4681 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3815 
       13.02       106.75        22.06         6.97         5.03        33.04 
TCGA-AA-A00E TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5860 
       30.02        58.39        12.76        51.32        21.14        32.02 
TCGA-D5-6540 TCGA-DM-A1D8 TCGA-G4-6309 
       16.14        12.59        85.48 

$`PSD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        85.45        15.62        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PSD MUTATED PSD WILD-TYPE 
         5.03          0.00 
  PSD MUTATED PSD WILD-TYPE 
       106.75        148.01 
  PSD MUTATED PSD WILD-TYPE 
        22.06         22.06 
[1] "5.0 - 106.8 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D175V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSD MUTATED         2        0        2         8         0         0
  PSD WILD-TYPE      62        1       24       100         8         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        17          6         43         33       34        12
               vv
clus            STAGE IVB
  PSD MUTATED           0
  PSD WILD-TYPE         1
D175V3, multiclass
            clus
vv           PSD MUTATED PSD WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            8           100
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  PSD MUTATED     1   1  13   1
  PSD WILD-TYPE   8  66 236  40
D175V4, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  T1           1             8
  T2           1            66
  T3          13           236
  T4           1            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
  PSD MUTATED    12   3   1
  PSD WILD-TYPE 208  78  65
D175V5, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  N0          12           208
  N1           3            78
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V6, binary
               cls
clus              0   1
  PSD MUTATED    13   1
  PSD WILD-TYPE 272  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     13    1
  PSD WILD-TYPE  272   47
   clus
vv  PSD MUTATED PSD WILD-TYPE
  0          13           272
  1           1            47
[1] 2 2
[1] FALSE
D175V7, binary
               cls
clus              0   1
  PSD MUTATED    10   6
  PSD WILD-TYPE 160 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     10    6
  PSD WILD-TYPE  160  191
        clus
vv       PSD MUTATED PSD WILD-TYPE
  FEMALE          10           160
  MALE             6           191
[1] 2 2
[1] FALSE
D175V8, binary
               cls
clus              0   1
  PSD MUTATED    14   0
  PSD WILD-TYPE 286   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     14    0
  PSD WILD-TYPE  286    8
     clus
vv    PSD MUTATED PSD WILD-TYPE
  NO           14           286
  YES           0             8
[1] 2 2
[1] FALSE
D175V9, binary
               cls
clus              0   1
  PSD MUTATED    13   3
  PSD WILD-TYPE 301  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     13    3
  PSD WILD-TYPE  301   45
                               clus
vv                              PSD MUTATED PSD WILD-TYPE
  COLON ADENOCARCINOMA                   13           301
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  PSD MUTATED    10   0   1   3
  PSD WILD-TYPE 249   3  21  18
D175V10, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  R0          10           249
  R1           0             3
  R2           1            21
  RX           3            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"
D175V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSD MUTATED                                  0     1
  PSD WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PSD MUTATED                           1     8
  PSD WILD-TYPE                        18   168
D175V12, multiclass
                                  clus
vv                                 PSD MUTATED PSD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      8           168
[1] 4 2
[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 = EP400 MUTATION ANALYSIS
D176V1, survival
                 sevent
clus2               0   1
  EP400 MUTATED    26   8
  EP400 WILD-TYPE 251  70
  EP400 MUTATED EP400 WILD-TYPE 
             34             321 
  EP400 MUTATED EP400 WILD-TYPE 
              8              70 
$`EP400 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6888 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-5661 
        0.92        19.04        15.52        26.17        46.65        33.53 
TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3850 TCGA-AA-3864 
        3.02         6.97        29.95         6.97         0.00        53.00 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R 
       25.02        30.02         4.01        34.98         1.02        35.01 
TCGA-AY-6386 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 TCGA-CM-4752 
       17.82        49.41        15.62        51.32        20.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6898 
       29.06        22.98        30.08        18.25        16.14         7.53 
TCGA-D5-7000 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6809 
       10.26        12.59        44.32        13.25 

$`EP400 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        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-A6-5662 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-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-3861 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56       148.01        85.45        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        23.05        37.02        25.02 
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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        11.38       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-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        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  EP400 MUTATED EP400 WILD-TYPE 
              0               0 
  EP400 MUTATED EP400 WILD-TYPE 
          53.00          148.01 
  EP400 MUTATED EP400 WILD-TYPE 
         18.645          22.090 
[1] "0.0 - 53.0 (18.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D176V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EP400 MUTATED         5        0        6        10         3         0
  EP400 WILD-TYPE      59        1       20        98         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP400 MUTATED           2          1          4          1        1         1
  EP400 WILD-TYPE        16          5         40         32       34        11
                 vv
clus              STAGE IVB
  EP400 MUTATED           0
  EP400 WILD-TYPE         1
D176V3, multiclass
            clus
vv           EP400 MUTATED EP400 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA             10              98
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  EP400 MUTATED     0   7  24   5
  EP400 WILD-TYPE   9  60 225  36
D176V4, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  T1             0               9
  T2             7              60
  T3            24             225
  T4             5              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
  EP400 MUTATED    26   8   2
  EP400 WILD-TYPE 194  73  64
D176V5, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  N0            26             194
  N1             8              73
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V6, binary
                 cls
clus                0   1
  EP400 MUTATED    29   2
  EP400 WILD-TYPE 256  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     29    2
  EP400 WILD-TYPE  256   46
   clus
vv  EP400 MUTATED EP400 WILD-TYPE
  0            29             256
  1             2              46
[1] 2 2
[1] FALSE
D176V7, binary
                 cls
clus                0   1
  EP400 MUTATED    20  16
  EP400 WILD-TYPE 150 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     20   16
  EP400 WILD-TYPE  150  181
        clus
vv       EP400 MUTATED EP400 WILD-TYPE
  FEMALE            20             150
  MALE              16             181
[1] 2 2
[1] FALSE
D176V8, binary
                 cls
clus                0   1
  EP400 MUTATED    26   2
  EP400 WILD-TYPE 274   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     26    2
  EP400 WILD-TYPE  274    6
     clus
vv    EP400 MUTATED EP400 WILD-TYPE
  NO             26             274
  YES             2               6
[1] 2 2
[1] FALSE
D176V9, binary
                 cls
clus                0   1
  EP400 MUTATED    30   6
  EP400 WILD-TYPE 284  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     30    6
  EP400 WILD-TYPE  284   42
                               clus
vv                              EP400 MUTATED EP400 WILD-TYPE
  COLON ADENOCARCINOMA                     30             284
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EP400 MUTATED    28   0   1   3
  EP400 WILD-TYPE 231   3  21  18
D176V10, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  R0            28             231
  R1             0               3
  R2             1              21
  RX             3              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"
D176V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP400 MUTATED                                  0     0
  EP400 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP400 MUTATED                           3    18
  EP400 WILD-TYPE                        16   158
D176V12, multiclass
                                  clus
vv                                 EP400 MUTATED EP400 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       18             158
[1] 4 2
[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 = DHRS7 MUTATION ANALYSIS
D177V1, survival
                 sevent
clus2               0   1
  DHRS7 MUTATED     9   1
  DHRS7 WILD-TYPE 268  77
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             345 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
              1              77 
$`DHRS7 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6781 TCGA-AA-3510 
       24.00       100.01        33.53        23.61        19.66        63.98 
TCGA-AU-6004 TCGA-AY-6197 TCGA-CK-4950 TCGA-CM-6172 
       27.09        21.44        85.45        11.01 

$`DHRS7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        29.19        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          21.990 
[1] "11.0 - 100.0 (25.5)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.3"
D177V2, continuous
                 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      63        1       24       105         8         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        18          6         42         32       35        11
                 vv
clus              STAGE IVB
  DHRS7 MUTATED           0
  DHRS7 WILD-TYPE         1
D177V3, multiclass
            clus
vv           DHRS7 MUTATED DHRS7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  DHRS7 MUTATED     0   1   8   1
  DHRS7 WILD-TYPE   9  66 241  40
D177V4, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             1              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
  DHRS7 MUTATED     6   3   1
  DHRS7 WILD-TYPE 214  78  65
D177V5, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V6, binary
                 cls
clus                0   1
  DHRS7 MUTATED     7   1
  DHRS7 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      7    1
  DHRS7 WILD-TYPE  278   47
   clus
vv  DHRS7 MUTATED DHRS7 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D177V7, binary
                 cls
clus                0   1
  DHRS7 MUTATED     5   5
  DHRS7 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      5    5
  DHRS7 WILD-TYPE  165  192
        clus
vv       DHRS7 MUTATED DHRS7 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D177V8, binary
                 cls
clus                0   1
  DHRS7 MUTATED     9   0
  DHRS7 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      9    0
  DHRS7 WILD-TYPE  291    8
     clus
vv    DHRS7 MUTATED DHRS7 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D177V9, binary
                 cls
clus                0   1
  DHRS7 MUTATED     7   3
  DHRS7 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      7    3
  DHRS7 WILD-TYPE  307   45
                               clus
vv                              DHRS7 MUTATED DHRS7 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHRS7 MUTATED     7   1   0   0
  DHRS7 WILD-TYPE 252   2  22  21
D177V10, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  R0             7             252
  R1             1               2
  R2             0              22
  RX             0              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"
D177V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHRS7 MUTATED                                  0     0
  DHRS7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHRS7 MUTATED                           2     6
  DHRS7 WILD-TYPE                        17   170
D177V12, multiclass
                                  clus
vv                                 DHRS7 MUTATED DHRS7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        6             170
[1] 4 2
[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 = ZNF486 MUTATION ANALYSIS
D178V1, survival
                  sevent
clus2                0   1
  ZNF486 MUTATED     6   5
  ZNF486 WILD-TYPE 271  73
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              11              344 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
               5               73 
$`ZNF486 MUTATED`
TCGA-A6-4105 TCGA-AD-6895 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6588 TCGA-A6-5661 
       14.53        25.08        49.08         5.88        26.17        33.53 
TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-A01P TCGA-CM-5861 TCGA-DM-A0XD 
       53.00        26.01        38.07        15.02        24.43 

$`ZNF486 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        1.94        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ZNF486 MUTATED ZNF486 WILD-TYPE 
            5.88             0.00 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
           53.00           148.01 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
           26.01            21.99 
[1] "5.9 - 53.0 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D178V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF486 MUTATED         1        0        1         5         1         0
  ZNF486 WILD-TYPE      63        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF486 MUTATED           1          0          2          0        1
  ZNF486 WILD-TYPE        17          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF486 MUTATED           0         0
  ZNF486 WILD-TYPE        12         1
D178V3, multiclass
            clus
vv           ZNF486 MUTATED ZNF486 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF486 MUTATED     0   1  10   1
  ZNF486 WILD-TYPE   9  66 239  40
D178V4, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             10              239
  T4              1               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
  ZNF486 MUTATED     8   3   1
  ZNF486 WILD-TYPE 212  78  65
D178V5, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  N0              8              212
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V6, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     9   1
  ZNF486 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      9    1
  ZNF486 WILD-TYPE  276   47
   clus
vv  ZNF486 MUTATED ZNF486 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D178V7, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     7   5
  ZNF486 WILD-TYPE 163 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      7    5
  ZNF486 WILD-TYPE  163  192
        clus
vv       ZNF486 MUTATED ZNF486 WILD-TYPE
  FEMALE              7              163
  MALE                5              192
[1] 2 2
[1] FALSE
D178V8, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     9   0
  ZNF486 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      9    0
  ZNF486 WILD-TYPE  291    8
     clus
vv    ZNF486 MUTATED ZNF486 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D178V9, binary
                  cls
clus                 0   1
  ZNF486 MUTATED    10   2
  ZNF486 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED     10    2
  ZNF486 WILD-TYPE  304   46
                               clus
vv                              ZNF486 MUTATED ZNF486 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF486 MUTATED     7   0   0   2
  ZNF486 WILD-TYPE 252   3  22  19
D178V10, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D178V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF486 MUTATED                                  0     0
  ZNF486 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF486 MUTATED                           1     8
  ZNF486 WILD-TYPE                        18   168
D178V12, multiclass
                                  clus
vv                                 ZNF486 MUTATED ZNF486 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = CLEC4F MUTATION ANALYSIS
D179V1, survival
                  sevent
clus2                0   1
  CLEC4F MUTATED    15   4
  CLEC4F WILD-TYPE 262  74
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              19              336 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
               4               74 
$`CLEC4F MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3534 
       19.04        10.88        26.17        24.39        63.98        29.00 
TCGA-AA-3864 TCGA-AA-A00N TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       53.00         4.01        12.16        33.01        17.82        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4752 TCGA-D5-6529 TCGA-D5-6532 
       12.76        10.06        23.05        13.02        20.19        18.25 
TCGA-DM-A28C 
       81.37 

$`CLEC4F WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        21.44 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4744 
       21.99        21.14        82.95         2.01       124.27        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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CLEC4F MUTATED CLEC4F WILD-TYPE 
            4.01             0.00 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
           81.37           148.01 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
          20.190           22.075 
[1] "4.0 - 81.4 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D179V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLEC4F MUTATED         2        0        2        10         1         0
  CLEC4F WILD-TYPE      62        1       24        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLEC4F MUTATED           0          0          1          0        1
  CLEC4F WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CLEC4F MUTATED           1         0
  CLEC4F WILD-TYPE        11         1
D179V3, multiclass
            clus
vv           CLEC4F MUTATED CLEC4F WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              10               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  CLEC4F MUTATED     0   2  15   2
  CLEC4F WILD-TYPE   9  65 234  39
D179V4, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  T1              0                9
  T2              2               65
  T3             15              234
  T4              2               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
  CLEC4F MUTATED    16   2   1
  CLEC4F WILD-TYPE 204  79  65
D179V5, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  N0             16              204
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V6, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    15   2
  CLEC4F WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     15    2
  CLEC4F WILD-TYPE  270   46
   clus
vv  CLEC4F MUTATED CLEC4F WILD-TYPE
  0             15              270
  1              2               46
[1] 2 2
[1] FALSE
D179V7, binary
                  cls
clus                 0   1
  CLEC4F MUTATED     4  15
  CLEC4F WILD-TYPE 166 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED      4   15
  CLEC4F WILD-TYPE  166  182
        clus
vv       CLEC4F MUTATED CLEC4F WILD-TYPE
  FEMALE              4              166
  MALE               15              182
[1] 2 2
[1] FALSE
D179V8, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    16   1
  CLEC4F WILD-TYPE 284   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     16    1
  CLEC4F WILD-TYPE  284    7
     clus
vv    CLEC4F MUTATED CLEC4F WILD-TYPE
  NO              16              284
  YES              1                7
[1] 2 2
[1] FALSE
D179V9, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    16   3
  CLEC4F WILD-TYPE 298  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     16    3
  CLEC4F WILD-TYPE  298   45
                               clus
vv                              CLEC4F MUTATED CLEC4F WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLEC4F MUTATED    13   0   1   2
  CLEC4F WILD-TYPE 246   3  21  19
D179V10, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  R0             13              246
  R1              0                3
  R2              1               21
  RX              2               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"
D179V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLEC4F MUTATED                                  0     2
  CLEC4F WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLEC4F MUTATED                           3     9
  CLEC4F WILD-TYPE                        16   167
D179V12, multiclass
                                  clus
vv                                 CLEC4F MUTATED CLEC4F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         9              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(180) Variable = MMP13 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2               0   1
  MMP13 MUTATED     9   4
  MMP13 WILD-TYPE 268  74
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             342 
  MMP13 MUTATED MMP13 WILD-TYPE 
              4              74 
$`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 
        6.18 

$`MMP13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       10.06        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MMP13 MUTATED MMP13 WILD-TYPE 
           6.18            0.00 
  MMP13 MUTATED MMP13 WILD-TYPE 
          49.41          148.01 
  MMP13 MUTATED MMP13 WILD-TYPE 
         21.140          22.075 
[1] "6.2 - 49.4 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D180V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP13 MUTATED         1        0        1         5         1         0
  MMP13 WILD-TYPE      63        1       25       103         7         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        18          5         40         33       35        12
                 vv
clus              STAGE IVB
  MMP13 MUTATED           0
  MMP13 WILD-TYPE         1
D180V3, multiclass
            clus
vv           MMP13 MUTATED MMP13 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MMP13 MUTATED     1   0  11   1
  MMP13 WILD-TYPE   8  67 238  40
D180V4, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  T1             1               8
  T2             0              67
  T3            11             238
  T4             1              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
  MMP13 MUTATED     8   4   1
  MMP13 WILD-TYPE 212  77  65
D180V5, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V6, binary
                 cls
clus                0   1
  MMP13 MUTATED    12   0
  MMP13 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     12    0
  MMP13 WILD-TYPE  273   48
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D180V7, binary
                 cls
clus                0   1
  MMP13 MUTATED     8   5
  MMP13 WILD-TYPE 162 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      8    5
  MMP13 WILD-TYPE  162  192
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             8             162
  MALE               5             192
[1] 2 2
[1] FALSE
D180V8, binary
                 cls
clus                0   1
  MMP13 MUTATED    12   0
  MMP13 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     12    0
  MMP13 WILD-TYPE  288    8
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D180V9, binary
                 cls
clus                0   1
  MMP13 MUTATED    10   3
  MMP13 WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     10    3
  MMP13 WILD-TYPE  304   45
                               clus
vv                              MMP13 MUTATED MMP13 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MMP13 MUTATED     7   0   0   3
  MMP13 WILD-TYPE 252   3  22  18
D180V10, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             3              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"
D180V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP13 MUTATED                                  0     2
  MMP13 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED                           0     9
  MMP13 WILD-TYPE                        19   167
D180V12, multiclass
                                  clus
vv                                 MMP13 MUTATED MMP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(181) Variable = KRT2 MUTATION ANALYSIS
D181V1, survival
                sevent
clus2              0   1
  KRT2 MUTATED    13   0
  KRT2 WILD-TYPE 264  78
  KRT2 MUTATED KRT2 WILD-TYPE 
            13            342 
  KRT2 MUTATED KRT2 WILD-TYPE 
             0             78 
$`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        12.39         9.04       119.70 
TCGA-DM-A28K 
       98.24 

$`KRT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        10.06        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        7.53        10.13        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-A0XD 
       13.41        13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  KRT2 MUTATED KRT2 WILD-TYPE 
          6.97           0.00 
  KRT2 MUTATED KRT2 WILD-TYPE 
        119.70         148.01 
  KRT2 MUTATED KRT2 WILD-TYPE 
         16.14          22.39 
[1] "7.0 - 119.7 (16.1)" "0.0 - 148.0 (22.4)"
[1] "hr="     "2.6e+07"
D181V2, continuous
                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      62        1       25       100         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT2 MUTATED           0          0          1          1        0         1
  KRT2 WILD-TYPE        18          6         43         32       35        11
                vv
clus             STAGE IVB
  KRT2 MUTATED           0
  KRT2 WILD-TYPE         1
D181V3, multiclass
            clus
vv           KRT2 MUTATED KRT2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  KRT2 MUTATED     0   2   8   4
  KRT2 WILD-TYPE   9  65 241  37
D181V4, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            4             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
  KRT2 MUTATED    11   3   0
  KRT2 WILD-TYPE 209  78  66
D181V5, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  N0           11            209
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V6, binary
                cls
clus               0   1
  KRT2 MUTATED    12   1
  KRT2 WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     12    1
  KRT2 WILD-TYPE  273   47
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D181V7, binary
                cls
clus               0   1
  KRT2 MUTATED     5   9
  KRT2 WILD-TYPE 165 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      5    9
  KRT2 WILD-TYPE  165  188
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  FEMALE            5            165
  MALE              9            188
[1] 2 2
[1] FALSE
D181V8, binary
                cls
clus               0   1
  KRT2 MUTATED    10   1
  KRT2 WILD-TYPE 290   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     10    1
  KRT2 WILD-TYPE  290    7
     clus
vv    KRT2 MUTATED KRT2 WILD-TYPE
  NO            10            290
  YES            1              7
[1] 2 2
[1] FALSE
D181V9, binary
                cls
clus               0   1
  KRT2 MUTATED    10   4
  KRT2 WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     10    4
  KRT2 WILD-TYPE  304   44
                               clus
vv                              KRT2 MUTATED KRT2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRT2 MUTATED     9   0   0   2
  KRT2 WILD-TYPE 250   3  22  19
D181V10, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            2             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"
D181V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT2 MUTATED                                  0     2
  KRT2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT2 MUTATED                           0    10
  KRT2 WILD-TYPE                        19   166
D181V12, multiclass
                                  clus
vv                                 KRT2 MUTATED KRT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(182) Variable = SLC12A6 MUTATION ANALYSIS
D182V1, survival
                   sevent
clus2                 0   1
  SLC12A6 MUTATED    16   4
  SLC12A6 WILD-TYPE 261  74
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               20               335 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                4                74 
$`SLC12A6 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3518 
        6.05        19.04       100.01        26.17        22.06         1.02 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 
       34.98        31.00        12.16        27.09        21.44        58.39 
TCGA-AZ-6598 TCGA-CM-4744 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-6536 TCGA-DM-A28H 
       49.41        20.02        12.00        12.03        17.85       117.07 
TCGA-F4-6570 TCGA-G4-6323 
        6.18        13.78 

$`SLC12A6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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-A01K 
       14.99        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
             1.02              0.00 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
           117.07            148.01 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
            20.73             22.09 
[1] "1.0 - 117.1 (20.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D182V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC12A6 MUTATED         4        1        3         7         1         0
  SLC12A6 WILD-TYPE      60        0       23       101         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A6 MUTATED           0          0          2          1        1
  SLC12A6 WILD-TYPE        18          6         42         32       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC12A6 MUTATED           0         0
  SLC12A6 WILD-TYPE        12         1
D182V3, multiclass
            clus
vv           SLC12A6 MUTATED SLC12A6 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 1                 0
  STAGE II                 3                23
  STAGE IIA                7               101
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC12A6 MUTATED     0   4  13   2
  SLC12A6 WILD-TYPE   9  63 236  39
D182V4, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3              13               236
  T4               2                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
  SLC12A6 MUTATED    16   1   3
  SLC12A6 WILD-TYPE 204  80  63
D182V5, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  N0              16               204
  N1               1                80
  N2               3                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"
D182V6, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    15   1
  SLC12A6 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     15    1
  SLC12A6 WILD-TYPE  270   47
   clus
vv  SLC12A6 MUTATED SLC12A6 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D182V7, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    10  10
  SLC12A6 WILD-TYPE 160 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     10   10
  SLC12A6 WILD-TYPE  160  187
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  FEMALE              10               160
  MALE                10               187
[1] 2 2
[1] FALSE
D182V8, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    17   0
  SLC12A6 WILD-TYPE 283   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     17    0
  SLC12A6 WILD-TYPE  283    8
     clus
vv    SLC12A6 MUTATED SLC12A6 WILD-TYPE
  NO               17               283
  YES               0                 8
[1] 2 2
[1] FALSE
D182V9, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    18   2
  SLC12A6 WILD-TYPE 296  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     18    2
  SLC12A6 WILD-TYPE  296   46
                               clus
vv                              SLC12A6 MUTATED SLC12A6 WILD-TYPE
  COLON ADENOCARCINOMA                       18               296
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC12A6 MUTATED    16   0   1   0
  SLC12A6 WILD-TYPE 243   3  21  21
D182V10, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  R0              16               243
  R1               0                 3
  R2               1                21
  RX               0                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"
D182V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC12A6 MUTATED                                  0     0
  SLC12A6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC12A6 MUTATED                           1    14
  SLC12A6 WILD-TYPE                        18   162
D182V12, multiclass
                                  clus
vv                                 SLC12A6 MUTATED SLC12A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         14               162
[1] 4 2
[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 = PRKCH MUTATION ANALYSIS
D183V1, survival
                 sevent
clus2               0   1
  PRKCH MUTATED     8   4
  PRKCH WILD-TYPE 269  74
  PRKCH MUTATED PRKCH WILD-TYPE 
             12             343 
  PRKCH MUTATED PRKCH WILD-TYPE 
              4              74 
$`PRKCH MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3989 TCGA-AD-6889 
      100.01        35.80        22.06        35.01         7.96        83.24 
TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6167 TCGA-D5-5540 TCGA-F4-6460 
       27.09        12.76        15.02        14.99        56.09        31.96 

$`PRKCH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        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-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PRKCH MUTATED PRKCH WILD-TYPE 
           7.96            0.00 
  PRKCH MUTATED PRKCH WILD-TYPE 
         100.01          148.01 
  PRKCH MUTATED PRKCH WILD-TYPE 
         29.525          21.990 
[1] "8.0 - 100.0 (29.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D183V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKCH MUTATED         3        0        1         6         0         0
  PRKCH WILD-TYPE      61        1       25       102         8         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        18          6         43         32       34        12
                 vv
clus              STAGE IVB
  PRKCH MUTATED           0
  PRKCH WILD-TYPE         1
D183V3, multiclass
            clus
vv           PRKCH MUTATED PRKCH WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  PRKCH MUTATED     0   3  10   0
  PRKCH WILD-TYPE   9  64 239  41
D183V4, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             0              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
  PRKCH MUTATED    10   1   2
  PRKCH WILD-TYPE 210  80  64
D183V5, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  N0            10             210
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V6, binary
                 cls
clus                0   1
  PRKCH MUTATED    12   1
  PRKCH WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     12    1
  PRKCH WILD-TYPE  273   47
   clus
vv  PRKCH MUTATED PRKCH WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D183V7, binary
                 cls
clus                0   1
  PRKCH MUTATED     6   7
  PRKCH WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED      6    7
  PRKCH WILD-TYPE  164  190
        clus
vv       PRKCH MUTATED PRKCH WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D183V8, binary
                 cls
clus                0   1
  PRKCH MUTATED    11   0
  PRKCH WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     11    0
  PRKCH WILD-TYPE  289    8
     clus
vv    PRKCH MUTATED PRKCH WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D183V9, binary
                 cls
clus                0   1
  PRKCH MUTATED    12   1
  PRKCH WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     12    1
  PRKCH WILD-TYPE  302   47
                               clus
vv                              PRKCH MUTATED PRKCH WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKCH MUTATED    10   0   1   1
  PRKCH WILD-TYPE 249   3  21  20
D183V10, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  R0            10             249
  R1             0               3
  R2             1              21
  RX             1              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"
D183V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCH MUTATED                                  0     2
  PRKCH WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCH MUTATED                           1     7
  PRKCH WILD-TYPE                        18   169
D183V12, multiclass
                                  clus
vv                                 PRKCH MUTATED PRKCH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = TUBA4A MUTATION ANALYSIS
D184V1, survival
                  sevent
clus2                0   1
  TUBA4A MUTATED     7   2
  TUBA4A WILD-TYPE 270  76
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               9              346 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               2               76 
$`TUBA4A MUTATED`
TCGA-AA-3662 TCGA-AZ-6601 TCGA-A6-5665 TCGA-AA-3977 TCGA-CK-4950 TCGA-CK-4952 
        6.05       100.01        22.06        25.02        85.45        15.62 
TCGA-CK-5916 TCGA-DM-A282 TCGA-F4-6856 
       21.14       139.17        35.31 

$`TUBA4A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
      148.01        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  TUBA4A MUTATED TUBA4A WILD-TYPE 
            6.05             0.00 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
          139.17           148.01 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
           25.02            22.01 
[1] "6.0 - 139.2 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D184V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUBA4A MUTATED         2        0        1         2         0         0
  TUBA4A WILD-TYPE      62        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TUBA4A MUTATED           0          0          1          1        1
  TUBA4A WILD-TYPE        18          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  TUBA4A MUTATED           0         0
  TUBA4A WILD-TYPE        12         1
D184V3, multiclass
            clus
vv           TUBA4A MUTATED TUBA4A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  TUBA4A MUTATED     1   2   4   2
  TUBA4A WILD-TYPE   8  65 245  39
D184V4, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  T1              1                8
  T2              2               65
  T3              4              245
  T4              2               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
  TUBA4A MUTATED     6   1   2
  TUBA4A WILD-TYPE 214  80  64
D184V5, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  N0              6              214
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V6, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     7   1
  TUBA4A WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      7    1
  TUBA4A WILD-TYPE  278   47
   clus
vv  TUBA4A MUTATED TUBA4A WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D184V7, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     6   3
  TUBA4A WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      6    3
  TUBA4A WILD-TYPE  164  194
        clus
vv       TUBA4A MUTATED TUBA4A WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D184V8, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     7   0
  TUBA4A WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      7    0
  TUBA4A WILD-TYPE  293    8
     clus
vv    TUBA4A MUTATED TUBA4A WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D184V9, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     6   3
  TUBA4A WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      6    3
  TUBA4A WILD-TYPE  308   45
                               clus
vv                              TUBA4A MUTATED TUBA4A WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TUBA4A MUTATED     2   1   1   2
  TUBA4A WILD-TYPE 257   2  21  19
D184V10, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  R0              2              257
  R1              1                2
  R2              1               21
  RX              2               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"
D184V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBA4A MUTATED                                  0     0
  TUBA4A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TUBA4A MUTATED                           1     6
  TUBA4A WILD-TYPE                        18   170
D184V12, multiclass
                                  clus
vv                                 TUBA4A MUTATED TUBA4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = ZFC3H1 MUTATION ANALYSIS
D185V1, survival
                  sevent
clus2                0   1
  ZFC3H1 MUTATED    12   6
  ZFC3H1 WILD-TYPE 265  72
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              18              337 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
               6               72 
$`ZFC3H1 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-CK-5912 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 
       19.04        24.00        49.08        33.53        22.06         6.97 
TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3975 TCGA-AA-A010 TCGA-AY-6386 
       33.04        53.00        18.05        34.06        34.98        17.82 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-D5-6927 
       49.41        12.10        12.76        10.06        21.14         9.44 

$`ZFC3H1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       31.07        30.05        17.03        27.02        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
            6.97             0.00 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           53.00           148.01 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           21.60            22.09 
[1] "7.0 - 53.0 (21.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D185V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFC3H1 MUTATED         4        0        4         7         2         0
  ZFC3H1 WILD-TYPE      60        1       22       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFC3H1 MUTATED           0          0          1          0        1
  ZFC3H1 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZFC3H1 MUTATED           0         0
  ZFC3H1 WILD-TYPE        12         1
D185V3, multiclass
            clus
vv           ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZFC3H1 MUTATED     2   2  12   3
  ZFC3H1 WILD-TYPE   7  65 237  38
D185V4, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  T1              2                7
  T2              2               65
  T3             12              237
  T4              3               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
  ZFC3H1 MUTATED    17   2   0
  ZFC3H1 WILD-TYPE 203  79  66
D185V5, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  N0             17              203
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V6, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    15   1
  ZFC3H1 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     15    1
  ZFC3H1 WILD-TYPE  270   47
   clus
vv  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  0             15              270
  1              1               47
[1] 2 2
[1] FALSE
D185V7, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    10   9
  ZFC3H1 WILD-TYPE 160 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     10    9
  ZFC3H1 WILD-TYPE  160  188
        clus
vv       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  FEMALE             10              160
  MALE                9              188
[1] 2 2
[1] FALSE
D185V8, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    18   0
  ZFC3H1 WILD-TYPE 282   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     18    0
  ZFC3H1 WILD-TYPE  282    8
     clus
vv    ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  NO              18              282
  YES              0                8
[1] 2 2
[1] FALSE
D185V9, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    17   2
  ZFC3H1 WILD-TYPE 297  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     17    2
  ZFC3H1 WILD-TYPE  297   46
                               clus
vv                              ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZFC3H1 MUTATED    12   0   0   5
  ZFC3H1 WILD-TYPE 247   3  22  16
D185V10, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              5               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"
D185V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFC3H1 MUTATED                                  0     2
  ZFC3H1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZFC3H1 MUTATED                           3     6
  ZFC3H1 WILD-TYPE                        16   170
D185V12, multiclass
                                  clus
vv                                 ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         6              170
[1] 4 2
[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 = FRMPD4 MUTATION ANALYSIS
D186V1, survival
                  sevent
clus2                0   1
  FRMPD4 MUTATED    23   6
  FRMPD4 WILD-TYPE 254  72
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              29              326 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
               6               72 
$`FRMPD4 MUTATED`
TCGA-G4-6310 TCGA-G4-6586 TCGA-A6-2672 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-6780 
       63.62        35.80        46.65        23.61        22.06        20.12 
TCGA-AA-A00N TCGA-AA-A01P TCGA-AD-6899 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 
        4.01        38.07         5.79        14.50        27.09        58.39 
TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5868 
       62.79        12.76        13.02        22.98        15.02        17.03 
TCGA-CM-6163 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6539 TCGA-DM-A0X9 
       14.04        56.09        55.92        18.25        12.49       119.70 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28H TCGA-F4-6856 
        7.50        44.32       139.17       117.07        35.31 

$`FRMPD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53        22.42        27.42        26.47 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        54.61 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       19.59        20.19        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F 
      140.38       131.51       135.65        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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
            4.01             0.00 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
          139.17           148.01 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
           23.61            21.99 
[1] "4.0 - 139.2 (23.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D186V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRMPD4 MUTATED         3        0        1        13         1         0
  FRMPD4 WILD-TYPE      61        1       25        95         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMPD4 MUTATED           1          0          4          3        1
  FRMPD4 WILD-TYPE        17          6         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  FRMPD4 MUTATED           2         0
  FRMPD4 WILD-TYPE        10         1
D186V3, multiclass
            clus
vv           FRMPD4 MUTATED FRMPD4 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              13               95
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              3               30
  STAGE IV                1               34
  STAGE IVA               2               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
  FRMPD4 MUTATED     1   2  24   3
  FRMPD4 WILD-TYPE   8  65 225  38
D186V4, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             24              225
  T4              3               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
  FRMPD4 MUTATED    19   6   5
  FRMPD4 WILD-TYPE 201  75  61
D186V5, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  N0             19              201
  N1              6               75
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V6, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    24   3
  FRMPD4 WILD-TYPE 261  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     24    3
  FRMPD4 WILD-TYPE  261   45
   clus
vv  FRMPD4 MUTATED FRMPD4 WILD-TYPE
  0             24              261
  1              3               45
[1] 2 2
[1] FALSE
D186V7, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    13  17
  FRMPD4 WILD-TYPE 157 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     13   17
  FRMPD4 WILD-TYPE  157  180
        clus
vv       FRMPD4 MUTATED FRMPD4 WILD-TYPE
  FEMALE             13              157
  MALE               17              180
[1] 2 2
[1] FALSE
D186V8, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    21   1
  FRMPD4 WILD-TYPE 279   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     21    1
  FRMPD4 WILD-TYPE  279    7
     clus
vv    FRMPD4 MUTATED FRMPD4 WILD-TYPE
  NO              21              279
  YES              1                7
[1] 2 2
[1] FALSE
D186V9, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    25   5
  FRMPD4 WILD-TYPE 289  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     25    5
  FRMPD4 WILD-TYPE  289   43
                               clus
vv                              FRMPD4 MUTATED FRMPD4 WILD-TYPE
  COLON ADENOCARCINOMA                      25              289
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FRMPD4 MUTATED    19   0   1   1
  FRMPD4 WILD-TYPE 240   3  21  20
D186V10, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  R0             19              240
  R1              0                3
  R2              1               21
  RX              1               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"
D186V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRMPD4 MUTATED                                  0     1
  FRMPD4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FRMPD4 MUTATED                           1    25
  FRMPD4 WILD-TYPE                        18   151
D186V12, multiclass
                                  clus
vv                                 FRMPD4 MUTATED FRMPD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        25              151
[1] 4 2
[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 = PRRG1 MUTATION ANALYSIS
D187V1, survival
                 sevent
clus2               0   1
  PRRG1 MUTATED     8   3
  PRRG1 WILD-TYPE 269  75
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             344 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              3              75 
$`PRRG1 MUTATED`
TCGA-G4-6586 TCGA-A6-5661 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 
       35.80        33.53        12.16        49.41        12.76        51.32 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-5538 TCGA-DM-A28K TCGA-G4-6303 
       12.00        14.04        54.61        98.24        65.85 

$`PRRG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PRRG1 MUTATED PRRG1 WILD-TYPE 
             12               0 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          98.24          148.01 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          35.80           22.01 
[1] "12.0 - 98.2 (35.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D187V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRRG1 MUTATED         2        0        1         5         0         0
  PRRG1 WILD-TYPE      62        1       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRRG1 MUTATED           0          0          2          0        1         0
  PRRG1 WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  PRRG1 MUTATED           0
  PRRG1 WILD-TYPE         1
D187V3, multiclass
            clus
vv           PRRG1 MUTATED PRRG1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  PRRG1 MUTATED     0   2   9   0
  PRRG1 WILD-TYPE   9  65 240  41
D187V4, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             0              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
  PRRG1 MUTATED     8   3   0
  PRRG1 WILD-TYPE 212  78  66
D187V5, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V6, binary
                 cls
clus                0   1
  PRRG1 MUTATED     7   1
  PRRG1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      7    1
  PRRG1 WILD-TYPE  278   47
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D187V7, binary
                 cls
clus                0   1
  PRRG1 MUTATED     8   3
  PRRG1 WILD-TYPE 162 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      8    3
  PRRG1 WILD-TYPE  162  194
        clus
vv       PRRG1 MUTATED PRRG1 WILD-TYPE
  FEMALE             8             162
  MALE               3             194
[1] 2 2
[1] FALSE
D187V8, binary
                 cls
clus                0   1
  PRRG1 MUTATED    10   0
  PRRG1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED     10    0
  PRRG1 WILD-TYPE  290    8
     clus
vv    PRRG1 MUTATED PRRG1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D187V9, binary
                 cls
clus                0   1
  PRRG1 MUTATED     7   4
  PRRG1 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      7    4
  PRRG1 WILD-TYPE  307   44
                               clus
vv                              PRRG1 MUTATED PRRG1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRRG1 MUTATED     7   0   0   2
  PRRG1 WILD-TYPE 252   3  22  19
D187V10, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             2              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"
D187V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRRG1 MUTATED                                  0     1
  PRRG1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRRG1 MUTATED                           1     9
  PRRG1 WILD-TYPE                        18   167
D187V12, multiclass
                                  clus
vv                                 PRRG1 MUTATED PRRG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(188) Variable = PAQR5 MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2               0   1
  PAQR5 MUTATED     6   2
  PAQR5 WILD-TYPE 271  76
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             347 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              2              76 
$`PAQR5 MUTATED`
TCGA-A6-4105 TCGA-AD-6895 TCGA-CK-5912 TCGA-AA-3663 TCGA-AY-5543 TCGA-D5-5541 
       14.53        25.08        49.08         6.97        33.01        55.92 
TCGA-D5-6540 TCGA-D5-6541 
       16.14        15.58 

$`PAQR5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PAQR5 MUTATED PAQR5 WILD-TYPE 
           6.97            0.00 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
          55.92          148.01 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
          20.61           22.06 
[1] "7.0 - 55.9 (20.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D188V2, continuous
                 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      62        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAQR5 MUTATED           0          0          2          0        0         1
  PAQR5 WILD-TYPE        18          6         42         33       35        11
                 vv
clus              STAGE IVB
  PAQR5 MUTATED           0
  PAQR5 WILD-TYPE         1
D188V3, multiclass
            clus
vv           PAQR5 MUTATED PAQR5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  PAQR5 MUTATED     0   2   6   0
  PAQR5 WILD-TYPE   9  65 243  41
D188V4, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             0              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
  PAQR5 MUTATED     5   3   0
  PAQR5 WILD-TYPE 215  78  66
D188V5, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  N0             5             215
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V6, binary
                 cls
clus                0   1
  PAQR5 MUTATED     6   1
  PAQR5 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      6    1
  PAQR5 WILD-TYPE  279   47
   clus
vv  PAQR5 MUTATED PAQR5 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D188V7, binary
                 cls
clus                0   1
  PAQR5 MUTATED     1   7
  PAQR5 WILD-TYPE 169 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      1    7
  PAQR5 WILD-TYPE  169  190
        clus
vv       PAQR5 MUTATED PAQR5 WILD-TYPE
  FEMALE             1             169
  MALE               7             190
[1] 2 2
[1] FALSE
D188V8, binary
                 cls
clus                0   1
  PAQR5 MUTATED     8   0
  PAQR5 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      8    0
  PAQR5 WILD-TYPE  292    8
     clus
vv    PAQR5 MUTATED PAQR5 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D188V9, binary
                 cls
clus                0   1
  PAQR5 MUTATED     7   1
  PAQR5 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      7    1
  PAQR5 WILD-TYPE  307   47
                               clus
vv                              PAQR5 MUTATED PAQR5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PAQR5 MUTATED     6   0   0   1
  PAQR5 WILD-TYPE 253   3  22  20
D188V10, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D188V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAQR5 MUTATED                                  0     0
  PAQR5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PAQR5 MUTATED                           1     6
  PAQR5 WILD-TYPE                        18   170
D188V12, multiclass
                                  clus
vv                                 PAQR5 MUTATED PAQR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = BIRC3 MUTATION ANALYSIS
D189V1, survival
                 sevent
clus2               0   1
  BIRC3 MUTATED    10   1
  BIRC3 WILD-TYPE 267  77
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             344 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
              1              77 
$`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-AY-6196 TCGA-CA-6718 TCGA-CM-5868 TCGA-D5-6929 TCGA-F4-6808 
        0.20        10.06        17.03        13.41        33.67 

$`BIRC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        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-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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  BIRC3 MUTATED BIRC3 WILD-TYPE 
            0.2             0.0 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          34.98          148.01 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          17.03           22.09 
[1] "0.2 - 35.0 (17.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D189V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BIRC3 MUTATED         2        0        1         2         2         0
  BIRC3 WILD-TYPE      62        1       25       106         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BIRC3 MUTATED           0          0          0          1        1         2
  BIRC3 WILD-TYPE        18          6         44         32       34        10
                 vv
clus              STAGE IVB
  BIRC3 MUTATED           0
  BIRC3 WILD-TYPE         1
D189V3, multiclass
            clus
vv           BIRC3 MUTATED BIRC3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              2              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
  BIRC3 MUTATED     1   1   6   3
  BIRC3 WILD-TYPE   8  66 243  38
D189V4, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             6             243
  T4             3              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
  BIRC3 MUTATED     7   3   1
  BIRC3 WILD-TYPE 213  78  65
D189V5, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V6, binary
                 cls
clus                0   1
  BIRC3 MUTATED     7   3
  BIRC3 WILD-TYPE 278  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      7    3
  BIRC3 WILD-TYPE  278   45
   clus
vv  BIRC3 MUTATED BIRC3 WILD-TYPE
  0             7             278
  1             3              45
[1] 2 2
[1] FALSE
D189V7, binary
                 cls
clus                0   1
  BIRC3 MUTATED     8   3
  BIRC3 WILD-TYPE 162 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      8    3
  BIRC3 WILD-TYPE  162  194
        clus
vv       BIRC3 MUTATED BIRC3 WILD-TYPE
  FEMALE             8             162
  MALE               3             194
[1] 2 2
[1] FALSE
D189V8, binary
                 cls
clus                0   1
  BIRC3 MUTATED    10   0
  BIRC3 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED     10    0
  BIRC3 WILD-TYPE  290    8
     clus
vv    BIRC3 MUTATED BIRC3 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D189V9, binary
                 cls
clus                0   1
  BIRC3 MUTATED     8   3
  BIRC3 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      8    3
  BIRC3 WILD-TYPE  306   45
                               clus
vv                              BIRC3 MUTATED BIRC3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BIRC3 MUTATED    10   0   0   1
  BIRC3 WILD-TYPE 249   3  22  20
D189V10, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             1              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"
D189V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BIRC3 MUTATED                                  0     1
  BIRC3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BIRC3 MUTATED                           1     6
  BIRC3 WILD-TYPE                        18   170
D189V12, multiclass
                                  clus
vv                                 BIRC3 MUTATED BIRC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = PPP1R12B MUTATION ANALYSIS
D190V1, survival
                    sevent
clus2                  0   1
  PPP1R12B MUTATED    10   2
  PPP1R12B WILD-TYPE 267  76
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                12                343 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                 2                 76 
$`PPP1R12B MUTATED`
TCGA-AA-3867 TCGA-G4-6310 TCGA-G4-6588 TCGA-AA-3842 TCGA-AA-A00N TCGA-AZ-4315 
       24.03        63.62        26.17        37.02         4.01        58.39 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-6162 TCGA-D5-6529 TCGA-D5-6536 TCGA-DM-A1D4 
       22.03        22.98        12.00        20.19        17.85        92.75 

$`PPP1R12B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
              4.01               0.00 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
             92.75             148.01 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
            23.505             21.990 
[1] "4.0 - 92.8 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D190V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP1R12B MUTATED         0        0        0         5         1         0
  PPP1R12B WILD-TYPE      64        1       26       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12B MUTATED           0          1          4          0        1
  PPP1R12B WILD-TYPE        18          5         40         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  PPP1R12B MUTATED           0         0
  PPP1R12B WILD-TYPE        12         1
D190V3, multiclass
            clus
vv           PPP1R12B MUTATED PPP1R12B WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                4                 40
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  PPP1R12B MUTATED     0   1  10   1
  PPP1R12B WILD-TYPE   9  66 239  40
D190V4, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3               10                239
  T4                1                 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
  PPP1R12B MUTATED     6   5   1
  PPP1R12B WILD-TYPE 214  76  65
D190V5, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  N0                6                214
  N1                5                 76
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V6, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    11   1
  PPP1R12B WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     11    1
  PPP1R12B WILD-TYPE  274   47
   clus
vv  PPP1R12B MUTATED PPP1R12B WILD-TYPE
  0               11                274
  1                1                 47
[1] 2 2
[1] FALSE
D190V7, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED     3   9
  PPP1R12B WILD-TYPE 167 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED      3    9
  PPP1R12B WILD-TYPE  167  188
        clus
vv       PPP1R12B MUTATED PPP1R12B WILD-TYPE
  FEMALE                3                167
  MALE                  9                188
[1] 2 2
[1] FALSE
D190V8, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED     9   1
  PPP1R12B WILD-TYPE 291   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED      9    1
  PPP1R12B WILD-TYPE  291    7
     clus
vv    PPP1R12B MUTATED PPP1R12B WILD-TYPE
  NO                 9                291
  YES                1                  7
[1] 2 2
[1] FALSE
D190V9, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    10   2
  PPP1R12B WILD-TYPE 304  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     10    2
  PPP1R12B WILD-TYPE  304   46
                               clus
vv                              PPP1R12B MUTATED PPP1R12B WILD-TYPE
  COLON ADENOCARCINOMA                        10                304
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPP1R12B MUTATED    10   0   1   0
  PPP1R12B WILD-TYPE 249   3  21  21
D190V10, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  R0               10                249
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D190V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP1R12B MUTATED                                  0     0
  PPP1R12B WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PPP1R12B MUTATED                           0     9
  PPP1R12B WILD-TYPE                        19   167
D190V12, multiclass
                                  clus
vv                                 PPP1R12B MUTATED PPP1R12B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           9                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(191) Variable = TFE3 MUTATION ANALYSIS
D191V1, survival
                sevent
clus2              0   1
  TFE3 MUTATED    10   1
  TFE3 WILD-TYPE 267  77
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            344 
  TFE3 MUTATED TFE3 WILD-TYPE 
             1             77 
$`TFE3 MUTATED`
TCGA-G4-6588 TCGA-AA-3532 TCGA-AA-3710 TCGA-AA-3947 TCGA-AD-6889 TCGA-AY-6197 
       26.17        29.00        26.99        33.01        83.24        21.44 
TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6920 TCGA-D5-6928 TCGA-F4-6703 
       51.32        14.04        12.39        11.64        47.87 

$`TFE3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07        19.07         0.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TFE3 MUTATED TFE3 WILD-TYPE 
         11.64           0.00 
  TFE3 MUTATED TFE3 WILD-TYPE 
         83.24         148.01 
  TFE3 MUTATED TFE3 WILD-TYPE 
         26.99          22.01 
[1] "11.6 - 83.2 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.9"
D191V2, continuous
                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      63        1       26        99         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  TFE3 MUTATED           0
  TFE3 WILD-TYPE         1
D191V3, multiclass
            clus
vv           TFE3 MUTATED TFE3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             9             99
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TFE3 MUTATED     0   1   9   1
  TFE3 WILD-TYPE   9  66 240  40
D191V4, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            9            240
  T4            1             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
  TFE3 MUTATED    11   0   0
  TFE3 WILD-TYPE 209  81  66
D191V5, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  N0           11            209
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V6, binary
                cls
clus               0   1
  TFE3 MUTATED     9   0
  TFE3 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    0
  TFE3 WILD-TYPE  276   48
   clus
vv  TFE3 MUTATED TFE3 WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D191V7, binary
                cls
clus               0   1
  TFE3 MUTATED     6   5
  TFE3 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      6    5
  TFE3 WILD-TYPE  164  192
        clus
vv       TFE3 MUTATED TFE3 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D191V8, binary
                cls
clus               0   1
  TFE3 MUTATED    11   0
  TFE3 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED     11    0
  TFE3 WILD-TYPE  289    8
     clus
vv    TFE3 MUTATED TFE3 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D191V9, binary
                cls
clus               0   1
  TFE3 MUTATED     9   2
  TFE3 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    2
  TFE3 WILD-TYPE  305   46
                               clus
vv                              TFE3 MUTATED TFE3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TFE3 MUTATED    10   0   0   1
  TFE3 WILD-TYPE 249   3  22  20
D191V10, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D191V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TFE3 MUTATED                                  0     1
  TFE3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TFE3 MUTATED                           0     7
  TFE3 WILD-TYPE                        19   169
D191V12, multiclass
                                  clus
vv                                 TFE3 MUTATED TFE3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = ZNF473 MUTATION ANALYSIS
D192V1, survival
                  sevent
clus2                0   1
  ZNF473 MUTATED    10   3
  ZNF473 WILD-TYPE 267  75
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              13              342 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
               3               75 
$`ZNF473 MUTATED`
TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3949 TCGA-AA-3975 TCGA-AA-A00N 
       26.17        42.90         8.38        26.01        34.06         4.01 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6678 
       10.06        85.45        30.08        32.02        15.02        11.01 
TCGA-D5-5540 
       56.09 

$`ZNF473 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       12.76        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-5868 TCGA-CM-6161 
       22.98        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        14.04        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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        19.59        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF473 MUTATED ZNF473 WILD-TYPE 
            4.01             0.00 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
           85.45           148.01 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
           26.17            22.01 
[1] "4.0 - 85.5 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D192V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF473 MUTATED         2        0        0         7         2         0
  ZNF473 WILD-TYPE      62        1       26       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF473 MUTATED           0          0          2          0        0
  ZNF473 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF473 MUTATED           1         0
  ZNF473 WILD-TYPE        11         1
D192V3, multiclass
            clus
vv           ZNF473 MUTATED ZNF473 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF473 MUTATED     0   2   9   3
  ZNF473 WILD-TYPE   9  65 240  38
D192V4, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              9              240
  T4              3               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
  ZNF473 MUTATED    11   3   0
  ZNF473 WILD-TYPE 209  78  66
D192V5, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  N0             11              209
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V6, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    13   1
  ZNF473 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     13    1
  ZNF473 WILD-TYPE  272   47
   clus
vv  ZNF473 MUTATED ZNF473 WILD-TYPE
  0             13              272
  1              1               47
[1] 2 2
[1] FALSE
D192V7, binary
                  cls
clus                 0   1
  ZNF473 MUTATED     7   7
  ZNF473 WILD-TYPE 163 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED      7    7
  ZNF473 WILD-TYPE  163  190
        clus
vv       ZNF473 MUTATED ZNF473 WILD-TYPE
  FEMALE              7              163
  MALE                7              190
[1] 2 2
[1] FALSE
D192V8, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    12   0
  ZNF473 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     12    0
  ZNF473 WILD-TYPE  288    8
     clus
vv    ZNF473 MUTATED ZNF473 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D192V9, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    11   3
  ZNF473 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     11    3
  ZNF473 WILD-TYPE  303   45
                               clus
vv                              ZNF473 MUTATED ZNF473 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF473 MUTATED    11   1   0   1
  ZNF473 WILD-TYPE 248   2  22  20
D192V10, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  R0             11              248
  R1              1                2
  R2              0               22
  RX              1               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"
D192V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF473 MUTATED                                  0     1
  ZNF473 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF473 MUTATED                           2     7
  ZNF473 WILD-TYPE                        17   169
D192V12, multiclass
                                  clus
vv                                 ZNF473 MUTATED ZNF473 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         7              169
[1] 4 2
[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 = SLAMF7 MUTATION ANALYSIS
D193V1, survival
                  sevent
clus2                0   1
  SLAMF7 MUTATED     9   2
  SLAMF7 WILD-TYPE 268  76
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              344 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
               2               76 
$`SLAMF7 MUTATED`
TCGA-AA-3662 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 
        6.05        26.17        22.06        63.98         4.01        34.98 
TCGA-CK-6748 TCGA-CM-5348 TCGA-CM-6168 TCGA-D5-6541 TCGA-F4-6809 
        2.01        22.98        12.99        15.58        13.25 

$`SLAMF7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        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-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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
            2.01             0.00 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
           63.98           148.01 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
           15.58            22.09 
[1] "2.0 - 64.0 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D193V2, continuous
                  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      64        1       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLAMF7 MUTATED           0          0          1          0        2
  SLAMF7 WILD-TYPE        18          6         43         33       33
                  vv
clus               STAGE IVA STAGE IVB
  SLAMF7 MUTATED           1         0
  SLAMF7 WILD-TYPE        11         1
D193V3, multiclass
            clus
vv           SLAMF7 MUTATED SLAMF7 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               1               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
  SLAMF7 MUTATED     0   0   8   3
  SLAMF7 WILD-TYPE   9  67 241  38
D193V4, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              8              241
  T4              3               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
  SLAMF7 MUTATED     7   3   1
  SLAMF7 WILD-TYPE 213  78  65
D193V5, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  N0              7              213
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V6, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     8   3
  SLAMF7 WILD-TYPE 277  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      8    3
  SLAMF7 WILD-TYPE  277   45
   clus
vv  SLAMF7 MUTATED SLAMF7 WILD-TYPE
  0              8              277
  1              3               45
[1] 2 2
[1] FALSE
D193V7, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     7   4
  SLAMF7 WILD-TYPE 163 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      7    4
  SLAMF7 WILD-TYPE  163  193
        clus
vv       SLAMF7 MUTATED SLAMF7 WILD-TYPE
  FEMALE              7              163
  MALE                4              193
[1] 2 2
[1] FALSE
D193V8, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED    10   0
  SLAMF7 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED     10    0
  SLAMF7 WILD-TYPE  290    8
     clus
vv    SLAMF7 MUTATED SLAMF7 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D193V9, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     9   2
  SLAMF7 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      9    2
  SLAMF7 WILD-TYPE  305   46
                               clus
vv                              SLAMF7 MUTATED SLAMF7 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLAMF7 MUTATED     9   0   1   1
  SLAMF7 WILD-TYPE 250   3  21  20
D193V10, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              1               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"
D193V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLAMF7 MUTATED                                  0     0
  SLAMF7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLAMF7 MUTATED                           1     6
  SLAMF7 WILD-TYPE                        18   170
D193V12, multiclass
                                  clus
vv                                 SLAMF7 MUTATED SLAMF7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = SNAI2 MUTATION ANALYSIS
D194V1, survival
                 sevent
clus2               0   1
  SNAI2 MUTATED     9   1
  SNAI2 WILD-TYPE 268  77
  SNAI2 MUTATED SNAI2 WILD-TYPE 
             10             345 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
              1              77 
$`SNAI2 MUTATED`
TCGA-G4-6321 TCGA-AA-3655 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6748 
       22.09        61.02         4.01        12.76        15.62         2.01 
TCGA-CM-4743 TCGA-CM-4752 TCGA-G4-6306 TCGA-G4-6323 
       23.05        13.02        44.68        13.78 

$`SNAI2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6626 
       61.91        36.00        46.75 

  SNAI2 MUTATED SNAI2 WILD-TYPE 
           2.01            0.00 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
          61.02          148.01 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
          14.70           22.09 
[1] "2.0 - 61.0 (14.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNAI2 MUTATED         0        1        1         3         1         0
  SNAI2 WILD-TYPE      64        0       25       105         7         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        17          6         44         32       34        12
                 vv
clus              STAGE IVB
  SNAI2 MUTATED           0
  SNAI2 WILD-TYPE         1
D194V3, multiclass
            clus
vv           SNAI2 MUTATED SNAI2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  SNAI2 MUTATED     0   2   5   2
  SNAI2 WILD-TYPE   9  65 244  39
D194V4, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             2              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
  SNAI2 MUTATED     7   2   1
  SNAI2 WILD-TYPE 213  79  65
D194V5, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V6, binary
                 cls
clus                0   1
  SNAI2 MUTATED     7   1
  SNAI2 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      7    1
  SNAI2 WILD-TYPE  278   47
   clus
vv  SNAI2 MUTATED SNAI2 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D194V7, binary
                 cls
clus                0   1
  SNAI2 MUTATED     3   7
  SNAI2 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      3    7
  SNAI2 WILD-TYPE  167  190
        clus
vv       SNAI2 MUTATED SNAI2 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D194V8, binary
                 cls
clus                0   1
  SNAI2 MUTATED     8   0
  SNAI2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      8    0
  SNAI2 WILD-TYPE  292    8
     clus
vv    SNAI2 MUTATED SNAI2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D194V9, binary
                 cls
clus                0   1
  SNAI2 MUTATED     6   4
  SNAI2 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      6    4
  SNAI2 WILD-TYPE  308   44
                               clus
vv                              SNAI2 MUTATED SNAI2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SNAI2 MUTATED     7   0   0   3
  SNAI2 WILD-TYPE 252   3  22  18
D194V10, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             3              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"
D194V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNAI2 MUTATED                                  0     1
  SNAI2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SNAI2 MUTATED                           2     5
  SNAI2 WILD-TYPE                        17   171
D194V12, multiclass
                                  clus
vv                                 SNAI2 MUTATED SNAI2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = B4GALNT4 MUTATION ANALYSIS
D195V1, survival
                    sevent
clus2                  0   1
  B4GALNT4 MUTATED     7   3
  B4GALNT4 WILD-TYPE 270  75
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                10                345 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                 3                 75 
$`B4GALNT4 MUTATED`
TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-2672 TCGA-AA-3510 TCGA-AU-6004 TCGA-AZ-6598 
       10.88        26.17        46.65        63.98        27.09        49.41 
TCGA-CK-5916 TCGA-CM-4743 TCGA-D5-6928 TCGA-DM-A1HB 
       21.14        23.05        11.64       135.65 

$`B4GALNT4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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              21.99 
[1] "10.9 - 135.7 (26.6)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1"  
D195V2, continuous
                    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      62        1       24       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALNT4 MUTATED           0          0          2          0        0
  B4GALNT4 WILD-TYPE        18          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  B4GALNT4 MUTATED           0         0
  B4GALNT4 WILD-TYPE        12         1
D195V3, multiclass
            clus
vv           B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 3                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  B4GALNT4 MUTATED     1   1   7   2
  B4GALNT4 WILD-TYPE   8  66 242  39
D195V4, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  T1                1                  8
  T2                1                 66
  T3                7                242
  T4                2                 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
  B4GALNT4 MUTATED     8   2   1
  B4GALNT4 WILD-TYPE 212  79  65
D195V5, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  N0                8                212
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V6, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     8   0
  B4GALNT4 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      8    0
  B4GALNT4 WILD-TYPE  277   48
   clus
vv  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  0                8                277
  1                0                 48
[1] 2 2
[1] FALSE
D195V7, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     6   5
  B4GALNT4 WILD-TYPE 164 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      6    5
  B4GALNT4 WILD-TYPE  164  192
        clus
vv       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  FEMALE                6                164
  MALE                  5                192
[1] 2 2
[1] FALSE
D195V8, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     8   0
  B4GALNT4 WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      8    0
  B4GALNT4 WILD-TYPE  292    8
     clus
vv    B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D195V9, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     9   1
  B4GALNT4 WILD-TYPE 305  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      9    1
  B4GALNT4 WILD-TYPE  305   47
                               clus
vv                              B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  B4GALNT4 MUTATED     6   0   0   2
  B4GALNT4 WILD-TYPE 253   3  22  19
D195V10, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D195V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B4GALNT4 MUTATED                                  0     0
  B4GALNT4 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  B4GALNT4 MUTATED                           0    10
  B4GALNT4 WILD-TYPE                        19   166
D195V12, multiclass
                                  clus
vv                                 B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          10                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(196) Variable = HIPK2 MUTATION ANALYSIS
D196V1, survival
                 sevent
clus2               0   1
  HIPK2 MUTATED    18   6
  HIPK2 WILD-TYPE 259  72
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             24             331 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
              6              72 
$`HIPK2 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3811 
       35.80        26.17        79.69        23.87         3.02        10.06 
TCGA-AA-3947 TCGA-AA-A02O TCGA-AD-6901 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 
       33.01         0.92        22.42        14.50        27.09        21.44 
TCGA-CK-4950 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6539 
       85.45        15.02        14.04        14.04        25.48        12.49 
TCGA-D5-6541 TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
       15.58        49.91        44.32        35.31        65.85        53.62 

$`HIPK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       22.09        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6780 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-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-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        54.61        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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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        43.04 
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-G4-6306 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-G4-6626 
       46.75 

  HIPK2 MUTATED HIPK2 WILD-TYPE 
           0.92            0.00 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
          85.45          148.01 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
         24.675          21.990 
[1] "0.9 - 85.5 (24.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D196V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIPK2 MUTATED         5        0        2         8         2         0
  HIPK2 WILD-TYPE      59        1       24       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIPK2 MUTATED           1          0          2          0        1         0
  HIPK2 WILD-TYPE        17          6         42         33       34        12
                 vv
clus              STAGE IVB
  HIPK2 MUTATED           0
  HIPK2 WILD-TYPE         1
D196V3, multiclass
            clus
vv           HIPK2 MUTATED HIPK2 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HIPK2 MUTATED     1   4  16   3
  HIPK2 WILD-TYPE   8  63 233  38
D196V4, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            16             233
  T4             3              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
  HIPK2 MUTATED    20   3   1
  HIPK2 WILD-TYPE 200  78  65
D196V5, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  N0            20             200
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V6, binary
                 cls
clus                0   1
  HIPK2 MUTATED    21   1
  HIPK2 WILD-TYPE 264  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     21    1
  HIPK2 WILD-TYPE  264   47
   clus
vv  HIPK2 MUTATED HIPK2 WILD-TYPE
  0            21             264
  1             1              47
[1] 2 2
[1] FALSE
D196V7, binary
                 cls
clus                0   1
  HIPK2 MUTATED    15   9
  HIPK2 WILD-TYPE 155 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     15    9
  HIPK2 WILD-TYPE  155  188
        clus
vv       HIPK2 MUTATED HIPK2 WILD-TYPE
  FEMALE            15             155
  MALE               9             188
[1] 2 2
[1] FALSE
D196V8, binary
                 cls
clus                0   1
  HIPK2 MUTATED    20   0
  HIPK2 WILD-TYPE 280   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     20    0
  HIPK2 WILD-TYPE  280    8
     clus
vv    HIPK2 MUTATED HIPK2 WILD-TYPE
  NO             20             280
  YES             0               8
[1] 2 2
[1] FALSE
D196V9, binary
                 cls
clus                0   1
  HIPK2 MUTATED    20   4
  HIPK2 WILD-TYPE 294  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     20    4
  HIPK2 WILD-TYPE  294   44
                               clus
vv                              HIPK2 MUTATED HIPK2 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HIPK2 MUTATED    19   1   0   0
  HIPK2 WILD-TYPE 240   2  22  21
D196V10, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  R0            19             240
  R1             1               2
  R2             0              22
  RX             0              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"
D196V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIPK2 MUTATED                                  0     0
  HIPK2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIPK2 MUTATED                           1    19
  HIPK2 WILD-TYPE                        18   157
D196V12, multiclass
                                  clus
vv                                 HIPK2 MUTATED HIPK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       19             157
[1] 4 2
[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 = SHROOM4 MUTATION ANALYSIS
D197V1, survival
                   sevent
clus2                 0   1
  SHROOM4 MUTATED    13   5
  SHROOM4 WILD-TYPE 264  73
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               18               337 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                5                73 
$`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        83.24 
TCGA-CA-5796 TCGA-CK-5913 TCGA-CM-6164 TCGA-CM-6678 TCGA-D5-6537 TCGA-D5-6540 
       12.39        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 
       10.13        10.26       135.65       139.17       119.93         6.18 

$`SHROOM4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       44.32       131.51        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             4.01              0.00 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           139.17            148.01 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           22.585            22.060 
[1] "4.0 - 139.2 (22.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D197V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SHROOM4 MUTATED         3        0        0        10         3         0
  SHROOM4 WILD-TYPE      61        1       26        98         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SHROOM4 MUTATED           1          1          2          0        0
  SHROOM4 WILD-TYPE        17          5         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SHROOM4 MUTATED           1         0
  SHROOM4 WILD-TYPE        11         1
D197V3, multiclass
            clus
vv           SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA               10                98
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  SHROOM4 MUTATED     0   3  14   4
  SHROOM4 WILD-TYPE   9  64 235  37
D197V4, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              14               235
  T4               4                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
  SHROOM4 MUTATED    16   4   1
  SHROOM4 WILD-TYPE 204  77  65
D197V5, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  N0              16               204
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V6, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    16   1
  SHROOM4 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     16    1
  SHROOM4 WILD-TYPE  269   47
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0              16               269
  1               1                47
[1] 2 2
[1] FALSE
D197V7, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    14   7
  SHROOM4 WILD-TYPE 156 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     14    7
  SHROOM4 WILD-TYPE  156  190
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE              14               156
  MALE                 7               190
[1] 2 2
[1] FALSE
D197V8, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    14   0
  SHROOM4 WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     14    0
  SHROOM4 WILD-TYPE  286    8
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D197V9, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    15   5
  SHROOM4 WILD-TYPE 299  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     15    5
  SHROOM4 WILD-TYPE  299   43
                               clus
vv                              SHROOM4 MUTATED SHROOM4 WILD-TYPE
  COLON ADENOCARCINOMA                       15               299
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SHROOM4 MUTATED    15   0   0   3
  SHROOM4 WILD-TYPE 244   3  22  18
D197V10, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0              15               244
  R1               0                 3
  R2               0                22
  RX               3                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"
D197V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SHROOM4 MUTATED                                  0     2
  SHROOM4 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED                           1    13
  SHROOM4 WILD-TYPE                        18   163
D197V12, multiclass
                                  clus
vv                                 SHROOM4 MUTATED SHROOM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         13               163
[1] 4 2
[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 = DDX43 MUTATION ANALYSIS
D198V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     9   2
  DDX43 WILD-TYPE 268  76
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             344 
  DDX43 MUTATED DDX43 WILD-TYPE 
              2              76 
$`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 
       21.14        14.04        43.27        85.48        46.75 

$`DDX43 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       27.09        22.52        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 
       36.00        13.78 

  DDX43 MUTATED DDX43 WILD-TYPE 
           8.38            0.00 
  DDX43 MUTATED DDX43 WILD-TYPE 
          85.48          148.01 
  DDX43 MUTATED DDX43 WILD-TYPE 
          33.04           21.99 
[1] "8.4 - 85.5 (33.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D198V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX43 MUTATED         3        0        1         5         0         0
  DDX43 WILD-TYPE      61        1       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX43 MUTATED           0          0          1          0        0         1
  DDX43 WILD-TYPE        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  DDX43 MUTATED           0
  DDX43 WILD-TYPE         1
D198V3, multiclass
            clus
vv           DDX43 MUTATED DDX43 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  DDX43 MUTATED     1   2   8   0
  DDX43 WILD-TYPE   8  65 241  41
D198V4, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             8             241
  T4             0              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
  DDX43 MUTATED     9   2   0
  DDX43 WILD-TYPE 211  79  66
D198V5, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V6, binary
                 cls
clus                0   1
  DDX43 MUTATED    10   1
  DDX43 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     10    1
  DDX43 WILD-TYPE  275   47
   clus
vv  DDX43 MUTATED DDX43 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D198V7, binary
                 cls
clus                0   1
  DDX43 MUTATED     6   5
  DDX43 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      6    5
  DDX43 WILD-TYPE  164  192
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D198V8, binary
                 cls
clus                0   1
  DDX43 MUTATED    11   0
  DDX43 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     11    0
  DDX43 WILD-TYPE  289    8
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D198V9, binary
                 cls
clus                0   1
  DDX43 MUTATED    10   1
  DDX43 WILD-TYPE 304  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     10    1
  DDX43 WILD-TYPE  304   47
                               clus
vv                              DDX43 MUTATED DDX43 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX43 MUTATED     7   0   0   1
  DDX43 WILD-TYPE 252   3  22  20
D198V10, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D198V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX43 MUTATED                                  0     0
  DDX43 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX43 MUTATED                           2     7
  DDX43 WILD-TYPE                        17   169
D198V12, multiclass
                                  clus
vv                                 DDX43 MUTATED DDX43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        7             169
[1] 4 2
[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 = LHCGR MUTATION ANALYSIS
D199V1, survival
                 sevent
clus2               0   1
  LHCGR MUTATED    18   5
  LHCGR WILD-TYPE 259  73
  LHCGR MUTATED LHCGR WILD-TYPE 
             23             332 
  LHCGR MUTATED LHCGR WILD-TYPE 
              5              73 
$`LHCGR MUTATED`
TCGA-AA-3662 TCGA-G4-6586 TCGA-A6-3808 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-A00O 
        6.05        35.80        33.34        63.98        61.02        27.02 
TCGA-AA-A029 TCGA-AD-6965 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6716 
       51.98        26.47        58.39        49.41         6.77        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6166 
       12.76        10.06         2.01        22.03        32.02        21.99 
TCGA-D5-6541 TCGA-D5-6932 TCGA-DM-A28G TCGA-F4-6570 TCGA-F4-6807 
       15.58        11.38        60.79         6.18        43.04 

$`LHCGR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        37.02        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        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        12.36        12.39        12.59        12.59 
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-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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-6167 TCGA-CM-6168 
       12.00        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-A28C TCGA-DM-A28E 
       44.32       131.51       135.65       139.17        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LHCGR MUTATED LHCGR WILD-TYPE 
           2.01            0.00 
  LHCGR MUTATED LHCGR WILD-TYPE 
          63.98          148.01 
  LHCGR MUTATED LHCGR WILD-TYPE 
         26.470          22.025 
[1] "2.0 - 64.0 (26.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D199V2, continuous
                 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      62        1       22        96         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LHCGR MUTATED           0          0          1          3        2         0
  LHCGR WILD-TYPE        18          6         43         30       33        12
                 vv
clus              STAGE IVB
  LHCGR MUTATED           0
  LHCGR WILD-TYPE         1
D199V3, multiclass
            clus
vv           LHCGR MUTATED LHCGR WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             12              96
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             3              30
  STAGE IV               2              33
  STAGE IVA              0              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
  LHCGR MUTATED     0   2  20   2
  LHCGR WILD-TYPE   9  65 229  39
D199V4, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  T1             0               9
  T2             2              65
  T3            20             229
  T4             2              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
  LHCGR MUTATED    18   2   4
  LHCGR WILD-TYPE 202  79  62
D199V5, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  N0            18             202
  N1             2              79
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V6, binary
                 cls
clus                0   1
  LHCGR MUTATED    20   2
  LHCGR WILD-TYPE 265  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     20    2
  LHCGR WILD-TYPE  265   46
   clus
vv  LHCGR MUTATED LHCGR WILD-TYPE
  0            20             265
  1             2              46
[1] 2 2
[1] FALSE
D199V7, binary
                 cls
clus                0   1
  LHCGR MUTATED    10  14
  LHCGR WILD-TYPE 160 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     10   14
  LHCGR WILD-TYPE  160  183
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  FEMALE            10             160
  MALE              14             183
[1] 2 2
[1] FALSE
D199V8, binary
                 cls
clus                0   1
  LHCGR MUTATED    22   0
  LHCGR WILD-TYPE 278   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     22    0
  LHCGR WILD-TYPE  278    8
     clus
vv    LHCGR MUTATED LHCGR WILD-TYPE
  NO             22             278
  YES             0               8
[1] 2 2
[1] FALSE
D199V9, binary
                 cls
clus                0   1
  LHCGR MUTATED    22   2
  LHCGR WILD-TYPE 292  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     22    2
  LHCGR WILD-TYPE  292   46
                               clus
vv                              LHCGR MUTATED LHCGR WILD-TYPE
  COLON ADENOCARCINOMA                     22             292
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LHCGR MUTATED    15   1   1   4
  LHCGR WILD-TYPE 244   2  21  17
D199V10, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  R0            15             244
  R1             1               2
  R2             1              21
  RX             4              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"
D199V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LHCGR MUTATED                                  0     3
  LHCGR WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LHCGR MUTATED                           0    15
  LHCGR WILD-TYPE                        19   161
D199V12, multiclass
                                  clus
vv                                 LHCGR MUTATED LHCGR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       15             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(200) Variable = USP34 MUTATION ANALYSIS
D200V1, survival
                 sevent
clus2               0   1
  USP34 MUTATED    29  12
  USP34 WILD-TYPE 248  66
  USP34 MUTATED USP34 WILD-TYPE 
             41             314 
  USP34 MUTATED USP34 WILD-TYPE 
             12              66 
$`USP34 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3867 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6321 
       19.04        19.04        24.03        25.08       100.01        22.09 
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3815 
       35.80        79.69        19.66         6.97        50.04        33.04 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6889 
       33.01        20.98        25.02         4.01        12.16        83.24 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 
       58.39        49.41        11.74        12.76        10.06        85.45 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-6535 
        2.01        23.05        13.02        14.99        14.04        15.12 
TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HB 
       16.14         9.44        11.38        13.32         7.50       135.65 
TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6626 
        6.18        65.85        85.48        61.91        46.75 

$`USP34 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       63.62        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3956 
       18.05        31.00         2.01        24.00        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       21.99        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        54.61        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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       49.91        12.59       140.38        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-F4-6703 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        43.04        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-G4-6317 TCGA-G4-6323 
       36.00        13.78 

  USP34 MUTATED USP34 WILD-TYPE 
           2.01            0.00 
  USP34 MUTATED USP34 WILD-TYPE 
         135.65          148.01 
  USP34 MUTATED USP34 WILD-TYPE 
         20.980          22.075 
[1] "2.0 - 135.7 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D200V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP34 MUTATED         4        0        5        13         3         0
  USP34 WILD-TYPE      60        1       21        95         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP34 MUTATED           1          0          6          3        6         0
  USP34 WILD-TYPE        17          6         38         30       29        12
                 vv
clus              STAGE IVB
  USP34 MUTATED           0
  USP34 WILD-TYPE         1
D200V3, multiclass
            clus
vv           USP34 MUTATED USP34 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             13              95
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             3              30
  STAGE IV               6              29
  STAGE IVA              0              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
  USP34 MUTATED     0   7  30   5
  USP34 WILD-TYPE   9  60 219  36
D200V4, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  T1             0               9
  T2             7              60
  T3            30             219
  T4             5              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
  USP34 MUTATED    27  10   5
  USP34 WILD-TYPE 193  71  61
D200V5, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  N0            27             193
  N1            10              71
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V6, binary
                 cls
clus                0   1
  USP34 MUTATED    29   6
  USP34 WILD-TYPE 256  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     29    6
  USP34 WILD-TYPE  256   42
   clus
vv  USP34 MUTATED USP34 WILD-TYPE
  0            29             256
  1             6              42
[1] 2 2
[1] FALSE
D200V7, binary
                 cls
clus                0   1
  USP34 MUTATED    16  26
  USP34 WILD-TYPE 154 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     16   26
  USP34 WILD-TYPE  154  171
        clus
vv       USP34 MUTATED USP34 WILD-TYPE
  FEMALE            16             154
  MALE              26             171
[1] 2 2
[1] FALSE
D200V8, binary
                 cls
clus                0   1
  USP34 MUTATED    36   1
  USP34 WILD-TYPE 264   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     36    1
  USP34 WILD-TYPE  264    7
     clus
vv    USP34 MUTATED USP34 WILD-TYPE
  NO             36             264
  YES             1               7
[1] 2 2
[1] FALSE
D200V9, binary
                 cls
clus                0   1
  USP34 MUTATED    32   8
  USP34 WILD-TYPE 282  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     32    8
  USP34 WILD-TYPE  282   40
                               clus
vv                              USP34 MUTATED USP34 WILD-TYPE
  COLON ADENOCARCINOMA                     32             282
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP34 MUTATED    27   1   2   5
  USP34 WILD-TYPE 232   2  20  16
D200V10, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  R0            27             232
  R1             1               2
  R2             2              20
  RX             5              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"
D200V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP34 MUTATED                                  0     3
  USP34 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP34 MUTATED                           4    25
  USP34 WILD-TYPE                        15   151
D200V12, multiclass
                                  clus
vv                                 USP34 MUTATED USP34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       25             151
[1] 4 2
[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 = ERCC5 MUTATION ANALYSIS
D201V1, survival
                 sevent
clus2               0   1
  ERCC5 MUTATED    12   8
  ERCC5 WILD-TYPE 265  70
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             20             335 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
              8              70 
$`ERCC5 MUTATED`
TCGA-AZ-6608 TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3655 
        1.94        46.65        22.06        20.12         3.02        61.02 
TCGA-AA-3815 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-6171 
       33.04         4.01        58.39        49.41        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 
       41.42        13.25 

$`ERCC5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      135.65        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-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       34.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ERCC5 MUTATED ERCC5 WILD-TYPE 
           1.94            0.00 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
         139.17          148.01 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
         28.735          21.990 
[1] "1.9 - 139.2 (28.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D201V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC5 MUTATED         2        0        3        10         1         0
  ERCC5 WILD-TYPE      62        1       23        98         7         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        18          5         42         33       35        11
                 vv
clus              STAGE IVB
  ERCC5 MUTATED           0
  ERCC5 WILD-TYPE         1
D201V3, multiclass
            clus
vv           ERCC5 MUTATED ERCC5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             10              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  ERCC5 MUTATED     0   3  16   1
  ERCC5 WILD-TYPE   9  64 233  40
D201V4, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            16             233
  T4             1              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
  ERCC5 MUTATED    15   4   1
  ERCC5 WILD-TYPE 205  77  65
D201V5, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  N0            15             205
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V6, binary
                 cls
clus                0   1
  ERCC5 MUTATED    16   1
  ERCC5 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     16    1
  ERCC5 WILD-TYPE  269   47
   clus
vv  ERCC5 MUTATED ERCC5 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D201V7, binary
                 cls
clus                0   1
  ERCC5 MUTATED    11   9
  ERCC5 WILD-TYPE 159 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     11    9
  ERCC5 WILD-TYPE  159  188
        clus
vv       ERCC5 MUTATED ERCC5 WILD-TYPE
  FEMALE            11             159
  MALE               9             188
[1] 2 2
[1] FALSE
D201V8, binary
                 cls
clus                0   1
  ERCC5 MUTATED    16   0
  ERCC5 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     16    0
  ERCC5 WILD-TYPE  284    8
     clus
vv    ERCC5 MUTATED ERCC5 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D201V9, binary
                 cls
clus                0   1
  ERCC5 MUTATED    18   2
  ERCC5 WILD-TYPE 296  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     18    2
  ERCC5 WILD-TYPE  296   46
                               clus
vv                              ERCC5 MUTATED ERCC5 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERCC5 MUTATED    13   0   0   1
  ERCC5 WILD-TYPE 246   3  22  20
D201V10, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             1              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"
D201V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC5 MUTATED                                  0     0
  ERCC5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERCC5 MUTATED                           0    16
  ERCC5 WILD-TYPE                        19   160
D201V12, multiclass
                                  clus
vv                                 ERCC5 MUTATED ERCC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       16             160
[1] 4 2
[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 = HIST1H1T MUTATION ANALYSIS
D202V1, survival
                    sevent
clus2                  0   1
  HIST1H1T MUTATED     6   3
  HIST1H1T WILD-TYPE 271  75
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 9                346 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 3                 75 
$`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        54.61        25.48        10.13 
TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1D6 
       13.35        92.75        49.91 

$`HIST1H1T WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-D5-6534 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         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
              6.97               0.00 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
             92.75             148.01 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
            25.480             22.045 
[1] "7.0 - 92.8 (25.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D202V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1T MUTATED         0        0        1         5         0         0
  HIST1H1T WILD-TYPE      64        1       25       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1T MUTATED           0          1          1          0        0
  HIST1H1T WILD-TYPE        18          5         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1T MUTATED           0         0
  HIST1H1T WILD-TYPE        12         1
D202V3, multiclass
            clus
vv           HIST1H1T MUTATED HIST1H1T WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  HIST1H1T MUTATED     0   0   8   1
  HIST1H1T WILD-TYPE   9  67 241  40
D202V4, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                8                241
  T4                1                 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
  HIST1H1T MUTATED     7   2   0
  HIST1H1T WILD-TYPE 213  79  66
D202V5, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  N0                7                213
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V6, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     9   0
  HIST1H1T WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      9    0
  HIST1H1T WILD-TYPE  276   48
   clus
vv  HIST1H1T MUTATED HIST1H1T WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D202V7, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     3   6
  HIST1H1T WILD-TYPE 167 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      3    6
  HIST1H1T WILD-TYPE  167  191
        clus
vv       HIST1H1T MUTATED HIST1H1T WILD-TYPE
  FEMALE                3                167
  MALE                  6                191
[1] 2 2
[1] FALSE
D202V8, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     7   0
  HIST1H1T WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      7    0
  HIST1H1T WILD-TYPE  293    8
     clus
vv    HIST1H1T MUTATED HIST1H1T WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D202V9, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     7   2
  HIST1H1T WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      7    2
  HIST1H1T WILD-TYPE  307   46
                               clus
vv                              HIST1H1T MUTATED HIST1H1T WILD-TYPE
  COLON ADENOCARCINOMA                         7                307
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1T MUTATED     6   0   0   0
  HIST1H1T WILD-TYPE 253   3  22  21
D202V10, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D202V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1T MUTATED                                  0     0
  HIST1H1T WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1T MUTATED                           2     6
  HIST1H1T WILD-TYPE                        17   170
D202V12, multiclass
                                  clus
vv                                 HIST1H1T MUTATED HIST1H1T WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                           6                170
[1] 4 2
[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 = RBPJ MUTATION ANALYSIS
D203V1, survival
                sevent
clus2              0   1
  RBPJ MUTATED    11   4
  RBPJ WILD-TYPE 266  74
  RBPJ MUTATED RBPJ WILD-TYPE 
            15            340 
  RBPJ MUTATED RBPJ WILD-TYPE 
             4             74 
$`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        12.16 
TCGA-AD-6889 TCGA-AY-6197 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6674 
       83.24        21.44        12.20        12.76        32.02        12.95 
TCGA-D5-6537 TCGA-G4-6303 TCGA-G4-6626 
        4.80        65.85        46.75 

$`RBPJ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        27.02         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       85.48        61.91        36.00        13.78 

  RBPJ MUTATED RBPJ WILD-TYPE 
           4.8            0.0 
  RBPJ MUTATED RBPJ WILD-TYPE 
         83.24         148.01 
  RBPJ MUTATED RBPJ WILD-TYPE 
        21.440         22.075 
[1] "4.8 - 83.2 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D203V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBPJ MUTATED         1        0        0         9         2         0
  RBPJ WILD-TYPE      63        1       26        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBPJ MUTATED           0          0          2          0        1         0
  RBPJ WILD-TYPE        18          6         42         33       34        12
                vv
clus             STAGE IVB
  RBPJ MUTATED           0
  RBPJ WILD-TYPE         1
D203V3, multiclass
            clus
vv           RBPJ MUTATED RBPJ WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             9             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  RBPJ MUTATED     0   1  11   3
  RBPJ WILD-TYPE   9  66 238  38
D203V4, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  T1            0              9
  T2            1             66
  T3           11            238
  T4            3             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
  RBPJ MUTATED    12   3   0
  RBPJ WILD-TYPE 208  78  66
D203V5, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  N0           12            208
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V6, binary
                cls
clus               0   1
  RBPJ MUTATED    10   1
  RBPJ WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     10    1
  RBPJ WILD-TYPE  275   47
   clus
vv  RBPJ MUTATED RBPJ WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D203V7, binary
                cls
clus               0   1
  RBPJ MUTATED     4  11
  RBPJ WILD-TYPE 166 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      4   11
  RBPJ WILD-TYPE  166  186
        clus
vv       RBPJ MUTATED RBPJ WILD-TYPE
  FEMALE            4            166
  MALE             11            186
[1] 2 2
[1] FALSE
D203V8, binary
                cls
clus               0   1
  RBPJ MUTATED    15   0
  RBPJ WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     15    0
  RBPJ WILD-TYPE  285    8
     clus
vv    RBPJ MUTATED RBPJ WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D203V9, binary
                cls
clus               0   1
  RBPJ MUTATED    12   3
  RBPJ WILD-TYPE 302  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     12    3
  RBPJ WILD-TYPE  302   45
                               clus
vv                              RBPJ MUTATED RBPJ WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBPJ MUTATED    11   0   0   2
  RBPJ WILD-TYPE 248   3  22  19
D203V10, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            2             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"
D203V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBPJ MUTATED                                  0     3
  RBPJ WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBPJ MUTATED                           1     9
  RBPJ WILD-TYPE                        18   167
D203V12, multiclass
                                  clus
vv                                 RBPJ MUTATED RBPJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       9            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(204) Variable = ADAM28 MUTATION ANALYSIS
D204V1, survival
                  sevent
clus2                0   1
  ADAM28 MUTATED     9   6
  ADAM28 WILD-TYPE 268  72
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              15              340 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
               6               72 
$`ADAM28 MUTATED`
TCGA-AA-3543 TCGA-A6-5660 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-A00N 
        0.99        29.19        24.69         3.02        63.98         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 
       35.97        35.74        46.75 

$`ADAM28 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-5864 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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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-F4-6570 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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  ADAM28 MUTATED ADAM28 WILD-TYPE 
            0.99             0.00 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
           63.98           148.01 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
          22.030           22.075 
[1] "1.0 - 64.0 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D204V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM28 MUTATED         3        0        2         4         2         0
  ADAM28 WILD-TYPE      61        1       24       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM28 MUTATED           0          0          4          1        0
  ADAM28 WILD-TYPE        18          6         40         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ADAM28 MUTATED           1         0
  ADAM28 WILD-TYPE        11         1
D204V3, multiclass
            clus
vv           ADAM28 MUTATED ADAM28 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  ADAM28 MUTATED     0   3  11   3
  ADAM28 WILD-TYPE   9  64 238  38
D204V4, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             11              238
  T4              3               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
  ADAM28 MUTATED    12   4   1
  ADAM28 WILD-TYPE 208  77  65
D204V5, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  N0             12              208
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V6, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    13   1
  ADAM28 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     13    1
  ADAM28 WILD-TYPE  272   47
   clus
vv  ADAM28 MUTATED ADAM28 WILD-TYPE
  0             13              272
  1              1               47
[1] 2 2
[1] FALSE
D204V7, binary
                  cls
clus                 0   1
  ADAM28 MUTATED     6  11
  ADAM28 WILD-TYPE 164 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED      6   11
  ADAM28 WILD-TYPE  164  186
        clus
vv       ADAM28 MUTATED ADAM28 WILD-TYPE
  FEMALE              6              164
  MALE               11              186
[1] 2 2
[1] FALSE
D204V8, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    13   0
  ADAM28 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     13    0
  ADAM28 WILD-TYPE  287    8
     clus
vv    ADAM28 MUTATED ADAM28 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D204V9, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    13   4
  ADAM28 WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     13    4
  ADAM28 WILD-TYPE  301   44
                               clus
vv                              ADAM28 MUTATED ADAM28 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ADAM28 MUTATED    10   0   0   2
  ADAM28 WILD-TYPE 249   3  22  19
D204V10, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D204V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM28 MUTATED                                  0     0
  ADAM28 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM28 MUTATED                           2    10
  ADAM28 WILD-TYPE                        17   166
D204V12, multiclass
                                  clus
vv                                 ADAM28 MUTATED ADAM28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        10              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(205) Variable = KDM5B MUTATION ANALYSIS
D205V1, survival
                 sevent
clus2               0   1
  KDM5B MUTATED    14   8
  KDM5B WILD-TYPE 263  70
  KDM5B MUTATED KDM5B WILD-TYPE 
             22             333 
  KDM5B MUTATED KDM5B WILD-TYPE 
              8              70 
$`KDM5B MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3818 
       19.04       100.01        32.75        33.53        63.98         0.99 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-6161 
       53.00        31.00        33.01        21.44        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 
      117.07         6.18        53.62        46.75 

$`KDM5B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
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-A6-6651 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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05        33.04        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       11.38        10.26       119.70        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59        44.32       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       61.91        36.00        13.78 

  KDM5B MUTATED KDM5B WILD-TYPE 
           0.99            0.00 
  KDM5B MUTATED KDM5B WILD-TYPE 
         140.38          148.01 
  KDM5B MUTATED KDM5B WILD-TYPE 
          32.88           21.99 
[1] "1.0 - 140.4 (32.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D205V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM5B MUTATED         2        0        4        11         3         0
  KDM5B WILD-TYPE      62        1       22        97         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM5B MUTATED           0          0          1          2        0         0
  KDM5B WILD-TYPE        18          6         43         31       35        12
                 vv
clus              STAGE IVB
  KDM5B MUTATED           0
  KDM5B WILD-TYPE         1
D205V3, multiclass
            clus
vv           KDM5B MUTATED KDM5B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             11              97
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  KDM5B MUTATED     1   1  18   3
  KDM5B WILD-TYPE   8  66 231  38
D205V4, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  T1             1               8
  T2             1              66
  T3            18             231
  T4             3              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
  KDM5B MUTATED    20   1   2
  KDM5B WILD-TYPE 200  80  64
D205V5, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  N0            20             200
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V6, binary
                 cls
clus                0   1
  KDM5B MUTATED    22   0
  KDM5B WILD-TYPE 263  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     22    0
  KDM5B WILD-TYPE  263   48
   clus
vv  KDM5B MUTATED KDM5B WILD-TYPE
  0            22             263
  1             0              48
[1] 2 2
[1] FALSE
D205V7, binary
                 cls
clus                0   1
  KDM5B MUTATED    12  11
  KDM5B WILD-TYPE 158 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     12   11
  KDM5B WILD-TYPE  158  186
        clus
vv       KDM5B MUTATED KDM5B WILD-TYPE
  FEMALE            12             158
  MALE              11             186
[1] 2 2
[1] FALSE
D205V8, binary
                 cls
clus                0   1
  KDM5B MUTATED    16   0
  KDM5B WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     16    0
  KDM5B WILD-TYPE  284    8
     clus
vv    KDM5B MUTATED KDM5B WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D205V9, binary
                 cls
clus                0   1
  KDM5B MUTATED    19   4
  KDM5B WILD-TYPE 295  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     19    4
  KDM5B WILD-TYPE  295   44
                               clus
vv                              KDM5B MUTATED KDM5B WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM5B MUTATED    16   0   0   1
  KDM5B WILD-TYPE 243   3  22  20
D205V10, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             1              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"
D205V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5B MUTATED                                  0     1
  KDM5B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5B MUTATED                           1    14
  KDM5B WILD-TYPE                        18   162
D205V12, multiclass
                                  clus
vv                                 KDM5B MUTATED KDM5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       14             162
[1] 4 2
[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 = RAG1AP1 MUTATION ANALYSIS
D206V1, survival
                   sevent
clus2                 0   1
  RAG1AP1 MUTATED     5   1
  RAG1AP1 WILD-TYPE 272  77
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                6               349 
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            21.990 
[1] "24.4 - 78.1 (33.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D206V2, continuous
                   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      62        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAG1AP1 MUTATED           0          0          0          0        1
  RAG1AP1 WILD-TYPE        18          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  RAG1AP1 MUTATED           0         0
  RAG1AP1 WILD-TYPE        12         1
D206V3, multiclass
            clus
vv           RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  RAG1AP1 MUTATED     0   2   4   0
  RAG1AP1 WILD-TYPE   9  65 245  41
D206V4, multiclass
    clus
vv   RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               4               245
  T4               0                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
  RAG1AP1 MUTATED     5   1   0
  RAG1AP1 WILD-TYPE 215  80  66
D206V5, multiclass
    clus
vv   RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  N0               5               215
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V6, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     5   1
  RAG1AP1 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      5    1
  RAG1AP1 WILD-TYPE  280   47
   clus
vv  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  0               5               280
  1               1                47
[1] 2 2
[1] FALSE
D206V7, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     5   1
  RAG1AP1 WILD-TYPE 165 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      5    1
  RAG1AP1 WILD-TYPE  165  196
        clus
vv       RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  FEMALE               5               165
  MALE                 1               196
[1] 2 2
[1] FALSE
D206V8, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     5   0
  RAG1AP1 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      5    0
  RAG1AP1 WILD-TYPE  295    8
     clus
vv    RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D206V9, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     6   0
  RAG1AP1 WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      6    0
  RAG1AP1 WILD-TYPE  308   48
                               clus
vv                              RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RAG1AP1 MUTATED     5   0   0   0
  RAG1AP1 WILD-TYPE 254   3  22  21
D206V10, multiclass
    clus
vv   RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D206V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAG1AP1 MUTATED                                  0     0
  RAG1AP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RAG1AP1 MUTATED                           1     3
  RAG1AP1 WILD-TYPE                        18   173
D206V12, multiclass
                                  clus
vv                                 RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = CNIH4 MUTATION ANALYSIS
D207V1, survival
                 sevent
clus2               0   1
  CNIH4 MUTATED     6   0
  CNIH4 WILD-TYPE 271  78
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             349 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              0              78 
$`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        43.04        33.67        74.56 

$`CNIH4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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-F4-6809 
        6.18        47.87         1.55        34.42        41.42        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-G4-6626 
       46.75 

  CNIH4 MUTATED CNIH4 WILD-TYPE 
          10.26            0.00 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
          74.56          148.01 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
         29.375          21.990 
[1] "10.3 - 74.6 (29.4)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D207V2, continuous
                 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      62        1       26       108         8         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        18          6         43         31       35        11
                 vv
clus              STAGE IVB
  CNIH4 MUTATED           0
  CNIH4 WILD-TYPE         1
D207V3, multiclass
            clus
vv           CNIH4 MUTATED CNIH4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              1              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
  CNIH4 MUTATED     1   1   4   0
  CNIH4 WILD-TYPE   8  66 245  41
D207V4, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             4             245
  T4             0              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
  CNIH4 MUTATED     2   2   2
  CNIH4 WILD-TYPE 218  79  64
D207V5, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  N0             2             218
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V6, binary
                 cls
clus                0   1
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  280   47
   clus
vv  CNIH4 MUTATED CNIH4 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D207V7, binary
                 cls
clus                0   1
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 165 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  165  196
        clus
vv       CNIH4 MUTATED CNIH4 WILD-TYPE
  FEMALE             5             165
  MALE               1             196
[1] 2 2
[1] FALSE
D207V8, binary
                 cls
clus                0   1
  CNIH4 MUTATED     6   0
  CNIH4 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      6    0
  CNIH4 WILD-TYPE  294    8
     clus
vv    CNIH4 MUTATED CNIH4 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D207V9, binary
                 cls
clus                0   1
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  309   47
                               clus
vv                              CNIH4 MUTATED CNIH4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CNIH4 MUTATED     5   0   0   0
  CNIH4 WILD-TYPE 254   3  22  21
D207V10, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D207V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNIH4 MUTATED                                  0     0
  CNIH4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNIH4 MUTATED                           0     6
  CNIH4 WILD-TYPE                        19   170
D207V12, multiclass
                                  clus
vv                                 CNIH4 MUTATED CNIH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = TRIM13 MUTATION ANALYSIS
D208V1, survival
                  sevent
clus2                0   1
  TRIM13 MUTATED     6   1
  TRIM13 WILD-TYPE 271  77
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               7              348 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               1               77 
$`TRIM13 MUTATED`
TCGA-AA-3662 TCGA-AA-3950 TCGA-AA-3660 TCGA-AA-3848 TCGA-AA-3977 TCGA-AY-5543 
        6.05        24.00        78.08        10.06        25.02        33.01 
TCGA-G4-6293 
      133.18 

$`TRIM13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TRIM13 MUTATED TRIM13 WILD-TYPE 
            6.05             0.00 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
          133.18           148.01 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
           25.02            22.01 
[1] "6.0 - 133.2 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D208V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM13 MUTATED         0        0        1         1         0         0
  TRIM13 WILD-TYPE      64        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM13 MUTATED           1          0          0          1        1
  TRIM13 WILD-TYPE        17          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM13 MUTATED           1         0
  TRIM13 WILD-TYPE        11         1
D208V3, multiclass
            clus
vv           TRIM13 MUTATED TRIM13 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  TRIM13 MUTATED     0   1   5   1
  TRIM13 WILD-TYPE   9  66 244  40
D208V4, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              1               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
  TRIM13 MUTATED     3   2   2
  TRIM13 WILD-TYPE 217  79  64
D208V5, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  N0              3              217
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V6, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     4   2
  TRIM13 WILD-TYPE 281  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      4    2
  TRIM13 WILD-TYPE  281   46
   clus
vv  TRIM13 MUTATED TRIM13 WILD-TYPE
  0              4              281
  1              2               46
[1] 2 2
[1] FALSE
D208V7, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     6   1
  TRIM13 WILD-TYPE 164 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      6    1
  TRIM13 WILD-TYPE  164  196
        clus
vv       TRIM13 MUTATED TRIM13 WILD-TYPE
  FEMALE              6              164
  MALE                1              196
[1] 2 2
[1] FALSE
D208V8, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     7   0
  TRIM13 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      7    0
  TRIM13 WILD-TYPE  293    8
     clus
vv    TRIM13 MUTATED TRIM13 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D208V9, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     6   1
  TRIM13 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      6    1
  TRIM13 WILD-TYPE  308   47
                               clus
vv                              TRIM13 MUTATED TRIM13 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM13 MUTATED     5   0   1   0
  TRIM13 WILD-TYPE 254   3  21  21
D208V10, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              1               21
  RX              0               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"
D208V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM13 MUTATED                                  0     0
  TRIM13 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM13 MUTATED                           1     1
  TRIM13 WILD-TYPE                        18   175
D208V12, multiclass
[1] "Remove cluster labels:" "TRIM13 MUTATED"        
clus
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"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-5913       TCGA-CK-5914       TCGA-CK-5915 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6299       TCGA-G4-6303 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 

Clustering(209) Variable = SNTN MUTATION ANALYSIS
D209V1, survival
                sevent
clus2              0   1
  SNTN MUTATED     5   0
  SNTN WILD-TYPE 272  78
  SNTN MUTATED SNTN WILD-TYPE 
             5            350 
  SNTN MUTATED SNTN WILD-TYPE 
             0             78 
$`SNTN MUTATED`
TCGA-AA-3496 TCGA-CA-6716 TCGA-CM-6676 TCGA-DM-A1HA TCGA-F4-6806 
        1.02        12.20        11.08       131.51        41.42 

$`SNTN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SNTN MUTATED SNTN WILD-TYPE 
          1.02           0.00 
  SNTN MUTATED SNTN WILD-TYPE 
        131.51         148.01 
  SNTN MUTATED SNTN WILD-TYPE 
        12.200         22.075 
[1] "1.0 - 131.5 (12.2)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D209V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNTN MUTATED         2        0        1         1         1         0
  SNTN WILD-TYPE      62        1       25       107         7         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        18          6         44         32       35        12
                vv
clus             STAGE IVB
  SNTN MUTATED           0
  SNTN WILD-TYPE         1
D209V3, multiclass
            clus
vv           SNTN MUTATED SNTN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  SNTN MUTATED     0   2   3   1
  SNTN WILD-TYPE   9  65 246  40
D209V4, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  T1            0              9
  T2            2             65
  T3            3            246
  T4            1             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
  SNTN MUTATED     5   0   1
  SNTN WILD-TYPE 215  81  65
D209V5, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  N0            5            215
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V6, binary
                cls
clus               0   1
  SNTN MUTATED     5   0
  SNTN WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      5    0
  SNTN WILD-TYPE  280   48
   clus
vv  SNTN MUTATED SNTN WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D209V7, binary
                cls
clus               0   1
  SNTN MUTATED     3   3
  SNTN WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      3    3
  SNTN WILD-TYPE  167  194
        clus
vv       SNTN MUTATED SNTN WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D209V8, binary
                cls
clus               0   1
  SNTN MUTATED     3   0
  SNTN WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      3    0
  SNTN WILD-TYPE  297    8
     clus
vv    SNTN MUTATED SNTN WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D209V9, binary
                cls
clus               0   1
  SNTN MUTATED     6   0
  SNTN WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      6    0
  SNTN WILD-TYPE  308   48
                               clus
vv                              SNTN MUTATED SNTN WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SNTN MUTATED     3   0   0   2
  SNTN WILD-TYPE 256   3  22  19
D209V10, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            2             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"
D209V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNTN MUTATED                                  0     1
  SNTN WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SNTN MUTATED                           0     4
  SNTN WILD-TYPE                        19   172
D209V12, multiclass
                                  clus
vv                                 SNTN MUTATED SNTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = SLC28A2 MUTATION ANALYSIS
D210V1, survival
                   sevent
clus2                 0   1
  SLC28A2 MUTATED     9   2
  SLC28A2 WILD-TYPE 268  76
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               11               344 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
                2                76 
$`SLC28A2 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3655 TCGA-AA-A02F TCGA-CA-6717 
        0.92       100.01        26.17        61.02        39.98        12.76 
TCGA-CK-4950 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5538 TCGA-G4-6293 
       85.45        12.99        12.95        54.61       133.18 

$`SLC28A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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-D5-5539 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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
             0.92              0.00 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
           133.18            148.01 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
            39.98             22.01 
[1] "0.9 - 133.2 (40.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D210V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC28A2 MUTATED         0        0        2         4         1         0
  SLC28A2 WILD-TYPE      64        1       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC28A2 MUTATED           3          0          2          0        1
  SLC28A2 WILD-TYPE        15          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC28A2 MUTATED           0         0
  SLC28A2 WILD-TYPE        12         1
D210V3, multiclass
            clus
vv           SLC28A2 MUTATED SLC28A2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                3                15
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC28A2 MUTATED     0   0  12   1
  SLC28A2 WILD-TYPE   9  67 237  40
D210V4, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3              12               237
  T4               1                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
  SLC28A2 MUTATED     7   5   1
  SLC28A2 WILD-TYPE 213  76  65
D210V5, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  N0               7               213
  N1               5                76
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V6, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    11   1
  SLC28A2 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     11    1
  SLC28A2 WILD-TYPE  274   47
   clus
vv  SLC28A2 MUTATED SLC28A2 WILD-TYPE
  0              11               274
  1               1                47
[1] 2 2
[1] FALSE
D210V7, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED     8   5
  SLC28A2 WILD-TYPE 162 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED      8    5
  SLC28A2 WILD-TYPE  162  192
        clus
vv       SLC28A2 MUTATED SLC28A2 WILD-TYPE
  FEMALE               8               162
  MALE                 5               192
[1] 2 2
[1] FALSE
D210V8, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    11   0
  SLC28A2 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     11    0
  SLC28A2 WILD-TYPE  289    8
     clus
vv    SLC28A2 MUTATED SLC28A2 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D210V9, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    11   2
  SLC28A2 WILD-TYPE 303  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     11    2
  SLC28A2 WILD-TYPE  303   46
                               clus
vv                              SLC28A2 MUTATED SLC28A2 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC28A2 MUTATED     8   1   1   2
  SLC28A2 WILD-TYPE 251   2  21  19
D210V10, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  R0               8               251
  R1               1                 2
  R2               1                21
  RX               2                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"
D210V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC28A2 MUTATED                                  0     1
  SLC28A2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC28A2 MUTATED                           2     6
  SLC28A2 WILD-TYPE                        17   170
D210V12, multiclass
                                  clus
vv                                 SLC28A2 MUTATED SLC28A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = OR2M3 MUTATION ANALYSIS
D211V1, survival
                 sevent
clus2               0   1
  OR2M3 MUTATED    11   3
  OR2M3 WILD-TYPE 266  75
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             14             341 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
              3              75 
$`OR2M3 MUTATED`
TCGA-CK-5912 TCGA-G4-6628 TCGA-AA-3949 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       49.08        79.69        26.01        58.39        12.76        10.06 
TCGA-CM-4744 TCGA-CM-5349 TCGA-CM-6163 TCGA-CM-6168 TCGA-D5-6540 TCGA-DM-A1D7 
       20.02        30.08        14.04        12.99        16.14        13.32 
TCGA-F4-6805 TCGA-F4-6855 
       34.42        47.41 

$`OR2M3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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-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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR2M3 MUTATED OR2M3 WILD-TYPE 
          10.06            0.00 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
          79.69          148.01 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
         23.015          22.060 
[1] "10.1 - 79.7 (23.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D211V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2M3 MUTATED         5        0        1         8         0         0
  OR2M3 WILD-TYPE      59        1       25       100         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  OR2M3 MUTATED           0
  OR2M3 WILD-TYPE         1
D211V3, multiclass
            clus
vv           OR2M3 MUTATED OR2M3 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              8             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR2M3 MUTATED     1   4   9   1
  OR2M3 WILD-TYPE   8  63 240  40
D211V4, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  T1             1               8
  T2             4              63
  T3             9             240
  T4             1              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
  OR2M3 MUTATED    14   1   0
  OR2M3 WILD-TYPE 206  80  66
D211V5, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  N0            14             206
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V6, binary
                 cls
clus                0   1
  OR2M3 MUTATED    14   0
  OR2M3 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     14    0
  OR2M3 WILD-TYPE  271   48
   clus
vv  OR2M3 MUTATED OR2M3 WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D211V7, binary
                 cls
clus                0   1
  OR2M3 MUTATED     6   9
  OR2M3 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED      6    9
  OR2M3 WILD-TYPE  164  188
        clus
vv       OR2M3 MUTATED OR2M3 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D211V8, binary
                 cls
clus                0   1
  OR2M3 MUTATED    13   0
  OR2M3 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     13    0
  OR2M3 WILD-TYPE  287    8
     clus
vv    OR2M3 MUTATED OR2M3 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D211V9, binary
                 cls
clus                0   1
  OR2M3 MUTATED    11   3
  OR2M3 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     11    3
  OR2M3 WILD-TYPE  303   45
                               clus
vv                              OR2M3 MUTATED OR2M3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2M3 MUTATED    11   0   0   3
  OR2M3 WILD-TYPE 248   3  22  18
D211V10, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             3              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"
D211V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2M3 MUTATED                                  0     2
  OR2M3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2M3 MUTATED                           1    10
  OR2M3 WILD-TYPE                        18   166
D211V12, multiclass
                                  clus
vv                                 OR2M3 MUTATED OR2M3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(212) Variable = MLL3 MUTATION ANALYSIS
D212V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    44  12
  MLL3 WILD-TYPE 233  66
  MLL3 MUTATED MLL3 WILD-TYPE 
            56            299 
  MLL3 MUTATED MLL3 WILD-TYPE 
            12             66 
$`MLL3 MUTATED`
TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6608 
        1.02         8.05         6.05        24.00        10.88         1.94 
TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       63.62        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6654 
       46.65        22.06        32.71        22.52         8.38        23.87 
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3845 
       19.66        63.98        78.08         6.97        26.99         0.00 
TCGA-AA-3846 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6899 TCGA-AU-3779 
       17.03        27.02        25.02         4.01         5.79        14.50 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-4950 
       58.39        88.21        49.41        29.56        12.76        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 
       15.62        51.32        22.03        15.02         5.03        17.03 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6540 
       12.00        14.99        12.95        19.59        18.25        16.14 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A1D7 
       12.39        12.43        11.64        13.41       130.65        13.32 
TCGA-DM-A28C TCGA-G4-6293 
       81.37       133.18 

$`MLL3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
       25.08       106.75       100.01        49.08         5.88        22.09 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 
       33.53        23.61        22.09        27.09        25.08        25.18 
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-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        61.02        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 
        1.02        17.98        15.95        38.99        37.02        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        53.00        17.03        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       24.53        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
        5.13        22.36        62.79         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 
       30.08        32.02        15.02        15.02        15.02        14.04 
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-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        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6924 
       17.13        12.49        15.58         7.53        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        13.35        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-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MLL3 MUTATED MLL3 WILD-TYPE 
             0              0 
  MLL3 MUTATED MLL3 WILD-TYPE 
        133.18         148.01 
  MLL3 MUTATED MLL3 WILD-TYPE 
        19.625         22.360 
[1] "0.0 - 133.2 (19.6)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D212V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL3 MUTATED         5        0        5        22         2         1
  MLL3 WILD-TYPE      59        1       21        86         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL3 MUTATED           1          2          7          4        4         2
  MLL3 WILD-TYPE        17          4         37         29       31        10
                vv
clus             STAGE IVB
  MLL3 MUTATED           0
  MLL3 WILD-TYPE         1
D212V3, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA            22             86
  STAGE IIB             2              6
  STAGE IIC             1              0
  STAGE III             1             17
  STAGE IIIA            2              4
  STAGE IIIB            7             37
  STAGE IIIC            4             29
  STAGE IV              4             31
  STAGE IVA             2             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
  MLL3 MUTATED     1   7  40  10
  MLL3 WILD-TYPE   8  60 209  31
D212V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1            1              8
  T2            7             60
  T3           40            209
  T4           10             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
  MLL3 MUTATED    36  15   7
  MLL3 WILD-TYPE 184  66  59
D212V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           36            184
  N1           15             66
  N2            7             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V6, binary
                cls
clus               0   1
  MLL3 MUTATED    44   6
  MLL3 WILD-TYPE 241  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     44    6
  MLL3 WILD-TYPE  241   42
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           44            241
  1            6             42
[1] 2 2
[1] FALSE
D212V7, binary
                cls
clus               0   1
  MLL3 MUTATED    32  26
  MLL3 WILD-TYPE 138 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     32   26
  MLL3 WILD-TYPE  138  171
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           32            138
  MALE             26            171
[1] 2 2
[1] FALSE
D212V8, binary
                cls
clus               0   1
  MLL3 MUTATED    48   1
  MLL3 WILD-TYPE 252   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     48    1
  MLL3 WILD-TYPE  252    7
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO            48            252
  YES            1              7
[1] 2 2
[1] FALSE
D212V9, binary
                cls
clus               0   1
  MLL3 MUTATED    46  11
  MLL3 WILD-TYPE 268  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     46   11
  MLL3 WILD-TYPE  268   37
                               clus
vv                              MLL3 MUTATED MLL3 WILD-TYPE
  COLON ADENOCARCINOMA                    46            268
  COLON MUCINOUS ADENOCARCINOMA           11             37
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    37   1   2   4
  MLL3 WILD-TYPE 222   2  20  17
D212V10, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           37            222
  R1            1              2
  R2            2             20
  RX            4             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"
D212V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL3 MUTATED                                  0     1
  MLL3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED                           3    40
  MLL3 WILD-TYPE                        16   136
D212V12, multiclass
                                  clus
vv                                 MLL3 MUTATED MLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      40            136
[1] 4 2
[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 = FIGNL1 MUTATION ANALYSIS
D213V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED    14   1
  FIGNL1 WILD-TYPE 263  77
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              15              340 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               1               77 
$`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 
       47.87       133.18        65.85 

$`FIGNL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3519 TCGA-AA-3526 
       35.01         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6704 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        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            1.02             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
          135.65           148.01 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           34.98            21.99 
[1] "1.0 - 135.7 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "6.1"
D213V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FIGNL1 MUTATED         0        0        1         8         1         0
  FIGNL1 WILD-TYPE      64        1       25       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIGNL1 MUTATED           1          0          2          1        1
  FIGNL1 WILD-TYPE        17          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  FIGNL1 MUTATED           1         0
  FIGNL1 WILD-TYPE        11         1
D213V3, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  FIGNL1 MUTATED     0   0  13   3
  FIGNL1 WILD-TYPE   9  67 236  38
D213V4, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             13              236
  T4              3               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
  FIGNL1 MUTATED    10   4   2
  FIGNL1 WILD-TYPE 210  77  64
D213V5, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0             10              210
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V6, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    14   2
  FIGNL1 WILD-TYPE 271  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     14    2
  FIGNL1 WILD-TYPE  271   46
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0             14              271
  1              2               46
[1] 2 2
[1] FALSE
D213V7, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     9   7
  FIGNL1 WILD-TYPE 161 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      9    7
  FIGNL1 WILD-TYPE  161  190
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  FEMALE              9              161
  MALE                7              190
[1] 2 2
[1] FALSE
D213V8, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    11   0
  FIGNL1 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     11    0
  FIGNL1 WILD-TYPE  289    8
     clus
vv    FIGNL1 MUTATED FIGNL1 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D213V9, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    12   3
  FIGNL1 WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     12    3
  FIGNL1 WILD-TYPE  302   45
                               clus
vv                              FIGNL1 MUTATED FIGNL1 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FIGNL1 MUTATED    11   0   0   2
  FIGNL1 WILD-TYPE 248   3  22  19
D213V10, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              2               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"
D213V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FIGNL1 MUTATED                                  0     1
  FIGNL1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FIGNL1 MUTATED                           1     9
  FIGNL1 WILD-TYPE                        18   167
D213V12, multiclass
                                  clus
vv                                 FIGNL1 MUTATED FIGNL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(214) Variable = COLEC10 MUTATION ANALYSIS
D214V1, survival
                   sevent
clus2                 0   1
  COLEC10 MUTATED     6   2
  COLEC10 WILD-TYPE 271  76
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                8               347 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                2                76 
$`COLEC10 MUTATED`
TCGA-AA-3715 TCGA-AZ-4681 TCGA-A6-5660 TCGA-AA-3821 TCGA-CM-5348 TCGA-CM-5862 
       19.04       106.75        29.19         1.02        22.98         5.03 
TCGA-D5-5541 TCGA-DM-A1HA 
       55.92       131.51 

$`COLEC10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       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 
       54.61        19.59        56.09        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50        44.32       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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  COLEC10 MUTATED COLEC10 WILD-TYPE 
             1.02              0.00 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
           131.51            148.01 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
           26.085            22.030 
[1] "1.0 - 131.5 (26.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D214V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COLEC10 MUTATED         1        0        1         1         0         0
  COLEC10 WILD-TYPE      63        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COLEC10 MUTATED           0          0          2          2        0
  COLEC10 WILD-TYPE        18          6         42         31       35
                   vv
clus                STAGE IVA STAGE IVB
  COLEC10 MUTATED           1         0
  COLEC10 WILD-TYPE        11         1
D214V3, multiclass
            clus
vv           COLEC10 MUTATED COLEC10 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                1                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
  COLEC10 MUTATED     0   1   7   0
  COLEC10 WILD-TYPE   9  66 242  41
D214V4, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               7               242
  T4               0                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
  COLEC10 MUTATED     3   3   2
  COLEC10 WILD-TYPE 217  78  64
D214V5, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  N0               3               217
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V6, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     7   1
  COLEC10 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      7    1
  COLEC10 WILD-TYPE  278   47
   clus
vv  COLEC10 MUTATED COLEC10 WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D214V7, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     2   6
  COLEC10 WILD-TYPE 168 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      2    6
  COLEC10 WILD-TYPE  168  191
        clus
vv       COLEC10 MUTATED COLEC10 WILD-TYPE
  FEMALE               2               168
  MALE                 6               191
[1] 2 2
[1] FALSE
D214V8, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     7   0
  COLEC10 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      7    0
  COLEC10 WILD-TYPE  293    8
     clus
vv    COLEC10 MUTATED COLEC10 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D214V9, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     7   1
  COLEC10 WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      7    1
  COLEC10 WILD-TYPE  307   47
                               clus
vv                              COLEC10 MUTATED COLEC10 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  COLEC10 MUTATED     6   0   0   0
  COLEC10 WILD-TYPE 253   3  22  21
D214V10, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               0                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"
D214V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COLEC10 MUTATED                                  0     0
  COLEC10 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COLEC10 MUTATED                           1     5
  COLEC10 WILD-TYPE                        18   171
D214V12, multiclass
                                  clus
vv                                 COLEC10 MUTATED COLEC10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = MYEOV MUTATION ANALYSIS
D215V1, survival
                 sevent
clus2               0   1
  MYEOV MUTATED     5   1
  MYEOV WILD-TYPE 272  77
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             349 
  MYEOV MUTATED MYEOV WILD-TYPE 
              1              77 
$`MYEOV MUTATED`
TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-A00E TCGA-AD-6889 TCGA-AU-6004 TCGA-D5-6923 
       26.17        33.53        30.02        83.24        27.09        12.43 

$`MYEOV WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYEOV MUTATED MYEOV WILD-TYPE 
          12.43            0.00 
  MYEOV MUTATED MYEOV WILD-TYPE 
          83.24          148.01 
  MYEOV MUTATED MYEOV WILD-TYPE 
         28.555          21.990 
[1] "12.4 - 83.2 (28.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D215V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYEOV MUTATED         2        0        0         4         0         0
  MYEOV WILD-TYPE      62        1       26       104         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  MYEOV MUTATED           0
  MYEOV WILD-TYPE         1
D215V3, multiclass
            clus
vv           MYEOV MUTATED MYEOV WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MYEOV MUTATED     0   2   4   0
  MYEOV WILD-TYPE   9  65 245  41
D215V4, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             0              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
  MYEOV MUTATED     6   0   0
  MYEOV WILD-TYPE 214  81  66
D215V5, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  N0             6             214
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V6, binary
                 cls
clus                0   1
  MYEOV MUTATED     6   0
  MYEOV WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      6    0
  MYEOV WILD-TYPE  279   48
   clus
vv  MYEOV MUTATED MYEOV WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D215V7, binary
                 cls
clus                0   1
  MYEOV MUTATED     3   3
  MYEOV WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      3    3
  MYEOV WILD-TYPE  167  194
        clus
vv       MYEOV MUTATED MYEOV WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D215V8, binary
                 cls
clus                0   1
  MYEOV MUTATED     5   0
  MYEOV WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      5    0
  MYEOV WILD-TYPE  295    8
     clus
vv    MYEOV MUTATED MYEOV WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D215V9, binary
                 cls
clus                0   1
  MYEOV MUTATED     6   0
  MYEOV WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      6    0
  MYEOV WILD-TYPE  308   48
                               clus
vv                              MYEOV MUTATED MYEOV WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYEOV MUTATED     6   0   0   0
  MYEOV WILD-TYPE 253   3  22  21
D215V10, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D215V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYEOV MUTATED                                  0     1
  MYEOV WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYEOV MUTATED                           1     3
  MYEOV WILD-TYPE                        18   173
D215V12, multiclass
                                  clus
vv                                 MYEOV MUTATED MYEOV WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = EFHC2 MUTATION ANALYSIS
D216V1, survival
                 sevent
clus2               0   1
  EFHC2 MUTATED    11   4
  EFHC2 WILD-TYPE 266  74
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             15             340 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
              4              74 
$`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        12.16        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 
       15.12        44.32        35.31 

$`EFHC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50       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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  EFHC2 MUTATED EFHC2 WILD-TYPE 
           3.02            0.00 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
          58.39          148.01 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
          15.12           22.09 
[1] "3.0 - 58.4 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D216V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFHC2 MUTATED         5        0        1         5         1         0
  EFHC2 WILD-TYPE      59        1       25       103         7         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  EFHC2 MUTATED           0
  EFHC2 WILD-TYPE         1
D216V3, multiclass
            clus
vv           EFHC2 MUTATED EFHC2 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  EFHC2 MUTATED     1   5   7   2
  EFHC2 WILD-TYPE   8  62 242  39
D216V4, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  T1             1               8
  T2             5              62
  T3             7             242
  T4             2              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
  EFHC2 MUTATED    13   1   1
  EFHC2 WILD-TYPE 207  80  65
D216V5, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  N0            13             207
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V6, binary
                 cls
clus                0   1
  EFHC2 MUTATED    12   0
  EFHC2 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED     12    0
  EFHC2 WILD-TYPE  273   48
   clus
vv  EFHC2 MUTATED EFHC2 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D216V7, binary
                 cls
clus                0   1
  EFHC2 MUTATED     6   9
  EFHC2 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED      6    9
  EFHC2 WILD-TYPE  164  188
        clus
vv       EFHC2 MUTATED EFHC2 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D216V8, binary
                 cls
clus                0   1
  EFHC2 MUTATED    12   0
  EFHC2 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED     12    0
  EFHC2 WILD-TYPE  288    8
     clus
vv    EFHC2 MUTATED EFHC2 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D216V9, binary
                 cls
clus                0   1
  EFHC2 MUTATED     9   6
  EFHC2 WILD-TYPE 305  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED      9    6
  EFHC2 WILD-TYPE  305   42
                               clus
vv                              EFHC2 MUTATED EFHC2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EFHC2 MUTATED     9   0   0   4
  EFHC2 WILD-TYPE 250   3  22  17
D216V10, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             4              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"
D216V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFHC2 MUTATED                                  0     2
  EFHC2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFHC2 MUTATED                           0     9
  EFHC2 WILD-TYPE                        19   167
D216V12, multiclass
                                  clus
vv                                 EFHC2 MUTATED EFHC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(217) Variable = MYL1 MUTATION ANALYSIS
D217V1, survival
                sevent
clus2              0   1
  MYL1 MUTATED     5   2
  MYL1 WILD-TYPE 272  76
  MYL1 MUTATED MYL1 WILD-TYPE 
             7            348 
  MYL1 MUTATED MYL1 WILD-TYPE 
             2             76 
$`MYL1 MUTATED`
TCGA-AA-3979 TCGA-A6-5662 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6172 
       24.00        23.61        21.14         5.03        14.04        11.01 
TCGA-D5-5540 
       56.09 

$`MYL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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-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-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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        19.59        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MYL1 MUTATED MYL1 WILD-TYPE 
          5.03           0.00 
  MYL1 MUTATED MYL1 WILD-TYPE 
         56.09         148.01 
  MYL1 MUTATED MYL1 WILD-TYPE 
        21.140         22.075 
[1] "5.0 - 56.1 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D217V2, continuous
                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      61        1       26       106         8         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        18          6         43         33       35        10
                vv
clus             STAGE IVB
  MYL1 MUTATED           0
  MYL1 WILD-TYPE         1
D217V3, multiclass
            clus
vv           MYL1 MUTATED MYL1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             2             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
  MYL1 MUTATED     2   1   5   0
  MYL1 WILD-TYPE   7  66 244  41
D217V4, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  T1            2              7
  T2            1             66
  T3            5            244
  T4            0             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
  MYL1 MUTATED     5   2   1
  MYL1 WILD-TYPE 215  79  65
D217V5, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  N0            5            215
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V6, binary
                cls
clus               0   1
  MYL1 MUTATED     5   2
  MYL1 WILD-TYPE 280  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      5    2
  MYL1 WILD-TYPE  280   46
   clus
vv  MYL1 MUTATED MYL1 WILD-TYPE
  0            5            280
  1            2             46
[1] 2 2
[1] FALSE
D217V7, binary
                cls
clus               0   1
  MYL1 MUTATED     2   6
  MYL1 WILD-TYPE 168 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      2    6
  MYL1 WILD-TYPE  168  191
        clus
vv       MYL1 MUTATED MYL1 WILD-TYPE
  FEMALE            2            168
  MALE              6            191
[1] 2 2
[1] FALSE
D217V8, binary
                cls
clus               0   1
  MYL1 MUTATED     7   0
  MYL1 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      7    0
  MYL1 WILD-TYPE  293    8
     clus
vv    MYL1 MUTATED MYL1 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D217V9, binary
                cls
clus               0   1
  MYL1 MUTATED     8   0
  MYL1 WILD-TYPE 306  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      8    0
  MYL1 WILD-TYPE  306   48
                               clus
vv                              MYL1 MUTATED MYL1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYL1 MUTATED     5   0   0   2
  MYL1 WILD-TYPE 254   3  22  19
D217V10, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            2             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"
D217V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYL1 MUTATED                                  0     0
  MYL1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYL1 MUTATED                           0     7
  MYL1 WILD-TYPE                        19   169
D217V12, multiclass
                                  clus
vv                                 MYL1 MUTATED MYL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = C12ORF5 MUTATION ANALYSIS
D218V1, survival
                   sevent
clus2                 0   1
  C12ORF5 MUTATED     5   1
  C12ORF5 WILD-TYPE 272  77
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               349 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                1                77 
$`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        54.61       133.18        44.68 

$`C12ORF5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
            29.03              0.00 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
           133.18            148.01 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
           49.645            21.990 
[1] "29.0 - 133.2 (49.6)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.5"
D218V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF5 MUTATED         0        0        0         2         0         0
  C12ORF5 WILD-TYPE      64        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF5 MUTATED           1          0          1          1        0
  C12ORF5 WILD-TYPE        17          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  C12ORF5 MUTATED           0         0
  C12ORF5 WILD-TYPE        12         1
D218V3, multiclass
            clus
vv           C12ORF5 MUTATED C12ORF5 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  C12ORF5 MUTATED     0   1   5   0
  C12ORF5 WILD-TYPE   9  66 244  41
D218V4, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               0                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
  C12ORF5 MUTATED     3   2   1
  C12ORF5 WILD-TYPE 217  79  65
D218V5, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  N0               3               217
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V6, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  279   48
   clus
vv  C12ORF5 MUTATED C12ORF5 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D218V7, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     3   3
  C12ORF5 WILD-TYPE 167 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      3    3
  C12ORF5 WILD-TYPE  167  194
        clus
vv       C12ORF5 MUTATED C12ORF5 WILD-TYPE
  FEMALE               3               167
  MALE                 3               194
[1] 2 2
[1] FALSE
D218V8, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  294    8
     clus
vv    C12ORF5 MUTATED C12ORF5 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D218V9, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  308   48
                               clus
vv                              C12ORF5 MUTATED C12ORF5 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C12ORF5 MUTATED     5   0   0   0
  C12ORF5 WILD-TYPE 254   3  22  21
D218V10, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D218V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF5 MUTATED                                  0     0
  C12ORF5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C12ORF5 MUTATED                           1     5
  C12ORF5 WILD-TYPE                        18   171
D218V12, multiclass
                                  clus
vv                                 C12ORF5 MUTATED C12ORF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = ZNF280B MUTATION ANALYSIS
D219V1, survival
                   sevent
clus2                 0   1
  ZNF280B MUTATED    11   0
  ZNF280B WILD-TYPE 266  78
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               11               344 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
                0                78 
$`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 
       51.32        15.02        13.35       133.18        74.56 

$`ZNF280B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00         2.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 
       33.67        13.25         0.53        47.41        35.31        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ZNF280B MUTATED ZNF280B WILD-TYPE 
             12.2               0.0 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
           133.18            148.01 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
            26.01             22.01 
[1] "12.2 - 133.2 (26.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D219V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF280B MUTATED         1        0        0         5         2         0
  ZNF280B WILD-TYPE      63        1       26       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF280B MUTATED           1          0          1          1        0
  ZNF280B WILD-TYPE        17          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF280B MUTATED           1         0
  ZNF280B WILD-TYPE        11         1
D219V3, multiclass
            clus
vv           ZNF280B MUTATED ZNF280B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  ZNF280B MUTATED     0   1   9   2
  ZNF280B WILD-TYPE   9  66 240  39
D219V4, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               9               240
  T4               2                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
  ZNF280B MUTATED     8   3   1
  ZNF280B WILD-TYPE 212  78  65
D219V5, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  N0               8               212
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V6, binary
                   cls
clus                  0   1
  ZNF280B MUTATED    10   1
  ZNF280B WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED     10    1
  ZNF280B WILD-TYPE  275   47
   clus
vv  ZNF280B MUTATED ZNF280B WILD-TYPE
  0              10               275
  1               1                47
[1] 2 2
[1] FALSE
D219V7, binary
                   cls
clus                  0   1
  ZNF280B MUTATED     8   4
  ZNF280B WILD-TYPE 162 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED      8    4
  ZNF280B WILD-TYPE  162  193
        clus
vv       ZNF280B MUTATED ZNF280B WILD-TYPE
  FEMALE               8               162
  MALE                 4               193
[1] 2 2
[1] FALSE
D219V8, binary
                   cls
clus                  0   1
  ZNF280B MUTATED    11   0
  ZNF280B WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED     11    0
  ZNF280B WILD-TYPE  289    8
     clus
vv    ZNF280B MUTATED ZNF280B WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D219V9, binary
                   cls
clus                  0   1
  ZNF280B MUTATED     8   4
  ZNF280B WILD-TYPE 306  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED      8    4
  ZNF280B WILD-TYPE  306   44
                               clus
vv                              ZNF280B MUTATED ZNF280B WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF280B MUTATED     8   0   0   3
  ZNF280B WILD-TYPE 251   3  22  18
D219V10, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               3                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"
D219V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF280B MUTATED                                  0     2
  ZNF280B WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF280B MUTATED                           0     6
  ZNF280B WILD-TYPE                        19   170
D219V12, multiclass
                                  clus
vv                                 ZNF280B MUTATED ZNF280B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = MIER3 MUTATION ANALYSIS
D220V1, survival
                 sevent
clus2               0   1
  MIER3 MUTATED    10   1
  MIER3 WILD-TYPE 267  77
  MIER3 MUTATED MIER3 WILD-TYPE 
             11             344 
  MIER3 MUTATED MIER3 WILD-TYPE 
              1              77 
$`MIER3 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3526 TCGA-AA-3555 
        0.92        19.04        46.65        22.06        19.07        29.95 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CM-5861 
       53.00        25.02        34.98        27.09        15.02 

$`MIER3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3529 
        6.97         1.02        38.99         1.02         9.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MIER3 MUTATED MIER3 WILD-TYPE 
           0.92            0.00 
  MIER3 MUTATED MIER3 WILD-TYPE 
          53.00          148.01 
  MIER3 MUTATED MIER3 WILD-TYPE 
          25.02           22.01 
[1] "0.9 - 53.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D220V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIER3 MUTATED         2        0        3         4         1         0
  MIER3 WILD-TYPE      62        1       23       104         7         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  MIER3 MUTATED           0
  MIER3 WILD-TYPE         1
D220V3, multiclass
            clus
vv           MIER3 MUTATED MIER3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MIER3 MUTATED     0   3   8   2
  MIER3 WILD-TYPE   9  64 241  39
D220V4, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             8             241
  T4             2              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
  MIER3 MUTATED    11   2   0
  MIER3 WILD-TYPE 209  79  66
D220V5, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V6, binary
                 cls
clus                0   1
  MIER3 MUTATED    12   0
  MIER3 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     12    0
  MIER3 WILD-TYPE  273   48
   clus
vv  MIER3 MUTATED MIER3 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D220V7, binary
                 cls
clus                0   1
  MIER3 MUTATED     9   4
  MIER3 WILD-TYPE 161 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED      9    4
  MIER3 WILD-TYPE  161  193
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  FEMALE             9             161
  MALE               4             193
[1] 2 2
[1] FALSE
D220V8, binary
                 cls
clus                0   1
  MIER3 MUTATED    10   0
  MIER3 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     10    0
  MIER3 WILD-TYPE  290    8
     clus
vv    MIER3 MUTATED MIER3 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D220V9, binary
                 cls
clus                0   1
  MIER3 MUTATED    12   1
  MIER3 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     12    1
  MIER3 WILD-TYPE  302   47
                               clus
vv                              MIER3 MUTATED MIER3 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MIER3 MUTATED    12   0   0   0
  MIER3 WILD-TYPE 247   3  22  21
D220V10, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             0              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"
D220V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIER3 MUTATED                                  0     0
  MIER3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MIER3 MUTATED                           0     4
  MIER3 WILD-TYPE                        19   172
D220V12, multiclass
                                  clus
vv                                 MIER3 MUTATED MIER3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SCLY MUTATION ANALYSIS
D221V1, survival
                sevent
clus2              0   1
  SCLY MUTATED     8   3
  SCLY WILD-TYPE 269  75
  SCLY MUTATED SCLY WILD-TYPE 
            11            344 
  SCLY MUTATED SCLY WILD-TYPE 
             3             75 
$`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 
       15.02        15.02        13.35        35.97        47.87 

$`SCLY WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SCLY MUTATED SCLY WILD-TYPE 
         13.35           0.00 
  SCLY MUTATED SCLY WILD-TYPE 
         49.41         148.01 
  SCLY MUTATED SCLY WILD-TYPE 
         31.00          22.01 
[1] "13.3 - 49.4 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D221V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCLY MUTATED         3        0        1         4         1         0
  SCLY WILD-TYPE      61        1       25       104         7         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        17          6         43         33       35        12
                vv
clus             STAGE IVB
  SCLY MUTATED           0
  SCLY WILD-TYPE         1
D221V3, multiclass
            clus
vv           SCLY MUTATED SCLY WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  SCLY MUTATED     2   2   6   1
  SCLY WILD-TYPE   7  65 243  40
D221V4, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  T1            2              7
  T2            2             65
  T3            6            243
  T4            1             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
  SCLY MUTATED     9   2   0
  SCLY WILD-TYPE 211  79  66
D221V5, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  N0            9            211
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V6, binary
                cls
clus               0   1
  SCLY MUTATED    10   0
  SCLY WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED     10    0
  SCLY WILD-TYPE  275   48
   clus
vv  SCLY MUTATED SCLY WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D221V7, binary
                cls
clus               0   1
  SCLY MUTATED     7   4
  SCLY WILD-TYPE 163 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      7    4
  SCLY WILD-TYPE  163  193
        clus
vv       SCLY MUTATED SCLY WILD-TYPE
  FEMALE            7            163
  MALE              4            193
[1] 2 2
[1] FALSE
D221V8, binary
                cls
clus               0   1
  SCLY MUTATED    10   0
  SCLY WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED     10    0
  SCLY WILD-TYPE  290    8
     clus
vv    SCLY MUTATED SCLY WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D221V9, binary
                cls
clus               0   1
  SCLY MUTATED     8   3
  SCLY WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      8    3
  SCLY WILD-TYPE  306   45
                               clus
vv                              SCLY MUTATED SCLY WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SCLY MUTATED     8   0   0   1
  SCLY WILD-TYPE 251   3  22  20
D221V10, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D221V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCLY MUTATED                                  0     0
  SCLY WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SCLY MUTATED                           0     9
  SCLY WILD-TYPE                        19   167
D221V12, multiclass
                                  clus
vv                                 SCLY MUTATED SCLY WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(222) Variable = SCLT1 MUTATION ANALYSIS
D222V1, survival
                 sevent
clus2               0   1
  SCLT1 MUTATED    12   5
  SCLT1 WILD-TYPE 265  73
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             17             338 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              5              73 
$`SCLT1 MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6782 TCGA-AA-3663 
        1.02         0.92       100.01        26.17        20.28         6.97 
TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 
        0.00        53.00        34.98         1.02        83.24        58.39 
TCGA-CA-6717 TCGA-DM-A0XD TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6307 
       12.76        24.43        35.97        74.56        55.04 

$`SCLT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
              0               0 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
         100.01          148.01 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          26.17           22.01 
[1] "0.0 - 100.0 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D222V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCLT1 MUTATED         0        0        5         6         3         0
  SCLT1 WILD-TYPE      64        1       21       102         5         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        17          6         42         32       35        12
                 vv
clus              STAGE IVB
  SCLT1 MUTATED           0
  SCLT1 WILD-TYPE         1
D222V3, multiclass
            clus
vv           SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA              6             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  SCLT1 MUTATED     0   0  15   3
  SCLT1 WILD-TYPE   9  67 234  38
D222V4, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            15             234
  T4             3              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
  SCLT1 MUTATED    14   3   1
  SCLT1 WILD-TYPE 206  78  65
D222V5, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  N0            14             206
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V6, binary
                 cls
clus                0   1
  SCLT1 MUTATED    16   0
  SCLT1 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     16    0
  SCLT1 WILD-TYPE  269   48
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0            16             269
  1             0              48
[1] 2 2
[1] FALSE
D222V7, binary
                 cls
clus                0   1
  SCLT1 MUTATED     8  10
  SCLT1 WILD-TYPE 162 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      8   10
  SCLT1 WILD-TYPE  162  187
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  FEMALE             8             162
  MALE              10             187
[1] 2 2
[1] FALSE
D222V8, binary
                 cls
clus                0   1
  SCLT1 MUTATED    12   0
  SCLT1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     12    0
  SCLT1 WILD-TYPE  288    8
     clus
vv    SCLT1 MUTATED SCLT1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D222V9, binary
                 cls
clus                0   1
  SCLT1 MUTATED    17   1
  SCLT1 WILD-TYPE 297  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     17    1
  SCLT1 WILD-TYPE  297   47
                               clus
vv                              SCLT1 MUTATED SCLT1 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCLT1 MUTATED    12   0   0   2
  SCLT1 WILD-TYPE 247   3  22  19
D222V10, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             2              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"
D222V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCLT1 MUTATED                                  0     2
  SCLT1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCLT1 MUTATED                           0     9
  SCLT1 WILD-TYPE                        19   167
D222V12, multiclass
                                  clus
vv                                 SCLT1 MUTATED SCLT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(223) Variable = ERBB2 MUTATION ANALYSIS
D223V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    19   8
  ERBB2 WILD-TYPE 258  70
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             27             328 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8              70 
$`ERBB2 MUTATED`
TCGA-A6-4105 TCGA-AD-6888 TCGA-AZ-6601 TCGA-A6-6138 TCGA-AA-3502 TCGA-AA-3660 
       14.53        15.52       100.01        22.52        35.01        78.08 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AY-5543 
       53.00        27.02        33.01        25.02        27.02        33.01 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6162 
        6.77        12.10        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 
       47.41        65.85        55.04 

$`ERBB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        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-A6-6651 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-3510 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        30.05        17.03        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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 
       14.04        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           6.77            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         100.01          148.01 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          27.02           21.99 
[1] "6.8 - 100.0 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D223V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB2 MUTATED         4        0        3         6         1         0
  ERBB2 WILD-TYPE      60        1       23       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED           0          0          5          1        3         1
  ERBB2 WILD-TYPE        18          6         39         32       32        11
                 vv
clus              STAGE IVB
  ERBB2 MUTATED           1
  ERBB2 WILD-TYPE         0
D223V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              1              11
  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   5  18   4
  ERBB2 WILD-TYPE   9  62 231  37
D223V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            18             231
  T4             4              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
  ERBB2 MUTATED    16   8   3
  ERBB2 WILD-TYPE 204  73  63
D223V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0            16             204
  N1             8              73
  N2             3              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"
D223V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    20   5
  ERBB2 WILD-TYPE 265  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     20    5
  ERBB2 WILD-TYPE  265   43
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            20             265
  1             5              43
[1] 2 2
[1] FALSE
D223V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED    12  15
  ERBB2 WILD-TYPE 158 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     12   15
  ERBB2 WILD-TYPE  158  182
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE            12             158
  MALE              15             182
[1] 2 2
[1] FALSE
D223V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED    26   0
  ERBB2 WILD-TYPE 274   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     26    0
  ERBB2 WILD-TYPE  274    8
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO             26             274
  YES             0               8
[1] 2 2
[1] FALSE
D223V9, binary
                 cls
clus                0   1
  ERBB2 MUTATED    23   3
  ERBB2 WILD-TYPE 291  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     23    3
  ERBB2 WILD-TYPE  291   45
                               clus
vv                              ERBB2 MUTATED ERBB2 WILD-TYPE
  COLON ADENOCARCINOMA                     23             291
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED    18   0   1   1
  ERBB2 WILD-TYPE 241   3  21  20
D223V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0            18             241
  R1             0               3
  R2             1              21
  RX             1              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"
D223V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2 MUTATED                                  0     0
  ERBB2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED                           3    17
  ERBB2 WILD-TYPE                        16   159
D223V12, multiclass
                                  clus
vv                                 ERBB2 MUTATED ERBB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       17             159
[1] 4 2
[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 = HM13 MUTATION ANALYSIS
D224V1, survival
                sevent
clus2              0   1
  HM13 MUTATED     4   1
  HM13 WILD-TYPE 273  77
  HM13 MUTATED HM13 WILD-TYPE 
             5            350 
  HM13 MUTATED HM13 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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         22.075 
[1] "8.6 - 47.9 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D224V2, continuous
                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      64        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HM13 MUTATED           0          0          1          0        0         0
  HM13 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  HM13 MUTATED           0
  HM13 WILD-TYPE         1
D224V3, multiclass
            clus
vv           HM13 MUTATED HM13 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  HM13 MUTATED     0   0   5   0
  HM13 WILD-TYPE   9  67 244  41
D224V4, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            0             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
  HM13 MUTATED     4   0   1
  HM13 WILD-TYPE 216  81  65
D224V5, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V6, binary
                cls
clus               0   1
  HM13 MUTATED     5   0
  HM13 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      5    0
  HM13 WILD-TYPE  280   48
   clus
vv  HM13 MUTATED HM13 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D224V7, binary
                cls
clus               0   1
  HM13 MUTATED     3   2
  HM13 WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      3    2
  HM13 WILD-TYPE  167  195
        clus
vv       HM13 MUTATED HM13 WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D224V8, binary
                cls
clus               0   1
  HM13 MUTATED     5   0
  HM13 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      5    0
  HM13 WILD-TYPE  295    8
     clus
vv    HM13 MUTATED HM13 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D224V9, binary
                cls
clus               0   1
  HM13 MUTATED     4   1
  HM13 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      4    1
  HM13 WILD-TYPE  310   47
                               clus
vv                              HM13 MUTATED HM13 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HM13 MUTATED     5   0   0   0
  HM13 WILD-TYPE 254   3  22  21
D224V10, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D224V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HM13 MUTATED                                  0     0
  HM13 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HM13 MUTATED                           0     4
  HM13 WILD-TYPE                        19   172
D224V12, multiclass
                                  clus
vv                                 HM13 MUTATED HM13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = RASAL2 MUTATION ANALYSIS
D225V1, survival
                  sevent
clus2                0   1
  RASAL2 MUTATED     9   5
  RASAL2 WILD-TYPE 268  73
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              14              341 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               5               73 
$`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 
       12.00        98.24 

$`RASAL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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-6163 
       32.02        15.02        15.02        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RASAL2 MUTATED RASAL2 WILD-TYPE 
            0.95             0.00 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           98.24           148.01 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           13.89            22.09 
[1] "0.9 - 98.2 (13.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D225V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASAL2 MUTATED         3        0        2         4         3         0
  RASAL2 WILD-TYPE      61        1       24       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASAL2 MUTATED           0          0          1          0        1
  RASAL2 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  RASAL2 MUTATED           1         0
  RASAL2 WILD-TYPE        11         1
D225V3, multiclass
            clus
vv           RASAL2 MUTATED RASAL2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  RASAL2 MUTATED     2   1   8   4
  RASAL2 WILD-TYPE   7  66 241  37
D225V4, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  T1              2                7
  T2              1               66
  T3              8              241
  T4              4               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
  RASAL2 MUTATED    12   2   1
  RASAL2 WILD-TYPE 208  79  65
D225V5, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  N0             12              208
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V6, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    12   2
  RASAL2 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     12    2
  RASAL2 WILD-TYPE  273   46
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0             12              273
  1              2               46
[1] 2 2
[1] FALSE
D225V7, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     8   7
  RASAL2 WILD-TYPE 162 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      8    7
  RASAL2 WILD-TYPE  162  190
        clus
vv       RASAL2 MUTATED RASAL2 WILD-TYPE
  FEMALE              8              162
  MALE                7              190
[1] 2 2
[1] FALSE
D225V8, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    11   0
  RASAL2 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     11    0
  RASAL2 WILD-TYPE  289    8
     clus
vv    RASAL2 MUTATED RASAL2 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D225V9, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     9   5
  RASAL2 WILD-TYPE 305  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      9    5
  RASAL2 WILD-TYPE  305   43
                               clus
vv                              RASAL2 MUTATED RASAL2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RASAL2 MUTATED    10   0   1   3
  RASAL2 WILD-TYPE 249   3  21  18
D225V10, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              3               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"
D225V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASAL2 MUTATED                                  0     2
  RASAL2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RASAL2 MUTATED                           0     6
  RASAL2 WILD-TYPE                        19   170
D225V12, multiclass
                                  clus
vv                                 RASAL2 MUTATED RASAL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = OSBPL2 MUTATION ANALYSIS
D226V1, survival
                  sevent
clus2                0   1
  OSBPL2 MUTATED    10   1
  OSBPL2 WILD-TYPE 267  77
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              11              344 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               1               77 
$`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        12.59        51.32 
TCGA-CM-5349 TCGA-CM-5862 TCGA-D5-7000 TCGA-DM-A28K TCGA-G4-6293 
       30.08         5.03        10.26        98.24       133.18 

$`OSBPL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5863 
       29.06        22.03        22.98        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
            5.03             0.00 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
          133.18           148.01 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
           30.08            21.99 
[1] "5.0 - 133.2 (30.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.7"
D226V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL2 MUTATED         2        0        0         5         0         0
  OSBPL2 WILD-TYPE      62        1       26       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL2 MUTATED           1          0          2          0        0
  OSBPL2 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OSBPL2 MUTATED           1         0
  OSBPL2 WILD-TYPE        11         1
D226V3, multiclass
            clus
vv           OSBPL2 MUTATED OSBPL2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  OSBPL2 MUTATED     0   2   9   0
  OSBPL2 WILD-TYPE   9  65 240  41
D226V4, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              9              240
  T4              0               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
  OSBPL2 MUTATED     7   4   0
  OSBPL2 WILD-TYPE 213  77  66
D226V5, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  N0              7              213
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V6, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     9   1
  OSBPL2 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      9    1
  OSBPL2 WILD-TYPE  276   47
   clus
vv  OSBPL2 MUTATED OSBPL2 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D226V7, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     7   4
  OSBPL2 WILD-TYPE 163 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      7    4
  OSBPL2 WILD-TYPE  163  193
        clus
vv       OSBPL2 MUTATED OSBPL2 WILD-TYPE
  FEMALE              7              163
  MALE                4              193
[1] 2 2
[1] FALSE
D226V8, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     9   0
  OSBPL2 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      9    0
  OSBPL2 WILD-TYPE  291    8
     clus
vv    OSBPL2 MUTATED OSBPL2 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D226V9, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     9   2
  OSBPL2 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      9    2
  OSBPL2 WILD-TYPE  305   46
                               clus
vv                              OSBPL2 MUTATED OSBPL2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OSBPL2 MUTATED     7   0   0   2
  OSBPL2 WILD-TYPE 252   3  22  19
D226V10, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D226V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSBPL2 MUTATED                                  0     1
  OSBPL2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OSBPL2 MUTATED                           1     9
  OSBPL2 WILD-TYPE                        18   167
D226V12, multiclass
                                  clus
vv                                 OSBPL2 MUTATED OSBPL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(227) Variable = OVGP1 MUTATION ANALYSIS
D227V1, survival
                 sevent
clus2               0   1
  OVGP1 MUTATED    12   2
  OVGP1 WILD-TYPE 265  76
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             14             341 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
              2              76 
$`OVGP1 MUTATED`
TCGA-AZ-4681 TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00A 
      106.75        32.71        63.98         6.97        53.00        38.04 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AU-3779 TCGA-AY-6386 TCGA-CM-6163 
       12.16        83.24         5.79        14.50        17.82        14.04 
TCGA-CM-6679 TCGA-D5-6536 
       10.06        17.85 

$`OVGP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       18.05        40.96        24.53        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OVGP1 MUTATED OVGP1 WILD-TYPE 
           5.79            0.00 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
         106.75          148.01 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
         17.835          22.090 
[1] "5.8 - 106.8 (17.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D227V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OVGP1 MUTATED         2        0        3         6         0         1
  OVGP1 WILD-TYPE      62        1       23       102         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OVGP1 MUTATED           0          0          1          1        0         0
  OVGP1 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  OVGP1 MUTATED           0
  OVGP1 WILD-TYPE         1
D227V3, multiclass
            clus
vv           OVGP1 MUTATED OVGP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OVGP1 MUTATED     1   1  10   2
  OVGP1 WILD-TYPE   8  66 239  39
D227V4, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            10             239
  T4             2              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
  OVGP1 MUTATED    12   1   1
  OVGP1 WILD-TYPE 208  80  65
D227V5, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V6, binary
                 cls
clus                0   1
  OVGP1 MUTATED    12   0
  OVGP1 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     12    0
  OVGP1 WILD-TYPE  273   48
   clus
vv  OVGP1 MUTATED OVGP1 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D227V7, binary
                 cls
clus                0   1
  OVGP1 MUTATED     3  11
  OVGP1 WILD-TYPE 167 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED      3   11
  OVGP1 WILD-TYPE  167  186
        clus
vv       OVGP1 MUTATED OVGP1 WILD-TYPE
  FEMALE             3             167
  MALE              11             186
[1] 2 2
[1] FALSE
D227V8, binary
                 cls
clus                0   1
  OVGP1 MUTATED    14   0
  OVGP1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     14    0
  OVGP1 WILD-TYPE  286    8
     clus
vv    OVGP1 MUTATED OVGP1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D227V9, binary
                 cls
clus                0   1
  OVGP1 MUTATED    12   2
  OVGP1 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     12    2
  OVGP1 WILD-TYPE  302   46
                               clus
vv                              OVGP1 MUTATED OVGP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OVGP1 MUTATED    12   0   0   0
  OVGP1 WILD-TYPE 247   3  22  21
D227V10, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             0              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"
D227V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OVGP1 MUTATED                                  0     1
  OVGP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OVGP1 MUTATED                           1     8
  OVGP1 WILD-TYPE                        18   168
D227V12, multiclass
                                  clus
vv                                 OVGP1 MUTATED OVGP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = GMCL1 MUTATION ANALYSIS
D228V1, survival
                 sevent
clus2               0   1
  GMCL1 MUTATED     7   2
  GMCL1 WILD-TYPE 270  76
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              9             346 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              2              76 
$`GMCL1 MUTATED`
TCGA-AD-6548 TCGA-AZ-6601 TCGA-G4-6625 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CM-5863 
       21.37       100.01        91.79        58.39         5.23        15.02 
TCGA-CM-6161 TCGA-DM-A1D9 TCGA-G4-6307 
       15.02       140.38        55.04 

$`GMCL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       15.02         5.03        15.02        17.03        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GMCL1 MUTATED GMCL1 WILD-TYPE 
           5.23            0.00 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
         140.38          148.01 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
         55.040          22.045 
[1] "5.2 - 140.4 (55.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D228V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GMCL1 MUTATED         2        0        1         3         1         0
  GMCL1 WILD-TYPE      62        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GMCL1 MUTATED           0          0          3          0        0         0
  GMCL1 WILD-TYPE        18          6         41         33       35        12
                 vv
clus              STAGE IVB
  GMCL1 MUTATED           0
  GMCL1 WILD-TYPE         1
D228V3, multiclass
            clus
vv           GMCL1 MUTATED GMCL1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GMCL1 MUTATED     0   2   6   2
  GMCL1 WILD-TYPE   9  65 243  39
D228V4, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  GMCL1 MUTATED     7   3   0
  GMCL1 WILD-TYPE 213  78  66
D228V5, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V6, binary
                 cls
clus                0   1
  GMCL1 MUTATED     9   0
  GMCL1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      9    0
  GMCL1 WILD-TYPE  276   48
   clus
vv  GMCL1 MUTATED GMCL1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D228V7, binary
                 cls
clus                0   1
  GMCL1 MUTATED     7   3
  GMCL1 WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      7    3
  GMCL1 WILD-TYPE  163  194
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D228V8, binary
                 cls
clus                0   1
  GMCL1 MUTATED     8   0
  GMCL1 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      8    0
  GMCL1 WILD-TYPE  292    8
     clus
vv    GMCL1 MUTATED GMCL1 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D228V9, binary
                 cls
clus                0   1
  GMCL1 MUTATED     9   1
  GMCL1 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      9    1
  GMCL1 WILD-TYPE  305   47
                               clus
vv                              GMCL1 MUTATED GMCL1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GMCL1 MUTATED     6   0   0   1
  GMCL1 WILD-TYPE 253   3  22  20
D228V10, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D228V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GMCL1 MUTATED                                  0     0
  GMCL1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GMCL1 MUTATED                           0    10
  GMCL1 WILD-TYPE                        19   166
D228V12, multiclass
                                  clus
vv                                 GMCL1 MUTATED GMCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(229) Variable = ZNF789 MUTATION ANALYSIS
D229V1, survival
                  sevent
clus2                0   1
  ZNF789 MUTATED     5   2
  ZNF789 WILD-TYPE 272  76
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              348 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               2               76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  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           22.045 
[1] "4.0 - 58.4 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D229V2, continuous
                  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      63        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF789 MUTATED           0          0          0          0        0
  ZNF789 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF789 MUTATED           0         0
  ZNF789 WILD-TYPE        12         1
D229V3, multiclass
            clus
vv           ZNF789 MUTATED ZNF789 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF789 MUTATED     0   2   4   1
  ZNF789 WILD-TYPE   9  65 245  40
D229V4, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              1               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
  ZNF789 MUTATED     7   0   0
  ZNF789 WILD-TYPE 213  81  66
D229V5, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V6, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     6   0
  ZNF789 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      6    0
  ZNF789 WILD-TYPE  279   48
   clus
vv  ZNF789 MUTATED ZNF789 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D229V7, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     2   5
  ZNF789 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      2    5
  ZNF789 WILD-TYPE  168  192
        clus
vv       ZNF789 MUTATED ZNF789 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D229V8, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     6   0
  ZNF789 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      6    0
  ZNF789 WILD-TYPE  294    8
     clus
vv    ZNF789 MUTATED ZNF789 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D229V9, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     5   2
  ZNF789 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      5    2
  ZNF789 WILD-TYPE  309   46
                               clus
vv                              ZNF789 MUTATED ZNF789 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF789 MUTATED     5   0   0   1
  ZNF789 WILD-TYPE 254   3  22  20
D229V10, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D229V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF789 MUTATED                                  0     1
  ZNF789 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF789 MUTATED                           0     4
  ZNF789 WILD-TYPE                        19   172
D229V12, multiclass
                                  clus
vv                                 ZNF789 MUTATED ZNF789 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = IVL MUTATION ANALYSIS
D230V1, survival
               sevent
clus2             0   1
  IVL MUTATED    12   4
  IVL WILD-TYPE 265  74
  IVL MUTATED IVL WILD-TYPE 
           16           339 
  IVL MUTATED IVL WILD-TYPE 
            4            74 
$`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 
       10.13        81.37       119.93        65.85 

$`IVL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        62.79        88.21        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28F 
        7.50        44.32       131.51       135.65       139.17        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 
       74.56        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  IVL MUTATED IVL WILD-TYPE 
         6.97          0.00 
  IVL MUTATED IVL WILD-TYPE 
       119.93        148.01 
  IVL MUTATED IVL WILD-TYPE 
        22.39         22.03 
[1] "7.0 - 119.9 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D230V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IVL MUTATED         3        0        2         4         0         0
  IVL WILD-TYPE      61        1       24       104         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVL MUTATED           1          1          1          1        1         1
  IVL WILD-TYPE        17          5         43         32       34        11
               vv
clus            STAGE IVB
  IVL MUTATED           0
  IVL WILD-TYPE         1
D230V3, multiclass
            clus
vv           IVL MUTATED IVL WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            4           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           1             5
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             1            34
  STAGE IVA            1            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
  IVL MUTATED     0   4  11   2
  IVL WILD-TYPE   9  63 238  39
D230V4, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  T1           0             9
  T2           4            63
  T3          11           238
  T4           2            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
  IVL MUTATED    12   4   1
  IVL WILD-TYPE 208  77  65
D230V5, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  N0          12           208
  N1           4            77
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V6, binary
               cls
clus              0   1
  IVL MUTATED    12   2
  IVL WILD-TYPE 273  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     12    2
  IVL WILD-TYPE  273   46
   clus
vv  IVL MUTATED IVL WILD-TYPE
  0          12           273
  1           2            46
[1] 2 2
[1] FALSE
D230V7, binary
               cls
clus              0   1
  IVL MUTATED     5  12
  IVL WILD-TYPE 165 185
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED      5   12
  IVL WILD-TYPE  165  185
        clus
vv       IVL MUTATED IVL WILD-TYPE
  FEMALE           5           165
  MALE            12           185
[1] 2 2
[1] FALSE
D230V8, binary
               cls
clus              0   1
  IVL MUTATED    14   0
  IVL WILD-TYPE 286   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     14    0
  IVL WILD-TYPE  286    8
     clus
vv    IVL MUTATED IVL WILD-TYPE
  NO           14           286
  YES           0             8
[1] 2 2
[1] FALSE
D230V9, binary
               cls
clus              0   1
  IVL MUTATED    15   2
  IVL WILD-TYPE 299  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     15    2
  IVL WILD-TYPE  299   46
                               clus
vv                              IVL MUTATED IVL WILD-TYPE
  COLON ADENOCARCINOMA                   15           299
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  IVL MUTATED    11   0   0   1
  IVL WILD-TYPE 248   3  22  20
D230V10, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  R0          11           248
  R1           0             3
  R2           0            22
  RX           1            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"
D230V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IVL MUTATED                                  0     0
  IVL WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IVL MUTATED                           2    11
  IVL WILD-TYPE                        17   165
D230V12, multiclass
                                  clus
vv                                 IVL MUTATED IVL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                     11           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(231) Variable = SPR MUTATION ANALYSIS
D231V1, survival
               sevent
clus2             0   1
  SPR MUTATED     4   3
  SPR WILD-TYPE 273  75
  SPR MUTATED SPR WILD-TYPE 
            7           348 
  SPR MUTATED SPR WILD-TYPE 
            3            75 
$`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-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        85.45        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SPR MUTATED SPR WILD-TYPE 
         3.02          0.00 
  SPR MUTATED SPR WILD-TYPE 
       133.18        148.01 
  SPR MUTATED SPR WILD-TYPE 
        14.53         22.09 
[1] "3.0 - 133.2 (14.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D231V2, continuous
               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      63        1       25       105         8         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        17          6         44         32       35        12
               vv
clus            STAGE IVB
  SPR MUTATED           0
  SPR WILD-TYPE         1
D231V3, multiclass
            clus
vv           SPR MUTATED SPR WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            3           105
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  SPR MUTATED     0   1   5   1
  SPR WILD-TYPE   9  66 244  40
D231V4, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  T1           0             9
  T2           1            66
  T3           5           244
  T4           1            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
  SPR MUTATED     5   1   1
  SPR WILD-TYPE 215  80  65
D231V5, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  N0           5           215
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V6, binary
               cls
clus              0   1
  SPR MUTATED     5   0
  SPR WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      5    0
  SPR WILD-TYPE  280   48
   clus
vv  SPR MUTATED SPR WILD-TYPE
  0           5           280
  1           0            48
[1] 2 2
[1] FALSE
D231V7, binary
               cls
clus              0   1
  SPR MUTATED     4   3
  SPR WILD-TYPE 166 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      4    3
  SPR WILD-TYPE  166  194
        clus
vv       SPR MUTATED SPR WILD-TYPE
  FEMALE           4           166
  MALE             3           194
[1] 2 2
[1] FALSE
D231V8, binary
               cls
clus              0   1
  SPR MUTATED     6   0
  SPR WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      6    0
  SPR WILD-TYPE  294    8
     clus
vv    SPR MUTATED SPR WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D231V9, binary
               cls
clus              0   1
  SPR MUTATED     5   2
  SPR WILD-TYPE 309  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      5    2
  SPR WILD-TYPE  309   46
                               clus
vv                              SPR MUTATED SPR WILD-TYPE
  COLON ADENOCARCINOMA                    5           309
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SPR MUTATED     3   0   0   2
  SPR WILD-TYPE 256   3  22  19
D231V10, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  R0           3           256
  R1           0             3
  R2           0            22
  RX           2            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"
D231V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPR MUTATED                                  0     0
  SPR WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SPR MUTATED                           0     6
  SPR WILD-TYPE                        19   170
D231V12, multiclass
                                  clus
vv                                 SPR MUTATED SPR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      6           170
[1] 4 2
[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 = C2ORF77 MUTATION ANALYSIS
D232V1, survival
                   sevent
clus2                 0   1
  C2ORF77 MUTATED     8   0
  C2ORF77 WILD-TYPE 269  78
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                8               347 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                0                78 
$`C2ORF77 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6586 TCGA-AA-3866 TCGA-AA-A010 TCGA-AD-5900 
       19.04        24.00        35.80        17.03        34.98        12.16 
TCGA-CA-6717 TCGA-D5-6928 
       12.76        11.64 

$`C2ORF77 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
            11.64              0.00 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
            35.80            148.01 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
           18.035            22.090 
[1] "11.6 - 35.8 (18.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D232V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2ORF77 MUTATED         2        0        0         4         1         0
  C2ORF77 WILD-TYPE      62        1       26       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF77 MUTATED           0          0          0          0        1
  C2ORF77 WILD-TYPE        18          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF77 MUTATED           0         0
  C2ORF77 WILD-TYPE        12         1
D232V3, multiclass
            clus
vv           C2ORF77 MUTATED C2ORF77 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  C2ORF77 MUTATED     0   2   5   1
  C2ORF77 WILD-TYPE   9  65 244  40
D232V4, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               1                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
  C2ORF77 MUTATED     8   0   0
  C2ORF77 WILD-TYPE 212  81  66
D232V5, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  N0               8               212
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V6, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     6   1
  C2ORF77 WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      6    1
  C2ORF77 WILD-TYPE  279   47
   clus
vv  C2ORF77 MUTATED C2ORF77 WILD-TYPE
  0               6               279
  1               1                47
[1] 2 2
[1] FALSE
D232V7, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     4   4
  C2ORF77 WILD-TYPE 166 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      4    4
  C2ORF77 WILD-TYPE  166  193
        clus
vv       C2ORF77 MUTATED C2ORF77 WILD-TYPE
  FEMALE               4               166
  MALE                 4               193
[1] 2 2
[1] FALSE
D232V8, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     7   1
  C2ORF77 WILD-TYPE 293   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      7    1
  C2ORF77 WILD-TYPE  293    7
     clus
vv    C2ORF77 MUTATED C2ORF77 WILD-TYPE
  NO                7               293
  YES               1                 7
[1] 2 2
[1] FALSE
D232V9, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     4   4
  C2ORF77 WILD-TYPE 310  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      4    4
  C2ORF77 WILD-TYPE  310   44
                               clus
vv                              C2ORF77 MUTATED C2ORF77 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C2ORF77 MUTATED     6   0   1   1
  C2ORF77 WILD-TYPE 253   3  21  20
D232V10, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               1                21
  RX               1                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"
D232V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2ORF77 MUTATED                                  0     1
  C2ORF77 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C2ORF77 MUTATED                           0     3
  C2ORF77 WILD-TYPE                        19   173
D232V12, multiclass
                                  clus
vv                                 C2ORF77 MUTATED C2ORF77 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = NT5DC3 MUTATION ANALYSIS
D233V1, survival
                  sevent
clus2                0   1
  NT5DC3 MUTATED     9   3
  NT5DC3 WILD-TYPE 268  75
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              12              343 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
               3               75 
$`NT5DC3 MUTATED`
TCGA-AA-3697 TCGA-AZ-6601 TCGA-G4-6310 TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3502 
       85.05       100.01        63.62        46.65        20.12        35.01 
TCGA-AZ-6598 TCGA-CM-6171 TCGA-D5-5539 TCGA-D5-6541 TCGA-D5-6929 TCGA-F4-6570 
       49.41        14.04        19.59        15.58        13.41         6.18 

$`NT5DC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        79.69        43.76        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        19.66 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
            6.18             0.00 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
          100.01           148.01 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
          27.565           22.060 
[1] "6.2 - 100.0 (27.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D233V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NT5DC3 MUTATED         2        0        3         3         0         0
  NT5DC3 WILD-TYPE      62        1       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5DC3 MUTATED           0          1          2          0        1
  NT5DC3 WILD-TYPE        18          5         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  NT5DC3 MUTATED           0         0
  NT5DC3 WILD-TYPE        12         1
D233V3, multiclass
            clus
vv           NT5DC3 MUTATED NT5DC3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  NT5DC3 MUTATED     0   2  10   0
  NT5DC3 WILD-TYPE   9  65 239  41
D233V4, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              0               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
  NT5DC3 MUTATED     8   4   0
  NT5DC3 WILD-TYPE 212  77  66
D233V5, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  N0              8              212
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V6, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED     9   1
  NT5DC3 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED      9    1
  NT5DC3 WILD-TYPE  276   47
   clus
vv  NT5DC3 MUTATED NT5DC3 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D233V7, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED     5   7
  NT5DC3 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED      5    7
  NT5DC3 WILD-TYPE  165  190
        clus
vv       NT5DC3 MUTATED NT5DC3 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D233V8, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED    11   1
  NT5DC3 WILD-TYPE 289   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED     11    1
  NT5DC3 WILD-TYPE  289    7
     clus
vv    NT5DC3 MUTATED NT5DC3 WILD-TYPE
  NO              11              289
  YES              1                7
[1] 2 2
[1] FALSE
D233V9, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED    10   2
  NT5DC3 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED     10    2
  NT5DC3 WILD-TYPE  304   46
                               clus
vv                              NT5DC3 MUTATED NT5DC3 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NT5DC3 MUTATED     9   0   0   0
  NT5DC3 WILD-TYPE 250   3  22  21
D233V10, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D233V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NT5DC3 MUTATED                                  0     0
  NT5DC3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NT5DC3 MUTATED                           0    10
  NT5DC3 WILD-TYPE                        19   166
D233V12, multiclass
                                  clus
vv                                 NT5DC3 MUTATED NT5DC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(234) Variable = ITPR1 MUTATION ANALYSIS
D234V1, survival
                 sevent
clus2               0   1
  ITPR1 MUTATED    25  10
  ITPR1 WILD-TYPE 252  68
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             35             320 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             10              68 
$`ITPR1 MUTATED`
TCGA-AA-3697 TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-5656 
       85.05        19.04        25.08       100.01        79.69        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3664 
       31.63        33.53        22.06        19.66        63.98        54.02 
TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3994 TCGA-AA-A00N 
       33.04        15.95         0.00        53.00        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A02Y TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        39.98        58.39        22.36        49.41        12.76 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6536 
       10.06        51.32        15.02        14.04        25.48        17.85 
TCGA-DM-A1DB TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6309 
       44.32        35.97         6.18        47.87        85.48 

$`ITPR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5659 TCGA-A6-5660 
       34.65        33.34        32.75        36.53        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19        18.25        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ITPR1 MUTATED ITPR1 WILD-TYPE 
              0               0 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
         100.01          148.01 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
          32.91           21.60 
[1] "0.0 - 100.0 (32.9)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1"  
D234V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITPR1 MUTATED         4        0        7        14         2         0
  ITPR1 WILD-TYPE      60        1       19        94         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITPR1 MUTATED           1          0          5          1        1         1
  ITPR1 WILD-TYPE        17          6         39         32       34        11
                 vv
clus              STAGE IVB
  ITPR1 MUTATED           0
  ITPR1 WILD-TYPE         1
D234V3, multiclass
            clus
vv           ITPR1 MUTATED ITPR1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               7              19
  STAGE IIA             14              94
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  ITPR1 MUTATED     0   4  29   4
  ITPR1 WILD-TYPE   9  63 220  37
D234V4, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            29             220
  T4             4              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
  ITPR1 MUTATED    29   6   2
  ITPR1 WILD-TYPE 191  75  64
D234V5, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  N0            29             191
  N1             6              75
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V6, binary
                 cls
clus                0   1
  ITPR1 MUTATED    32   2
  ITPR1 WILD-TYPE 253  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     32    2
  ITPR1 WILD-TYPE  253   46
   clus
vv  ITPR1 MUTATED ITPR1 WILD-TYPE
  0            32             253
  1             2              46
[1] 2 2
[1] FALSE
D234V7, binary
                 cls
clus                0   1
  ITPR1 MUTATED    15  22
  ITPR1 WILD-TYPE 155 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     15   22
  ITPR1 WILD-TYPE  155  175
        clus
vv       ITPR1 MUTATED ITPR1 WILD-TYPE
  FEMALE            15             155
  MALE              22             175
[1] 2 2
[1] FALSE
D234V8, binary
                 cls
clus                0   1
  ITPR1 MUTATED    31   0
  ITPR1 WILD-TYPE 269   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     31    0
  ITPR1 WILD-TYPE  269    8
     clus
vv    ITPR1 MUTATED ITPR1 WILD-TYPE
  NO             31             269
  YES             0               8
[1] 2 2
[1] FALSE
D234V9, binary
                 cls
clus                0   1
  ITPR1 MUTATED    33   4
  ITPR1 WILD-TYPE 281  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     33    4
  ITPR1 WILD-TYPE  281   44
                               clus
vv                              ITPR1 MUTATED ITPR1 WILD-TYPE
  COLON ADENOCARCINOMA                     33             281
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITPR1 MUTATED    28   0   1   3
  ITPR1 WILD-TYPE 231   3  21  18
D234V10, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  R0            28             231
  R1             0               3
  R2             1              21
  RX             3              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"
D234V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITPR1 MUTATED                                  0     2
  ITPR1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITPR1 MUTATED                           3    18
  ITPR1 WILD-TYPE                        16   158
D234V12, multiclass
                                  clus
vv                                 ITPR1 MUTATED ITPR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       18             158
[1] 4 2
[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 = PDCD5 MUTATION ANALYSIS
D235V1, survival
                 sevent
clus2               0   1
  PDCD5 MUTATED     8   0
  PDCD5 WILD-TYPE 269  78
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              8             347 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              0              78 
$`PDCD5 MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-A6-6651 TCGA-AA-3502 TCGA-AZ-4315 TCGA-CK-5914 
        0.92        25.08        21.76        35.01        58.39        21.99 
TCGA-D5-6920 TCGA-F4-6855 
       12.39        47.41 

$`PDCD5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PDCD5 MUTATED PDCD5 WILD-TYPE 
           0.92            0.00 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
          58.39          148.01 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
         23.535          22.060 
[1] "0.9 - 58.4 (23.5)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D235V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDCD5 MUTATED         1        0        0         3         0         0
  PDCD5 WILD-TYPE      63        1       26       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDCD5 MUTATED           1          0          3          0        0         0
  PDCD5 WILD-TYPE        17          6         41         33       35        12
                 vv
clus              STAGE IVB
  PDCD5 MUTATED           0
  PDCD5 WILD-TYPE         1
D235V3, multiclass
            clus
vv           PDCD5 MUTATED PDCD5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PDCD5 MUTATED     0   1   7   0
  PDCD5 WILD-TYPE   9  66 242  41
D235V4, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             0              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
  PDCD5 MUTATED     4   4   0
  PDCD5 WILD-TYPE 216  77  66
D235V5, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  N0             4             216
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V6, binary
                 cls
clus                0   1
  PDCD5 MUTATED     6   0
  PDCD5 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      6    0
  PDCD5 WILD-TYPE  279   48
   clus
vv  PDCD5 MUTATED PDCD5 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D235V7, binary
                 cls
clus                0   1
  PDCD5 MUTATED     4   4
  PDCD5 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      4    4
  PDCD5 WILD-TYPE  166  193
        clus
vv       PDCD5 MUTATED PDCD5 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D235V8, binary
                 cls
clus                0   1
  PDCD5 MUTATED     7   0
  PDCD5 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      7    0
  PDCD5 WILD-TYPE  293    8
     clus
vv    PDCD5 MUTATED PDCD5 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D235V9, binary
                 cls
clus                0   1
  PDCD5 MUTATED     8   0
  PDCD5 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      8    0
  PDCD5 WILD-TYPE  306   48
                               clus
vv                              PDCD5 MUTATED PDCD5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PDCD5 MUTATED     6   0   0   1
  PDCD5 WILD-TYPE 253   3  22  20
D235V10, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D235V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDCD5 MUTATED                                  0     0
  PDCD5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDCD5 MUTATED                           0     6
  PDCD5 WILD-TYPE                        19   170
D235V12, multiclass
                                  clus
vv                                 PDCD5 MUTATED PDCD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = AKAP3 MUTATION ANALYSIS
D236V1, survival
                 sevent
clus2               0   1
  AKAP3 MUTATED    19   2
  AKAP3 WILD-TYPE 258  76
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             21             334 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
              2              76 
$`AKAP3 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3655 
       19.04        26.17         8.38         3.02        35.01        61.02 
TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A02F 
       21.99        25.02        34.98         1.02        35.01        39.98 
TCGA-AD-6963 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 
       27.42        58.39        12.10        12.76        15.62        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6931 
       32.02        15.02        12.00 

$`AKAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-3510 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  AKAP3 MUTATED AKAP3 WILD-TYPE 
           1.02            0.00 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
          61.02          148.01 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
         22.980          22.045 
[1] "1.0 - 61.0 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D236V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP3 MUTATED         2        0        3         6         1         0
  AKAP3 WILD-TYPE      62        1       23       102         7         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        17          6         43         31       32        12
                 vv
clus              STAGE IVB
  AKAP3 MUTATED           0
  AKAP3 WILD-TYPE         1
D236V3, multiclass
            clus
vv           AKAP3 MUTATED AKAP3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              0              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
  AKAP3 MUTATED     0   3  14   4
  AKAP3 WILD-TYPE   9  64 235  37
D236V4, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            14             235
  T4             4              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
  AKAP3 MUTATED    15   3   3
  AKAP3 WILD-TYPE 205  78  63
D236V5, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  N0            15             205
  N1             3              78
  N2             3              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"
D236V6, binary
                 cls
clus                0   1
  AKAP3 MUTATED    16   3
  AKAP3 WILD-TYPE 269  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     16    3
  AKAP3 WILD-TYPE  269   45
   clus
vv  AKAP3 MUTATED AKAP3 WILD-TYPE
  0            16             269
  1             3              45
[1] 2 2
[1] FALSE
D236V7, binary
                 cls
clus                0   1
  AKAP3 MUTATED     8  13
  AKAP3 WILD-TYPE 162 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED      8   13
  AKAP3 WILD-TYPE  162  184
        clus
vv       AKAP3 MUTATED AKAP3 WILD-TYPE
  FEMALE             8             162
  MALE              13             184
[1] 2 2
[1] FALSE
D236V8, binary
                 cls
clus                0   1
  AKAP3 MUTATED    17   2
  AKAP3 WILD-TYPE 283   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     17    2
  AKAP3 WILD-TYPE  283    6
     clus
vv    AKAP3 MUTATED AKAP3 WILD-TYPE
  NO             17             283
  YES             2               6
[1] 2 2
[1] FALSE
D236V9, binary
                 cls
clus                0   1
  AKAP3 MUTATED    18   3
  AKAP3 WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     18    3
  AKAP3 WILD-TYPE  296   45
                               clus
vv                              AKAP3 MUTATED AKAP3 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AKAP3 MUTATED    13   0   2   2
  AKAP3 WILD-TYPE 246   3  20  19
D236V10, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             2              20
  RX             2              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"
D236V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP3 MUTATED                                  0     1
  AKAP3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP3 MUTATED                           2     8
  AKAP3 WILD-TYPE                        17   168
D236V12, multiclass
                                  clus
vv                                 AKAP3 MUTATED AKAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = TNFAIP3 MUTATION ANALYSIS
D237V1, survival
                   sevent
clus2                 0   1
  TNFAIP3 MUTATED    30   4
  TNFAIP3 WILD-TYPE 247  74
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               34               321 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                4                74 
$`TNFAIP3 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5661 
       19.04        24.00        25.08        35.80        79.69        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3975 TCGA-AU-3779 
       22.06        22.52        63.98        10.06        34.06        14.50 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 
       58.39        88.21         6.77        12.76        10.06        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-6169 TCGA-D5-6535 
       15.62        21.99        23.05        20.02        13.02        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A28K 
       17.85         4.80        15.58        13.41       135.65        98.24 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6315 TCGA-G4-6323 
      133.18        74.56        61.91        13.78 

$`TNFAIP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79        49.41        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 
       51.32        21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6317 TCGA-G4-6626 
       85.48        36.00        46.75 

  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
              4.8               0.0 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           135.65            148.01 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
            22.29             22.03 
[1] "4.8 - 135.7 (22.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.7"
D237V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNFAIP3 MUTATED         6        1        1        13         0         0
  TNFAIP3 WILD-TYPE      58        0       25        95         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFAIP3 MUTATED           2          0          6          2        3
  TNFAIP3 WILD-TYPE        16          6         38         31       32
                   vv
clus                STAGE IVA STAGE IVB
  TNFAIP3 MUTATED           0         0
  TNFAIP3 WILD-TYPE        12         1
D237V3, multiclass
            clus
vv           TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 1                 0
  STAGE II                 1                25
  STAGE IIA               13                95
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               6                38
  STAGE IIIC               2                31
  STAGE IV                 3                32
  STAGE IVA                0                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
  TNFAIP3 MUTATED     1   5  26   1
  TNFAIP3 WILD-TYPE   8  62 223  40
D237V4, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  T1               1                 8
  T2               5                62
  T3              26               223
  T4               1                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
  TNFAIP3 MUTATED    22   9   3
  TNFAIP3 WILD-TYPE 198  72  63
D237V5, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  N0              22               198
  N1               9                72
  N2               3                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"
D237V6, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    26   3
  TNFAIP3 WILD-TYPE 259  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     26    3
  TNFAIP3 WILD-TYPE  259   45
   clus
vv  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  0              26               259
  1               3                45
[1] 2 2
[1] FALSE
D237V7, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    12  22
  TNFAIP3 WILD-TYPE 158 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     12   22
  TNFAIP3 WILD-TYPE  158  175
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  FEMALE              12               158
  MALE                22               175
[1] 2 2
[1] FALSE
D237V8, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    29   1
  TNFAIP3 WILD-TYPE 271   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     29    1
  TNFAIP3 WILD-TYPE  271    7
     clus
vv    TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  NO               29               271
  YES               1                 7
[1] 2 2
[1] FALSE
D237V9, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    28   5
  TNFAIP3 WILD-TYPE 286  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     28    5
  TNFAIP3 WILD-TYPE  286   43
                               clus
vv                              TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  COLON ADENOCARCINOMA                       28               286
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TNFAIP3 MUTATED    22   1   1   5
  TNFAIP3 WILD-TYPE 237   2  21  16
D237V10, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  R0              22               237
  R1               1                 2
  R2               1                21
  RX               5                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"
D237V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNFAIP3 MUTATED                                  0     2
  TNFAIP3 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TNFAIP3 MUTATED                           4    23
  TNFAIP3 WILD-TYPE                        15   153
D237V12, multiclass
                                  clus
vv                                 TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      4                15
  WHITE                                         23               153
[1] 4 2
[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 = GFI1 MUTATION ANALYSIS
D238V1, survival
                sevent
clus2              0   1
  GFI1 MUTATED     6   4
  GFI1 WILD-TYPE 271  74
  GFI1 MUTATED GFI1 WILD-TYPE 
            10            345 
  GFI1 MUTATED GFI1 WILD-TYPE 
             4             74 
$`GFI1 MUTATED`
TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3950 TCGA-AZ-6608 TCGA-AA-3947 TCGA-AZ-4682 
       14.53        13.02        24.00         1.94        33.01        22.36 
TCGA-CM-5860 TCGA-D5-6539 TCGA-D5-6541 TCGA-F4-6703 
       32.02        12.49        15.58        47.87 

$`GFI1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 
       15.52        25.08        10.88       106.75       100.01        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GFI1 MUTATED GFI1 WILD-TYPE 
          1.94           0.00 
  GFI1 MUTATED GFI1 WILD-TYPE 
         47.87         148.01 
  GFI1 MUTATED GFI1 WILD-TYPE 
         18.97          22.06 
[1] "1.9 - 47.9 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D238V2, continuous
                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      64        1       26       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GFI1 MUTATED           1          1          0          0        0         1
  GFI1 WILD-TYPE        17          5         44         33       35        11
                vv
clus             STAGE IVB
  GFI1 MUTATED           0
  GFI1 WILD-TYPE         1
D238V3, multiclass
            clus
vv           GFI1 MUTATED GFI1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  GFI1 MUTATED     0   1   8   1
  GFI1 WILD-TYPE   9  66 241  40
D238V4, multiclass
    clus
vv   GFI1 MUTATED GFI1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            1             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
  GFI1 MUTATED     8   1   1
  GFI1 WILD-TYPE 212  80  65
D238V5, multiclass
    clus
vv   GFI1 MUTATED GFI1 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V6, binary
                cls
clus               0   1
  GFI1 MUTATED     9   1
  GFI1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED      9    1
  GFI1 WILD-TYPE  276   47
   clus
vv  GFI1 MUTATED GFI1 WILD-TYPE
  0            9            276
  1            1             47
[1] 2 2
[1] FALSE
D238V7, binary
                cls
clus               0   1
  GFI1 MUTATED     5   5
  GFI1 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED      5    5
  GFI1 WILD-TYPE  165  192
        clus
vv       GFI1 MUTATED GFI1 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D238V8, binary
                cls
clus               0   1
  GFI1 MUTATED    10   0
  GFI1 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED     10    0
  GFI1 WILD-TYPE  290    8
     clus
vv    GFI1 MUTATED GFI1 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D238V9, binary
                cls
clus               0   1
  GFI1 MUTATED     7   3
  GFI1 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED      7    3
  GFI1 WILD-TYPE  307   45
                               clus
vv                              GFI1 MUTATED GFI1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GFI1 MUTATED     7   0   0   0
  GFI1 WILD-TYPE 252   3  22  21
D238V10, multiclass
    clus
vv   GFI1 MUTATED GFI1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            0             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"
D238V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFI1 MUTATED                                  0     0
  GFI1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GFI1 MUTATED                           0     7
  GFI1 WILD-TYPE                        19   169
D238V12, multiclass
                                  clus
vv                                 GFI1 MUTATED GFI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = TWISTNB MUTATION ANALYSIS
D239V1, survival
                   sevent
clus2                 0   1
  TWISTNB MUTATED     7   1
  TWISTNB WILD-TYPE 270  77
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                8               347 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                1                77 
$`TWISTNB MUTATED`
TCGA-G4-6625 TCGA-AA-3977 TCGA-AZ-6603 TCGA-CM-4743 TCGA-CM-5344 TCGA-D5-6926 
       91.79        25.02        29.56        23.05        22.03         9.04 
TCGA-DM-A28H TCGA-G4-6309 
      117.07        85.48 

$`TWISTNB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  TWISTNB MUTATED TWISTNB WILD-TYPE 
             9.04              0.00 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
           117.07            148.01 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
            27.29             21.99 
[1] "9.0 - 117.1 (27.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.1"
D239V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TWISTNB MUTATED         0        0        0         2         0         0
  TWISTNB WILD-TYPE      64        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TWISTNB MUTATED           0          0          3          1        0
  TWISTNB WILD-TYPE        18          6         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  TWISTNB MUTATED           0         0
  TWISTNB WILD-TYPE        12         1
D239V3, multiclass
            clus
vv           TWISTNB MUTATED TWISTNB WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  TWISTNB MUTATED     0   2   5   1
  TWISTNB WILD-TYPE   9  65 244  40
D239V4, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               1                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
  TWISTNB MUTATED     3   4   1
  TWISTNB WILD-TYPE 217  77  65
D239V5, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  N0               3               217
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V6, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     6   0
  TWISTNB WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      6    0
  TWISTNB WILD-TYPE  279   48
   clus
vv  TWISTNB MUTATED TWISTNB WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D239V7, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     4   4
  TWISTNB WILD-TYPE 166 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      4    4
  TWISTNB WILD-TYPE  166  193
        clus
vv       TWISTNB MUTATED TWISTNB WILD-TYPE
  FEMALE               4               166
  MALE                 4               193
[1] 2 2
[1] FALSE
D239V8, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     6   1
  TWISTNB WILD-TYPE 294   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      6    1
  TWISTNB WILD-TYPE  294    7
     clus
vv    TWISTNB MUTATED TWISTNB WILD-TYPE
  NO                6               294
  YES               1                 7
[1] 2 2
[1] FALSE
D239V9, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     8   0
  TWISTNB WILD-TYPE 306  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      8    0
  TWISTNB WILD-TYPE  306   48
                               clus
vv                              TWISTNB MUTATED TWISTNB WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TWISTNB MUTATED     5   0   0   0
  TWISTNB WILD-TYPE 254   3  22  21
D239V10, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D239V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TWISTNB MUTATED                                  0     0
  TWISTNB WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TWISTNB MUTATED                           1     6
  TWISTNB WILD-TYPE                        18   170
D239V12, multiclass
                                  clus
vv                                 TWISTNB MUTATED TWISTNB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[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 = ASB11 MUTATION ANALYSIS
D240V1, survival
                 sevent
clus2               0   1
  ASB11 MUTATED     7   1
  ASB11 WILD-TYPE 270  77
  ASB11 MUTATED ASB11 WILD-TYPE 
              8             347 
  ASB11 MUTATED ASB11 WILD-TYPE 
              1              77 
$`ASB11 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-AD-6901 TCGA-AZ-4315 TCGA-CA-6717 
       26.17        79.69        22.06        22.42        58.39        12.76 
TCGA-CK-5913 TCGA-F4-6856 
       51.32        35.31 

$`ASB11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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           21.99 
[1] "12.8 - 79.7 (30.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D240V2, continuous
                 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      62        1       26       103         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  ASB11 MUTATED           0
  ASB11 WILD-TYPE         1
D240V3, multiclass
            clus
vv           ASB11 MUTATED ASB11 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ASB11 MUTATED     0   2   6   0
  ASB11 WILD-TYPE   9  65 243  41
D240V4, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             0              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
  ASB11 MUTATED     8   0   0
  ASB11 WILD-TYPE 212  81  66
D240V5, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V6, binary
                 cls
clus                0   1
  ASB11 MUTATED     6   0
  ASB11 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      6    0
  ASB11 WILD-TYPE  279   48
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D240V7, binary
                 cls
clus                0   1
  ASB11 MUTATED     3   5
  ASB11 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      3    5
  ASB11 WILD-TYPE  167  192
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D240V8, binary
                 cls
clus                0   1
  ASB11 MUTATED     8   0
  ASB11 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      8    0
  ASB11 WILD-TYPE  292    8
     clus
vv    ASB11 MUTATED ASB11 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D240V9, binary
                 cls
clus                0   1
  ASB11 MUTATED     6   2
  ASB11 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      6    2
  ASB11 WILD-TYPE  308   46
                               clus
vv                              ASB11 MUTATED ASB11 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASB11 MUTATED     5   0   0   2
  ASB11 WILD-TYPE 254   3  22  19
D240V10, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D240V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASB11 MUTATED                                  0     1
  ASB11 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASB11 MUTATED                           0     7
  ASB11 WILD-TYPE                        19   169
D240V12, multiclass
                                  clus
vv                                 ASB11 MUTATED ASB11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = ETAA1 MUTATION ANALYSIS
D241V1, survival
                 sevent
clus2               0   1
  ETAA1 MUTATED    14   2
  ETAA1 WILD-TYPE 263  76
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             16             339 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
              2              76 
$`ETAA1 MUTATED`
TCGA-AA-3525 TCGA-G4-6588 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3866 TCGA-AA-3977 
        8.05        26.17         3.02         6.97        17.03        25.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-5541 
       34.98        12.16        58.39        88.21        12.76        55.92 
TCGA-D5-6539 TCGA-D5-6927 TCGA-DM-A1HA TCGA-F4-6459 
       12.49         9.44       131.51         8.61 

$`ETAA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ETAA1 MUTATED ETAA1 WILD-TYPE 
           3.02            0.00 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
         131.51          148.01 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
         14.895          22.090 
[1] "3.0 - 131.5 (14.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D241V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ETAA1 MUTATED         3        0        2         4         1         0
  ETAA1 WILD-TYPE      61        1       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETAA1 MUTATED           0          0          3          1        0         0
  ETAA1 WILD-TYPE        18          6         41         32       35        12
                 vv
clus              STAGE IVB
  ETAA1 MUTATED           0
  ETAA1 WILD-TYPE         1
D241V3, multiclass
            clus
vv           ETAA1 MUTATED ETAA1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ETAA1 MUTATED     1   3  11   1
  ETAA1 WILD-TYPE   8  64 238  40
D241V4, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            11             238
  T4             1              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
  ETAA1 MUTATED    12   2   2
  ETAA1 WILD-TYPE 208  79  64
D241V5, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V6, binary
                 cls
clus                0   1
  ETAA1 MUTATED    14   0
  ETAA1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     14    0
  ETAA1 WILD-TYPE  271   48
   clus
vv  ETAA1 MUTATED ETAA1 WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D241V7, binary
                 cls
clus                0   1
  ETAA1 MUTATED     7   9
  ETAA1 WILD-TYPE 163 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED      7    9
  ETAA1 WILD-TYPE  163  188
        clus
vv       ETAA1 MUTATED ETAA1 WILD-TYPE
  FEMALE             7             163
  MALE               9             188
[1] 2 2
[1] FALSE
D241V8, binary
                 cls
clus                0   1
  ETAA1 MUTATED    15   0
  ETAA1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     15    0
  ETAA1 WILD-TYPE  285    8
     clus
vv    ETAA1 MUTATED ETAA1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D241V9, binary
                 cls
clus                0   1
  ETAA1 MUTATED    14   2
  ETAA1 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     14    2
  ETAA1 WILD-TYPE  300   46
                               clus
vv                              ETAA1 MUTATED ETAA1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ETAA1 MUTATED    12   0   0   1
  ETAA1 WILD-TYPE 247   3  22  20
D241V10, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D241V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ETAA1 MUTATED                                  0     1
  ETAA1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ETAA1 MUTATED                           0     9
  ETAA1 WILD-TYPE                        19   167
D241V12, multiclass
                                  clus
vv                                 ETAA1 MUTATED ETAA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(242) Variable = NUP188 MUTATION ANALYSIS
D242V1, survival
                  sevent
clus2                0   1
  NUP188 MUTATED    13   5
  NUP188 WILD-TYPE 264  73
  NUP188 MUTATED NUP188 WILD-TYPE 
              18              337 
  NUP188 MUTATED NUP188 WILD-TYPE 
               5               73 
$`NUP188 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-5657 TCGA-A6-6653 TCGA-AA-3510 
       19.04        25.08       100.01        31.63        24.39        63.98 
TCGA-AA-3955 TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-5403 
       20.98         0.99        34.98         1.02        58.39        62.79 
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 

$`NUP188 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
        4.01        27.02        42.02        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-F4-6703 
       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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  NUP188 MUTATED NUP188 WILD-TYPE 
            0.99             0.00 
  NUP188 MUTATED NUP188 WILD-TYPE 
          100.01           148.01 
  NUP188 MUTATED NUP188 WILD-TYPE 
          22.685           22.060 
[1] "1.0 - 100.0 (22.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D242V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP188 MUTATED         5        0        4         3         1         0
  NUP188 WILD-TYPE      59        1       22       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP188 MUTATED           0          0          4          1        1
  NUP188 WILD-TYPE        18          6         40         32       34
                  vv
clus               STAGE IVA STAGE IVB
  NUP188 MUTATED           0         0
  NUP188 WILD-TYPE        12         1
D242V3, multiclass
            clus
vv           NUP188 MUTATED NUP188 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  NUP188 MUTATED     0   6  12   1
  NUP188 WILD-TYPE   9  61 237  40
D242V4, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  T1              0                9
  T2              6               61
  T3             12              237
  T4              1               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
  NUP188 MUTATED    14   2   3
  NUP188 WILD-TYPE 206  79  63
D242V5, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  N0             14              206
  N1              2               79
  N2              3               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"
D242V6, binary
                  cls
clus                 0   1
  NUP188 MUTATED    17   1
  NUP188 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     17    1
  NUP188 WILD-TYPE  268   47
   clus
vv  NUP188 MUTATED NUP188 WILD-TYPE
  0             17              268
  1              1               47
[1] 2 2
[1] FALSE
D242V7, binary
                  cls
clus                 0   1
  NUP188 MUTATED     8  11
  NUP188 WILD-TYPE 162 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED      8   11
  NUP188 WILD-TYPE  162  186
        clus
vv       NUP188 MUTATED NUP188 WILD-TYPE
  FEMALE              8              162
  MALE               11              186
[1] 2 2
[1] FALSE
D242V8, binary
                  cls
clus                 0   1
  NUP188 MUTATED    14   1
  NUP188 WILD-TYPE 286   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     14    1
  NUP188 WILD-TYPE  286    7
     clus
vv    NUP188 MUTATED NUP188 WILD-TYPE
  NO              14              286
  YES              1                7
[1] 2 2
[1] FALSE
D242V9, binary
                  cls
clus                 0   1
  NUP188 MUTATED    18   1
  NUP188 WILD-TYPE 296  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     18    1
  NUP188 WILD-TYPE  296   47
                               clus
vv                              NUP188 MUTATED NUP188 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUP188 MUTATED    14   0   1   0
  NUP188 WILD-TYPE 245   3  21  21
D242V10, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              1               21
  RX              0               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"
D242V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP188 MUTATED                                  0     0
  NUP188 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP188 MUTATED                           1    11
  NUP188 WILD-TYPE                        18   165
D242V12, multiclass
                                  clus
vv                                 NUP188 MUTATED NUP188 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(243) Variable = GNPAT MUTATION ANALYSIS
D243V1, survival
                 sevent
clus2               0   1
  GNPAT MUTATED    12   5
  GNPAT WILD-TYPE 265  73
  GNPAT MUTATED GNPAT WILD-TYPE 
             17             338 
  GNPAT MUTATED GNPAT WILD-TYPE 
              5              73 
$`GNPAT MUTATED`
TCGA-G4-6321 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AY-6197 TCGA-AZ-6598 
       22.09        22.06        19.66        26.99        21.44        49.41 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-6163 TCGA-CM-6675 
       12.59        12.76        21.99        21.14        14.04        13.05 
TCGA-D5-5541 TCGA-DM-A1D4 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6315 
       55.92        92.75        31.96         6.18        61.91 

$`GNPAT WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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-6715 TCGA-CA-6716 TCGA-CA-6718 
       12.69        12.36        12.39        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       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 
       54.61        19.59        56.09        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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-F4-6569 
       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GNPAT MUTATED GNPAT WILD-TYPE 
           6.18            0.00 
  GNPAT MUTATED GNPAT WILD-TYPE 
          92.75          148.01 
  GNPAT MUTATED GNPAT WILD-TYPE 
         21.990          22.225 
[1] "6.2 - 92.8 (22.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D243V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNPAT MUTATED         2        0        1         7         0         0
  GNPAT WILD-TYPE      62        1       25       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNPAT MUTATED           1          0          3          1        1         0
  GNPAT WILD-TYPE        17          6         41         32       34        12
                 vv
clus              STAGE IVB
  GNPAT MUTATED           1
  GNPAT WILD-TYPE         0
D243V3, multiclass
            clus
vv           GNPAT MUTATED GNPAT WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              12
  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  13   1
  GNPAT WILD-TYPE   7  66 236  40
D243V4, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  T1             2               7
  T2             1              66
  T3            13             236
  T4             1              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
  GNPAT MUTATED    10   6   1
  GNPAT WILD-TYPE 210  75  65
D243V5, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  N0            10             210
  N1             6              75
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V6, binary
                 cls
clus                0   1
  GNPAT MUTATED    10   2
  GNPAT WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     10    2
  GNPAT WILD-TYPE  275   46
   clus
vv  GNPAT MUTATED GNPAT WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D243V7, binary
                 cls
clus                0   1
  GNPAT MUTATED     7  10
  GNPAT WILD-TYPE 163 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED      7   10
  GNPAT WILD-TYPE  163  187
        clus
vv       GNPAT MUTATED GNPAT WILD-TYPE
  FEMALE             7             163
  MALE              10             187
[1] 2 2
[1] FALSE
D243V8, binary
                 cls
clus                0   1
  GNPAT MUTATED    15   0
  GNPAT WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     15    0
  GNPAT WILD-TYPE  285    8
     clus
vv    GNPAT MUTATED GNPAT WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D243V9, binary
                 cls
clus                0   1
  GNPAT MUTATED    15   2
  GNPAT WILD-TYPE 299  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     15    2
  GNPAT WILD-TYPE  299   46
                               clus
vv                              GNPAT MUTATED GNPAT WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GNPAT MUTATED    12   0   0   3
  GNPAT WILD-TYPE 247   3  22  18
D243V10, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             3              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"
D243V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNPAT MUTATED                                  0     2
  GNPAT WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNPAT MUTATED                           1    13
  GNPAT WILD-TYPE                        18   163
D243V12, multiclass
                                  clus
vv                                 GNPAT MUTATED GNPAT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       13             163
[1] 4 2
[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 = TRIM32 MUTATION ANALYSIS
D244V1, survival
                  sevent
clus2                0   1
  TRIM32 MUTATED     9   3
  TRIM32 WILD-TYPE 268  75
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              12              343 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
               3               75 
$`TRIM32 MUTATED`
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3715 TCGA-G4-6628 TCGA-AA-3710 TCGA-AA-3968 
       13.02        37.05        19.04        79.69        26.99        21.99 
TCGA-AA-A01R TCGA-AZ-5403 TCGA-F4-6808 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6315 
       35.01        62.79        33.67        74.56        53.62        61.91 

$`TRIM32 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3524 
       24.33        14.53        24.16         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        88.21        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 
       65.85        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            21.99 
[1] "13.0 - 79.7 (36.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D244V2, continuous
                  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      61        1       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM32 MUTATED           2          0          0          1        1
  TRIM32 WILD-TYPE        16          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM32 MUTATED           0         0
  TRIM32 WILD-TYPE        12         1
D244V3, multiclass
            clus
vv           TRIM32 MUTATED TRIM32 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  TRIM32 MUTATED     1   2   8   1
  TRIM32 WILD-TYPE   8  65 241  40
D244V4, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              8              241
  T4              1               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
  TRIM32 MUTATED     8   1   3
  TRIM32 WILD-TYPE 212  80  63
D244V5, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              3               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"
D244V6, binary
                  cls
clus                 0   1
  TRIM32 MUTATED    10   1
  TRIM32 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED     10    1
  TRIM32 WILD-TYPE  275   47
   clus
vv  TRIM32 MUTATED TRIM32 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D244V7, binary
                  cls
clus                 0   1
  TRIM32 MUTATED     5   7
  TRIM32 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED      5    7
  TRIM32 WILD-TYPE  165  190
        clus
vv       TRIM32 MUTATED TRIM32 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D244V8, binary
                  cls
clus                 0   1
  TRIM32 MUTATED    11   1
  TRIM32 WILD-TYPE 289   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED     11    1
  TRIM32 WILD-TYPE  289    7
     clus
vv    TRIM32 MUTATED TRIM32 WILD-TYPE
  NO              11              289
  YES              1                7
[1] 2 2
[1] FALSE
D244V9, binary
                  cls
clus                 0   1
  TRIM32 MUTATED    10   2
  TRIM32 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED     10    2
  TRIM32 WILD-TYPE  304   46
                               clus
vv                              TRIM32 MUTATED TRIM32 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM32 MUTATED    10   0   0   0
  TRIM32 WILD-TYPE 249   3  22  21
D244V10, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              0               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"
D244V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM32 MUTATED                                  0     0
  TRIM32 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM32 MUTATED                           0     6
  TRIM32 WILD-TYPE                        19   170
D244V12, multiclass
                                  clus
vv                                 TRIM32 MUTATED TRIM32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = HAS2 MUTATION ANALYSIS
D245V1, survival
                sevent
clus2              0   1
  HAS2 MUTATED     6   3
  HAS2 WILD-TYPE 271  75
  HAS2 MUTATED HAS2 WILD-TYPE 
             9            346 
  HAS2 MUTATED HAS2 WILD-TYPE 
             3             75 
$`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        83.24        21.44 
TCGA-AY-6386 TCGA-CA-6716 TCGA-G4-6306 
       17.82        12.20        44.68 

$`HAS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  HAS2 MUTATED HAS2 WILD-TYPE 
          1.02           0.00 
  HAS2 MUTATED HAS2 WILD-TYPE 
         83.24         148.01 
  HAS2 MUTATED HAS2 WILD-TYPE 
        17.820         22.225 
[1] "1.0 - 83.2 (17.8)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.8"
D245V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAS2 MUTATED         1        0        1         4         1         0
  HAS2 WILD-TYPE      63        1       25       104         7         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  HAS2 MUTATED           0
  HAS2 WILD-TYPE         1
D245V3, multiclass
            clus
vv           HAS2 MUTATED HAS2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  HAS2 MUTATED     0   2   6   1
  HAS2 WILD-TYPE   9  65 243  40
D245V4, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            1             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
  HAS2 MUTATED     8   1   0
  HAS2 WILD-TYPE 212  80  66
D245V5, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V6, binary
                cls
clus               0   1
  HAS2 MUTATED     7   0
  HAS2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      7    0
  HAS2 WILD-TYPE  278   48
   clus
vv  HAS2 MUTATED HAS2 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D245V7, binary
                cls
clus               0   1
  HAS2 MUTATED     3   6
  HAS2 WILD-TYPE 167 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      3    6
  HAS2 WILD-TYPE  167  191
        clus
vv       HAS2 MUTATED HAS2 WILD-TYPE
  FEMALE            3            167
  MALE              6            191
[1] 2 2
[1] FALSE
D245V8, binary
                cls
clus               0   1
  HAS2 MUTATED     8   0
  HAS2 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      8    0
  HAS2 WILD-TYPE  292    8
     clus
vv    HAS2 MUTATED HAS2 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D245V9, binary
                cls
clus               0   1
  HAS2 MUTATED     6   3
  HAS2 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      6    3
  HAS2 WILD-TYPE  308   45
                               clus
vv                              HAS2 MUTATED HAS2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HAS2 MUTATED     7   0   0   1
  HAS2 WILD-TYPE 252   3  22  20
D245V10, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D245V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAS2 MUTATED                                  0     2
  HAS2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HAS2 MUTATED                           1     3
  HAS2 WILD-TYPE                        18   173
D245V12, multiclass
                                  clus
vv                                 HAS2 MUTATED HAS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = MKL2 MUTATION ANALYSIS
D246V1, survival
                sevent
clus2              0   1
  MKL2 MUTATED     6   4
  MKL2 WILD-TYPE 271  74
  MKL2 MUTATED MKL2 WILD-TYPE 
            10            345 
  MKL2 MUTATED MKL2 WILD-TYPE 
             4             74 
$`MKL2 MUTATED`
TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3518 TCGA-AD-5900 TCGA-AD-6963 
       10.88        22.06         3.02         1.02        12.16        27.42 
TCGA-AU-6004 TCGA-CK-5916 TCGA-F4-6570 TCGA-G4-6307 
       27.09        21.14         6.18        55.04 

$`MKL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MKL2 MUTATED MKL2 WILD-TYPE 
          1.02           0.00 
  MKL2 MUTATED MKL2 WILD-TYPE 
         55.04         148.01 
  MKL2 MUTATED MKL2 WILD-TYPE 
         16.65          22.09 
[1] "1.0 - 55.0 (16.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D246V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MKL2 MUTATED         3        0        1         3         0         0
  MKL2 WILD-TYPE      61        1       25       105         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  MKL2 MUTATED           0
  MKL2 WILD-TYPE         1
D246V3, multiclass
            clus
vv           MKL2 MUTATED MKL2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MKL2 MUTATED     1   2   6   1
  MKL2 WILD-TYPE   8  65 243  40
D246V4, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            6            243
  T4            1             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
  MKL2 MUTATED     8   1   1
  MKL2 WILD-TYPE 212  80  65
D246V5, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V6, binary
                cls
clus               0   1
  MKL2 MUTATED     7   0
  MKL2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      7    0
  MKL2 WILD-TYPE  278   48
   clus
vv  MKL2 MUTATED MKL2 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D246V7, binary
                cls
clus               0   1
  MKL2 MUTATED     7   3
  MKL2 WILD-TYPE 163 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      7    3
  MKL2 WILD-TYPE  163  194
        clus
vv       MKL2 MUTATED MKL2 WILD-TYPE
  FEMALE            7            163
  MALE              3            194
[1] 2 2
[1] FALSE
D246V8, binary
                cls
clus               0   1
  MKL2 MUTATED     8   0
  MKL2 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      8    0
  MKL2 WILD-TYPE  292    8
     clus
vv    MKL2 MUTATED MKL2 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D246V9, binary
                cls
clus               0   1
  MKL2 MUTATED     9   1
  MKL2 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      9    1
  MKL2 WILD-TYPE  305   47
                               clus
vv                              MKL2 MUTATED MKL2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MKL2 MUTATED     7   0   0   1
  MKL2 WILD-TYPE 252   3  22  20
D246V10, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D246V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKL2 MUTATED                                  0     0
  MKL2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MKL2 MUTATED                           0     8
  MKL2 WILD-TYPE                        19   168
D246V12, multiclass
                                  clus
vv                                 MKL2 MUTATED MKL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = PCSK1 MUTATION ANALYSIS
D247V1, survival
                 sevent
clus2               0   1
  PCSK1 MUTATED    12   4
  PCSK1 WILD-TYPE 265  74
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             16             339 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
              4              74 
$`PCSK1 MUTATED`
TCGA-AD-6964 TCGA-G4-6628 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-A010 
       10.88        79.69        29.95         6.97         2.01        34.98 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-5254 
        5.79        27.42        58.39        62.79        49.41        12.69 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4746 TCGA-D5-6536 
       12.76        85.45        37.02        17.85 

$`PCSK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 
       18.05        40.96        12.16        83.24        24.53        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PCSK1 MUTATED PCSK1 WILD-TYPE 
           2.01            0.00 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
          85.45          148.01 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
         28.685          22.030 
[1] "2.0 - 85.5 (28.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D247V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCSK1 MUTATED         2        0        3         6         1         0
  PCSK1 WILD-TYPE      62        1       23       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCSK1 MUTATED           0          0          1          1        0         0
  PCSK1 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  PCSK1 MUTATED           0
  PCSK1 WILD-TYPE         1
D247V3, multiclass
            clus
vv           PCSK1 MUTATED PCSK1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  PCSK1 MUTATED     0   2  11   3
  PCSK1 WILD-TYPE   9  65 238  38
D247V4, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            11             238
  T4             3              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
  PCSK1 MUTATED    13   1   2
  PCSK1 WILD-TYPE 207  80  64
D247V5, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  N0            13             207
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V6, binary
                 cls
clus                0   1
  PCSK1 MUTATED    11   0
  PCSK1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     11    0
  PCSK1 WILD-TYPE  274   48
   clus
vv  PCSK1 MUTATED PCSK1 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D247V7, binary
                 cls
clus                0   1
  PCSK1 MUTATED     6  10
  PCSK1 WILD-TYPE 164 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED      6   10
  PCSK1 WILD-TYPE  164  187
        clus
vv       PCSK1 MUTATED PCSK1 WILD-TYPE
  FEMALE             6             164
  MALE              10             187
[1] 2 2
[1] FALSE
D247V8, binary
                 cls
clus                0   1
  PCSK1 MUTATED    15   0
  PCSK1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     15    0
  PCSK1 WILD-TYPE  285    8
     clus
vv    PCSK1 MUTATED PCSK1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D247V9, binary
                 cls
clus                0   1
  PCSK1 MUTATED    11   5
  PCSK1 WILD-TYPE 303  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     11    5
  PCSK1 WILD-TYPE  303   43
                               clus
vv                              PCSK1 MUTATED PCSK1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCSK1 MUTATED     7   1   0   2
  PCSK1 WILD-TYPE 252   2  22  19
D247V10, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  R0             7             252
  R1             1               2
  R2             0              22
  RX             2              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"
D247V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCSK1 MUTATED                                  0     2
  PCSK1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCSK1 MUTATED                           2     8
  PCSK1 WILD-TYPE                        17   168
D247V12, multiclass
                                  clus
vv                                 PCSK1 MUTATED PCSK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = TIAL1 MUTATION ANALYSIS
D248V1, survival
                 sevent
clus2               0   1
  TIAL1 MUTATED     7   4
  TIAL1 WILD-TYPE 270  74
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             11             344 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
              4              74 
$`TIAL1 MUTATED`
TCGA-AA-3715 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00J TCGA-AZ-6599 TCGA-CA-6718 
       19.04         6.97        53.00        18.05         6.77        10.06 
TCGA-CM-5862 TCGA-CM-6675 TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1HB 
        5.03        13.05        12.39        11.64       135.65 

$`TIAL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TIAL1 MUTATED TIAL1 WILD-TYPE 
           5.03            0.00 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
         135.65          148.01 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
          12.39           22.39 
[1] "5.0 - 135.7 (12.4)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.9"
D248V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TIAL1 MUTATED         1        0        3         3         1         0
  TIAL1 WILD-TYPE      63        1       23       105         7         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        18          6         42         33       35        11
                 vv
clus              STAGE IVB
  TIAL1 MUTATED           1
  TIAL1 WILD-TYPE         0
D248V3, multiclass
            clus
vv           TIAL1 MUTATED TIAL1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              11
  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     0   1   9   2
  TIAL1 WILD-TYPE   9  66 240  39
D248V4, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             2              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
  TIAL1 MUTATED     8   3   1
  TIAL1 WILD-TYPE 212  78  65
D248V5, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V6, binary
                 cls
clus                0   1
  TIAL1 MUTATED     8   2
  TIAL1 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      8    2
  TIAL1 WILD-TYPE  277   46
   clus
vv  TIAL1 MUTATED TIAL1 WILD-TYPE
  0             8             277
  1             2              46
[1] 2 2
[1] FALSE
D248V7, binary
                 cls
clus                0   1
  TIAL1 MUTATED     2  10
  TIAL1 WILD-TYPE 168 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      2   10
  TIAL1 WILD-TYPE  168  187
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  FEMALE             2             168
  MALE              10             187
[1] 2 2
[1] FALSE
D248V8, binary
                 cls
clus                0   1
  TIAL1 MUTATED    10   0
  TIAL1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED     10    0
  TIAL1 WILD-TYPE  290    8
     clus
vv    TIAL1 MUTATED TIAL1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D248V9, binary
                 cls
clus                0   1
  TIAL1 MUTATED     9   2
  TIAL1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      9    2
  TIAL1 WILD-TYPE  305   46
                               clus
vv                              TIAL1 MUTATED TIAL1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TIAL1 MUTATED     8   0   0   2
  TIAL1 WILD-TYPE 251   3  22  19
D248V10, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D248V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIAL1 MUTATED                                  0     1
  TIAL1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TIAL1 MUTATED                           1     6
  TIAL1 WILD-TYPE                        18   170
D248V12, multiclass
                                  clus
vv                                 TIAL1 MUTATED TIAL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = NBEA MUTATION ANALYSIS
D249V1, survival
                sevent
clus2              0   1
  NBEA MUTATED    37   7
  NBEA WILD-TYPE 240  71
  NBEA MUTATED NBEA WILD-TYPE 
            44            311 
  NBEA MUTATED NBEA WILD-TYPE 
             7             71 
$`NBEA MUTATED`
TCGA-AA-3688 TCGA-AA-3713 TCGA-AZ-6608 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-5665 
       19.00        19.04         1.94        35.80        91.79        22.06 
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-3971 
       24.39        20.12         3.02        63.98        26.01        16.08 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A017 TCGA-AD-5900 
       25.02        27.02         4.01        34.98        15.02        12.16 
TCGA-AD-6899 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6606 
        5.79        14.50        27.09        16.31        58.39        11.74 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-5348 TCGA-CM-5860 
       12.20        12.76        10.06        82.95        22.98        32.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-6529 
       15.02        12.00        21.99        15.02        11.01        20.19 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6932 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6806 
       10.13         9.44        11.38        35.74        47.87        41.42 
TCGA-G4-6293 TCGA-G4-6299 
      133.18        74.56 

$`NBEA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 
       49.08         5.88        63.62        22.09        26.17        79.69 
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-A6-5656 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.69        23.87        19.66        20.28         7.04        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       33.01        20.98        34.03         2.01        21.99        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        27.02        27.02         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01D TCGA-AA-A01F 
       42.02         0.99        17.03        14.99        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 
       39.98        18.05        40.96        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.42        26.47         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41         6.77        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        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        13.41        13.35        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-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-F4-6570 
       60.79       117.07        98.24         8.61        31.96         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NBEA MUTATED NBEA WILD-TYPE 
          1.94           0.00 
  NBEA MUTATED NBEA WILD-TYPE 
        133.18         148.01 
  NBEA MUTATED NBEA WILD-TYPE 
         19.58          22.42 
[1] "1.9 - 133.2 (19.6)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D249V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NBEA MUTATED         8        0        2        17         3         0
  NBEA WILD-TYPE      56        1       24        91         5         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        16          4         39         30       32        12
                vv
clus             STAGE IVB
  NBEA MUTATED           0
  NBEA WILD-TYPE         1
D249V3, multiclass
            clus
vv           NBEA MUTATED NBEA WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            17             91
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            2              4
  STAGE IIIB            5             39
  STAGE IIIC            3             30
  STAGE IV              3             32
  STAGE IVA             0             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
  NBEA MUTATED     0  10  31   5
  NBEA WILD-TYPE   9  57 218  36
D249V4, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  T1            0              9
  T2           10             57
  T3           31            218
  T4            5             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
  NBEA MUTATED    32  10   4
  NBEA WILD-TYPE 188  71  62
D249V5, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  N0           32            188
  N1           10             71
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V6, binary
                cls
clus               0   1
  NBEA MUTATED    37   3
  NBEA WILD-TYPE 248  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     37    3
  NBEA WILD-TYPE  248   45
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0           37            248
  1            3             45
[1] 2 2
[1] FALSE
D249V7, binary
                cls
clus               0   1
  NBEA MUTATED    20  26
  NBEA WILD-TYPE 150 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     20   26
  NBEA WILD-TYPE  150  171
        clus
vv       NBEA MUTATED NBEA WILD-TYPE
  FEMALE           20            150
  MALE             26            171
[1] 2 2
[1] FALSE
D249V8, binary
                cls
clus               0   1
  NBEA MUTATED    41   1
  NBEA WILD-TYPE 259   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     41    1
  NBEA WILD-TYPE  259    7
     clus
vv    NBEA MUTATED NBEA WILD-TYPE
  NO            41            259
  YES            1              7
[1] 2 2
[1] FALSE
D249V9, binary
                cls
clus               0   1
  NBEA MUTATED    38   8
  NBEA WILD-TYPE 276  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     38    8
  NBEA WILD-TYPE  276   40
                               clus
vv                              NBEA MUTATED NBEA WILD-TYPE
  COLON ADENOCARCINOMA                    38            276
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NBEA MUTATED    32   1   2   5
  NBEA WILD-TYPE 227   2  20  16
D249V10, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  R0           32            227
  R1            1              2
  R2            2             20
  RX            5             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"
D249V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBEA MUTATED                                  0     3
  NBEA WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NBEA MUTATED                           1    30
  NBEA WILD-TYPE                        18   146
D249V12, multiclass
                                  clus
vv                                 NBEA MUTATED NBEA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      30            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(250) Variable = F2RL1 MUTATION ANALYSIS
D250V1, survival
                 sevent
clus2               0   1
  F2RL1 MUTATED     6   0
  F2RL1 WILD-TYPE 271  78
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              6             349 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              0              78 
$`F2RL1 MUTATED`
TCGA-AZ-4315 TCGA-CM-4744 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5539 
       58.39        20.02        14.04        11.08        11.01        19.59 

$`F2RL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-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-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  F2RL1 MUTATED F2RL1 WILD-TYPE 
          11.01            0.00 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
          58.39          148.01 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
         16.815          22.090 
[1] "11.0 - 58.4 (16.8)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D250V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F2RL1 MUTATED         3        0        0         2         0         0
  F2RL1 WILD-TYPE      61        1       26       106         8         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        18          5         44         33       35        11
                 vv
clus              STAGE IVB
  F2RL1 MUTATED           0
  F2RL1 WILD-TYPE         1
D250V3, multiclass
            clus
vv           F2RL1 MUTATED F2RL1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  F2RL1 MUTATED     1   2   3   1
  F2RL1 WILD-TYPE   8  65 246  40
D250V4, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             3             246
  T4             1              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
  F2RL1 MUTATED     5   2   0
  F2RL1 WILD-TYPE 215  79  66
D250V5, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V6, binary
                 cls
clus                0   1
  F2RL1 MUTATED     5   1
  F2RL1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      5    1
  F2RL1 WILD-TYPE  280   47
   clus
vv  F2RL1 MUTATED F2RL1 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D250V7, binary
                 cls
clus                0   1
  F2RL1 MUTATED     2   5
  F2RL1 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      2    5
  F2RL1 WILD-TYPE  168  192
        clus
vv       F2RL1 MUTATED F2RL1 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D250V8, binary
                 cls
clus                0   1
  F2RL1 MUTATED     6   0
  F2RL1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      6    0
  F2RL1 WILD-TYPE  294    8
     clus
vv    F2RL1 MUTATED F2RL1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D250V9, binary
                 cls
clus                0   1
  F2RL1 MUTATED     6   1
  F2RL1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      6    1
  F2RL1 WILD-TYPE  308   47
                               clus
vv                              F2RL1 MUTATED F2RL1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  F2RL1 MUTATED     6   0   0   1
  F2RL1 WILD-TYPE 253   3  22  20
D250V10, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D250V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  F2RL1 MUTATED                                  0     0
  F2RL1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  F2RL1 MUTATED                           0     7
  F2RL1 WILD-TYPE                        19   169
D250V12, multiclass
                                  clus
vv                                 F2RL1 MUTATED F2RL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = ALG2 MUTATION ANALYSIS
D251V1, survival
                sevent
clus2              0   1
  ALG2 MUTATED     5   3
  ALG2 WILD-TYPE 272  75
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            347 
  ALG2 MUTATED ALG2 WILD-TYPE 
             3             75 
$`ALG2 MUTATED`
TCGA-G4-6588 TCGA-AA-3518 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-5403 TCGA-AZ-5407 
       26.17         1.02         4.01        34.98        62.79        88.21 
TCGA-CM-5349 TCGA-D5-6537 
       30.08         4.80 

$`ALG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 
       17.82        58.39         1.41         5.13        22.36        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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         22.030 
[1] "1.0 - 88.2 (28.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D251V2, continuous
                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      63        1       25       105         6         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  ALG2 MUTATED           0
  ALG2 WILD-TYPE         1
D251V3, multiclass
            clus
vv           ALG2 MUTATED ALG2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ALG2 MUTATED     1   0   5   2
  ALG2 WILD-TYPE   8  67 244  39
D251V4, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  T1            1              8
  T2            0             67
  T3            5            244
  T4            2             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
  ALG2 MUTATED     7   1   0
  ALG2 WILD-TYPE 213  80  66
D251V5, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V6, binary
                cls
clus               0   1
  ALG2 MUTATED     6   0
  ALG2 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      6    0
  ALG2 WILD-TYPE  279   48
   clus
vv  ALG2 MUTATED ALG2 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D251V7, binary
                cls
clus               0   1
  ALG2 MUTATED     5   3
  ALG2 WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      5    3
  ALG2 WILD-TYPE  165  194
        clus
vv       ALG2 MUTATED ALG2 WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D251V8, binary
                cls
clus               0   1
  ALG2 MUTATED     6   0
  ALG2 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      6    0
  ALG2 WILD-TYPE  294    8
     clus
vv    ALG2 MUTATED ALG2 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D251V9, binary
                cls
clus               0   1
  ALG2 MUTATED     7   1
  ALG2 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      7    1
  ALG2 WILD-TYPE  307   47
                               clus
vv                              ALG2 MUTATED ALG2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ALG2 MUTATED     6   0   0   0
  ALG2 WILD-TYPE 253   3  22  21
D251V10, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D251V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG2 MUTATED                                  0     0
  ALG2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALG2 MUTATED                           0     5
  ALG2 WILD-TYPE                        19   171
D251V12, multiclass
                                  clus
vv                                 ALG2 MUTATED ALG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = STBD1 MUTATION ANALYSIS
D252V1, survival
                 sevent
clus2               0   1
  STBD1 MUTATED     5   1
  STBD1 WILD-TYPE 272  77
  STBD1 MUTATED STBD1 WILD-TYPE 
              6             349 
  STBD1 MUTATED STBD1 WILD-TYPE 
              1              77 
$`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 

$`STBD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  STBD1 MUTATED STBD1 WILD-TYPE 
          15.58            0.00 
  STBD1 MUTATED STBD1 WILD-TYPE 
         148.01          140.38 
  STBD1 MUTATED STBD1 WILD-TYPE 
         39.815          21.990 
[1] "15.6 - 148.0 (39.8)" "0.0 - 140.4 (22.0)" 
[1] "hr=" "2.1"
D252V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STBD1 MUTATED         1        0        0         2         0         1
  STBD1 WILD-TYPE      63        1       26       106         8         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        16          6         44         33       35        12
                 vv
clus              STAGE IVB
  STBD1 MUTATED           0
  STBD1 WILD-TYPE         1
D252V3, multiclass
            clus
vv           STBD1 MUTATED STBD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  STBD1 MUTATED     0   2   3   1
  STBD1 WILD-TYPE   9  65 246  40
D252V4, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             1              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
  STBD1 MUTATED     4   2   0
  STBD1 WILD-TYPE 216  79  66
D252V5, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V6, binary
                 cls
clus                0   1
  STBD1 MUTATED     6   0
  STBD1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      6    0
  STBD1 WILD-TYPE  279   48
   clus
vv  STBD1 MUTATED STBD1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D252V7, binary
                 cls
clus                0   1
  STBD1 MUTATED     2   4
  STBD1 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      2    4
  STBD1 WILD-TYPE  168  193
        clus
vv       STBD1 MUTATED STBD1 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D252V8, binary
                 cls
clus                0   1
  STBD1 MUTATED     5   0
  STBD1 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      5    0
  STBD1 WILD-TYPE  295    8
     clus
vv    STBD1 MUTATED STBD1 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D252V9, binary
                 cls
clus                0   1
  STBD1 MUTATED     5   1
  STBD1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      5    1
  STBD1 WILD-TYPE  309   47
                               clus
vv                              STBD1 MUTATED STBD1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STBD1 MUTATED     4   0   0   0
  STBD1 WILD-TYPE 255   3  22  21
D252V10, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D252V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STBD1 MUTATED                                  0     0
  STBD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STBD1 MUTATED                           0     5
  STBD1 WILD-TYPE                        19   171
D252V12, multiclass
                                  clus
vv                                 STBD1 MUTATED STBD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = C12ORF40 MUTATION ANALYSIS
D253V1, survival
                    sevent
clus2                  0   1
  C12ORF40 MUTATED    15   5
  C12ORF40 WILD-TYPE 262  73
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                20                335 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 5                 73 
$`C12ORF40 MUTATED`
TCGA-AA-3713 TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-A00N 
       19.04        49.08        26.17        33.53        25.18         4.01 
TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-6598 TCGA-CA-6717 
       83.24        14.50        27.09         0.20        49.41        12.76 
TCGA-CK-4947 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6931 
       17.56         2.01        22.03        14.04        11.08        12.00 
TCGA-DM-A1D6 TCGA-DM-A1HB 
       49.91       135.65 

$`C12ORF40 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       27.42        26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
               0.2                0.0 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            135.65             148.01 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            20.535             22.090 
[1] "0.2 - 135.7 (20.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D253V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF40 MUTATED         4        0        1         6         1         0
  C12ORF40 WILD-TYPE      60        1       25       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF40 MUTATED           0          0          3          2        3
  C12ORF40 WILD-TYPE        18          6         41         31       32
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF40 MUTATED           1         0
  C12ORF40 WILD-TYPE        11         1
D253V3, multiclass
            clus
vv           C12ORF40 MUTATED C12ORF40 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 6                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                2                 31
  STAGE IV                  3                 32
  STAGE IVA                 1                 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
  C12ORF40 MUTATED     0   4  13   4
  C12ORF40 WILD-TYPE   9  63 236  37
D253V4, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  T1                0                  9
  T2                4                 63
  T3               13                236
  T4                4                 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
  C12ORF40 MUTATED    14   4   3
  C12ORF40 WILD-TYPE 206  77  63
D253V5, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  N0               14                206
  N1                4                 77
  N2                3                 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"
D253V6, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    14   4
  C12ORF40 WILD-TYPE 271  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     14    4
  C12ORF40 WILD-TYPE  271   44
   clus
vv  C12ORF40 MUTATED C12ORF40 WILD-TYPE
  0               14                271
  1                4                 44
[1] 2 2
[1] FALSE
D253V7, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED     9  12
  C12ORF40 WILD-TYPE 161 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED      9   12
  C12ORF40 WILD-TYPE  161  185
        clus
vv       C12ORF40 MUTATED C12ORF40 WILD-TYPE
  FEMALE                9                161
  MALE                 12                185
[1] 2 2
[1] FALSE
D253V8, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    14   1
  C12ORF40 WILD-TYPE 286   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     14    1
  C12ORF40 WILD-TYPE  286    7
     clus
vv    C12ORF40 MUTATED C12ORF40 WILD-TYPE
  NO                14                286
  YES                1                  7
[1] 2 2
[1] FALSE
D253V9, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    15   5
  C12ORF40 WILD-TYPE 299  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     15    5
  C12ORF40 WILD-TYPE  299   43
                               clus
vv                              C12ORF40 MUTATED C12ORF40 WILD-TYPE
  COLON ADENOCARCINOMA                        15                299
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF40 MUTATED    11   0   2   4
  C12ORF40 WILD-TYPE 248   3  20  17
D253V10, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  R0               11                248
  R1                0                  3
  R2                2                 20
  RX                4                 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"
D253V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF40 MUTATED                                  0     2
  C12ORF40 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF40 MUTATED                           1    15
  C12ORF40 WILD-TYPE                        18   161
D253V12, multiclass
                                  clus
vv                                 C12ORF40 MUTATED C12ORF40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          15                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(254) Variable = GNAS MUTATION ANALYSIS
D254V1, survival
                sevent
clus2              0   1
  GNAS MUTATED    23   9
  GNAS WILD-TYPE 254  69
  GNAS MUTATED GNAS WILD-TYPE 
            32            323 
  GNAS MUTATED GNAS WILD-TYPE 
             9             69 
$`GNAS MUTATED`
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2678 TCGA-A6-6141 TCGA-AA-3489 
       22.09        35.80        26.17        42.28         8.38         7.04 
TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3679 TCGA-AA-3681 
       35.01         1.02        78.08         6.97        15.02         5.98 
TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-3869 TCGA-AA-3989 TCGA-AD-5900 TCGA-AD-6889 
       33.04        30.05        27.02         7.96        12.16        83.24 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6718 
       27.09        49.41         6.77        12.10        29.56        10.06 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6675 TCGA-D5-6928 TCGA-DM-A1HA TCGA-G4-6306 
       15.62        23.05        13.05        11.64       131.51        44.68 
TCGA-G4-6315 TCGA-G4-6317 
       61.91        36.00 

$`GNAS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
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-A6-6651 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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       20.28         3.02        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        61.02        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       50.04        47.01        11.01        37.05         5.03        26.99 
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-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-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6605 TCGA-AZ-6606 
        5.13        22.36        62.79        88.21         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6323 TCGA-G4-6626 
       53.62        55.04        85.48        13.78        46.75 

  GNAS MUTATED GNAS WILD-TYPE 
          1.02           0.00 
  GNAS MUTATED GNAS WILD-TYPE 
        131.51         148.01 
  GNAS MUTATED GNAS WILD-TYPE 
         24.61          21.99 
[1] "1.0 - 131.5 (24.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D254V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNAS MUTATED         4        0        4        10         0         0
  GNAS WILD-TYPE      60        1       22        98         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNAS MUTATED           2          0          1          3        5         0
  GNAS WILD-TYPE        16          6         43         30       30        12
                vv
clus             STAGE IVB
  GNAS MUTATED           1
  GNAS WILD-TYPE         0
D254V3, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            10             98
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            3             30
  STAGE IV              5             30
  STAGE IVA             0             12
  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   7  22   3
  GNAS WILD-TYPE   9  60 227  38
D254V4, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  T1            0              9
  T2            7             60
  T3           22            227
  T4            3             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
  GNAS MUTATED    19   6   7
  GNAS WILD-TYPE 201  75  59
D254V5, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  N0           19            201
  N1            6             75
  N2            7             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V6, binary
                cls
clus               0   1
  GNAS MUTATED    20   6
  GNAS WILD-TYPE 265  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     20    6
  GNAS WILD-TYPE  265   42
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0           20            265
  1            6             42
[1] 2 2
[1] FALSE
D254V7, binary
                cls
clus               0   1
  GNAS MUTATED    13  19
  GNAS WILD-TYPE 157 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     13   19
  GNAS WILD-TYPE  157  178
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE           13            157
  MALE             19            178
[1] 2 2
[1] FALSE
D254V8, binary
                cls
clus               0   1
  GNAS MUTATED    28   0
  GNAS WILD-TYPE 272   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     28    0
  GNAS WILD-TYPE  272    8
     clus
vv    GNAS MUTATED GNAS WILD-TYPE
  NO            28            272
  YES            0              8
[1] 2 2
[1] FALSE
D254V9, binary
                cls
clus               0   1
  GNAS MUTATED    29   3
  GNAS WILD-TYPE 285  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     29    3
  GNAS WILD-TYPE  285   45
                               clus
vv                              GNAS MUTATED GNAS WILD-TYPE
  COLON ADENOCARCINOMA                    29            285
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GNAS MUTATED    21   0   3   2
  GNAS WILD-TYPE 238   3  19  19
D254V10, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0           21            238
  R1            0              3
  R2            3             19
  RX            2             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"
D254V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNAS MUTATED                                  0     2
  GNAS WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED                           3    16
  GNAS WILD-TYPE                        16   160
D254V12, multiclass
                                  clus
vv                                 GNAS MUTATED GNAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      16            160
[1] 4 2
[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 = RBM7 MUTATION ANALYSIS
D255V1, survival
                sevent
clus2              0   1
  RBM7 MUTATED     6   4
  RBM7 WILD-TYPE 271  74
  RBM7 MUTATED RBM7 WILD-TYPE 
            10            345 
  RBM7 MUTATED RBM7 WILD-TYPE 
             4             74 
$`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 
       15.62        11.01        15.12        65.85 

$`RBM7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        49.41        12.10         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 
       74.56        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RBM7 MUTATED RBM7 WILD-TYPE 
          4.01           0.00 
  RBM7 MUTATED RBM7 WILD-TYPE 
         65.85         148.01 
  RBM7 MUTATED RBM7 WILD-TYPE 
         15.37          22.09 
[1] "4.0 - 65.8 (15.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D255V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM7 MUTATED         1        0        0         3         1         0
  RBM7 WILD-TYPE      63        1       26       105         7         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        18          6         43         32       34        11
                vv
clus             STAGE IVB
  RBM7 MUTATED           0
  RBM7 WILD-TYPE         1
D255V3, multiclass
            clus
vv           RBM7 MUTATED RBM7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  RBM7 MUTATED     0   2   5   3
  RBM7 WILD-TYPE   9  65 244  38
D255V4, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            3             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
  RBM7 MUTATED     5   4   1
  RBM7 WILD-TYPE 215  77  65
D255V5, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  N0            5            215
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V6, binary
                cls
clus               0   1
  RBM7 MUTATED     5   2
  RBM7 WILD-TYPE 280  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      5    2
  RBM7 WILD-TYPE  280   46
   clus
vv  RBM7 MUTATED RBM7 WILD-TYPE
  0            5            280
  1            2             46
[1] 2 2
[1] FALSE
D255V7, binary
                cls
clus               0   1
  RBM7 MUTATED     5   5
  RBM7 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      5    5
  RBM7 WILD-TYPE  165  192
        clus
vv       RBM7 MUTATED RBM7 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D255V8, binary
                cls
clus               0   1
  RBM7 MUTATED     8   0
  RBM7 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      8    0
  RBM7 WILD-TYPE  292    8
     clus
vv    RBM7 MUTATED RBM7 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D255V9, binary
                cls
clus               0   1
  RBM7 MUTATED     6   4
  RBM7 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      6    4
  RBM7 WILD-TYPE  308   44
                               clus
vv                              RBM7 MUTATED RBM7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBM7 MUTATED     5   0   0   3
  RBM7 WILD-TYPE 254   3  22  18
D255V10, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            3             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"
D255V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM7 MUTATED                                  0     1
  RBM7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBM7 MUTATED                           0     7
  RBM7 WILD-TYPE                        19   169
D255V12, multiclass
                                  clus
vv                                 RBM7 MUTATED RBM7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = RUNX1 MUTATION ANALYSIS
D256V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED    28   8
  RUNX1 WILD-TYPE 249  70
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             36             319 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
              8              70 
$`RUNX1 MUTATED`
TCGA-A6-4105 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-4681 
       14.53         0.92        85.05        19.04        24.00       106.75 
TCGA-G4-6628 TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3818 TCGA-AA-3861 TCGA-AA-A01T 
       79.69        31.63        19.66         0.99        30.05        33.04 
TCGA-AD-6889 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       83.24        33.01        58.39        49.41         6.77        29.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 
       85.45        15.62        30.08        32.02        15.02        12.99 
TCGA-CM-6171 TCGA-D5-6533 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28H TCGA-DM-A28K 
       14.04        25.48        44.32       135.65       117.07        98.24 
TCGA-F4-6569 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       35.74       133.18        53.62        36.00        13.78        46.75 

$`RUNX1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       10.88       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79        88.21        12.10         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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5913 
       12.76        10.06        14.30        17.56       148.01        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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        54.61 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        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        43.04        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 
       61.91 

  RUNX1 MUTATED RUNX1 WILD-TYPE 
           0.92            0.00 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         135.65          148.01 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         32.515          21.440 
[1] "0.9 - 135.7 (32.5)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.6"
D256V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUNX1 MUTATED         4        1        2        14         1         0
  RUNX1 WILD-TYPE      60        0       24        94         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUNX1 MUTATED           4          0          3          4        1         1
  RUNX1 WILD-TYPE        14          6         41         29       34        11
                 vv
clus              STAGE IVB
  RUNX1 MUTATED           0
  RUNX1 WILD-TYPE         1
D256V3, multiclass
            clus
vv           RUNX1 MUTATED RUNX1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA             14              94
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              4              14
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             4              29
  STAGE IV               1              34
  STAGE IVA              1              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
  RUNX1 MUTATED     0   5  27   4
  RUNX1 WILD-TYPE   9  62 222  37
D256V4, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            27             222
  T4             4              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
  RUNX1 MUTATED    24   9   4
  RUNX1 WILD-TYPE 196  72  62
D256V5, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  N0            24             196
  N1             9              72
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V6, binary
                 cls
clus                0   1
  RUNX1 MUTATED    29   2
  RUNX1 WILD-TYPE 256  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     29    2
  RUNX1 WILD-TYPE  256   46
   clus
vv  RUNX1 MUTATED RUNX1 WILD-TYPE
  0            29             256
  1             2              46
[1] 2 2
[1] FALSE
D256V7, binary
                 cls
clus                0   1
  RUNX1 MUTATED    18  19
  RUNX1 WILD-TYPE 152 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     18   19
  RUNX1 WILD-TYPE  152  178
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  FEMALE            18             152
  MALE              19             178
[1] 2 2
[1] FALSE
D256V8, binary
                 cls
clus                0   1
  RUNX1 MUTATED    29   1
  RUNX1 WILD-TYPE 271   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     29    1
  RUNX1 WILD-TYPE  271    7
     clus
vv    RUNX1 MUTATED RUNX1 WILD-TYPE
  NO             29             271
  YES             1               7
[1] 2 2
[1] FALSE
D256V9, binary
                 cls
clus                0   1
  RUNX1 MUTATED    31   5
  RUNX1 WILD-TYPE 283  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     31    5
  RUNX1 WILD-TYPE  283   43
                               clus
vv                              RUNX1 MUTATED RUNX1 WILD-TYPE
  COLON ADENOCARCINOMA                     31             283
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUNX1 MUTATED    26   1   1   1
  RUNX1 WILD-TYPE 233   2  21  20
D256V10, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  R0            26             233
  R1             1               2
  R2             1              21
  RX             1              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"
D256V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUNX1 MUTATED                                  0     1
  RUNX1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUNX1 MUTATED                           5    23
  RUNX1 WILD-TYPE                        14   153
D256V12, multiclass
                                  clus
vv                                 RUNX1 MUTATED RUNX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       23             153
[1] 4 2
[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 = FAM133B MUTATION ANALYSIS
D257V1, survival
                   sevent
clus2                 0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 273  77
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               350 
  FAM133B MUTATED FAM133B WILD-TYPE 
                1                77 
$`FAM133B MUTATED`
TCGA-G4-6628 TCGA-A6-3809 TCGA-CK-5916 TCGA-CM-6167 TCGA-G4-6309 
       79.69        32.75        21.14        14.99        85.48 

$`FAM133B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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            22.045 
[1] "15.0 - 85.5 (32.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D257V2, continuous
                   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      62        1       26       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133B MUTATED           0          0          1          1        0
  FAM133B WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM133B MUTATED           0         0
  FAM133B WILD-TYPE        12         1
D257V3, multiclass
            clus
vv           FAM133B MUTATED FAM133B WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                0               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM133B MUTATED     1   1   2   1
  FAM133B WILD-TYPE   8  66 247  40
D257V4, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               2               247
  T4               1                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
  FAM133B MUTATED     3   1   1
  FAM133B WILD-TYPE 217  80  65
D257V5, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  N0               3               217
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V6, binary
                   cls
clus                  0   1
  FAM133B MUTATED     5   0
  FAM133B WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      5    0
  FAM133B WILD-TYPE  280   48
   clus
vv  FAM133B MUTATED FAM133B WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D257V7, binary
                   cls
clus                  0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 166 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      4    1
  FAM133B WILD-TYPE  166  196
        clus
vv       FAM133B MUTATED FAM133B WILD-TYPE
  FEMALE               4               166
  MALE                 1               196
[1] 2 2
[1] FALSE
D257V8, binary
                   cls
clus                  0   1
  FAM133B MUTATED     5   0
  FAM133B WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      5    0
  FAM133B WILD-TYPE  295    8
     clus
vv    FAM133B MUTATED FAM133B WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D257V9, binary
                   cls
clus                  0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      4    1
  FAM133B WILD-TYPE  310   47
                               clus
vv                              FAM133B MUTATED FAM133B WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM133B MUTATED     4   0   0   1
  FAM133B WILD-TYPE 255   3  22  20
D257V10, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               1                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"
D257V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM133B MUTATED                                  0     0
  FAM133B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM133B MUTATED                           2     3
  FAM133B WILD-TYPE                        17   173
D257V12, multiclass
                                  clus
vv                                 FAM133B MUTATED FAM133B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          3               173
[1] 4 2
[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 = CARD11 MUTATION ANALYSIS
D258V1, survival
                  sevent
clus2                0   1
  CARD11 MUTATED    32   7
  CARD11 WILD-TYPE 245  71
  CARD11 MUTATED CARD11 WILD-TYPE 
              39              316 
  CARD11 MUTATED CARD11 WILD-TYPE 
               7               71 
$`CARD11 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6964 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6651 
       19.04        24.00        10.88        32.91        30.44        21.76 
TCGA-A6-6652 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3980 TCGA-AA-A00R TCGA-AY-4071 
       24.69         6.97        53.00        27.02         0.99         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        12.39        12.59 
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 
      131.51         1.55        13.78 

$`CARD11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6653 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       16.31         0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6717 
       11.74         3.19        12.69        12.36        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       10.06        14.30        17.56        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 
       21.14        82.95         2.01       124.27        23.05        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-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        15.02        14.04        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        54.61        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        25.48        43.27        15.12        17.85        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        13.41        13.35        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-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       13.32        12.59         7.50       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-F4-6805 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 
       43.04        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-G4-6626 
       85.48        61.91        36.00        46.75 

  CARD11 MUTATED CARD11 WILD-TYPE 
            0.95             0.00 
  CARD11 MUTATED CARD11 WILD-TYPE 
          148.01           139.17 
  CARD11 MUTATED CARD11 WILD-TYPE 
           20.02            22.47 
[1] "0.9 - 148.0 (20.0)" "0.0 - 139.2 (22.5)"
[1] "hr=" "1.4"
D258V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CARD11 MUTATED         8        1        3        12         0         0
  CARD11 WILD-TYPE      56        0       23        96         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CARD11 MUTATED           2          0          7          2        1
  CARD11 WILD-TYPE        16          6         37         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CARD11 MUTATED           3         0
  CARD11 WILD-TYPE         9         1
D258V3, multiclass
            clus
vv           CARD11 MUTATED CARD11 WILD-TYPE
  STAGE I                 8               56
  STAGE IA                1                0
  STAGE II                3               23
  STAGE IIA              12               96
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              7               37
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               3                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
  CARD11 MUTATED     1   7  28   4
  CARD11 WILD-TYPE   8  60 221  37
D258V4, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  T1              1                8
  T2              7               60
  T3             28              221
  T4              4               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
  CARD11 MUTATED    26  10   5
  CARD11 WILD-TYPE 194  71  61
D258V5, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  N0             26              194
  N1             10               71
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V6, binary
                  cls
clus                 0   1
  CARD11 MUTATED    30   4
  CARD11 WILD-TYPE 255  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     30    4
  CARD11 WILD-TYPE  255   44
   clus
vv  CARD11 MUTATED CARD11 WILD-TYPE
  0             30              255
  1              4               44
[1] 2 2
[1] FALSE
D258V7, binary
                  cls
clus                 0   1
  CARD11 MUTATED    17  24
  CARD11 WILD-TYPE 153 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     17   24
  CARD11 WILD-TYPE  153  173
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  FEMALE             17              153
  MALE               24              173
[1] 2 2
[1] FALSE
D258V8, binary
                  cls
clus                 0   1
  CARD11 MUTATED    32   1
  CARD11 WILD-TYPE 268   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     32    1
  CARD11 WILD-TYPE  268    7
     clus
vv    CARD11 MUTATED CARD11 WILD-TYPE
  NO              32              268
  YES              1                7
[1] 2 2
[1] FALSE
D258V9, binary
                  cls
clus                 0   1
  CARD11 MUTATED    33   7
  CARD11 WILD-TYPE 281  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     33    7
  CARD11 WILD-TYPE  281   41
                               clus
vv                              CARD11 MUTATED CARD11 WILD-TYPE
  COLON ADENOCARCINOMA                      33              281
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CARD11 MUTATED    29   1   0   1
  CARD11 WILD-TYPE 230   2  22  20
D258V10, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  R0             29              230
  R1              1                2
  R2              0               22
  RX              1               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"
D258V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CARD11 MUTATED                                  1     3
  CARD11 WILD-TYPE                                0     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CARD11 MUTATED                           5    24
  CARD11 WILD-TYPE                        14   152
D258V12, multiclass
                                  clus
vv                                 CARD11 MUTATED CARD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     5               14
  WHITE                                        24              152
[1] 4 2
[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 = IFT57 MUTATION ANALYSIS
D259V1, survival
                 sevent
clus2               0   1
  IFT57 MUTATED     8   2
  IFT57 WILD-TYPE 269  76
  IFT57 MUTATED IFT57 WILD-TYPE 
             10             345 
  IFT57 MUTATED IFT57 WILD-TYPE 
              2              76 
$`IFT57 MUTATED`
TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CM-4743 
       26.17        22.06        32.71         4.01        58.39        23.05 
TCGA-CM-5868 TCGA-CM-6162 TCGA-DM-A1DA TCGA-G4-6323 
       17.03        12.00         7.50        13.78 

$`IFT57 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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-6163 TCGA-CM-6164 
        5.03        15.02        15.02        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-F4-6459 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        46.75 

  IFT57 MUTATED IFT57 WILD-TYPE 
           4.01            0.00 
  IFT57 MUTATED IFT57 WILD-TYPE 
          58.39          148.01 
  IFT57 MUTATED IFT57 WILD-TYPE 
         19.545          22.090 
[1] "4.0 - 58.4 (19.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D259V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFT57 MUTATED         0        1        0         4         1         1
  IFT57 WILD-TYPE      64        0       26       104         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFT57 MUTATED           0          0          1          1        0         1
  IFT57 WILD-TYPE        18          6         43         32       35        11
                 vv
clus              STAGE IVB
  IFT57 MUTATED           0
  IFT57 WILD-TYPE         1
D259V3, multiclass
            clus
vv           IFT57 MUTATED IFT57 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  IFT57 MUTATED     0   0   6   3
  IFT57 WILD-TYPE   9  67 243  38
D259V4, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             3              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
  IFT57 MUTATED     7   2   1
  IFT57 WILD-TYPE 213  79  65
D259V5, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V6, binary
                 cls
clus                0   1
  IFT57 MUTATED     8   1
  IFT57 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      8    1
  IFT57 WILD-TYPE  277   47
   clus
vv  IFT57 MUTATED IFT57 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D259V7, binary
                 cls
clus                0   1
  IFT57 MUTATED     5   5
  IFT57 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      5    5
  IFT57 WILD-TYPE  165  192
        clus
vv       IFT57 MUTATED IFT57 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D259V8, binary
                 cls
clus                0   1
  IFT57 MUTATED     8   0
  IFT57 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      8    0
  IFT57 WILD-TYPE  292    8
     clus
vv    IFT57 MUTATED IFT57 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D259V9, binary
                 cls
clus                0   1
  IFT57 MUTATED     8   2
  IFT57 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      8    2
  IFT57 WILD-TYPE  306   46
                               clus
vv                              IFT57 MUTATED IFT57 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IFT57 MUTATED     8   0   0   0
  IFT57 WILD-TYPE 251   3  22  21
D259V10, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D259V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFT57 MUTATED                                  0     0
  IFT57 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFT57 MUTATED                           1     8
  IFT57 WILD-TYPE                        18   168
D259V12, multiclass
                                  clus
vv                                 IFT57 MUTATED IFT57 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = TNFRSF9 MUTATION ANALYSIS
D260V1, survival
                   sevent
clus2                 0   1
  TNFRSF9 MUTATED     8   1
  TNFRSF9 WILD-TYPE 269  77
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               346 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                1                77 
$`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        12.39        12.76 
TCGA-CM-5341 TCGA-CM-6167 TCGA-D5-6538 
       29.06        14.99        17.13 

$`TNFRSF9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            12.39              0.00 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            38.07            148.01 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
           18.050            22.075 
[1] "12.4 - 38.1 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D260V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNFRSF9 MUTATED         1        0        0         2         0         1
  TNFRSF9 WILD-TYPE      63        1       26       106         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF9 MUTATED           1          1          2          1        0
  TNFRSF9 WILD-TYPE        17          5         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  TNFRSF9 MUTATED           0         0
  TNFRSF9 WILD-TYPE        12         1
D260V3, multiclass
            clus
vv           TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  TNFRSF9 MUTATED     0   2   5   2
  TNFRSF9 WILD-TYPE   9  65 244  39
D260V4, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               2                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
  TNFRSF9 MUTATED     4   3   2
  TNFRSF9 WILD-TYPE 216  78  64
D260V5, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  N0               4               216
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V6, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     9   0
  TNFRSF9 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      9    0
  TNFRSF9 WILD-TYPE  276   48
   clus
vv  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D260V7, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     5   4
  TNFRSF9 WILD-TYPE 165 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      5    4
  TNFRSF9 WILD-TYPE  165  193
        clus
vv       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  FEMALE               5               165
  MALE                 4               193
[1] 2 2
[1] FALSE
D260V8, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     9   0
  TNFRSF9 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      9    0
  TNFRSF9 WILD-TYPE  291    8
     clus
vv    TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D260V9, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     6   3
  TNFRSF9 WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      6    3
  TNFRSF9 WILD-TYPE  308   45
                               clus
vv                              TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TNFRSF9 MUTATED     6   0   0   1
  TNFRSF9 WILD-TYPE 253   3  22  20
D260V10, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D260V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNFRSF9 MUTATED                                  0     2
  TNFRSF9 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TNFRSF9 MUTATED                           1     4
  TNFRSF9 WILD-TYPE                        18   172
D260V12, multiclass
                                  clus
vv                                 TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = WNT16 MUTATION ANALYSIS
D261V1, survival
                 sevent
clus2               0   1
  WNT16 MUTATED     5   2
  WNT16 WILD-TYPE 272  76
  WNT16 MUTATED WNT16 WILD-TYPE 
              7             348 
  WNT16 MUTATED WNT16 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.045 
[1] "3.0 - 78.1 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D261V2, continuous
                 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      64        1       23       106         6         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  WNT16 MUTATED           0
  WNT16 WILD-TYPE         1
D261V3, multiclass
            clus
vv           WNT16 MUTATED WNT16 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  WNT16 MUTATED     0   0   5   3
  WNT16 WILD-TYPE   9  67 244  38
D261V4, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             3              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
  WNT16 MUTATED     7   1   0
  WNT16 WILD-TYPE 213  80  66
D261V5, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V6, binary
                 cls
clus                0   1
  WNT16 MUTATED     5   0
  WNT16 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      5    0
  WNT16 WILD-TYPE  280   48
   clus
vv  WNT16 MUTATED WNT16 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D261V7, binary
                 cls
clus                0   1
  WNT16 MUTATED     4   4
  WNT16 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      4    4
  WNT16 WILD-TYPE  166  193
        clus
vv       WNT16 MUTATED WNT16 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D261V8, binary
                 cls
clus                0   1
  WNT16 MUTATED     7   0
  WNT16 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      7    0
  WNT16 WILD-TYPE  293    8
     clus
vv    WNT16 MUTATED WNT16 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D261V9, binary
                 cls
clus                0   1
  WNT16 MUTATED     6   2
  WNT16 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      6    2
  WNT16 WILD-TYPE  308   46
                               clus
vv                              WNT16 MUTATED WNT16 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WNT16 MUTATED     6   0   0   1
  WNT16 WILD-TYPE 253   3  22  20
D261V10, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D261V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNT16 MUTATED                                  0     0
  WNT16 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WNT16 MUTATED                           0     5
  WNT16 WILD-TYPE                        19   171
D261V12, multiclass
                                  clus
vv                                 WNT16 MUTATED WNT16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = SLC9A10 MUTATION ANALYSIS
D262V1, survival
                   sevent
clus2                 0   1
  SLC9A10 MUTATED    16   2
  SLC9A10 WILD-TYPE 261  76
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               18               337 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
                2                76 
$`SLC9A10 MUTATED`
TCGA-AA-3713 TCGA-A6-6780 TCGA-AA-3534 TCGA-AA-3710 TCGA-AA-A010 TCGA-AA-A01Q 
       19.04        20.12        29.00        26.99        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 

$`SLC9A10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       12.00        14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
             1.02              0.00 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           140.38            148.01 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           22.095            22.060 
[1] "1.0 - 140.4 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D262V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC9A10 MUTATED         3        0        1        11         1         0
  SLC9A10 WILD-TYPE      61        1       25        97         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A10 MUTATED           0          0          1          0        1
  SLC9A10 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC9A10 MUTATED           0         0
  SLC9A10 WILD-TYPE        12         1
D262V3, multiclass
            clus
vv           SLC9A10 MUTATED SLC9A10 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA               11                97
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC9A10 MUTATED     1   2  14   1
  SLC9A10 WILD-TYPE   8  65 235  40
D262V4, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3              14               235
  T4               1                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
  SLC9A10 MUTATED    17   1   0
  SLC9A10 WILD-TYPE 203  80  66
D262V5, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  N0              17               203
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V6, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    16   1
  SLC9A10 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     16    1
  SLC9A10 WILD-TYPE  269   47
   clus
vv  SLC9A10 MUTATED SLC9A10 WILD-TYPE
  0              16               269
  1               1                47
[1] 2 2
[1] FALSE
D262V7, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED     9   9
  SLC9A10 WILD-TYPE 161 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED      9    9
  SLC9A10 WILD-TYPE  161  188
        clus
vv       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  FEMALE               9               161
  MALE                 9               188
[1] 2 2
[1] FALSE
D262V8, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    14   1
  SLC9A10 WILD-TYPE 286   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     14    1
  SLC9A10 WILD-TYPE  286    7
     clus
vv    SLC9A10 MUTATED SLC9A10 WILD-TYPE
  NO               14               286
  YES               1                 7
[1] 2 2
[1] FALSE
D262V9, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    15   3
  SLC9A10 WILD-TYPE 299  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     15    3
  SLC9A10 WILD-TYPE  299   45
                               clus
vv                              SLC9A10 MUTATED SLC9A10 WILD-TYPE
  COLON ADENOCARCINOMA                       15               299
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC9A10 MUTATED    12   0   1   2
  SLC9A10 WILD-TYPE 247   3  21  19
D262V10, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               1                21
  RX               2                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"
D262V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A10 MUTATED                                  0     1
  SLC9A10 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC9A10 MUTATED                           1    11
  SLC9A10 WILD-TYPE                        18   165
D262V12, multiclass
                                  clus
vv                                 SLC9A10 MUTATED SLC9A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               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(263) Variable = VAV2 MUTATION ANALYSIS
D263V1, survival
                sevent
clus2              0   1
  VAV2 MUTATED    14   3
  VAV2 WILD-TYPE 263  75
  VAV2 MUTATED VAV2 WILD-TYPE 
            17            338 
  VAV2 MUTATED VAV2 WILD-TYPE 
             3             75 
$`VAV2 MUTATED`
TCGA-AA-3662 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3534 
        6.05        35.80        91.79        79.69        19.66        29.00 
TCGA-AA-3663 TCGA-AA-A01R TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-5862 
        6.97        35.01        17.56        23.05        15.02         5.03 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6541 TCGA-G4-6626 
       25.48        17.85         4.80        15.58        46.75 

$`VAV2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       26.17        43.76        46.65        43.76        42.90        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-A6-6651 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       43.27        15.12        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 
       36.00        13.78 

  VAV2 MUTATED VAV2 WILD-TYPE 
           4.8            0.0 
  VAV2 MUTATED VAV2 WILD-TYPE 
         91.79         148.01 
  VAV2 MUTATED VAV2 WILD-TYPE 
        19.660         22.075 
[1] "4.8 - 91.8 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D263V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VAV2 MUTATED         1        0        1         8         0         0
  VAV2 WILD-TYPE      63        1       25       100         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VAV2 MUTATED           1          0          2          1        1         1
  VAV2 WILD-TYPE        17          6         42         32       34        11
                vv
clus             STAGE IVB
  VAV2 MUTATED           0
  VAV2 WILD-TYPE         1
D263V3, multiclass
            clus
vv           VAV2 MUTATED VAV2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  VAV2 MUTATED     0   1  12   4
  VAV2 WILD-TYPE   9  66 237  37
D263V4, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           12            237
  T4            4             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
  VAV2 MUTATED    11   4   2
  VAV2 WILD-TYPE 209  77  64
D263V5, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  N0           11            209
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V6, binary
                cls
clus               0   1
  VAV2 MUTATED    13   2
  VAV2 WILD-TYPE 272  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     13    2
  VAV2 WILD-TYPE  272   46
   clus
vv  VAV2 MUTATED VAV2 WILD-TYPE
  0           13            272
  1            2             46
[1] 2 2
[1] FALSE
D263V7, binary
                cls
clus               0   1
  VAV2 MUTATED     7  10
  VAV2 WILD-TYPE 163 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED      7   10
  VAV2 WILD-TYPE  163  187
        clus
vv       VAV2 MUTATED VAV2 WILD-TYPE
  FEMALE            7            163
  MALE             10            187
[1] 2 2
[1] FALSE
D263V8, binary
                cls
clus               0   1
  VAV2 MUTATED    16   1
  VAV2 WILD-TYPE 284   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     16    1
  VAV2 WILD-TYPE  284    7
     clus
vv    VAV2 MUTATED VAV2 WILD-TYPE
  NO            16            284
  YES            1              7
[1] 2 2
[1] FALSE
D263V9, binary
                cls
clus               0   1
  VAV2 MUTATED    15   2
  VAV2 WILD-TYPE 299  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     15    2
  VAV2 WILD-TYPE  299   46
                               clus
vv                              VAV2 MUTATED VAV2 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  VAV2 MUTATED    15   0   1   1
  VAV2 WILD-TYPE 244   3  21  20
D263V10, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  R0           15            244
  R1            0              3
  R2            1             21
  RX            1             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"
D263V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VAV2 MUTATED                                  0     0
  VAV2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VAV2 MUTATED                           0    13
  VAV2 WILD-TYPE                        19   163
D263V12, multiclass
                                  clus
vv                                 VAV2 MUTATED VAV2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      13            163
[1] 4 2
[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 = HMG20A MUTATION ANALYSIS
D264V1, survival
                  sevent
clus2                0   1
  HMG20A MUTATED    10   3
  HMG20A WILD-TYPE 267  75
  HMG20A MUTATED HMG20A WILD-TYPE 
              13              342 
  HMG20A MUTATED HMG20A WILD-TYPE 
               3               75 
$`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 
      135.65 

$`HMG20A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       26.01        12.99        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HMG20A MUTATED HMG20A WILD-TYPE 
               0                0 
  HMG20A MUTATED HMG20A WILD-TYPE 
          135.65           148.01 
  HMG20A MUTATED HMG20A WILD-TYPE 
           21.14            22.09 
[1] "0.0 - 135.7 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D264V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMG20A MUTATED         3        0        0         5         1         0
  HMG20A WILD-TYPE      61        1       26       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HMG20A MUTATED           0          0          3          0        0
  HMG20A WILD-TYPE        18          6         41         33       35
                  vv
clus               STAGE IVA STAGE IVB
  HMG20A MUTATED           0         0
  HMG20A WILD-TYPE        12         1
D264V3, multiclass
            clus
vv           HMG20A MUTATED HMG20A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  HMG20A MUTATED     1   2   9   1
  HMG20A WILD-TYPE   8  65 240  40
D264V4, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  T1              1                8
  T2              2               65
  T3              9              240
  T4              1               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
  HMG20A MUTATED     9   4   0
  HMG20A WILD-TYPE 211  77  66
D264V5, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  N0              9              211
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V6, binary
                  cls
clus                 0   1
  HMG20A MUTATED    12   0
  HMG20A WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     12    0
  HMG20A WILD-TYPE  273   48
   clus
vv  HMG20A MUTATED HMG20A WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D264V7, binary
                  cls
clus                 0   1
  HMG20A MUTATED     8   5
  HMG20A WILD-TYPE 162 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED      8    5
  HMG20A WILD-TYPE  162  192
        clus
vv       HMG20A MUTATED HMG20A WILD-TYPE
  FEMALE              8              162
  MALE                5              192
[1] 2 2
[1] FALSE
D264V8, binary
                  cls
clus                 0   1
  HMG20A MUTATED    10   0
  HMG20A WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     10    0
  HMG20A WILD-TYPE  290    8
     clus
vv    HMG20A MUTATED HMG20A WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D264V9, binary
                  cls
clus                 0   1
  HMG20A MUTATED    10   2
  HMG20A WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     10    2
  HMG20A WILD-TYPE  304   46
                               clus
vv                              HMG20A MUTATED HMG20A WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HMG20A MUTATED     7   1   0   2
  HMG20A WILD-TYPE 252   2  22  19
D264V10, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  R0              7              252
  R1              1                2
  R2              0               22
  RX              2               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"
D264V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HMG20A MUTATED                                  0     1
  HMG20A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HMG20A MUTATED                           3     5
  HMG20A WILD-TYPE                        16   171
D264V12, multiclass
                                  clus
vv                                 HMG20A MUTATED HMG20A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         5              171
[1] 4 2
[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 = ETF1 MUTATION ANALYSIS
D265V1, survival
                sevent
clus2              0   1
  ETF1 MUTATED     9   1
  ETF1 WILD-TYPE 268  77
  ETF1 MUTATED ETF1 WILD-TYPE 
            10            345 
  ETF1 MUTATED ETF1 WILD-TYPE 
             1             77 
$`ETF1 MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3663 TCGA-AA-3966 
        0.92        35.80        22.06        23.87         6.97         2.01 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-6168 TCGA-F4-6809 
       12.59        12.20        12.99        13.25 

$`ETF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.69        12.36        12.39        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ETF1 MUTATED ETF1 WILD-TYPE 
          0.92           0.00 
  ETF1 MUTATED ETF1 WILD-TYPE 
         35.80         148.01 
  ETF1 MUTATED ETF1 WILD-TYPE 
         12.79          22.36 
[1] "0.9 - 35.8 (12.8)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D265V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ETF1 MUTATED         0        0        1         6         0         0
  ETF1 WILD-TYPE      64        1       25       102         8         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        17          6         43         33       35        11
                vv
clus             STAGE IVB
  ETF1 MUTATED           0
  ETF1 WILD-TYPE         1
D265V3, multiclass
            clus
vv           ETF1 MUTATED ETF1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  ETF1 MUTATED     0   0  10   0
  ETF1 WILD-TYPE   9  67 239  41
D265V4, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3           10            239
  T4            0             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
  ETF1 MUTATED     7   3   0
  ETF1 WILD-TYPE 213  78  66
D265V5, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  N0            7            213
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V6, binary
                cls
clus               0   1
  ETF1 MUTATED     9   1
  ETF1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      9    1
  ETF1 WILD-TYPE  276   47
   clus
vv  ETF1 MUTATED ETF1 WILD-TYPE
  0            9            276
  1            1             47
[1] 2 2
[1] FALSE
D265V7, binary
                cls
clus               0   1
  ETF1 MUTATED     7   3
  ETF1 WILD-TYPE 163 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      7    3
  ETF1 WILD-TYPE  163  194
        clus
vv       ETF1 MUTATED ETF1 WILD-TYPE
  FEMALE            7            163
  MALE              3            194
[1] 2 2
[1] FALSE
D265V8, binary
                cls
clus               0   1
  ETF1 MUTATED     9   0
  ETF1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      9    0
  ETF1 WILD-TYPE  291    8
     clus
vv    ETF1 MUTATED ETF1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D265V9, binary
                cls
clus               0   1
  ETF1 MUTATED     9   1
  ETF1 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      9    1
  ETF1 WILD-TYPE  305   47
                               clus
vv                              ETF1 MUTATED ETF1 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ETF1 MUTATED     7   0   0   1
  ETF1 WILD-TYPE 252   3  22  20
D265V10, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D265V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ETF1 MUTATED                                  0     2
  ETF1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ETF1 MUTATED                           1     4
  ETF1 WILD-TYPE                        18   172
D265V12, multiclass
                                  clus
vv                                 ETF1 MUTATED ETF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = CBL MUTATION ANALYSIS
D266V1, survival
               sevent
clus2             0   1
  CBL MUTATED    27   7
  CBL WILD-TYPE 250  71
  CBL MUTATED CBL WILD-TYPE 
           34           321 
  CBL MUTATED CBL WILD-TYPE 
            7            71 
$`CBL MUTATED`
TCGA-AA-3662 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6628 TCGA-A6-5657 
        6.05       100.01         1.94        63.62        79.69        31.63 
TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3968 TCGA-AA-A010 
       23.61        63.98         6.97         1.02        21.99        34.98 
TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6600 
       12.16        33.01        17.82        58.39        88.21        12.10 
TCGA-AZ-6603 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-4752 
       29.56        10.06        14.30        17.56        23.05        13.02 
TCGA-CM-5862 TCGA-CM-6164 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-6533 TCGA-D5-6923 
        5.03        29.03        11.01        11.08        25.48        12.43 
TCGA-DM-A1DB TCGA-DM-A28E TCGA-DM-A28K TCGA-G4-6309 
       44.32       119.93        98.24        85.48 

$`CBL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        22.09        35.80        26.17        91.79 
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-A6-5656 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
        3.02        35.01         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       33.01        26.01        20.98        34.03         2.01        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44         1.41         5.13        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77         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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       131.51       135.65       139.17        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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CBL MUTATED CBL WILD-TYPE 
         1.02          0.00 
  CBL MUTATED CBL WILD-TYPE 
       119.93        148.01 
  CBL MUTATED CBL WILD-TYPE 
        23.33         22.03 
[1] "1.0 - 119.9 (23.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D266V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBL MUTATED         6        0        3        10         1         0
  CBL WILD-TYPE      58        1       23        98         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBL MUTATED           0          1          6          0        2         3
  CBL WILD-TYPE        18          5         38         33       33         9
               vv
clus            STAGE IVB
  CBL MUTATED           0
  CBL WILD-TYPE         1
D266V3, multiclass
            clus
vv           CBL MUTATED CBL WILD-TYPE
  STAGE I              6            58
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA           10            98
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           1             5
  STAGE IIIB           6            38
  STAGE IIIC           0            33
  STAGE IV             2            33
  STAGE IVA            3             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
  CBL MUTATED     1   7  20   6
  CBL WILD-TYPE   8  60 229  35
D266V4, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  T1           1             8
  T2           7            60
  T3          20           229
  T4           6            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
  CBL MUTATED    21  11   2
  CBL WILD-TYPE 199  70  64
D266V5, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  N0          21           199
  N1          11            70
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V6, binary
               cls
clus              0   1
  CBL MUTATED    27   5
  CBL WILD-TYPE 258  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     27    5
  CBL WILD-TYPE  258   43
   clus
vv  CBL MUTATED CBL WILD-TYPE
  0          27           258
  1           5            43
[1] 2 2
[1] FALSE
D266V7, binary
               cls
clus              0   1
  CBL MUTATED    15  19
  CBL WILD-TYPE 155 178
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     15   19
  CBL WILD-TYPE  155  178
        clus
vv       CBL MUTATED CBL WILD-TYPE
  FEMALE          15           155
  MALE            19           178
[1] 2 2
[1] FALSE
D266V8, binary
               cls
clus              0   1
  CBL MUTATED    29   1
  CBL WILD-TYPE 271   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     29    1
  CBL WILD-TYPE  271    7
     clus
vv    CBL MUTATED CBL WILD-TYPE
  NO           29           271
  YES           1             7
[1] 2 2
[1] FALSE
D266V9, binary
               cls
clus              0   1
  CBL MUTATED    32   2
  CBL WILD-TYPE 282  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     32    2
  CBL WILD-TYPE  282   46
                               clus
vv                              CBL MUTATED CBL WILD-TYPE
  COLON ADENOCARCINOMA                   32           282
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CBL MUTATED    21   0   1   3
  CBL WILD-TYPE 238   3  21  18
D266V10, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  R0          21           238
  R1           0             3
  R2           1            21
  RX           3            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"
D266V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBL MUTATED                                  0     2
  CBL WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CBL MUTATED                           6    20
  CBL WILD-TYPE                        13   156
D266V12, multiclass
                                  clus
vv                                 CBL MUTATED CBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  6            13
  WHITE                                     20           156
[1] 4 2
[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 = PRB4 MUTATION ANALYSIS
D267V1, survival
                sevent
clus2              0   1
  PRB4 MUTATED    10   0
  PRB4 WILD-TYPE 267  78
  PRB4 MUTATED PRB4 WILD-TYPE 
            10            345 
  PRB4 MUTATED PRB4 WILD-TYPE 
             0             78 
$`PRB4 MUTATED`
TCGA-G4-6625 TCGA-A6-6651 TCGA-AA-3812 TCGA-AA-3855 TCGA-AA-A010 TCGA-CA-6717 
       91.79        21.76        35.05        32.05        34.98        12.76 
TCGA-CM-6169 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6898 
       13.02        18.25        25.48         7.53 

$`PRB4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
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-D5-6540 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 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PRB4 MUTATED PRB4 WILD-TYPE 
          7.53           0.00 
  PRB4 MUTATED PRB4 WILD-TYPE 
         91.79         148.01 
  PRB4 MUTATED PRB4 WILD-TYPE 
         23.62          22.06 
[1] "7.5 - 91.8 (23.6)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "2.5e+07"
D267V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRB4 MUTATED         2        0        0         5         1         0
  PRB4 WILD-TYPE      62        1       26       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRB4 MUTATED           0          0          1          0        0         0
  PRB4 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  PRB4 MUTATED           0
  PRB4 WILD-TYPE         1
D267V3, multiclass
            clus
vv           PRB4 MUTATED PRB4 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PRB4 MUTATED     0   2   6   2
  PRB4 WILD-TYPE   9  65 243  39
D267V4, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            2             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
  PRB4 MUTATED     9   1   0
  PRB4 WILD-TYPE 211  80  66
D267V5, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  N0            9            211
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V6, binary
                cls
clus               0   1
  PRB4 MUTATED     9   0
  PRB4 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      9    0
  PRB4 WILD-TYPE  276   48
   clus
vv  PRB4 MUTATED PRB4 WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D267V7, binary
                cls
clus               0   1
  PRB4 MUTATED     6   4
  PRB4 WILD-TYPE 164 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      6    4
  PRB4 WILD-TYPE  164  193
        clus
vv       PRB4 MUTATED PRB4 WILD-TYPE
  FEMALE            6            164
  MALE              4            193
[1] 2 2
[1] FALSE
D267V8, binary
                cls
clus               0   1
  PRB4 MUTATED    10   0
  PRB4 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED     10    0
  PRB4 WILD-TYPE  290    8
     clus
vv    PRB4 MUTATED PRB4 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D267V9, binary
                cls
clus               0   1
  PRB4 MUTATED     9   1
  PRB4 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      9    1
  PRB4 WILD-TYPE  305   47
                               clus
vv                              PRB4 MUTATED PRB4 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PRB4 MUTATED     8   0   0   1
  PRB4 WILD-TYPE 251   3  22  20
D267V10, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D267V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRB4 MUTATED                                  0     1
  PRB4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PRB4 MUTATED                           1     5
  PRB4 WILD-TYPE                        18   171
D267V12, multiclass
                                  clus
vv                                 PRB4 MUTATED PRB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = SOX7 MUTATION ANALYSIS
D268V1, survival
                sevent
clus2              0   1
  SOX7 MUTATED     9   2
  SOX7 WILD-TYPE 268  76
  SOX7 MUTATED SOX7 WILD-TYPE 
            11            344 
  SOX7 MUTATED SOX7 WILD-TYPE 
             2             76 
$`SOX7 MUTATED`
TCGA-AA-3672 TCGA-A6-6780 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A010 TCGA-AY-6197 
        0.92        20.12        33.04        33.01        34.98        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6171 TCGA-DM-A1D7 
       58.39        49.41        12.76        14.04        13.32 

$`SOX7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SOX7 MUTATED SOX7 WILD-TYPE 
          0.92           0.00 
  SOX7 MUTATED SOX7 WILD-TYPE 
         58.39         148.01 
  SOX7 MUTATED SOX7 WILD-TYPE 
        21.440         22.075 
[1] "0.9 - 58.4 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D268V2, continuous
                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      63        1       25       102         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX7 MUTATED           1          0          0          0        0         0
  SOX7 WILD-TYPE        17          6         44         33       35        12
                vv
clus             STAGE IVB
  SOX7 MUTATED           0
  SOX7 WILD-TYPE         1
D268V3, multiclass
            clus
vv           SOX7 MUTATED SOX7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  SOX7 MUTATED     0   1   8   2
  SOX7 WILD-TYPE   9  66 241  39
D268V4, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            2             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
  SOX7 MUTATED    10   1   0
  SOX7 WILD-TYPE 210  80  66
D268V5, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V6, binary
                cls
clus               0   1
  SOX7 MUTATED     8   0
  SOX7 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      8    0
  SOX7 WILD-TYPE  277   48
   clus
vv  SOX7 MUTATED SOX7 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D268V7, binary
                cls
clus               0   1
  SOX7 MUTATED     6   5
  SOX7 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      6    5
  SOX7 WILD-TYPE  164  192
        clus
vv       SOX7 MUTATED SOX7 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D268V8, binary
                cls
clus               0   1
  SOX7 MUTATED    10   0
  SOX7 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     10    0
  SOX7 WILD-TYPE  290    8
     clus
vv    SOX7 MUTATED SOX7 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D268V9, binary
                cls
clus               0   1
  SOX7 MUTATED     7   3
  SOX7 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      7    3
  SOX7 WILD-TYPE  307   45
                               clus
vv                              SOX7 MUTATED SOX7 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SOX7 MUTATED     7   0   0   1
  SOX7 WILD-TYPE 252   3  22  20
D268V10, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D268V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOX7 MUTATED                                  0     1
  SOX7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOX7 MUTATED                           0     6
  SOX7 WILD-TYPE                        19   170
D268V12, multiclass
                                  clus
vv                                 SOX7 MUTATED SOX7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = ARHGAP5 MUTATION ANALYSIS
D269V1, survival
                   sevent
clus2                 0   1
  ARHGAP5 MUTATED    13   6
  ARHGAP5 WILD-TYPE 264  72
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               336 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                6                72 
$`ARHGAP5 MUTATED`
TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3821 TCGA-AA-3845 
       79.69         3.02        63.98        29.95         1.02         0.00 
TCGA-AA-3973 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6899 TCGA-CA-6717 TCGA-CA-6718 
       13.05        35.01        83.24         5.79        12.76        10.06 
TCGA-CK-5913 TCGA-CM-5860 TCGA-CM-6678 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB 
       51.32        32.02        11.01        16.14        13.35       135.65 
TCGA-F4-6570 
        6.18 

$`ARHGAP5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 
       25.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       12.16        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                0                 0 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
           135.65            148.01 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            13.35             22.09 
[1] "0.0 - 135.7 (13.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D269V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP5 MUTATED         3        0        2         9         0         0
  ARHGAP5 WILD-TYPE      61        1       24        99         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP5 MUTATED           1          0          1          1        1
  ARHGAP5 WILD-TYPE        17          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  ARHGAP5 MUTATED           1         0
  ARHGAP5 WILD-TYPE        11         1
D269V3, multiclass
            clus
vv           ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                9                99
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                1                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
  ARHGAP5 MUTATED     0   3  13   3
  ARHGAP5 WILD-TYPE   9  64 236  38
D269V4, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              13               236
  T4               3                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
  ARHGAP5 MUTATED    14   3   2
  ARHGAP5 WILD-TYPE 206  78  64
D269V5, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  N0              14               206
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V6, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    15   2
  ARHGAP5 WILD-TYPE 270  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     15    2
  ARHGAP5 WILD-TYPE  270   46
   clus
vv  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  0              15               270
  1               2                46
[1] 2 2
[1] FALSE
D269V7, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     7  12
  ARHGAP5 WILD-TYPE 163 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      7   12
  ARHGAP5 WILD-TYPE  163  185
        clus
vv       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  FEMALE               7               163
  MALE                12               185
[1] 2 2
[1] FALSE
D269V8, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    16   1
  ARHGAP5 WILD-TYPE 284   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     16    1
  ARHGAP5 WILD-TYPE  284    7
     clus
vv    ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  NO               16               284
  YES               1                 7
[1] 2 2
[1] FALSE
D269V9, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    11   7
  ARHGAP5 WILD-TYPE 303  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     11    7
  ARHGAP5 WILD-TYPE  303   41
                               clus
vv                              ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGAP5 MUTATED    13   0   1   3
  ARHGAP5 WILD-TYPE 246   3  21  18
D269V10, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               1                21
  RX               3                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"
D269V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP5 MUTATED                                  0     3
  ARHGAP5 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP5 MUTATED                           0     9
  ARHGAP5 WILD-TYPE                        19   167
D269V12, multiclass
                                  clus
vv                                 ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(270) Variable = MAGEC1 MUTATION ANALYSIS
D270V1, survival
                  sevent
clus2                0   1
  MAGEC1 MUTATED    20   6
  MAGEC1 WILD-TYPE 257  72
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              26              329 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
               6               72 
$`MAGEC1 MUTATED`
TCGA-AA-3662 TCGA-G4-6586 TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-5666 
        6.05        35.80        46.65        32.75        22.09        32.71 
TCGA-AA-3502 TCGA-AA-3955 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N 
       35.01        20.98        34.06        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6901 TCGA-CA-6717 TCGA-D5-5538 TCGA-D5-6538 
       34.98        83.24        22.42        12.76        54.61        17.13 
TCGA-D5-6898 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-F4-6808 
        7.53        12.00        11.38        24.43        38.20        33.67 
TCGA-F4-6855 TCGA-G4-6304 
       47.41        53.62 

$`MAGEC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        36.53        32.91 
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-A6-6137 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-A6-6780 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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3989 
        2.01        21.99        16.08        13.05        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       40.96        12.16        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
            4.01             0.00 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
           83.24           148.01 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
          29.865           21.990 
[1] "4.0 - 83.2 (29.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D270V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEC1 MUTATED         5        0        0         7         4         1
  MAGEC1 WILD-TYPE      59        1       26       101         4         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEC1 MUTATED           0          0          4          3        2
  MAGEC1 WILD-TYPE        18          6         40         30       33
                  vv
clus               STAGE IVA STAGE IVB
  MAGEC1 MUTATED           0         0
  MAGEC1 WILD-TYPE        12         1
D270V3, multiclass
            clus
vv           MAGEC1 MUTATED MAGEC1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               4                4
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              3               30
  STAGE IV                2               33
  STAGE IVA               0               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
  MAGEC1 MUTATED     1   6  12   9
  MAGEC1 WILD-TYPE   8  61 237  32
D270V4, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  T1              1                8
  T2              6               61
  T3             12              237
  T4              9               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
  MAGEC1 MUTATED    19   3   6
  MAGEC1 WILD-TYPE 201  78  60
D270V5, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  N0             19              201
  N1              3               78
  N2              6               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V6, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    23   2
  MAGEC1 WILD-TYPE 262  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     23    2
  MAGEC1 WILD-TYPE  262   46
   clus
vv  MAGEC1 MUTATED MAGEC1 WILD-TYPE
  0             23              262
  1              2               46
[1] 2 2
[1] FALSE
D270V7, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    15  13
  MAGEC1 WILD-TYPE 155 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     15   13
  MAGEC1 WILD-TYPE  155  184
        clus
vv       MAGEC1 MUTATED MAGEC1 WILD-TYPE
  FEMALE             15              155
  MALE               13              184
[1] 2 2
[1] FALSE
D270V8, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    23   0
  MAGEC1 WILD-TYPE 277   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     23    0
  MAGEC1 WILD-TYPE  277    8
     clus
vv    MAGEC1 MUTATED MAGEC1 WILD-TYPE
  NO              23              277
  YES              0                8
[1] 2 2
[1] FALSE
D270V9, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    24   3
  MAGEC1 WILD-TYPE 290  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     24    3
  MAGEC1 WILD-TYPE  290   45
                               clus
vv                              MAGEC1 MUTATED MAGEC1 WILD-TYPE
  COLON ADENOCARCINOMA                      24              290
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGEC1 MUTATED    18   0   2   1
  MAGEC1 WILD-TYPE 241   3  20  20
D270V10, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  R0             18              241
  R1              0                3
  R2              2               20
  RX              1               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"
D270V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEC1 MUTATED                                  0     2
  MAGEC1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEC1 MUTATED                           1    15
  MAGEC1 WILD-TYPE                        18   161
D270V12, multiclass
                                  clus
vv                                 MAGEC1 MUTATED MAGEC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        15              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(271) Variable = RAB28 MUTATION ANALYSIS
D271V1, survival
                 sevent
clus2               0   1
  RAB28 MUTATED     4   2
  RAB28 WILD-TYPE 273  76
  RAB28 MUTATED RAB28 WILD-TYPE 
              6             349 
  RAB28 MUTATED RAB28 WILD-TYPE 
              2              76 
$`RAB28 MUTATED`
TCGA-G4-6588 TCGA-AY-6197 TCGA-AZ-6598 TCGA-D5-6541 TCGA-DM-A28G TCGA-F4-6856 
       26.17        21.44        49.41        15.58        60.79        35.31 

$`RAB28 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RAB28 MUTATED RAB28 WILD-TYPE 
          15.58            0.00 
  RAB28 MUTATED RAB28 WILD-TYPE 
          60.79          148.01 
  RAB28 MUTATED RAB28 WILD-TYPE 
          30.74           22.03 
[1] "15.6 - 60.8 (30.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D271V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB28 MUTATED         1        0        1         4         0         0
  RAB28 WILD-TYPE      63        1       25       104         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  RAB28 MUTATED           0
  RAB28 WILD-TYPE         1
D271V3, multiclass
            clus
vv           RAB28 MUTATED RAB28 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RAB28 MUTATED     0   1   5   0
  RAB28 WILD-TYPE   9  66 244  41
D271V4, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             0              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
  RAB28 MUTATED     6   0   0
  RAB28 WILD-TYPE 214  81  66
D271V5, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  N0             6             214
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V6, binary
                 cls
clus                0   1
  RAB28 MUTATED     4   0
  RAB28 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      4    0
  RAB28 WILD-TYPE  281   48
   clus
vv  RAB28 MUTATED RAB28 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D271V7, binary
                 cls
clus                0   1
  RAB28 MUTATED     2   4
  RAB28 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      2    4
  RAB28 WILD-TYPE  168  193
        clus
vv       RAB28 MUTATED RAB28 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D271V8, binary
                 cls
clus                0   1
  RAB28 MUTATED     5   0
  RAB28 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      5    0
  RAB28 WILD-TYPE  295    8
     clus
vv    RAB28 MUTATED RAB28 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D271V9, binary
                 cls
clus                0   1
  RAB28 MUTATED     5   1
  RAB28 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      5    1
  RAB28 WILD-TYPE  309   47
                               clus
vv                              RAB28 MUTATED RAB28 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RAB28 MUTATED     4   0   0   0
  RAB28 WILD-TYPE 255   3  22  21
D271V10, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D271V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB28 MUTATED                                  0     0
  RAB28 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB28 MUTATED                           0     6
  RAB28 WILD-TYPE                        19   170
D271V12, multiclass
                                  clus
vv                                 RAB28 MUTATED RAB28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = UBR4 MUTATION ANALYSIS
D272V1, survival
                sevent
clus2              0   1
  UBR4 MUTATED    30   7
  UBR4 WILD-TYPE 247  71
  UBR4 MUTATED UBR4 WILD-TYPE 
            37            318 
  UBR4 MUTATED UBR4 WILD-TYPE 
             7             71 
$`UBR4 MUTATED`
TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 
       13.02        85.05        19.04        24.00        25.08        10.88 
TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5660 TCGA-A6-6780 TCGA-AA-3542 
      100.01        26.17        42.90        29.19        20.12        12.99 
TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A02K 
        6.97        26.99        10.06        53.00        34.98        14.01 
TCGA-AD-6963 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5863 
       27.42        33.01        58.39        12.76        23.05        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       14.04        12.95        11.08        18.25        25.48        15.12 
TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-7000 TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6856 
       16.14         9.44        10.26       135.65         6.18        35.31 
TCGA-G4-6304 
       53.62 

$`UBR4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3812 TCGA-AA-3815 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        11.01        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.19        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         7.53        12.39        10.13        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        13.41        13.35        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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  UBR4 MUTATED UBR4 WILD-TYPE 
          6.18           0.00 
  UBR4 MUTATED UBR4 WILD-TYPE 
        135.65         148.01 
  UBR4 MUTATED UBR4 WILD-TYPE 
        20.120         22.075 
[1] "6.2 - 135.7 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D272V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBR4 MUTATED         5        0        4        12         4         0
  UBR4 WILD-TYPE      59        1       22        96         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR4 MUTATED           2          0          4          2        2         1
  UBR4 WILD-TYPE        16          6         40         31       33        11
                vv
clus             STAGE IVB
  UBR4 MUTATED           0
  UBR4 WILD-TYPE         1
D272V3, multiclass
            clus
vv           UBR4 MUTATED UBR4 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            12             96
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            2             31
  STAGE IV              2             33
  STAGE IVA             1             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
  UBR4 MUTATED     0   5  27   7
  UBR4 WILD-TYPE   9  62 222  34
D272V4, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           27            222
  T4            7             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
  UBR4 MUTATED    28   5   6
  UBR4 WILD-TYPE 192  76  60
D272V5, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  N0           28            192
  N1            5             76
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V6, binary
                cls
clus               0   1
  UBR4 MUTATED    31   3
  UBR4 WILD-TYPE 254  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     31    3
  UBR4 WILD-TYPE  254   45
   clus
vv  UBR4 MUTATED UBR4 WILD-TYPE
  0           31            254
  1            3             45
[1] 2 2
[1] FALSE
D272V7, binary
                cls
clus               0   1
  UBR4 MUTATED    17  22
  UBR4 WILD-TYPE 153 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     17   22
  UBR4 WILD-TYPE  153  175
        clus
vv       UBR4 MUTATED UBR4 WILD-TYPE
  FEMALE           17            153
  MALE             22            175
[1] 2 2
[1] FALSE
D272V8, binary
                cls
clus               0   1
  UBR4 MUTATED    35   1
  UBR4 WILD-TYPE 265   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     35    1
  UBR4 WILD-TYPE  265    7
     clus
vv    UBR4 MUTATED UBR4 WILD-TYPE
  NO            35            265
  YES            1              7
[1] 2 2
[1] FALSE
D272V9, binary
                cls
clus               0   1
  UBR4 MUTATED    30   8
  UBR4 WILD-TYPE 284  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     30    8
  UBR4 WILD-TYPE  284   40
                               clus
vv                              UBR4 MUTATED UBR4 WILD-TYPE
  COLON ADENOCARCINOMA                    30            284
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UBR4 MUTATED    27   0   2   3
  UBR4 WILD-TYPE 232   3  20  18
D272V10, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  R0           27            232
  R1            0              3
  R2            2             20
  RX            3             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"
D272V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBR4 MUTATED                                  0     1
  UBR4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBR4 MUTATED                           2    24
  UBR4 WILD-TYPE                        17   152
D272V12, multiclass
                                  clus
vv                                 UBR4 MUTATED UBR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      24            152
[1] 4 2
[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 = OR2T33 MUTATION ANALYSIS
D273V1, survival
                  sevent
clus2                0   1
  OR2T33 MUTATED    11   4
  OR2T33 WILD-TYPE 266  74
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              15              340 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               4               74 
$`OR2T33 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-G4-6625 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3977 
        6.05        19.04        91.79        20.12         3.02        25.02 
TCGA-AA-A010 TCGA-AA-A03J TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5349 
       34.98        40.96        58.39        12.10        12.76        30.08 
TCGA-CM-6168 TCGA-D5-6532 TCGA-DM-A1DB 
       12.99        18.25        44.32 

$`OR2T33 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6169 
       14.04        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        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.075 
[1] "3.0 - 91.8 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D273V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2T33 MUTATED         1        0        2         9         1         0
  OR2T33 WILD-TYPE      63        1       24        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2T33 MUTATED           0          0          0          0        2
  OR2T33 WILD-TYPE        18          6         44         33       33
                  vv
clus               STAGE IVA STAGE IVB
  OR2T33 MUTATED           0         0
  OR2T33 WILD-TYPE        12         1
D273V3, multiclass
            clus
vv           OR2T33 MUTATED OR2T33 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               9               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  OR2T33 MUTATED     0   2  11   3
  OR2T33 WILD-TYPE   9  65 238  38
D273V4, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             11              238
  T4              3               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
  OR2T33 MUTATED    14   1   1
  OR2T33 WILD-TYPE 206  80  65
D273V5, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  N0             14              206
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V6, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    12   2
  OR2T33 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     12    2
  OR2T33 WILD-TYPE  273   46
   clus
vv  OR2T33 MUTATED OR2T33 WILD-TYPE
  0             12              273
  1              2               46
[1] 2 2
[1] FALSE
D273V7, binary
                  cls
clus                 0   1
  OR2T33 MUTATED     8   8
  OR2T33 WILD-TYPE 162 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED      8    8
  OR2T33 WILD-TYPE  162  189
        clus
vv       OR2T33 MUTATED OR2T33 WILD-TYPE
  FEMALE              8              162
  MALE                8              189
[1] 2 2
[1] FALSE
D273V8, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    14   0
  OR2T33 WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     14    0
  OR2T33 WILD-TYPE  286    8
     clus
vv    OR2T33 MUTATED OR2T33 WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D273V9, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    14   2
  OR2T33 WILD-TYPE 300  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     14    2
  OR2T33 WILD-TYPE  300   46
                               clus
vv                              OR2T33 MUTATED OR2T33 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR2T33 MUTATED    10   0   1   1
  OR2T33 WILD-TYPE 249   3  21  20
D273V10, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              1               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"
D273V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2T33 MUTATED                                  0     1
  OR2T33 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR2T33 MUTATED                           2     6
  OR2T33 WILD-TYPE                        17   170
D273V12, multiclass
                                  clus
vv                                 OR2T33 MUTATED OR2T33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         6              170
[1] 4 2
[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 = TRIP11 MUTATION ANALYSIS
D274V1, survival
                  sevent
clus2                0   1
  TRIP11 MUTATED    16   2
  TRIP11 WILD-TYPE 261  76
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              18              337 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               2               76 
$`TRIP11 MUTATED`
TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 
       79.69        33.53        22.06         6.97         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6603 
        4.01        34.98        21.44        17.82        58.39        29.56 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6168 TCGA-D5-6532 TCGA-D5-6540 
       12.76        51.32        21.99        12.99        18.25        16.14 

$`TRIP11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20         1.41         5.13        22.36        62.79        88.21 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TRIP11 MUTATED TRIP11 WILD-TYPE 
            2.01             0.00 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
           79.69           148.01 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
          21.715           22.090 
[1] "2.0 - 79.7 (21.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D274V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIP11 MUTATED         2        0        1        10         2         0
  TRIP11 WILD-TYPE      62        1       25        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP11 MUTATED           0          0          2          0        0
  TRIP11 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIP11 MUTATED           0         0
  TRIP11 WILD-TYPE        12         1
D274V3, multiclass
            clus
vv           TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              10               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TRIP11 MUTATED     0   4  13   2
  TRIP11 WILD-TYPE   9  63 236  39
D274V4, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             13              236
  T4              2               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
  TRIP11 MUTATED    16   3   0
  TRIP11 WILD-TYPE 204  78  66
D274V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0             16              204
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V6, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    14   0
  TRIP11 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     14    0
  TRIP11 WILD-TYPE  271   48
   clus
vv  TRIP11 MUTATED TRIP11 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D274V7, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     9  10
  TRIP11 WILD-TYPE 161 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      9   10
  TRIP11 WILD-TYPE  161  187
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  FEMALE              9              161
  MALE               10              187
[1] 2 2
[1] FALSE
D274V8, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    15   0
  TRIP11 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     15    0
  TRIP11 WILD-TYPE  285    8
     clus
vv    TRIP11 MUTATED TRIP11 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D274V9, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    15   4
  TRIP11 WILD-TYPE 299  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     15    4
  TRIP11 WILD-TYPE  299   44
                               clus
vv                              TRIP11 MUTATED TRIP11 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIP11 MUTATED    13   0   0   3
  TRIP11 WILD-TYPE 246   3  22  18
D274V10, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              3               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"
D274V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP11 MUTATED                                  0     1
  TRIP11 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIP11 MUTATED                           3     9
  TRIP11 WILD-TYPE                        16   167
D274V12, multiclass
                                  clus
vv                                 TRIP11 MUTATED TRIP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         9              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(275) Variable = ZBTB7C MUTATION ANALYSIS
D275V1, survival
                  sevent
clus2                0   1
  ZBTB7C MUTATED     8   5
  ZBTB7C WILD-TYPE 269  73
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              13              342 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               5               73 
$`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 
       83.24        27.09        51.32        15.02        60.79         8.61 
TCGA-G4-6309 
       85.48 

$`ZBTB7C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               0                0 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
           85.48           148.01 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
          26.990           22.045 
[1] "0.0 - 85.5 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D275V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB7C MUTATED         2        0        3         6         0         0
  ZBTB7C WILD-TYPE      62        1       23       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB7C MUTATED           0          0          2          0        1
  ZBTB7C WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB7C MUTATED           0         0
  ZBTB7C WILD-TYPE        12         1
D275V3, multiclass
            clus
vv           ZBTB7C MUTATED ZBTB7C WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZBTB7C MUTATED     0   2  11   1
  ZBTB7C WILD-TYPE   9  65 238  40
D275V4, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  T1              0                9
  T2              2               65
  T3             11              238
  T4              1               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
  ZBTB7C MUTATED    11   1   2
  ZBTB7C WILD-TYPE 209  80  64
D275V5, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  N0             11              209
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V6, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    12   1
  ZBTB7C WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     12    1
  ZBTB7C WILD-TYPE  273   47
   clus
vv  ZBTB7C MUTATED ZBTB7C WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D275V7, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     8   6
  ZBTB7C WILD-TYPE 162 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      8    6
  ZBTB7C WILD-TYPE  162  191
        clus
vv       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  FEMALE              8              162
  MALE                6              191
[1] 2 2
[1] FALSE
D275V8, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     9   0
  ZBTB7C WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      9    0
  ZBTB7C WILD-TYPE  291    8
     clus
vv    ZBTB7C MUTATED ZBTB7C WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D275V9, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    12   2
  ZBTB7C WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     12    2
  ZBTB7C WILD-TYPE  302   46
                               clus
vv                              ZBTB7C MUTATED ZBTB7C WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB7C MUTATED    10   0   1   1
  ZBTB7C WILD-TYPE 249   3  21  20
D275V10, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              1               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"
D275V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB7C MUTATED                                  0     1
  ZBTB7C WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7C MUTATED                           1     5
  ZBTB7C WILD-TYPE                        18   171
D275V12, multiclass
                                  clus
vv                                 ZBTB7C MUTATED ZBTB7C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = ABCC4 MUTATION ANALYSIS
D276V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    13   4
  ABCC4 WILD-TYPE 264  74
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             17             338 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              4              74 
$`ABCC4 MUTATED`
TCGA-AA-3516 TCGA-AZ-6601 TCGA-DM-A285 TCGA-A6-5666 TCGA-AA-3534 TCGA-AA-3955 
       13.02       100.01         5.88        32.71        29.00        20.98 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-5797 
        4.01        34.98        35.01        27.09        58.39        12.59 
TCGA-CK-6747 TCGA-CM-4743 TCGA-D5-5539 TCGA-D5-6534 TCGA-G4-6306 
       82.95        23.05        19.59        43.27        44.68 

$`ABCC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.39        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           4.01            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         100.01          148.01 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
          29.00           21.99 
[1] "4.0 - 100.0 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D276V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCC4 MUTATED         1        0        2         7         3         1
  ABCC4 WILD-TYPE      63        1       24       101         5         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        16          5         43         33       34        12
                 vv
clus              STAGE IVB
  ABCC4 MUTATED           0
  ABCC4 WILD-TYPE         1
D276V3, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ABCC4 MUTATED     0   3  12   5
  ABCC4 WILD-TYPE   9  64 237  36
D276V4, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             5              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
  ABCC4 MUTATED    15   1   4
  ABCC4 WILD-TYPE 205  80  62
D276V5, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  N0            15             205
  N1             1              80
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V6, binary
                 cls
clus                0   1
  ABCC4 MUTATED    17   1
  ABCC4 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     17    1
  ABCC4 WILD-TYPE  268   47
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            17             268
  1             1              47
[1] 2 2
[1] FALSE
D276V7, binary
                 cls
clus                0   1
  ABCC4 MUTATED    10  10
  ABCC4 WILD-TYPE 160 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     10   10
  ABCC4 WILD-TYPE  160  187
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  FEMALE            10             160
  MALE              10             187
[1] 2 2
[1] FALSE
D276V8, binary
                 cls
clus                0   1
  ABCC4 MUTATED    13   1
  ABCC4 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     13    1
  ABCC4 WILD-TYPE  287    7
     clus
vv    ABCC4 MUTATED ABCC4 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D276V9, binary
                 cls
clus                0   1
  ABCC4 MUTATED    14   6
  ABCC4 WILD-TYPE 300  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     14    6
  ABCC4 WILD-TYPE  300   42
                               clus
vv                              ABCC4 MUTATED ABCC4 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCC4 MUTATED    14   0   0   2
  ABCC4 WILD-TYPE 245   3  22  19
D276V10, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D276V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCC4 MUTATED                                  0     1
  ABCC4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCC4 MUTATED                           0    11
  ABCC4 WILD-TYPE                        19   165
D276V12, multiclass
                                  clus
vv                                 ABCC4 MUTATED ABCC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(277) Variable = CENPF MUTATION ANALYSIS
D277V1, survival
                 sevent
clus2               0   1
  CENPF MUTATED    36   5
  CENPF WILD-TYPE 241  73
  CENPF MUTATED CENPF WILD-TYPE 
             41             314 
  CENPF MUTATED CENPF WILD-TYPE 
              5              73 
$`CENPF MUTATED`
TCGA-AA-3525 TCGA-G4-6625 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5661 
        8.05        91.79        42.90        32.75        32.91        33.53 
TCGA-A6-6648 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 
       25.18        63.98        29.95        78.08         6.97        33.04 
TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 
        0.00        25.02        18.05         4.01         0.99        34.98 
TCGA-AA-A01Q TCGA-AA-A02O TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6719 
        1.02         0.92        12.16        58.39        12.76        14.30 
TCGA-CK-4952 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6162 
       15.62        82.95       124.27        13.02        15.02        12.00 
TCGA-CM-6675 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6569 
       13.05        15.12        16.14         7.53        13.32        35.74 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6307 
       33.67        35.31       133.18        65.85        55.04 

$`CENPF WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5657 
       42.28        16.57        34.65        33.34        36.53        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-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.08        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        10.06        17.56       148.01        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.99        21.14         2.01        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-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 
       14.04        29.03        16.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       74.56        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CENPF MUTATED CENPF WILD-TYPE 
              0               0 
  CENPF MUTATED CENPF WILD-TYPE 
         133.18          148.01 
  CENPF MUTATED CENPF WILD-TYPE 
         25.020          22.045 
[1] "0.0 - 133.2 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D277V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CENPF MUTATED         9        0        5        12         4         0
  CENPF WILD-TYPE      55        1       21        96         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CENPF MUTATED           1          0          5          1        1         1
  CENPF WILD-TYPE        17          6         39         32       34        11
                 vv
clus              STAGE IVB
  CENPF MUTATED           1
  CENPF WILD-TYPE         0
D277V3, multiclass
            clus
vv           CENPF MUTATED CENPF WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             12              96
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              11
  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     1   9  25   6
  CENPF WILD-TYPE   8  58 224  35
D277V4, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  T1             1               8
  T2             9              58
  T3            25             224
  T4             6              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
  CENPF MUTATED    32   7   2
  CENPF WILD-TYPE 188  74  64
D277V5, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  N0            32             188
  N1             7              74
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V6, binary
                 cls
clus                0   1
  CENPF MUTATED    33   3
  CENPF WILD-TYPE 252  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     33    3
  CENPF WILD-TYPE  252   45
   clus
vv  CENPF MUTATED CENPF WILD-TYPE
  0            33             252
  1             3              45
[1] 2 2
[1] FALSE
D277V7, binary
                 cls
clus                0   1
  CENPF MUTATED    22  19
  CENPF WILD-TYPE 148 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     22   19
  CENPF WILD-TYPE  148  178
        clus
vv       CENPF MUTATED CENPF WILD-TYPE
  FEMALE            22             148
  MALE              19             178
[1] 2 2
[1] FALSE
D277V8, binary
                 cls
clus                0   1
  CENPF MUTATED    34   0
  CENPF WILD-TYPE 266   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     34    0
  CENPF WILD-TYPE  266    8
     clus
vv    CENPF MUTATED CENPF WILD-TYPE
  NO             34             266
  YES             0               8
[1] 2 2
[1] FALSE
D277V9, binary
                 cls
clus                0   1
  CENPF MUTATED    29  11
  CENPF WILD-TYPE 285  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     29   11
  CENPF WILD-TYPE  285   37
                               clus
vv                              CENPF MUTATED CENPF WILD-TYPE
  COLON ADENOCARCINOMA                     29             285
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CENPF MUTATED    31   0   0   6
  CENPF WILD-TYPE 228   3  22  15
D277V10, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  R0            31             228
  R1             0               3
  R2             0              22
  RX             6              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"
D277V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CENPF MUTATED                                  0     2
  CENPF WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CENPF MUTATED                           3    22
  CENPF WILD-TYPE                        16   154
D277V12, multiclass
                                  clus
vv                                 CENPF MUTATED CENPF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       22             154
[1] 4 2
[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 = MYO3B MUTATION ANALYSIS
D278V1, survival
                 sevent
clus2               0   1
  MYO3B MUTATED    24   6
  MYO3B WILD-TYPE 253  72
  MYO3B MUTATED MYO3B WILD-TYPE 
             30             325 
  MYO3B MUTATED MYO3B WILD-TYPE 
              6              72 
$`MYO3B MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6964 TCGA-G4-6321 TCGA-G4-6586 
        6.05        85.05        19.04        10.88        22.09        35.80 
TCGA-A6-2671 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3845 TCGA-AA-A00N TCGA-AU-3779 
       43.76         8.38        19.66         0.00         4.01        14.50 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-4743 
       33.01        58.39         3.19        12.76       124.27        23.05 
TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6676 
       13.02        32.02        21.99        13.02        12.95        11.08 
TCGA-D5-6532 TCGA-D5-6927 TCGA-D5-6931 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6315 
       18.25         9.44        12.00         6.18        35.31        61.91 

$`MYO3B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 
        5.88        63.62        26.17        91.79        79.69        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
       82.95         2.01        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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYO3B MUTATED MYO3B WILD-TYPE 
              0               0 
  MYO3B MUTATED MYO3B WILD-TYPE 
         124.27          148.01 
  MYO3B MUTATED MYO3B WILD-TYPE 
         16.375          22.520 
[1] "0.0 - 124.3 (16.4)" "0.0 - 148.0 (22.5)"
[1] "hr=" "1"  
D278V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO3B MUTATED         4        0        1        14         1         0
  MYO3B WILD-TYPE      60        1       25        94         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3B MUTATED           2          0          0          2        5         1
  MYO3B WILD-TYPE        16          6         44         31       30        11
                 vv
clus              STAGE IVB
  MYO3B MUTATED           0
  MYO3B WILD-TYPE         1
D278V3, multiclass
            clus
vv           MYO3B MUTATED MYO3B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             14              94
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               5              30
  STAGE IVA              1              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
  MYO3B MUTATED     0   5  20   6
  MYO3B WILD-TYPE   9  62 229  35
D278V4, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  T1             0               9
  T2             5              62
  T3            20             229
  T4             6              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
  MYO3B MUTATED    21   4   6
  MYO3B WILD-TYPE 199  77  60
D278V5, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  N0            21             199
  N1             4              77
  N2             6              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V6, binary
                 cls
clus                0   1
  MYO3B MUTATED    21   6
  MYO3B WILD-TYPE 264  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     21    6
  MYO3B WILD-TYPE  264   42
   clus
vv  MYO3B MUTATED MYO3B WILD-TYPE
  0            21             264
  1             6              42
[1] 2 2
[1] FALSE
D278V7, binary
                 cls
clus                0   1
  MYO3B MUTATED     9  22
  MYO3B WILD-TYPE 161 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED      9   22
  MYO3B WILD-TYPE  161  175
        clus
vv       MYO3B MUTATED MYO3B WILD-TYPE
  FEMALE             9             161
  MALE              22             175
[1] 2 2
[1] FALSE
D278V8, binary
                 cls
clus                0   1
  MYO3B MUTATED    27   1
  MYO3B WILD-TYPE 273   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     27    1
  MYO3B WILD-TYPE  273    7
     clus
vv    MYO3B MUTATED MYO3B WILD-TYPE
  NO             27             273
  YES             1               7
[1] 2 2
[1] FALSE
D278V9, binary
                 cls
clus                0   1
  MYO3B MUTATED    26   5
  MYO3B WILD-TYPE 288  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     26    5
  MYO3B WILD-TYPE  288   43
                               clus
vv                              MYO3B MUTATED MYO3B WILD-TYPE
  COLON ADENOCARCINOMA                     26             288
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYO3B MUTATED    24   0   2   2
  MYO3B WILD-TYPE 235   3  20  19
D278V10, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  R0            24             235
  R1             0               3
  R2             2              20
  RX             2              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"
D278V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO3B MUTATED                                  0     1
  MYO3B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO3B MUTATED                           4    20
  MYO3B WILD-TYPE                        15   156
D278V12, multiclass
                                  clus
vv                                 MYO3B MUTATED MYO3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       20             156
[1] 4 2
[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 = G3BP2 MUTATION ANALYSIS
D279V1, survival
                 sevent
clus2               0   1
  G3BP2 MUTATED     7   2
  G3BP2 WILD-TYPE 270  76
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              9             346 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              2              76 
$`G3BP2 MUTATED`
TCGA-AD-6548 TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 
       21.37        79.69        33.53         4.01        34.98        12.76 
TCGA-D5-6536 TCGA-D5-6540 TCGA-DM-A0XD 
       17.85        16.14        24.43 

$`G3BP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        43.27        15.12         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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  G3BP2 MUTATED G3BP2 WILD-TYPE 
           4.01            0.00 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
          79.69          148.01 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
         21.370          22.075 
[1] "4.0 - 79.7 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D279V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  G3BP2 MUTATED         3        0        0         4         2         0
  G3BP2 WILD-TYPE      61        1       26       104         6         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  G3BP2 MUTATED           0
  G3BP2 WILD-TYPE         1
D279V3, multiclass
            clus
vv           G3BP2 MUTATED G3BP2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  G3BP2 MUTATED     0   3   4   2
  G3BP2 WILD-TYPE   9  64 245  39
D279V4, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             4             245
  T4             2              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
  G3BP2 MUTATED     9   0   0
  G3BP2 WILD-TYPE 211  81  66
D279V5, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V6, binary
                 cls
clus                0   1
  G3BP2 MUTATED     9   0
  G3BP2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      9    0
  G3BP2 WILD-TYPE  276   48
   clus
vv  G3BP2 MUTATED G3BP2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D279V7, binary
                 cls
clus                0   1
  G3BP2 MUTATED     3   6
  G3BP2 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      3    6
  G3BP2 WILD-TYPE  167  191
        clus
vv       G3BP2 MUTATED G3BP2 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D279V8, binary
                 cls
clus                0   1
  G3BP2 MUTATED     7   0
  G3BP2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      7    0
  G3BP2 WILD-TYPE  293    8
     clus
vv    G3BP2 MUTATED G3BP2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D279V9, binary
                 cls
clus                0   1
  G3BP2 MUTATED     6   3
  G3BP2 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      6    3
  G3BP2 WILD-TYPE  308   45
                               clus
vv                              G3BP2 MUTATED G3BP2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  G3BP2 MUTATED     7   0   0   1
  G3BP2 WILD-TYPE 252   3  22  20
D279V10, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D279V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G3BP2 MUTATED                                  0     1
  G3BP2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  G3BP2 MUTATED                           1     5
  G3BP2 WILD-TYPE                        18   171
D279V12, multiclass
                                  clus
vv                                 G3BP2 MUTATED G3BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = MBD6 MUTATION ANALYSIS
D280V1, survival
                sevent
clus2              0   1
  MBD6 MUTATED     9   5
  MBD6 WILD-TYPE 268  73
  MBD6 MUTATED MBD6 WILD-TYPE 
            14            341 
  MBD6 MUTATED MBD6 WILD-TYPE 
             5             73 
$`MBD6 MUTATED`
TCGA-AD-6895 TCGA-AZ-6608 TCGA-AA-3492 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       25.08         1.94         3.02         4.01        34.98        35.01 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6930 
       27.09        49.41        51.32        14.04        11.64        13.35 
TCGA-F4-6570 TCGA-G4-6304 
        6.18        53.62 

$`MBD6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MBD6 MUTATED MBD6 WILD-TYPE 
          1.94           0.00 
  MBD6 MUTATED MBD6 WILD-TYPE 
         53.62         148.01 
  MBD6 MUTATED MBD6 WILD-TYPE 
         19.56          22.06 
[1] "1.9 - 53.6 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D280V2, continuous
                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      62        1       24       104         5         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        16          5         43         33       35        12
                vv
clus             STAGE IVB
  MBD6 MUTATED           0
  MBD6 WILD-TYPE         1
D280V3, multiclass
            clus
vv           MBD6 MUTATED MBD6 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MBD6 MUTATED     0   3   9   3
  MBD6 WILD-TYPE   9  64 240  38
D280V4, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            9            240
  T4            3             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
  MBD6 MUTATED    11   2   2
  MBD6 WILD-TYPE 209  79  64
D280V5, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  N0           11            209
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V6, binary
                cls
clus               0   1
  MBD6 MUTATED    13   0
  MBD6 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     13    0
  MBD6 WILD-TYPE  272   48
   clus
vv  MBD6 MUTATED MBD6 WILD-TYPE
  0           13            272
  1            0             48
[1] 2 2
[1] FALSE
D280V7, binary
                cls
clus               0   1
  MBD6 MUTATED     9   6
  MBD6 WILD-TYPE 161 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED      9    6
  MBD6 WILD-TYPE  161  191
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  FEMALE            9            161
  MALE              6            191
[1] 2 2
[1] FALSE
D280V8, binary
                cls
clus               0   1
  MBD6 MUTATED    11   1
  MBD6 WILD-TYPE 289   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     11    1
  MBD6 WILD-TYPE  289    7
     clus
vv    MBD6 MUTATED MBD6 WILD-TYPE
  NO            11            289
  YES            1              7
[1] 2 2
[1] FALSE
D280V9, binary
                cls
clus               0   1
  MBD6 MUTATED    11   4
  MBD6 WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     11    4
  MBD6 WILD-TYPE  303   44
                               clus
vv                              MBD6 MUTATED MBD6 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MBD6 MUTATED    12   0   0   1
  MBD6 WILD-TYPE 247   3  22  20
D280V10, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            1             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"
D280V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBD6 MUTATED                                  0     0
  MBD6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MBD6 MUTATED                           0    10
  MBD6 WILD-TYPE                        19   166
D280V12, multiclass
                                  clus
vv                                 MBD6 MUTATED MBD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(281) Variable = ANAPC4 MUTATION ANALYSIS
D281V1, survival
                  sevent
clus2                0   1
  ANAPC4 MUTATED     8   2
  ANAPC4 WILD-TYPE 269  76
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              10              345 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
               2               76 
$`ANAPC4 MUTATED`
TCGA-AA-3697 TCGA-A6-6141 TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4950 
       85.05         8.38         4.01        12.16        12.76        85.45 
TCGA-CM-6676 TCGA-D5-6538 TCGA-DM-A1D4 TCGA-G4-6315 
       11.08        17.13        92.75        61.91 

$`ANAPC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
            4.01             0.00 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
           92.75           148.01 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
          14.945           22.090 
[1] "4.0 - 92.8 (14.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D281V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANAPC4 MUTATED         2        0        1         3         1         0
  ANAPC4 WILD-TYPE      62        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC4 MUTATED           0          0          2          0        1
  ANAPC4 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ANAPC4 MUTATED           0         0
  ANAPC4 WILD-TYPE        12         1
D281V3, multiclass
            clus
vv           ANAPC4 MUTATED ANAPC4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ANAPC4 MUTATED     0   2   7   1
  ANAPC4 WILD-TYPE   9  65 242  40
D281V4, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              1               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
  ANAPC4 MUTATED     7   2   1
  ANAPC4 WILD-TYPE 213  79  65
D281V5, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V6, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     8   1
  ANAPC4 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      8    1
  ANAPC4 WILD-TYPE  277   47
   clus
vv  ANAPC4 MUTATED ANAPC4 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D281V7, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     2   8
  ANAPC4 WILD-TYPE 168 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      2    8
  ANAPC4 WILD-TYPE  168  189
        clus
vv       ANAPC4 MUTATED ANAPC4 WILD-TYPE
  FEMALE              2              168
  MALE                8              189
[1] 2 2
[1] FALSE
D281V8, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     8   0
  ANAPC4 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      8    0
  ANAPC4 WILD-TYPE  292    8
     clus
vv    ANAPC4 MUTATED ANAPC4 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D281V9, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     6   4
  ANAPC4 WILD-TYPE 308  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      6    4
  ANAPC4 WILD-TYPE  308   44
                               clus
vv                              ANAPC4 MUTATED ANAPC4 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ANAPC4 MUTATED     6   1   0   1
  ANAPC4 WILD-TYPE 253   2  22  20
D281V10, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  R0              6              253
  R1              1                2
  R2              0               22
  RX              1               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"
D281V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANAPC4 MUTATED                                  0     1
  ANAPC4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANAPC4 MUTATED                           2     5
  ANAPC4 WILD-TYPE                        17   171
D281V12, multiclass
                                  clus
vv                                 ANAPC4 MUTATED ANAPC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         5              171
[1] 4 2
[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 = TTF1 MUTATION ANALYSIS
D282V1, survival
                sevent
clus2              0   1
  TTF1 MUTATED     6   2
  TTF1 WILD-TYPE 271  76
  TTF1 MUTATED TTF1 WILD-TYPE 
             8            347 
  TTF1 MUTATED TTF1 WILD-TYPE 
             2             76 
$`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 
       15.02        12.03 

$`TTF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-5662 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-A6-6142 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TTF1 MUTATED TTF1 WILD-TYPE 
          3.02           0.00 
  TTF1 MUTATED TTF1 WILD-TYPE 
         33.53         148.01 
  TTF1 MUTATED TTF1 WILD-TYPE 
        12.395         22.090 
[1] "3.0 - 33.5 (12.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D282V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTF1 MUTATED         1        0        1         5         1         0
  TTF1 WILD-TYPE      63        1       25       103         7         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  TTF1 MUTATED           0
  TTF1 WILD-TYPE         1
D282V3, multiclass
            clus
vv           TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TTF1 MUTATED     0   1   7   1
  TTF1 WILD-TYPE   9  66 242  40
D282V4, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            1             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
  TTF1 MUTATED     8   0   1
  TTF1 WILD-TYPE 212  81  65
D282V5, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V6, binary
                cls
clus               0   1
  TTF1 MUTATED     8   0
  TTF1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      8    0
  TTF1 WILD-TYPE  277   48
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D282V7, binary
                cls
clus               0   1
  TTF1 MUTATED     5   4
  TTF1 WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      5    4
  TTF1 WILD-TYPE  165  193
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D282V8, binary
                cls
clus               0   1
  TTF1 MUTATED     8   0
  TTF1 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      8    0
  TTF1 WILD-TYPE  292    8
     clus
vv    TTF1 MUTATED TTF1 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D282V9, binary
                cls
clus               0   1
  TTF1 MUTATED     8   1
  TTF1 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      8    1
  TTF1 WILD-TYPE  306   47
                               clus
vv                              TTF1 MUTATED TTF1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TTF1 MUTATED     5   0   0   3
  TTF1 WILD-TYPE 254   3  22  18
D282V10, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            3             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"
D282V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTF1 MUTATED                                  0     2
  TTF1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TTF1 MUTATED                           2     4
  TTF1 WILD-TYPE                        17   172
D282V12, multiclass
                                  clus
vv                                 TTF1 MUTATED TTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       4            172
[1] 4 2
[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 = FAM134A MUTATION ANALYSIS
D283V1, survival
                   sevent
clus2                 0   1
  FAM134A MUTATED     5   3
  FAM134A WILD-TYPE 272  75
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               347 
  FAM134A MUTATED FAM134A WILD-TYPE 
                3                75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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            22.090 
[1] "4.0 - 85.5 (17.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D283V2, continuous
                   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      64        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM134A MUTATED           0          0          1          0        0
  FAM134A WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM134A MUTATED           1         0
  FAM134A WILD-TYPE        11         1
D283V3, multiclass
            clus
vv           FAM134A MUTATED FAM134A WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  FAM134A MUTATED     0   0   7   1
  FAM134A WILD-TYPE   9  67 242  40
D283V4, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               7               242
  T4               1                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
  FAM134A MUTATED     6   2   0
  FAM134A WILD-TYPE 214  79  66
D283V5, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  N0               6               214
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V6, binary
                   cls
clus                  0   1
  FAM134A MUTATED     6   1
  FAM134A WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      6    1
  FAM134A WILD-TYPE  279   47
   clus
vv  FAM134A MUTATED FAM134A WILD-TYPE
  0               6               279
  1               1                47
[1] 2 2
[1] FALSE
D283V7, binary
                   cls
clus                  0   1
  FAM134A MUTATED     5   3
  FAM134A WILD-TYPE 165 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      5    3
  FAM134A WILD-TYPE  165  194
        clus
vv       FAM134A MUTATED FAM134A WILD-TYPE
  FEMALE               5               165
  MALE                 3               194
[1] 2 2
[1] FALSE
D283V8, binary
                   cls
clus                  0   1
  FAM134A MUTATED     6   0
  FAM134A WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      6    0
  FAM134A WILD-TYPE  294    8
     clus
vv    FAM134A MUTATED FAM134A WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D283V9, binary
                   cls
clus                  0   1
  FAM134A MUTATED     5   2
  FAM134A WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      5    2
  FAM134A WILD-TYPE  309   46
                               clus
vv                              FAM134A MUTATED FAM134A WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM134A MUTATED     5   1   0   0
  FAM134A WILD-TYPE 254   2  22  21
D283V10, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  R0               5               254
  R1               1                 2
  R2               0                22
  RX               0                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"
D283V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM134A MUTATED                                  0     0
  FAM134A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM134A MUTATED                           2     3
  FAM134A WILD-TYPE                        17   173
D283V12, multiclass
                                  clus
vv                                 FAM134A MUTATED FAM134A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          3               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(284) Variable = ZKSCAN2 MUTATION ANALYSIS
D284V1, survival
                   sevent
clus2                 0   1
  ZKSCAN2 MUTATED    11   2
  ZKSCAN2 WILD-TYPE 266  76
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               13               342 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
                2                76 
$`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 
       26.47        58.39        17.56        30.08        11.08        11.64 
TCGA-G4-6306 
       44.68 

$`ZKSCAN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
        2.01        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
             1.02              0.00 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
            58.39            148.01 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
           17.560            22.075 
[1] "1.0 - 58.4 (17.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D284V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZKSCAN2 MUTATED         2        0        1         4         1         0
  ZKSCAN2 WILD-TYPE      62        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN2 MUTATED           0          0          1          1        0
  ZKSCAN2 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ZKSCAN2 MUTATED           1         0
  ZKSCAN2 WILD-TYPE        11         1
D284V3, multiclass
            clus
vv           ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  ZKSCAN2 MUTATED     0   4   5   4
  ZKSCAN2 WILD-TYPE   9  63 244  37
D284V4, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               5               244
  T4               4                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
  ZKSCAN2 MUTATED    10   2   1
  ZKSCAN2 WILD-TYPE 210  79  65
D284V5, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  N0              10               210
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V6, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED    11   1
  ZKSCAN2 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED     11    1
  ZKSCAN2 WILD-TYPE  274   47
   clus
vv  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  0              11               274
  1               1                47
[1] 2 2
[1] FALSE
D284V7, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED     6   7
  ZKSCAN2 WILD-TYPE 164 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED      6    7
  ZKSCAN2 WILD-TYPE  164  190
        clus
vv       ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  FEMALE               6               164
  MALE                 7               190
[1] 2 2
[1] FALSE
D284V8, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED    11   0
  ZKSCAN2 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED     11    0
  ZKSCAN2 WILD-TYPE  289    8
     clus
vv    ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D284V9, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED     9   4
  ZKSCAN2 WILD-TYPE 305  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED      9    4
  ZKSCAN2 WILD-TYPE  305   44
                               clus
vv                              ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN2 MUTATED     9   1   0   1
  ZKSCAN2 WILD-TYPE 250   2  22  20
D284V10, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  R0               9               250
  R1               1                 2
  R2               0                22
  RX               1                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"
D284V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZKSCAN2 MUTATED                                  0     0
  ZKSCAN2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZKSCAN2 MUTATED                           0     7
  ZKSCAN2 WILD-TYPE                        19   169
D284V12, multiclass
                                  clus
vv                                 ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = RNF182 MUTATION ANALYSIS
D285V1, survival
                  sevent
clus2                0   1
  RNF182 MUTATED    11   2
  RNF182 WILD-TYPE 266  76
  RNF182 MUTATED RNF182 WILD-TYPE 
              13              342 
  RNF182 MUTATED RNF182 WILD-TYPE 
               2               76 
$`RNF182 MUTATED`
TCGA-AA-3713 TCGA-AD-6888 TCGA-A6-3810 TCGA-AA-3558 TCGA-AA-3655 TCGA-AZ-4315 
       19.04        15.52        36.53        20.98        61.02        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 
       13.25 

$`RNF182 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        29.95        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RNF182 MUTATED RNF182 WILD-TYPE 
              12                0 
  RNF182 MUTATED RNF182 WILD-TYPE 
          139.17           148.01 
  RNF182 MUTATED RNF182 WILD-TYPE 
          36.530           22.045 
[1] "12.0 - 139.2 (36.5)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.5"
D285V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF182 MUTATED         3        0        1         4         0         0
  RNF182 WILD-TYPE      61        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF182 MUTATED           0          0          2          1        1
  RNF182 WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  RNF182 MUTATED           1         0
  RNF182 WILD-TYPE        11         1
D285V3, multiclass
            clus
vv           RNF182 MUTATED RNF182 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  RNF182 MUTATED     1   2   9   1
  RNF182 WILD-TYPE   8  65 240  40
D285V4, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              9              240
  T4              1               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
  RNF182 MUTATED     9   3   1
  RNF182 WILD-TYPE 211  78  65
D285V5, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V6, binary
                  cls
clus                 0   1
  RNF182 MUTATED    11   2
  RNF182 WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     11    2
  RNF182 WILD-TYPE  274   46
   clus
vv  RNF182 MUTATED RNF182 WILD-TYPE
  0             11              274
  1              2               46
[1] 2 2
[1] FALSE
D285V7, binary
                  cls
clus                 0   1
  RNF182 MUTATED     3  10
  RNF182 WILD-TYPE 167 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED      3   10
  RNF182 WILD-TYPE  167  187
        clus
vv       RNF182 MUTATED RNF182 WILD-TYPE
  FEMALE              3              167
  MALE               10              187
[1] 2 2
[1] FALSE
D285V8, binary
                  cls
clus                 0   1
  RNF182 MUTATED    10   1
  RNF182 WILD-TYPE 290   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     10    1
  RNF182 WILD-TYPE  290    7
     clus
vv    RNF182 MUTATED RNF182 WILD-TYPE
  NO              10              290
  YES              1                7
[1] 2 2
[1] FALSE
D285V9, binary
                  cls
clus                 0   1
  RNF182 MUTATED    11   1
  RNF182 WILD-TYPE 303  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     11    1
  RNF182 WILD-TYPE  303   47
                               clus
vv                              RNF182 MUTATED RNF182 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF182 MUTATED     8   0   2   0
  RNF182 WILD-TYPE 251   3  20  21
D285V10, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              2               20
  RX              0               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"
D285V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF182 MUTATED                                  0     0
  RNF182 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF182 MUTATED                           0    10
  RNF182 WILD-TYPE                        19   166
D285V12, multiclass
                                  clus
vv                                 RNF182 MUTATED RNF182 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(286) Variable = RBBP7 MUTATION ANALYSIS
D286V1, survival
                 sevent
clus2               0   1
  RBBP7 MUTATED    11   4
  RBBP7 WILD-TYPE 266  74
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             15             340 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
              4              74 
$`RBBP7 MUTATED`
TCGA-AA-3662 TCGA-A6-2671 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-A00N TCGA-AA-A010 
        6.05        43.76        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        12.16        58.39        12.76        21.14        22.03 
TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5538 
       15.02        14.04        54.61 

$`RBBP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  RBBP7 MUTATED RBBP7 WILD-TYPE 
           1.02            0.00 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
          58.39          148.01 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
          21.14           22.09 
[1] "1.0 - 58.4 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D286V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBBP7 MUTATED         3        0        2         3         2         0
  RBBP7 WILD-TYPE      61        1       24       105         6         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        18          6         42         33       33        11
                 vv
clus              STAGE IVB
  RBBP7 MUTATED           0
  RBBP7 WILD-TYPE         1
D286V3, multiclass
            clus
vv           RBBP7 MUTATED RBBP7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              1              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
  RBBP7 MUTATED     1   2   8   4
  RBBP7 WILD-TYPE   8  65 241  37
D286V4, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             8             241
  T4             4              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
  RBBP7 MUTATED    10   3   2
  RBBP7 WILD-TYPE 210  78  64
D286V5, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  N0            10             210
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V6, binary
                 cls
clus                0   1
  RBBP7 MUTATED    11   3
  RBBP7 WILD-TYPE 274  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     11    3
  RBBP7 WILD-TYPE  274   45
   clus
vv  RBBP7 MUTATED RBBP7 WILD-TYPE
  0            11             274
  1             3              45
[1] 2 2
[1] FALSE
D286V7, binary
                 cls
clus                0   1
  RBBP7 MUTATED     9   6
  RBBP7 WILD-TYPE 161 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED      9    6
  RBBP7 WILD-TYPE  161  191
        clus
vv       RBBP7 MUTATED RBBP7 WILD-TYPE
  FEMALE             9             161
  MALE               6             191
[1] 2 2
[1] FALSE
D286V8, binary
                 cls
clus                0   1
  RBBP7 MUTATED    13   0
  RBBP7 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     13    0
  RBBP7 WILD-TYPE  287    8
     clus
vv    RBBP7 MUTATED RBBP7 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D286V9, binary
                 cls
clus                0   1
  RBBP7 MUTATED    12   3
  RBBP7 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     12    3
  RBBP7 WILD-TYPE  302   45
                               clus
vv                              RBBP7 MUTATED RBBP7 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBBP7 MUTATED    12   0   1   2
  RBBP7 WILD-TYPE 247   3  21  19
D286V10, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             1              21
  RX             2              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"
D286V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBBP7 MUTATED                                  0     1
  RBBP7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBBP7 MUTATED                           0     8
  RBBP7 WILD-TYPE                        19   168
D286V12, multiclass
                                  clus
vv                                 RBBP7 MUTATED RBBP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = MAGEA1 MUTATION ANALYSIS
D287V1, survival
                  sevent
clus2                0   1
  MAGEA1 MUTATED    10   3
  MAGEA1 WILD-TYPE 267  75
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              13              342 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
               3               75 
$`MAGEA1 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3510 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4616 
       26.17        79.69        63.98        33.01        21.44         5.13 
TCGA-AZ-5403 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-D5-6539 TCGA-F4-6805 
       62.79       148.01        21.99         2.01        12.49        34.42 
TCGA-G4-6303 
       65.85 

$`MAGEA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 
       14.50        27.09        16.31         0.95         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       58.39         1.41        22.36        88.21        49.41         6.77 
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 
       12.36        12.39        12.59        12.59        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-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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
            2.01             0.00 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
          148.01           140.38 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
           33.01            22.01 
[1] "2.0 - 148.0 (33.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.4"
D287V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEA1 MUTATED         1        0        2         3         0         0
  MAGEA1 WILD-TYPE      63        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEA1 MUTATED           1          0          1          0        3
  MAGEA1 WILD-TYPE        17          6         43         33       32
                  vv
clus               STAGE IVA STAGE IVB
  MAGEA1 MUTATED           1         0
  MAGEA1 WILD-TYPE        11         1
D287V3, multiclass
            clus
vv           MAGEA1 MUTATED MAGEA1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                3               32
  STAGE IVA               1               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
  MAGEA1 MUTATED     0   1  12   0
  MAGEA1 WILD-TYPE   9  66 237  41
D287V4, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             12              237
  T4              0               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
  MAGEA1 MUTATED     7   5   1
  MAGEA1 WILD-TYPE 213  76  65
D287V5, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  N0              7              213
  N1              5               76
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V6, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED     6   4
  MAGEA1 WILD-TYPE 279  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED      6    4
  MAGEA1 WILD-TYPE  279   44
   clus
vv  MAGEA1 MUTATED MAGEA1 WILD-TYPE
  0              6              279
  1              4               44
[1] 2 2
[1] FALSE
D287V7, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED     8   5
  MAGEA1 WILD-TYPE 162 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED      8    5
  MAGEA1 WILD-TYPE  162  192
        clus
vv       MAGEA1 MUTATED MAGEA1 WILD-TYPE
  FEMALE              8              162
  MALE                5              192
[1] 2 2
[1] FALSE
D287V8, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED    12   0
  MAGEA1 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED     12    0
  MAGEA1 WILD-TYPE  288    8
     clus
vv    MAGEA1 MUTATED MAGEA1 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D287V9, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED    12   1
  MAGEA1 WILD-TYPE 302  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED     12    1
  MAGEA1 WILD-TYPE  302   47
                               clus
vv                              MAGEA1 MUTATED MAGEA1 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGEA1 MUTATED     9   0   0   2
  MAGEA1 WILD-TYPE 250   3  22  19
D287V10, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              2               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"
D287V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEA1 MUTATED                                  0     0
  MAGEA1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEA1 MUTATED                           1    11
  MAGEA1 WILD-TYPE                        18   165
D287V12, multiclass
                                  clus
vv                                 MAGEA1 MUTATED MAGEA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(288) Variable = HEPACAM2 MUTATION ANALYSIS
D288V1, survival
                    sevent
clus2                  0   1
  HEPACAM2 MUTATED    10   3
  HEPACAM2 WILD-TYPE 267  75
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                13                342 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 3                 75 
$`HEPACAM2 MUTATED`
TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3845 TCGA-AA-3977 TCGA-AU-6004 
       79.69        32.75        19.66         0.00        25.02        27.09 
TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5348 TCGA-D5-6930 
       12.10        10.06        15.62        23.05        22.98        13.35 
TCGA-G4-6315 
       61.91 

$`HEPACAM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 0                  0 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
             79.69             148.01 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
            22.980             22.045 
[1] "0.0 - 79.7 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D288V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEPACAM2 MUTATED         2        0        0         4         1         0
  HEPACAM2 WILD-TYPE      62        1       26       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEPACAM2 MUTATED           0          0          1          2        2
  HEPACAM2 WILD-TYPE        18          6         43         31       33
                    vv
clus                 STAGE IVA STAGE IVB
  HEPACAM2 MUTATED           0         0
  HEPACAM2 WILD-TYPE        12         1
D288V3, multiclass
            clus
vv           HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 4                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                2                 31
  STAGE IV                  2                 33
  STAGE IVA                 0                 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
  HEPACAM2 MUTATED     0   3   6   4
  HEPACAM2 WILD-TYPE   9  64 243  37
D288V4, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3                6                243
  T4                4                 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
  HEPACAM2 MUTATED     8   4   1
  HEPACAM2 WILD-TYPE 212  77  65
D288V5, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  N0                8                212
  N1                4                 77
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V6, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     9   2
  HEPACAM2 WILD-TYPE 276  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      9    2
  HEPACAM2 WILD-TYPE  276   46
   clus
vv  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  0                9                276
  1                2                 46
[1] 2 2
[1] FALSE
D288V7, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     4   9
  HEPACAM2 WILD-TYPE 166 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      4    9
  HEPACAM2 WILD-TYPE  166  188
        clus
vv       HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  FEMALE                4                166
  MALE                  9                188
[1] 2 2
[1] FALSE
D288V8, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED    10   0
  HEPACAM2 WILD-TYPE 290   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED     10    0
  HEPACAM2 WILD-TYPE  290    8
     clus
vv    HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  NO                10                290
  YES                0                  8
[1] 2 2
[1] FALSE
D288V9, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     9   4
  HEPACAM2 WILD-TYPE 305  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      9    4
  HEPACAM2 WILD-TYPE  305   44
                               clus
vv                              HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HEPACAM2 MUTATED     9   0   0   2
  HEPACAM2 WILD-TYPE 250   3  22  19
D288V10, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D288V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEPACAM2 MUTATED                                  0     1
  HEPACAM2 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HEPACAM2 MUTATED                           1     9
  HEPACAM2 WILD-TYPE                        18   167
D288V12, multiclass
                                  clus
vv                                 HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           9                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(289) Variable = DHX35 MUTATION ANALYSIS
D289V1, survival
                 sevent
clus2               0   1
  DHX35 MUTATED     7   3
  DHX35 WILD-TYPE 270  75
  DHX35 MUTATED DHX35 WILD-TYPE 
             10             345 
  DHX35 MUTATED DHX35 WILD-TYPE 
              3              75 
$`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 
       12.10        32.02        14.04        61.91 

$`DHX35 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DHX35 MUTATED DHX35 WILD-TYPE 
           1.02            0.00 
  DHX35 MUTATED DHX35 WILD-TYPE 
          61.91          148.01 
  DHX35 MUTATED DHX35 WILD-TYPE 
         32.775          22.030 
[1] "1.0 - 61.9 (32.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D289V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHX35 MUTATED         1        0        1         5         1         0
  DHX35 WILD-TYPE      63        1       25       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHX35 MUTATED           0          0          0          0        3         0
  DHX35 WILD-TYPE        18          6         44         33       32        12
                 vv
clus              STAGE IVB
  DHX35 MUTATED           0
  DHX35 WILD-TYPE         1
D289V3, multiclass
            clus
vv           DHX35 MUTATED DHX35 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              0              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
  DHX35 MUTATED     0   1   7   3
  DHX35 WILD-TYPE   9  66 242  38
D289V4, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             3              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
  DHX35 MUTATED     8   2   1
  DHX35 WILD-TYPE 212  79  65
D289V5, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V6, binary
                 cls
clus                0   1
  DHX35 MUTATED     7   3
  DHX35 WILD-TYPE 278  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      7    3
  DHX35 WILD-TYPE  278   45
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             7             278
  1             3              45
[1] 2 2
[1] FALSE
D289V7, binary
                 cls
clus                0   1
  DHX35 MUTATED     6   5
  DHX35 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      6    5
  DHX35 WILD-TYPE  164  192
        clus
vv       DHX35 MUTATED DHX35 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D289V8, binary
                 cls
clus                0   1
  DHX35 MUTATED     9   0
  DHX35 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      9    0
  DHX35 WILD-TYPE  291    8
     clus
vv    DHX35 MUTATED DHX35 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D289V9, binary
                 cls
clus                0   1
  DHX35 MUTATED    11   0
  DHX35 WILD-TYPE 303  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED     11    0
  DHX35 WILD-TYPE  303   48
                               clus
vv                              DHX35 MUTATED DHX35 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHX35 MUTATED     8   0   1   0
  DHX35 WILD-TYPE 251   3  21  21
D289V10, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             0              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"
D289V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHX35 MUTATED                                  0     0
  DHX35 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHX35 MUTATED                           2     5
  DHX35 WILD-TYPE                        17   171
D289V12, multiclass
                                  clus
vv                                 DHX35 MUTATED DHX35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = PARP12 MUTATION ANALYSIS
D290V1, survival
                  sevent
clus2                0   1
  PARP12 MUTATED     7   2
  PARP12 WILD-TYPE 270  76
  PARP12 MUTATED PARP12 WILD-TYPE 
               9              346 
  PARP12 MUTATED PARP12 WILD-TYPE 
               2               76 
$`PARP12 MUTATED`
TCGA-AA-3950 TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3966 
       24.00        22.09        79.69        20.12        78.08         2.01 
TCGA-AZ-6598 TCGA-CK-4947 TCGA-F4-6460 
       49.41        17.56        31.96 

$`PARP12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6569 
       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PARP12 MUTATED PARP12 WILD-TYPE 
            2.01             0.00 
  PARP12 MUTATED PARP12 WILD-TYPE 
           79.69           148.01 
  PARP12 MUTATED PARP12 WILD-TYPE 
           24.00            22.01 
[1] "2.0 - 79.7 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D290V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARP12 MUTATED         1        0        2         3         0         0
  PARP12 WILD-TYPE      63        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PARP12 MUTATED           1          0          2          0        0
  PARP12 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  PARP12 MUTATED           0         0
  PARP12 WILD-TYPE        12         1
D290V3, multiclass
            clus
vv           PARP12 MUTATED PARP12 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  PARP12 MUTATED     0   2   6   1
  PARP12 WILD-TYPE   9  65 243  40
D290V4, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              6              243
  T4              1               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
  PARP12 MUTATED     6   3   0
  PARP12 WILD-TYPE 214  78  66
D290V5, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  N0              6              214
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V6, binary
                  cls
clus                 0   1
  PARP12 MUTATED     6   0
  PARP12 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      6    0
  PARP12 WILD-TYPE  279   48
   clus
vv  PARP12 MUTATED PARP12 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D290V7, binary
                  cls
clus                 0   1
  PARP12 MUTATED     7   2
  PARP12 WILD-TYPE 163 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      7    2
  PARP12 WILD-TYPE  163  195
        clus
vv       PARP12 MUTATED PARP12 WILD-TYPE
  FEMALE              7              163
  MALE                2              195
[1] 2 2
[1] FALSE
D290V8, binary
                  cls
clus                 0   1
  PARP12 MUTATED     8   0
  PARP12 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      8    0
  PARP12 WILD-TYPE  292    8
     clus
vv    PARP12 MUTATED PARP12 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D290V9, binary
                  cls
clus                 0   1
  PARP12 MUTATED     6   3
  PARP12 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      6    3
  PARP12 WILD-TYPE  308   45
                               clus
vv                              PARP12 MUTATED PARP12 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PARP12 MUTATED     5   0   0   1
  PARP12 WILD-TYPE 254   3  22  20
D290V10, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D290V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARP12 MUTATED                                  0     0
  PARP12 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PARP12 MUTATED                           0     6
  PARP12 WILD-TYPE                        19   170
D290V12, multiclass
                                  clus
vv                                 PARP12 MUTATED PARP12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = BRCA2 MUTATION ANALYSIS
D291V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED    37   9
  BRCA2 WILD-TYPE 240  69
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             46             309 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              9              69 
$`BRCA2 MUTATED`
TCGA-AA-3496 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        1.02        19.99         6.05        85.05        19.04        19.04 
TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5656 TCGA-A6-5665 
       10.88       100.01        26.17        79.69        32.91        22.06 
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-A00N 
       23.87        63.98         1.02         6.97        26.99         4.01 
TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6715 
       34.98        27.09        58.39        49.41         6.77        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5863 
       12.76        10.06        51.32        23.05        13.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       17.03        12.00        11.01        11.08        11.01        10.06 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 
       17.85        16.14        12.43         9.04        13.41        13.35 
TCGA-DM-A0XD TCGA-DM-A1D9 TCGA-F4-6460 TCGA-G4-6307 
       24.43       140.38        31.96        55.04 

$`BRCA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99         0.92        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5666 
       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-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        3.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        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-6716 
        3.19        12.69        12.36        12.39        12.59        12.20 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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-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-F4-6569 
       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           1.02            0.00 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         140.38          148.01 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          17.44           22.52 
[1] "1.0 - 140.4 (17.4)" "0.0 - 148.0 (22.5)"
[1] "hr=" "1.1"
D291V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRCA2 MUTATED         6        0        7        16         2         0
  BRCA2 WILD-TYPE      58        1       19        92         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA2 MUTATED           1          0          8          1        3         2
  BRCA2 WILD-TYPE        17          6         36         32       32        10
                 vv
clus              STAGE IVB
  BRCA2 MUTATED           0
  BRCA2 WILD-TYPE         1
D291V3, multiclass
            clus
vv           BRCA2 MUTATED BRCA2 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               7              19
  STAGE IIA             16              92
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             8              36
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              2              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
  BRCA2 MUTATED     0   6  34   7
  BRCA2 WILD-TYPE   9  61 215  34
D291V4, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  T1             0               9
  T2             6              61
  T3            34             215
  T4             7              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
  BRCA2 MUTATED    32  11   4
  BRCA2 WILD-TYPE 188  70  62
D291V5, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  N0            32             188
  N1            11              70
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V6, binary
                 cls
clus                0   1
  BRCA2 MUTATED    38   5
  BRCA2 WILD-TYPE 247  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     38    5
  BRCA2 WILD-TYPE  247   43
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0            38             247
  1             5              43
[1] 2 2
[1] FALSE
D291V7, binary
                 cls
clus                0   1
  BRCA2 MUTATED    21  26
  BRCA2 WILD-TYPE 149 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     21   26
  BRCA2 WILD-TYPE  149  171
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  FEMALE            21             149
  MALE              26             171
[1] 2 2
[1] FALSE
D291V8, binary
                 cls
clus                0   1
  BRCA2 MUTATED    38   2
  BRCA2 WILD-TYPE 262   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     38    2
  BRCA2 WILD-TYPE  262    6
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO             38             262
  YES             2               6
[1] 2 2
[1] FALSE
D291V9, binary
                 cls
clus                0   1
  BRCA2 MUTATED    41   6
  BRCA2 WILD-TYPE 273  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     41    6
  BRCA2 WILD-TYPE  273   42
                               clus
vv                              BRCA2 MUTATED BRCA2 WILD-TYPE
  COLON ADENOCARCINOMA                     41             273
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRCA2 MUTATED    33   0   2   4
  BRCA2 WILD-TYPE 226   3  20  17
D291V10, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  R0            33             226
  R1             0               3
  R2             2              20
  RX             4              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"
D291V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA2 MUTATED                                  0     3
  BRCA2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA2 MUTATED                           1    30
  BRCA2 WILD-TYPE                        18   146
D291V12, multiclass
                                  clus
vv                                 BRCA2 MUTATED BRCA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       30             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(292) Variable = IFIT2 MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2               0   1
  IFIT2 MUTATED     5   2
  IFIT2 WILD-TYPE 272  76
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              7             348 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              2              76 
$`IFIT2 MUTATED`
TCGA-AA-3950 TCGA-AA-3492 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6534 
       24.00         3.02        25.02        12.76        10.06        43.27 
TCGA-G4-6309 
       85.48 

$`IFIT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  IFIT2 MUTATED IFIT2 WILD-TYPE 
           3.02            0.00 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
          85.48          148.01 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
         24.000          22.045 
[1] "3.0 - 85.5 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D292V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFIT2 MUTATED         0        0        1         4         0         0
  IFIT2 WILD-TYPE      64        1       25       104         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  IFIT2 MUTATED           0
  IFIT2 WILD-TYPE         1
D292V3, multiclass
            clus
vv           IFIT2 MUTATED IFIT2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  IFIT2 MUTATED     0   1   6   0
  IFIT2 WILD-TYPE   9  66 243  41
D292V4, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             0              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
  IFIT2 MUTATED     6   1   0
  IFIT2 WILD-TYPE 214  80  66
D292V5, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V6, binary
                 cls
clus                0   1
  IFIT2 MUTATED     6   0
  IFIT2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      6    0
  IFIT2 WILD-TYPE  279   48
   clus
vv  IFIT2 MUTATED IFIT2 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D292V7, binary
                 cls
clus                0   1
  IFIT2 MUTATED     4   3
  IFIT2 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      4    3
  IFIT2 WILD-TYPE  166  194
        clus
vv       IFIT2 MUTATED IFIT2 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D292V8, binary
                 cls
clus                0   1
  IFIT2 MUTATED     7   0
  IFIT2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      7    0
  IFIT2 WILD-TYPE  293    8
     clus
vv    IFIT2 MUTATED IFIT2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D292V9, binary
                 cls
clus                0   1
  IFIT2 MUTATED     4   3
  IFIT2 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      4    3
  IFIT2 WILD-TYPE  310   45
                               clus
vv                              IFIT2 MUTATED IFIT2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IFIT2 MUTATED     4   0   0   2
  IFIT2 WILD-TYPE 255   3  22  19
D292V10, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             2              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"
D292V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFIT2 MUTATED                                  0     2
  IFIT2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFIT2 MUTATED                           1     1
  IFIT2 WILD-TYPE                        18   175
D292V12, multiclass
                                  clus
vv                                 IFIT2 MUTATED IFIT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        1             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(293) Variable = MUC17 MUTATION ANALYSIS
D293V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED    36   8
  MUC17 WILD-TYPE 241  70
  MUC17 MUTATED MUC17 WILD-TYPE 
             44             311 
  MUC17 MUTATED MUC17 WILD-TYPE 
              8              70 
$`MUC17 MUTATED`
TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 
       24.16        13.02        85.05        19.04        24.00        25.08 
TCGA-AZ-4681 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-3807 
      106.75        22.09        35.80        26.17        46.65        34.65 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3660 
       33.53        22.06        19.66        20.28        63.98        78.08 
TCGA-AA-3696 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N 
        5.03        33.04        53.00        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A029 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 
       34.98        31.00        51.98        83.24         5.79        58.39 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CK-5916 TCGA-CM-6161 TCGA-CM-6674 
       88.21        12.10        12.20        21.14        15.02        12.95 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28H 
       17.13        16.14        10.13        11.64        13.41       117.07 
TCGA-DM-A28K TCGA-G4-6626 
       98.24        46.75 

$`MUC17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        15.52        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 
      100.01         1.94        49.08         5.88        63.62        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.12         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3710 TCGA-AA-3811 
       15.02        11.01         5.98        37.05        26.99        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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-A01K 
       14.99        15.02        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         1.02 
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        12.16 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        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        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6459 
      139.17        81.37       119.93        35.97        60.79         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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 
       55.04        85.48        61.91        36.00        13.78 

  MUC17 MUTATED MUC17 WILD-TYPE 
           4.01            0.00 
  MUC17 MUTATED MUC17 WILD-TYPE 
         117.07          148.01 
  MUC17 MUTATED MUC17 WILD-TYPE 
          25.05           21.99 
[1] "4.0 - 117.1 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D293V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUC17 MUTATED         6        0        5        15         4         0
  MUC17 WILD-TYPE      58        1       21        93         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC17 MUTATED           2          1          4          4        4         0
  MUC17 WILD-TYPE        16          5         40         29       31        12
                 vv
clus              STAGE IVB
  MUC17 MUTATED           0
  MUC17 WILD-TYPE         1
D293V3, multiclass
            clus
vv           MUC17 MUTATED MUC17 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             15              93
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             4              29
  STAGE IV               4              31
  STAGE IVA              0              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
  MUC17 MUTATED     2   6  31   7
  MUC17 WILD-TYPE   7  61 218  34
D293V4, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  T1             2               7
  T2             6              61
  T3            31             218
  T4             7              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
  MUC17 MUTATED    32   9   5
  MUC17 WILD-TYPE 188  72  61
D293V5, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  N0            32             188
  N1             9              72
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V6, binary
                 cls
clus                0   1
  MUC17 MUTATED    36   4
  MUC17 WILD-TYPE 249  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     36    4
  MUC17 WILD-TYPE  249   44
   clus
vv  MUC17 MUTATED MUC17 WILD-TYPE
  0            36             249
  1             4              44
[1] 2 2
[1] FALSE
D293V7, binary
                 cls
clus                0   1
  MUC17 MUTATED    22  24
  MUC17 WILD-TYPE 148 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     22   24
  MUC17 WILD-TYPE  148  173
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE            22             148
  MALE              24             173
[1] 2 2
[1] FALSE
D293V8, binary
                 cls
clus                0   1
  MUC17 MUTATED    40   1
  MUC17 WILD-TYPE 260   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     40    1
  MUC17 WILD-TYPE  260    7
     clus
vv    MUC17 MUTATED MUC17 WILD-TYPE
  NO             40             260
  YES             1               7
[1] 2 2
[1] FALSE
D293V9, binary
                 cls
clus                0   1
  MUC17 MUTATED    38   8
  MUC17 WILD-TYPE 276  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     38    8
  MUC17 WILD-TYPE  276   40
                               clus
vv                              MUC17 MUTATED MUC17 WILD-TYPE
  COLON ADENOCARCINOMA                     38             276
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MUC17 MUTATED    31   0   2   3
  MUC17 WILD-TYPE 228   3  20  18
D293V10, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  R0            31             228
  R1             0               3
  R2             2              20
  RX             3              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"
D293V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC17 MUTATED                                  0     2
  MUC17 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED                           2    26
  MUC17 WILD-TYPE                        17   150
D293V12, multiclass
                                  clus
vv                                 MUC17 MUTATED MUC17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       26             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(294) Variable = TET3 MUTATION ANALYSIS
D294V1, survival
                sevent
clus2              0   1
  TET3 MUTATED    14   4
  TET3 WILD-TYPE 263  74
  TET3 MUTATED TET3 WILD-TYPE 
            18            337 
  TET3 MUTATED TET3 WILD-TYPE 
             4             74 
$`TET3 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6321 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3673 
       19.04        24.00        22.09        24.39         6.97        50.04 
TCGA-AA-3846 TCGA-AA-3864 TCGA-AD-6889 TCGA-CA-6715 TCGA-CA-6718 TCGA-CK-5913 
       17.03        53.00        83.24        12.59        10.06        51.32 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6533 TCGA-DM-A1D4 TCGA-F4-6570 
       23.05        37.02        14.04        25.48        92.75         6.18 

$`TET3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       61.02        78.08        54.02         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 
       17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95         2.01 
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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TET3 MUTATED TET3 WILD-TYPE 
          6.18           0.00 
  TET3 MUTATED TET3 WILD-TYPE 
         92.75         148.01 
  TET3 MUTATED TET3 WILD-TYPE 
        23.525         21.990 
[1] "6.2 - 92.8 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D294V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TET3 MUTATED         3        0        4         8         1         0
  TET3 WILD-TYPE      61        1       22       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TET3 MUTATED           1          0          1          0        1         0
  TET3 WILD-TYPE        17          6         43         33       34        12
                vv
clus             STAGE IVB
  TET3 MUTATED           0
  TET3 WILD-TYPE         1
D294V3, multiclass
            clus
vv           TET3 MUTATED TET3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  TET3 MUTATED     0   4  13   3
  TET3 WILD-TYPE   9  63 236  38
D294V4, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           13            236
  T4            3             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
  TET3 MUTATED    18   2   0
  TET3 WILD-TYPE 202  79  66
D294V5, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  N0           18            202
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V6, binary
                cls
clus               0   1
  TET3 MUTATED    16   1
  TET3 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     16    1
  TET3 WILD-TYPE  269   47
   clus
vv  TET3 MUTATED TET3 WILD-TYPE
  0           16            269
  1            1             47
[1] 2 2
[1] FALSE
D294V7, binary
                cls
clus               0   1
  TET3 MUTATED    10  10
  TET3 WILD-TYPE 160 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     10   10
  TET3 WILD-TYPE  160  187
        clus
vv       TET3 MUTATED TET3 WILD-TYPE
  FEMALE           10            160
  MALE             10            187
[1] 2 2
[1] FALSE
D294V8, binary
                cls
clus               0   1
  TET3 MUTATED    16   1
  TET3 WILD-TYPE 284   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     16    1
  TET3 WILD-TYPE  284    7
     clus
vv    TET3 MUTATED TET3 WILD-TYPE
  NO            16            284
  YES            1              7
[1] 2 2
[1] FALSE
D294V9, binary
                cls
clus               0   1
  TET3 MUTATED    19   1
  TET3 WILD-TYPE 295  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     19    1
  TET3 WILD-TYPE  295   47
                               clus
vv                              TET3 MUTATED TET3 WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TET3 MUTATED    13   0   1   4
  TET3 WILD-TYPE 246   3  21  17
D294V10, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            1             21
  RX            4             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"
D294V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TET3 MUTATED                                  0     3
  TET3 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TET3 MUTATED                           1     9
  TET3 WILD-TYPE                        18   167
D294V12, multiclass
                                  clus
vv                                 TET3 MUTATED TET3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       9            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(295) Variable = TOB1 MUTATION ANALYSIS
D295V1, survival
                sevent
clus2              0   1
  TOB1 MUTATED     6   0
  TOB1 WILD-TYPE 271  78
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            349 
  TOB1 MUTATED TOB1 WILD-TYPE 
             0             78 
$`TOB1 MUTATED`
TCGA-G4-6310 TCGA-G4-6586 TCGA-A6-6780 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5863 
       63.62        35.80        20.12        15.62       124.27        15.02 

$`TOB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TOB1 MUTATED TOB1 WILD-TYPE 
         15.02           0.00 
  TOB1 MUTATED TOB1 WILD-TYPE 
        124.27         148.01 
  TOB1 MUTATED TOB1 WILD-TYPE 
         27.96          22.06 
[1] "15.0 - 124.3 (28.0)" "0.0 - 148.0 (22.1)" 
[1] "hr="     "9400000"
D295V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOB1 MUTATED         1        0        0         2         0         0
  TOB1 WILD-TYPE      63        1       26       106         8         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        18          6         42         32       35        12
                vv
clus             STAGE IVB
  TOB1 MUTATED           0
  TOB1 WILD-TYPE         1
D295V3, multiclass
            clus
vv           TOB1 MUTATED TOB1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TOB1 MUTATED     0   1   4   1
  TOB1 WILD-TYPE   9  66 245  40
D295V4, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            1             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
  TOB1 MUTATED     3   2   1
  TOB1 WILD-TYPE 217  79  65
D295V5, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  N0            3            217
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V6, binary
                cls
clus               0   1
  TOB1 MUTATED     4   0
  TOB1 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      4    0
  TOB1 WILD-TYPE  281   48
   clus
vv  TOB1 MUTATED TOB1 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D295V7, binary
                cls
clus               0   1
  TOB1 MUTATED     4   2
  TOB1 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      4    2
  TOB1 WILD-TYPE  166  195
        clus
vv       TOB1 MUTATED TOB1 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D295V8, binary
                cls
clus               0   1
  TOB1 MUTATED     4   1
  TOB1 WILD-TYPE 296   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      4    1
  TOB1 WILD-TYPE  296    7
     clus
vv    TOB1 MUTATED TOB1 WILD-TYPE
  NO             4            296
  YES            1              7
[1] 2 2
[1] FALSE
D295V9, binary
                cls
clus               0   1
  TOB1 MUTATED     2   4
  TOB1 WILD-TYPE 312  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      2    4
  TOB1 WILD-TYPE  312   44
                               clus
vv                              TOB1 MUTATED TOB1 WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TOB1 MUTATED     3   0   0   2
  TOB1 WILD-TYPE 256   3  22  19
D295V10, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            2             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"
D295V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOB1 MUTATED                                  0     0
  TOB1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TOB1 MUTATED                           0     6
  TOB1 WILD-TYPE                        19   170
D295V12, multiclass
                                  clus
vv                                 TOB1 MUTATED TOB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = GOLPH3L MUTATION ANALYSIS
D296V1, survival
                   sevent
clus2                 0   1
  GOLPH3L MUTATED     2   3
  GOLPH3L WILD-TYPE 275  75
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                5               350 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                3                75 
$`GOLPH3L MUTATED`
TCGA-AA-3529 TCGA-AY-6386 TCGA-AZ-4315 TCGA-DM-A1D4 TCGA-G4-6303 
        0.00        17.82        58.39        92.75        65.85 

$`GOLPH3L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02         9.07        19.07        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                0                 0 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
            92.75            148.01 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
           58.390            22.045 
[1] "0.0 - 92.8 (58.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D296V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLPH3L MUTATED         0        0        0         2         0         0
  GOLPH3L WILD-TYPE      64        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLPH3L MUTATED           0          0          1          1        1
  GOLPH3L WILD-TYPE        18          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  GOLPH3L MUTATED           0         0
  GOLPH3L WILD-TYPE        12         1
D296V3, multiclass
            clus
vv           GOLPH3L MUTATED GOLPH3L WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  GOLPH3L MUTATED     0   0   5   0
  GOLPH3L WILD-TYPE   9  67 244  41
D296V4, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  GOLPH3L MUTATED     2   2   1
  GOLPH3L WILD-TYPE 218  79  65
D296V5, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  N0               2               218
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V6, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     4   1
  GOLPH3L WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      4    1
  GOLPH3L WILD-TYPE  281   47
   clus
vv  GOLPH3L MUTATED GOLPH3L WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D296V7, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     3   2
  GOLPH3L WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      3    2
  GOLPH3L WILD-TYPE  167  195
        clus
vv       GOLPH3L MUTATED GOLPH3L WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D296V8, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     3   0
  GOLPH3L WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      3    0
  GOLPH3L WILD-TYPE  297    8
     clus
vv    GOLPH3L MUTATED GOLPH3L WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D296V9, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     5   0
  GOLPH3L WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      5    0
  GOLPH3L WILD-TYPE  309   48
                               clus
vv                              GOLPH3L MUTATED GOLPH3L WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GOLPH3L MUTATED     4   0   0   0
  GOLPH3L WILD-TYPE 255   3  22  21
D296V10, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D296V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLPH3L MUTATED                                  0     0
  GOLPH3L WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GOLPH3L MUTATED                           1     3
  GOLPH3L WILD-TYPE                        18   173
D296V12, multiclass
                                  clus
vv                                 GOLPH3L MUTATED GOLPH3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = TSHR MUTATION ANALYSIS
D297V1, survival
                sevent
clus2              0   1
  TSHR MUTATED    30  14
  TSHR WILD-TYPE 247  64
  TSHR MUTATED TSHR WILD-TYPE 
            44            311 
  TSHR MUTATED TSHR WILD-TYPE 
            14             64 
$`TSHR MUTATED`
TCGA-AA-3516 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.02        49.08         5.88        26.17        91.79        79.69 
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3947 
       22.06         8.38        29.95        78.08         6.97        33.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02K TCGA-AD-6890 TCGA-AY-6386 
       34.98        38.07         1.02        14.01        24.53        17.82 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6717 
       58.39        62.79        49.41         6.77        29.56        12.76 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-5538 TCGA-D5-6536 TCGA-D5-6541 
       17.03        29.03        11.01        54.61        17.85        15.58 
TCGA-D5-6926 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A282 TCGA-DM-A28C 
        9.04        12.00        10.26        38.20       139.17        81.37 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      117.07        31.96        47.87        44.68        55.04        85.48 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

$`TSHR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-A6-2671 
      100.01         1.94        63.62        22.09        35.80        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
        5.13        22.36        88.21        12.10         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-D5-5539 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-D5-6537 
       20.19        18.25        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38       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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
      135.65       119.93        35.97        60.79        98.24         8.61 
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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 
       74.56        65.85        53.62        61.91        36.00 

  TSHR MUTATED TSHR WILD-TYPE 
          1.02           0.00 
  TSHR MUTATED TSHR WILD-TYPE 
        139.17         148.01 
  TSHR MUTATED TSHR WILD-TYPE 
        29.755         21.990 
[1] "1.0 - 139.2 (29.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D297V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSHR MUTATED         4        1        5        14         2         0
  TSHR WILD-TYPE      60        0       21        94         6         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        16          6         37         30       33        11
                vv
clus             STAGE IVB
  TSHR MUTATED           0
  TSHR WILD-TYPE         1
D297V3, multiclass
            clus
vv           TSHR MUTATED TSHR WILD-TYPE
  STAGE I               4             60
  STAGE IA              1              0
  STAGE II              5             21
  STAGE IIA            14             94
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            7             37
  STAGE IIIC            3             30
  STAGE IV              2             33
  STAGE IVA             1             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
  TSHR MUTATED     1   6  30   6
  TSHR WILD-TYPE   8  61 219  35
D297V4, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  T1            1              8
  T2            6             61
  T3           30            219
  T4            6             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
  TSHR MUTATED    28  10   6
  TSHR WILD-TYPE 192  71  60
D297V5, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  N0           28            192
  N1           10             71
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V6, binary
                cls
clus               0   1
  TSHR MUTATED    34   3
  TSHR WILD-TYPE 251  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     34    3
  TSHR WILD-TYPE  251   45
   clus
vv  TSHR MUTATED TSHR WILD-TYPE
  0           34            251
  1            3             45
[1] 2 2
[1] FALSE
D297V7, binary
                cls
clus               0   1
  TSHR MUTATED    24  20
  TSHR WILD-TYPE 146 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     24   20
  TSHR WILD-TYPE  146  177
        clus
vv       TSHR MUTATED TSHR WILD-TYPE
  FEMALE           24            146
  MALE             20            177
[1] 2 2
[1] FALSE
D297V8, binary
                cls
clus               0   1
  TSHR MUTATED    37   1
  TSHR WILD-TYPE 263   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     37    1
  TSHR WILD-TYPE  263    7
     clus
vv    TSHR MUTATED TSHR WILD-TYPE
  NO            37            263
  YES            1              7
[1] 2 2
[1] FALSE
D297V9, binary
                cls
clus               0   1
  TSHR MUTATED    37   6
  TSHR WILD-TYPE 277  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     37    6
  TSHR WILD-TYPE  277   42
                               clus
vv                              TSHR MUTATED TSHR WILD-TYPE
  COLON ADENOCARCINOMA                    37            277
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TSHR MUTATED    29   0   1   2
  TSHR WILD-TYPE 230   3  21  19
D297V10, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  R0           29            230
  R1            0              3
  R2            1             21
  RX            2             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"
D297V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSHR MUTATED                                  0     1
  TSHR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSHR MUTATED                           4    30
  TSHR WILD-TYPE                        15   146
D297V12, multiclass
                                  clus
vv                                 TSHR MUTATED TSHR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      30            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(298) Variable = C14ORF102 MUTATION ANALYSIS
D298V1, survival
                     sevent
clus2                   0   1
  C14ORF102 MUTATED    12   5
  C14ORF102 WILD-TYPE 265  73
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 17                 338 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                  5                  73 
$`C14ORF102 MUTATED`
TCGA-AA-3516 TCGA-G4-6310 TCGA-A6-5661 TCGA-A6-5664 TCGA-AA-3663 TCGA-AA-3664 
       13.02        63.62        33.53        22.09         6.97        54.02 
TCGA-AA-3815 TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 
       33.04        18.05        34.98        58.39        49.41        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6537 TCGA-F4-6459 
       12.76        10.06        14.04         4.80         8.61 

$`C14ORF102 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        78.08         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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              22.075 
[1] "4.8 - 63.6 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D298V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF102 MUTATED         1        0        3         6         1         0
  C14ORF102 WILD-TYPE      63        1       23       102         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF102 MUTATED           1          0          4          1        0
  C14ORF102 WILD-TYPE        17          6         40         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF102 MUTATED           0         0
  C14ORF102 WILD-TYPE        12         1
D298V3, multiclass
            clus
vv           C14ORF102 MUTATED C14ORF102 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   3                  23
  STAGE IIA                  6                 102
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  1                  17
  STAGE IIIA                 0                   6
  STAGE IIIB                 4                  40
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C14ORF102 MUTATED     0   1  13   3
  C14ORF102 WILD-TYPE   9  66 236  38
D298V4, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                13                 236
  T4                 3                  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
  C14ORF102 MUTATED    11   3   3
  C14ORF102 WILD-TYPE 209  78  63
D298V5, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  N0                11                 209
  N1                 3                  78
  N2                 3                  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"
D298V6, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    14   0
  C14ORF102 WILD-TYPE 271  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     14    0
  C14ORF102 WILD-TYPE  271   48
   clus
vv  C14ORF102 MUTATED C14ORF102 WILD-TYPE
  0                14                 271
  1                 0                  48
[1] 2 2
[1] FALSE
D298V7, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED     8   9
  C14ORF102 WILD-TYPE 162 188
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED      8    9
  C14ORF102 WILD-TYPE  162  188
        clus
vv       C14ORF102 MUTATED C14ORF102 WILD-TYPE
  FEMALE                 8                 162
  MALE                   9                 188
[1] 2 2
[1] FALSE
D298V8, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    16   1
  C14ORF102 WILD-TYPE 284   7
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     16    1
  C14ORF102 WILD-TYPE  284    7
     clus
vv    C14ORF102 MUTATED C14ORF102 WILD-TYPE
  NO                 16                 284
  YES                 1                   7
[1] 2 2
[1] FALSE
D298V9, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    14   3
  C14ORF102 WILD-TYPE 300  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     14    3
  C14ORF102 WILD-TYPE  300   45
                               clus
vv                              C14ORF102 MUTATED C14ORF102 WILD-TYPE
  COLON ADENOCARCINOMA                         14                 300
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF102 MUTATED    11   0   0   3
  C14ORF102 WILD-TYPE 248   3  22  18
D298V10, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  R0                11                 248
  R1                 0                   3
  R2                 0                  22
  RX                 3                  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"
D298V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF102 MUTATED                                  0     3
  C14ORF102 WILD-TYPE                                1     7
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF102 MUTATED                           2     6
  C14ORF102 WILD-TYPE                        17   170
D298V12, multiclass
                                  clus
vv                                 C14ORF102 MUTATED C14ORF102 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            3                   7
  BLACK OR AFRICAN AMERICAN                        2                  17
  WHITE                                            6                 170
[1] 4 2
[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 = EXOC4 MUTATION ANALYSIS
D299V1, survival
                 sevent
clus2               0   1
  EXOC4 MUTATED    14   3
  EXOC4 WILD-TYPE 263  75
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             17             338 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              3              75 
$`EXOC4 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6780 
       19.04        25.08        79.69        33.53         8.38        20.12 
TCGA-AA-3845 TCGA-AA-3854 TCGA-AA-3864 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-4948 
        0.00        36.03        53.00        58.39         6.77       148.01 
TCGA-D5-6540 TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A1HB 
       16.14        14.30       119.70         7.50       135.65 

$`EXOC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  EXOC4 MUTATED EXOC4 WILD-TYPE 
              0               0 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         148.01          140.38 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         25.080          22.045 
[1] "0.0 - 148.0 (25.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.9"
D299V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXOC4 MUTATED         4        0        1         7         0         0
  EXOC4 WILD-TYPE      60        1       25       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXOC4 MUTATED           2          0          2          1        1         0
  EXOC4 WILD-TYPE        16          6         42         32       34        12
                 vv
clus              STAGE IVB
  EXOC4 MUTATED           0
  EXOC4 WILD-TYPE         1
D299V3, multiclass
            clus
vv           EXOC4 MUTATED EXOC4 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  EXOC4 MUTATED     0   4  14   0
  EXOC4 WILD-TYPE   9  63 235  41
D299V4, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            14             235
  T4             0              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
  EXOC4 MUTATED    13   3   2
  EXOC4 WILD-TYPE 207  78  64
D299V5, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  N0            13             207
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V6, binary
                 cls
clus                0   1
  EXOC4 MUTATED    15   1
  EXOC4 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     15    1
  EXOC4 WILD-TYPE  270   47
   clus
vv  EXOC4 MUTATED EXOC4 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D299V7, binary
                 cls
clus                0   1
  EXOC4 MUTATED     6  12
  EXOC4 WILD-TYPE 164 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      6   12
  EXOC4 WILD-TYPE  164  185
        clus
vv       EXOC4 MUTATED EXOC4 WILD-TYPE
  FEMALE             6             164
  MALE              12             185
[1] 2 2
[1] FALSE
D299V8, binary
                 cls
clus                0   1
  EXOC4 MUTATED    12   1
  EXOC4 WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     12    1
  EXOC4 WILD-TYPE  288    7
     clus
vv    EXOC4 MUTATED EXOC4 WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D299V9, binary
                 cls
clus                0   1
  EXOC4 MUTATED    14   3
  EXOC4 WILD-TYPE 300  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     14    3
  EXOC4 WILD-TYPE  300   45
                               clus
vv                              EXOC4 MUTATED EXOC4 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EXOC4 MUTATED    11   0   1   0
  EXOC4 WILD-TYPE 248   3  21  21
D299V10, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             0              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"
D299V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXOC4 MUTATED                                  0     0
  EXOC4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EXOC4 MUTATED                           2    11
  EXOC4 WILD-TYPE                        17   165
D299V12, multiclass
                                  clus
vv                                 EXOC4 MUTATED EXOC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       11             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(300) Variable = RPS6KA3 MUTATION ANALYSIS
D300V1, survival
                   sevent
clus2                 0   1
  RPS6KA3 MUTATED    11   2
  RPS6KA3 WILD-TYPE 266  76
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               13               342 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
                2                76 
$`RPS6KA3 MUTATED`
TCGA-AA-3662 TCGA-AA-3950 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3854 TCGA-AA-3877 
        6.05        24.00         3.02        63.98        36.03        31.00 
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 
      119.93 

$`RPS6KA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
             3.02              0.00 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
           119.93            148.01 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
           24.000            22.045 
[1] "3.0 - 119.9 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D300V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPS6KA3 MUTATED         3        0        3         2         1         0
  RPS6KA3 WILD-TYPE      61        1       23       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA3 MUTATED           0          0          1          1        1
  RPS6KA3 WILD-TYPE        18          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KA3 MUTATED           0         0
  RPS6KA3 WILD-TYPE        12         1
D300V3, multiclass
            clus
vv           RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  RPS6KA3 MUTATED     1   2   7   3
  RPS6KA3 WILD-TYPE   8  65 242  38
D300V4, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               7               242
  T4               3                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
  RPS6KA3 MUTATED    10   0   3
  RPS6KA3 WILD-TYPE 210  81  63
D300V5, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  N0              10               210
  N1               0                81
  N2               3                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"
D300V6, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    11   1
  RPS6KA3 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     11    1
  RPS6KA3 WILD-TYPE  274   47
   clus
vv  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  0              11               274
  1               1                47
[1] 2 2
[1] FALSE
D300V7, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    12   1
  RPS6KA3 WILD-TYPE 158 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     12    1
  RPS6KA3 WILD-TYPE  158  196
        clus
vv       RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  FEMALE              12               158
  MALE                 1               196
[1] 2 2
[1] FALSE
D300V8, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    11   0
  RPS6KA3 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     11    0
  RPS6KA3 WILD-TYPE  289    8
     clus
vv    RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D300V9, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED     8   5
  RPS6KA3 WILD-TYPE 306  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED      8    5
  RPS6KA3 WILD-TYPE  306   43
                               clus
vv                              RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RPS6KA3 MUTATED     9   0   1   1
  RPS6KA3 WILD-TYPE 250   3  21  20
D300V10, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               1                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"
D300V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KA3 MUTATED                                  0     0
  RPS6KA3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA3 MUTATED                           0     6
  RPS6KA3 WILD-TYPE                        19   170
D300V12, multiclass
                                  clus
vv                                 RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = ZNF438 MUTATION ANALYSIS
D301V1, survival
                  sevent
clus2                0   1
  ZNF438 MUTATED     7   3
  ZNF438 WILD-TYPE 270  75
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              10              345 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
               3               75 
$`ZNF438 MUTATED`
TCGA-G4-6588 TCGA-A6-2671 TCGA-A6-6137 TCGA-AA-3845 TCGA-AA-A00N TCGA-CA-6717 
       26.17        43.76        27.09         0.00         4.01        12.76 
TCGA-CK-4952 TCGA-CM-6167 TCGA-D5-6541 TCGA-D5-6927 
       15.62        14.99        15.58         9.44 

$`ZNF438 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF438 MUTATED ZNF438 WILD-TYPE 
               0                0 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
           43.76           148.01 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
          15.285           22.090 
[1] "0.0 - 43.8 (15.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D301V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF438 MUTATED         1        0        0         5         1         0
  ZNF438 WILD-TYPE      63        1       26       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF438 MUTATED           1          0          1          2        1
  ZNF438 WILD-TYPE        17          6         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF438 MUTATED           0         0
  ZNF438 WILD-TYPE        12         1
D301V3, multiclass
            clus
vv           ZNF438 MUTATED ZNF438 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF438 MUTATED     0   1   9   2
  ZNF438 WILD-TYPE   9  66 240  39
D301V4, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              9              240
  T4              2               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
  ZNF438 MUTATED     7   1   4
  ZNF438 WILD-TYPE 213  80  62
D301V5, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V6, binary
                  cls
clus                 0   1
  ZNF438 MUTATED    10   1
  ZNF438 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED     10    1
  ZNF438 WILD-TYPE  275   47
   clus
vv  ZNF438 MUTATED ZNF438 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D301V7, binary
                  cls
clus                 0   1
  ZNF438 MUTATED     4   8
  ZNF438 WILD-TYPE 166 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED      4    8
  ZNF438 WILD-TYPE  166  189
        clus
vv       ZNF438 MUTATED ZNF438 WILD-TYPE
  FEMALE              4              166
  MALE                8              189
[1] 2 2
[1] FALSE
D301V8, binary
                  cls
clus                 0   1
  ZNF438 MUTATED     7   0
  ZNF438 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED      7    0
  ZNF438 WILD-TYPE  293    8
     clus
vv    ZNF438 MUTATED ZNF438 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D301V9, binary
                  cls
clus                 0   1
  ZNF438 MUTATED     9   3
  ZNF438 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED      9    3
  ZNF438 WILD-TYPE  305   45
                               clus
vv                              ZNF438 MUTATED ZNF438 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF438 MUTATED     8   0   0   3
  ZNF438 WILD-TYPE 251   3  22  18
D301V10, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              3               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"
D301V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF438 MUTATED                                  0     1
  ZNF438 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF438 MUTATED                           1     7
  ZNF438 WILD-TYPE                        18   169
D301V12, multiclass
                                  clus
vv                                 ZNF438 MUTATED ZNF438 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = MST4 MUTATION ANALYSIS
D302V1, survival
                sevent
clus2              0   1
  MST4 MUTATED     5   2
  MST4 WILD-TYPE 272  76
  MST4 MUTATED MST4 WILD-TYPE 
             7            348 
  MST4 MUTATED MST4 WILD-TYPE 
             2             76 
$`MST4 MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-A00N TCGA-AU-6004 
       14.53         1.02        33.53        23.61         4.01        27.09 
TCGA-DM-A28K 
       98.24 

$`MST4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        29.19        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MST4 MUTATED MST4 WILD-TYPE 
          1.02           0.00 
  MST4 MUTATED MST4 WILD-TYPE 
         98.24         148.01 
  MST4 MUTATED MST4 WILD-TYPE 
        23.610         22.045 
[1] "1.0 - 98.2 (23.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D302V2, continuous
                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      63        1       25       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MST4 MUTATED           0          0          0          0        0         1
  MST4 WILD-TYPE        18          6         44         33       35        11
                vv
clus             STAGE IVB
  MST4 MUTATED           0
  MST4 WILD-TYPE         1
D302V3, multiclass
            clus
vv           MST4 MUTATED MST4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  MST4 MUTATED     0   1   5   1
  MST4 WILD-TYPE   9  66 244  40
D302V4, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            1             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
  MST4 MUTATED     6   0   1
  MST4 WILD-TYPE 214  81  65
D302V5, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V6, binary
                cls
clus               0   1
  MST4 MUTATED     6   1
  MST4 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      6    1
  MST4 WILD-TYPE  279   47
   clus
vv  MST4 MUTATED MST4 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D302V7, binary
                cls
clus               0   1
  MST4 MUTATED     3   4
  MST4 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      3    4
  MST4 WILD-TYPE  167  193
        clus
vv       MST4 MUTATED MST4 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D302V8, binary
                cls
clus               0   1
  MST4 MUTATED     3   0
  MST4 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      3    0
  MST4 WILD-TYPE  297    8
     clus
vv    MST4 MUTATED MST4 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D302V9, binary
                cls
clus               0   1
  MST4 MUTATED     5   2
  MST4 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      5    2
  MST4 WILD-TYPE  309   46
                               clus
vv                              MST4 MUTATED MST4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MST4 MUTATED     4   0   0   0
  MST4 WILD-TYPE 255   3  22  21
D302V10, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D302V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MST4 MUTATED                                  0     0
  MST4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MST4 MUTATED                           1     4
  MST4 WILD-TYPE                        18   172
D302V12, multiclass
                                  clus
vv                                 MST4 MUTATED MST4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = RIF1 MUTATION ANALYSIS
D303V1, survival
                sevent
clus2              0   1
  RIF1 MUTATED    28   6
  RIF1 WILD-TYPE 249  72
  RIF1 MUTATED RIF1 WILD-TYPE 
            34            321 
  RIF1 MUTATED RIF1 WILD-TYPE 
             6             72 
$`RIF1 MUTATED`
TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-2672 
        6.05        19.04        19.04        22.09        79.69        46.65 
TCGA-A6-3807 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3655 
       34.65        22.06        20.12        19.66        63.98        61.02 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P 
       33.04         1.02        18.05         4.01        34.98        38.07 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6718 
       33.01         0.20        58.39        29.56        12.59        10.06 
TCGA-CK-4952 TCGA-CM-5868 TCGA-CM-6167 TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6927 
       15.62        17.03        14.99        25.48        15.58         9.44 
TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6304 
        6.18        33.67       133.18        53.62 

$`RIF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        35.80        26.17        91.79 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 
       43.76        43.76        42.90        42.28        16.57        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.95        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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        54.61        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RIF1 MUTATED RIF1 WILD-TYPE 
           0.2            0.0 
  RIF1 MUTATED RIF1 WILD-TYPE 
        133.18         148.01 
  RIF1 MUTATED RIF1 WILD-TYPE 
         21.09          22.09 
[1] "0.2 - 133.2 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D303V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RIF1 MUTATED         3        0        3         9         3         0
  RIF1 WILD-TYPE      61        1       23        99         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIF1 MUTATED           4          0          2          5        2         2
  RIF1 WILD-TYPE        14          6         42         28       33        10
                vv
clus             STAGE IVB
  RIF1 MUTATED           0
  RIF1 WILD-TYPE         1
D303V3, multiclass
            clus
vv           RIF1 MUTATED RIF1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             9             99
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             4             14
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            5             28
  STAGE IV              2             33
  STAGE IVA             2             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
  RIF1 MUTATED     1   4  21   9
  RIF1 WILD-TYPE   8  63 228  32
D303V4, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  T1            1              8
  T2            4             63
  T3           21            228
  T4            9             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
  RIF1 MUTATED    20   9   6
  RIF1 WILD-TYPE 200  72  60
D303V5, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  N0           20            200
  N1            9             72
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V6, binary
                cls
clus               0   1
  RIF1 MUTATED    26   4
  RIF1 WILD-TYPE 259  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     26    4
  RIF1 WILD-TYPE  259   44
   clus
vv  RIF1 MUTATED RIF1 WILD-TYPE
  0           26            259
  1            4             44
[1] 2 2
[1] FALSE
D303V7, binary
                cls
clus               0   1
  RIF1 MUTATED    19  16
  RIF1 WILD-TYPE 151 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     19   16
  RIF1 WILD-TYPE  151  181
        clus
vv       RIF1 MUTATED RIF1 WILD-TYPE
  FEMALE           19            151
  MALE             16            181
[1] 2 2
[1] FALSE
D303V8, binary
                cls
clus               0   1
  RIF1 MUTATED    30   1
  RIF1 WILD-TYPE 270   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     30    1
  RIF1 WILD-TYPE  270    7
     clus
vv    RIF1 MUTATED RIF1 WILD-TYPE
  NO            30            270
  YES            1              7
[1] 2 2
[1] FALSE
D303V9, binary
                cls
clus               0   1
  RIF1 MUTATED    28   7
  RIF1 WILD-TYPE 286  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     28    7
  RIF1 WILD-TYPE  286   41
                               clus
vv                              RIF1 MUTATED RIF1 WILD-TYPE
  COLON ADENOCARCINOMA                    28            286
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RIF1 MUTATED    29   0   2   2
  RIF1 WILD-TYPE 230   3  20  19
D303V10, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  R0           29            230
  R1            0              3
  R2            2             20
  RX            2             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"
D303V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIF1 MUTATED                                  0     2
  RIF1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RIF1 MUTATED                           2    19
  RIF1 WILD-TYPE                        17   157
D303V12, multiclass
                                  clus
vv                                 RIF1 MUTATED RIF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      19            157
[1] 4 2
[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 = INPP1 MUTATION ANALYSIS
D304V1, survival
                 sevent
clus2               0   1
  INPP1 MUTATED     4   2
  INPP1 WILD-TYPE 273  76
  INPP1 MUTATED INPP1 WILD-TYPE 
              6             349 
  INPP1 MUTATED INPP1 WILD-TYPE 
              2              76 
$`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        14.04         6.18 

$`INPP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  INPP1 MUTATED INPP1 WILD-TYPE 
           6.18            0.00 
  INPP1 MUTATED INPP1 WILD-TYPE 
          85.05          148.01 
  INPP1 MUTATED INPP1 WILD-TYPE 
         19.085          22.090 
[1] "6.2 - 85.0 (19.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D304V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INPP1 MUTATED         4        0        1         1         1         0
  INPP1 WILD-TYPE      60        1       25       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INPP1 MUTATED           0          0          0          0        0         0
  INPP1 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  INPP1 MUTATED           0
  INPP1 WILD-TYPE         1
D304V3, multiclass
            clus
vv           INPP1 MUTATED INPP1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  INPP1 MUTATED     2   2   2   1
  INPP1 WILD-TYPE   7  65 247  40
D304V4, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  T1             2               7
  T2             2              65
  T3             2             247
  T4             1              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
  INPP1 MUTATED     7   0   0
  INPP1 WILD-TYPE 213  81  66
D304V5, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V6, binary
                 cls
clus                0   1
  INPP1 MUTATED     6   0
  INPP1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      6    0
  INPP1 WILD-TYPE  279   48
   clus
vv  INPP1 MUTATED INPP1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D304V7, binary
                 cls
clus                0   1
  INPP1 MUTATED     4   3
  INPP1 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      4    3
  INPP1 WILD-TYPE  166  194
        clus
vv       INPP1 MUTATED INPP1 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D304V8, binary
                 cls
clus                0   1
  INPP1 MUTATED     6   0
  INPP1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      6    0
  INPP1 WILD-TYPE  294    8
     clus
vv    INPP1 MUTATED INPP1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D304V9, binary
                 cls
clus                0   1
  INPP1 MUTATED     7   0
  INPP1 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      7    0
  INPP1 WILD-TYPE  307   48
                               clus
vv                              INPP1 MUTATED INPP1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INPP1 MUTATED     5   0   0   2
  INPP1 WILD-TYPE 254   3  22  19
D304V10, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D304V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INPP1 MUTATED                                  0     0
  INPP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INPP1 MUTATED                           0     4
  INPP1 WILD-TYPE                        19   172
D304V12, multiclass
                                  clus
vv                                 INPP1 MUTATED INPP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SAPS2 MUTATION ANALYSIS
D305V1, survival
                 sevent
clus2               0   1
  SAPS2 MUTATED     8   3
  SAPS2 WILD-TYPE 269  75
  SAPS2 MUTATED SAPS2 WILD-TYPE 
             11             344 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
              3              75 
$`SAPS2 MUTATED`
TCGA-AA-3713 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3966 TCGA-AD-6889 TCGA-AZ-6598 
       19.04         1.02         6.97         2.01        83.24        49.41 
TCGA-CM-4746 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6930 TCGA-F4-6570 
       37.02        14.04        12.95        13.35         6.18 

$`SAPS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SAPS2 MUTATED SAPS2 WILD-TYPE 
           1.02            0.00 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
          83.24          148.01 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
         13.350          22.225 
[1] "1.0 - 83.2 (13.3)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.5"
D305V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAPS2 MUTATED         2        0        2         6         0         0
  SAPS2 WILD-TYPE      62        1       24       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAPS2 MUTATED           0          0          0          0        1         0
  SAPS2 WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  SAPS2 MUTATED           0
  SAPS2 WILD-TYPE         1
D305V3, multiclass
            clus
vv           SAPS2 MUTATED SAPS2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  SAPS2 MUTATED     0   2   9   0
  SAPS2 WILD-TYPE   9  65 240  41
D305V4, multiclass
    clus
vv   SAPS2 MUTATED SAPS2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             0              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
  SAPS2 MUTATED    11   0   0
  SAPS2 WILD-TYPE 209  81  66
D305V5, multiclass
    clus
vv   SAPS2 MUTATED SAPS2 WILD-TYPE
  N0            11             209
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V6, binary
                 cls
clus                0   1
  SAPS2 MUTATED     9   1
  SAPS2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED      9    1
  SAPS2 WILD-TYPE  276   47
   clus
vv  SAPS2 MUTATED SAPS2 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D305V7, binary
                 cls
clus                0   1
  SAPS2 MUTATED     5   6
  SAPS2 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED      5    6
  SAPS2 WILD-TYPE  165  191
        clus
vv       SAPS2 MUTATED SAPS2 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D305V8, binary
                 cls
clus                0   1
  SAPS2 MUTATED     8   1
  SAPS2 WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED      8    1
  SAPS2 WILD-TYPE  292    7
     clus
vv    SAPS2 MUTATED SAPS2 WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D305V9, binary
                 cls
clus                0   1
  SAPS2 MUTATED     9   2
  SAPS2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED      9    2
  SAPS2 WILD-TYPE  305   46
                               clus
vv                              SAPS2 MUTATED SAPS2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SAPS2 MUTATED     8   0   1   0
  SAPS2 WILD-TYPE 251   3  21  21
D305V10, multiclass
    clus
vv   SAPS2 MUTATED SAPS2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             0              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"
D305V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAPS2 MUTATED                                  0     1
  SAPS2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SAPS2 MUTATED                           1     5
  SAPS2 WILD-TYPE                        18   171
D305V12, multiclass
                                  clus
vv                                 SAPS2 MUTATED SAPS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = CEP135 MUTATION ANALYSIS
D306V1, survival
                  sevent
clus2                0   1
  CEP135 MUTATED    13   6
  CEP135 WILD-TYPE 264  72
  CEP135 MUTATED CEP135 WILD-TYPE 
              19              336 
  CEP135 MUTATED CEP135 WILD-TYPE 
               6               72 
$`CEP135 MUTATED`
TCGA-AA-3554 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-6782 TCGA-AA-3811 
       17.95       100.01        35.80        79.69        20.28        10.06 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 
       25.02        30.02         4.01        58.39        12.59        12.76 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-6538 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
       11.08        10.06        17.13        12.59        44.32       135.65 
TCGA-F4-6570 
        6.18 

$`CEP135 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CEP135 MUTATED CEP135 WILD-TYPE 
            4.01             0.00 
  CEP135 MUTATED CEP135 WILD-TYPE 
          135.65           148.01 
  CEP135 MUTATED CEP135 WILD-TYPE 
           17.95            22.09 
[1] "4.0 - 135.7 (17.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D306V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEP135 MUTATED         2        0        1         9         3         0
  CEP135 WILD-TYPE      62        1       25        99         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP135 MUTATED           1          0          3          0        0
  CEP135 WILD-TYPE        17          6         41         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CEP135 MUTATED           0         0
  CEP135 WILD-TYPE        12         1
D306V3, multiclass
            clus
vv           CEP135 MUTATED CEP135 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               9               99
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CEP135 MUTATED     0   3  15   3
  CEP135 WILD-TYPE   9  64 234  38
D306V4, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             15              234
  T4              3               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
  CEP135 MUTATED    16   3   2
  CEP135 WILD-TYPE 204  78  64
D306V5, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  N0             16              204
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V6, binary
                  cls
clus                 0   1
  CEP135 MUTATED    17   0
  CEP135 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     17    0
  CEP135 WILD-TYPE  268   48
   clus
vv  CEP135 MUTATED CEP135 WILD-TYPE
  0             17              268
  1              0               48
[1] 2 2
[1] FALSE
D306V7, binary
                  cls
clus                 0   1
  CEP135 MUTATED     8  13
  CEP135 WILD-TYPE 162 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED      8   13
  CEP135 WILD-TYPE  162  184
        clus
vv       CEP135 MUTATED CEP135 WILD-TYPE
  FEMALE              8              162
  MALE               13              184
[1] 2 2
[1] FALSE
D306V8, binary
                  cls
clus                 0   1
  CEP135 MUTATED    15   0
  CEP135 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     15    0
  CEP135 WILD-TYPE  285    8
     clus
vv    CEP135 MUTATED CEP135 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D306V9, binary
                  cls
clus                 0   1
  CEP135 MUTATED    18   2
  CEP135 WILD-TYPE 296  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     18    2
  CEP135 WILD-TYPE  296   46
                               clus
vv                              CEP135 MUTATED CEP135 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CEP135 MUTATED    12   0   0   3
  CEP135 WILD-TYPE 247   3  22  18
D306V10, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              3               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"
D306V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEP135 MUTATED                                  0     2
  CEP135 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CEP135 MUTATED                           0    13
  CEP135 WILD-TYPE                        19   163
D306V12, multiclass
                                  clus
vv                                 CEP135 MUTATED CEP135 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        13              163
[1] 4 2
[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 = PPP2R1A MUTATION ANALYSIS
D307V1, survival
                   sevent
clus2                 0   1
  PPP2R1A MUTATED    12   2
  PPP2R1A WILD-TYPE 265  76
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               341 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                2                76 
$`PPP2R1A MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6653 TCGA-AA-3514 TCGA-AA-3663 TCGA-AA-3846 
      100.01        26.17        24.39         1.02         6.97        17.03 
TCGA-AA-A01R TCGA-AA-A02O TCGA-AD-5900 TCGA-AZ-5407 TCGA-CK-4952 TCGA-D5-6540 
       35.01         0.92        12.16        88.21        15.62        16.14 
TCGA-D5-6928 TCGA-G4-6626 
       11.64        46.75 

$`PPP2R1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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 
       55.04        85.48        61.91        36.00        13.78 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             0.92              0.00 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           100.01            148.01 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           16.585            22.090 
[1] "0.9 - 100.0 (16.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D307V2, continuous
                   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      59        1       23       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R1A MUTATED           1          0          0          1        0
  PPP2R1A WILD-TYPE        17          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R1A MUTATED           0         0
  PPP2R1A WILD-TYPE        12         1
D307V3, multiclass
            clus
vv           PPP2R1A MUTATED PPP2R1A WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  PPP2R1A MUTATED     1   4   8   1
  PPP2R1A WILD-TYPE   8  63 241  40
D307V4, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  T1               1                 8
  T2               4                63
  T3               8               241
  T4               1                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
  PPP2R1A MUTATED    12   0   2
  PPP2R1A WILD-TYPE 208  81  64
D307V5, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  N0              12               208
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V6, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    13   0
  PPP2R1A WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     13    0
  PPP2R1A WILD-TYPE  272   48
   clus
vv  PPP2R1A MUTATED PPP2R1A WILD-TYPE
  0              13               272
  1               0                48
[1] 2 2
[1] FALSE
D307V7, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED     5   9
  PPP2R1A WILD-TYPE 165 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      5    9
  PPP2R1A WILD-TYPE  165  188
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  FEMALE               5               165
  MALE                 9               188
[1] 2 2
[1] FALSE
D307V8, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    11   1
  PPP2R1A WILD-TYPE 289   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     11    1
  PPP2R1A WILD-TYPE  289    7
     clus
vv    PPP2R1A MUTATED PPP2R1A WILD-TYPE
  NO               11               289
  YES               1                 7
[1] 2 2
[1] FALSE
D307V9, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED     9   5
  PPP2R1A WILD-TYPE 305  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      9    5
  PPP2R1A WILD-TYPE  305   43
                               clus
vv                              PPP2R1A MUTATED PPP2R1A WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PPP2R1A MUTATED    10   0   0   1
  PPP2R1A WILD-TYPE 249   3  22  20
D307V10, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               1                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"
D307V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R1A MUTATED                                  0     0
  PPP2R1A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R1A MUTATED                           0     9
  PPP2R1A WILD-TYPE                        19   167
D307V12, multiclass
                                  clus
vv                                 PPP2R1A MUTATED PPP2R1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(308) Variable = RNF160 MUTATION ANALYSIS
D308V1, survival
                  sevent
clus2                0   1
  RNF160 MUTATED    13   3
  RNF160 WILD-TYPE 264  75
  RNF160 MUTATED RNF160 WILD-TYPE 
              16              339 
  RNF160 MUTATED RNF160 WILD-TYPE 
               3               75 
$`RNF160 MUTATED`
TCGA-AZ-4681 TCGA-A6-5657 TCGA-AA-3949 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00O 
      106.75        31.63        26.01        38.04         4.01        27.02 
TCGA-AA-A01R TCGA-AD-6965 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-6747 
       35.01        26.47        12.76        10.06       148.01        82.95 
TCGA-CM-5861 TCGA-DM-A1DB TCGA-G4-6293 TCGA-G4-6315 
       15.02        44.32       133.18        61.91 

$`RNF160 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50       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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RNF160 MUTATED RNF160 WILD-TYPE 
            4.01             0.00 
  RNF160 MUTATED RNF160 WILD-TYPE 
          148.01           140.38 
  RNF160 MUTATED RNF160 WILD-TYPE 
           33.32            21.99 
[1] "4.0 - 148.0 (33.3)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.9"
D308V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF160 MUTATED         0        0        0         7         1         0
  RNF160 WILD-TYPE      64        1       26       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF160 MUTATED           3          0          2          2        1
  RNF160 WILD-TYPE        15          6         42         31       34
                  vv
clus               STAGE IVA STAGE IVB
  RNF160 MUTATED           0         0
  RNF160 WILD-TYPE        12         1
D308V3, multiclass
            clus
vv           RNF160 MUTATED RNF160 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               15
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  RNF160 MUTATED     0   0  14   2
  RNF160 WILD-TYPE   9  67 235  39
D308V4, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             14              235
  T4              2               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
  RNF160 MUTATED     8   5   3
  RNF160 WILD-TYPE 212  76  63
D308V5, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  N0              8              212
  N1              5               76
  N2              3               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"
D308V6, binary
                  cls
clus                 0   1
  RNF160 MUTATED    14   1
  RNF160 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     14    1
  RNF160 WILD-TYPE  271   47
   clus
vv  RNF160 MUTATED RNF160 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D308V7, binary
                  cls
clus                 0   1
  RNF160 MUTATED     7   9
  RNF160 WILD-TYPE 163 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED      7    9
  RNF160 WILD-TYPE  163  188
        clus
vv       RNF160 MUTATED RNF160 WILD-TYPE
  FEMALE              7              163
  MALE                9              188
[1] 2 2
[1] FALSE
D308V8, binary
                  cls
clus                 0   1
  RNF160 MUTATED    13   1
  RNF160 WILD-TYPE 287   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     13    1
  RNF160 WILD-TYPE  287    7
     clus
vv    RNF160 MUTATED RNF160 WILD-TYPE
  NO              13              287
  YES              1                7
[1] 2 2
[1] FALSE
D308V9, binary
                  cls
clus                 0   1
  RNF160 MUTATED    12   4
  RNF160 WILD-TYPE 302  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     12    4
  RNF160 WILD-TYPE  302   44
                               clus
vv                              RNF160 MUTATED RNF160 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF160 MUTATED    11   1   0   3
  RNF160 WILD-TYPE 248   2  22  18
D308V10, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  R0             11              248
  R1              1                2
  R2              0               22
  RX              3               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"
D308V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF160 MUTATED                                  0     2
  RNF160 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF160 MUTATED                           1     8
  RNF160 WILD-TYPE                        18   168
D308V12, multiclass
                                  clus
vv                                 RNF160 MUTATED RNF160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = ECM2 MUTATION ANALYSIS
D309V1, survival
                sevent
clus2              0   1
  ECM2 MUTATED    13   3
  ECM2 WILD-TYPE 264  75
  ECM2 MUTATED ECM2 WILD-TYPE 
            16            339 
  ECM2 MUTATED ECM2 WILD-TYPE 
             3             75 
$`ECM2 MUTATED`
TCGA-AA-3713 TCGA-A6-3808 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3815 
       19.04        33.34        24.39        63.98        10.06        33.04 
TCGA-AA-A00N TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 
        4.01        14.50        27.09         0.20        58.39        88.21 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6164 
        6.77        12.76        13.02        29.03 

$`ECM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        34.65        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       27.42        26.47        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-6598 
       17.82         1.41         5.13        22.36        62.79        49.41 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ECM2 MUTATED ECM2 WILD-TYPE 
           0.2            0.0 
  ECM2 MUTATED ECM2 WILD-TYPE 
         88.21         148.01 
  ECM2 MUTATED ECM2 WILD-TYPE 
        21.715         22.060 
[1] "0.2 - 88.2 (21.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D309V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ECM2 MUTATED         4        0        1         7         2         0
  ECM2 WILD-TYPE      60        1       25       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ECM2 MUTATED           1          0          0          1        1         0
  ECM2 WILD-TYPE        17          6         44         32       34        12
                vv
clus             STAGE IVB
  ECM2 MUTATED           0
  ECM2 WILD-TYPE         1
D309V3, multiclass
            clus
vv           ECM2 MUTATED ECM2 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  ECM2 MUTATED     1   3  11   2
  ECM2 WILD-TYPE   8  64 238  39
D309V4, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  T1            1              8
  T2            3             64
  T3           11            238
  T4            2             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
  ECM2 MUTATED    15   0   2
  ECM2 WILD-TYPE 205  81  64
D309V5, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  N0           15            205
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V6, binary
                cls
clus               0   1
  ECM2 MUTATED    13   1
  ECM2 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     13    1
  ECM2 WILD-TYPE  272   47
   clus
vv  ECM2 MUTATED ECM2 WILD-TYPE
  0           13            272
  1            1             47
[1] 2 2
[1] FALSE
D309V7, binary
                cls
clus               0   1
  ECM2 MUTATED     7  10
  ECM2 WILD-TYPE 163 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED      7   10
  ECM2 WILD-TYPE  163  187
        clus
vv       ECM2 MUTATED ECM2 WILD-TYPE
  FEMALE            7            163
  MALE             10            187
[1] 2 2
[1] FALSE
D309V8, binary
                cls
clus               0   1
  ECM2 MUTATED    12   1
  ECM2 WILD-TYPE 288   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     12    1
  ECM2 WILD-TYPE  288    7
     clus
vv    ECM2 MUTATED ECM2 WILD-TYPE
  NO            12            288
  YES            1              7
[1] 2 2
[1] FALSE
D309V9, binary
                cls
clus               0   1
  ECM2 MUTATED    14   3
  ECM2 WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     14    3
  ECM2 WILD-TYPE  300   45
                               clus
vv                              ECM2 MUTATED ECM2 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ECM2 MUTATED    11   0   1   2
  ECM2 WILD-TYPE 248   3  21  19
D309V10, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            1             21
  RX            2             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"
D309V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ECM2 MUTATED                                  0     1
  ECM2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ECM2 MUTATED                           1    10
  ECM2 WILD-TYPE                        18   166
D309V12, multiclass
                                  clus
vv                                 ECM2 MUTATED ECM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(310) Variable = MSH2 MUTATION ANALYSIS
D310V1, survival
                sevent
clus2              0   1
  MSH2 MUTATED    24   8
  MSH2 WILD-TYPE 253  70
  MSH2 MUTATED MSH2 WILD-TYPE 
            32            323 
  MSH2 MUTATED MSH2 WILD-TYPE 
             8             70 
$`MSH2 MUTATED`
TCGA-AA-3496 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AA-3492 TCGA-AA-3968 
        1.02        25.08       106.75       100.01         3.02        21.99 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 
       25.02         4.01        34.98        83.24        14.50        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       21.44        17.82        58.39        49.41         6.77        12.10 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5348 TCGA-CM-6162 
        5.23        12.76        21.99        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        13.35       135.65       117.07        41.42 
TCGA-G4-6307 TCGA-G4-6315 
       55.04        61.91 

$`MSH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6608 TCGA-CK-5912 
       39.06        21.37        15.52        10.88         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       24.53         5.79        22.42        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.95        33.01         0.20         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       62.79        88.21        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-6718 
       12.36        12.39        12.59        12.59        12.20        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        36.00        13.78        46.75 

  MSH2 MUTATED MSH2 WILD-TYPE 
          1.02           0.00 
  MSH2 MUTATED MSH2 WILD-TYPE 
        135.65         148.01 
  MSH2 MUTATED MSH2 WILD-TYPE 
        22.485         22.060 
[1] "1.0 - 135.7 (22.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D310V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH2 MUTATED         5        0        4         8         2         0
  MSH2 WILD-TYPE      59        1       22       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH2 MUTATED           1          0          9          1        2         0
  MSH2 WILD-TYPE        17          6         35         32       33        12
                vv
clus             STAGE IVB
  MSH2 MUTATED           0
  MSH2 WILD-TYPE         1
D310V3, multiclass
            clus
vv           MSH2 MUTATED MSH2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            9             35
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  MSH2 MUTATED     0   6  23   4
  MSH2 WILD-TYPE   9  61 226  37
D310V4, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  T1            0              9
  T2            6             61
  T3           23            226
  T4            4             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
  MSH2 MUTATED    20  11   2
  MSH2 WILD-TYPE 200  70  64
D310V5, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  N0           20            200
  N1           11             70
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V6, binary
                cls
clus               0   1
  MSH2 MUTATED    26   2
  MSH2 WILD-TYPE 259  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     26    2
  MSH2 WILD-TYPE  259   46
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0           26            259
  1            2             46
[1] 2 2
[1] FALSE
D310V7, binary
                cls
clus               0   1
  MSH2 MUTATED    13  20
  MSH2 WILD-TYPE 157 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     13   20
  MSH2 WILD-TYPE  157  177
        clus
vv       MSH2 MUTATED MSH2 WILD-TYPE
  FEMALE           13            157
  MALE             20            177
[1] 2 2
[1] FALSE
D310V8, binary
                cls
clus               0   1
  MSH2 MUTATED    26   0
  MSH2 WILD-TYPE 274   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     26    0
  MSH2 WILD-TYPE  274    8
     clus
vv    MSH2 MUTATED MSH2 WILD-TYPE
  NO            26            274
  YES            0              8
[1] 2 2
[1] FALSE
D310V9, binary
                cls
clus               0   1
  MSH2 MUTATED    28   4
  MSH2 WILD-TYPE 286  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     28    4
  MSH2 WILD-TYPE  286   44
                               clus
vv                              MSH2 MUTATED MSH2 WILD-TYPE
  COLON ADENOCARCINOMA                    28            286
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH2 MUTATED    23   0   0   2
  MSH2 WILD-TYPE 236   3  22  19
D310V10, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  R0           23            236
  R1            0              3
  R2            0             22
  RX            2             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"
D310V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH2 MUTATED                                  0     2
  MSH2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH2 MUTATED                           3    21
  MSH2 WILD-TYPE                        16   155
D310V12, multiclass
                                  clus
vv                                 MSH2 MUTATED MSH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      21            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(311) Variable = IL1RAPL1 MUTATION ANALYSIS
D311V1, survival
                    sevent
clus2                  0   1
  IL1RAPL1 MUTATED    15   5
  IL1RAPL1 WILD-TYPE 262  73
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                20                335 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                 5                 73 
$`IL1RAPL1 MUTATED`
TCGA-AA-3554 TCGA-DM-A285 TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-3518 TCGA-AA-3663 
       17.95         5.88        79.69        33.53         1.02         6.97 
TCGA-AA-3977 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6164 
       25.02        49.41         3.19        12.76        12.00        29.03 
TCGA-D5-6532 TCGA-D5-6533 TCGA-DM-A1DA TCGA-DM-A28E TCGA-DM-A28G TCGA-F4-6855 
       18.25        25.48         7.50       119.93        60.79        47.41 
TCGA-G4-6304 TCGA-G4-6307 
       53.62        55.04 

$`IL1RAPL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 
       54.61        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
              1.02               0.00 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
            119.93             148.01 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
             25.25              22.03 
[1] "1.0 - 119.9 (25.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D311V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL1RAPL1 MUTATED         1        0        2        11         2         0
  IL1RAPL1 WILD-TYPE      63        1       24        97         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1RAPL1 MUTATED           0          0          2          1        2
  IL1RAPL1 WILD-TYPE        18          6         42         32       33
                    vv
clus                 STAGE IVA STAGE IVB
  IL1RAPL1 MUTATED           0         0
  IL1RAPL1 WILD-TYPE        12         1
D311V3, multiclass
            clus
vv           IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                11                 97
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                1                 32
  STAGE IV                  2                 33
  STAGE IVA                 0                 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
  IL1RAPL1 MUTATED     0   2  17   4
  IL1RAPL1 WILD-TYPE   9  65 232  37
D311V4, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3               17                232
  T4                4                 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
  IL1RAPL1 MUTATED    18   2   3
  IL1RAPL1 WILD-TYPE 202  79  63
D311V5, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  N0               18                202
  N1                2                 79
  N2                3                 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"
D311V6, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    18   2
  IL1RAPL1 WILD-TYPE 267  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     18    2
  IL1RAPL1 WILD-TYPE  267   46
   clus
vv  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  0               18                267
  1                2                 46
[1] 2 2
[1] FALSE
D311V7, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    16   7
  IL1RAPL1 WILD-TYPE 154 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     16    7
  IL1RAPL1 WILD-TYPE  154  190
        clus
vv       IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  FEMALE               16                154
  MALE                  7                190
[1] 2 2
[1] FALSE
D311V8, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    15   0
  IL1RAPL1 WILD-TYPE 285   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     15    0
  IL1RAPL1 WILD-TYPE  285    8
     clus
vv    IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  NO                15                285
  YES                0                  8
[1] 2 2
[1] FALSE
D311V9, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    20   3
  IL1RAPL1 WILD-TYPE 294  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     20    3
  IL1RAPL1 WILD-TYPE  294   45
                               clus
vv                              IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  COLON ADENOCARCINOMA                        20                294
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  IL1RAPL1 MUTATED    14   0   0   2
  IL1RAPL1 WILD-TYPE 245   3  22  19
D311V10, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  R0               14                245
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D311V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL1RAPL1 MUTATED                                  0     1
  IL1RAPL1 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  IL1RAPL1 MUTATED                           1    15
  IL1RAPL1 WILD-TYPE                        18   161
D311V12, multiclass
                                  clus
vv                                 IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          15                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(312) Variable = C6ORF170 MUTATION ANALYSIS
D312V1, survival
                    sevent
clus2                  0   1
  C6ORF170 MUTATED    12   5
  C6ORF170 WILD-TYPE 265  73
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                17                338 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                 5                 73 
$`C6ORF170 MUTATED`
TCGA-AA-3715 TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3710 TCGA-AA-3977 
       19.04        25.08        63.98         6.97        26.99        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 
       15.02        12.00         7.53        35.97         1.55 

$`C6ORF170 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6163 TCGA-CM-6164 
        5.03        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
              1.55               0.00 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
             63.98             148.01 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
            22.420             22.045 
[1] "1.6 - 64.0 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D312V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF170 MUTATED         2        0        4         5         1         0
  C6ORF170 WILD-TYPE      62        1       22       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF170 MUTATED           0          0          2          1        0
  C6ORF170 WILD-TYPE        18          6         42         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF170 MUTATED           1         0
  C6ORF170 WILD-TYPE        11         1
D312V3, multiclass
            clus
vv           C6ORF170 MUTATED C6ORF170 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  C6ORF170 MUTATED     0   3  13   2
  C6ORF170 WILD-TYPE   9  64 236  39
D312V4, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3               13                236
  T4                2                 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
  C6ORF170 MUTATED    14   3   1
  C6ORF170 WILD-TYPE 206  78  65
D312V5, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  N0               14                206
  N1                3                 78
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V6, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    13   1
  C6ORF170 WILD-TYPE 272  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     13    1
  C6ORF170 WILD-TYPE  272   47
   clus
vv  C6ORF170 MUTATED C6ORF170 WILD-TYPE
  0               13                272
  1                1                 47
[1] 2 2
[1] FALSE
D312V7, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED     7  11
  C6ORF170 WILD-TYPE 163 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED      7   11
  C6ORF170 WILD-TYPE  163  186
        clus
vv       C6ORF170 MUTATED C6ORF170 WILD-TYPE
  FEMALE                7                163
  MALE                 11                186
[1] 2 2
[1] FALSE
D312V8, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    15   0
  C6ORF170 WILD-TYPE 285   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     15    0
  C6ORF170 WILD-TYPE  285    8
     clus
vv    C6ORF170 MUTATED C6ORF170 WILD-TYPE
  NO                15                285
  YES                0                  8
[1] 2 2
[1] FALSE
D312V9, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    15   3
  C6ORF170 WILD-TYPE 299  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     15    3
  C6ORF170 WILD-TYPE  299   45
                               clus
vv                              C6ORF170 MUTATED C6ORF170 WILD-TYPE
  COLON ADENOCARCINOMA                        15                299
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C6ORF170 MUTATED    11   0   0   2
  C6ORF170 WILD-TYPE 248   3  22  19
D312V10, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  R0               11                248
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D312V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF170 MUTATED                                  1     2
  C6ORF170 WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF170 MUTATED                           0     8
  C6ORF170 WILD-TYPE                        19   168
D312V12, multiclass
                                  clus
vv                                 C6ORF170 MUTATED C6ORF170 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           8                168
[1] 4 2
[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 = STAB2 MUTATION ANALYSIS
D313V1, survival
                 sevent
clus2               0   1
  STAB2 MUTATED    27   4
  STAB2 WILD-TYPE 250  74
  STAB2 MUTATED STAB2 WILD-TYPE 
             31             324 
  STAB2 MUTATED STAB2 WILD-TYPE 
              4              74 
$`STAB2 MUTATED`
TCGA-AA-3554 TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       17.95        46.65        32.75         8.38        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3947 
        3.02        63.98         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        12.59        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 
       13.78 

$`STAB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.69        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3861 TCGA-AA-3866 
        0.00        36.03        32.05         0.99        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 
       27.02        18.05        31.00         2.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A029 
       35.01         1.02         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
      117.07         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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  STAB2 MUTATED STAB2 WILD-TYPE 
              0               0 
  STAB2 MUTATED STAB2 WILD-TYPE 
         135.65          148.01 
  STAB2 MUTATED STAB2 WILD-TYPE 
         24.390          22.045 
[1] "0.0 - 135.7 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D313V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAB2 MUTATED         4        1        3        13         3         0
  STAB2 WILD-TYPE      60        0       23        95         5         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        17          6         40         32       34        12
                 vv
clus              STAGE IVB
  STAB2 MUTATED           0
  STAB2 WILD-TYPE         1
D313V3, multiclass
            clus
vv           STAB2 MUTATED STAB2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               3              23
  STAGE IIA             13              95
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  STAB2 MUTATED     0   5  22   4
  STAB2 WILD-TYPE   9  62 227  37
D313V4, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            22             227
  T4             4              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
  STAB2 MUTATED    25   5   2
  STAB2 WILD-TYPE 195  76  64
D313V5, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  N0            25             195
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V6, binary
                 cls
clus                0   1
  STAB2 MUTATED    27   1
  STAB2 WILD-TYPE 258  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     27    1
  STAB2 WILD-TYPE  258   47
   clus
vv  STAB2 MUTATED STAB2 WILD-TYPE
  0            27             258
  1             1              47
[1] 2 2
[1] FALSE
D313V7, binary
                 cls
clus                0   1
  STAB2 MUTATED    12  20
  STAB2 WILD-TYPE 158 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     12   20
  STAB2 WILD-TYPE  158  177
        clus
vv       STAB2 MUTATED STAB2 WILD-TYPE
  FEMALE            12             158
  MALE              20             177
[1] 2 2
[1] FALSE
D313V8, binary
                 cls
clus                0   1
  STAB2 MUTATED    26   0
  STAB2 WILD-TYPE 274   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     26    0
  STAB2 WILD-TYPE  274    8
     clus
vv    STAB2 MUTATED STAB2 WILD-TYPE
  NO             26             274
  YES             0               8
[1] 2 2
[1] FALSE
D313V9, binary
                 cls
clus                0   1
  STAB2 MUTATED    25   6
  STAB2 WILD-TYPE 289  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     25    6
  STAB2 WILD-TYPE  289   42
                               clus
vv                              STAB2 MUTATED STAB2 WILD-TYPE
  COLON ADENOCARCINOMA                     25             289
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAB2 MUTATED    22   0   0   2
  STAB2 WILD-TYPE 237   3  22  19
D313V10, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  R0            22             237
  R1             0               3
  R2             0              22
  RX             2              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"
D313V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAB2 MUTATED                                  0     2
  STAB2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAB2 MUTATED                           4    14
  STAB2 WILD-TYPE                        15   162
D313V12, multiclass
                                  clus
vv                                 STAB2 MUTATED STAB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       14             162
[1] 4 2
[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 = ERBB3 MUTATION ANALYSIS
D314V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    23   1
  ERBB3 WILD-TYPE 254  77
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             24             331 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              1              77 
$`ERBB3 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3976 TCGA-A6-5657 
        0.92        19.04        19.04        24.00        26.01        31.63 
TCGA-AA-3519 TCGA-AA-3819 TCGA-AA-3864 TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 
        9.07        25.02        53.00        38.04         0.99        34.98 
TCGA-AD-6890 TCGA-AY-6197 TCGA-CA-5254 TCGA-CK-4947 TCGA-CM-4746 TCGA-CM-5348 
       24.53        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 

$`ERBB3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 
       29.98        12.99         2.01        50.99        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        32.91        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        83.24         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74         3.19        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.92            0.00 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          53.62          148.01 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         24.265          21.990 
[1] "0.9 - 53.6 (24.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "4.9"
D314V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB3 MUTATED         3        0        3         8         2         0
  ERBB3 WILD-TYPE      61        1       23       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB3 MUTATED           2          1          3          1        2         0
  ERBB3 WILD-TYPE        16          5         41         32       33        12
                 vv
clus              STAGE IVB
  ERBB3 MUTATED           0
  ERBB3 WILD-TYPE         1
D314V3, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  ERBB3 MUTATED     1   4  16   5
  ERBB3 WILD-TYPE   8  63 233  36
D314V4, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            16             233
  T4             5              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
  ERBB3 MUTATED    18   6   2
  ERBB3 WILD-TYPE 202  75  64
D314V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            18             202
  N1             6              75
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    22   2
  ERBB3 WILD-TYPE 263  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     22    2
  ERBB3 WILD-TYPE  263   46
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            22             263
  1             2              46
[1] 2 2
[1] FALSE
D314V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED    12  14
  ERBB3 WILD-TYPE 158 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     12   14
  ERBB3 WILD-TYPE  158  183
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE            12             158
  MALE              14             183
[1] 2 2
[1] FALSE
D314V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED    22   1
  ERBB3 WILD-TYPE 278   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     22    1
  ERBB3 WILD-TYPE  278    7
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO             22             278
  YES             1               7
[1] 2 2
[1] FALSE
D314V9, binary
                 cls
clus                0   1
  ERBB3 MUTATED    22   4
  ERBB3 WILD-TYPE 292  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     22    4
  ERBB3 WILD-TYPE  292   44
                               clus
vv                              ERBB3 MUTATED ERBB3 WILD-TYPE
  COLON ADENOCARCINOMA                     22             292
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    21   0   2   2
  ERBB3 WILD-TYPE 238   3  20  19
D314V10, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            21             238
  R1             0               3
  R2             2              20
  RX             2              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"
D314V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB3 MUTATED                                  0     1
  ERBB3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB3 MUTATED                           2    10
  ERBB3 WILD-TYPE                        17   166
D314V12, multiclass
                                  clus
vv                                 ERBB3 MUTATED ERBB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       10             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(315) Variable = ZNF708 MUTATION ANALYSIS
D315V1, survival
                  sevent
clus2                0   1
  ZNF708 MUTATED     6   4
  ZNF708 WILD-TYPE 271  74
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              10              345 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
               4               74 
$`ZNF708 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-6964 TCGA-A6-5666 TCGA-AA-A00N TCGA-AA-A010 
       85.05        19.04        10.88        32.71         4.01        34.98 
TCGA-AY-5543 TCGA-CA-6718 TCGA-D5-6928 TCGA-DM-A28G 
       33.01        10.06        11.64        60.79 

$`ZNF708 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF708 MUTATED ZNF708 WILD-TYPE 
            4.01             0.00 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
           85.05           148.01 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
          25.875           22.060 
[1] "4.0 - 85.0 (25.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D315V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF708 MUTATED         1        0        1         4         2         1
  ZNF708 WILD-TYPE      63        1       25       104         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF708 MUTATED           0          0          0          0        1
  ZNF708 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF708 MUTATED           1         0
  ZNF708 WILD-TYPE        11         1
D315V3, multiclass
            clus
vv           ZNF708 MUTATED ZNF708 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  ZNF708 MUTATED     0   1   7   4
  ZNF708 WILD-TYPE   9  66 242  37
D315V4, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              4               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
  ZNF708 MUTATED    10   1   1
  ZNF708 WILD-TYPE 210  80  65
D315V5, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  N0             10              210
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V6, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     8   2
  ZNF708 WILD-TYPE 277  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      8    2
  ZNF708 WILD-TYPE  277   46
   clus
vv  ZNF708 MUTATED ZNF708 WILD-TYPE
  0              8              277
  1              2               46
[1] 2 2
[1] FALSE
D315V7, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     3   9
  ZNF708 WILD-TYPE 167 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      3    9
  ZNF708 WILD-TYPE  167  188
        clus
vv       ZNF708 MUTATED ZNF708 WILD-TYPE
  FEMALE              3              167
  MALE                9              188
[1] 2 2
[1] FALSE
D315V8, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     7   1
  ZNF708 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      7    1
  ZNF708 WILD-TYPE  293    7
     clus
vv    ZNF708 MUTATED ZNF708 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D315V9, binary
                  cls
clus                 0   1
  ZNF708 MUTATED    10   2
  ZNF708 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED     10    2
  ZNF708 WILD-TYPE  304   46
                               clus
vv                              ZNF708 MUTATED ZNF708 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF708 MUTATED     6   0   1   2
  ZNF708 WILD-TYPE 253   3  21  19
D315V10, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              2               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"
D315V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF708 MUTATED                                  0     1
  ZNF708 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF708 MUTATED                           1     5
  ZNF708 WILD-TYPE                        18   171
D315V12, multiclass
                                  clus
vv                                 ZNF708 MUTATED ZNF708 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = MBTD1 MUTATION ANALYSIS
D316V1, survival
                 sevent
clus2               0   1
  MBTD1 MUTATED     6   3
  MBTD1 WILD-TYPE 271  75
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              9             346 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              3              75 
$`MBTD1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-AA-3492 TCGA-AD-6889 TCGA-CK-4948 TCGA-CK-5913 
      100.01        79.69         3.02        83.24       148.01        51.32 
TCGA-CK-6747 TCGA-D5-5539 TCGA-D5-6922 
       82.95        19.59        10.13 

$`MBTD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       85.45        15.62        21.99        21.14         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MBTD1 MUTATED MBTD1 WILD-TYPE 
           3.02            0.00 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
         148.01          140.38 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
          79.69           22.01 
[1] "3.0 - 148.0 (79.7)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.4"
D316V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MBTD1 MUTATED         1        0        2         3         0         0
  MBTD1 WILD-TYPE      63        1       24       105         8         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        17          4         44         33       35        12
                 vv
clus              STAGE IVB
  MBTD1 MUTATED           0
  MBTD1 WILD-TYPE         1
D316V3, multiclass
            clus
vv           MBTD1 MUTATED MBTD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             2               4
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MBTD1 MUTATED     0   1   8   0
  MBTD1 WILD-TYPE   9  66 241  41
D316V4, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             0              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
  MBTD1 MUTATED     6   3   0
  MBTD1 WILD-TYPE 214  78  66
D316V5, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V6, binary
                 cls
clus                0   1
  MBTD1 MUTATED     7   0
  MBTD1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      7    0
  MBTD1 WILD-TYPE  278   48
   clus
vv  MBTD1 MUTATED MBTD1 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D316V7, binary
                 cls
clus                0   1
  MBTD1 MUTATED     4   5
  MBTD1 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      4    5
  MBTD1 WILD-TYPE  166  192
        clus
vv       MBTD1 MUTATED MBTD1 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D316V8, binary
                 cls
clus                0   1
  MBTD1 MUTATED     9   0
  MBTD1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      9    0
  MBTD1 WILD-TYPE  291    8
     clus
vv    MBTD1 MUTATED MBTD1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D316V9, binary
                 cls
clus                0   1
  MBTD1 MUTATED     8   1
  MBTD1 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      8    1
  MBTD1 WILD-TYPE  306   47
                               clus
vv                              MBTD1 MUTATED MBTD1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MBTD1 MUTATED     6   0   0   2
  MBTD1 WILD-TYPE 253   3  22  19
D316V10, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D316V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBTD1 MUTATED                                  0     1
  MBTD1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MBTD1 MUTATED                           0     7
  MBTD1 WILD-TYPE                        19   169
D316V12, multiclass
                                  clus
vv                                 MBTD1 MUTATED MBTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = ZNF189 MUTATION ANALYSIS
D317V1, survival
                  sevent
clus2                0   1
  ZNF189 MUTATED    17   0
  ZNF189 WILD-TYPE 260  78
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              17              338 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
               0               78 
$`ZNF189 MUTATED`
TCGA-AZ-4681 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3815 
      106.75        30.44        22.06        19.66        63.98        33.04 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 
       12.16        58.39        12.20        12.76        29.03        12.99 
TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6541 TCGA-D5-6926 TCGA-G4-6317 
       11.01        18.25        15.58         9.04        36.00 

$`ZNF189 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        14.04        16.04        21.99        14.99 
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        54.61 
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        25.48        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-D5-6927 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ZNF189 MUTATED ZNF189 WILD-TYPE 
            9.04             0.00 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
          106.75           148.01 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
           19.66            22.09 
[1] "9.0 - 106.8 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr="     "2.6e+07"
D317V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF189 MUTATED         2        0        1        10         0         0
  ZNF189 WILD-TYPE      62        1       25        98         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF189 MUTATED           0          0          2          2        0
  ZNF189 WILD-TYPE        18          6         42         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF189 MUTATED           0         0
  ZNF189 WILD-TYPE        12         1
D317V3, multiclass
            clus
vv           ZNF189 MUTATED ZNF189 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              10               98
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF189 MUTATED     0   2  13   2
  ZNF189 WILD-TYPE   9  65 236  39
D317V4, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             13              236
  T4              2               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
  ZNF189 MUTATED    13   3   1
  ZNF189 WILD-TYPE 207  78  65
D317V5, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  N0             13              207
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V6, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    14   0
  ZNF189 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     14    0
  ZNF189 WILD-TYPE  271   48
   clus
vv  ZNF189 MUTATED ZNF189 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D317V7, binary
                  cls
clus                 0   1
  ZNF189 MUTATED     7  10
  ZNF189 WILD-TYPE 163 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED      7   10
  ZNF189 WILD-TYPE  163  187
        clus
vv       ZNF189 MUTATED ZNF189 WILD-TYPE
  FEMALE              7              163
  MALE               10              187
[1] 2 2
[1] FALSE
D317V8, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    16   1
  ZNF189 WILD-TYPE 284   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     16    1
  ZNF189 WILD-TYPE  284    7
     clus
vv    ZNF189 MUTATED ZNF189 WILD-TYPE
  NO              16              284
  YES              1                7
[1] 2 2
[1] FALSE
D317V9, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    14   3
  ZNF189 WILD-TYPE 300  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     14    3
  ZNF189 WILD-TYPE  300   45
                               clus
vv                              ZNF189 MUTATED ZNF189 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF189 MUTATED    15   0   0   2
  ZNF189 WILD-TYPE 244   3  22  19
D317V10, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              2               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"
D317V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF189 MUTATED                                  0     2
  ZNF189 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF189 MUTATED                           1    12
  ZNF189 WILD-TYPE                        18   164
D317V12, multiclass
                                  clus
vv                                 ZNF189 MUTATED ZNF189 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = ACP6 MUTATION ANALYSIS
D318V1, survival
                sevent
clus2              0   1
  ACP6 MUTATED     4   2
  ACP6 WILD-TYPE 273  76
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            349 
  ACP6 MUTATED ACP6 WILD-TYPE 
             2             76 
$`ACP6 MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-6648 TCGA-CK-4948 TCGA-F4-6460 
       19.04        10.88        26.17        25.18       148.01        31.96 

$`ACP6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.030 
[1] "10.9 - 148.0 (25.7)" "0.0 - 140.4 (22.0)" 
[1] "hr=" "1.2"
D318V2, continuous
                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      64        1       26       107         8         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        17          6         43         33       34        11
                vv
clus             STAGE IVB
  ACP6 MUTATED           0
  ACP6 WILD-TYPE         1
D318V3, multiclass
            clus
vv           ACP6 MUTATED ACP6 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  ACP6 MUTATED     0   0   5   1
  ACP6 WILD-TYPE   9  67 244  40
D318V4, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            1             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
  ACP6 MUTATED     3   2   1
  ACP6 WILD-TYPE 217  79  65
D318V5, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  N0            3            217
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V6, binary
                cls
clus               0   1
  ACP6 MUTATED     3   2
  ACP6 WILD-TYPE 282  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      3    2
  ACP6 WILD-TYPE  282   46
   clus
vv  ACP6 MUTATED ACP6 WILD-TYPE
  0            3            282
  1            2             46
[1] 2 2
[1] FALSE
D318V7, binary
                cls
clus               0   1
  ACP6 MUTATED     3   3
  ACP6 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      3    3
  ACP6 WILD-TYPE  167  194
        clus
vv       ACP6 MUTATED ACP6 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D318V8, binary
                cls
clus               0   1
  ACP6 MUTATED     5   1
  ACP6 WILD-TYPE 295   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      5    1
  ACP6 WILD-TYPE  295    7
     clus
vv    ACP6 MUTATED ACP6 WILD-TYPE
  NO             5            295
  YES            1              7
[1] 2 2
[1] FALSE
D318V9, binary
                cls
clus               0   1
  ACP6 MUTATED     6   0
  ACP6 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      6    0
  ACP6 WILD-TYPE  308   48
                               clus
vv                              ACP6 MUTATED ACP6 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ACP6 MUTATED     3   0   1   0
  ACP6 WILD-TYPE 256   3  21  21
D318V10, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            1             21
  RX            0             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"
D318V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACP6 MUTATED                                  0     0
  ACP6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ACP6 MUTATED                           0     5
  ACP6 WILD-TYPE                        19   171
D318V12, multiclass
                                  clus
vv                                 ACP6 MUTATED ACP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = PRKCI MUTATION ANALYSIS
D319V1, survival
                 sevent
clus2               0   1
  PRKCI MUTATED    15   2
  PRKCI WILD-TYPE 262  76
  PRKCI MUTATED PRKCI WILD-TYPE 
             17             338 
  PRKCI MUTATED PRKCI WILD-TYPE 
              2              76 
$`PRKCI MUTATED`
TCGA-G4-6586 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 
       35.80         8.38        20.12        63.98        29.95         6.97 
TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6169 
       33.04        25.02        34.98        58.39         6.77        13.02 
TCGA-CM-6171 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1D4 
       14.04        56.09        15.12        16.14        92.75 

$`PRKCI WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        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        54.61 
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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PRKCI MUTATED PRKCI WILD-TYPE 
           6.77            0.00 
  PRKCI MUTATED PRKCI WILD-TYPE 
          92.75          148.01 
  PRKCI MUTATED PRKCI WILD-TYPE 
         25.020          22.045 
[1] "6.8 - 92.8 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D319V2, continuous
                 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      61        1       24        98         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCI MUTATED           0          0          1          0        0         0
  PRKCI WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  PRKCI MUTATED           0
  PRKCI WILD-TYPE         1
D319V3, multiclass
            clus
vv           PRKCI MUTATED PRKCI WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             10              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PRKCI MUTATED     0   4  13   1
  PRKCI WILD-TYPE   9  63 236  40
D319V4, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  T1             0               9
  T2             4              63
  T3            13             236
  T4             1              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
  PRKCI MUTATED    17   1   0
  PRKCI WILD-TYPE 203  80  66
D319V5, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  N0            17             203
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V6, binary
                 cls
clus                0   1
  PRKCI MUTATED    14   0
  PRKCI WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     14    0
  PRKCI WILD-TYPE  271   48
   clus
vv  PRKCI MUTATED PRKCI WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D319V7, binary
                 cls
clus                0   1
  PRKCI MUTATED     7  11
  PRKCI WILD-TYPE 163 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED      7   11
  PRKCI WILD-TYPE  163  186
        clus
vv       PRKCI MUTATED PRKCI WILD-TYPE
  FEMALE             7             163
  MALE              11             186
[1] 2 2
[1] FALSE
D319V8, binary
                 cls
clus                0   1
  PRKCI MUTATED    16   0
  PRKCI WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     16    0
  PRKCI WILD-TYPE  284    8
     clus
vv    PRKCI MUTATED PRKCI WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D319V9, binary
                 cls
clus                0   1
  PRKCI MUTATED    15   3
  PRKCI WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     15    3
  PRKCI WILD-TYPE  299   45
                               clus
vv                              PRKCI MUTATED PRKCI WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKCI MUTATED    12   0   0   1
  PRKCI WILD-TYPE 247   3  22  20
D319V10, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D319V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCI MUTATED                                  0     0
  PRKCI WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCI MUTATED                           2     9
  PRKCI WILD-TYPE                        17   167
D319V12, multiclass
                                  clus
vv                                 PRKCI MUTATED PRKCI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(320) Variable = ANKRD50 MUTATION ANALYSIS
D320V1, survival
                   sevent
clus2                 0   1
  ANKRD50 MUTATED     7   7
  ANKRD50 WILD-TYPE 270  71
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               14               341 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
                7                71 
$`ANKRD50 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-6601 TCGA-AA-3492 TCGA-AA-3977 
       13.02        19.04        19.04       100.01         3.02        25.02 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-6598 TCGA-CK-4948 
       30.02         4.01        34.98        38.07        49.41       148.01 
TCGA-CM-6171 TCGA-DM-A1HB 
       14.04       135.65 

$`ANKRD50 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
             3.02              0.00 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
           148.01            140.38 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
            27.52             22.03 
[1] "3.0 - 148.0 (27.5)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.7"
D320V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD50 MUTATED         1        0        5         1         2         0
  ANKRD50 WILD-TYPE      63        1       21       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD50 MUTATED           3          0          1          0        1
  ANKRD50 WILD-TYPE        15          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD50 MUTATED           0         0
  ANKRD50 WILD-TYPE        12         1
D320V3, multiclass
            clus
vv           ANKRD50 MUTATED ANKRD50 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 5                21
  STAGE IIA                1               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                3                15
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  ANKRD50 MUTATED     0   2  10   3
  ANKRD50 WILD-TYPE   9  65 239  38
D320V4, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              10               239
  T4               3                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
  ANKRD50 MUTATED    11   3   1
  ANKRD50 WILD-TYPE 209  78  65
D320V5, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  N0              11               209
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V6, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    12   1
  ANKRD50 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     12    1
  ANKRD50 WILD-TYPE  273   47
   clus
vv  ANKRD50 MUTATED ANKRD50 WILD-TYPE
  0              12               273
  1               1                47
[1] 2 2
[1] FALSE
D320V7, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED     8   7
  ANKRD50 WILD-TYPE 162 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED      8    7
  ANKRD50 WILD-TYPE  162  190
        clus
vv       ANKRD50 MUTATED ANKRD50 WILD-TYPE
  FEMALE               8               162
  MALE                 7               190
[1] 2 2
[1] FALSE
D320V8, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    11   1
  ANKRD50 WILD-TYPE 289   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     11    1
  ANKRD50 WILD-TYPE  289    7
     clus
vv    ANKRD50 MUTATED ANKRD50 WILD-TYPE
  NO               11               289
  YES               1                 7
[1] 2 2
[1] FALSE
D320V9, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    12   2
  ANKRD50 WILD-TYPE 302  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     12    2
  ANKRD50 WILD-TYPE  302   46
                               clus
vv                              ANKRD50 MUTATED ANKRD50 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD50 MUTATED     9   0   1   0
  ANKRD50 WILD-TYPE 250   3  21  21
D320V10, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               0                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"
D320V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD50 MUTATED                                  0     0
  ANKRD50 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD50 MUTATED                           0     5
  ANKRD50 WILD-TYPE                        19   171
D320V12, multiclass
                                  clus
vv                                 ANKRD50 MUTATED ANKRD50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = IL12RB2 MUTATION ANALYSIS
D321V1, survival
                   sevent
clus2                 0   1
  IL12RB2 MUTATED     7   6
  IL12RB2 WILD-TYPE 270  72
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               13               342 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
                6                72 
$`IL12RB2 MUTATED`
TCGA-AA-3525 TCGA-G4-6588 TCGA-AA-3811 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6889 
        8.05        26.17        10.06        34.98        31.00        83.24 
TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-D5-5538 
       27.09        12.76        10.06        85.45        21.14        54.61 
TCGA-DM-A28C 
       81.37 

$`IL12RB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
             8.05              0.00 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
            85.45            148.01 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
            27.09             22.01 
[1] "8.1 - 85.5 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D321V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL12RB2 MUTATED         3        0        0         6         1         0
  IL12RB2 WILD-TYPE      61        1       26       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL12RB2 MUTATED           1          0          3          0        0
  IL12RB2 WILD-TYPE        17          6         41         33       35
                   vv
clus                STAGE IVA STAGE IVB
  IL12RB2 MUTATED           0         0
  IL12RB2 WILD-TYPE        12         1
D321V3, multiclass
            clus
vv           IL12RB2 MUTATED IL12RB2 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                6               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  IL12RB2 MUTATED     1   2  10   1
  IL12RB2 WILD-TYPE   8  65 239  40
D321V4, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3              10               239
  T4               1                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
  IL12RB2 MUTATED    10   3   1
  IL12RB2 WILD-TYPE 210  78  65
D321V5, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  N0              10               210
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V6, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    14   0
  IL12RB2 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     14    0
  IL12RB2 WILD-TYPE  271   48
   clus
vv  IL12RB2 MUTATED IL12RB2 WILD-TYPE
  0              14               271
  1               0                48
[1] 2 2
[1] FALSE
D321V7, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED     8   6
  IL12RB2 WILD-TYPE 162 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED      8    6
  IL12RB2 WILD-TYPE  162  191
        clus
vv       IL12RB2 MUTATED IL12RB2 WILD-TYPE
  FEMALE               8               162
  MALE                 6               191
[1] 2 2
[1] FALSE
D321V8, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    11   0
  IL12RB2 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     11    0
  IL12RB2 WILD-TYPE  289    8
     clus
vv    IL12RB2 MUTATED IL12RB2 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D321V9, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    12   2
  IL12RB2 WILD-TYPE 302  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     12    2
  IL12RB2 WILD-TYPE  302   46
                               clus
vv                              IL12RB2 MUTATED IL12RB2 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  IL12RB2 MUTATED     9   1   0   3
  IL12RB2 WILD-TYPE 250   2  22  18
D321V10, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  R0               9               250
  R1               1                 2
  R2               0                22
  RX               3                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"
D321V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL12RB2 MUTATED                                  0     3
  IL12RB2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  IL12RB2 MUTATED                           1     5
  IL12RB2 WILD-TYPE                        18   171
D321V12, multiclass
                                  clus
vv                                 IL12RB2 MUTATED IL12RB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = GPNMB MUTATION ANALYSIS
D322V1, survival
                 sevent
clus2               0   1
  GPNMB MUTATED     8   3
  GPNMB WILD-TYPE 269  75
  GPNMB MUTATED GPNMB WILD-TYPE 
             11             344 
  GPNMB MUTATED GPNMB WILD-TYPE 
              3              75 
$`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 
       17.85        44.32       135.65        81.37       117.07 

$`GPNMB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28E TCGA-DM-A28F TCGA-DM-A28G 
        7.50       131.51       139.17       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GPNMB MUTATED GPNMB WILD-TYPE 
           0.92            0.00 
  GPNMB MUTATED GPNMB WILD-TYPE 
         135.65          148.01 
  GPNMB MUTATED GPNMB WILD-TYPE 
         17.850          22.075 
[1] "0.9 - 135.7 (17.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D322V2, continuous
                 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      64        1       25       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPNMB MUTATED           2          0          1          1        0         1
  GPNMB WILD-TYPE        16          6         43         32       35        11
                 vv
clus              STAGE IVB
  GPNMB MUTATED           0
  GPNMB WILD-TYPE         1
D322V3, multiclass
            clus
vv           GPNMB MUTATED GPNMB WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  GPNMB MUTATED     0   1  10   2
  GPNMB WILD-TYPE   9  66 239  39
D322V4, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             2              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
  GPNMB MUTATED     8   3   2
  GPNMB WILD-TYPE 212  78  64
D322V5, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  N0             8             212
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V6, binary
                 cls
clus                0   1
  GPNMB MUTATED    10   1
  GPNMB WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED     10    1
  GPNMB WILD-TYPE  275   47
   clus
vv  GPNMB MUTATED GPNMB WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D322V7, binary
                 cls
clus                0   1
  GPNMB MUTATED     4   9
  GPNMB WILD-TYPE 166 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED      4    9
  GPNMB WILD-TYPE  166  188
        clus
vv       GPNMB MUTATED GPNMB WILD-TYPE
  FEMALE             4             166
  MALE               9             188
[1] 2 2
[1] FALSE
D322V8, binary
                 cls
clus                0   1
  GPNMB MUTATED     6   0
  GPNMB WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED      6    0
  GPNMB WILD-TYPE  294    8
     clus
vv    GPNMB MUTATED GPNMB WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D322V9, binary
                 cls
clus                0   1
  GPNMB MUTATED    11   1
  GPNMB WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED     11    1
  GPNMB WILD-TYPE  303   47
                               clus
vv                              GPNMB MUTATED GPNMB WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPNMB MUTATED     5   0   0   3
  GPNMB WILD-TYPE 254   3  22  18
D322V10, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             3              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"
D322V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPNMB MUTATED                                  0     2
  GPNMB WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPNMB MUTATED                           0     7
  GPNMB WILD-TYPE                        19   169
D322V12, multiclass
                                  clus
vv                                 GPNMB MUTATED GPNMB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = GLI2 MUTATION ANALYSIS
D323V1, survival
                sevent
clus2              0   1
  GLI2 MUTATED    13   6
  GLI2 WILD-TYPE 264  72
  GLI2 MUTATED GLI2 WILD-TYPE 
            19            336 
  GLI2 MUTATED GLI2 WILD-TYPE 
             6             72 
$`GLI2 MUTATED`
TCGA-G4-6625 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-A01P TCGA-AY-5543 TCGA-AY-6196 
       91.79        79.69         3.02        38.07        33.01         0.20 
TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
       12.36        12.76        10.06         5.03        15.02        14.04 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6928 
       14.04         4.80        12.49        10.13        12.43        11.64 
TCGA-DM-A1DA 
        7.50 

$`GLI2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        26.17        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-5868 TCGA-CM-6161 
       30.08        32.02        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-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        7.53        12.39        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GLI2 MUTATED GLI2 WILD-TYPE 
           0.2            0.0 
  GLI2 MUTATED GLI2 WILD-TYPE 
         91.79         148.01 
  GLI2 MUTATED GLI2 WILD-TYPE 
         12.43          22.75 
[1] "0.2 - 91.8 (12.4)"  "0.0 - 148.0 (22.8)"
[1] "hr=" "2"  
D323V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLI2 MUTATED         5        0        2         5         0         0
  GLI2 WILD-TYPE      59        1       24       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI2 MUTATED           1          1          1          2        0         2
  GLI2 WILD-TYPE        17          5         43         31       35        10
                vv
clus             STAGE IVB
  GLI2 MUTATED           0
  GLI2 WILD-TYPE         1
D323V3, multiclass
            clus
vv           GLI2 MUTATED GLI2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             2             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
  GLI2 MUTATED     1   4  14   1
  GLI2 WILD-TYPE   8  63 235  40
D323V4, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  T1            1              8
  T2            4             63
  T3           14            235
  T4            1             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
  GLI2 MUTATED    13   5   2
  GLI2 WILD-TYPE 207  76  64
D323V5, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  N0           13            207
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V6, binary
                cls
clus               0   1
  GLI2 MUTATED    16   2
  GLI2 WILD-TYPE 269  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     16    2
  GLI2 WILD-TYPE  269   46
   clus
vv  GLI2 MUTATED GLI2 WILD-TYPE
  0           16            269
  1            2             46
[1] 2 2
[1] FALSE
D323V7, binary
                cls
clus               0   1
  GLI2 MUTATED     8  12
  GLI2 WILD-TYPE 162 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED      8   12
  GLI2 WILD-TYPE  162  185
        clus
vv       GLI2 MUTATED GLI2 WILD-TYPE
  FEMALE            8            162
  MALE             12            185
[1] 2 2
[1] FALSE
D323V8, binary
                cls
clus               0   1
  GLI2 MUTATED    16   1
  GLI2 WILD-TYPE 284   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     16    1
  GLI2 WILD-TYPE  284    7
     clus
vv    GLI2 MUTATED GLI2 WILD-TYPE
  NO            16            284
  YES            1              7
[1] 2 2
[1] FALSE
D323V9, binary
                cls
clus               0   1
  GLI2 MUTATED    17   3
  GLI2 WILD-TYPE 297  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     17    3
  GLI2 WILD-TYPE  297   45
                               clus
vv                              GLI2 MUTATED GLI2 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GLI2 MUTATED    16   0   0   3
  GLI2 WILD-TYPE 243   3  22  18
D323V10, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            3             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"
D323V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLI2 MUTATED                                  0     3
  GLI2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLI2 MUTATED                           1    13
  GLI2 WILD-TYPE                        18   163
D323V12, multiclass
                                  clus
vv                                 GLI2 MUTATED GLI2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      13            163
[1] 4 2
[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 = OR51E1 MUTATION ANALYSIS
D324V1, survival
                  sevent
clus2                0   1
  OR51E1 MUTATED     9   4
  OR51E1 WILD-TYPE 268  74
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              13              342 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
               4               74 
$`OR51E1 MUTATED`
TCGA-AA-3950 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3866 TCGA-AY-6197 TCGA-CK-5913 
       24.00        22.06         3.02        17.03        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 
       74.56 

$`OR51E1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-6165 
       15.02        17.03        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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            22.01 
[1] "3.0 - 135.7 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D324V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51E1 MUTATED         1        0        1         6         0         0
  OR51E1 WILD-TYPE      63        1       25       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51E1 MUTATED           0          0          3          1        0
  OR51E1 WILD-TYPE        18          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51E1 MUTATED           1         0
  OR51E1 WILD-TYPE        11         1
D324V3, multiclass
            clus
vv           OR51E1 MUTATED OR51E1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  OR51E1 MUTATED     0   1  12   0
  OR51E1 WILD-TYPE   9  66 237  41
D324V4, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             12              237
  T4              0               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
  OR51E1 MUTATED     8   4   1
  OR51E1 WILD-TYPE 212  77  65
D324V5, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  N0              8              212
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V6, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    10   1
  OR51E1 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     10    1
  OR51E1 WILD-TYPE  275   47
   clus
vv  OR51E1 MUTATED OR51E1 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D324V7, binary
                  cls
clus                 0   1
  OR51E1 MUTATED     6   7
  OR51E1 WILD-TYPE 164 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED      6    7
  OR51E1 WILD-TYPE  164  190
        clus
vv       OR51E1 MUTATED OR51E1 WILD-TYPE
  FEMALE              6              164
  MALE                7              190
[1] 2 2
[1] FALSE
D324V8, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    10   0
  OR51E1 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     10    0
  OR51E1 WILD-TYPE  290    8
     clus
vv    OR51E1 MUTATED OR51E1 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D324V9, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    10   1
  OR51E1 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     10    1
  OR51E1 WILD-TYPE  304   47
                               clus
vv                              OR51E1 MUTATED OR51E1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51E1 MUTATED     9   0   0   1
  OR51E1 WILD-TYPE 250   3  22  20
D324V10, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D324V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51E1 MUTATED                                  0     0
  OR51E1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51E1 MUTATED                           0    10
  OR51E1 WILD-TYPE                        19   166
D324V12, multiclass
                                  clus
vv                                 OR51E1 MUTATED OR51E1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(325) Variable = AGFG1 MUTATION ANALYSIS
D325V1, survival
                 sevent
clus2               0   1
  AGFG1 MUTATED     8   4
  AGFG1 WILD-TYPE 269  74
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             12             343 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
              4              74 
$`AGFG1 MUTATED`
TCGA-AD-6895 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3968 TCGA-AA-A00N TCGA-AA-A010 
       25.08        22.06        63.98        21.99         4.01        34.98 
TCGA-AY-6196 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-5349 TCGA-DM-A0X9 
        0.20        22.36        49.41        10.06        30.08       119.70 

$`AGFG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        62.79        88.21         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  AGFG1 MUTATED AGFG1 WILD-TYPE 
            0.2             0.0 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
         119.70          148.01 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
          23.72           21.99 
[1] "0.2 - 119.7 (23.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D325V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGFG1 MUTATED         1        0        3         4         3         0
  AGFG1 WILD-TYPE      63        1       23       104         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGFG1 MUTATED           1          0          1          1        0         1
  AGFG1 WILD-TYPE        17          6         43         32       35        11
                 vv
clus              STAGE IVB
  AGFG1 MUTATED           0
  AGFG1 WILD-TYPE         1
D325V3, multiclass
            clus
vv           AGFG1 MUTATED AGFG1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  AGFG1 MUTATED     0   1  11   3
  AGFG1 WILD-TYPE   9  66 238  38
D325V4, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             3              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
  AGFG1 MUTATED    12   1   2
  AGFG1 WILD-TYPE 208  80  64
D325V5, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V6, binary
                 cls
clus                0   1
  AGFG1 MUTATED    11   1
  AGFG1 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED     11    1
  AGFG1 WILD-TYPE  274   47
   clus
vv  AGFG1 MUTATED AGFG1 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D325V7, binary
                 cls
clus                0   1
  AGFG1 MUTATED     7   8
  AGFG1 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED      7    8
  AGFG1 WILD-TYPE  163  189
        clus
vv       AGFG1 MUTATED AGFG1 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D325V8, binary
                 cls
clus                0   1
  AGFG1 MUTATED     9   0
  AGFG1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED      9    0
  AGFG1 WILD-TYPE  291    8
     clus
vv    AGFG1 MUTATED AGFG1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D325V9, binary
                 cls
clus                0   1
  AGFG1 MUTATED    13   2
  AGFG1 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED     13    2
  AGFG1 WILD-TYPE  301   46
                               clus
vv                              AGFG1 MUTATED AGFG1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGFG1 MUTATED    11   0   0   2
  AGFG1 WILD-TYPE 248   3  22  19
D325V10, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             2              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"
D325V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGFG1 MUTATED                                  0     1
  AGFG1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGFG1 MUTATED                           0     8
  AGFG1 WILD-TYPE                        19   168
D325V12, multiclass
                                  clus
vv                                 AGFG1 MUTATED AGFG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = NRAS MUTATION ANALYSIS
D326V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    26   7
  NRAS WILD-TYPE 251  71
  NRAS MUTATED NRAS WILD-TYPE 
            33            322 
  NRAS MUTATED NRAS WILD-TYPE 
             7             71 
$`NRAS MUTATED`
TCGA-AA-3713 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A024 TCGA-A6-2678 TCGA-A6-5656 
       19.04        50.99        26.01        39.06        42.28        32.91 
TCGA-A6-5666 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3666 TCGA-AA-3819 TCGA-AA-3850 
       32.71        21.01        20.98         2.01        25.02         0.00 
TCGA-AA-3864 TCGA-AA-3973 TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A02F 
       53.00        13.05        34.03         4.01         1.02        39.98 
TCGA-AY-5543 TCGA-CA-5797 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-5538 
       33.01        12.59        15.02        12.00        12.03        54.61 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-F4-6809 
       12.49        10.13        11.38       140.38         7.50        13.25 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6315 
       53.62        55.04        61.91 

$`NRAS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        42.90        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 
       26.01        12.99        14.01        33.99        24.00        29.95 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        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-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-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        21.99        16.08        34.06        25.02 
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-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A029 
       35.01         1.02        33.04        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        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-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-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-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-D5-5539 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 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         7.53        12.39        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        13.41        13.35        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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59        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-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  NRAS MUTATED NRAS WILD-TYPE 
             0              0 
  NRAS MUTATED NRAS WILD-TYPE 
        140.38         148.01 
  NRAS MUTATED NRAS WILD-TYPE 
        21.010         22.075 
[1] "0.0 - 140.4 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D326V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRAS MUTATED         6        0        2         4         2         1
  NRAS WILD-TYPE      58        1       24       104         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED           1          2          5          2        5         2
  NRAS WILD-TYPE        17          4         39         31       30        10
                vv
clus             STAGE IVB
  NRAS MUTATED           0
  NRAS WILD-TYPE         1
D326V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             1              0
  STAGE III             1             17
  STAGE IIIA            2              4
  STAGE IIIB            5             39
  STAGE IIIC            2             31
  STAGE IV              5             30
  STAGE IVA             2             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
  NRAS MUTATED     0   7  22   4
  NRAS WILD-TYPE   9  60 227  37
D326V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            0              9
  T2            7             60
  T3           22            227
  T4            4             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
  NRAS MUTATED    17  13   3
  NRAS WILD-TYPE 203  68  63
D326V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           17            203
  N1           13             68
  N2            3             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"
D326V6, binary
                cls
clus               0   1
  NRAS MUTATED    26   7
  NRAS WILD-TYPE 259  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     26    7
  NRAS WILD-TYPE  259   41
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           26            259
  1            7             41
[1] 2 2
[1] FALSE
D326V7, binary
                cls
clus               0   1
  NRAS MUTATED    13  20
  NRAS WILD-TYPE 157 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13   20
  NRAS WILD-TYPE  157  177
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           13            157
  MALE             20            177
[1] 2 2
[1] FALSE
D326V8, binary
                cls
clus               0   1
  NRAS MUTATED    25   2
  NRAS WILD-TYPE 275   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     25    2
  NRAS WILD-TYPE  275    6
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            25            275
  YES            2              6
[1] 2 2
[1] FALSE
D326V9, binary
                cls
clus               0   1
  NRAS MUTATED    30   3
  NRAS WILD-TYPE 284  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     30    3
  NRAS WILD-TYPE  284   45
                               clus
vv                              NRAS MUTATED NRAS WILD-TYPE
  COLON ADENOCARCINOMA                    30            284
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED    24   0   5   0
  NRAS WILD-TYPE 235   3  17  21
D326V10, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           24            235
  R1            0              3
  R2            5             17
  RX            0             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"
D326V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     1
  NRAS WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED                           1    16
  NRAS WILD-TYPE                        18   160
D326V12, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      16            160
[1] 4 2
[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 = MPO MUTATION ANALYSIS
D327V1, survival
               sevent
clus2             0   1
  MPO MUTATED     9   2
  MPO WILD-TYPE 268  76
  MPO MUTATED MPO WILD-TYPE 
           11           344 
  MPO MUTATED MPO WILD-TYPE 
            2            76 
$`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 
       29.03        14.99       135.65        43.04        13.25 

$`MPO WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6168 TCGA-CM-6169 TCGA-CM-6170 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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-F4-6808 
        6.18        47.87         1.55        34.42        41.42        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MPO MUTATED MPO WILD-TYPE 
        12.76          0.00 
  MPO MUTATED MPO WILD-TYPE 
       135.65        148.01 
  MPO MUTATED MPO WILD-TYPE 
       25.020        22.045 
[1] "12.8 - 135.7 (25.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.5"
D327V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MPO MUTATED         1        0        0         5         0         0
  MPO WILD-TYPE      63        1       26       103         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MPO MUTATED           0          0          1          2        1         1
  MPO WILD-TYPE        18          6         43         31       34        11
               vv
clus            STAGE IVB
  MPO MUTATED           0
  MPO WILD-TYPE         1
D327V3, multiclass
            clus
vv           MPO MUTATED MPO WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            5           103
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           2            31
  STAGE IV             1            34
  STAGE IVA            1            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
  MPO MUTATED     1   1   9   1
  MPO WILD-TYPE   8  66 240  40
D327V4, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  T1           1             8
  T2           1            66
  T3           9           240
  T4           1            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
  MPO MUTATED     7   2   3
  MPO WILD-TYPE 213  79  63
D327V5, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  N0           7           213
  N1           2            79
  N2           3            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"
D327V6, binary
               cls
clus              0   1
  MPO MUTATED     8   2
  MPO WILD-TYPE 277  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED      8    2
  MPO WILD-TYPE  277   46
   clus
vv  MPO MUTATED MPO WILD-TYPE
  0           8           277
  1           2            46
[1] 2 2
[1] FALSE
D327V7, binary
               cls
clus              0   1
  MPO MUTATED     6   6
  MPO WILD-TYPE 164 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED      6    6
  MPO WILD-TYPE  164  191
        clus
vv       MPO MUTATED MPO WILD-TYPE
  FEMALE           6           164
  MALE             6           191
[1] 2 2
[1] FALSE
D327V8, binary
               cls
clus              0   1
  MPO MUTATED    10   0
  MPO WILD-TYPE 290   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED     10    0
  MPO WILD-TYPE  290    8
     clus
vv    MPO MUTATED MPO WILD-TYPE
  NO           10           290
  YES           0             8
[1] 2 2
[1] FALSE
D327V9, binary
               cls
clus              0   1
  MPO MUTATED     8   3
  MPO WILD-TYPE 306  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED      8    3
  MPO WILD-TYPE  306   45
                               clus
vv                              MPO MUTATED MPO WILD-TYPE
  COLON ADENOCARCINOMA                    8           306
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MPO MUTATED     7   0   1   1
  MPO WILD-TYPE 252   3  21  20
D327V10, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  R0           7           252
  R1           0             3
  R2           1            21
  RX           1            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"
D327V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPO MUTATED                                  0     1
  MPO WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MPO MUTATED                           1     6
  MPO WILD-TYPE                        18   170
D327V12, multiclass
                                  clus
vv                                 MPO MUTATED MPO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      6           170
[1] 4 2
[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 = TRRAP MUTATION ANALYSIS
D328V1, survival
                 sevent
clus2               0   1
  TRRAP MUTATED    34  11
  TRRAP WILD-TYPE 243  67
  TRRAP MUTATED TRRAP WILD-TYPE 
             45             310 
  TRRAP MUTATED TRRAP WILD-TYPE 
             11              67 
$`TRRAP MUTATED`
TCGA-AA-3496 TCGA-AA-3552 TCGA-AA-3672 TCGA-AA-3715 TCGA-AZ-4681 TCGA-G4-6586 
        1.02        13.02         0.92        19.04       106.75        35.80 
TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 
       79.69        42.90        42.28        31.63        29.19        23.61 
TCGA-A6-6138 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3678 
       22.52        19.66         3.02        63.98         6.97        47.01 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01P 
       26.99        10.06        33.04        38.04        34.98        38.07 
TCGA-AA-A01R TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6718 
       35.01        22.42        58.39        88.21         6.77        10.06 
TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5860 
       17.56        15.62        51.32        21.14        13.02        32.02 
TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6930 TCGA-DM-A1D4 
       15.02        14.04        19.59        15.12        13.35        92.75 
TCGA-DM-A1HA TCGA-F4-6808 TCGA-G4-6306 
      131.51        33.67        44.68 

$`TRRAP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       63.62        22.09        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       43.76        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       32.91        30.44        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        20.12        20.28         7.04        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        54.02         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3812 
       15.02        11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 
       12.20        12.76        14.30       148.01        85.45        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        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-A28C 
      140.38         7.50        44.32       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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  TRRAP MUTATED TRRAP WILD-TYPE 
           0.92            0.00 
  TRRAP MUTATED TRRAP WILD-TYPE 
         131.51          148.01 
  TRRAP MUTATED TRRAP WILD-TYPE 
          26.99           21.99 
[1] "0.9 - 131.5 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D328V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRRAP MUTATED         8        0        6        14         3         0
  TRRAP WILD-TYPE      56        1       20        94         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRRAP MUTATED           5          1          4          5        0         1
  TRRAP WILD-TYPE        13          5         40         28       35        11
                 vv
clus              STAGE IVB
  TRRAP MUTATED           0
  TRRAP WILD-TYPE         1
D328V3, multiclass
            clus
vv           TRRAP MUTATED TRRAP WILD-TYPE
  STAGE I                8              56
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA             14              94
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              5              13
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             5              28
  STAGE IV               0              35
  STAGE IVA              1              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
  TRRAP MUTATED     3   7  32   7
  TRRAP WILD-TYPE   6  60 217  34
D328V4, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  T1             3               6
  T2             7              60
  T3            32             217
  T4             7              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
  TRRAP MUTATED    33   9   7
  TRRAP WILD-TYPE 187  72  59
D328V5, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  N0            33             187
  N1             9              72
  N2             7              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V6, binary
                 cls
clus                0   1
  TRRAP MUTATED    41   1
  TRRAP WILD-TYPE 244  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     41    1
  TRRAP WILD-TYPE  244   47
   clus
vv  TRRAP MUTATED TRRAP WILD-TYPE
  0            41             244
  1             1              47
[1] 2 2
[1] FALSE
D328V7, binary
                 cls
clus                0   1
  TRRAP MUTATED    25  24
  TRRAP WILD-TYPE 145 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     25   24
  TRRAP WILD-TYPE  145  173
        clus
vv       TRRAP MUTATED TRRAP WILD-TYPE
  FEMALE            25             145
  MALE              24             173
[1] 2 2
[1] FALSE
D328V8, binary
                 cls
clus                0   1
  TRRAP MUTATED    40   1
  TRRAP WILD-TYPE 260   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     40    1
  TRRAP WILD-TYPE  260    7
     clus
vv    TRRAP MUTATED TRRAP WILD-TYPE
  NO             40             260
  YES             1               7
[1] 2 2
[1] FALSE
D328V9, binary
                 cls
clus                0   1
  TRRAP MUTATED    44   5
  TRRAP WILD-TYPE 270  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     44    5
  TRRAP WILD-TYPE  270   43
                               clus
vv                              TRRAP MUTATED TRRAP WILD-TYPE
  COLON ADENOCARCINOMA                     44             270
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRRAP MUTATED    33   0   0   8
  TRRAP WILD-TYPE 226   3  22  13
D328V10, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  R0            33             226
  R1             0               3
  R2             0              22
  RX             8              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"
D328V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRRAP MUTATED                                  0     1
  TRRAP WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRRAP MUTATED                           3    28
  TRRAP WILD-TYPE                        16   148
D328V12, multiclass
                                  clus
vv                                 TRRAP MUTATED TRRAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       28             148
[1] 4 2
[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 = OR11G2 MUTATION ANALYSIS
D329V1, survival
                  sevent
clus2                0   1
  OR11G2 MUTATED     3   2
  OR11G2 WILD-TYPE 274  76
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               5              350 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               2               76 
$`OR11G2 MUTATED`
TCGA-AA-3489 TCGA-AA-A00N TCGA-D5-5541 TCGA-DM-A28E TCGA-G4-6307 
        7.04         4.01        55.92       119.93        55.04 

$`OR11G2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OR11G2 MUTATED OR11G2 WILD-TYPE 
            4.01             0.00 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
          119.93           148.01 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
          55.040           22.045 
[1] "4.0 - 119.9 (55.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D329V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR11G2 MUTATED         0        0        1         1         1         0
  OR11G2 WILD-TYPE      64        1       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR11G2 MUTATED           0          0          2          0        0
  OR11G2 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR11G2 MUTATED           0         0
  OR11G2 WILD-TYPE        12         1
D329V3, multiclass
            clus
vv           OR11G2 MUTATED OR11G2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  OR11G2 MUTATED     0   0   4   1
  OR11G2 WILD-TYPE   9  67 245  40
D329V4, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              1               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
  OR11G2 MUTATED     3   2   0
  OR11G2 WILD-TYPE 217  79  66
D329V5, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  N0              3              217
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V6, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     5   0
  OR11G2 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      5    0
  OR11G2 WILD-TYPE  280   48
   clus
vv  OR11G2 MUTATED OR11G2 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D329V7, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     2   3
  OR11G2 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      2    3
  OR11G2 WILD-TYPE  168  194
        clus
vv       OR11G2 MUTATED OR11G2 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D329V8, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     3   0
  OR11G2 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      3    0
  OR11G2 WILD-TYPE  297    8
     clus
vv    OR11G2 MUTATED OR11G2 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D329V9, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     4   1
  OR11G2 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      4    1
  OR11G2 WILD-TYPE  310   47
                               clus
vv                              OR11G2 MUTATED OR11G2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR11G2 MUTATED     4   0   0   0
  OR11G2 WILD-TYPE 255   3  22  21
D329V10, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D329V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR11G2 MUTATED                                  0     0
  OR11G2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR11G2 MUTATED                           0     3
  OR11G2 WILD-TYPE                        19   173
D329V12, multiclass
                                  clus
vv                                 OR11G2 MUTATED OR11G2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = TRIM23 MUTATION ANALYSIS
D330V1, survival
                  sevent
clus2                0   1
  TRIM23 MUTATED     8   2
  TRIM23 WILD-TYPE 269  76
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              10              345 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
               2               76 
$`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 
      133.18        74.56        61.91        36.00 

$`TRIM23 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        13.78        46.75 

  TRIM23 MUTATED TRIM23 WILD-TYPE 
            1.02             0.00 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
          133.18           148.01 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
          42.705           21.990 
[1] "1.0 - 133.2 (42.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D330V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM23 MUTATED         1        0        2         2         0         0
  TRIM23 WILD-TYPE      63        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM23 MUTATED           1          0          1          2        1
  TRIM23 WILD-TYPE        17          6         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM23 MUTATED           0         0
  TRIM23 WILD-TYPE        12         1
D330V3, multiclass
            clus
vv           TRIM23 MUTATED TRIM23 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  TRIM23 MUTATED     0   2   9   0
  TRIM23 WILD-TYPE   9  65 240  41
D330V4, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              9              240
  T4              0               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
  TRIM23 MUTATED     6   3   2
  TRIM23 WILD-TYPE 214  78  64
D330V5, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  N0              6              214
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V6, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     7   1
  TRIM23 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      7    1
  TRIM23 WILD-TYPE  278   47
   clus
vv  TRIM23 MUTATED TRIM23 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D330V7, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     7   4
  TRIM23 WILD-TYPE 163 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      7    4
  TRIM23 WILD-TYPE  163  193
        clus
vv       TRIM23 MUTATED TRIM23 WILD-TYPE
  FEMALE              7              163
  MALE                4              193
[1] 2 2
[1] FALSE
D330V8, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     8   0
  TRIM23 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      8    0
  TRIM23 WILD-TYPE  292    8
     clus
vv    TRIM23 MUTATED TRIM23 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D330V9, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     9   2
  TRIM23 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      9    2
  TRIM23 WILD-TYPE  305   46
                               clus
vv                              TRIM23 MUTATED TRIM23 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM23 MUTATED     8   0   0   0
  TRIM23 WILD-TYPE 251   3  22  21
D330V10, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              0               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"
D330V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM23 MUTATED                                  0     0
  TRIM23 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM23 MUTATED                           0     7
  TRIM23 WILD-TYPE                        19   169
D330V12, multiclass
                                  clus
vv                                 TRIM23 MUTATED TRIM23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = BRAF MUTATION ANALYSIS
D331V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    67  25
  BRAF WILD-TYPE 210  53
  BRAF MUTATED BRAF WILD-TYPE 
            92            263 
  BRAF MUTATED BRAF WILD-TYPE 
            25             53 
$`BRAF MUTATED`
TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3713 TCGA-AA-3715 
       24.16        13.02         8.05         0.99        19.04        19.04 
TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
       24.00        25.08        10.88         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2676 
       35.80        26.17        91.79        79.69        46.65        42.90 
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6653 
       32.75        31.63        33.53        22.09        22.06        24.39 
TCGA-AA-3492 TCGA-AA-3664 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3877 
        3.02        54.02        33.04         1.02        15.95        31.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A01D 
       33.01        26.01         2.01        19.00        18.05        10.98 
TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AU-6004 TCGA-AY-6196 
       38.07        12.16        83.24        27.42        27.09         0.20 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
       88.21        49.41        29.56        11.74        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       10.06        17.56        85.45        15.62        51.32        21.99 
TCGA-CK-6747 TCGA-CM-4744 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       82.95        20.02        22.98        30.08        32.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       15.02        17.03        12.00        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6534 
       14.04        12.95        13.05        54.61        20.19        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 
       15.12        17.85        12.49        16.14        11.64        13.35 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
       24.43        38.20        92.75        49.91        13.32         7.50 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6303 
      135.65        81.37        31.96         6.18        74.56        65.85 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

$`BRAF WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53         1.02        24.03        37.05        36.03 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       49.08        43.76        43.76        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       33.34        36.53        32.91        30.44        29.19        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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        0.99        25.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       27.02        18.05         2.01        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       40.96        24.53         5.79        22.42        26.47        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-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79         6.77        12.10 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        5.23         3.19        12.69        12.36        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       12.20        14.30       148.01        21.14         2.01       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        14.04        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        25.48         4.80        17.13        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        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        43.04        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 
       44.68        55.04        85.48        61.91        36.00 

  BRAF MUTATED BRAF WILD-TYPE 
           0.2            0.0 
  BRAF MUTATED BRAF WILD-TYPE 
        135.65         148.01 
  BRAF MUTATED BRAF WILD-TYPE 
        22.075         22.030 
[1] "0.2 - 135.7 (22.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D331V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRAF MUTATED        14        1        5        33         4         0
  BRAF WILD-TYPE      50        0       21        75         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED           4          0         17          7        5         1
  BRAF WILD-TYPE        14          6         27         26       30        11
                vv
clus             STAGE IVB
  BRAF MUTATED           1
  BRAF WILD-TYPE         0
D331V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I              14             50
  STAGE IA              1              0
  STAGE II              5             21
  STAGE IIA            33             75
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             4             14
  STAGE IIIA            0              6
  STAGE IIIB           17             27
  STAGE IIIC            7             26
  STAGE IV              5             30
  STAGE IVA             1             11
  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  14  66  13
  BRAF WILD-TYPE   7  53 183  28
D331V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            2              7
  T2           14             53
  T3           66            183
  T4           13             28
[1] 4 2
[1] TRUE
[1] "dimension 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    60  22  14
  BRAF WILD-TYPE 160  59  52
D331V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           60            160
  N1           22             59
  N2           14             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V6, binary
                cls
clus               0   1
  BRAF MUTATED    75   7
  BRAF WILD-TYPE 210  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     75    7
  BRAF WILD-TYPE  210   41
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           75            210
  1            7             41
[1] 2 2
[1] FALSE
D331V7, binary
                cls
clus               0   1
  BRAF MUTATED    52  44
  BRAF WILD-TYPE 118 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     52   44
  BRAF WILD-TYPE  118  153
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           52            118
  MALE             44            153
[1] 2 2
[1] FALSE
D331V8, binary
                cls
clus               0   1
  BRAF MUTATED    76   2
  BRAF WILD-TYPE 224   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     76    2
  BRAF WILD-TYPE  224    6
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            76            224
  YES            2              6
[1] 2 2
[1] FALSE
D331V9, binary
                cls
clus               0   1
  BRAF MUTATED    68  25
  BRAF WILD-TYPE 246  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     68   25
  BRAF WILD-TYPE  246   23
                               clus
vv                              BRAF MUTATED BRAF WILD-TYPE
  COLON ADENOCARCINOMA                    68            246
  COLON MUCINOUS ADENOCARCINOMA           25             23
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    64   1   2   9
  BRAF WILD-TYPE 195   2  20  12
D331V10, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           64            195
  R1            1              2
  R2            2             20
  RX            9             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     4
  BRAF WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           8    62
  BRAF WILD-TYPE                        11   114
D331V12, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   8             11
  WHITE                                      62            114
[1] 4 2
[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 = GTF2B MUTATION ANALYSIS
D332V1, survival
                 sevent
clus2               0   1
  GTF2B MUTATED    10   0
  GTF2B WILD-TYPE 267  78
  GTF2B MUTATED GTF2B WILD-TYPE 
             10             345 
  GTF2B MUTATED GTF2B WILD-TYPE 
              0              78 
$`GTF2B MUTATED`
TCGA-AA-3713 TCGA-AZ-4681 TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3877 
       19.04       106.75        35.80        63.98        78.08        31.00 
TCGA-AZ-4315 TCGA-CM-5344 TCGA-DM-A1HB TCGA-G4-6323 
       58.39        22.03       135.65        13.78 

$`GTF2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        46.75 

  GTF2B MUTATED GTF2B WILD-TYPE 
          13.78            0.00 
  GTF2B MUTATED GTF2B WILD-TYPE 
         135.65          148.01 
  GTF2B MUTATED GTF2B WILD-TYPE 
         47.095          21.990 
[1] "13.8 - 135.7 (47.1)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.7e+07"
D332V2, continuous
                 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      63        0       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GTF2B MUTATED           0          0          2          0        1         0
  GTF2B WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  GTF2B MUTATED           0
  GTF2B WILD-TYPE         1
D332V3, multiclass
            clus
vv           GTF2B MUTATED GTF2B WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GTF2B MUTATED     1   0   8   1
  GTF2B WILD-TYPE   8  67 241  40
D332V4, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  T1             1               8
  T2             0              67
  T3             8             241
  T4             1              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
  GTF2B MUTATED     9   2   0
  GTF2B WILD-TYPE 211  79  66
D332V5, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  N0             9             211
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V6, binary
                 cls
clus                0   1
  GTF2B MUTATED     8   1
  GTF2B WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      8    1
  GTF2B WILD-TYPE  277   47
   clus
vv  GTF2B MUTATED GTF2B WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D332V7, binary
                 cls
clus                0   1
  GTF2B MUTATED     6   5
  GTF2B WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      6    5
  GTF2B WILD-TYPE  164  192
        clus
vv       GTF2B MUTATED GTF2B WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D332V8, binary
                 cls
clus                0   1
  GTF2B MUTATED     8   1
  GTF2B WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      8    1
  GTF2B WILD-TYPE  292    7
     clus
vv    GTF2B MUTATED GTF2B WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D332V9, binary
                 cls
clus                0   1
  GTF2B MUTATED     9   1
  GTF2B WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      9    1
  GTF2B WILD-TYPE  305   47
                               clus
vv                              GTF2B MUTATED GTF2B WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GTF2B MUTATED     8   0   1   1
  GTF2B WILD-TYPE 251   3  21  20
D332V10, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             1              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"
D332V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2B MUTATED                                  0     0
  GTF2B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GTF2B MUTATED                           1     6
  GTF2B WILD-TYPE                        18   170
D332V12, multiclass
                                  clus
vv                                 GTF2B MUTATED GTF2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = DDB1 MUTATION ANALYSIS
D333V1, survival
                sevent
clus2              0   1
  DDB1 MUTATED     7   6
  DDB1 WILD-TYPE 270  72
  DDB1 MUTATED DDB1 WILD-TYPE 
            13            342 
  DDB1 MUTATED DDB1 WILD-TYPE 
             6             72 
$`DDB1 MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AD-6964 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3949 
        1.02        13.02        10.88        33.53        20.12        26.01 
TCGA-AA-A01Q TCGA-AZ-6599 TCGA-CM-5862 TCGA-D5-6537 TCGA-D5-7000 TCGA-DM-A1HB 
        1.02         6.77         5.03         4.80        10.26       135.65 
TCGA-F4-6460 
       31.96 

$`DDB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6569 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DDB1 MUTATED DDB1 WILD-TYPE 
          1.02           0.00 
  DDB1 MUTATED DDB1 WILD-TYPE 
        135.65         148.01 
  DDB1 MUTATED DDB1 WILD-TYPE 
        10.880         22.225 
[1] "1.0 - 135.7 (10.9)" "0.0 - 148.0 (22.2)"
[1] "hr=" "3"  
D333V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDB1 MUTATED         2        0        2         2         0         0
  DDB1 WILD-TYPE      62        1       24       106         8         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        17          6         40         33       35        11
                vv
clus             STAGE IVB
  DDB1 MUTATED           0
  DDB1 WILD-TYPE         1
D333V3, multiclass
            clus
vv           DDB1 MUTATED DDB1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  DDB1 MUTATED     0   2  10   1
  DDB1 WILD-TYPE   9  65 239  40
D333V4, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           10            239
  T4            1             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
  DDB1 MUTATED     6   5   2
  DDB1 WILD-TYPE 214  76  64
D333V5, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  N0            6            214
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V6, binary
                cls
clus               0   1
  DDB1 MUTATED     8   1
  DDB1 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      8    1
  DDB1 WILD-TYPE  277   47
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D333V7, binary
                cls
clus               0   1
  DDB1 MUTATED     7   6
  DDB1 WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      7    6
  DDB1 WILD-TYPE  163  191
        clus
vv       DDB1 MUTATED DDB1 WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D333V8, binary
                cls
clus               0   1
  DDB1 MUTATED    10   0
  DDB1 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED     10    0
  DDB1 WILD-TYPE  290    8
     clus
vv    DDB1 MUTATED DDB1 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D333V9, binary
                cls
clus               0   1
  DDB1 MUTATED     8   4
  DDB1 WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      8    4
  DDB1 WILD-TYPE  306   44
                               clus
vv                              DDB1 MUTATED DDB1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DDB1 MUTATED     8   0   0   0
  DDB1 WILD-TYPE 251   3  22  21
D333V10, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D333V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDB1 MUTATED                                  0     0
  DDB1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DDB1 MUTATED                           1     8
  DDB1 WILD-TYPE                        18   168
D333V12, multiclass
                                  clus
vv                                 DDB1 MUTATED DDB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = EZH2 MUTATION ANALYSIS
D334V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED    32  11
  EZH2 WILD-TYPE 245  67
  EZH2 MUTATED EZH2 WILD-TYPE 
            43            312 
  EZH2 MUTATED EZH2 WILD-TYPE 
            11             67 
$`EZH2 MUTATED`
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6964 TCGA-AZ-6608 TCGA-G4-6586 
        6.05         0.92        19.04        10.88         1.94        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5661 
       26.17        79.69        42.90        32.75        29.19        33.53 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 
       22.06         8.38        24.39        19.66        63.98         6.97 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-6599 TCGA-CA-6717 
        4.01        34.98         0.20        21.44         6.77        12.76 
TCGA-CA-6718 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 TCGA-D5-5540 TCGA-D5-6535 
       10.06        22.03        15.02        15.02        56.09        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-DM-A1DB 
       17.85         4.80        16.14        15.58        12.39        44.32 
TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6317 
      135.65        35.97        33.67        65.85        44.68        36.00 
TCGA-G4-6626 
       46.75 

$`EZH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       13.02        17.95        23.01        19.99        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       15.52        25.08       106.75       100.01        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       63.62        22.09        91.79        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        36.53        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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       22.52        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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-5868 
       22.98        30.08        32.02        15.02         5.03        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        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        54.61        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       18.25        25.48        43.27        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
       12.59       140.38         7.50       131.51       139.17        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6323 
       74.56        53.62        55.04        85.48        61.91        13.78 

  EZH2 MUTATED EZH2 WILD-TYPE 
           0.2            0.0 
  EZH2 MUTATED EZH2 WILD-TYPE 
        135.65         148.01 
  EZH2 MUTATED EZH2 WILD-TYPE 
        21.440         22.225 
[1] "0.2 - 135.7 (21.4)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D334V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EZH2 MUTATED         6        0        2        14         4         0
  EZH2 WILD-TYPE      58        1       24        94         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EZH2 MUTATED           2          1          6          4        3         0
  EZH2 WILD-TYPE        16          5         38         29       32        12
                vv
clus             STAGE IVB
  EZH2 MUTATED           0
  EZH2 WILD-TYPE         1
D334V3, multiclass
            clus
vv           EZH2 MUTATED EZH2 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            14             94
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            1              5
  STAGE IIIB            6             38
  STAGE IIIC            4             29
  STAGE IV              3             32
  STAGE IVA             0             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
  EZH2 MUTATED     1   7  29   7
  EZH2 WILD-TYPE   8  60 220  34
D334V4, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  T1            1              8
  T2            7             60
  T3           29            220
  T4            7             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
  EZH2 MUTATED    28  10   6
  EZH2 WILD-TYPE 192  71  60
D334V5, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  N0           28            192
  N1           10             71
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V6, binary
                cls
clus               0   1
  EZH2 MUTATED    33   3
  EZH2 WILD-TYPE 252  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     33    3
  EZH2 WILD-TYPE  252   45
   clus
vv  EZH2 MUTATED EZH2 WILD-TYPE
  0           33            252
  1            3             45
[1] 2 2
[1] FALSE
D334V7, binary
                cls
clus               0   1
  EZH2 MUTATED    17  27
  EZH2 WILD-TYPE 153 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     17   27
  EZH2 WILD-TYPE  153  170
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  FEMALE           17            153
  MALE             27            170
[1] 2 2
[1] FALSE
D334V8, binary
                cls
clus               0   1
  EZH2 MUTATED    37   1
  EZH2 WILD-TYPE 263   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     37    1
  EZH2 WILD-TYPE  263    7
     clus
vv    EZH2 MUTATED EZH2 WILD-TYPE
  NO            37            263
  YES            1              7
[1] 2 2
[1] FALSE
D334V9, binary
                cls
clus               0   1
  EZH2 MUTATED    36   7
  EZH2 WILD-TYPE 278  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     36    7
  EZH2 WILD-TYPE  278   41
                               clus
vv                              EZH2 MUTATED EZH2 WILD-TYPE
  COLON ADENOCARCINOMA                    36            278
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EZH2 MUTATED    30   0   2   3
  EZH2 WILD-TYPE 229   3  20  18
D334V10, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  R0           30            229
  R1            0              3
  R2            2             20
  RX            3             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"
D334V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EZH2 MUTATED                                  0     2
  EZH2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EZH2 MUTATED                           3    31
  EZH2 WILD-TYPE                        16   145
D334V12, multiclass
                                  clus
vv                                 EZH2 MUTATED EZH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      31            145
[1] 4 2
[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 = PRDM1 MUTATION ANALYSIS
D335V1, survival
                 sevent
clus2               0   1
  PRDM1 MUTATED    15   4
  PRDM1 WILD-TYPE 262  74
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             19             336 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
              4              74 
$`PRDM1 MUTATED`
TCGA-AA-3662 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3968 TCGA-AA-A00J TCGA-AA-A00N 
        6.05        32.71         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 
       55.04 

$`PRDM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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        54.61 
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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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        43.04        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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  PRDM1 MUTATED PRDM1 WILD-TYPE 
           4.01            0.00 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
         133.18          148.01 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
         21.990          22.075 
[1] "4.0 - 133.2 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRDM1 MUTATED         6        0        1         4         2         1
  PRDM1 WILD-TYPE      58        1       25       104         6         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        17          6         40         33       34        12
                 vv
clus              STAGE IVB
  PRDM1 MUTATED           0
  PRDM1 WILD-TYPE         1
D335V3, multiclass
            clus
vv           PRDM1 MUTATED PRDM1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  PRDM1 MUTATED     0   6   9   5
  PRDM1 WILD-TYPE   9  61 240  36
D335V4, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  T1             0               9
  T2             6              61
  T3             9             240
  T4             5              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
  PRDM1 MUTATED    14   5   1
  PRDM1 WILD-TYPE 206  76  65
D335V5, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  N0            14             206
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V6, binary
                 cls
clus                0   1
  PRDM1 MUTATED    16   1
  PRDM1 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     16    1
  PRDM1 WILD-TYPE  269   47
   clus
vv  PRDM1 MUTATED PRDM1 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D335V7, binary
                 cls
clus                0   1
  PRDM1 MUTATED    10  10
  PRDM1 WILD-TYPE 160 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     10   10
  PRDM1 WILD-TYPE  160  187
        clus
vv       PRDM1 MUTATED PRDM1 WILD-TYPE
  FEMALE            10             160
  MALE              10             187
[1] 2 2
[1] FALSE
D335V8, binary
                 cls
clus                0   1
  PRDM1 MUTATED    16   0
  PRDM1 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     16    0
  PRDM1 WILD-TYPE  284    8
     clus
vv    PRDM1 MUTATED PRDM1 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D335V9, binary
                 cls
clus                0   1
  PRDM1 MUTATED    15   5
  PRDM1 WILD-TYPE 299  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     15    5
  PRDM1 WILD-TYPE  299   43
                               clus
vv                              PRDM1 MUTATED PRDM1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRDM1 MUTATED    14   1   1   1
  PRDM1 WILD-TYPE 245   2  21  20
D335V10, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  R0            14             245
  R1             1               2
  R2             1              21
  RX             1              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"
D335V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRDM1 MUTATED                                  0     0
  PRDM1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRDM1 MUTATED                           2    13
  PRDM1 WILD-TYPE                        17   163
D335V12, multiclass
                                  clus
vv                                 PRDM1 MUTATED PRDM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       13             163
[1] 4 2
[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 = USP26 MUTATION ANALYSIS
D336V1, survival
                 sevent
clus2               0   1
  USP26 MUTATED    20   2
  USP26 WILD-TYPE 257  76
  USP26 MUTATED USP26 WILD-TYPE 
             22             333 
  USP26 MUTATED USP26 WILD-TYPE 
              2              76 
$`USP26 MUTATED`
TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 
       24.00        46.65        22.06        24.39        19.66        63.98 
TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00E TCGA-AA-A010 TCGA-AU-6004 
        6.97        53.00        33.01        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 
       11.38         6.18        41.42        35.31 

$`USP26 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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-F4-6807 
       31.96        35.74        47.87         1.55        34.42        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  USP26 MUTATED USP26 WILD-TYPE 
           6.18            0.00 
  USP26 MUTATED USP26 WILD-TYPE 
          63.98          148.01 
  USP26 MUTATED USP26 WILD-TYPE 
         24.195          21.990 
[1] "6.2 - 64.0 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D336V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP26 MUTATED         6        0        3        10         2         0
  USP26 WILD-TYPE      58        1       23        98         6         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  USP26 MUTATED           0
  USP26 WILD-TYPE         1
D336V3, multiclass
            clus
vv           USP26 MUTATED USP26 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  USP26 MUTATED     0   6  14   3
  USP26 WILD-TYPE   9  61 235  38
D336V4, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  T1             0               9
  T2             6              61
  T3            14             235
  T4             3              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
  USP26 MUTATED    21   2   0
  USP26 WILD-TYPE 199  79  66
D336V5, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  N0            21             199
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V6, binary
                 cls
clus                0   1
  USP26 MUTATED    20   0
  USP26 WILD-TYPE 265  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     20    0
  USP26 WILD-TYPE  265   48
   clus
vv  USP26 MUTATED USP26 WILD-TYPE
  0            20             265
  1             0              48
[1] 2 2
[1] FALSE
D336V7, binary
                 cls
clus                0   1
  USP26 MUTATED    10  13
  USP26 WILD-TYPE 160 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     10   13
  USP26 WILD-TYPE  160  184
        clus
vv       USP26 MUTATED USP26 WILD-TYPE
  FEMALE            10             160
  MALE              13             184
[1] 2 2
[1] FALSE
D336V8, binary
                 cls
clus                0   1
  USP26 MUTATED    21   0
  USP26 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     21    0
  USP26 WILD-TYPE  279    8
     clus
vv    USP26 MUTATED USP26 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D336V9, binary
                 cls
clus                0   1
  USP26 MUTATED    17   6
  USP26 WILD-TYPE 297  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     17    6
  USP26 WILD-TYPE  297   42
                               clus
vv                              USP26 MUTATED USP26 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP26 MUTATED    20   0   0   1
  USP26 WILD-TYPE 239   3  22  20
D336V10, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  R0            20             239
  R1             0               3
  R2             0              22
  RX             1              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"
D336V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP26 MUTATED                                  0     1
  USP26 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP26 MUTATED                           0    14
  USP26 WILD-TYPE                        19   162
D336V12, multiclass
                                  clus
vv                                 USP26 MUTATED USP26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       14             162
[1] 4 2
[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 = TXNDC15 MUTATION ANALYSIS
D337V1, survival
                   sevent
clus2                 0   1
  TXNDC15 MUTATED     4   2
  TXNDC15 WILD-TYPE 273  76
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                6               349 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                2                76 
$`TXNDC15 MUTATED`
TCGA-AA-3950 TCGA-DM-A285 TCGA-AA-A00N TCGA-CM-4746 TCGA-CM-6163 TCGA-G4-6307 
       24.00         5.88         4.01        37.02        14.04        55.04 

$`TXNDC15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
             4.01              0.00 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
            55.04            148.01 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
            19.02             22.06 
[1] "4.0 - 55.0 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D337V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC15 MUTATED         2        0        0         1         1         0
  TXNDC15 WILD-TYPE      62        1       26       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC15 MUTATED           0          0          1          0        1
  TXNDC15 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  TXNDC15 MUTATED           0         0
  TXNDC15 WILD-TYPE        12         1
D337V3, multiclass
            clus
vv           TXNDC15 MUTATED TXNDC15 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  TXNDC15 MUTATED     1   1   3   1
  TXNDC15 WILD-TYPE   8  66 246  40
D337V4, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               3               246
  T4               1                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
  TXNDC15 MUTATED     4   1   1
  TXNDC15 WILD-TYPE 216  80  65
D337V5, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V6, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     5   1
  TXNDC15 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      5    1
  TXNDC15 WILD-TYPE  280   47
   clus
vv  TXNDC15 MUTATED TXNDC15 WILD-TYPE
  0               5               280
  1               1                47
[1] 2 2
[1] FALSE
D337V7, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     3   3
  TXNDC15 WILD-TYPE 167 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      3    3
  TXNDC15 WILD-TYPE  167  194
        clus
vv       TXNDC15 MUTATED TXNDC15 WILD-TYPE
  FEMALE               3               167
  MALE                 3               194
[1] 2 2
[1] FALSE
D337V8, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     4   0
  TXNDC15 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      4    0
  TXNDC15 WILD-TYPE  296    8
     clus
vv    TXNDC15 MUTATED TXNDC15 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D337V9, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     3   3
  TXNDC15 WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      3    3
  TXNDC15 WILD-TYPE  311   45
                               clus
vv                              TXNDC15 MUTATED TXNDC15 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TXNDC15 MUTATED     5   0   0   0
  TXNDC15 WILD-TYPE 254   3  22  21
D337V10, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D337V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC15 MUTATED                                  0     0
  TXNDC15 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TXNDC15 MUTATED                           1     3
  TXNDC15 WILD-TYPE                        18   173
D337V12, multiclass
                                  clus
vv                                 TXNDC15 MUTATED TXNDC15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = OR1I1 MUTATION ANALYSIS
D338V1, survival
                 sevent
clus2               0   1
  OR1I1 MUTATED     9   1
  OR1I1 WILD-TYPE 268  77
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             10             345 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
              1              77 
$`OR1I1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6625 TCGA-A6-5659 TCGA-AA-3864 TCGA-AU-3779 TCGA-CA-6717 
      100.01        91.79        30.44        53.00        14.50        12.76 
TCGA-CM-5861 TCGA-D5-6930 TCGA-F4-6569 TCGA-G4-6293 
       15.02        13.35        35.74       133.18 

$`OR1I1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  OR1I1 MUTATED OR1I1 WILD-TYPE 
          12.76            0.00 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
         133.18          148.01 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
          33.09           22.03 
[1] "12.8 - 133.2 (33.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.9"
D338V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR1I1 MUTATED         2        0        2         5         0         0
  OR1I1 WILD-TYPE      62        1       24       103         8         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  OR1I1 MUTATED           0
  OR1I1 WILD-TYPE         1
D338V3, multiclass
            clus
vv           OR1I1 MUTATED OR1I1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR1I1 MUTATED     0   2   8   0
  OR1I1 WILD-TYPE   9  65 241  41
D338V4, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             0              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
  OR1I1 MUTATED     9   1   0
  OR1I1 WILD-TYPE 211  80  66
D338V5, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V6, binary
                 cls
clus                0   1
  OR1I1 MUTATED    10   0
  OR1I1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED     10    0
  OR1I1 WILD-TYPE  275   48
   clus
vv  OR1I1 MUTATED OR1I1 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D338V7, binary
                 cls
clus                0   1
  OR1I1 MUTATED     4   6
  OR1I1 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED      4    6
  OR1I1 WILD-TYPE  166  191
        clus
vv       OR1I1 MUTATED OR1I1 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D338V8, binary
                 cls
clus                0   1
  OR1I1 MUTATED    10   0
  OR1I1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED     10    0
  OR1I1 WILD-TYPE  290    8
     clus
vv    OR1I1 MUTATED OR1I1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D338V9, binary
                 cls
clus                0   1
  OR1I1 MUTATED     8   2
  OR1I1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED      8    2
  OR1I1 WILD-TYPE  306   46
                               clus
vv                              OR1I1 MUTATED OR1I1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR1I1 MUTATED     8   0   0   1
  OR1I1 WILD-TYPE 251   3  22  20
D338V10, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D338V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR1I1 MUTATED                                  0     1
  OR1I1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR1I1 MUTATED                           0     8
  OR1I1 WILD-TYPE                        19   168
D338V12, multiclass
                                  clus
vv                                 OR1I1 MUTATED OR1I1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = CUL2 MUTATION ANALYSIS
D339V1, survival
                sevent
clus2              0   1
  CUL2 MUTATED    11   2
  CUL2 WILD-TYPE 266  76
  CUL2 MUTATED CUL2 WILD-TYPE 
            13            342 
  CUL2 MUTATED CUL2 WILD-TYPE 
             2             76 
$`CUL2 MUTATED`
TCGA-G4-6628 TCGA-AA-3555 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 
       79.69        29.95         2.01        34.98         1.02        83.24 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6532 TCGA-D5-6538 
       58.39        49.41        12.76        23.05        18.25        17.13 
TCGA-D5-6928 
       11.64 

$`CUL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CUL2 MUTATED CUL2 WILD-TYPE 
          1.02           0.00 
  CUL2 MUTATED CUL2 WILD-TYPE 
         83.24         148.01 
  CUL2 MUTATED CUL2 WILD-TYPE 
        23.050         22.045 
[1] "1.0 - 83.2 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D339V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUL2 MUTATED         1        0        2         8         2         0
  CUL2 WILD-TYPE      63        1       24       100         6         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  CUL2 MUTATED           0
  CUL2 WILD-TYPE         1
D339V3, multiclass
            clus
vv           CUL2 MUTATED CUL2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CUL2 MUTATED     0   1  11   2
  CUL2 WILD-TYPE   9  66 238  39
D339V4, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           11            238
  T4            2             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
  CUL2 MUTATED    13   0   1
  CUL2 WILD-TYPE 207  81  65
D339V5, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  N0           13            207
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V6, binary
                cls
clus               0   1
  CUL2 MUTATED    12   0
  CUL2 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     12    0
  CUL2 WILD-TYPE  273   48
   clus
vv  CUL2 MUTATED CUL2 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D339V7, binary
                cls
clus               0   1
  CUL2 MUTATED     7   7
  CUL2 WILD-TYPE 163 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      7    7
  CUL2 WILD-TYPE  163  190
        clus
vv       CUL2 MUTATED CUL2 WILD-TYPE
  FEMALE            7            163
  MALE              7            190
[1] 2 2
[1] FALSE
D339V8, binary
                cls
clus               0   1
  CUL2 MUTATED    11   0
  CUL2 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     11    0
  CUL2 WILD-TYPE  289    8
     clus
vv    CUL2 MUTATED CUL2 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D339V9, binary
                cls
clus               0   1
  CUL2 MUTATED    10   4
  CUL2 WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     10    4
  CUL2 WILD-TYPE  304   44
                               clus
vv                              CUL2 MUTATED CUL2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CUL2 MUTATED    10   0   0   2
  CUL2 WILD-TYPE 249   3  22  19
D339V10, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            2             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"
D339V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL2 MUTATED                                  0     2
  CUL2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL2 MUTATED                           0     8
  CUL2 WILD-TYPE                        19   168
D339V12, multiclass
                                  clus
vv                                 CUL2 MUTATED CUL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = TMEM169 MUTATION ANALYSIS
D340V1, survival
                   sevent
clus2                 0   1
  TMEM169 MUTATED     5   8
  TMEM169 WILD-TYPE 272  70
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               13               342 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
                8                70 
$`TMEM169 MUTATED`
TCGA-A6-4105 TCGA-AA-3713 TCGA-AA-3489 TCGA-AA-3510 TCGA-AD-6889 TCGA-CK-5916 
       14.53        19.04         7.04        63.98        83.24        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 
       65.85 

$`TMEM169 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TMEM169 MUTATED TMEM169 WILD-TYPE 
             6.18              0.00 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
           124.27            148.01 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
            20.19             22.09 
[1] "6.2 - 124.3 (20.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D340V2, continuous
                   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      62        1       24       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM169 MUTATED           0          0          1          0        2
  TMEM169 WILD-TYPE        18          6         43         33       33
                   vv
clus                STAGE IVA STAGE IVB
  TMEM169 MUTATED           0         0
  TMEM169 WILD-TYPE        12         1
D340V3, multiclass
            clus
vv           TMEM169 MUTATED TMEM169 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  TMEM169 MUTATED     1   1  11   0
  TMEM169 WILD-TYPE   8  66 238  41
D340V4, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3              11               238
  T4               0                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
  TMEM169 MUTATED    11   2   0
  TMEM169 WILD-TYPE 209  79  66
D340V5, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  N0              11               209
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V6, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    10   2
  TMEM169 WILD-TYPE 275  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     10    2
  TMEM169 WILD-TYPE  275   46
   clus
vv  TMEM169 MUTATED TMEM169 WILD-TYPE
  0              10               275
  1               2                46
[1] 2 2
[1] FALSE
D340V7, binary
                   cls
clus                  0   1
  TMEM169 MUTATED     5   8
  TMEM169 WILD-TYPE 165 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED      5    8
  TMEM169 WILD-TYPE  165  189
        clus
vv       TMEM169 MUTATED TMEM169 WILD-TYPE
  FEMALE               5               165
  MALE                 8               189
[1] 2 2
[1] FALSE
D340V8, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    10   1
  TMEM169 WILD-TYPE 290   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     10    1
  TMEM169 WILD-TYPE  290    7
     clus
vv    TMEM169 MUTATED TMEM169 WILD-TYPE
  NO               10               290
  YES               1                 7
[1] 2 2
[1] FALSE
D340V9, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    11   1
  TMEM169 WILD-TYPE 303  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     11    1
  TMEM169 WILD-TYPE  303   47
                               clus
vv                              TMEM169 MUTATED TMEM169 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM169 MUTATED     7   0   1   2
  TMEM169 WILD-TYPE 252   3  21  19
D340V10, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               1                21
  RX               2                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"
D340V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM169 MUTATED                                  0     1
  TMEM169 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM169 MUTATED                           0     9
  TMEM169 WILD-TYPE                        19   167
D340V12, multiclass
                                  clus
vv                                 TMEM169 MUTATED TMEM169 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(341) Variable = PIK3C2A MUTATION ANALYSIS
D341V1, survival
                   sevent
clus2                 0   1
  PIK3C2A MUTATED    13   1
  PIK3C2A WILD-TYPE 264  77
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               14               341 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
                1                77 
$`PIK3C2A MUTATED`
TCGA-AA-3496 TCGA-A6-5660 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-3877 TCGA-AA-3977 
        1.02        29.19         8.38        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 
       85.48        61.91 

$`PIK3C2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        36.00        13.78        46.75 

  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
             1.02              0.00 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
            85.48            148.01 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
           27.105            22.030 
[1] "1.0 - 85.5 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "4.2"
D341V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C2A MUTATED         2        0        3         4         0         0
  PIK3C2A WILD-TYPE      62        1       23       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2A MUTATED           0          0          2          1        1
  PIK3C2A WILD-TYPE        18          6         42         32       34
                   vv
clus                STAGE IVA STAGE IVB
  PIK3C2A MUTATED           0         0
  PIK3C2A WILD-TYPE        12         1
D341V3, multiclass
            clus
vv           PIK3C2A MUTATED PIK3C2A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  PIK3C2A MUTATED     1   2  11   0
  PIK3C2A WILD-TYPE   8  65 238  41
D341V4, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  T1               1                 8
  T2               2                65
  T3              11               238
  T4               0                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
  PIK3C2A MUTATED    10   3   1
  PIK3C2A WILD-TYPE 210  78  65
D341V5, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  N0              10               210
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V6, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    11   1
  PIK3C2A WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     11    1
  PIK3C2A WILD-TYPE  274   47
   clus
vv  PIK3C2A MUTATED PIK3C2A WILD-TYPE
  0              11               274
  1               1                47
[1] 2 2
[1] FALSE
D341V7, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED     7   7
  PIK3C2A WILD-TYPE 163 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED      7    7
  PIK3C2A WILD-TYPE  163  190
        clus
vv       PIK3C2A MUTATED PIK3C2A WILD-TYPE
  FEMALE               7               163
  MALE                 7               190
[1] 2 2
[1] FALSE
D341V8, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    13   0
  PIK3C2A WILD-TYPE 287   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     13    0
  PIK3C2A WILD-TYPE  287    8
     clus
vv    PIK3C2A MUTATED PIK3C2A WILD-TYPE
  NO               13               287
  YES               0                 8
[1] 2 2
[1] FALSE
D341V9, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    10   4
  PIK3C2A WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     10    4
  PIK3C2A WILD-TYPE  304   44
                               clus
vv                              PIK3C2A MUTATED PIK3C2A WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PIK3C2A MUTATED     8   1   0   1
  PIK3C2A WILD-TYPE 251   2  22  20
D341V10, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  R0               8               251
  R1               1                 2
  R2               0                22
  RX               1                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"
D341V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C2A MUTATED                                  0     1
  PIK3C2A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3C2A MUTATED                           4     5
  PIK3C2A WILD-TYPE                        15   171
D341V12, multiclass
                                  clus
vv                                 PIK3C2A MUTATED PIK3C2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      4                15
  WHITE                                          5               171
[1] 4 2
[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 = MSH6 MUTATION ANALYSIS
D342V1, survival
                sevent
clus2              0   1
  MSH6 MUTATED    33   6
  MSH6 WILD-TYPE 244  72
  MSH6 MUTATED MSH6 WILD-TYPE 
            39            316 
  MSH6 MUTATED MSH6 WILD-TYPE 
             6             72 
$`MSH6 MUTATED`
TCGA-AA-3525 TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6321 TCGA-A6-3809 
        8.05        19.04        24.00       100.01        22.09        32.75 
TCGA-A6-5662 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3949 TCGA-AA-3968 
       23.61        61.02        78.08        26.99        26.01        21.99 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6963 TCGA-AU-3779 
       25.02         4.01        34.98        24.53        27.42        14.50 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5255 
       58.39        62.79        88.21        49.41        12.10        12.36 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5344 
       12.76       148.01        85.45        15.62       124.27        22.03 
TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6929 TCGA-D5-6930 
       29.03        13.02        25.48        15.58        13.41        13.35 
TCGA-DM-A1HB TCGA-DM-A28H TCGA-G4-6307 
      135.65       117.07        55.04 

$`MSH6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        35.80        26.17        91.79        79.69 
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-A6-3810 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-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       29.95        20.98        13.94         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       33.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       83.24         5.79        22.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        5.13        22.36         6.77        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        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       10.06        14.30        17.56        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  MSH6 MUTATED MSH6 WILD-TYPE 
          4.01           0.00 
  MSH6 MUTATED MSH6 WILD-TYPE 
        148.01         140.38 
  MSH6 MUTATED MSH6 WILD-TYPE 
        25.480         21.405 
[1] "4.0 - 148.0 (25.5)" "0.0 - 140.4 (21.4)"
[1] "hr=" "2.3"
D342V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH6 MUTATED         3        0        6        10         3         0
  MSH6 WILD-TYPE      61        1       20        98         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH6 MUTATED           2          0          6          2        2         1
  MSH6 WILD-TYPE        16          6         38         31       33        11
                vv
clus             STAGE IVB
  MSH6 MUTATED           0
  MSH6 WILD-TYPE         1
D342V3, multiclass
            clus
vv           MSH6 MUTATED MSH6 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA            10             98
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            6             38
  STAGE IIIC            2             31
  STAGE IV              2             33
  STAGE IVA             1             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
  MSH6 MUTATED     2   4  27   6
  MSH6 WILD-TYPE   7  63 222  35
D342V4, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  T1            2              7
  T2            4             63
  T3           27            222
  T4            6             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
  MSH6 MUTATED    26  10   3
  MSH6 WILD-TYPE 194  71  63
D342V5, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  N0           26            194
  N1           10             71
  N2            3             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"
D342V6, binary
                cls
clus               0   1
  MSH6 MUTATED    29   3
  MSH6 WILD-TYPE 256  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     29    3
  MSH6 WILD-TYPE  256   45
   clus
vv  MSH6 MUTATED MSH6 WILD-TYPE
  0           29            256
  1            3             45
[1] 2 2
[1] FALSE
D342V7, binary
                cls
clus               0   1
  MSH6 MUTATED    20  19
  MSH6 WILD-TYPE 150 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     20   19
  MSH6 WILD-TYPE  150  178
        clus
vv       MSH6 MUTATED MSH6 WILD-TYPE
  FEMALE           20            150
  MALE             19            178
[1] 2 2
[1] FALSE
D342V8, binary
                cls
clus               0   1
  MSH6 MUTATED    34   1
  MSH6 WILD-TYPE 266   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     34    1
  MSH6 WILD-TYPE  266    7
     clus
vv    MSH6 MUTATED MSH6 WILD-TYPE
  NO            34            266
  YES            1              7
[1] 2 2
[1] FALSE
D342V9, binary
                cls
clus               0   1
  MSH6 MUTATED    29   9
  MSH6 WILD-TYPE 285  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     29    9
  MSH6 WILD-TYPE  285   39
                               clus
vv                              MSH6 MUTATED MSH6 WILD-TYPE
  COLON ADENOCARCINOMA                    29            285
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH6 MUTATED    23   1   0   4
  MSH6 WILD-TYPE 236   2  22  17
D342V10, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  R0           23            236
  R1            1              2
  R2            0             22
  RX            4             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"
D342V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH6 MUTATED                                  0     2
  MSH6 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH6 MUTATED                           3    23
  MSH6 WILD-TYPE                        16   153
D342V12, multiclass
                                  clus
vv                                 MSH6 MUTATED MSH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      23            153
[1] 4 2
[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 = KRAS MUTATION ANALYSIS
D343V1, survival
                sevent
clus2              0   1
  KRAS MUTATED   126  39
  KRAS WILD-TYPE 151  39
  KRAS MUTATED KRAS WILD-TYPE 
           165            190 
  KRAS MUTATED KRAS WILD-TYPE 
            39             39 
$`KRAS MUTATED`
TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3556 TCGA-AA-3560 
       14.53        24.03        37.05        19.07        23.01        19.99 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3939 
        0.92        19.04        19.04        14.93        29.98        12.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       24.00        19.07        21.37        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2683 TCGA-A6-3808 
        1.94         5.88        35.80        91.79        16.57        33.34 
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-A6-6138 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       32.71        22.52         8.38        24.39        23.87        20.28 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3558 
       35.01         6.97        29.00        33.99        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3680 
       13.94        61.02        78.08         6.97        50.04        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        5.98         5.03         0.99        38.99        37.02         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-3930 TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
        2.01        24.00        34.06        25.02        27.02        38.04 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       18.05         4.01        42.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02K 
       31.00        35.01        26.01        37.02        51.98        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 
       22.42        26.47        33.01        17.82        58.39         5.13 
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-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 
        3.19        12.36        12.39        12.20        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
      148.01        85.45         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 
       37.02        25.02         5.03        15.02        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       29.03        21.99        14.99        12.99        14.04        12.95 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       11.01        45.40        54.61        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       15.58        12.43         9.44        13.35        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-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6805 
      119.93        60.79       117.07        98.24        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6304 
       41.42        43.04         0.53        47.41        35.31        53.62 
TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6626 
       44.68        13.78        46.75 

$`KRAS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3524 TCGA-AA-3525 
       24.33        24.16         1.02        13.02        36.03         8.05 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3562 TCGA-AA-3662 
       34.03         0.99        13.02        17.95        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 
       19.00        36.00        85.05        31.07        24.03        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
        2.01        50.99        26.01        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
       15.52       106.75        49.08        63.62        22.09        26.17 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.08        25.18        21.76        24.69        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04         3.02        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       14.01        21.01        24.00        54.02         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       47.01        15.02        37.05        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3846 
       33.04        25.02         1.02        17.98        15.95        17.03 
TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
        0.00        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3980 TCGA-AA-3982 
        2.01        21.99        16.08        13.05        27.02        27.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
        7.96        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       10.98        38.07         1.02         1.02        33.04         1.02 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 
       39.98         2.01         5.03        12.16        24.53         5.79 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       27.42        14.50        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CA-5254 
       21.44         1.41        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-5913 
       12.59        12.59        12.76        14.30        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       21.99        21.14        82.95        13.02        29.06        22.03 
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-6165 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       12.00        16.04        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5541 TCGA-D5-6533 
       11.08        11.08        10.06        12.03        55.92        25.48 
TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       43.27        16.14         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1HB 
        9.04        11.64        13.41        38.20         7.50       135.65 
TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       81.37        35.97         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        1.55        33.67        13.25       133.18        74.56        65.85 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       55.04        85.48        61.91        36.00 

  KRAS MUTATED KRAS WILD-TYPE 
             0              0 
  KRAS MUTATED KRAS WILD-TYPE 
        148.01         135.65 
  KRAS MUTATED KRAS WILD-TYPE 
         23.05          21.60 
[1] "0.0 - 148.0 (23.1)" "0.0 - 135.7 (21.6)"
[1] "hr=" "1.1"
D343V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRAS MUTATED        28        1       14        59         3         1
  KRAS WILD-TYPE      36        0       12        49         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED           6          3         15         12       14         6
  KRAS WILD-TYPE        12          3         29         21       21         6
                vv
clus             STAGE IVB
  KRAS MUTATED           0
  KRAS WILD-TYPE         1
D343V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              28             36
  STAGE IA              1              0
  STAGE II             14             12
  STAGE IIA            59             49
  STAGE IIB             3              5
  STAGE IIC             1              0
  STAGE III             6             12
  STAGE IIIA            3              3
  STAGE IIIB           15             29
  STAGE IIIC           12             21
  STAGE IV             14             21
  STAGE IVA             6              6
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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     2  31 113  21
  KRAS WILD-TYPE   7  36 136  20
D343V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            2              7
  T2           31             36
  T3          113            136
  T4           21             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"
                vv
clus              N0  N1  N2
  KRAS MUTATED   111  30  27
  KRAS WILD-TYPE 109  51  39
D343V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0          111            109
  N1           30             51
  N2           27             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V6, binary
                cls
clus               0   1
  KRAS MUTATED   135  20
  KRAS WILD-TYPE 150  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    135   20
  KRAS WILD-TYPE  150   28
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0          135            150
  1           20             28
[1] 2 2
[1] FALSE
D343V7, binary
                cls
clus               0   1
  KRAS MUTATED    70  98
  KRAS WILD-TYPE 100  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     70   98
  KRAS WILD-TYPE  100   99
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           70            100
  MALE             98             99
[1] 2 2
[1] FALSE
D343V8, binary
                cls
clus               0   1
  KRAS MUTATED   138   4
  KRAS WILD-TYPE 162   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    138    4
  KRAS WILD-TYPE  162    4
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO           138            162
  YES            4              4
[1] 2 2
[1] FALSE
D343V9, binary
                cls
clus               0   1
  KRAS MUTATED   145  21
  KRAS WILD-TYPE 169  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    145   21
  KRAS WILD-TYPE  169   27
                               clus
vv                              KRAS MUTATED KRAS WILD-TYPE
  COLON ADENOCARCINOMA                   145            169
  COLON MUCINOUS ADENOCARCINOMA           21             27
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED   112   2   7   9
  KRAS WILD-TYPE 147   1  15  12
D343V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0          112            147
  R1            2              1
  R2            7             15
  RX            9             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     5
  KRAS WILD-TYPE                                1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                          12    88
  KRAS WILD-TYPE                         7    88
D343V12, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       5              5
  BLACK OR AFRICAN AMERICAN                  12              7
  WHITE                                      88             88
[1] 4 2
[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 = NEXN MUTATION ANALYSIS
D344V1, survival
                sevent
clus2              0   1
  NEXN MUTATED    13   4
  NEXN WILD-TYPE 264  74
  NEXN MUTATED NEXN WILD-TYPE 
            17            338 
  NEXN MUTATED NEXN WILD-TYPE 
             4             74 
$`NEXN MUTATED`
TCGA-AA-3976 TCGA-DM-A285 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 
       26.01         5.88        33.53        63.98         4.01        34.98 
TCGA-AA-A01I TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6747 TCGA-CM-6171 
       31.00        29.56        12.76        14.30        82.95        14.04 
TCGA-CM-6679 TCGA-D5-6920 TCGA-F4-6805 TCGA-G4-6293 TCGA-G4-6303 
       10.06        12.39        34.42       133.18        65.85 

$`NEXN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        10.06        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        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         7.53        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        41.42        43.04 
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-G4-6304 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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NEXN MUTATED NEXN WILD-TYPE 
          4.01           0.00 
  NEXN MUTATED NEXN WILD-TYPE 
        133.18         148.01 
  NEXN MUTATED NEXN WILD-TYPE 
         29.56          22.01 
[1] "4.0 - 133.2 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D344V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEXN MUTATED         2        0        1         7         2         0
  NEXN WILD-TYPE      62        1       25       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEXN MUTATED           1          1          0          0        2         0
  NEXN WILD-TYPE        17          5         44         33       33        12
                vv
clus             STAGE IVB
  NEXN MUTATED           0
  NEXN WILD-TYPE         1
D344V3, multiclass
            clus
vv           NEXN MUTATED NEXN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  NEXN MUTATED     0   4  11   2
  NEXN WILD-TYPE   9  63 238  39
D344V4, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  T1            0              9
  T2            4             63
  T3           11            238
  T4            2             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
  NEXN MUTATED    12   4   1
  NEXN WILD-TYPE 208  77  65
D344V5, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  N0           12            208
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V6, binary
                cls
clus               0   1
  NEXN MUTATED    13   2
  NEXN WILD-TYPE 272  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     13    2
  NEXN WILD-TYPE  272   46
   clus
vv  NEXN MUTATED NEXN WILD-TYPE
  0           13            272
  1            2             46
[1] 2 2
[1] FALSE
D344V7, binary
                cls
clus               0   1
  NEXN MUTATED    10   7
  NEXN WILD-TYPE 160 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     10    7
  NEXN WILD-TYPE  160  190
        clus
vv       NEXN MUTATED NEXN WILD-TYPE
  FEMALE           10            160
  MALE              7            190
[1] 2 2
[1] FALSE
D344V8, binary
                cls
clus               0   1
  NEXN MUTATED    15   0
  NEXN WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     15    0
  NEXN WILD-TYPE  285    8
     clus
vv    NEXN MUTATED NEXN WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D344V9, binary
                cls
clus               0   1
  NEXN MUTATED    14   3
  NEXN WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     14    3
  NEXN WILD-TYPE  300   45
                               clus
vv                              NEXN MUTATED NEXN WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEXN MUTATED    12   0   0   3
  NEXN WILD-TYPE 247   3  22  18
D344V10, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            3             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"
D344V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEXN MUTATED                                  0     2
  NEXN WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEXN MUTATED                           1     9
  NEXN WILD-TYPE                        18   167
D344V12, multiclass
                                  clus
vv                                 NEXN MUTATED NEXN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       9            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(345) Variable = SP110 MUTATION ANALYSIS
D345V1, survival
                 sevent
clus2               0   1
  SP110 MUTATED     8   2
  SP110 WILD-TYPE 269  76
  SP110 MUTATED SP110 WILD-TYPE 
             10             345 
  SP110 MUTATED SP110 WILD-TYPE 
              2              76 
$`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        13.35         7.50 

$`SP110 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SP110 MUTATED SP110 WILD-TYPE 
           5.79            0.00 
  SP110 MUTATED SP110 WILD-TYPE 
          26.99          148.01 
  SP110 MUTATED SP110 WILD-TYPE 
          12.92           22.42 
[1] "5.8 - 27.0 (12.9)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D345V2, continuous
                 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      62        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SP110 MUTATED           0          0          1          2        0         0
  SP110 WILD-TYPE        18          6         43         31       35        12
                 vv
clus              STAGE IVB
  SP110 MUTATED           0
  SP110 WILD-TYPE         1
D345V3, multiclass
            clus
vv           SP110 MUTATED SP110 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  SP110 MUTATED     0   2   7   1
  SP110 WILD-TYPE   9  65 242  40
D345V4, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             1              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
  SP110 MUTATED     7   1   2
  SP110 WILD-TYPE 213  80  64
D345V5, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V6, binary
                 cls
clus                0   1
  SP110 MUTATED     9   0
  SP110 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      9    0
  SP110 WILD-TYPE  276   48
   clus
vv  SP110 MUTATED SP110 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D345V7, binary
                 cls
clus                0   1
  SP110 MUTATED     7   3
  SP110 WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      7    3
  SP110 WILD-TYPE  163  194
        clus
vv       SP110 MUTATED SP110 WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D345V8, binary
                 cls
clus                0   1
  SP110 MUTATED     9   0
  SP110 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      9    0
  SP110 WILD-TYPE  291    8
     clus
vv    SP110 MUTATED SP110 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D345V9, binary
                 cls
clus                0   1
  SP110 MUTATED     8   2
  SP110 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      8    2
  SP110 WILD-TYPE  306   46
                               clus
vv                              SP110 MUTATED SP110 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SP110 MUTATED     8   0   0   0
  SP110 WILD-TYPE 251   3  22  21
D345V10, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D345V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SP110 MUTATED                                  0     0
  SP110 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SP110 MUTATED                           0     9
  SP110 WILD-TYPE                        19   167
D345V12, multiclass
                                  clus
vv                                 SP110 MUTATED SP110 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(346) Variable = MYST4 MUTATION ANALYSIS
D346V1, survival
                 sevent
clus2               0   1
  MYST4 MUTATED    19   4
  MYST4 WILD-TYPE 258  74
  MYST4 MUTATED MYST4 WILD-TYPE 
             23             332 
  MYST4 MUTATED MYST4 WILD-TYPE 
              4              74 
$`MYST4 MUTATED`
TCGA-A6-4105 TCGA-AA-3554 TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AA-3492 
       14.53        17.95        24.00        25.08       100.01         3.02 
TCGA-AA-3502 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3966 TCGA-AU-6004 
       35.01        29.95        26.99        53.00         2.01        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 
       21.44        58.39        88.21        12.76        10.06        20.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-D5-6532 TCGA-F4-6856 TCGA-G4-6309 
       22.03        22.98        18.25        35.31        85.48 

$`MYST4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 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-A6-6648 
       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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       124.27        23.05        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-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MYST4 MUTATED MYST4 WILD-TYPE 
           2.01            0.00 
  MYST4 MUTATED MYST4 WILD-TYPE 
         100.01          148.01 
  MYST4 MUTATED MYST4 WILD-TYPE 
          24.00           21.99 
[1] "2.0 - 100.0 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D346V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYST4 MUTATED         5        0        3        11         0         0
  MYST4 WILD-TYPE      59        1       23        97         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYST4 MUTATED           0          0          4          0        0         0
  MYST4 WILD-TYPE        18          6         40         33       35        12
                 vv
clus              STAGE IVB
  MYST4 MUTATED           0
  MYST4 WILD-TYPE         1
D346V3, multiclass
            clus
vv           MYST4 MUTATED MYST4 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             11              97
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MYST4 MUTATED     1   4  18   0
  MYST4 WILD-TYPE   8  63 231  41
D346V4, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            18             231
  T4             0              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
  MYST4 MUTATED    19   4   0
  MYST4 WILD-TYPE 201  77  66
D346V5, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  N0            19             201
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V6, binary
                 cls
clus                0   1
  MYST4 MUTATED    22   0
  MYST4 WILD-TYPE 263  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     22    0
  MYST4 WILD-TYPE  263   48
   clus
vv  MYST4 MUTATED MYST4 WILD-TYPE
  0            22             263
  1             0              48
[1] 2 2
[1] FALSE
D346V7, binary
                 cls
clus                0   1
  MYST4 MUTATED    10  13
  MYST4 WILD-TYPE 160 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     10   13
  MYST4 WILD-TYPE  160  184
        clus
vv       MYST4 MUTATED MYST4 WILD-TYPE
  FEMALE            10             160
  MALE              13             184
[1] 2 2
[1] FALSE
D346V8, binary
                 cls
clus                0   1
  MYST4 MUTATED    21   0
  MYST4 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     21    0
  MYST4 WILD-TYPE  279    8
     clus
vv    MYST4 MUTATED MYST4 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D346V9, binary
                 cls
clus                0   1
  MYST4 MUTATED    18   5
  MYST4 WILD-TYPE 296  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     18    5
  MYST4 WILD-TYPE  296   43
                               clus
vv                              MYST4 MUTATED MYST4 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYST4 MUTATED    17   0   0   2
  MYST4 WILD-TYPE 242   3  22  19
D346V10, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  R0            17             242
  R1             0               3
  R2             0              22
  RX             2              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"
D346V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYST4 MUTATED                                  0     2
  MYST4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYST4 MUTATED                           1    12
  MYST4 WILD-TYPE                        18   164
D346V12, multiclass
                                  clus
vv                                 MYST4 MUTATED MYST4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = PPARGC1A MUTATION ANALYSIS
D347V1, survival
                    sevent
clus2                  0   1
  PPARGC1A MUTATED    15   7
  PPARGC1A WILD-TYPE 262  71
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                22                333 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                 7                 71 
$`PPARGC1A MUTATED`
TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-5666 
        6.05        19.04        19.04        32.75        22.06        32.71 
TCGA-A6-6648 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3947 
       25.18        20.12        20.28        26.99        53.00        33.01 
TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       83.24        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.08        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.39        23.87        19.66         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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
               4.8                0.0 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
             83.24             148.01 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
             20.20              22.09 
[1] "4.8 - 83.2 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D347V2, continuous
                    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      63        1       22       101         5         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARGC1A MUTATED           0          0          3          0        3
  PPARGC1A WILD-TYPE        18          6         41         33       32
                    vv
clus                 STAGE IVA STAGE IVB
  PPARGC1A MUTATED           1         0
  PPARGC1A WILD-TYPE        11         1
D347V3, multiclass
            clus
vv           PPARGC1A MUTATED PPARGC1A WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                 7                101
  STAGE IIB                 3                  5
  STAGE IIC                 1                  0
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                0                 33
  STAGE IV                  3                 32
  STAGE IVA                 1                 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
  PPARGC1A MUTATED     0   1  15   7
  PPARGC1A WILD-TYPE   9  66 234  34
D347V4, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3               15                234
  T4                7                 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
  PPARGC1A MUTATED    18   3   2
  PPARGC1A WILD-TYPE 202  78  64
D347V5, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  N0               18                202
  N1                3                 78
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V6, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    15   4
  PPARGC1A WILD-TYPE 270  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     15    4
  PPARGC1A WILD-TYPE  270   44
   clus
vv  PPARGC1A MUTATED PPARGC1A WILD-TYPE
  0               15                270
  1                4                 44
[1] 2 2
[1] FALSE
D347V7, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED     9  14
  PPARGC1A WILD-TYPE 161 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED      9   14
  PPARGC1A WILD-TYPE  161  183
        clus
vv       PPARGC1A MUTATED PPARGC1A WILD-TYPE
  FEMALE                9                161
  MALE                 14                183
[1] 2 2
[1] FALSE
D347V8, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    21   1
  PPARGC1A WILD-TYPE 279   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     21    1
  PPARGC1A WILD-TYPE  279    7
     clus
vv    PPARGC1A MUTATED PPARGC1A WILD-TYPE
  NO                21                279
  YES                1                  7
[1] 2 2
[1] FALSE
D347V9, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    18   5
  PPARGC1A WILD-TYPE 296  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     18    5
  PPARGC1A WILD-TYPE  296   43
                               clus
vv                              PPARGC1A MUTATED PPARGC1A WILD-TYPE
  COLON ADENOCARCINOMA                        18                296
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPARGC1A MUTATED    13   0   2   2
  PPARGC1A WILD-TYPE 246   3  20  19
D347V10, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  R0               13                246
  R1                0                  3
  R2                2                 20
  RX                2                 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"
D347V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPARGC1A MUTATED                                  0     3
  PPARGC1A WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PPARGC1A MUTATED                           1    12
  PPARGC1A WILD-TYPE                        18   164
D347V12, multiclass
                                  clus
vv                                 PPARGC1A MUTATED PPARGC1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          12                164
[1] 4 2
[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 = CLIP4 MUTATION ANALYSIS
D348V1, survival
                 sevent
clus2               0   1
  CLIP4 MUTATED     8   5
  CLIP4 WILD-TYPE 269  73
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             13             342 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              5              73 
$`CLIP4 MUTATED`
TCGA-AA-3662 TCGA-AD-6964 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-3977 
        6.05        10.88        63.98        29.95        33.04        25.02 
TCGA-AA-A00N TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-6386 TCGA-AZ-6598 TCGA-CM-6677 
        4.01        18.05        40.96        17.82        49.41        11.08 
TCGA-DM-A1D4 
       92.75 

$`CLIP4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-AD-5900 
        5.03        14.01         0.92        41.00        39.98        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.045 
[1] "4.0 - 92.8 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D348V2, continuous
                 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      63        1       24       103         7         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        17          6         43         33       34        12
                 vv
clus              STAGE IVB
  CLIP4 MUTATED           0
  CLIP4 WILD-TYPE         1
D348V3, multiclass
            clus
vv           CLIP4 MUTATED CLIP4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  CLIP4 MUTATED     0   2   9   3
  CLIP4 WILD-TYPE   9  65 240  38
D348V4, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             3              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
  CLIP4 MUTATED    10   1   3
  CLIP4 WILD-TYPE 210  80  63
D348V5, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             3              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"
D348V6, binary
                 cls
clus                0   1
  CLIP4 MUTATED    10   1
  CLIP4 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     10    1
  CLIP4 WILD-TYPE  275   47
   clus
vv  CLIP4 MUTATED CLIP4 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D348V7, binary
                 cls
clus                0   1
  CLIP4 MUTATED     9   5
  CLIP4 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      9    5
  CLIP4 WILD-TYPE  161  192
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D348V8, binary
                 cls
clus                0   1
  CLIP4 MUTATED    11   0
  CLIP4 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     11    0
  CLIP4 WILD-TYPE  289    8
     clus
vv    CLIP4 MUTATED CLIP4 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D348V9, binary
                 cls
clus                0   1
  CLIP4 MUTATED    11   3
  CLIP4 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     11    3
  CLIP4 WILD-TYPE  303   45
                               clus
vv                              CLIP4 MUTATED CLIP4 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLIP4 MUTATED     9   0   1   0
  CLIP4 WILD-TYPE 250   3  21  21
D348V10, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             0              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"
D348V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLIP4 MUTATED                                  0     0
  CLIP4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLIP4 MUTATED                           1     4
  CLIP4 WILD-TYPE                        18   172
D348V12, multiclass
                                  clus
vv                                 CLIP4 MUTATED CLIP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = PAK3 MUTATION ANALYSIS
D349V1, survival
                sevent
clus2              0   1
  PAK3 MUTATED    15   2
  PAK3 WILD-TYPE 262  76
  PAK3 MUTATED PAK3 WILD-TYPE 
            17            338 
  PAK3 MUTATED PAK3 WILD-TYPE 
             2             76 
$`PAK3 MUTATED`
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2676 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3663 
       35.80        91.79        42.90        63.98        61.02         6.97 
TCGA-AA-3681 TCGA-AA-3977 TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6676 
        5.98        25.02        10.06        29.03        14.04        11.08 
TCGA-D5-6536 TCGA-D5-6541 TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6569 
       17.85        15.58       135.65        98.24        35.74 

$`PAK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
       60.79       117.07         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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PAK3 MUTATED PAK3 WILD-TYPE 
          5.98           0.00 
  PAK3 MUTATED PAK3 WILD-TYPE 
        135.65         148.01 
  PAK3 MUTATED PAK3 WILD-TYPE 
         29.03          22.01 
[1] "6.0 - 135.7 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.7"
D349V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK3 MUTATED         3        0        3         7         1         0
  PAK3 WILD-TYPE      61        1       23       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK3 MUTATED           1          0          1          0        0         0
  PAK3 WILD-TYPE        17          6         43         33       35        12
                vv
clus             STAGE IVB
  PAK3 MUTATED           0
  PAK3 WILD-TYPE         1
D349V3, multiclass
            clus
vv           PAK3 MUTATED PAK3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PAK3 MUTATED     0   4  12   1
  PAK3 WILD-TYPE   9  63 237  40
D349V4, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           12            237
  T4            1             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
  PAK3 MUTATED    15   2   0
  PAK3 WILD-TYPE 205  79  66
D349V5, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  N0           15            205
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V6, binary
                cls
clus               0   1
  PAK3 MUTATED    16   0
  PAK3 WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     16    0
  PAK3 WILD-TYPE  269   48
   clus
vv  PAK3 MUTATED PAK3 WILD-TYPE
  0           16            269
  1            0             48
[1] 2 2
[1] FALSE
D349V7, binary
                cls
clus               0   1
  PAK3 MUTATED     6  11
  PAK3 WILD-TYPE 164 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      6   11
  PAK3 WILD-TYPE  164  186
        clus
vv       PAK3 MUTATED PAK3 WILD-TYPE
  FEMALE            6            164
  MALE             11            186
[1] 2 2
[1] FALSE
D349V8, binary
                cls
clus               0   1
  PAK3 MUTATED    15   0
  PAK3 WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     15    0
  PAK3 WILD-TYPE  285    8
     clus
vv    PAK3 MUTATED PAK3 WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D349V9, binary
                cls
clus               0   1
  PAK3 MUTATED    15   1
  PAK3 WILD-TYPE 299  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     15    1
  PAK3 WILD-TYPE  299   47
                               clus
vv                              PAK3 MUTATED PAK3 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAK3 MUTATED    13   0   0   1
  PAK3 WILD-TYPE 246   3  22  20
D349V10, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            1             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"
D349V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK3 MUTATED                                  0     1
  PAK3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK3 MUTATED                           0    11
  PAK3 WILD-TYPE                        19   165
D349V12, multiclass
                                  clus
vv                                 PAK3 MUTATED PAK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      11            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(350) Variable = KCNS3 MUTATION ANALYSIS
D350V1, survival
                 sevent
clus2               0   1
  KCNS3 MUTATED    16   3
  KCNS3 WILD-TYPE 261  75
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             19             336 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
              3              75 
$`KCNS3 MUTATED`
TCGA-AA-3496 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-6780 TCGA-AA-3812 TCGA-AA-A010 
        1.02        79.69        32.75        20.12        35.05        34.98 
TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-4746 
       12.16        33.01        21.44        49.41         6.77        37.02 
TCGA-CM-4752 TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5540 TCGA-D5-6533 TCGA-DM-A28C 
       13.02        15.02        11.01        56.09        25.48        81.37 
TCGA-G4-6299 
       74.56 

$`KCNS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 
        2.01       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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-D5-5541 
       10.06        12.03        45.40        54.61        19.59        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  KCNS3 MUTATED KCNS3 WILD-TYPE 
           1.02            0.00 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
          81.37          148.01 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
          32.75           22.01 
[1] "1.0 - 81.4 (32.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D350V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNS3 MUTATED         5        0        2         6         2         0
  KCNS3 WILD-TYPE      59        1       24       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNS3 MUTATED           0          0          0          1        0         2
  KCNS3 WILD-TYPE        18          6         44         32       35        10
                 vv
clus              STAGE IVB
  KCNS3 MUTATED           0
  KCNS3 WILD-TYPE         1
D350V3, multiclass
            clus
vv           KCNS3 MUTATED KCNS3 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              2              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
  KCNS3 MUTATED     0   5  10   4
  KCNS3 WILD-TYPE   9  62 239  37
D350V4, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            10             239
  T4             4              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
  KCNS3 MUTATED    16   2   1
  KCNS3 WILD-TYPE 204  79  65
D350V5, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  N0            16             204
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V6, binary
                 cls
clus                0   1
  KCNS3 MUTATED    12   2
  KCNS3 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     12    2
  KCNS3 WILD-TYPE  273   46
   clus
vv  KCNS3 MUTATED KCNS3 WILD-TYPE
  0            12             273
  1             2              46
[1] 2 2
[1] FALSE
D350V7, binary
                 cls
clus                0   1
  KCNS3 MUTATED     8  11
  KCNS3 WILD-TYPE 162 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED      8   11
  KCNS3 WILD-TYPE  162  186
        clus
vv       KCNS3 MUTATED KCNS3 WILD-TYPE
  FEMALE             8             162
  MALE              11             186
[1] 2 2
[1] FALSE
D350V8, binary
                 cls
clus                0   1
  KCNS3 MUTATED    17   0
  KCNS3 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     17    0
  KCNS3 WILD-TYPE  283    8
     clus
vv    KCNS3 MUTATED KCNS3 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D350V9, binary
                 cls
clus                0   1
  KCNS3 MUTATED    16   3
  KCNS3 WILD-TYPE 298  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     16    3
  KCNS3 WILD-TYPE  298   45
                               clus
vv                              KCNS3 MUTATED KCNS3 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNS3 MUTATED    15   0   0   0
  KCNS3 WILD-TYPE 244   3  22  21
D350V10, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             0              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"
D350V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNS3 MUTATED                                  0     0
  KCNS3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNS3 MUTATED                           3    13
  KCNS3 WILD-TYPE                        16   163
D350V12, multiclass
                                  clus
vv                                 KCNS3 MUTATED KCNS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       13             163
[1] 4 2
[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 = TRPM7 MUTATION ANALYSIS
D351V1, survival
                 sevent
clus2               0   1
  TRPM7 MUTATED    19   8
  TRPM7 WILD-TYPE 258  70
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             27             328 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
              8              70 
$`TRPM7 MUTATED`
TCGA-A6-6649 TCGA-AA-3672 TCGA-AD-6964 TCGA-AZ-4681 TCGA-A6-5660 TCGA-A6-5666 
       24.16         0.92        10.88       106.75        29.19        32.71 
TCGA-A6-6653 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01V 
       24.39        33.01        25.02         4.01        34.98         1.02 
TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
       12.16         0.20        12.10         3.19        12.76        10.06 
TCGA-CK-4952 TCGA-D5-5538 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6928 TCGA-DM-A1D4 
       15.62        54.61        43.27        17.85        11.64        92.75 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28H 
       44.32       135.65       117.07 

$`TRPM7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6137 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-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-A029 TCGA-AA-A02F 
        1.02        33.04        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-6603 
       22.36        62.79        88.21        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        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-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      140.38         7.50       131.51       139.17        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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TRPM7 MUTATED TRPM7 WILD-TYPE 
            0.2             0.0 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
         135.65          148.01 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
         24.160          22.045 
[1] "0.2 - 135.7 (24.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D351V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPM7 MUTATED         3        0        0         9         3         1
  TRPM7 WILD-TYPE      61        1       26        99         5         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        17          6         41         29       33        12
                 vv
clus              STAGE IVB
  TRPM7 MUTATED           0
  TRPM7 WILD-TYPE         1
D351V3, multiclass
            clus
vv           TRPM7 MUTATED TRPM7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              9              99
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             4              29
  STAGE IV               2              33
  STAGE IVA              0              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
  TRPM7 MUTATED     0   4  16   8
  TRPM7 WILD-TYPE   9  63 233  33
D351V4, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            16             233
  T4             8              33
[1] 4 2
[1] TRUE
[1] "dimension 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    17   5   6
  TRPM7 WILD-TYPE 203  76  60
D351V5, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  N0            17             203
  N1             5              76
  N2             6              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V6, binary
                 cls
clus                0   1
  TRPM7 MUTATED    22   2
  TRPM7 WILD-TYPE 263  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     22    2
  TRPM7 WILD-TYPE  263   46
   clus
vv  TRPM7 MUTATED TRPM7 WILD-TYPE
  0            22             263
  1             2              46
[1] 2 2
[1] FALSE
D351V7, binary
                 cls
clus                0   1
  TRPM7 MUTATED     8  20
  TRPM7 WILD-TYPE 162 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED      8   20
  TRPM7 WILD-TYPE  162  177
        clus
vv       TRPM7 MUTATED TRPM7 WILD-TYPE
  FEMALE             8             162
  MALE              20             177
[1] 2 2
[1] FALSE
D351V8, binary
                 cls
clus                0   1
  TRPM7 MUTATED    19   0
  TRPM7 WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     19    0
  TRPM7 WILD-TYPE  281    8
     clus
vv    TRPM7 MUTATED TRPM7 WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D351V9, binary
                 cls
clus                0   1
  TRPM7 MUTATED    19   8
  TRPM7 WILD-TYPE 295  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     19    8
  TRPM7 WILD-TYPE  295   40
                               clus
vv                              TRPM7 MUTATED TRPM7 WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRPM7 MUTATED    13   0   0   3
  TRPM7 WILD-TYPE 246   3  22  18
D351V10, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             3              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"
D351V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPM7 MUTATED                                  0     2
  TRPM7 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPM7 MUTATED                           2    17
  TRPM7 WILD-TYPE                        17   159
D351V12, multiclass
                                  clus
vv                                 TRPM7 MUTATED TRPM7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       17             159
[1] 4 2
[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 = DSG1 MUTATION ANALYSIS
D352V1, survival
                sevent
clus2              0   1
  DSG1 MUTATED    16   2
  DSG1 WILD-TYPE 261  76
  DSG1 MUTATED DSG1 WILD-TYPE 
            18            337 
  DSG1 MUTATED DSG1 WILD-TYPE 
             2             76 
$`DSG1 MUTATED`
TCGA-AA-3950 TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00N 
       24.00        35.80        63.98        26.01         2.01         4.01 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 
       34.98        32.02        35.01        27.09        58.39        12.76 
TCGA-CA-6718 TCGA-CM-6169 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6931 TCGA-G4-6307 
       10.06        13.02        12.49        15.58        12.00        55.04 

$`DSG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        33.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        15.02        10.98        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DSG1 MUTATED DSG1 WILD-TYPE 
          2.01           0.00 
  DSG1 MUTATED DSG1 WILD-TYPE 
         63.98         148.01 
  DSG1 MUTATED DSG1 WILD-TYPE 
        25.005         22.030 
[1] "2.0 - 64.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D352V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSG1 MUTATED         1        0        1         8         2         0
  DSG1 WILD-TYPE      63        1       25       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSG1 MUTATED           1          0          3          1        0         0
  DSG1 WILD-TYPE        17          6         41         32       35        12
                vv
clus             STAGE IVB
  DSG1 MUTATED           0
  DSG1 WILD-TYPE         1
D352V3, multiclass
            clus
vv           DSG1 MUTATED DSG1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  DSG1 MUTATED     0   1  14   3
  DSG1 WILD-TYPE   9  66 235  38
D352V4, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           14            235
  T4            3             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
  DSG1 MUTATED    13   3   2
  DSG1 WILD-TYPE 207  78  64
D352V5, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  N0           13            207
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V6, binary
                cls
clus               0   1
  DSG1 MUTATED    18   0
  DSG1 WILD-TYPE 267  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     18    0
  DSG1 WILD-TYPE  267   48
   clus
vv  DSG1 MUTATED DSG1 WILD-TYPE
  0           18            267
  1            0             48
[1] 2 2
[1] FALSE
D352V7, binary
                cls
clus               0   1
  DSG1 MUTATED     8  10
  DSG1 WILD-TYPE 162 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED      8   10
  DSG1 WILD-TYPE  162  187
        clus
vv       DSG1 MUTATED DSG1 WILD-TYPE
  FEMALE            8            162
  MALE             10            187
[1] 2 2
[1] FALSE
D352V8, binary
                cls
clus               0   1
  DSG1 MUTATED    14   1
  DSG1 WILD-TYPE 286   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     14    1
  DSG1 WILD-TYPE  286    7
     clus
vv    DSG1 MUTATED DSG1 WILD-TYPE
  NO            14            286
  YES            1              7
[1] 2 2
[1] FALSE
D352V9, binary
                cls
clus               0   1
  DSG1 MUTATED    12   6
  DSG1 WILD-TYPE 302  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     12    6
  DSG1 WILD-TYPE  302   42
                               clus
vv                              DSG1 MUTATED DSG1 WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DSG1 MUTATED    15   0   0   2
  DSG1 WILD-TYPE 244   3  22  19
D352V10, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  R0           15            244
  R1            0              3
  R2            0             22
  RX            2             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"
D352V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSG1 MUTATED                                  0     2
  DSG1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSG1 MUTATED                           1     7
  DSG1 WILD-TYPE                        18   169
D352V12, multiclass
                                  clus
vv                                 DSG1 MUTATED DSG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = ZNF585A MUTATION ANALYSIS
D353V1, survival
                   sevent
clus2                 0   1
  ZNF585A MUTATED    10   5
  ZNF585A WILD-TYPE 267  73
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               15               340 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
                5                73 
$`ZNF585A MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6895 
        1.02        13.02         8.05        19.04        19.04        25.08 
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6718 
       63.98         6.97        25.02         4.01        34.98        10.06 
TCGA-D5-6534 TCGA-G4-6293 TCGA-G4-6626 
       43.27       133.18        46.75 

$`ZNF585A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       85.05        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        15.52        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  ZNF585A MUTATED ZNF585A WILD-TYPE 
             1.02              0.00 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
           133.18            148.01 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
           19.040            22.075 
[1] "1.0 - 133.2 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D353V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF585A MUTATED         0        0        4         4         2         0
  ZNF585A WILD-TYPE      64        1       22       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF585A MUTATED           2          0          2          0        1
  ZNF585A WILD-TYPE        16          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  ZNF585A MUTATED           0         0
  ZNF585A WILD-TYPE        12         1
D353V3, multiclass
            clus
vv           ZNF585A MUTATED ZNF585A WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 4                22
  STAGE IIA                4               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  ZNF585A MUTATED     0   1  13   2
  ZNF585A WILD-TYPE   9  66 236  39
D353V4, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              13               236
  T4               2                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
  ZNF585A MUTATED    12   3   1
  ZNF585A WILD-TYPE 208  78  65
D353V5, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  N0              12               208
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V6, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    14   1
  ZNF585A WILD-TYPE 271  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     14    1
  ZNF585A WILD-TYPE  271   47
   clus
vv  ZNF585A MUTATED ZNF585A WILD-TYPE
  0              14               271
  1               1                47
[1] 2 2
[1] FALSE
D353V7, binary
                   cls
clus                  0   1
  ZNF585A MUTATED     6  10
  ZNF585A WILD-TYPE 164 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED      6   10
  ZNF585A WILD-TYPE  164  187
        clus
vv       ZNF585A MUTATED ZNF585A WILD-TYPE
  FEMALE               6               164
  MALE                10               187
[1] 2 2
[1] FALSE
D353V8, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    12   1
  ZNF585A WILD-TYPE 288   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     12    1
  ZNF585A WILD-TYPE  288    7
     clus
vv    ZNF585A MUTATED ZNF585A WILD-TYPE
  NO               12               288
  YES               1                 7
[1] 2 2
[1] FALSE
D353V9, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    13   3
  ZNF585A WILD-TYPE 301  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     13    3
  ZNF585A WILD-TYPE  301   45
                               clus
vv                              ZNF585A MUTATED ZNF585A WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF585A MUTATED    12   0   1   1
  ZNF585A WILD-TYPE 247   3  21  20
D353V10, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               1                21
  RX               1                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"
D353V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF585A MUTATED                                  0     1
  ZNF585A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF585A MUTATED                           0     4
  ZNF585A WILD-TYPE                        19   172
D353V12, multiclass
                                  clus
vv                                 ZNF585A MUTATED ZNF585A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = KPNA5 MUTATION ANALYSIS
D354V1, survival
                 sevent
clus2               0   1
  KPNA5 MUTATED     7   3
  KPNA5 WILD-TYPE 270  75
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             10             345 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
              3              75 
$`KPNA5 MUTATED`
TCGA-AA-3524 TCGA-AA-3713 TCGA-AZ-6608 TCGA-AA-3973 TCGA-AA-A00N TCGA-CK-5913 
       36.03        19.04         1.94        13.05         4.01        51.32 
TCGA-D5-6930 TCGA-DM-A28E TCGA-G4-6315 TCGA-G4-6626 
       13.35       119.93        61.91        46.75 

$`KPNA5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6317 TCGA-G4-6323 
       85.48        36.00        13.78 

  KPNA5 MUTATED KPNA5 WILD-TYPE 
           1.94            0.00 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
         119.93          148.01 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
         27.535          22.060 
[1] "1.9 - 119.9 (27.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D354V2, continuous
                 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      64        1       25       104         6         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        18          5         44         33       32        12
                 vv
clus              STAGE IVB
  KPNA5 MUTATED           0
  KPNA5 WILD-TYPE         1
D354V3, multiclass
            clus
vv           KPNA5 MUTATED KPNA5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              0              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
  KPNA5 MUTATED     0   1   7   3
  KPNA5 WILD-TYPE   9  66 242  38
D354V4, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             3              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
  KPNA5 MUTATED     8   3   0
  KPNA5 WILD-TYPE 212  78  66
D354V5, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V6, binary
                 cls
clus                0   1
  KPNA5 MUTATED     6   3
  KPNA5 WILD-TYPE 279  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      6    3
  KPNA5 WILD-TYPE  279   45
   clus
vv  KPNA5 MUTATED KPNA5 WILD-TYPE
  0             6             279
  1             3              45
[1] 2 2
[1] FALSE
D354V7, binary
                 cls
clus                0   1
  KPNA5 MUTATED     4   7
  KPNA5 WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      4    7
  KPNA5 WILD-TYPE  166  190
        clus
vv       KPNA5 MUTATED KPNA5 WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D354V8, binary
                 cls
clus                0   1
  KPNA5 MUTATED     7   1
  KPNA5 WILD-TYPE 293   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      7    1
  KPNA5 WILD-TYPE  293    7
     clus
vv    KPNA5 MUTATED KPNA5 WILD-TYPE
  NO              7             293
  YES             1               7
[1] 2 2
[1] FALSE
D354V9, binary
                 cls
clus                0   1
  KPNA5 MUTATED     9   2
  KPNA5 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      9    2
  KPNA5 WILD-TYPE  305   46
                               clus
vv                              KPNA5 MUTATED KPNA5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KPNA5 MUTATED     5   0   2   2
  KPNA5 WILD-TYPE 254   3  20  19
D354V10, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             2              20
  RX             2              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"
D354V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KPNA5 MUTATED                                  0     0
  KPNA5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KPNA5 MUTATED                           0     7
  KPNA5 WILD-TYPE                        19   169
D354V12, multiclass
                                  clus
vv                                 KPNA5 MUTATED KPNA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = CDC42BPA MUTATION ANALYSIS
D355V1, survival
                    sevent
clus2                  0   1
  CDC42BPA MUTATED    17  12
  CDC42BPA WILD-TYPE 260  66
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                29                326 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                12                 66 
$`CDC42BPA MUTATED`
TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6888 
       14.53        13.02        85.05        19.04        24.00        15.52 
TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3492 
      100.01        26.17        46.65        31.63        33.53         3.02 
TCGA-AA-3655 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
       61.02        26.99        53.00        25.02        18.05         4.01 
TCGA-AA-A02J TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-CM-5349 
        5.03        83.24        58.39         5.13        12.76        30.08 
TCGA-DM-A1DB TCGA-DM-A28G TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6626 
       44.32        60.79        47.87        35.31        46.75 

$`CDC42BPA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44        17.82         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       131.51       135.65       139.17        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        43.04 
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-G4-6323 
       36.00        13.78 

  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
              3.02               0.00 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
            100.01             148.01 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
             30.08              21.99 
[1] "3.0 - 100.0 (30.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D355V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC42BPA MUTATED         1        0        5        13         1         0
  CDC42BPA WILD-TYPE      63        1       21        95         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC42BPA MUTATED           1          0          4          0        3
  CDC42BPA WILD-TYPE        17          6         40         33       32
                    vv
clus                 STAGE IVA STAGE IVB
  CDC42BPA MUTATED           0         0
  CDC42BPA WILD-TYPE        12         1
D355V3, multiclass
            clus
vv           CDC42BPA MUTATED CDC42BPA WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  5                 21
  STAGE IIA                13                 95
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                4                 40
  STAGE IIIC                0                 33
  STAGE IV                  3                 32
  STAGE IVA                 0                 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
  CDC42BPA MUTATED     0   2  25   2
  CDC42BPA WILD-TYPE   9  65 224  39
D355V4, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3               25                224
  T4                2                 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
  CDC42BPA MUTATED    23   4   2
  CDC42BPA WILD-TYPE 197  77  64
D355V5, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  N0               23                197
  N1                4                 77
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V6, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    25   3
  CDC42BPA WILD-TYPE 260  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     25    3
  CDC42BPA WILD-TYPE  260   45
   clus
vv  CDC42BPA MUTATED CDC42BPA WILD-TYPE
  0               25                260
  1                3                 45
[1] 2 2
[1] FALSE
D355V7, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    10  19
  CDC42BPA WILD-TYPE 160 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     10   19
  CDC42BPA WILD-TYPE  160  178
        clus
vv       CDC42BPA MUTATED CDC42BPA WILD-TYPE
  FEMALE               10                160
  MALE                 19                178
[1] 2 2
[1] FALSE
D355V8, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    24   1
  CDC42BPA WILD-TYPE 276   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     24    1
  CDC42BPA WILD-TYPE  276    7
     clus
vv    CDC42BPA MUTATED CDC42BPA WILD-TYPE
  NO                24                276
  YES                1                  7
[1] 2 2
[1] FALSE
D355V9, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    23   6
  CDC42BPA WILD-TYPE 291  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     23    6
  CDC42BPA WILD-TYPE  291   42
                               clus
vv                              CDC42BPA MUTATED CDC42BPA WILD-TYPE
  COLON ADENOCARCINOMA                        23                291
  COLON MUCINOUS ADENOCARCINOMA                6                 42
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CDC42BPA MUTATED    19   0   2   1
  CDC42BPA WILD-TYPE 240   3  20  20
D355V10, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  R0               19                240
  R1                0                  3
  R2                2                 20
  RX                1                 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"
D355V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC42BPA MUTATED                                  0     2
  CDC42BPA WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CDC42BPA MUTATED                           2    13
  CDC42BPA WILD-TYPE                        17   163
D355V12, multiclass
                                  clus
vv                                 CDC42BPA MUTATED CDC42BPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          13                163
[1] 4 2
[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 = KIR2DL3 MUTATION ANALYSIS
D356V1, survival
                   sevent
clus2                 0   1
  KIR2DL3 MUTATED    13   5
  KIR2DL3 WILD-TYPE 264  73
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               18               337 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
                5                73 
$`KIR2DL3 MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AZ-6601 TCGA-A6-5665 TCGA-A6-6648 TCGA-A6-6651 
       14.53         1.02       100.01        22.06        25.18        21.76 
TCGA-AA-3815 TCGA-AY-5543 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-CM-4747 TCGA-CM-4752 
       33.04        33.01        22.36        62.79        25.02        13.02 
TCGA-CM-5341 TCGA-CM-6163 TCGA-CM-6168 TCGA-D5-6537 TCGA-D5-6928 TCGA-DM-A28H 
       29.06        14.04        12.99         4.80        11.64       117.07 

$`KIR2DL3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6652 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
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-6164 
       15.02        15.02        17.03        15.02        12.00        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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             22.03 
[1] "1.0 - 117.1 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D356V2, continuous
                   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      63        1       23       101         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIR2DL3 MUTATED           0          1          2          1        0
  KIR2DL3 WILD-TYPE        18          5         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  KIR2DL3 MUTATED           4         0
  KIR2DL3 WILD-TYPE         8         1
D356V3, multiclass
            clus
vv           KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                7               101
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                4                 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
  KIR2DL3 MUTATED     1   1  16   1
  KIR2DL3 WILD-TYPE   8  66 233  40
D356V4, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3              16               233
  T4               1                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
  KIR2DL3 MUTATED    13   5   1
  KIR2DL3 WILD-TYPE 207  76  65
D356V5, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  N0              13               207
  N1               5                76
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V6, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    12   4
  KIR2DL3 WILD-TYPE 273  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     12    4
  KIR2DL3 WILD-TYPE  273   44
   clus
vv  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  0              12               273
  1               4                44
[1] 2 2
[1] FALSE
D356V7, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED     8  11
  KIR2DL3 WILD-TYPE 162 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED      8   11
  KIR2DL3 WILD-TYPE  162  186
        clus
vv       KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  FEMALE               8               162
  MALE                11               186
[1] 2 2
[1] FALSE
D356V8, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    16   0
  KIR2DL3 WILD-TYPE 284   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     16    0
  KIR2DL3 WILD-TYPE  284    8
     clus
vv    KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  NO               16               284
  YES               0                 8
[1] 2 2
[1] FALSE
D356V9, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    18   1
  KIR2DL3 WILD-TYPE 296  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     18    1
  KIR2DL3 WILD-TYPE  296   47
                               clus
vv                              KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  COLON ADENOCARCINOMA                       18               296
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KIR2DL3 MUTATED    13   0   0   0
  KIR2DL3 WILD-TYPE 246   3  22  21
D356V10, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               0                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"
D356V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIR2DL3 MUTATED                                  0     0
  KIR2DL3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  KIR2DL3 MUTATED                           3    13
  KIR2DL3 WILD-TYPE                        16   163
D356V12, multiclass
                                  clus
vv                                 KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      3                16
  WHITE                                         13               163
[1] 4 2
[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 = C5ORF22 MUTATION ANALYSIS
D357V1, survival
                   sevent
clus2                 0   1
  C5ORF22 MUTATED     7   3
  C5ORF22 WILD-TYPE 270  75
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               10               345 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
                3                75 
$`C5ORF22 MUTATED`
TCGA-AA-3672 TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-3850 
        0.92        49.08        26.17        33.53        61.02         0.00 
TCGA-DM-A1D4 TCGA-F4-6805 TCGA-G4-6309 TCGA-G4-6315 
       92.75        34.42        85.48        61.91 

$`C5ORF22 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6806 
       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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
                0                 0 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
            92.75            148.01 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
            41.75             21.99 
[1] "0.0 - 92.8 (41.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D357V2, continuous
                   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      61        1       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF22 MUTATED           1          0          1          0        1
  C5ORF22 WILD-TYPE        17          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF22 MUTATED           0         0
  C5ORF22 WILD-TYPE        12         1
D357V3, multiclass
            clus
vv           C5ORF22 MUTATED C5ORF22 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  C5ORF22 MUTATED     0   3   8   0
  C5ORF22 WILD-TYPE   9  64 241  41
D357V4, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               8               241
  T4               0                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
  C5ORF22 MUTATED     8   3   0
  C5ORF22 WILD-TYPE 212  78  66
D357V5, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  N0               8               212
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V6, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     8   1
  C5ORF22 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      8    1
  C5ORF22 WILD-TYPE  277   47
   clus
vv  C5ORF22 MUTATED C5ORF22 WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D357V7, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     5   6
  C5ORF22 WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      5    6
  C5ORF22 WILD-TYPE  165  191
        clus
vv       C5ORF22 MUTATED C5ORF22 WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D357V8, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     8   0
  C5ORF22 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      8    0
  C5ORF22 WILD-TYPE  292    8
     clus
vv    C5ORF22 MUTATED C5ORF22 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D357V9, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED    11   0
  C5ORF22 WILD-TYPE 303  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED     11    0
  C5ORF22 WILD-TYPE  303   48
                               clus
vv                              C5ORF22 MUTATED C5ORF22 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C5ORF22 MUTATED     8   0   0   2
  C5ORF22 WILD-TYPE 251   3  22  19
D357V10, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               2                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"
D357V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF22 MUTATED                                  0     0
  C5ORF22 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF22 MUTATED                           2     6
  C5ORF22 WILD-TYPE                        17   170
D357V12, multiclass
                                  clus
vv                                 C5ORF22 MUTATED C5ORF22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = CSNK1D MUTATION ANALYSIS
D358V1, survival
                  sevent
clus2                0   1
  CSNK1D MUTATED    13   1
  CSNK1D WILD-TYPE 264  77
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              14              341 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
               1               77 
$`CSNK1D MUTATED`
TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-A00R 
       79.69        33.53        23.61         1.02        53.00         0.99 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6679 
       33.01        58.39         5.23        12.76        15.02        10.06 
TCGA-D5-6533 TCGA-D5-6928 
       25.48        11.64 

$`CSNK1D WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CSNK1D MUTATED CSNK1D WILD-TYPE 
            0.99             0.00 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
           79.69           148.01 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
          19.315           22.060 
[1] "1.0 - 79.7 (19.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.9"
D358V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSNK1D MUTATED         3        0        1         6         0         0
  CSNK1D WILD-TYPE      61        1       25       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1D MUTATED           0          0          1          0        0
  CSNK1D WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CSNK1D MUTATED           2         0
  CSNK1D WILD-TYPE        10         1
D358V3, multiclass
            clus
vv           CSNK1D MUTATED CSNK1D WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               2               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
  CSNK1D MUTATED     0   3   9   2
  CSNK1D WILD-TYPE   9  64 240  39
D358V4, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  T1              0                9
  T2              3               64
  T3              9              240
  T4              2               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
  CSNK1D MUTATED    11   2   1
  CSNK1D WILD-TYPE 209  79  65
D358V5, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  N0             11              209
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V6, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    12   2
  CSNK1D WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     12    2
  CSNK1D WILD-TYPE  273   46
   clus
vv  CSNK1D MUTATED CSNK1D WILD-TYPE
  0             12              273
  1              2               46
[1] 2 2
[1] FALSE
D358V7, binary
                  cls
clus                 0   1
  CSNK1D MUTATED     6   8
  CSNK1D WILD-TYPE 164 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED      6    8
  CSNK1D WILD-TYPE  164  189
        clus
vv       CSNK1D MUTATED CSNK1D WILD-TYPE
  FEMALE              6              164
  MALE                8              189
[1] 2 2
[1] FALSE
D358V8, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    13   0
  CSNK1D WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     13    0
  CSNK1D WILD-TYPE  287    8
     clus
vv    CSNK1D MUTATED CSNK1D WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D358V9, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    11   3
  CSNK1D WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     11    3
  CSNK1D WILD-TYPE  303   45
                               clus
vv                              CSNK1D MUTATED CSNK1D WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CSNK1D MUTATED    11   0   0   1
  CSNK1D WILD-TYPE 248   3  22  20
D358V10, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              1               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"
D358V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK1D MUTATED                                  0     1
  CSNK1D WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CSNK1D MUTATED                           2     8
  CSNK1D WILD-TYPE                        17   168
D358V12, multiclass
                                  clus
vv                                 CSNK1D MUTATED CSNK1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         8              168
[1] 4 2
[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 = IQSEC2 MUTATION ANALYSIS
D359V1, survival
                  sevent
clus2                0   1
  IQSEC2 MUTATED    14   1
  IQSEC2 WILD-TYPE 263  77
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              15              340 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
               1               77 
$`IQSEC2 MUTATED`
TCGA-AA-3560 TCGA-AA-3662 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3821 TCGA-AA-3877 
       19.99         6.05        26.17        22.06         1.02        31.00 
TCGA-AA-3947 TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 
       33.01        33.01        49.41        51.32        23.05        14.04 
TCGA-D5-6535 TCGA-DM-A1HB TCGA-F4-6856 
       15.12       135.65        35.31 

$`IQSEC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       13.02        17.95        23.01        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       27.02        18.05         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
            1.02             0.00 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
          135.65           148.01 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
           26.17            21.99 
[1] "1.0 - 135.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.7"
D359V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQSEC2 MUTATED         4        0        1         4         2         0
  IQSEC2 WILD-TYPE      60        1       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQSEC2 MUTATED           0          0          2          1        1
  IQSEC2 WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  IQSEC2 MUTATED           1         0
  IQSEC2 WILD-TYPE        11         1
D359V3, multiclass
            clus
vv           IQSEC2 MUTATED IQSEC2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  IQSEC2 MUTATED     1   3   9   3
  IQSEC2 WILD-TYPE   8  64 240  38
D359V4, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  T1              1                8
  T2              3               64
  T3              9              240
  T4              3               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
  IQSEC2 MUTATED    11   3   2
  IQSEC2 WILD-TYPE 209  78  64
D359V5, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  N0             11              209
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V6, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    10   2
  IQSEC2 WILD-TYPE 275  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     10    2
  IQSEC2 WILD-TYPE  275   46
   clus
vv  IQSEC2 MUTATED IQSEC2 WILD-TYPE
  0             10              275
  1              2               46
[1] 2 2
[1] FALSE
D359V7, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    13   3
  IQSEC2 WILD-TYPE 157 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     13    3
  IQSEC2 WILD-TYPE  157  194
        clus
vv       IQSEC2 MUTATED IQSEC2 WILD-TYPE
  FEMALE             13              157
  MALE                3              194
[1] 2 2
[1] FALSE
D359V8, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    14   0
  IQSEC2 WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     14    0
  IQSEC2 WILD-TYPE  286    8
     clus
vv    IQSEC2 MUTATED IQSEC2 WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D359V9, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    11   4
  IQSEC2 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     11    4
  IQSEC2 WILD-TYPE  303   44
                               clus
vv                              IQSEC2 MUTATED IQSEC2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IQSEC2 MUTATED    10   0   1   3
  IQSEC2 WILD-TYPE 249   3  21  18
D359V10, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              3               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"
D359V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQSEC2 MUTATED                                  0     0
  IQSEC2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IQSEC2 MUTATED                           1    10
  IQSEC2 WILD-TYPE                        18   166
D359V12, multiclass
                                  clus
vv                                 IQSEC2 MUTATED IQSEC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(360) Variable = RAB6C MUTATION ANALYSIS
D360V1, survival
                 sevent
clus2               0   1
  RAB6C MUTATED     3   2
  RAB6C WILD-TYPE 274  76
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             350 
  RAB6C MUTATED RAB6C WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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          22.075 
[1] "10.1 - 78.1 (15.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D360V2, continuous
                 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      64        1       25       105         8         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  RAB6C MUTATED           0
  RAB6C WILD-TYPE         1
D360V3, multiclass
            clus
vv           RAB6C MUTATED RAB6C WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RAB6C MUTATED     0   0   4   1
  RAB6C WILD-TYPE   9  67 245  40
D360V4, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  RAB6C MUTATED     3   0   2
  RAB6C WILD-TYPE 217  81  64
D360V5, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  N0             3             217
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V6, binary
                 cls
clus                0   1
  RAB6C MUTATED     4   0
  RAB6C WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      4    0
  RAB6C WILD-TYPE  281   48
   clus
vv  RAB6C MUTATED RAB6C WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D360V7, binary
                 cls
clus                0   1
  RAB6C MUTATED     2   3
  RAB6C WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      2    3
  RAB6C WILD-TYPE  168  194
        clus
vv       RAB6C MUTATED RAB6C WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D360V8, binary
                 cls
clus                0   1
  RAB6C MUTATED     4   0
  RAB6C WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      4    0
  RAB6C WILD-TYPE  296    8
     clus
vv    RAB6C MUTATED RAB6C WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D360V9, binary
                 cls
clus                0   1
  RAB6C MUTATED     3   2
  RAB6C WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      3    2
  RAB6C WILD-TYPE  311   46
                               clus
vv                              RAB6C MUTATED RAB6C WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RAB6C MUTATED     1   0   0   4
  RAB6C WILD-TYPE 258   3  22  17
D360V10, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  R0             1             258
  R1             0               3
  R2             0              22
  RX             4              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"
D360V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB6C MUTATED                                  0     2
  RAB6C WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB6C MUTATED                           0     2
  RAB6C WILD-TYPE                        19   174
D360V12, multiclass
                                  clus
vv                                 RAB6C MUTATED RAB6C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        2             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(361) Variable = C9ORF131 MUTATION ANALYSIS
D361V1, survival
                    sevent
clus2                  0   1
  C9ORF131 MUTATED     9   2
  C9ORF131 WILD-TYPE 268  76
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                11                344 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 2                 76 
$`C9ORF131 MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 
       25.08        79.69        22.06        29.95         4.01        34.98 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6540 
       27.09        49.41        12.76        51.32        16.14 

$`C9ORF131 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
              4.01               0.00 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             79.69             148.01 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             27.09              21.99 
[1] "4.0 - 79.7 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D361V2, continuous
                    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      61        1       25       103         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF131 MUTATED           0          0          1          0        0
  C9ORF131 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF131 MUTATED           0         0
  C9ORF131 WILD-TYPE        12         1
D361V3, multiclass
            clus
vv           C9ORF131 MUTATED C9ORF131 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C9ORF131 MUTATED     0   3   7   3
  C9ORF131 WILD-TYPE   9  64 242  38
D361V4, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3                7                242
  T4                3                 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
  C9ORF131 MUTATED    12   1   0
  C9ORF131 WILD-TYPE 208  80  66
D361V5, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  N0               12                208
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V6, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    10   0
  C9ORF131 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     10    0
  C9ORF131 WILD-TYPE  275   48
   clus
vv  C9ORF131 MUTATED C9ORF131 WILD-TYPE
  0               10                275
  1                0                 48
[1] 2 2
[1] FALSE
D361V7, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     8   5
  C9ORF131 WILD-TYPE 162 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      8    5
  C9ORF131 WILD-TYPE  162  192
        clus
vv       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  FEMALE                8                162
  MALE                  5                192
[1] 2 2
[1] FALSE
D361V8, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     9   0
  C9ORF131 WILD-TYPE 291   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      9    0
  C9ORF131 WILD-TYPE  291    8
     clus
vv    C9ORF131 MUTATED C9ORF131 WILD-TYPE
  NO                 9                291
  YES                0                  8
[1] 2 2
[1] FALSE
D361V9, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     9   4
  C9ORF131 WILD-TYPE 305  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      9    4
  C9ORF131 WILD-TYPE  305   44
                               clus
vv                              C9ORF131 MUTATED C9ORF131 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF131 MUTATED     9   0   0   3
  C9ORF131 WILD-TYPE 250   3  22  18
D361V10, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D361V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF131 MUTATED                                  0     1
  C9ORF131 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF131 MUTATED                           0     8
  C9ORF131 WILD-TYPE                        19   168
D361V12, multiclass
                                  clus
vv                                 C9ORF131 MUTATED C9ORF131 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           8                168
[1] 4 2
[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 = C12ORF10 MUTATION ANALYSIS
D362V1, survival
                    sevent
clus2                  0   1
  C12ORF10 MUTATED     2   2
  C12ORF10 WILD-TYPE 275  76
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                351 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 2                 76 
$`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-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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             22.090 
[1] "6.2 - 133.2 (14.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D362V2, continuous
                    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      64        1       26       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF10 MUTATED           1          0          0          0        0
  C12ORF10 WILD-TYPE        17          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF10 MUTATED           0         0
  C12ORF10 WILD-TYPE        12         1
D362V3, multiclass
            clus
vv           C12ORF10 MUTATED C12ORF10 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 3                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C12ORF10 MUTATED     0   0   4   0
  C12ORF10 WILD-TYPE   9  67 245  41
D362V4, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                4                245
  T4                0                 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
  C12ORF10 MUTATED     3   1   0
  C12ORF10 WILD-TYPE 217  80  66
D362V5, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  N0                3                217
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V6, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  281   48
   clus
vv  C12ORF10 MUTATED C12ORF10 WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D362V7, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     3   1
  C12ORF10 WILD-TYPE 167 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      3    1
  C12ORF10 WILD-TYPE  167  196
        clus
vv       C12ORF10 MUTATED C12ORF10 WILD-TYPE
  FEMALE                3                167
  MALE                  1                196
[1] 2 2
[1] FALSE
D362V8, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 296   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  296    8
     clus
vv    C12ORF10 MUTATED C12ORF10 WILD-TYPE
  NO                 4                296
  YES                0                  8
[1] 2 2
[1] FALSE
D362V9, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 310  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  310   48
                               clus
vv                              C12ORF10 MUTATED C12ORF10 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF10 MUTATED     3   0   0   0
  C12ORF10 WILD-TYPE 256   3  22  21
D362V10, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D362V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF10 MUTATED                                  0     0
  C12ORF10 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF10 MUTATED                           0     4
  C12ORF10 WILD-TYPE                        19   172
D362V12, multiclass
                                  clus
vv                                 C12ORF10 MUTATED C12ORF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = NUP54 MUTATION ANALYSIS
D363V1, survival
                 sevent
clus2               0   1
  NUP54 MUTATED     6   2
  NUP54 WILD-TYPE 271  76
  NUP54 MUTATED NUP54 WILD-TYPE 
              8             347 
  NUP54 MUTATED NUP54 WILD-TYPE 
              2              76 
$`NUP54 MUTATED`
TCGA-G4-6321 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-6600 TCGA-CM-5864 
       22.09         8.38        63.98        34.98        12.10        15.02 
TCGA-CM-6678 TCGA-DM-A1D4 
       11.01        92.75 

$`NUP54 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NUP54 MUTATED NUP54 WILD-TYPE 
           8.38            0.00 
  NUP54 MUTATED NUP54 WILD-TYPE 
          92.75          148.01 
  NUP54 MUTATED NUP54 WILD-TYPE 
         18.555          22.060 
[1] "8.4 - 92.8 (18.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D363V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP54 MUTATED         1        0        1         2         1         0
  NUP54 WILD-TYPE      63        1       25       106         7         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        17          6         44         33       34        11
                 vv
clus              STAGE IVB
  NUP54 MUTATED           0
  NUP54 WILD-TYPE         1
D363V3, multiclass
            clus
vv           NUP54 MUTATED NUP54 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  NUP54 MUTATED     0   2   3   3
  NUP54 WILD-TYPE   9  65 246  38
D363V4, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             3              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
  NUP54 MUTATED     5   3   0
  NUP54 WILD-TYPE 215  78  66
D363V5, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  N0             5             215
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V6, binary
                 cls
clus                0   1
  NUP54 MUTATED     5   2
  NUP54 WILD-TYPE 280  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      5    2
  NUP54 WILD-TYPE  280   46
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             5             280
  1             2              46
[1] 2 2
[1] FALSE
D363V7, binary
                 cls
clus                0   1
  NUP54 MUTATED     3   5
  NUP54 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      3    5
  NUP54 WILD-TYPE  167  192
        clus
vv       NUP54 MUTATED NUP54 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D363V8, binary
                 cls
clus                0   1
  NUP54 MUTATED     7   0
  NUP54 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      7    0
  NUP54 WILD-TYPE  293    8
     clus
vv    NUP54 MUTATED NUP54 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D363V9, binary
                 cls
clus                0   1
  NUP54 MUTATED     8   0
  NUP54 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      8    0
  NUP54 WILD-TYPE  306   48
                               clus
vv                              NUP54 MUTATED NUP54 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NUP54 MUTATED     5   0   0   0
  NUP54 WILD-TYPE 254   3  22  21
D363V10, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D363V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP54 MUTATED                                  0     0
  NUP54 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NUP54 MUTATED                           2     4
  NUP54 WILD-TYPE                        17   172
D363V12, multiclass
                                  clus
vv                                 NUP54 MUTATED NUP54 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = PLEKHA6 MUTATION ANALYSIS
D364V1, survival
                   sevent
clus2                 0   1
  PLEKHA6 MUTATED    15   3
  PLEKHA6 WILD-TYPE 262  75
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               18               337 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
                3                75 
$`PLEKHA6 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 
        0.92        19.04        19.04        24.39        19.66         6.97 
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        83.24        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 

$`PLEKHA6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
             0.92              0.00 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            83.24            148.01 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            19.35             22.09 
[1] "0.9 - 83.2 (19.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D364V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHA6 MUTATED         5        0        3         8         0         0
  PLEKHA6 WILD-TYPE      59        1       23       100         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA6 MUTATED           1          0          0          1        1
  PLEKHA6 WILD-TYPE        17          6         44         32       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHA6 MUTATED           0         0
  PLEKHA6 WILD-TYPE        12         1
D364V3, multiclass
            clus
vv           PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                8               100
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  PLEKHA6 MUTATED     0   5  13   1
  PLEKHA6 WILD-TYPE   9  62 236  40
D364V4, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3              13               236
  T4               1                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
  PLEKHA6 MUTATED    17   2   0
  PLEKHA6 WILD-TYPE 203  79  66
D364V5, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  N0              17               203
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V6, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    15   1
  PLEKHA6 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     15    1
  PLEKHA6 WILD-TYPE  270   47
   clus
vv  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D364V7, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED     8  11
  PLEKHA6 WILD-TYPE 162 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED      8   11
  PLEKHA6 WILD-TYPE  162  186
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  FEMALE               8               162
  MALE                11               186
[1] 2 2
[1] FALSE
D364V8, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    15   1
  PLEKHA6 WILD-TYPE 285   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     15    1
  PLEKHA6 WILD-TYPE  285    7
     clus
vv    PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  NO               15               285
  YES               1                 7
[1] 2 2
[1] FALSE
D364V9, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    13   6
  PLEKHA6 WILD-TYPE 301  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     13    6
  PLEKHA6 WILD-TYPE  301   42
                               clus
vv                              PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHA6 MUTATED    15   0   1   0
  PLEKHA6 WILD-TYPE 244   3  21  21
D364V10, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  R0              15               244
  R1               0                 3
  R2               1                21
  RX               0                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"
D364V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHA6 MUTATED                                  0     1
  PLEKHA6 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHA6 MUTATED                           0     9
  PLEKHA6 WILD-TYPE                        19   167
D364V12, multiclass
                                  clus
vv                                 PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(365) Variable = CYP4X1 MUTATION ANALYSIS
D365V1, survival
                  sevent
clus2                0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 273  77
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               5              350 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               1               77 
$`CYP4X1 MUTATED`
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-4947 TCGA-F4-6809 TCGA-G4-6309 
       88.21        12.76        17.56        13.25        85.48 

$`CYP4X1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
           12.76             0.00 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
           88.21           148.01 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
          17.560           22.075 
[1] "12.8 - 88.2 (17.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D365V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP4X1 MUTATED         1        0        0         1         0         0
  CYP4X1 WILD-TYPE      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4X1 MUTATED           0          0          2          0        0
  CYP4X1 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CYP4X1 MUTATED           1         0
  CYP4X1 WILD-TYPE        11         1
D365V3, multiclass
            clus
vv           CYP4X1 MUTATED CYP4X1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  CYP4X1 MUTATED     1   0   3   1
  CYP4X1 WILD-TYPE   8  67 246  40
D365V4, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              3              246
  T4              1               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
  CYP4X1 MUTATED     2   3   0
  CYP4X1 WILD-TYPE 218  78  66
D365V5, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  N0              2              218
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V6, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      4    1
  CYP4X1 WILD-TYPE  281   47
   clus
vv  CYP4X1 MUTATED CYP4X1 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D365V7, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 166 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      4    1
  CYP4X1 WILD-TYPE  166  196
        clus
vv       CYP4X1 MUTATED CYP4X1 WILD-TYPE
  FEMALE              4              166
  MALE                1              196
[1] 2 2
[1] FALSE
D365V8, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     5   0
  CYP4X1 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      5    0
  CYP4X1 WILD-TYPE  295    8
     clus
vv    CYP4X1 MUTATED CYP4X1 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D365V9, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      4    1
  CYP4X1 WILD-TYPE  310   47
                               clus
vv                              CYP4X1 MUTATED CYP4X1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CYP4X1 MUTATED     2   0   0   2
  CYP4X1 WILD-TYPE 257   3  22  19
D365V10, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              2               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"
D365V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4X1 MUTATED                                  0     1
  CYP4X1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP4X1 MUTATED                           1     3
  CYP4X1 WILD-TYPE                        18   173
D365V12, multiclass
                                  clus
vv                                 CYP4X1 MUTATED CYP4X1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = DAXX MUTATION ANALYSIS
D366V1, survival
                sevent
clus2              0   1
  DAXX MUTATED     9   2
  DAXX WILD-TYPE 268  76
  DAXX MUTATED DAXX WILD-TYPE 
            11            344 
  DAXX MUTATED DAXX WILD-TYPE 
             2             76 
$`DAXX MUTATED`
TCGA-G4-6586 TCGA-A6-5657 TCGA-A6-5661 TCGA-AU-6004 TCGA-CK-5916 TCGA-CM-5862 
       35.80        31.63        33.53        27.09        21.14         5.03 
TCGA-CM-5868 TCGA-CM-6166 TCGA-D5-6536 TCGA-G4-6309 TCGA-G4-6317 
       17.03        21.99        17.85        85.48        36.00 

$`DAXX WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.75        36.53        32.91        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        15.02        15.02        12.00        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DAXX MUTATED DAXX WILD-TYPE 
          5.03           0.00 
  DAXX MUTATED DAXX WILD-TYPE 
         85.48         148.01 
  DAXX MUTATED DAXX WILD-TYPE 
        27.090         22.045 
[1] "5.0 - 85.5 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D366V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DAXX MUTATED         3        0        0         3         0         0
  DAXX WILD-TYPE      61        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DAXX MUTATED           1          0          2          1        0         2
  DAXX WILD-TYPE        17          6         42         32       35        10
                vv
clus             STAGE IVB
  DAXX MUTATED           0
  DAXX WILD-TYPE         1
D366V3, multiclass
            clus
vv           DAXX MUTATED DAXX WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             2             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
  DAXX MUTATED     1   2   8   1
  DAXX WILD-TYPE   8  65 241  40
D366V4, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  T1            1              8
  T2            2             65
  T3            8            241
  T4            1             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
  DAXX MUTATED     6   4   2
  DAXX WILD-TYPE 214  77  64
D366V5, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  N0            6            214
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V6, binary
                cls
clus               0   1
  DAXX MUTATED     9   2
  DAXX WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED      9    2
  DAXX WILD-TYPE  276   46
   clus
vv  DAXX MUTATED DAXX WILD-TYPE
  0            9            276
  1            2             46
[1] 2 2
[1] FALSE
D366V7, binary
                cls
clus               0   1
  DAXX MUTATED     8   4
  DAXX WILD-TYPE 162 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED      8    4
  DAXX WILD-TYPE  162  193
        clus
vv       DAXX MUTATED DAXX WILD-TYPE
  FEMALE            8            162
  MALE              4            193
[1] 2 2
[1] FALSE
D366V8, binary
                cls
clus               0   1
  DAXX MUTATED    10   0
  DAXX WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     10    0
  DAXX WILD-TYPE  290    8
     clus
vv    DAXX MUTATED DAXX WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D366V9, binary
                cls
clus               0   1
  DAXX MUTATED    12   0
  DAXX WILD-TYPE 302  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     12    0
  DAXX WILD-TYPE  302   48
                               clus
vv                              DAXX MUTATED DAXX WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DAXX MUTATED    11   0   0   1
  DAXX WILD-TYPE 248   3  22  20
D366V10, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            1             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"
D366V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DAXX MUTATED                                  0     0
  DAXX WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DAXX MUTATED                           3     8
  DAXX WILD-TYPE                        16   168
D366V12, multiclass
                                  clus
vv                                 DAXX MUTATED DAXX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                       8            168
[1] 4 2
[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 = CDK17 MUTATION ANALYSIS
D367V1, survival
                 sevent
clus2               0   1
  CDK17 MUTATED     7   4
  CDK17 WILD-TYPE 270  74
  CDK17 MUTATED CDK17 WILD-TYPE 
             11             344 
  CDK17 MUTATED CDK17 WILD-TYPE 
              4              74 
$`CDK17 MUTATED`
TCGA-G4-6588 TCGA-AA-3558 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6963 
       26.17        20.98        27.02         4.01        34.98        27.42 
TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4950 TCGA-G4-6323 TCGA-G4-6626 
       49.41        10.06        85.45        13.78        46.75 

$`CDK17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00 

  CDK17 MUTATED CDK17 WILD-TYPE 
           4.01            0.00 
  CDK17 MUTATED CDK17 WILD-TYPE 
          85.45          148.01 
  CDK17 MUTATED CDK17 WILD-TYPE 
          27.02           22.01 
[1] "4.0 - 85.5 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D367V2, continuous
                 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      63        0       25       105         6         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  CDK17 MUTATED           0
  CDK17 WILD-TYPE         1
D367V3, multiclass
            clus
vv           CDK17 MUTATED CDK17 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CDK17 MUTATED     0   1   7   2
  CDK17 WILD-TYPE   9  66 242  39
D367V4, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             2              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
  CDK17 MUTATED     9   2   0
  CDK17 WILD-TYPE 211  79  66
D367V5, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V6, binary
                 cls
clus                0   1
  CDK17 MUTATED     8   0
  CDK17 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      8    0
  CDK17 WILD-TYPE  277   48
   clus
vv  CDK17 MUTATED CDK17 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D367V7, binary
                 cls
clus                0   1
  CDK17 MUTATED     4   7
  CDK17 WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      4    7
  CDK17 WILD-TYPE  166  190
        clus
vv       CDK17 MUTATED CDK17 WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D367V8, binary
                 cls
clus                0   1
  CDK17 MUTATED    10   0
  CDK17 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED     10    0
  CDK17 WILD-TYPE  290    8
     clus
vv    CDK17 MUTATED CDK17 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D367V9, binary
                 cls
clus                0   1
  CDK17 MUTATED     8   3
  CDK17 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      8    3
  CDK17 WILD-TYPE  306   45
                               clus
vv                              CDK17 MUTATED CDK17 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK17 MUTATED     6   1   1   1
  CDK17 WILD-TYPE 253   2  21  20
D367V10, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  R0             6             253
  R1             1               2
  R2             1              21
  RX             1              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"
D367V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK17 MUTATED                                  0     1
  CDK17 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK17 MUTATED                           2     4
  CDK17 WILD-TYPE                        17   172
D367V12, multiclass
                                  clus
vv                                 CDK17 MUTATED CDK17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = SYNCRIP MUTATION ANALYSIS
D368V1, survival
                   sevent
clus2                 0   1
  SYNCRIP MUTATED     7   3
  SYNCRIP WILD-TYPE 270  75
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               10               345 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                3                75 
$`SYNCRIP MUTATED`
TCGA-AA-A010 TCGA-AA-A017 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5348 
       34.98        15.02         6.77        12.76        10.06        22.98 
TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6536 TCGA-F4-6460 
       14.04        15.12        17.85        31.96 

$`SYNCRIP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             6.77              0.00 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            34.98            148.01 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            15.07             22.09 
[1] "6.8 - 35.0 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D368V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNCRIP MUTATED         2        0        0         4         1         0
  SYNCRIP WILD-TYPE      62        1       26       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNCRIP MUTATED           0          0          3          0        0
  SYNCRIP WILD-TYPE        18          6         41         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SYNCRIP MUTATED           0         0
  SYNCRIP WILD-TYPE        12         1
D368V3, multiclass
            clus
vv           SYNCRIP MUTATED SYNCRIP WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SYNCRIP MUTATED     0   2   7   1
  SYNCRIP WILD-TYPE   9  65 242  40
D368V4, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               7               242
  T4               1                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
  SYNCRIP MUTATED     7   3   0
  SYNCRIP WILD-TYPE 213  78  66
D368V5, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  N0               7               213
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V6, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     8   0
  SYNCRIP WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      8    0
  SYNCRIP WILD-TYPE  277   48
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D368V7, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     5   5
  SYNCRIP WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      5    5
  SYNCRIP WILD-TYPE  165  192
        clus
vv       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D368V8, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    10   0
  SYNCRIP WILD-TYPE 290   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     10    0
  SYNCRIP WILD-TYPE  290    8
     clus
vv    SYNCRIP MUTATED SYNCRIP WILD-TYPE
  NO               10               290
  YES               0                 8
[1] 2 2
[1] FALSE
D368V9, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     9   1
  SYNCRIP WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      9    1
  SYNCRIP WILD-TYPE  305   47
                               clus
vv                              SYNCRIP MUTATED SYNCRIP WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SYNCRIP MUTATED     6   0   0   3
  SYNCRIP WILD-TYPE 253   3  22  18
D368V10, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               3                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"
D368V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNCRIP MUTATED                                  0     2
  SYNCRIP WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SYNCRIP MUTATED                           0     6
  SYNCRIP WILD-TYPE                        19   170
D368V12, multiclass
                                  clus
vv                                 SYNCRIP MUTATED SYNCRIP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = ENPEP MUTATION ANALYSIS
D369V1, survival
                 sevent
clus2               0   1
  ENPEP MUTATED    12   9
  ENPEP WILD-TYPE 265  69
  ENPEP MUTATED ENPEP WILD-TYPE 
             21             334 
  ENPEP MUTATED ENPEP WILD-TYPE 
              9              69 
$`ENPEP MUTATED`
TCGA-AA-3516 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-6141 
       13.02        10.88       100.01        46.65        33.53         8.38 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3977 TCGA-AA-A00U TCGA-AA-A010 
        3.02        63.98        54.02        25.02        17.03        34.98 
TCGA-AD-6890 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-5796 TCGA-CA-6717 TCGA-D5-5538 
       24.53         6.77        12.10        12.39        12.76        54.61 
TCGA-D5-6536 TCGA-DM-A1D7 TCGA-F4-6809 
       17.85        13.32        13.25 

$`ENPEP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        79.69        43.76        43.76        42.90        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
        0.99        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        83.24         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 
        5.13        22.36        62.79        88.21        49.41        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.36        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ENPEP MUTATED ENPEP WILD-TYPE 
           3.02            0.00 
  ENPEP MUTATED ENPEP WILD-TYPE 
         100.01          148.01 
  ENPEP MUTATED ENPEP WILD-TYPE 
          17.03           22.09 
[1] "3.0 - 100.0 (17.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D369V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPEP MUTATED         1        0        4         6         1         0
  ENPEP WILD-TYPE      63        1       22       102         7         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        17          6         41         33       34        11
                 vv
clus              STAGE IVB
  ENPEP MUTATED           0
  ENPEP WILD-TYPE         1
D369V3, multiclass
            clus
vv           ENPEP MUTATED ENPEP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  ENPEP MUTATED     1   2  15   3
  ENPEP WILD-TYPE   8  65 234  38
D369V4, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  T1             1               8
  T2             2              65
  T3            15             234
  T4             3              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
  ENPEP MUTATED    14   5   2
  ENPEP WILD-TYPE 206  76  64
D369V5, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  N0            14             206
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V6, binary
                 cls
clus                0   1
  ENPEP MUTATED    15   2
  ENPEP WILD-TYPE 270  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     15    2
  ENPEP WILD-TYPE  270   46
   clus
vv  ENPEP MUTATED ENPEP WILD-TYPE
  0            15             270
  1             2              46
[1] 2 2
[1] FALSE
D369V7, binary
                 cls
clus                0   1
  ENPEP MUTATED     9  12
  ENPEP WILD-TYPE 161 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED      9   12
  ENPEP WILD-TYPE  161  185
        clus
vv       ENPEP MUTATED ENPEP WILD-TYPE
  FEMALE             9             161
  MALE              12             185
[1] 2 2
[1] FALSE
D369V8, binary
                 cls
clus                0   1
  ENPEP MUTATED    20   0
  ENPEP WILD-TYPE 280   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     20    0
  ENPEP WILD-TYPE  280    8
     clus
vv    ENPEP MUTATED ENPEP WILD-TYPE
  NO             20             280
  YES             0               8
[1] 2 2
[1] FALSE
D369V9, binary
                 cls
clus                0   1
  ENPEP MUTATED    17   3
  ENPEP WILD-TYPE 297  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     17    3
  ENPEP WILD-TYPE  297   45
                               clus
vv                              ENPEP MUTATED ENPEP WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ENPEP MUTATED    11   0   0   1
  ENPEP WILD-TYPE 248   3  22  20
D369V10, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D369V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENPEP MUTATED                                  0     2
  ENPEP WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ENPEP MUTATED                           3     9
  ENPEP WILD-TYPE                        16   167
D369V12, multiclass
                                  clus
vv                                 ENPEP MUTATED ENPEP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        9             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(370) Variable = C6ORF89 MUTATION ANALYSIS
D370V1, survival
                   sevent
clus2                 0   1
  C6ORF89 MUTATED     3   2
  C6ORF89 WILD-TYPE 274  76
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                5               350 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                2                76 
$`C6ORF89 MUTATED`
TCGA-AA-3811 TCGA-AA-3977 TCGA-AY-6196 TCGA-CM-6678 TCGA-F4-6809 
       10.06        25.02         0.20        11.01        13.25 

$`C6ORF89 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
              0.2               0.0 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            25.02            148.01 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            11.01             22.09 
[1] "0.2 - 25.0 (11.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.8"
D370V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF89 MUTATED         0        0        0         1         0         0
  C6ORF89 WILD-TYPE      64        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF89 MUTATED           1          0          0          1        0
  C6ORF89 WILD-TYPE        17          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  C6ORF89 MUTATED           2         0
  C6ORF89 WILD-TYPE        10         1
D370V3, multiclass
            clus
vv           C6ORF89 MUTATED C6ORF89 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                2                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
  C6ORF89 MUTATED     0   1   4   1
  C6ORF89 WILD-TYPE   9  66 245  40
D370V4, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               1                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
  C6ORF89 MUTATED     2   2   2
  C6ORF89 WILD-TYPE 218  79  64
D370V5, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  N0               2               218
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V6, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     2   2
  C6ORF89 WILD-TYPE 283  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      2    2
  C6ORF89 WILD-TYPE  283   46
   clus
vv  C6ORF89 MUTATED C6ORF89 WILD-TYPE
  0               2               283
  1               2                46
[1] 2 2
[1] FALSE
D370V7, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     4   2
  C6ORF89 WILD-TYPE 166 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      4    2
  C6ORF89 WILD-TYPE  166  195
        clus
vv       C6ORF89 MUTATED C6ORF89 WILD-TYPE
  FEMALE               4               166
  MALE                 2               195
[1] 2 2
[1] FALSE
D370V8, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     4   0
  C6ORF89 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      4    0
  C6ORF89 WILD-TYPE  296    8
     clus
vv    C6ORF89 MUTATED C6ORF89 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D370V9, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     5   1
  C6ORF89 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      5    1
  C6ORF89 WILD-TYPE  309   47
                               clus
vv                              C6ORF89 MUTATED C6ORF89 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C6ORF89 MUTATED     5   0   0   0
  C6ORF89 WILD-TYPE 254   3  22  21
D370V10, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D370V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF89 MUTATED                                  0     0
  C6ORF89 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C6ORF89 MUTATED                           0     3
  C6ORF89 WILD-TYPE                        19   173
D370V12, multiclass
                                  clus
vv                                 C6ORF89 MUTATED C6ORF89 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = USP7 MUTATION ANALYSIS
D371V1, survival
                sevent
clus2              0   1
  USP7 MUTATED    15   7
  USP7 WILD-TYPE 262  71
  USP7 MUTATED USP7 WILD-TYPE 
            22            333 
  USP7 MUTATED USP7 WILD-TYPE 
             7             71 
$`USP7 MUTATED`
TCGA-AA-3715 TCGA-G4-6588 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-A00N 
       19.04        26.17        63.98         1.02         6.97         4.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-5543 
       34.98        38.07        35.01        83.24        27.09        33.01 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       58.39        49.41        11.74        12.76        10.06        17.56 
TCGA-D5-6540 TCGA-D5-6541 TCGA-F4-6856 TCGA-G4-6317 
       16.14        15.58        35.31        36.00 

$`USP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3519 TCGA-AA-3526 
       35.01         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.59        12.20        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  USP7 MUTATED USP7 WILD-TYPE 
          1.02           0.00 
  USP7 MUTATED USP7 WILD-TYPE 
         83.24         148.01 
  USP7 MUTATED USP7 WILD-TYPE 
         26.63          22.03 
[1] "1.0 - 83.2 (26.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D371V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP7 MUTATED         3        0        4         8         2         0
  USP7 WILD-TYPE      61        1       22       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP7 MUTATED           3          0          1          1        1         1
  USP7 WILD-TYPE        15          6         43         32       34        11
                vv
clus             STAGE IVB
  USP7 MUTATED           0
  USP7 WILD-TYPE         1
D371V3, multiclass
            clus
vv           USP7 MUTATED USP7 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  USP7 MUTATED     0   3  17   4
  USP7 WILD-TYPE   9  64 232  37
D371V4, multiclass
    clus
vv   USP7 MUTATED USP7 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           17            232
  T4            4             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
  USP7 MUTATED    17   3   4
  USP7 WILD-TYPE 203  78  62
D371V5, multiclass
    clus
vv   USP7 MUTATED USP7 WILD-TYPE
  N0           17            203
  N1            3             78
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V6, binary
                cls
clus               0   1
  USP7 MUTATED    20   2
  USP7 WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     20    2
  USP7 WILD-TYPE  265   46
   clus
vv  USP7 MUTATED USP7 WILD-TYPE
  0           20            265
  1            2             46
[1] 2 2
[1] FALSE
D371V7, binary
                cls
clus               0   1
  USP7 MUTATED    10  14
  USP7 WILD-TYPE 160 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     10   14
  USP7 WILD-TYPE  160  183
        clus
vv       USP7 MUTATED USP7 WILD-TYPE
  FEMALE           10            160
  MALE             14            183
[1] 2 2
[1] FALSE
D371V8, binary
                cls
clus               0   1
  USP7 MUTATED    18   1
  USP7 WILD-TYPE 282   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     18    1
  USP7 WILD-TYPE  282    7
     clus
vv    USP7 MUTATED USP7 WILD-TYPE
  NO            18            282
  YES            1              7
[1] 2 2
[1] FALSE
D371V9, binary
                cls
clus               0   1
  USP7 MUTATED    19   5
  USP7 WILD-TYPE 295  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     19    5
  USP7 WILD-TYPE  295   43
                               clus
vv                              USP7 MUTATED USP7 WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  USP7 MUTATED    19   0   0   3
  USP7 WILD-TYPE 240   3  22  18
D371V10, multiclass
    clus
vv   USP7 MUTATED USP7 WILD-TYPE
  R0           19            240
  R1            0              3
  R2            0             22
  RX            3             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"
D371V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP7 MUTATED                                  0     3
  USP7 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USP7 MUTATED                           1    10
  USP7 WILD-TYPE                        18   166
D371V12, multiclass
                                  clus
vv                                 USP7 MUTATED USP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(372) Variable = CCAR1 MUTATION ANALYSIS
D372V1, survival
                 sevent
clus2               0   1
  CCAR1 MUTATED    14   3
  CCAR1 WILD-TYPE 263  75
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             17             338 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
              3              75 
$`CCAR1 MUTATED`
TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3855 
       79.69        22.06        21.76        19.66        63.98        32.05 
TCGA-AA-3966 TCGA-AA-A00J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CM-6162 
        2.01        18.05        58.39        49.41        14.30        12.00 
TCGA-CM-6680 TCGA-D5-6929 TCGA-DM-A1D4 TCGA-G4-6304 TCGA-G4-6626 
       12.03        13.41        92.75        53.62        46.75 

$`CCAR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

  CCAR1 MUTATED CCAR1 WILD-TYPE 
           2.01            0.00 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          92.75          148.01 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          22.06           22.06 
[1] "2.0 - 92.8 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D372V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCAR1 MUTATED         2        0        2         7         1         0
  CCAR1 WILD-TYPE      62        1       24       101         7         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        18          6         40         32       34        12
                 vv
clus              STAGE IVB
  CCAR1 MUTATED           0
  CCAR1 WILD-TYPE         1
D372V3, multiclass
            clus
vv           CCAR1 MUTATED CCAR1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  CCAR1 MUTATED     0   2  13   3
  CCAR1 WILD-TYPE   9  65 236  38
D372V4, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            13             236
  T4             3              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
  CCAR1 MUTATED    12   5   1
  CCAR1 WILD-TYPE 208  76  65
D372V5, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  N0            12             208
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V6, binary
                 cls
clus                0   1
  CCAR1 MUTATED    14   1
  CCAR1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     14    1
  CCAR1 WILD-TYPE  271   47
   clus
vv  CCAR1 MUTATED CCAR1 WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D372V7, binary
                 cls
clus                0   1
  CCAR1 MUTATED     9   9
  CCAR1 WILD-TYPE 161 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED      9    9
  CCAR1 WILD-TYPE  161  188
        clus
vv       CCAR1 MUTATED CCAR1 WILD-TYPE
  FEMALE             9             161
  MALE               9             188
[1] 2 2
[1] FALSE
D372V8, binary
                 cls
clus                0   1
  CCAR1 MUTATED    15   0
  CCAR1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     15    0
  CCAR1 WILD-TYPE  285    8
     clus
vv    CCAR1 MUTATED CCAR1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D372V9, binary
                 cls
clus                0   1
  CCAR1 MUTATED    14   4
  CCAR1 WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     14    4
  CCAR1 WILD-TYPE  300   44
                               clus
vv                              CCAR1 MUTATED CCAR1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCAR1 MUTATED    13   0   0   1
  CCAR1 WILD-TYPE 246   3  22  20
D372V10, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             1              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"
D372V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCAR1 MUTATED                                  0     1
  CCAR1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCAR1 MUTATED                           0    12
  CCAR1 WILD-TYPE                        19   164
D372V12, multiclass
                                  clus
vv                                 CCAR1 MUTATED CCAR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = SLC7A10 MUTATION ANALYSIS
D373V1, survival
                   sevent
clus2                 0   1
  SLC7A10 MUTATED     4   3
  SLC7A10 WILD-TYPE 273  75
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                7               348 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                3                75 
$`SLC7A10 MUTATED`
TCGA-AA-3715 TCGA-AA-3664 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-6674 
       19.04        54.02        83.24        27.09        49.41        12.95 
TCGA-D5-6928 
       11.64 

$`SLC7A10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            11.64              0.00 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            83.24            148.01 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
           27.090            22.045 
[1] "11.6 - 83.2 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D373V2, continuous
                   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      63        1       23       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A10 MUTATED           0          0          0          0        0
  SLC7A10 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC7A10 MUTATED           0         0
  SLC7A10 WILD-TYPE        12         1
D373V3, multiclass
            clus
vv           SLC7A10 MUTATED SLC7A10 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                3               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC7A10 MUTATED     0   1   6   1
  SLC7A10 WILD-TYPE   9  66 243  40
D373V4, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               1                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
  SLC7A10 MUTATED     8   0   0
  SLC7A10 WILD-TYPE 212  81  66
D373V5, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  N0               8               212
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V6, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     6   0
  SLC7A10 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      6    0
  SLC7A10 WILD-TYPE  279   48
   clus
vv  SLC7A10 MUTATED SLC7A10 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D373V7, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     4   4
  SLC7A10 WILD-TYPE 166 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      4    4
  SLC7A10 WILD-TYPE  166  193
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  FEMALE               4               166
  MALE                 4               193
[1] 2 2
[1] FALSE
D373V8, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     6   0
  SLC7A10 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      6    0
  SLC7A10 WILD-TYPE  294    8
     clus
vv    SLC7A10 MUTATED SLC7A10 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D373V9, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     7   1
  SLC7A10 WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      7    1
  SLC7A10 WILD-TYPE  307   47
                               clus
vv                              SLC7A10 MUTATED SLC7A10 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC7A10 MUTATED     6   0   0   1
  SLC7A10 WILD-TYPE 253   3  22  20
D373V10, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D373V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC7A10 MUTATED                                  0     1
  SLC7A10 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC7A10 MUTATED                           0     5
  SLC7A10 WILD-TYPE                        19   171
D373V12, multiclass
                                  clus
vv                                 SLC7A10 MUTATED SLC7A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = GTF2IRD2 MUTATION ANALYSIS
D374V1, survival
                    sevent
clus2                  0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 271  78
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                349 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 0                 78 
$`GTF2IRD2 MUTATED`
TCGA-G4-6588 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6165 TCGA-F4-6856 
       26.17        12.59        12.76        32.02        16.04        35.31 

$`GTF2IRD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.39        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6166 TCGA-CM-6167 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
             12.59               0.00 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
             35.31             148.01 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
            21.105             22.060 
[1] "12.6 - 35.3 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D374V2, continuous
                    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      63        1       26       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF2IRD2 MUTATED           0          0          0          0        0
  GTF2IRD2 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  GTF2IRD2 MUTATED           0         0
  GTF2IRD2 WILD-TYPE        12         1
D374V3, multiclass
            clus
vv           GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 5                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  GTF2IRD2 MUTATED     0   1   5   0
  GTF2IRD2 WILD-TYPE   9  66 244  41
D374V4, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                5                244
  T4                0                 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
  GTF2IRD2 MUTATED     6   0   0
  GTF2IRD2 WILD-TYPE 214  81  66
D374V5, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  N0                6                214
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V6, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      6    0
  GTF2IRD2 WILD-TYPE  279   48
   clus
vv  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D374V7, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     1   5
  GTF2IRD2 WILD-TYPE 169 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      1    5
  GTF2IRD2 WILD-TYPE  169  192
        clus
vv       GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  FEMALE                1                169
  MALE                  5                192
[1] 2 2
[1] FALSE
D374V8, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      6    0
  GTF2IRD2 WILD-TYPE  294    8
     clus
vv    GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D374V9, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     4   2
  GTF2IRD2 WILD-TYPE 310  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      4    2
  GTF2IRD2 WILD-TYPE  310   46
                               clus
vv                              GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  GTF2IRD2 MUTATED     5   0   0   1
  GTF2IRD2 WILD-TYPE 254   3  22  20
D374V10, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D374V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2IRD2 MUTATED                                  0     2
  GTF2IRD2 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  GTF2IRD2 MUTATED                           0     4
  GTF2IRD2 WILD-TYPE                        19   172
D374V12, multiclass
                                  clus
vv                                 GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = TIFA MUTATION ANALYSIS
D375V1, survival
                sevent
clus2              0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 272  78
  TIFA MUTATED TIFA WILD-TYPE 
             5            350 
  TIFA MUTATED TIFA WILD-TYPE 
             0             78 
$`TIFA MUTATED`
TCGA-AA-3663 TCGA-CA-6715 TCGA-CM-5348 TCGA-D5-5541 TCGA-G4-6317 
        6.97        12.59        22.98        55.92        36.00 

$`TIFA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TIFA MUTATED TIFA WILD-TYPE 
          6.97           0.00 
  TIFA MUTATED TIFA WILD-TYPE 
         55.92         148.01 
  TIFA MUTATED TIFA WILD-TYPE 
        22.980         22.045 
[1] "7.0 - 55.9 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D375V2, continuous
                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      64        1       25       107         8         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        18          6         41         32       35        12
                vv
clus             STAGE IVB
  TIFA MUTATED           0
  TIFA WILD-TYPE         1
D375V3, multiclass
            clus
vv           TIFA MUTATED TIFA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TIFA MUTATED     0   0   6   0
  TIFA WILD-TYPE   9  67 243  41
D375V4, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            0             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
  TIFA MUTATED     2   3   1
  TIFA WILD-TYPE 218  78  65
D375V5, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  N0            2            218
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V6, binary
                cls
clus               0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      5    0
  TIFA WILD-TYPE  280   48
   clus
vv  TIFA MUTATED TIFA WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D375V7, binary
                cls
clus               0   1
  TIFA MUTATED     2   4
  TIFA WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      2    4
  TIFA WILD-TYPE  168  193
        clus
vv       TIFA MUTATED TIFA WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D375V8, binary
                cls
clus               0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      5    0
  TIFA WILD-TYPE  295    8
     clus
vv    TIFA MUTATED TIFA WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D375V9, binary
                cls
clus               0   1
  TIFA MUTATED     6   0
  TIFA WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      6    0
  TIFA WILD-TYPE  308   48
                               clus
vv                              TIFA MUTATED TIFA WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TIFA MUTATED     5   0   0   1
  TIFA WILD-TYPE 254   3  22  20
D375V10, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D375V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIFA MUTATED                                  0     1
  TIFA WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TIFA MUTATED                           0     3
  TIFA WILD-TYPE                        19   173
D375V12, multiclass
                                  clus
vv                                 TIFA MUTATED TIFA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = MFN1 MUTATION ANALYSIS
D376V1, survival
                sevent
clus2              0   1
  MFN1 MUTATED     9   4
  MFN1 WILD-TYPE 268  74
  MFN1 MUTATED MFN1 WILD-TYPE 
            13            342 
  MFN1 MUTATED MFN1 WILD-TYPE 
             4             74 
$`MFN1 MUTATED`
TCGA-AA-3516 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-5665 TCGA-A6-6780 TCGA-CA-6715 
       13.02        25.08       100.01        22.06        20.12        12.59 
TCGA-CK-5916 TCGA-D5-6532 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DA TCGA-F4-6808 
       21.14        18.25        10.13        13.35         7.50        33.67 
TCGA-G4-6299 
       74.56 

$`MFN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-6716 
        3.19        12.69        12.36        12.39        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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         7.53        12.39        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MFN1 MUTATED MFN1 WILD-TYPE 
           7.5            0.0 
  MFN1 MUTATED MFN1 WILD-TYPE 
        100.01         148.01 
  MFN1 MUTATED MFN1 WILD-TYPE 
        20.120         22.225 
[1] "7.5 - 100.0 (20.1)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D376V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFN1 MUTATED         2        0        1         4         0         0
  MFN1 WILD-TYPE      62        1       25       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFN1 MUTATED           1          1          2          2        0         0
  MFN1 WILD-TYPE        17          5         42         31       35        12
                vv
clus             STAGE IVB
  MFN1 MUTATED           0
  MFN1 WILD-TYPE         1
D376V3, multiclass
            clus
vv           MFN1 MUTATED MFN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  MFN1 MUTATED     2   0  11   0
  MFN1 WILD-TYPE   7  67 238  41
D376V4, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  T1            2              7
  T2            0             67
  T3           11            238
  T4            0             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
  MFN1 MUTATED     7   3   3
  MFN1 WILD-TYPE 213  78  63
D376V5, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  N0            7            213
  N1            3             78
  N2            3             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"
D376V6, binary
                cls
clus               0   1
  MFN1 MUTATED    12   0
  MFN1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     12    0
  MFN1 WILD-TYPE  273   48
   clus
vv  MFN1 MUTATED MFN1 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D376V7, binary
                cls
clus               0   1
  MFN1 MUTATED     5   8
  MFN1 WILD-TYPE 165 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      5    8
  MFN1 WILD-TYPE  165  189
        clus
vv       MFN1 MUTATED MFN1 WILD-TYPE
  FEMALE            5            165
  MALE              8            189
[1] 2 2
[1] FALSE
D376V8, binary
                cls
clus               0   1
  MFN1 MUTATED    12   0
  MFN1 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     12    0
  MFN1 WILD-TYPE  288    8
     clus
vv    MFN1 MUTATED MFN1 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D376V9, binary
                cls
clus               0   1
  MFN1 MUTATED    10   3
  MFN1 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     10    3
  MFN1 WILD-TYPE  304   45
                               clus
vv                              MFN1 MUTATED MFN1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MFN1 MUTATED     7   0   0   2
  MFN1 WILD-TYPE 252   3  22  19
D376V10, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            2             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"
D376V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFN1 MUTATED                                  0     1
  MFN1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MFN1 MUTATED                           0    11
  MFN1 WILD-TYPE                        19   165
D376V12, multiclass
                                  clus
vv                                 MFN1 MUTATED MFN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      11            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(377) Variable = AMOT MUTATION ANALYSIS
D377V1, survival
                sevent
clus2              0   1
  AMOT MUTATED     7   4
  AMOT WILD-TYPE 270  74
  AMOT MUTATED AMOT WILD-TYPE 
            11            344 
  AMOT MUTATED AMOT WILD-TYPE 
             4             74 
$`AMOT MUTATED`
TCGA-AA-3713 TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-A00R TCGA-AA-A01P 
       19.04        42.90        19.66         3.02         0.99        38.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1D8 
       21.44        58.39        12.76        12.00        12.59 

$`AMOT WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  AMOT MUTATED AMOT WILD-TYPE 
          0.99           0.00 
  AMOT MUTATED AMOT WILD-TYPE 
         58.39         148.01 
  AMOT MUTATED AMOT WILD-TYPE 
        19.040         22.225 
[1] "1.0 - 58.4 (19.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.1"
D377V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMOT MUTATED         2        0        1         3         2         0
  AMOT WILD-TYPE      62        1       25       105         6         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        17          6         43         32       34        12
                vv
clus             STAGE IVB
  AMOT MUTATED           0
  AMOT WILD-TYPE         1
D377V3, multiclass
            clus
vv           AMOT MUTATED AMOT WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  AMOT MUTATED     0   2   8   3
  AMOT WILD-TYPE   9  65 241  38
D377V4, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            3             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
  AMOT MUTATED     9   4   0
  AMOT WILD-TYPE 211  77  66
D377V5, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  N0            9            211
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V6, binary
                cls
clus               0   1
  AMOT MUTATED     7   1
  AMOT WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED      7    1
  AMOT WILD-TYPE  278   47
   clus
vv  AMOT MUTATED AMOT WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D377V7, binary
                cls
clus               0   1
  AMOT MUTATED     7   6
  AMOT WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED      7    6
  AMOT WILD-TYPE  163  191
        clus
vv       AMOT MUTATED AMOT WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D377V8, binary
                cls
clus               0   1
  AMOT MUTATED     8   1
  AMOT WILD-TYPE 292   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED      8    1
  AMOT WILD-TYPE  292    7
     clus
vv    AMOT MUTATED AMOT WILD-TYPE
  NO             8            292
  YES            1              7
[1] 2 2
[1] FALSE
D377V9, binary
                cls
clus               0   1
  AMOT MUTATED    10   3
  AMOT WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED     10    3
  AMOT WILD-TYPE  304   45
                               clus
vv                              AMOT MUTATED AMOT WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AMOT MUTATED     8   0   1   3
  AMOT WILD-TYPE 251   3  21  18
D377V10, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            3             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"
D377V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMOT MUTATED                                  0     1
  AMOT WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AMOT MUTATED                           0     8
  AMOT WILD-TYPE                        19   168
D377V12, multiclass
                                  clus
vv                                 AMOT MUTATED AMOT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = ZNF449 MUTATION ANALYSIS
D378V1, survival
                  sevent
clus2                0   1
  ZNF449 MUTATED    10   0
  ZNF449 WILD-TYPE 267  78
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              10              345 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
               0               78 
$`ZNF449 MUTATED`
TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A01Q TCGA-AD-5900 
       26.17        33.53        22.06         6.97         1.02        12.16 
TCGA-AU-6004 TCGA-CA-6716 TCGA-D5-6931 TCGA-F4-6805 
       27.09        12.20        12.00        34.42 

$`ZNF449 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF449 MUTATED ZNF449 WILD-TYPE 
            1.02             0.00 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
           34.42           148.01 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
           17.13            22.09 
[1] "1.0 - 34.4 (17.1)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D378V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF449 MUTATED         2        0        2         5         0         0
  ZNF449 WILD-TYPE      62        1       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF449 MUTATED           0          0          0          1        0
  ZNF449 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF449 MUTATED           0         0
  ZNF449 WILD-TYPE        12         1
D378V3, multiclass
            clus
vv           ZNF449 MUTATED ZNF449 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF449 MUTATED     0   2   7   1
  ZNF449 WILD-TYPE   9  65 242  40
D378V4, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              1               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
  ZNF449 MUTATED     9   0   1
  ZNF449 WILD-TYPE 211  81  65
D378V5, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V6, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     9   0
  ZNF449 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      9    0
  ZNF449 WILD-TYPE  276   48
   clus
vv  ZNF449 MUTATED ZNF449 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D378V7, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     6   4
  ZNF449 WILD-TYPE 164 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      6    4
  ZNF449 WILD-TYPE  164  193
        clus
vv       ZNF449 MUTATED ZNF449 WILD-TYPE
  FEMALE              6              164
  MALE                4              193
[1] 2 2
[1] FALSE
D378V8, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     8   0
  ZNF449 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      8    0
  ZNF449 WILD-TYPE  292    8
     clus
vv    ZNF449 MUTATED ZNF449 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D378V9, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     9   1
  ZNF449 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      9    1
  ZNF449 WILD-TYPE  305   47
                               clus
vv                              ZNF449 MUTATED ZNF449 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF449 MUTATED     9   0   0   1
  ZNF449 WILD-TYPE 250   3  22  20
D378V10, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D378V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF449 MUTATED                                  0     1
  ZNF449 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF449 MUTATED                           1     6
  ZNF449 WILD-TYPE                        18   170
D378V12, multiclass
                                  clus
vv                                 ZNF449 MUTATED ZNF449 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = SMARCA4 MUTATION ANALYSIS
D379V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    23   6
  SMARCA4 WILD-TYPE 254  72
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               29               326 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                6                72 
$`SMARCA4 MUTATED`
TCGA-AA-3524 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6310 TCGA-G4-6588 TCGA-A6-6653 
       36.03        10.88       100.01        63.62        26.17        24.39 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3558 TCGA-AA-3663 
       19.66         3.02         1.02         0.00        20.98         6.97 
TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6598 
       33.04        25.02        34.98        83.24        21.44        49.41 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       12.76        85.45        37.02        13.02        22.03        22.98 
TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6928 
       15.02        12.95        43.27        17.85        11.64 

$`SMARCA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        22.09        35.80        91.79        79.69 
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-A6-5656 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-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
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-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-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                0                 0 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           100.01            148.01 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           22.030            22.075 
[1] "0.0 - 100.0 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D379V2, continuous
                   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      60        1       21        97         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA4 MUTATED           1          0          4          2        0
  SMARCA4 WILD-TYPE        17          6         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SMARCA4 MUTATED           0         0
  SMARCA4 WILD-TYPE        12         1
D379V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 5                21
  STAGE IIA               11                97
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  SMARCA4 MUTATED     0   5  22   3
  SMARCA4 WILD-TYPE   9  62 227  38
D379V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3              22               227
  T4               3                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
  SMARCA4 MUTATED    22   5   3
  SMARCA4 WILD-TYPE 198  76  63
D379V5, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0              22               198
  N1               5                76
  N2               3                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"
D379V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    25   0
  SMARCA4 WILD-TYPE 260  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     25    0
  SMARCA4 WILD-TYPE  260   48
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              25               260
  1               0                48
[1] 2 2
[1] FALSE
D379V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    11  19
  SMARCA4 WILD-TYPE 159 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     11   19
  SMARCA4 WILD-TYPE  159  178
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE              11               159
  MALE                19               178
[1] 2 2
[1] FALSE
D379V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    26   1
  SMARCA4 WILD-TYPE 274   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     26    1
  SMARCA4 WILD-TYPE  274    7
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO               26               274
  YES               1                 7
[1] 2 2
[1] FALSE
D379V9, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    25   5
  SMARCA4 WILD-TYPE 289  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     25    5
  SMARCA4 WILD-TYPE  289   43
                               clus
vv                              SMARCA4 MUTATED SMARCA4 WILD-TYPE
  COLON ADENOCARCINOMA                       25               289
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED    22   1   1   1
  SMARCA4 WILD-TYPE 237   2  21  20
D379V10, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              22               237
  R1               1                 2
  R2               1                21
  RX               1                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"
D379V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     2
  SMARCA4 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           3    15
  SMARCA4 WILD-TYPE                        16   161
D379V12, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      3                16
  WHITE                                         15               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(380) Variable = IGFBP7 MUTATION ANALYSIS
D380V1, survival
                  sevent
clus2                0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 273  78
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              351 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               0               78 
$`IGFBP7 MUTATED`
TCGA-A6-5657 TCGA-AA-3815 TCGA-D5-5541 TCGA-F4-6808 
       31.63        33.04        55.92        33.67 

$`IGFBP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           31.63             0.00 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           55.92           148.01 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
          33.355           21.990 
[1] "31.6 - 55.9 (33.4)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D380V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFBP7 MUTATED         1        0        0         1         0         0
  IGFBP7 WILD-TYPE      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP7 MUTATED           0          0          2          0        0
  IGFBP7 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  IGFBP7 MUTATED           0         0
  IGFBP7 WILD-TYPE        12         1
D380V3, multiclass
            clus
vv           IGFBP7 MUTATED IGFBP7 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  IGFBP7 MUTATED     1   0   3   0
  IGFBP7 WILD-TYPE   8  67 246  41
D380V4, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              3              246
  T4              0               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
  IGFBP7 MUTATED     2   2   0
  IGFBP7 WILD-TYPE 218  79  66
D380V5, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  N0              2              218
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V6, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  281   48
   clus
vv  IGFBP7 MUTATED IGFBP7 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D380V7, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     2   2
  IGFBP7 WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      2    2
  IGFBP7 WILD-TYPE  168  195
        clus
vv       IGFBP7 MUTATED IGFBP7 WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D380V8, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  296    8
     clus
vv    IGFBP7 MUTATED IGFBP7 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D380V9, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  310   48
                               clus
vv                              IGFBP7 MUTATED IGFBP7 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IGFBP7 MUTATED     4   0   0   0
  IGFBP7 WILD-TYPE 255   3  22  21
D380V10, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D380V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFBP7 MUTATED                                  0     0
  IGFBP7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IGFBP7 MUTATED                           1     2
  IGFBP7 WILD-TYPE                        18   174
D380V12, multiclass
                                  clus
vv                                 IGFBP7 MUTATED IGFBP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(381) Variable = MARK1 MUTATION ANALYSIS
D381V1, survival
                 sevent
clus2               0   1
  MARK1 MUTATED    20   4
  MARK1 WILD-TYPE 257  74
  MARK1 MUTATED MARK1 WILD-TYPE 
             24             331 
  MARK1 MUTATED MARK1 WILD-TYPE 
              4              74 
$`MARK1 MUTATED`
TCGA-AA-A024 TCGA-AZ-4681 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5665 TCGA-AA-3510 
       39.06       106.75        31.63        30.44        22.06        63.98 
TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3977 TCGA-AU-3779 TCGA-AZ-4315 
       29.95        26.99         1.02        25.02        14.50        58.39 
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 

$`MARK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       21.99        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       36.53        32.91        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6167 TCGA-CM-6168 
       12.00        14.04        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-D5-5538 
       11.08        11.08        11.01        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          21.990 
[1] "1.0 - 117.1 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D381V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MARK1 MUTATED         5        0        2         9         0         0
  MARK1 WILD-TYPE      59        1       24        99         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MARK1 MUTATED           0          0          3          2        1         1
  MARK1 WILD-TYPE        18          6         41         31       34        11
                 vv
clus              STAGE IVB
  MARK1 MUTATED           0
  MARK1 WILD-TYPE         1
D381V3, multiclass
            clus
vv           MARK1 MUTATED MARK1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              9              99
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  MARK1 MUTATED     0   6  16   3
  MARK1 WILD-TYPE   9  61 233  38
D381V4, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  T1             0               9
  T2             6              61
  T3            16             233
  T4             3              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
  MARK1 MUTATED    17   5   3
  MARK1 WILD-TYPE 203  76  63
D381V5, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  N0            17             203
  N1             5              76
  N2             3              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"
D381V6, binary
                 cls
clus                0   1
  MARK1 MUTATED    20   2
  MARK1 WILD-TYPE 265  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     20    2
  MARK1 WILD-TYPE  265   46
   clus
vv  MARK1 MUTATED MARK1 WILD-TYPE
  0            20             265
  1             2              46
[1] 2 2
[1] FALSE
D381V7, binary
                 cls
clus                0   1
  MARK1 MUTATED    11  14
  MARK1 WILD-TYPE 159 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     11   14
  MARK1 WILD-TYPE  159  183
        clus
vv       MARK1 MUTATED MARK1 WILD-TYPE
  FEMALE            11             159
  MALE              14             183
[1] 2 2
[1] FALSE
D381V8, binary
                 cls
clus                0   1
  MARK1 MUTATED    23   0
  MARK1 WILD-TYPE 277   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     23    0
  MARK1 WILD-TYPE  277    8
     clus
vv    MARK1 MUTATED MARK1 WILD-TYPE
  NO             23             277
  YES             0               8
[1] 2 2
[1] FALSE
D381V9, binary
                 cls
clus                0   1
  MARK1 MUTATED    21   4
  MARK1 WILD-TYPE 293  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     21    4
  MARK1 WILD-TYPE  293   44
                               clus
vv                              MARK1 MUTATED MARK1 WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MARK1 MUTATED    18   0   0   3
  MARK1 WILD-TYPE 241   3  22  18
D381V10, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  R0            18             241
  R1             0               3
  R2             0              22
  RX             3              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"
D381V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARK1 MUTATED                                  0     1
  MARK1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MARK1 MUTATED                           3    14
  MARK1 WILD-TYPE                        16   162
D381V12, multiclass
                                  clus
vv                                 MARK1 MUTATED MARK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       14             162
[1] 4 2
[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 = CCR2 MUTATION ANALYSIS
D382V1, survival
                sevent
clus2              0   1
  CCR2 MUTATED     7   0
  CCR2 WILD-TYPE 270  78
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            348 
  CCR2 MUTATED CCR2 WILD-TYPE 
             0             78 
$`CCR2 MUTATED`
TCGA-AD-6548 TCGA-A6-5666 TCGA-A6-6781 TCGA-CA-6717 TCGA-CK-4950 TCGA-D5-5541 
       21.37        32.71        19.66        12.76        85.45        55.92 
TCGA-D5-6540 
       16.14 

$`CCR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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         22.075 
[1] "12.8 - 85.5 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D382V2, continuous
                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      62        1       26       107         8         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        18          6         42         32       35        12
                vv
clus             STAGE IVB
  CCR2 MUTATED           0
  CCR2 WILD-TYPE         1
D382V3, multiclass
            clus
vv           CCR2 MUTATED CCR2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  CCR2 MUTATED     0   2   3   2
  CCR2 WILD-TYPE   9  65 246  39
D382V4, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            3            246
  T4            2             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
  CCR2 MUTATED     4   3   0
  CCR2 WILD-TYPE 216  78  66
D382V5, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  N0            4            216
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V6, binary
                cls
clus               0   1
  CCR2 MUTATED     6   0
  CCR2 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      6    0
  CCR2 WILD-TYPE  279   48
   clus
vv  CCR2 MUTATED CCR2 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D382V7, binary
                cls
clus               0   1
  CCR2 MUTATED     2   5
  CCR2 WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      2    5
  CCR2 WILD-TYPE  168  192
        clus
vv       CCR2 MUTATED CCR2 WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D382V8, binary
                cls
clus               0   1
  CCR2 MUTATED     7   0
  CCR2 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      7    0
  CCR2 WILD-TYPE  293    8
     clus
vv    CCR2 MUTATED CCR2 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D382V9, binary
                cls
clus               0   1
  CCR2 MUTATED     3   4
  CCR2 WILD-TYPE 311  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      3    4
  CCR2 WILD-TYPE  311   44
                               clus
vv                              CCR2 MUTATED CCR2 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCR2 MUTATED     4   1   0   1
  CCR2 WILD-TYPE 255   2  22  20
D382V10, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  R0            4            255
  R1            1              2
  R2            0             22
  RX            1             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"
D382V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCR2 MUTATED                                  0     1
  CCR2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCR2 MUTATED                           1     5
  CCR2 WILD-TYPE                        18   171
D382V12, multiclass
                                  clus
vv                                 CCR2 MUTATED CCR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = NUP160 MUTATION ANALYSIS
D383V1, survival
                  sevent
clus2                0   1
  NUP160 MUTATED     8   2
  NUP160 WILD-TYPE 269  76
  NUP160 MUTATED NUP160 WILD-TYPE 
              10              345 
  NUP160 MUTATED NUP160 WILD-TYPE 
               2               76 
$`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 
       13.35         7.50        85.48        13.78 

$`NUP160 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6626 
       61.91        36.00        46.75 

  NUP160 MUTATED NUP160 WILD-TYPE 
             4.8              0.0 
  NUP160 MUTATED NUP160 WILD-TYPE 
           85.48           148.01 
  NUP160 MUTATED NUP160 WILD-TYPE 
          15.915           22.090 
[1] "4.8 - 85.5 (15.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D383V2, continuous
                  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      62        0       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP160 MUTATED           0          0          3          1        0
  NUP160 WILD-TYPE        18          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  NUP160 MUTATED           0         0
  NUP160 WILD-TYPE        12         1
D383V3, multiclass
            clus
vv           NUP160 MUTATED NUP160 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  NUP160 MUTATED     0   3   5   2
  NUP160 WILD-TYPE   9  64 244  39
D383V4, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              2               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
  NUP160 MUTATED     7   3   1
  NUP160 WILD-TYPE 213  78  65
D383V5, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  N0              7              213
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V6, binary
                  cls
clus                 0   1
  NUP160 MUTATED     8   0
  NUP160 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      8    0
  NUP160 WILD-TYPE  277   48
   clus
vv  NUP160 MUTATED NUP160 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D383V7, binary
                  cls
clus                 0   1
  NUP160 MUTATED     4   7
  NUP160 WILD-TYPE 166 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      4    7
  NUP160 WILD-TYPE  166  190
        clus
vv       NUP160 MUTATED NUP160 WILD-TYPE
  FEMALE              4              166
  MALE                7              190
[1] 2 2
[1] FALSE
D383V8, binary
                  cls
clus                 0   1
  NUP160 MUTATED     9   0
  NUP160 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      9    0
  NUP160 WILD-TYPE  291    8
     clus
vv    NUP160 MUTATED NUP160 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D383V9, binary
                  cls
clus                 0   1
  NUP160 MUTATED     9   2
  NUP160 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      9    2
  NUP160 WILD-TYPE  305   46
                               clus
vv                              NUP160 MUTATED NUP160 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUP160 MUTATED     8   0   0   0
  NUP160 WILD-TYPE 251   3  22  21
D383V10, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              0               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"
D383V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP160 MUTATED                                  0     0
  NUP160 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP160 MUTATED                           2     5
  NUP160 WILD-TYPE                        17   171
D383V12, multiclass
                                  clus
vv                                 NUP160 MUTATED NUP160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         5              171
[1] 4 2
[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 = CYLC1 MUTATION ANALYSIS
D384V1, survival
                 sevent
clus2               0   1
  CYLC1 MUTATED    19   7
  CYLC1 WILD-TYPE 258  71
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             26             329 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
              7              71 
$`CYLC1 MUTATED`
TCGA-AD-6548 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3511 
       21.37        26.17        32.75        22.06        24.39         6.97 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-4616 
       34.98        38.07        83.24         5.79        58.39         5.13 
TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6929 
       12.76        32.02        14.99        45.40        56.09        13.41 
TCGA-DM-A1DA TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6805 TCGA-G4-6293 TCGA-G4-6299 
        7.50       119.93         6.18        34.42       133.18        74.56 
TCGA-G4-6315 TCGA-G4-6317 
       61.91        36.00 

$`CYLC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6654 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-3502 TCGA-AA-3510 TCGA-AA-3514 
       20.28         7.04         3.02        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        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         1.02 
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-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       12.16        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       17.82         1.41        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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        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-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        13.78        46.75 

  CYLC1 MUTATED CYLC1 WILD-TYPE 
           5.13            0.00 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
         133.18          148.01 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
         32.385          21.990 
[1] "5.1 - 133.2 (32.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D384V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYLC1 MUTATED         2        0        1        11         3         0
  CYLC1 WILD-TYPE      62        1       25        97         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYLC1 MUTATED           2          0          0          5        3         0
  CYLC1 WILD-TYPE        16          6         44         28       32        12
                 vv
clus              STAGE IVB
  CYLC1 MUTATED           0
  CYLC1 WILD-TYPE         1
D384V3, multiclass
            clus
vv           CYLC1 MUTATED CYLC1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             11              97
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             5              28
  STAGE IV               3              32
  STAGE IVA              0              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
  CYLC1 MUTATED     0   2  20   5
  CYLC1 WILD-TYPE   9  65 229  36
D384V4, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            20             229
  T4             5              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
  CYLC1 MUTATED    16   4   7
  CYLC1 WILD-TYPE 204  77  59
D384V5, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  N0            16             204
  N1             4              77
  N2             7              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V6, binary
                 cls
clus                0   1
  CYLC1 MUTATED    20   3
  CYLC1 WILD-TYPE 265  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     20    3
  CYLC1 WILD-TYPE  265   45
   clus
vv  CYLC1 MUTATED CYLC1 WILD-TYPE
  0            20             265
  1             3              45
[1] 2 2
[1] FALSE
D384V7, binary
                 cls
clus                0   1
  CYLC1 MUTATED    16  11
  CYLC1 WILD-TYPE 154 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     16   11
  CYLC1 WILD-TYPE  154  186
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  FEMALE            16             154
  MALE              11             186
[1] 2 2
[1] FALSE
D384V8, binary
                 cls
clus                0   1
  CYLC1 MUTATED    24   0
  CYLC1 WILD-TYPE 276   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     24    0
  CYLC1 WILD-TYPE  276    8
     clus
vv    CYLC1 MUTATED CYLC1 WILD-TYPE
  NO             24             276
  YES             0               8
[1] 2 2
[1] FALSE
D384V9, binary
                 cls
clus                0   1
  CYLC1 MUTATED    24   3
  CYLC1 WILD-TYPE 290  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     24    3
  CYLC1 WILD-TYPE  290   45
                               clus
vv                              CYLC1 MUTATED CYLC1 WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CYLC1 MUTATED    19   0   0   3
  CYLC1 WILD-TYPE 240   3  22  18
D384V10, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             0              22
  RX             3              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"
D384V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYLC1 MUTATED                                  0     2
  CYLC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CYLC1 MUTATED                           1    21
  CYLC1 WILD-TYPE                        18   155
D384V12, multiclass
                                  clus
vv                                 CYLC1 MUTATED CYLC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       21             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(385) Variable = PRAMEF12 MUTATION ANALYSIS
D385V1, survival
                    sevent
clus2                  0   1
  PRAMEF12 MUTATED     2   3
  PRAMEF12 WILD-TYPE 275  75
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 5                350 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 3                 75 
$`PRAMEF12 MUTATED`
TCGA-AA-3715 TCGA-AZ-6603 TCGA-CM-6171 TCGA-DM-A28F TCGA-G4-6309 
       19.04        29.56        14.04        35.97        85.48 

$`PRAMEF12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
             14.04               0.00 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
             85.48             148.01 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
            29.560             22.045 
[1] "14.0 - 85.5 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D385V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRAMEF12 MUTATED         1        0        1         0         0         0
  PRAMEF12 WILD-TYPE      63        1       25       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRAMEF12 MUTATED           0          0          2          0        0
  PRAMEF12 WILD-TYPE        18          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  PRAMEF12 MUTATED           0         0
  PRAMEF12 WILD-TYPE        12         1
D385V3, multiclass
            clus
vv           PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 0                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  PRAMEF12 MUTATED     0   2   3   0
  PRAMEF12 WILD-TYPE   9  65 246  41
D385V4, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                3                246
  T4                0                 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
  PRAMEF12 MUTATED     2   3   0
  PRAMEF12 WILD-TYPE 218  78  66
D385V5, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  N0                2                218
  N1                3                 78
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V6, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     4   0
  PRAMEF12 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      4    0
  PRAMEF12 WILD-TYPE  281   48
   clus
vv  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D385V7, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     3   2
  PRAMEF12 WILD-TYPE 167 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      3    2
  PRAMEF12 WILD-TYPE  167  195
        clus
vv       PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  FEMALE                3                167
  MALE                  2                195
[1] 2 2
[1] FALSE
D385V8, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     4   0
  PRAMEF12 WILD-TYPE 296   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      4    0
  PRAMEF12 WILD-TYPE  296    8
     clus
vv    PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  NO                 4                296
  YES                0                  8
[1] 2 2
[1] FALSE
D385V9, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     5   0
  PRAMEF12 WILD-TYPE 309  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      5    0
  PRAMEF12 WILD-TYPE  309   48
                               clus
vv                              PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PRAMEF12 MUTATED     3   0   0   0
  PRAMEF12 WILD-TYPE 256   3  22  21
D385V10, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D385V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRAMEF12 MUTATED                                  0     0
  PRAMEF12 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PRAMEF12 MUTATED                           1     3
  PRAMEF12 WILD-TYPE                        18   173
D385V12, multiclass
                                  clus
vv                                 PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           3                173
[1] 4 2
[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 = C1ORF59 MUTATION ANALYSIS
D386V1, survival
                   sevent
clus2                 0   1
  C1ORF59 MUTATED     7   3
  C1ORF59 WILD-TYPE 270  75
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               345 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
                3                75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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            22.030 
[1] "4.0 - 62.8 (23.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D386V2, continuous
                   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      64        1       25       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF59 MUTATED           0          0          1          2        0
  C1ORF59 WILD-TYPE        18          6         43         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF59 MUTATED           0         0
  C1ORF59 WILD-TYPE        12         1
D386V3, multiclass
            clus
vv           C1ORF59 MUTATED C1ORF59 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  C1ORF59 MUTATED     0   0   8   2
  C1ORF59 WILD-TYPE   9  67 241  39
D386V4, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               8               241
  T4               2                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
  C1ORF59 MUTATED     7   2   1
  C1ORF59 WILD-TYPE 213  79  65
D386V5, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  N0               7               213
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V6, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   0
  C1ORF59 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    0
  C1ORF59 WILD-TYPE  277   48
   clus
vv  C1ORF59 MUTATED C1ORF59 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D386V7, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     0  10
  C1ORF59 WILD-TYPE 170 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      0   10
  C1ORF59 WILD-TYPE  170  187
        clus
vv       C1ORF59 MUTATED C1ORF59 WILD-TYPE
  FEMALE               0               170
  MALE                10               187
[1] 2 2
[1] FALSE
D386V8, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   0
  C1ORF59 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    0
  C1ORF59 WILD-TYPE  292    8
     clus
vv    C1ORF59 MUTATED C1ORF59 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D386V9, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   2
  C1ORF59 WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    2
  C1ORF59 WILD-TYPE  306   46
                               clus
vv                              C1ORF59 MUTATED C1ORF59 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C1ORF59 MUTATED     6   0   0   1
  C1ORF59 WILD-TYPE 253   3  22  20
D386V10, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D386V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF59 MUTATED                                  0     1
  C1ORF59 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF59 MUTATED                           2     6
  C1ORF59 WILD-TYPE                        17   170
D386V12, multiclass
                                  clus
vv                                 C1ORF59 MUTATED C1ORF59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = MEPE MUTATION ANALYSIS
D387V1, survival
                sevent
clus2              0   1
  MEPE MUTATED    10   5
  MEPE WILD-TYPE 267  73
  MEPE MUTATED MEPE WILD-TYPE 
            15            340 
  MEPE MUTATED MEPE WILD-TYPE 
             5             73 
$`MEPE MUTATED`
TCGA-AA-3697 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A01P 
       85.05        22.06         8.38        29.95         4.01        38.07 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5868 
       83.24        27.09         5.23        12.76        10.06        17.03 
TCGA-D5-6924 TCGA-D5-6930 TCGA-F4-6703 
       14.30        13.35        47.87 

$`MEPE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MEPE MUTATED MEPE WILD-TYPE 
          4.01           0.00 
  MEPE MUTATED MEPE WILD-TYPE 
         85.05         148.01 
  MEPE MUTATED MEPE WILD-TYPE 
         17.03          22.09 
[1] "4.0 - 85.0 (17.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D387V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEPE MUTATED         1        0        1         9         1         0
  MEPE WILD-TYPE      63        1       25        99         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEPE MUTATED           1          0          1          0        0         1
  MEPE WILD-TYPE        17          6         43         33       35        11
                vv
clus             STAGE IVB
  MEPE MUTATED           0
  MEPE WILD-TYPE         1
D387V3, multiclass
            clus
vv           MEPE MUTATED MEPE WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             9             99
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  MEPE MUTATED     0   1  11   3
  MEPE WILD-TYPE   9  66 238  38
D387V4, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  T1            0              9
  T2            1             66
  T3           11            238
  T4            3             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
  MEPE MUTATED    12   3   0
  MEPE WILD-TYPE 208  78  66
D387V5, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  N0           12            208
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V6, binary
                cls
clus               0   1
  MEPE MUTATED    14   1
  MEPE WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     14    1
  MEPE WILD-TYPE  271   47
   clus
vv  MEPE MUTATED MEPE WILD-TYPE
  0           14            271
  1            1             47
[1] 2 2
[1] FALSE
D387V7, binary
                cls
clus               0   1
  MEPE MUTATED     5  10
  MEPE WILD-TYPE 165 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED      5   10
  MEPE WILD-TYPE  165  187
        clus
vv       MEPE MUTATED MEPE WILD-TYPE
  FEMALE            5            165
  MALE             10            187
[1] 2 2
[1] FALSE
D387V8, binary
                cls
clus               0   1
  MEPE MUTATED    13   0
  MEPE WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     13    0
  MEPE WILD-TYPE  287    8
     clus
vv    MEPE MUTATED MEPE WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D387V9, binary
                cls
clus               0   1
  MEPE MUTATED    11   4
  MEPE WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     11    4
  MEPE WILD-TYPE  303   44
                               clus
vv                              MEPE MUTATED MEPE WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MEPE MUTATED    11   0   0   2
  MEPE WILD-TYPE 248   3  22  19
D387V10, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            2             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"
D387V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEPE MUTATED                                  0     3
  MEPE WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MEPE MUTATED                           1     7
  MEPE WILD-TYPE                        18   169
D387V12, multiclass
                                  clus
vv                                 MEPE MUTATED MEPE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = ZNF384 MUTATION ANALYSIS
D388V1, survival
                  sevent
clus2                0   1
  ZNF384 MUTATED     7   2
  ZNF384 WILD-TYPE 270  76
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              346 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               2               76 
$`ZNF384 MUTATED`
TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-5864 TCGA-CM-6674 
       33.04        83.24        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        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        14.04        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.045 
[1] "12.9 - 135.7 (33.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.7"
D388V2, continuous
                  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      62        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF384 MUTATED           0          1          1          0        0
  ZNF384 WILD-TYPE        18          5         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF384 MUTATED           0         0
  ZNF384 WILD-TYPE        12         1
D388V3, multiclass
            clus
vv           ZNF384 MUTATED ZNF384 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF384 MUTATED     0   2   7   0
  ZNF384 WILD-TYPE   9  65 242  41
D388V4, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              0               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
  ZNF384 MUTATED     7   2   0
  ZNF384 WILD-TYPE 213  79  66
D388V5, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V6, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     8   0
  ZNF384 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      8    0
  ZNF384 WILD-TYPE  277   48
   clus
vv  ZNF384 MUTATED ZNF384 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D388V7, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     1   8
  ZNF384 WILD-TYPE 169 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      1    8
  ZNF384 WILD-TYPE  169  189
        clus
vv       ZNF384 MUTATED ZNF384 WILD-TYPE
  FEMALE              1              169
  MALE                8              189
[1] 2 2
[1] FALSE
D388V8, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     8   0
  ZNF384 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      8    0
  ZNF384 WILD-TYPE  292    8
     clus
vv    ZNF384 MUTATED ZNF384 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D388V9, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     6   2
  ZNF384 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      6    2
  ZNF384 WILD-TYPE  308   46
                               clus
vv                              ZNF384 MUTATED ZNF384 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF384 MUTATED     7   0   0   0
  ZNF384 WILD-TYPE 252   3  22  21
D388V10, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D388V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF384 MUTATED                                  0     1
  ZNF384 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF384 MUTATED                           0     7
  ZNF384 WILD-TYPE                        19   169
D388V12, multiclass
                                  clus
vv                                 ZNF384 MUTATED ZNF384 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = MOBKL2B MUTATION ANALYSIS
D389V1, survival
                   sevent
clus2                 0   1
  MOBKL2B MUTATED     6   1
  MOBKL2B WILD-TYPE 271  77
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                7               348 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                1                77 
$`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        21.99        82.95 
TCGA-DM-A1HA 
      131.51 

$`MOBKL2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 
      148.01        85.45        15.62        51.32        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C 
      140.38         7.50        44.32       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
            14.01              0.00 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
           131.51            148.01 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
           21.990            22.075 
[1] "14.0 - 131.5 (22.0)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "2.3"
D389V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOBKL2B MUTATED         0        0        0         1         0         0
  MOBKL2B WILD-TYPE      64        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOBKL2B MUTATED           0          0          2          2        1
  MOBKL2B WILD-TYPE        18          6         42         31       34
                   vv
clus                STAGE IVA STAGE IVB
  MOBKL2B MUTATED           0         0
  MOBKL2B WILD-TYPE        12         1
D389V3, multiclass
            clus
vv           MOBKL2B MUTATED MOBKL2B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  MOBKL2B MUTATED     0   0   5   2
  MOBKL2B WILD-TYPE   9  67 244  39
D389V4, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               2                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
  MOBKL2B MUTATED     2   3   2
  MOBKL2B WILD-TYPE 218  78  64
D389V5, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  N0               2               218
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V6, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     2   1
  MOBKL2B WILD-TYPE 283  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      2    1
  MOBKL2B WILD-TYPE  283   47
   clus
vv  MOBKL2B MUTATED MOBKL2B WILD-TYPE
  0               2               283
  1               1                47
[1] 2 2
[1] FALSE
D389V7, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     2   5
  MOBKL2B WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      2    5
  MOBKL2B WILD-TYPE  168  192
        clus
vv       MOBKL2B MUTATED MOBKL2B WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D389V8, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     5   0
  MOBKL2B WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      5    0
  MOBKL2B WILD-TYPE  295    8
     clus
vv    MOBKL2B MUTATED MOBKL2B WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D389V9, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     6   1
  MOBKL2B WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      6    1
  MOBKL2B WILD-TYPE  308   47
                               clus
vv                              MOBKL2B MUTATED MOBKL2B WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  MOBKL2B MUTATED     2   0   1   2
  MOBKL2B WILD-TYPE 257   3  21  19
D389V10, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  R0               2               257
  R1               0                 3
  R2               1                21
  RX               2                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"
D389V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOBKL2B MUTATED                                  0     0
  MOBKL2B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MOBKL2B MUTATED                           1     5
  MOBKL2B WILD-TYPE                        18   171
D389V12, multiclass
                                  clus
vv                                 MOBKL2B MUTATED MOBKL2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = GPR112 MUTATION ANALYSIS
D390V1, survival
                  sevent
clus2                0   1
  GPR112 MUTATED    20  10
  GPR112 WILD-TYPE 257  68
  GPR112 MUTATED GPR112 WILD-TYPE 
              30              325 
  GPR112 MUTATED GPR112 WILD-TYPE 
              10               68 
$`GPR112 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-DM-A285 TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-3809 
       24.00       100.01         5.88        46.65        42.28        32.75 
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3678 TCGA-AA-3710 
       22.06        19.66        63.98        29.95        47.01        26.99 
TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02J TCGA-AD-6889 TCGA-AD-6890 
       10.06        25.02         4.01         5.03        83.24        24.53 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5349 
       58.39        88.21        29.56        12.76        10.06        30.08 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6678 TCGA-DM-A28F TCGA-G4-6303 
       15.02        15.02        13.02        11.01        35.97        65.85 

$`GPR112 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 
       91.79        79.69        43.76        43.76        42.90        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-A6-5666 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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O 
       37.02        51.98        39.98         2.01        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        12.16         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        12.00        14.04        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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GPR112 MUTATED GPR112 WILD-TYPE 
            4.01             0.00 
  GPR112 MUTATED GPR112 WILD-TYPE 
          100.01           148.01 
  GPR112 MUTATED GPR112 WILD-TYPE 
          26.005           21.990 
[1] "4.0 - 100.0 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D390V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR112 MUTATED         3        0        2        10         2         0
  GPR112 WILD-TYPE      61        1       24        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR112 MUTATED           2          0          3          1        3
  GPR112 WILD-TYPE        16          6         41         32       32
                  vv
clus               STAGE IVA STAGE IVB
  GPR112 MUTATED           1         0
  GPR112 WILD-TYPE        11         1
D390V3, multiclass
            clus
vv           GPR112 MUTATED GPR112 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              10               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                3               32
  STAGE IVA               1               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
  GPR112 MUTATED     2   5  19   4
  GPR112 WILD-TYPE   7  62 230  37
D390V4, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  T1              2                7
  T2              5               62
  T3             19              230
  T4              4               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
  GPR112 MUTATED    20   8   2
  GPR112 WILD-TYPE 200  73  64
D390V5, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  N0             20              200
  N1              8               73
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V6, binary
                  cls
clus                 0   1
  GPR112 MUTATED    22   4
  GPR112 WILD-TYPE 263  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     22    4
  GPR112 WILD-TYPE  263   44
   clus
vv  GPR112 MUTATED GPR112 WILD-TYPE
  0             22              263
  1              4               44
[1] 2 2
[1] FALSE
D390V7, binary
                  cls
clus                 0   1
  GPR112 MUTATED    17  13
  GPR112 WILD-TYPE 153 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     17   13
  GPR112 WILD-TYPE  153  184
        clus
vv       GPR112 MUTATED GPR112 WILD-TYPE
  FEMALE             17              153
  MALE               13              184
[1] 2 2
[1] FALSE
D390V8, binary
                  cls
clus                 0   1
  GPR112 MUTATED    26   0
  GPR112 WILD-TYPE 274   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     26    0
  GPR112 WILD-TYPE  274    8
     clus
vv    GPR112 MUTATED GPR112 WILD-TYPE
  NO              26              274
  YES              0                8
[1] 2 2
[1] FALSE
D390V9, binary
                  cls
clus                 0   1
  GPR112 MUTATED    23   7
  GPR112 WILD-TYPE 291  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     23    7
  GPR112 WILD-TYPE  291   41
                               clus
vv                              GPR112 MUTATED GPR112 WILD-TYPE
  COLON ADENOCARCINOMA                      23              291
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR112 MUTATED    20   0   1   2
  GPR112 WILD-TYPE 239   3  21  19
D390V10, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  R0             20              239
  R1              0                3
  R2              1               21
  RX              2               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"
D390V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR112 MUTATED                                  0     3
  GPR112 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR112 MUTATED                           1    17
  GPR112 WILD-TYPE                        18   159
D390V12, multiclass
                                  clus
vv                                 GPR112 MUTATED GPR112 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        17              159
[1] 4 2
[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 = MET MUTATION ANALYSIS
D391V1, survival
               sevent
clus2             0   1
  MET MUTATED    27  14
  MET WILD-TYPE 250  64
  MET MUTATED MET WILD-TYPE 
           41           314 
  MET MUTATED MET WILD-TYPE 
           14            64 
$`MET MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3950 TCGA-DM-A285 TCGA-G4-6310 
       14.53         6.05        19.04        24.00         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-A00N TCGA-AA-A010 
       22.09        79.69        32.71         8.38         4.01        34.98 
TCGA-AA-A02K TCGA-AD-6889 TCGA-AD-6890 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-6598 
       14.01        83.24        24.53        14.50        21.44        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4952 
       12.10        29.56        12.59        10.06        14.30        15.62 
TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-5864 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6674 
       23.05        29.06        15.02        14.99        15.02        12.95 
TCGA-CM-6675 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       13.05        25.48        14.30        12.59         7.50        44.32 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-G4-6293 TCGA-G4-6304 
      117.07         8.61        31.96       133.18        53.62 

$`MET WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        22.06        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        12.16         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        6.77         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 
       12.39        12.59        12.20        12.76        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
      124.27        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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       21.99        12.99        13.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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-D5-6926 
       15.58         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       49.91        13.32       140.38       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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
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-G4-6306 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-G4-6626 
       13.78        46.75 

  MET MUTATED MET WILD-TYPE 
         4.01          0.00 
  MET MUTATED MET WILD-TYPE 
       133.18        148.01 
  MET MUTATED MET WILD-TYPE 
        15.62         22.39 
[1] "4.0 - 133.2 (15.6)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D391V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MET MUTATED         3        0        1        13         3         1
  MET WILD-TYPE      61        1       25        95         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MET MUTATED           2          1          4          4        5         0
  MET WILD-TYPE        16          5         40         29       30        12
               vv
clus            STAGE IVB
  MET MUTATED           1
  MET WILD-TYPE         0
D391V3, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA           13            95
  STAGE IIB            3             5
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           1             5
  STAGE IIIB           4            40
  STAGE IIIC           4            29
  STAGE IV             5            30
  STAGE IVA            0            12
  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     1   6  26   9
  MET WILD-TYPE   8  61 223  32
D391V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           1             8
  T2           6            61
  T3          26           223
  T4           9            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
  MET MUTATED    24   9   9
  MET WILD-TYPE 196  72  57
D391V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0          24           196
  N1           9            72
  N2           9            57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V6, binary
               cls
clus              0   1
  MET MUTATED    30   6
  MET WILD-TYPE 255  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     30    6
  MET WILD-TYPE  255   42
   clus
vv  MET MUTATED MET WILD-TYPE
  0          30           255
  1           6            42
[1] 2 2
[1] FALSE
D391V7, binary
               cls
clus              0   1
  MET MUTATED    20  22
  MET WILD-TYPE 150 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     20   22
  MET WILD-TYPE  150  175
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE          20           150
  MALE            22           175
[1] 2 2
[1] FALSE
D391V8, binary
               cls
clus              0   1
  MET MUTATED    32   2
  MET WILD-TYPE 268   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     32    2
  MET WILD-TYPE  268    6
     clus
vv    MET MUTATED MET WILD-TYPE
  NO           32           268
  YES           2             6
[1] 2 2
[1] FALSE
D391V9, binary
               cls
clus              0   1
  MET MUTATED    38   4
  MET WILD-TYPE 276  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     38    4
  MET WILD-TYPE  276   44
                               clus
vv                              MET MUTATED MET WILD-TYPE
  COLON ADENOCARCINOMA                   38           276
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MET MUTATED    23   0   3   4
  MET WILD-TYPE 236   3  19  17
D391V10, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0          23           236
  R1           0             3
  R2           3            19
  RX           4            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"
D391V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     4
  MET WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           4    27
  MET WILD-TYPE                        15   149
D391V12, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      4             6
  BLACK OR AFRICAN AMERICAN                  4            15
  WHITE                                     27           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(392) Variable = FUT10 MUTATION ANALYSIS
D392V1, survival
                 sevent
clus2               0   1
  FUT10 MUTATED     5   0
  FUT10 WILD-TYPE 272  78
  FUT10 MUTATED FUT10 WILD-TYPE 
              5             350 
  FUT10 MUTATED FUT10 WILD-TYPE 
              0              78 
$`FUT10 MUTATED`
TCGA-A6-6649 TCGA-G4-6586 TCGA-A6-5661 TCGA-A6-5662 TCGA-AD-6963 
       24.16        35.80        33.53        23.61        27.42 

$`FUT10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        29.19        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FUT10 MUTATED FUT10 WILD-TYPE 
          23.61            0.00 
  FUT10 MUTATED FUT10 WILD-TYPE 
          35.80          148.01 
  FUT10 MUTATED FUT10 WILD-TYPE 
          27.42           21.99 
[1] "23.6 - 35.8 (27.4)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D392V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FUT10 MUTATED         0        0        0         3         0         0
  FUT10 WILD-TYPE      64        1       26       105         8         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        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  FUT10 MUTATED           0
  FUT10 WILD-TYPE         1
D392V3, multiclass
            clus
vv           FUT10 MUTATED FUT10 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  FUT10 MUTATED     0   0   6   0
  FUT10 WILD-TYPE   9  67 243  41
D392V4, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             0              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
  FUT10 MUTATED     4   1   1
  FUT10 WILD-TYPE 216  80  65
D392V5, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V6, binary
                 cls
clus                0   1
  FUT10 MUTATED     4   1
  FUT10 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      4    1
  FUT10 WILD-TYPE  281   47
   clus
vv  FUT10 MUTATED FUT10 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D392V7, binary
                 cls
clus                0   1
  FUT10 MUTATED     3   3
  FUT10 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      3    3
  FUT10 WILD-TYPE  167  194
        clus
vv       FUT10 MUTATED FUT10 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D392V8, binary
                 cls
clus                0   1
  FUT10 MUTATED     5   0
  FUT10 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      5    0
  FUT10 WILD-TYPE  295    8
     clus
vv    FUT10 MUTATED FUT10 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D392V9, binary
                 cls
clus                0   1
  FUT10 MUTATED     6   0
  FUT10 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      6    0
  FUT10 WILD-TYPE  308   48
                               clus
vv                              FUT10 MUTATED FUT10 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FUT10 MUTATED     3   0   0   0
  FUT10 WILD-TYPE 256   3  22  21
D392V10, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D392V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUT10 MUTATED                                  0     0
  FUT10 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FUT10 MUTATED                           1     4
  FUT10 WILD-TYPE                        18   172
D392V12, multiclass
                                  clus
vv                                 FUT10 MUTATED FUT10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = BAG4 MUTATION ANALYSIS
D393V1, survival
                sevent
clus2              0   1
  BAG4 MUTATED     8   0
  BAG4 WILD-TYPE 269  78
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            347 
  BAG4 MUTATED BAG4 WILD-TYPE 
             0             78 
$`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        24.53        12.76        15.62 
TCGA-CM-4744 TCGA-G4-6323 
       20.02        13.78 

$`BAG4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  BAG4 MUTATED BAG4 WILD-TYPE 
         12.76           0.00 
  BAG4 MUTATED BAG4 WILD-TYPE 
         29.95         148.01 
  BAG4 MUTATED BAG4 WILD-TYPE 
         21.04          22.09 
[1] "12.8 - 29.9 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D393V2, continuous
                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      63        0       26       105         8         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        18          6         44         32       35        12
                vv
clus             STAGE IVB
  BAG4 MUTATED           0
  BAG4 WILD-TYPE         1
D393V3, multiclass
            clus
vv           BAG4 MUTATED BAG4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  BAG4 MUTATED     1   2   3   1
  BAG4 WILD-TYPE   8  65 246  40
D393V4, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            3            246
  T4            1             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
  BAG4 MUTATED     7   0   1
  BAG4 WILD-TYPE 213  81  65
D393V5, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  N0            7            213
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V6, binary
                cls
clus               0   1
  BAG4 MUTATED     5   0
  BAG4 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    0
  BAG4 WILD-TYPE  280   48
   clus
vv  BAG4 MUTATED BAG4 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D393V7, binary
                cls
clus               0   1
  BAG4 MUTATED     3   5
  BAG4 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      3    5
  BAG4 WILD-TYPE  167  192
        clus
vv       BAG4 MUTATED BAG4 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D393V8, binary
                cls
clus               0   1
  BAG4 MUTATED     7   0
  BAG4 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      7    0
  BAG4 WILD-TYPE  293    8
     clus
vv    BAG4 MUTATED BAG4 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D393V9, binary
                cls
clus               0   1
  BAG4 MUTATED     5   3
  BAG4 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    3
  BAG4 WILD-TYPE  309   45
                               clus
vv                              BAG4 MUTATED BAG4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BAG4 MUTATED     4   0   0   2
  BAG4 WILD-TYPE 255   3  22  19
D393V10, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            2             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"
D393V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAG4 MUTATED                                  0     1
  BAG4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAG4 MUTATED                           1     4
  BAG4 WILD-TYPE                        18   172
D393V12, multiclass
                                  clus
vv                                 BAG4 MUTATED BAG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = GPR87 MUTATION ANALYSIS
D394V1, survival
                 sevent
clus2               0   1
  GPR87 MUTATED     8   1
  GPR87 WILD-TYPE 269  77
  GPR87 MUTATED GPR87 WILD-TYPE 
              9             346 
  GPR87 MUTATED GPR87 WILD-TYPE 
              1              77 
$`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 
       12.95        16.14        41.42 

$`GPR87 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6807 
       35.74         6.18        47.87         1.55        34.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  GPR87 MUTATED GPR87 WILD-TYPE 
           5.03            0.00 
  GPR87 MUTATED GPR87 WILD-TYPE 
          41.42          148.01 
  GPR87 MUTATED GPR87 WILD-TYPE 
         25.020          22.045 
[1] "5.0 - 41.4 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D394V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR87 MUTATED         3        0        1         3         0         0
  GPR87 WILD-TYPE      61        1       25       105         8         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        18          6         44         33       34        11
                 vv
clus              STAGE IVB
  GPR87 MUTATED           0
  GPR87 WILD-TYPE         1
D394V3, multiclass
            clus
vv           GPR87 MUTATED GPR87 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  GPR87 MUTATED     0   4   5   1
  GPR87 WILD-TYPE   9  63 244  40
D394V4, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             5             244
  T4             1              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
  GPR87 MUTATED     8   1   1
  GPR87 WILD-TYPE 212  80  65
D394V5, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V6, binary
                 cls
clus                0   1
  GPR87 MUTATED     7   2
  GPR87 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      7    2
  GPR87 WILD-TYPE  278   46
   clus
vv  GPR87 MUTATED GPR87 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D394V7, binary
                 cls
clus                0   1
  GPR87 MUTATED     4   6
  GPR87 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      4    6
  GPR87 WILD-TYPE  166  191
        clus
vv       GPR87 MUTATED GPR87 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D394V8, binary
                 cls
clus                0   1
  GPR87 MUTATED     8   0
  GPR87 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      8    0
  GPR87 WILD-TYPE  292    8
     clus
vv    GPR87 MUTATED GPR87 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D394V9, binary
                 cls
clus                0   1
  GPR87 MUTATED     6   4
  GPR87 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      6    4
  GPR87 WILD-TYPE  308   44
                               clus
vv                              GPR87 MUTATED GPR87 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR87 MUTATED     7   0   1   1
  GPR87 WILD-TYPE 252   3  21  20
D394V10, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             1              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"
D394V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR87 MUTATED                                  0     1
  GPR87 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR87 MUTATED                           0     5
  GPR87 WILD-TYPE                        19   171
D394V12, multiclass
                                  clus
vv                                 GPR87 MUTATED GPR87 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = RASA2 MUTATION ANALYSIS
D395V1, survival
                 sevent
clus2               0   1
  RASA2 MUTATED    12   3
  RASA2 WILD-TYPE 265  75
  RASA2 MUTATED RASA2 WILD-TYPE 
             15             340 
  RASA2 MUTATED RASA2 WILD-TYPE 
              3              75 
$`RASA2 MUTATED`
TCGA-AA-3697 TCGA-AD-6964 TCGA-G4-6321 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3655 
       85.05        10.88        22.09         8.38        63.98        61.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-6751 TCGA-CM-5344 
       34.98        12.16        83.24        58.39       124.27        22.03 
TCGA-D5-6926 TCGA-DM-A1D6 TCGA-F4-6703 
        9.04        49.91        47.87 

$`RASA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  RASA2 MUTATED RASA2 WILD-TYPE 
           8.38            0.00 
  RASA2 MUTATED RASA2 WILD-TYPE 
         124.27          148.01 
  RASA2 MUTATED RASA2 WILD-TYPE 
          47.87           21.99 
[1] "8.4 - 124.3 (47.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D395V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASA2 MUTATED         2        0        3         5         1         0
  RASA2 WILD-TYPE      62        1       23       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RASA2 MUTATED           1          0          2          0        0         0
  RASA2 WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  RASA2 MUTATED           0
  RASA2 WILD-TYPE         1
D395V3, multiclass
            clus
vv           RASA2 MUTATED RASA2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RASA2 MUTATED     0   3   9   3
  RASA2 WILD-TYPE   9  64 240  38
D395V4, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             3              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
  RASA2 MUTATED    11   3   1
  RASA2 WILD-TYPE 209  78  65
D395V5, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  N0            11             209
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V6, binary
                 cls
clus                0   1
  RASA2 MUTATED    11   0
  RASA2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     11    0
  RASA2 WILD-TYPE  274   48
   clus
vv  RASA2 MUTATED RASA2 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D395V7, binary
                 cls
clus                0   1
  RASA2 MUTATED     4  11
  RASA2 WILD-TYPE 166 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED      4   11
  RASA2 WILD-TYPE  166  186
        clus
vv       RASA2 MUTATED RASA2 WILD-TYPE
  FEMALE             4             166
  MALE              11             186
[1] 2 2
[1] FALSE
D395V8, binary
                 cls
clus                0   1
  RASA2 MUTATED    13   1
  RASA2 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     13    1
  RASA2 WILD-TYPE  287    7
     clus
vv    RASA2 MUTATED RASA2 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D395V9, binary
                 cls
clus                0   1
  RASA2 MUTATED    12   3
  RASA2 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     12    3
  RASA2 WILD-TYPE  302   45
                               clus
vv                              RASA2 MUTATED RASA2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RASA2 MUTATED    11   0   0   1
  RASA2 WILD-TYPE 248   3  22  20
D395V10, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D395V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA2 MUTATED                                  0     1
  RASA2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RASA2 MUTATED                           1     9
  RASA2 WILD-TYPE                        18   167
D395V12, multiclass
                                  clus
vv                                 RASA2 MUTATED RASA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(396) Variable = TNNI3K MUTATION ANALYSIS
D396V1, survival
                  sevent
clus2                0   1
  TNNI3K MUTATED    20   3
  TNNI3K WILD-TYPE 257  75
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              23              332 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
               3               75 
$`TNNI3K MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5665 
        0.92        24.00        46.65        32.75        29.19        22.06 
TCGA-A6-6137 TCGA-AA-3510 TCGA-AA-3667 TCGA-AA-3696 TCGA-AA-3833 TCGA-AA-A00N 
       27.09        63.98        14.01         5.03        15.95         4.01 
TCGA-AA-A00R TCGA-AY-6196 TCGA-AZ-4315 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-6168 
        0.99         0.20        58.39        21.99        23.05        12.99 
TCGA-D5-6533 TCGA-D5-6541 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-DM-A28H 
       25.48        15.58       119.70        35.97       117.07 

$`TNNI3K WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        36.53        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05        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-3845 
       25.02         1.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        18.05        27.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-4682 
       33.01        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         7.53        12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28G 
      131.51       135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TNNI3K MUTATED TNNI3K WILD-TYPE 
             0.2              0.0 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
          119.70           148.01 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
           23.05            22.01 
[1] "0.2 - 119.7 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D396V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNNI3K MUTATED         2        0        1         8         2         0
  TNNI3K WILD-TYPE      62        1       25       100         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNNI3K MUTATED           1          0          4          3        2
  TNNI3K WILD-TYPE        17          6         40         30       33
                  vv
clus               STAGE IVA STAGE IVB
  TNNI3K MUTATED           0         0
  TNNI3K WILD-TYPE        12         1
D396V3, multiclass
            clus
vv           TNNI3K MUTATED TNNI3K WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              3               30
  STAGE IV                2               33
  STAGE IVA               0               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
  TNNI3K MUTATED     0   2  19   3
  TNNI3K WILD-TYPE   9  65 230  38
D396V4, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  T1              0                9
  T2              2               65
  T3             19              230
  T4              3               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
  TNNI3K MUTATED    14   6   4
  TNNI3K WILD-TYPE 206  75  62
D396V5, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  N0             14              206
  N1              6               75
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V6, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    20   2
  TNNI3K WILD-TYPE 265  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     20    2
  TNNI3K WILD-TYPE  265   46
   clus
vv  TNNI3K MUTATED TNNI3K WILD-TYPE
  0             20              265
  1              2               46
[1] 2 2
[1] FALSE
D396V7, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    13  11
  TNNI3K WILD-TYPE 157 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     13   11
  TNNI3K WILD-TYPE  157  186
        clus
vv       TNNI3K MUTATED TNNI3K WILD-TYPE
  FEMALE             13              157
  MALE               11              186
[1] 2 2
[1] FALSE
D396V8, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    16   0
  TNNI3K WILD-TYPE 284   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     16    0
  TNNI3K WILD-TYPE  284    8
     clus
vv    TNNI3K MUTATED TNNI3K WILD-TYPE
  NO              16              284
  YES              0                8
[1] 2 2
[1] FALSE
D396V9, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    20   4
  TNNI3K WILD-TYPE 294  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     20    4
  TNNI3K WILD-TYPE  294   44
                               clus
vv                              TNNI3K MUTATED TNNI3K WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TNNI3K MUTATED    16   0   2   1
  TNNI3K WILD-TYPE 243   3  20  20
D396V10, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  R0             16              243
  R1              0                3
  R2              2               20
  RX              1               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"
D396V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNNI3K MUTATED                                  0     0
  TNNI3K WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TNNI3K MUTATED                           2    13
  TNNI3K WILD-TYPE                        17   163
D396V12, multiclass
                                  clus
vv                                 TNNI3K MUTATED TNNI3K WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        13              163
[1] 4 2
[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 = RELN MUTATION ANALYSIS
D397V1, survival
                sevent
clus2              0   1
  RELN MUTATED    46  16
  RELN WILD-TYPE 231  62
  RELN MUTATED RELN WILD-TYPE 
            62            293 
  RELN MUTATED RELN WILD-TYPE 
            16             62 
$`RELN MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
       13.02         8.05         0.92        19.04        19.04        24.00 
TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       10.88       100.01        63.62        35.80        26.17        79.69 
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-3532 TCGA-AA-3555 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3818 
       24.69        29.00        29.95        54.02        11.01         0.99 
TCGA-AA-3837 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       38.99        33.01        26.01        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5796 
       83.24        22.42         0.20        58.39        88.21        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-5348 TCGA-CM-5349 
       12.76        10.06        23.05        20.02        22.98        30.08 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6532 
        5.03        15.02        17.03        12.95        13.05        18.25 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 
        4.80        12.49        15.58        12.43        11.64        13.41 
TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28E 
       13.35        38.20        92.75         7.50        44.32       119.93 
TCGA-G4-6307 TCGA-G4-6309 
       55.04        85.48 

$`RELN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       85.05        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 
        1.94        49.08         5.88        22.09        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 
       46.65        43.76        42.90        42.28        16.57        33.34 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       22.09        27.09        22.52        25.08        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07        19.07         0.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00         2.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        12.16        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.59        12.59        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-CK-6751 TCGA-CM-4746 
       21.99        21.14        82.95         2.01       124.27        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-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
       25.48        43.27        15.12        17.85        17.13        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        14.30         9.04         9.44 
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-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        61.91        36.00        13.78        46.75 

  RELN MUTATED RELN WILD-TYPE 
           0.2            0.0 
  RELN MUTATED RELN WILD-TYPE 
        119.93         148.01 
  RELN MUTATED RELN WILD-TYPE 
         22.70          21.99 
[1] "0.2 - 119.9 (22.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D397V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RELN MUTATED         5        0        3        26         5         1
  RELN WILD-TYPE      59        1       23        82         3         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELN MUTATED           2          0          7          4        4         3
  RELN WILD-TYPE        16          6         37         29       31         9
                vv
clus             STAGE IVB
  RELN MUTATED           1
  RELN WILD-TYPE         0
D397V3, multiclass
            clus
vv           RELN MUTATED RELN WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            26             82
  STAGE IIB             5              3
  STAGE IIC             1              0
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            7             37
  STAGE IIIC            4             29
  STAGE IV              4             31
  STAGE IVA             3              9
  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     1   5  50   9
  RELN WILD-TYPE   8  62 199  32
D397V4, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  T1            1              8
  T2            5             62
  T3           50            199
  T4            9             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
  RELN MUTATED    45  11   9
  RELN WILD-TYPE 175  70  57
D397V5, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  N0           45            175
  N1           11             70
  N2            9             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V6, binary
                cls
clus               0   1
  RELN MUTATED    51   8
  RELN WILD-TYPE 234  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     51    8
  RELN WILD-TYPE  234   40
   clus
vv  RELN MUTATED RELN WILD-TYPE
  0           51            234
  1            8             40
[1] 2 2
[1] FALSE
D397V7, binary
                cls
clus               0   1
  RELN MUTATED    30  35
  RELN WILD-TYPE 140 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     30   35
  RELN WILD-TYPE  140  162
        clus
vv       RELN MUTATED RELN WILD-TYPE
  FEMALE           30            140
  MALE             35            162
[1] 2 2
[1] FALSE
D397V8, binary
                cls
clus               0   1
  RELN MUTATED    52   2
  RELN WILD-TYPE 248   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     52    2
  RELN WILD-TYPE  248    6
     clus
vv    RELN MUTATED RELN WILD-TYPE
  NO            52            248
  YES            2              6
[1] 2 2
[1] FALSE
D397V9, binary
                cls
clus               0   1
  RELN MUTATED    51  13
  RELN WILD-TYPE 263  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     51   13
  RELN WILD-TYPE  263   35
                               clus
vv                              RELN MUTATED RELN WILD-TYPE
  COLON ADENOCARCINOMA                    51            263
  COLON MUCINOUS ADENOCARCINOMA           13             35
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RELN MUTATED    45   0   3   3
  RELN WILD-TYPE 214   3  19  18
D397V10, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  R0           45            214
  R1            0              3
  R2            3             19
  RX            3             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"
D397V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RELN MUTATED                                  0     4
  RELN WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RELN MUTATED                           5    37
  RELN WILD-TYPE                        14   139
D397V12, multiclass
                                  clus
vv                                 RELN MUTATED RELN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   5             14
  WHITE                                      37            139
[1] 4 2
[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    16   3
  USP25 WILD-TYPE 261  75
  USP25 MUTATED USP25 WILD-TYPE 
             19             336 
  USP25 MUTATED USP25 WILD-TYPE 
              3              75 
$`USP25 MUTATED`
TCGA-AD-6895 TCGA-A6-5656 TCGA-A6-6654 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 
       25.08        32.91        23.87        25.02         4.01        83.24 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
       14.50        58.39        29.56        12.59        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 
       12.39 

$`USP25 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        10.06        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-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-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  USP25 MUTATED USP25 WILD-TYPE 
           4.01            0.00 
  USP25 MUTATED USP25 WILD-TYPE 
         124.27          148.01 
  USP25 MUTATED USP25 WILD-TYPE 
          23.87           22.01 
[1] "4.0 - 124.3 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D398V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP25 MUTATED         3        0        0         8         1         0
  USP25 WILD-TYPE      61        1       26       100         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP25 MUTATED           0          0          5          0        0         0
  USP25 WILD-TYPE        18          6         39         33       35        12
                 vv
clus              STAGE IVB
  USP25 MUTATED           0
  USP25 WILD-TYPE         1
D398V3, multiclass
            clus
vv           USP25 MUTATED USP25 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  USP25 MUTATED     0   5  13   1
  USP25 WILD-TYPE   9  62 236  40
D398V4, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            13             236
  T4             1              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
  USP25 MUTATED    13   6   0
  USP25 WILD-TYPE 207  75  66
D398V5, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  N0            13             207
  N1             6              75
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V6, binary
                 cls
clus                0   1
  USP25 MUTATED    16   0
  USP25 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     16    0
  USP25 WILD-TYPE  269   48
   clus
vv  USP25 MUTATED USP25 WILD-TYPE
  0            16             269
  1             0              48
[1] 2 2
[1] FALSE
D398V7, binary
                 cls
clus                0   1
  USP25 MUTATED     7  12
  USP25 WILD-TYPE 163 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED      7   12
  USP25 WILD-TYPE  163  185
        clus
vv       USP25 MUTATED USP25 WILD-TYPE
  FEMALE             7             163
  MALE              12             185
[1] 2 2
[1] FALSE
D398V8, binary
                 cls
clus                0   1
  USP25 MUTATED    18   0
  USP25 WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     18    0
  USP25 WILD-TYPE  282    8
     clus
vv    USP25 MUTATED USP25 WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D398V9, binary
                 cls
clus                0   1
  USP25 MUTATED    15   4
  USP25 WILD-TYPE 299  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     15    4
  USP25 WILD-TYPE  299   44
                               clus
vv                              USP25 MUTATED USP25 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP25 MUTATED    11   0   0   4
  USP25 WILD-TYPE 248   3  22  17
D398V10, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             4              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"
D398V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP25 MUTATED                                  0     4
  USP25 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP25 MUTATED                           0    13
  USP25 WILD-TYPE                        19   163
D398V12, multiclass
                                  clus
vv                                 USP25 MUTATED USP25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               6
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       13             163
[1] 4 2
[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 = NCOA7 MUTATION ANALYSIS
D399V1, survival
                 sevent
clus2               0   1
  NCOA7 MUTATED    14   1
  NCOA7 WILD-TYPE 263  77
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             15             340 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              77 
$`NCOA7 MUTATED`
TCGA-AA-3496 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3966 
        1.02        24.39        23.87         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        12.16        27.09         5.13        15.02        15.02 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6317 
       14.04        11.64        36.00 

$`NCOA7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6780 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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82        58.39         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  NCOA7 MUTATED NCOA7 WILD-TYPE 
           1.02            0.00 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          61.02          148.01 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
         15.020          22.225 
[1] "1.0 - 61.0 (15.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.3"
D399V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA7 MUTATED         5        0        2         4         0         0
  NCOA7 WILD-TYPE      59        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA7 MUTATED           0          0          2          1        1         0
  NCOA7 WILD-TYPE        18          6         42         32       34        12
                 vv
clus              STAGE IVB
  NCOA7 MUTATED           0
  NCOA7 WILD-TYPE         1
D399V3, multiclass
            clus
vv           NCOA7 MUTATED NCOA7 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  NCOA7 MUTATED     0   5   9   1
  NCOA7 WILD-TYPE   9  62 240  40
D399V4, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             9             240
  T4             1              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
  NCOA7 MUTATED    11   2   2
  NCOA7 WILD-TYPE 209  79  64
D399V5, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V6, binary
                 cls
clus                0   1
  NCOA7 MUTATED    12   1
  NCOA7 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     12    1
  NCOA7 WILD-TYPE  273   47
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D399V7, binary
                 cls
clus                0   1
  NCOA7 MUTATED    10   5
  NCOA7 WILD-TYPE 160 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     10    5
  NCOA7 WILD-TYPE  160  192
        clus
vv       NCOA7 MUTATED NCOA7 WILD-TYPE
  FEMALE            10             160
  MALE               5             192
[1] 2 2
[1] FALSE
D399V8, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   0
  NCOA7 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    0
  NCOA7 WILD-TYPE  289    8
     clus
vv    NCOA7 MUTATED NCOA7 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D399V9, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   4
  NCOA7 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    4
  NCOA7 WILD-TYPE  303   44
                               clus
vv                              NCOA7 MUTATED NCOA7 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NCOA7 MUTATED    11   0   0   0
  NCOA7 WILD-TYPE 248   3  22  21
D399V10, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D399V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA7 MUTATED                                  0     0
  NCOA7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA7 MUTATED                           0    10
  NCOA7 WILD-TYPE                        19   166
D399V12, multiclass
                                  clus
vv                                 NCOA7 MUTATED NCOA7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(400) Variable = DDX23 MUTATION ANALYSIS
D400V1, survival
                 sevent
clus2               0   1
  DDX23 MUTATED    14   3
  DDX23 WILD-TYPE 263  75
  DDX23 MUTATED DDX23 WILD-TYPE 
             17             338 
  DDX23 MUTATED DDX23 WILD-TYPE 
              3              75 
$`DDX23 MUTATED`
TCGA-AA-3713 TCGA-AD-6548 TCGA-A6-6781 TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-A004 
       19.04        21.37        19.66        78.08        33.04        13.94 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        4.01         0.99        21.44        58.39        49.41        12.76 
TCGA-CK-4952 TCGA-CM-5349 TCGA-DM-A1D4 TCGA-F4-6854 TCGA-G4-6315 
       15.62        30.08        92.75         0.53        61.91 

$`DDX23 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       18.05        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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        43.04 
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-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DDX23 MUTATED DDX23 WILD-TYPE 
           0.53            0.00 
  DDX23 MUTATED DDX23 WILD-TYPE 
          92.75          148.01 
  DDX23 MUTATED DDX23 WILD-TYPE 
          21.37           22.09 
[1] "0.5 - 92.8 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D400V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX23 MUTATED         2        0        2         9         1         0
  DDX23 WILD-TYPE      62        1       24        99         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX23 MUTATED           0          0          0          2        2         0
  DDX23 WILD-TYPE        18          6         44         31       33        12
                 vv
clus              STAGE IVB
  DDX23 MUTATED           0
  DDX23 WILD-TYPE         1
D400V3, multiclass
            clus
vv           DDX23 MUTATED DDX23 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              9              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  DDX23 MUTATED     0   2  13   3
  DDX23 WILD-TYPE   9  65 236  38
D400V4, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            13             236
  T4             3              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
  DDX23 MUTATED    15   2   1
  DDX23 WILD-TYPE 205  79  65
D400V5, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  N0            15             205
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V6, binary
                 cls
clus                0   1
  DDX23 MUTATED    13   2
  DDX23 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     13    2
  DDX23 WILD-TYPE  272   46
   clus
vv  DDX23 MUTATED DDX23 WILD-TYPE
  0            13             272
  1             2              46
[1] 2 2
[1] FALSE
D400V7, binary
                 cls
clus                0   1
  DDX23 MUTATED     9   9
  DDX23 WILD-TYPE 161 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED      9    9
  DDX23 WILD-TYPE  161  188
        clus
vv       DDX23 MUTATED DDX23 WILD-TYPE
  FEMALE             9             161
  MALE               9             188
[1] 2 2
[1] FALSE
D400V8, binary
                 cls
clus                0   1
  DDX23 MUTATED    12   1
  DDX23 WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     12    1
  DDX23 WILD-TYPE  288    7
     clus
vv    DDX23 MUTATED DDX23 WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D400V9, binary
                 cls
clus                0   1
  DDX23 MUTATED    14   4
  DDX23 WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     14    4
  DDX23 WILD-TYPE  300   44
                               clus
vv                              DDX23 MUTATED DDX23 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX23 MUTATED    13   0   1   2
  DDX23 WILD-TYPE 246   3  21  19
D400V10, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             1              21
  RX             2              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"
D400V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX23 MUTATED                                  0     1
  DDX23 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX23 MUTATED                           0    10
  DDX23 WILD-TYPE                        19   166
D400V12, multiclass
                                  clus
vv                                 DDX23 MUTATED DDX23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(401) Variable = IGF2R MUTATION ANALYSIS
D401V1, survival
                 sevent
clus2               0   1
  IGF2R MUTATED    28   7
  IGF2R WILD-TYPE 249  71
  IGF2R MUTATED IGF2R WILD-TYPE 
             35             320 
  IGF2R MUTATED IGF2R WILD-TYPE 
              7              71 
$`IGF2R MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3672 TCGA-AD-6895 TCGA-AZ-6601 
       13.02         8.05         0.99         0.92        25.08       100.01 
TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 
       26.17        32.75        20.12        19.66         3.02         6.97 
TCGA-AA-3679 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 
       15.02        53.00        33.01        38.04         4.01        34.98 
TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
       35.01        83.24        58.39        88.21        49.41        12.76 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4746 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 
       10.06        15.62        37.02        16.14        11.64        13.35 
TCGA-DM-A28H TCGA-DM-A28K TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 
      117.07        98.24        44.68        55.04        36.00 

$`IGF2R WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       36.03        19.07        34.03        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       10.88       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       23.87        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       12.20        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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 
       43.04        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-G4-6315 
      133.18        74.56        65.85        53.62        85.48        61.91 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  IGF2R MUTATED IGF2R WILD-TYPE 
           0.92            0.00 
  IGF2R MUTATED IGF2R WILD-TYPE 
         117.07          148.01 
  IGF2R MUTATED IGF2R WILD-TYPE 
          26.17           22.01 
[1] "0.9 - 117.1 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D401V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGF2R MUTATED         4        0        5        11         5         0
  IGF2R WILD-TYPE      60        1       21        97         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGF2R MUTATED           3          0          3          4        1         0
  IGF2R WILD-TYPE        15          6         41         29       34        12
                 vv
clus              STAGE IVB
  IGF2R MUTATED           0
  IGF2R WILD-TYPE         1
D401V3, multiclass
            clus
vv           IGF2R MUTATED IGF2R WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             11              97
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             4              29
  STAGE IV               1              34
  STAGE IVA              0              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
  IGF2R MUTATED     1   4  25   7
  IGF2R WILD-TYPE   8  63 224  34
D401V4, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  T1             1               8
  T2             4              63
  T3            25             224
  T4             7              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
  IGF2R MUTATED    26   5   6
  IGF2R WILD-TYPE 194  76  60
D401V5, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  N0            26             194
  N1             5              76
  N2             6              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V6, binary
                 cls
clus                0   1
  IGF2R MUTATED    31   1
  IGF2R WILD-TYPE 254  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     31    1
  IGF2R WILD-TYPE  254   47
   clus
vv  IGF2R MUTATED IGF2R WILD-TYPE
  0            31             254
  1             1              47
[1] 2 2
[1] FALSE
D401V7, binary
                 cls
clus                0   1
  IGF2R MUTATED    14  23
  IGF2R WILD-TYPE 156 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     14   23
  IGF2R WILD-TYPE  156  174
        clus
vv       IGF2R MUTATED IGF2R WILD-TYPE
  FEMALE            14             156
  MALE              23             174
[1] 2 2
[1] FALSE
D401V8, binary
                 cls
clus                0   1
  IGF2R MUTATED    30   1
  IGF2R WILD-TYPE 270   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     30    1
  IGF2R WILD-TYPE  270    7
     clus
vv    IGF2R MUTATED IGF2R WILD-TYPE
  NO             30             270
  YES             1               7
[1] 2 2
[1] FALSE
D401V9, binary
                 cls
clus                0   1
  IGF2R MUTATED    23  14
  IGF2R WILD-TYPE 291  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     23   14
  IGF2R WILD-TYPE  291   34
                               clus
vv                              IGF2R MUTATED IGF2R WILD-TYPE
  COLON ADENOCARCINOMA                     23             291
  COLON MUCINOUS ADENOCARCINOMA            14              34
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IGF2R MUTATED    25   0   1   4
  IGF2R WILD-TYPE 234   3  21  17
D401V10, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  R0            25             234
  R1             0               3
  R2             1              21
  RX             4              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"
D401V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGF2R MUTATED                                  0     3
  IGF2R WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGF2R MUTATED                           1    19
  IGF2R WILD-TYPE                        18   157
D401V12, multiclass
                                  clus
vv                                 IGF2R MUTATED IGF2R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       19             157
[1] 4 2
[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 = TMEM92 MUTATION ANALYSIS
D402V1, survival
                  sevent
clus2                0   1
  TMEM92 MUTATED     2   1
  TMEM92 WILD-TYPE 275  77
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              352 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               1               77 
$`TMEM92 MUTATED`
TCGA-AA-3947 TCGA-AD-6889 TCGA-CK-5913 
       33.01        83.24        51.32 

$`TMEM92 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TMEM92 MUTATED TMEM92 WILD-TYPE 
           33.01             0.00 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
           83.24           148.01 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
           51.32            22.01 
[1] "33.0 - 83.2 (51.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D402V2, continuous
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              364 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3516       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-3527       TCGA-AA-3530 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6964       TCGA-AZ-4681       TCGA-AZ-6601       TCGA-AZ-6608 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5912       TCGA-DM-A285       TCGA-G4-6310       TCGA-G4-6321 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      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-A6-2678       TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5656       TCGA-A6-5657 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5660       TCGA-A6-5661       TCGA-A6-5662 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5664       TCGA-A6-5665       TCGA-A6-5666       TCGA-A6-6137 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142       TCGA-A6-6648 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6651       TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3492       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-3517       TCGA-AA-3518       TCGA-AA-3519 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532       TCGA-AA-3534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544       TCGA-AA-3548 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555       TCGA-AA-3558 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660       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-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-3693       TCGA-AA-3695 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3811 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3812       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-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-3861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       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-3941 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00K       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-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-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-6890       TCGA-AD-6899 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       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-4315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"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-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-5914       TCGA-CK-5915       TCGA-CK-5916 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
                  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      64        1       26       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM92 MUTATED           0          0          0          0        0
  TMEM92 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM92 MUTATED           0         0
  TMEM92 WILD-TYPE        12         1
D402V3, multiclass
            clus
vv           TMEM92 MUTATED TMEM92 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TMEM92 MUTATED     0   0   2   1
  TMEM92 WILD-TYPE   9  67 247  40
D402V4, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              2              247
  T4              1               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
  TMEM92 MUTATED     3   0   0
  TMEM92 WILD-TYPE 217  81  66
D402V5, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  N0              3              217
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V6, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   0
  TMEM92 WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    0
  TMEM92 WILD-TYPE  283   48
   clus
vv  TMEM92 MUTATED TMEM92 WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D402V7, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   1
  TMEM92 WILD-TYPE 168 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    1
  TMEM92 WILD-TYPE  168  196
        clus
vv       TMEM92 MUTATED TMEM92 WILD-TYPE
  FEMALE              2              168
  MALE                1              196
[1] 2 2
[1] FALSE
D402V8, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     3   0
  TMEM92 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      3    0
  TMEM92 WILD-TYPE  297    8
     clus
vv    TMEM92 MUTATED TMEM92 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D402V9, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   1
  TMEM92 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    1
  TMEM92 WILD-TYPE  312   47
                               clus
vv                              TMEM92 MUTATED TMEM92 WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM92 MUTATED     2   0   0   1
  TMEM92 WILD-TYPE 257   3  22  20
D402V10, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              1               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"
D402V11, continuous
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              344 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3516       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-3527       TCGA-AA-3530 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6964       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-DM-A285 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       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-3526       TCGA-AA-3529 
"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-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3655       TCGA-AA-3660 
"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-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-3693 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       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-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3949       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-3973 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3977       TCGA-AA-3980       TCGA-AA-3982 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3984       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-A00N       TCGA-AA-A00O 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"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-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-6890 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       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-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"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-CA-6715       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-A28C       TCGA-DM-A28E 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806       TCGA-F4-6807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"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     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM92 MUTATED                           0     1
  TMEM92 WILD-TYPE                        19   175
D402V12, multiclass
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6890       TCGA-AD-6899 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       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-4315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"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-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-5914       TCGA-CK-5915       TCGA-CK-5916 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 

Clustering(403) Variable = ODZ1 MUTATION ANALYSIS
D403V1, survival
                sevent
clus2              0   1
  ODZ1 MUTATED    45  14
  ODZ1 WILD-TYPE 232  64
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            59            296 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            14             64 
$`ODZ1 MUTATED`
TCGA-AA-3516 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-4681 
       13.02        19.99         6.05        19.04        19.04       106.75 
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6652 TCGA-AA-3502 
       35.80        26.17        31.63        33.53        24.69        35.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       24.00        29.95        10.06        33.04         0.99         1.02 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-3980 TCGA-AA-A00Q TCGA-AA-A01P 
       38.99         0.00        33.01        27.02        42.02        38.07 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 
       18.05        83.24        14.50         0.95         0.20        17.82 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       58.39        12.76        10.06        85.45        15.62        51.32 
TCGA-CK-6747 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6167 TCGA-CM-6674 
       82.95        22.03        15.02        15.02        14.99        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6540 TCGA-D5-6541 
       11.08        11.01        54.61        56.09        16.14        15.58 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6570 TCGA-F4-6703 
       12.00        11.38        12.59        44.32         6.18        47.87 
TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6323 
       33.67       133.18        53.62        55.04        13.78 

$`ODZ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       85.05        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       10.88       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       36.53        32.91        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-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        24.39        23.87        20.12        19.66 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 
        5.98        37.05         5.03        26.99        35.05        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       17.98        15.95        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        27.02         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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 
       26.47        27.09        16.31        33.01        21.44         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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       17.56       148.01        21.99        21.14         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 
       11.08        10.06        12.03        45.40        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       13.35        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-A1HA 
       92.75        49.91        13.32       140.38         7.50       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-F4-6704 
      117.07        98.24         8.61        31.96        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       35.31        74.56        65.85        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6626 
       36.00        46.75 

  ODZ1 MUTATED ODZ1 WILD-TYPE 
             0              0 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
        133.18         148.01 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
         19.99          22.09 
[1] "0.0 - 133.2 (20.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D403V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ODZ1 MUTATED         8        1        1        26         3         0
  ODZ1 WILD-TYPE      56        0       25        82         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ODZ1 MUTATED           5          0          7          5        2         2
  ODZ1 WILD-TYPE        13          6         37         28       33        10
                vv
clus             STAGE IVB
  ODZ1 MUTATED           0
  ODZ1 WILD-TYPE         1
D403V3, multiclass
            clus
vv           ODZ1 MUTATED ODZ1 WILD-TYPE
  STAGE I               8             56
  STAGE IA              1              0
  STAGE II              1             25
  STAGE IIA            26             82
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             5             13
  STAGE IIIA            0              6
  STAGE IIIB            7             37
  STAGE IIIC            5             28
  STAGE IV              2             33
  STAGE IVA             2             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
  ODZ1 MUTATED     2   6  44   8
  ODZ1 WILD-TYPE   7  61 205  33
D403V4, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  T1            2              7
  T2            6             61
  T3           44            205
  T4            8             33
[1] 4 2
[1] TRUE
[1] "dimension 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    41  11   9
  ODZ1 WILD-TYPE 179  70  57
D403V5, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  N0           41            179
  N1           11             70
  N2            9             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V6, binary
                cls
clus               0   1
  ODZ1 MUTATED    50   4
  ODZ1 WILD-TYPE 235  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     50    4
  ODZ1 WILD-TYPE  235   44
   clus
vv  ODZ1 MUTATED ODZ1 WILD-TYPE
  0           50            235
  1            4             44
[1] 2 2
[1] FALSE
D403V7, binary
                cls
clus               0   1
  ODZ1 MUTATED    41  20
  ODZ1 WILD-TYPE 129 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     41   20
  ODZ1 WILD-TYPE  129  177
        clus
vv       ODZ1 MUTATED ODZ1 WILD-TYPE
  FEMALE           41            129
  MALE             20            177
[1] 2 2
[1] FALSE
D403V8, binary
                cls
clus               0   1
  ODZ1 MUTATED    52   1
  ODZ1 WILD-TYPE 248   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     52    1
  ODZ1 WILD-TYPE  248    7
     clus
vv    ODZ1 MUTATED ODZ1 WILD-TYPE
  NO            52            248
  YES            1              7
[1] 2 2
[1] FALSE
D403V9, binary
                cls
clus               0   1
  ODZ1 MUTATED    49  11
  ODZ1 WILD-TYPE 265  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     49   11
  ODZ1 WILD-TYPE  265   37
                               clus
vv                              ODZ1 MUTATED ODZ1 WILD-TYPE
  COLON ADENOCARCINOMA                    49            265
  COLON MUCINOUS ADENOCARCINOMA           11             37
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ODZ1 MUTATED    47   1   2   6
  ODZ1 WILD-TYPE 212   2  20  15
D403V10, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  R0           47            212
  R1            1              2
  R2            2             20
  RX            6             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"
D403V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ODZ1 MUTATED                                  0     3
  ODZ1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ODZ1 MUTATED                           7    31
  ODZ1 WILD-TYPE                        12   145
D403V12, multiclass
                                  clus
vv                                 ODZ1 MUTATED ODZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   7             12
  WHITE                                      31            145
[1] 4 2
[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 = FLG2 MUTATION ANALYSIS
D404V1, survival
                sevent
clus2              0   1
  FLG2 MUTATED    20   7
  FLG2 WILD-TYPE 257  71
  FLG2 MUTATED FLG2 WILD-TYPE 
            27            328 
  FLG2 MUTATED FLG2 WILD-TYPE 
             7             71 
$`FLG2 MUTATED`
TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-3986 TCGA-AA-3510 TCGA-AA-3532 TCGA-AA-3663 
        1.02         8.05        19.07        63.98        29.00         6.97 
TCGA-AA-3710 TCGA-AA-3837 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-A00N 
       26.99        38.99        31.00         2.01        33.01         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 
       92.75         6.18        85.48 

$`FLG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 
       30.05        53.00        17.03        27.02        18.05        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       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        14.04        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-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-D5-5541 TCGA-D5-6532 
       12.03        45.40        54.61        19.59        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  FLG2 MUTATED FLG2 WILD-TYPE 
          1.02           0.00 
  FLG2 MUTATED FLG2 WILD-TYPE 
         92.75         148.01 
  FLG2 MUTATED FLG2 WILD-TYPE 
        25.020         22.045 
[1] "1.0 - 92.8 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D404V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLG2 MUTATED         3        0        4        12         2         0
  FLG2 WILD-TYPE      61        1       22        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLG2 MUTATED           0          0          2          1        2         1
  FLG2 WILD-TYPE        18          6         42         32       33        11
                vv
clus             STAGE IVB
  FLG2 MUTATED           1
  FLG2 WILD-TYPE         0
D404V3, multiclass
            clus
vv           FLG2 MUTATED FLG2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            12             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             1             11
  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   2  21   4
  FLG2 WILD-TYPE   8  65 228  37
D404V4, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  T1            1              8
  T2            2             65
  T3           21            228
  T4            4             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
  FLG2 MUTATED    21   3   4
  FLG2 WILD-TYPE 199  78  62
D404V5, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  N0           21            199
  N1            3             78
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V6, binary
                cls
clus               0   1
  FLG2 MUTATED    22   4
  FLG2 WILD-TYPE 263  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     22    4
  FLG2 WILD-TYPE  263   44
   clus
vv  FLG2 MUTATED FLG2 WILD-TYPE
  0           22            263
  1            4             44
[1] 2 2
[1] FALSE
D404V7, binary
                cls
clus               0   1
  FLG2 MUTATED    11  17
  FLG2 WILD-TYPE 159 180
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     11   17
  FLG2 WILD-TYPE  159  180
        clus
vv       FLG2 MUTATED FLG2 WILD-TYPE
  FEMALE           11            159
  MALE             17            180
[1] 2 2
[1] FALSE
D404V8, binary
                cls
clus               0   1
  FLG2 MUTATED    23   0
  FLG2 WILD-TYPE 277   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     23    0
  FLG2 WILD-TYPE  277    8
     clus
vv    FLG2 MUTATED FLG2 WILD-TYPE
  NO            23            277
  YES            0              8
[1] 2 2
[1] FALSE
D404V9, binary
                cls
clus               0   1
  FLG2 MUTATED    23   5
  FLG2 WILD-TYPE 291  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     23    5
  FLG2 WILD-TYPE  291   43
                               clus
vv                              FLG2 MUTATED FLG2 WILD-TYPE
  COLON ADENOCARCINOMA                    23            291
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FLG2 MUTATED    21   0   1   3
  FLG2 WILD-TYPE 238   3  21  18
D404V10, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  R0           21            238
  R1            0              3
  R2            1             21
  RX            3             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"
D404V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLG2 MUTATED                                  0     2
  FLG2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLG2 MUTATED                           3    10
  FLG2 WILD-TYPE                        16   166
D404V12, multiclass
                                  clus
vv                                 FLG2 MUTATED FLG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      10            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(405) Variable = TRMT5 MUTATION ANALYSIS
D405V1, survival
                 sevent
clus2               0   1
  TRMT5 MUTATED     4   2
  TRMT5 WILD-TYPE 273  76
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              6             349 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              2              76 
$`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 

$`TRMT5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.09 
[1] "4.0 - 85.0 (13.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D405V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRMT5 MUTATED         1        0        1         2         1         0
  TRMT5 WILD-TYPE      63        1       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRMT5 MUTATED           0          0          0          0        1         0
  TRMT5 WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  TRMT5 MUTATED           0
  TRMT5 WILD-TYPE         1
D405V3, multiclass
            clus
vv           TRMT5 MUTATED TRMT5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TRMT5 MUTATED     0   1   3   2
  TRMT5 WILD-TYPE   9  66 246  39
D405V4, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             2              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
  TRMT5 MUTATED     5   1   0
  TRMT5 WILD-TYPE 215  80  66
D405V5, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V6, binary
                 cls
clus                0   1
  TRMT5 MUTATED     5   1
  TRMT5 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      5    1
  TRMT5 WILD-TYPE  280   47
   clus
vv  TRMT5 MUTATED TRMT5 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D405V7, binary
                 cls
clus                0   1
  TRMT5 MUTATED     2   4
  TRMT5 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      2    4
  TRMT5 WILD-TYPE  168  193
        clus
vv       TRMT5 MUTATED TRMT5 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D405V8, binary
                 cls
clus                0   1
  TRMT5 MUTATED     5   0
  TRMT5 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      5    0
  TRMT5 WILD-TYPE  295    8
     clus
vv    TRMT5 MUTATED TRMT5 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D405V9, binary
                 cls
clus                0   1
  TRMT5 MUTATED     5   1
  TRMT5 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      5    1
  TRMT5 WILD-TYPE  309   47
                               clus
vv                              TRMT5 MUTATED TRMT5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRMT5 MUTATED     5   0   0   0
  TRMT5 WILD-TYPE 254   3  22  21
D405V10, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D405V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRMT5 MUTATED                                  0     0
  TRMT5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRMT5 MUTATED                           1     3
  TRMT5 WILD-TYPE                        18   173
D405V12, multiclass
                                  clus
vv                                 TRMT5 MUTATED TRMT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = CHML MUTATION ANALYSIS
D406V1, survival
                sevent
clus2              0   1
  CHML MUTATED    15   5
  CHML WILD-TYPE 262  73
  CHML MUTATED CHML WILD-TYPE 
            20            335 
  CHML MUTATED CHML WILD-TYPE 
             5             73 
$`CHML MUTATED`
TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3672 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6625 
        8.05         6.05         0.92        10.88       100.01        91.79 
TCGA-A6-3809 TCGA-A6-6138 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3947 TCGA-AU-6004 
       32.75        22.52         8.38         3.02        33.01        27.09 
TCGA-CM-5348 TCGA-CM-6162 TCGA-D5-5537 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 
       22.98        12.00        45.40        12.43        11.64        13.41 
TCGA-F4-6460 TCGA-G4-6323 
       31.96        13.78 

$`CHML WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52        25.08       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 
       63.62        22.09        35.80        26.17        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6651 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        14.30         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6569 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  CHML MUTATED CHML WILD-TYPE 
          0.92           0.00 
  CHML MUTATED CHML WILD-TYPE 
        100.01         148.01 
  CHML MUTATED CHML WILD-TYPE 
        13.595         22.090 
[1] "0.9 - 100.0 (13.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D406V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHML MUTATED         3        1        2         4         2         0
  CHML WILD-TYPE      61        0       24       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHML MUTATED           1          0          4          0        2         0
  CHML WILD-TYPE        17          6         40         33       33        12
                vv
clus             STAGE IVB
  CHML MUTATED           0
  CHML WILD-TYPE         1
D406V3, multiclass
            clus
vv           CHML MUTATED CHML WILD-TYPE
  STAGE I               3             61
  STAGE IA              1              0
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  CHML MUTATED     0   3  12   4
  CHML WILD-TYPE   9  64 237  37
D406V4, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  T1            0              9
  T2            3             64
  T3           12            237
  T4            4             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
  CHML MUTATED    11   6   3
  CHML WILD-TYPE 209  75  63
D406V5, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  N0           11            209
  N1            6             75
  N2            3             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"
D406V6, binary
                cls
clus               0   1
  CHML MUTATED    15   2
  CHML WILD-TYPE 270  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     15    2
  CHML WILD-TYPE  270   46
   clus
vv  CHML MUTATED CHML WILD-TYPE
  0           15            270
  1            2             46
[1] 2 2
[1] FALSE
D406V7, binary
                cls
clus               0   1
  CHML MUTATED    10  10
  CHML WILD-TYPE 160 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     10   10
  CHML WILD-TYPE  160  187
        clus
vv       CHML MUTATED CHML WILD-TYPE
  FEMALE           10            160
  MALE             10            187
[1] 2 2
[1] FALSE
D406V8, binary
                cls
clus               0   1
  CHML MUTATED    19   0
  CHML WILD-TYPE 281   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     19    0
  CHML WILD-TYPE  281    8
     clus
vv    CHML MUTATED CHML WILD-TYPE
  NO            19            281
  YES            0              8
[1] 2 2
[1] FALSE
D406V9, binary
                cls
clus               0   1
  CHML MUTATED    16   4
  CHML WILD-TYPE 298  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     16    4
  CHML WILD-TYPE  298   44
                               clus
vv                              CHML MUTATED CHML WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHML MUTATED    14   0   1   1
  CHML WILD-TYPE 245   3  21  20
D406V10, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  R0           14            245
  R1            0              3
  R2            1             21
  RX            1             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"
D406V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHML MUTATED                                  0     0
  CHML WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHML MUTATED                           2    13
  CHML WILD-TYPE                        17   163
D406V12, multiclass
                                  clus
vv                                 CHML MUTATED CHML WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      13            163
[1] 4 2
[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 = AURKA MUTATION ANALYSIS
D407V1, survival
                 sevent
clus2               0   1
  AURKA MUTATED     4   3
  AURKA WILD-TYPE 273  75
  AURKA MUTATED AURKA WILD-TYPE 
              7             348 
  AURKA MUTATED AURKA WILD-TYPE 
              3              75 
$`AURKA MUTATED`
TCGA-AZ-6608 TCGA-AA-3864 TCGA-AA-A00J TCGA-AZ-6605 TCGA-CM-6674 TCGA-CM-6677 
        1.94        53.00        18.05         5.23        12.95        11.08 
TCGA-G4-6626 
       46.75 

$`AURKA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  AURKA MUTATED AURKA WILD-TYPE 
           1.94            0.00 
  AURKA MUTATED AURKA WILD-TYPE 
          53.00          148.01 
  AURKA MUTATED AURKA WILD-TYPE 
          12.95           22.09 
[1] "1.9 - 53.0 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D407V2, continuous
                 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      64        1       25       105         8         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        18          5         42         33       35        12
                 vv
clus              STAGE IVB
  AURKA MUTATED           0
  AURKA WILD-TYPE         1
D407V3, multiclass
            clus
vv           AURKA MUTATED AURKA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  AURKA MUTATED     0   1   4   2
  AURKA WILD-TYPE   9  66 245  39
D407V4, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             2              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
  AURKA MUTATED     4   3   0
  AURKA WILD-TYPE 216  78  66
D407V5, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  N0             4             216
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V6, binary
                 cls
clus                0   1
  AURKA MUTATED     7   0
  AURKA WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      7    0
  AURKA WILD-TYPE  278   48
   clus
vv  AURKA MUTATED AURKA WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D407V7, binary
                 cls
clus                0   1
  AURKA MUTATED     2   5
  AURKA WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      2    5
  AURKA WILD-TYPE  168  192
        clus
vv       AURKA MUTATED AURKA WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D407V8, binary
                 cls
clus                0   1
  AURKA MUTATED     7   0
  AURKA WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      7    0
  AURKA WILD-TYPE  293    8
     clus
vv    AURKA MUTATED AURKA WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D407V9, binary
                 cls
clus                0   1
  AURKA MUTATED     6   1
  AURKA WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      6    1
  AURKA WILD-TYPE  308   47
                               clus
vv                              AURKA MUTATED AURKA WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AURKA MUTATED     5   0   0   0
  AURKA WILD-TYPE 254   3  22  21
D407V10, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D407V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AURKA MUTATED                                  0     0
  AURKA WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AURKA MUTATED                           0     5
  AURKA WILD-TYPE                        19   171
D407V12, multiclass
                                  clus
vv                                 AURKA MUTATED AURKA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = LRRC23 MUTATION ANALYSIS
D408V1, survival
                  sevent
clus2                0   1
  LRRC23 MUTATED     7   2
  LRRC23 WILD-TYPE 270  76
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               9              346 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               2               76 
$`LRRC23 MUTATED`
TCGA-AD-6889 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6677 
       83.24        62.79        12.76        15.02        14.04        11.08 
TCGA-CM-6680 TCGA-D5-6923 TCGA-D5-6927 
       12.03        12.43         9.44 

$`LRRC23 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        88.21        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        10.06        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LRRC23 MUTATED LRRC23 WILD-TYPE 
            9.44             0.00 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
           83.24           148.01 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
          12.760           22.225 
[1] "9.4 - 83.2 (12.8)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1"  
D408V2, continuous
                  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      61        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC23 MUTATED           0          0          1          0        0
  LRRC23 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRC23 MUTATED           0         0
  LRRC23 WILD-TYPE        12         1
D408V3, multiclass
            clus
vv           LRRC23 MUTATED LRRC23 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  LRRC23 MUTATED     1   2   6   0
  LRRC23 WILD-TYPE   8  65 243  41
D408V4, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              6              243
  T4              0               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
  LRRC23 MUTATED     8   0   1
  LRRC23 WILD-TYPE 212  81  65
D408V5, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V6, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     8   0
  LRRC23 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      8    0
  LRRC23 WILD-TYPE  277   48
   clus
vv  LRRC23 MUTATED LRRC23 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D408V7, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     2   7
  LRRC23 WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      2    7
  LRRC23 WILD-TYPE  168  190
        clus
vv       LRRC23 MUTATED LRRC23 WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D408V8, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     9   0
  LRRC23 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      9    0
  LRRC23 WILD-TYPE  291    8
     clus
vv    LRRC23 MUTATED LRRC23 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D408V9, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     8   1
  LRRC23 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      8    1
  LRRC23 WILD-TYPE  306   47
                               clus
vv                              LRRC23 MUTATED LRRC23 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LRRC23 MUTATED     7   0   0   1
  LRRC23 WILD-TYPE 252   3  22  20
D408V10, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D408V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC23 MUTATED                                  0     2
  LRRC23 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRC23 MUTATED                           0     7
  LRRC23 WILD-TYPE                        19   169
D408V12, multiclass
                                  clus
vv                                 LRRC23 MUTATED LRRC23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = PHF3 MUTATION ANALYSIS
D409V1, survival
                sevent
clus2              0   1
  PHF3 MUTATED    17   3
  PHF3 WILD-TYPE 260  75
  PHF3 MUTATED PHF3 WILD-TYPE 
            20            335 
  PHF3 MUTATED PHF3 WILD-TYPE 
             3             75 
$`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        12.16        27.09 
TCGA-AY-6197 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-6169 
       21.44        12.59        12.76        10.06       148.01        13.02 
TCGA-D5-6541 TCGA-DM-A28F 
       15.58        35.97 

$`PHF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.36        12.39        12.59        12.20        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PHF3 MUTATED PHF3 WILD-TYPE 
          2.01           0.00 
  PHF3 MUTATED PHF3 WILD-TYPE 
        148.01         140.38 
  PHF3 MUTATED PHF3 WILD-TYPE 
         23.26          22.06 
[1] "2.0 - 148.0 (23.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.4"
D409V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF3 MUTATED         2        0        2         9         3         0
  PHF3 WILD-TYPE      62        1       24        99         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF3 MUTATED           2          0          1          2        1         1
  PHF3 WILD-TYPE        16          6         43         31       34        11
                vv
clus             STAGE IVB
  PHF3 MUTATED           0
  PHF3 WILD-TYPE         1
D409V3, multiclass
            clus
vv           PHF3 MUTATED PHF3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             9             99
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             1             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
  PHF3 MUTATED     0   2  16   5
  PHF3 WILD-TYPE   9  65 233  36
D409V4, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           16            233
  T4            5             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
  PHF3 MUTATED    16   4   3
  PHF3 WILD-TYPE 204  77  63
D409V5, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  N0           16            204
  N1            4             77
  N2            3             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"
D409V6, binary
                cls
clus               0   1
  PHF3 MUTATED    18   2
  PHF3 WILD-TYPE 267  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     18    2
  PHF3 WILD-TYPE  267   46
   clus
vv  PHF3 MUTATED PHF3 WILD-TYPE
  0           18            267
  1            2             46
[1] 2 2
[1] FALSE
D409V7, binary
                cls
clus               0   1
  PHF3 MUTATED     9  14
  PHF3 WILD-TYPE 161 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED      9   14
  PHF3 WILD-TYPE  161  183
        clus
vv       PHF3 MUTATED PHF3 WILD-TYPE
  FEMALE            9            161
  MALE             14            183
[1] 2 2
[1] FALSE
D409V8, binary
                cls
clus               0   1
  PHF3 MUTATED    16   0
  PHF3 WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     16    0
  PHF3 WILD-TYPE  284    8
     clus
vv    PHF3 MUTATED PHF3 WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D409V9, binary
                cls
clus               0   1
  PHF3 MUTATED    17   6
  PHF3 WILD-TYPE 297  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     17    6
  PHF3 WILD-TYPE  297   42
                               clus
vv                              PHF3 MUTATED PHF3 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PHF3 MUTATED    16   0   1   2
  PHF3 WILD-TYPE 243   3  21  19
D409V10, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            1             21
  RX            2             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"
D409V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF3 MUTATED                                  0     3
  PHF3 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PHF3 MUTATED                           2     8
  PHF3 WILD-TYPE                        17   168
D409V12, multiclass
                                  clus
vv                                 PHF3 MUTATED PHF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       8            168
[1] 4 2
[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 = CNTNAP5 MUTATION ANALYSIS
D410V1, survival
                   sevent
clus2                 0   1
  CNTNAP5 MUTATED    28  11
  CNTNAP5 WILD-TYPE 249  67
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               39               316 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               11                67 
$`CNTNAP5 MUTATED`
TCGA-AD-6964 TCGA-AZ-6608 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5665 
       10.88         1.94        79.69        43.76        33.53        22.06 
TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3947 TCGA-AA-3977 
        8.38        23.87        20.12        78.08        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A01Z TCGA-AD-5900 TCGA-AD-6889 
        4.01        34.98        35.01        37.02        12.16        83.24 
TCGA-AD-6901 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6716 
       22.42        27.09        58.39        62.79        49.41        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-6166 
       12.76        10.06        21.99        37.02        29.06        21.99 
TCGA-D5-6532 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-F4-6569 TCGA-F4-6570 
       18.25        13.35       130.65        49.91        35.74         6.18 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6323 
       85.48        61.91        13.78 

$`CNTNAP5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       26.17        91.79        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.39        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6626 
       44.68        55.04        36.00        46.75 

  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
             1.94              0.00 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
           130.65            148.01 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
            27.09             21.60 
[1] "1.9 - 130.7 (27.1)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1.1"
D410V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNTNAP5 MUTATED         6        1        4        15         3         0
  CNTNAP5 WILD-TYPE      58        0       22        93         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNTNAP5 MUTATED           1          2          3          0        2
  CNTNAP5 WILD-TYPE        17          4         41         33       33
                   vv
clus                STAGE IVA STAGE IVB
  CNTNAP5 MUTATED           0         0
  CNTNAP5 WILD-TYPE        12         1
D410V3, multiclass
            clus
vv           CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 1                 0
  STAGE II                 4                22
  STAGE IIA               15                93
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               2                 4
  STAGE IIIB               3                41
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  CNTNAP5 MUTATED     0   9  26   4
  CNTNAP5 WILD-TYPE   9  58 223  37
D410V4, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  T1               0                 9
  T2               9                58
  T3              26               223
  T4               4                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
  CNTNAP5 MUTATED    31   6   3
  CNTNAP5 WILD-TYPE 189  75  63
D410V5, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  N0              31               189
  N1               6                75
  N2               3                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"
D410V6, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    29   2
  CNTNAP5 WILD-TYPE 256  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     29    2
  CNTNAP5 WILD-TYPE  256   46
   clus
vv  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  0              29               256
  1               2                46
[1] 2 2
[1] FALSE
D410V7, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    15  25
  CNTNAP5 WILD-TYPE 155 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     15   25
  CNTNAP5 WILD-TYPE  155  172
        clus
vv       CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  FEMALE              15               155
  MALE                25               172
[1] 2 2
[1] FALSE
D410V8, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    33   1
  CNTNAP5 WILD-TYPE 267   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     33    1
  CNTNAP5 WILD-TYPE  267    7
     clus
vv    CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  NO               33               267
  YES               1                 7
[1] 2 2
[1] FALSE
D410V9, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    32   8
  CNTNAP5 WILD-TYPE 282  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     32    8
  CNTNAP5 WILD-TYPE  282   40
                               clus
vv                              CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       32               282
  COLON MUCINOUS ADENOCARCINOMA               8                40
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CNTNAP5 MUTATED    25   0   0   4
  CNTNAP5 WILD-TYPE 234   3  22  17
D410V10, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  R0              25               234
  R1               0                 3
  R2               0                22
  RX               4                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"
D410V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNTNAP5 MUTATED                                  0     4
  CNTNAP5 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CNTNAP5 MUTATED                           5    23
  CNTNAP5 WILD-TYPE                        14   153
D410V12, multiclass
                                  clus
vv                                 CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 6
  BLACK OR AFRICAN AMERICAN                      5                14
  WHITE                                         23               153
[1] 4 2
[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 = KRT14 MUTATION ANALYSIS
D411V1, survival
                 sevent
clus2               0   1
  KRT14 MUTATED     5   3
  KRT14 WILD-TYPE 272  75
  KRT14 MUTATED KRT14 WILD-TYPE 
              8             347 
  KRT14 MUTATED KRT14 WILD-TYPE 
              3              75 
$`KRT14 MUTATED`
TCGA-AA-3662 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5665 TCGA-AZ-4682 TCGA-AZ-6599 
        6.05        10.88        26.17        22.06        22.36         6.77 
TCGA-CM-6674 TCGA-DM-A28E 
       12.95       119.93 

$`KRT14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KRT14 MUTATED KRT14 WILD-TYPE 
           6.05            0.00 
  KRT14 MUTATED KRT14 WILD-TYPE 
         119.93          148.01 
  KRT14 MUTATED KRT14 WILD-TYPE 
         17.505          22.090 
[1] "6.0 - 119.9 (17.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D411V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT14 MUTATED         1        0        0         4         0         0
  KRT14 WILD-TYPE      63        1       26       104         8         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        18          6         44         33       34        11
                 vv
clus              STAGE IVB
  KRT14 MUTATED           0
  KRT14 WILD-TYPE         1
D411V3, multiclass
            clus
vv           KRT14 MUTATED KRT14 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  KRT14 MUTATED     0   1   5   2
  KRT14 WILD-TYPE   9  66 244  39
D411V4, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             2              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
  KRT14 MUTATED     6   0   2
  KRT14 WILD-TYPE 214  81  64
D411V5, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  N0             6             214
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V6, binary
                 cls
clus                0   1
  KRT14 MUTATED     4   2
  KRT14 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      4    2
  KRT14 WILD-TYPE  281   46
   clus
vv  KRT14 MUTATED KRT14 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D411V7, binary
                 cls
clus                0   1
  KRT14 MUTATED     4   4
  KRT14 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      4    4
  KRT14 WILD-TYPE  166  193
        clus
vv       KRT14 MUTATED KRT14 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D411V8, binary
                 cls
clus                0   1
  KRT14 MUTATED     7   0
  KRT14 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      7    0
  KRT14 WILD-TYPE  293    8
     clus
vv    KRT14 MUTATED KRT14 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D411V9, binary
                 cls
clus                0   1
  KRT14 MUTATED     8   0
  KRT14 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      8    0
  KRT14 WILD-TYPE  306   48
                               clus
vv                              KRT14 MUTATED KRT14 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KRT14 MUTATED     4   0   1   0
  KRT14 WILD-TYPE 255   3  21  21
D411V10, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D411V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT14 MUTATED                                  0     0
  KRT14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT14 MUTATED                           0     7
  KRT14 WILD-TYPE                        19   169
D411V12, multiclass
                                  clus
vv                                 KRT14 MUTATED KRT14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = JAK2 MUTATION ANALYSIS
D412V1, survival
                sevent
clus2              0   1
  JAK2 MUTATED    30   8
  JAK2 WILD-TYPE 247  70
  JAK2 MUTATED JAK2 WILD-TYPE 
            38            317 
  JAK2 MUTATED JAK2 WILD-TYPE 
             8             70 
$`JAK2 MUTATED`
TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6625 TCGA-A6-5662 TCGA-A6-5666 
        6.05        19.04        24.00        91.79        23.61        32.71 
TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K 
       78.08        33.04         2.01         4.01        34.98        14.01 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6606 
       27.09        33.01         0.20         5.13        49.41        11.74 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5862 
       12.76        10.06        14.30        37.02        32.02         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-6532 TCGA-D5-6533 
       17.03        15.02        13.02        15.02        18.25        25.48 
TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A0XD TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6807 
       15.58        13.41        24.43        35.74         1.55        43.04 
TCGA-G4-6293 TCGA-G4-6309 
      133.18        85.48 

$`JAK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82        58.39         1.41        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       88.21         6.77        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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         7.53        12.39        10.13        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        13.35        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-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-F4-6570 
       60.79       117.07        98.24         8.61        31.96         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       47.87        34.42        41.42        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  JAK2 MUTATED JAK2 WILD-TYPE 
           0.2            0.0 
  JAK2 MUTATED JAK2 WILD-TYPE 
        133.18         148.01 
  JAK2 MUTATED JAK2 WILD-TYPE 
        18.645         22.090 
[1] "0.2 - 133.2 (18.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D412V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JAK2 MUTATED         5        0        2        13         3         1
  JAK2 WILD-TYPE      59        1       24        95         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK2 MUTATED           1          0          1          3        6         4
  JAK2 WILD-TYPE        17          6         43         30       29         8
                vv
clus             STAGE IVB
  JAK2 MUTATED           0
  JAK2 WILD-TYPE         1
D412V3, multiclass
            clus
vv           JAK2 MUTATED JAK2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            13             95
  STAGE IIB             3              5
  STAGE IIC             1              0
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            3             30
  STAGE IV              6             29
  STAGE IVA             4              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
  JAK2 MUTATED     0   5  26   9
  JAK2 WILD-TYPE   9  62 223  32
D412V4, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           26            223
  T4            9             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
  JAK2 MUTATED    26   6   8
  JAK2 WILD-TYPE 194  75  58
D412V5, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  N0           26            194
  N1            6             75
  N2            8             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"
D412V6, binary
                cls
clus               0   1
  JAK2 MUTATED    26  10
  JAK2 WILD-TYPE 259  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     26   10
  JAK2 WILD-TYPE  259   38
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0           26            259
  1           10             38
[1] 2 2
[1] FALSE
D412V7, binary
                cls
clus               0   1
  JAK2 MUTATED    21  19
  JAK2 WILD-TYPE 149 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     21   19
  JAK2 WILD-TYPE  149  178
        clus
vv       JAK2 MUTATED JAK2 WILD-TYPE
  FEMALE           21            149
  MALE             19            178
[1] 2 2
[1] FALSE
D412V8, binary
                cls
clus               0   1
  JAK2 MUTATED    31   1
  JAK2 WILD-TYPE 269   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     31    1
  JAK2 WILD-TYPE  269    7
     clus
vv    JAK2 MUTATED JAK2 WILD-TYPE
  NO            31            269
  YES            1              7
[1] 2 2
[1] FALSE
D412V9, binary
                cls
clus               0   1
  JAK2 MUTATED    34   6
  JAK2 WILD-TYPE 280  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     34    6
  JAK2 WILD-TYPE  280   42
                               clus
vv                              JAK2 MUTATED JAK2 WILD-TYPE
  COLON ADENOCARCINOMA                    34            280
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  JAK2 MUTATED    26   0   3   4
  JAK2 WILD-TYPE 233   3  19  17
D412V10, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  R0           26            233
  R1            0              3
  R2            3             19
  RX            4             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"
D412V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK2 MUTATED                                  1     3
  JAK2 WILD-TYPE                                0     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK2 MUTATED                           4    22
  JAK2 WILD-TYPE                        15   154
D412V12, multiclass
                                  clus
vv                                 JAK2 MUTATED JAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      22            154
[1] 4 2
[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 = ANKHD1 MUTATION ANALYSIS
D413V1, survival
                  sevent
clus2                0   1
  ANKHD1 MUTATED    22   6
  ANKHD1 WILD-TYPE 255  72
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              28              327 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
               6               72 
$`ANKHD1 MUTATED`
TCGA-AA-3496 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-3807 TCGA-A6-5666 
        1.02        24.00       100.01        26.17        34.65        32.71 
TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3549 TCGA-AA-3660 TCGA-AA-3977 
        8.38         7.04        63.98        21.01        78.08        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 
        4.01        34.98        12.16        21.44        58.39        49.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6533 
        6.77        12.76        22.98        12.00        12.95        25.48 
TCGA-DM-A1D7 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6323 
       13.32        53.62        85.48        13.78 

$`ANKHD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       16.57        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-3492 
       24.39        23.87        20.12        19.66        20.28         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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       61.91        36.00        46.75 

  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
            1.02             0.00 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
          100.01           148.01 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
           23.49            22.03 
[1] "1.0 - 100.0 (23.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D413V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKHD1 MUTATED         3        1        6         9         3         1
  ANKHD1 WILD-TYPE      61        0       20        99         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKHD1 MUTATED           0          0          3          1        0
  ANKHD1 WILD-TYPE        18          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ANKHD1 MUTATED           0         0
  ANKHD1 WILD-TYPE        12         1
D413V3, multiclass
            clus
vv           ANKHD1 MUTATED ANKHD1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                1                0
  STAGE II                6               20
  STAGE IIA               9               99
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ANKHD1 MUTATED     0   4  19   5
  ANKHD1 WILD-TYPE   9  63 230  36
D413V4, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             19              230
  T4              5               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
  ANKHD1 MUTATED    25   3   1
  ANKHD1 WILD-TYPE 195  78  65
D413V5, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  N0             25              195
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V6, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    23   0
  ANKHD1 WILD-TYPE 262  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     23    0
  ANKHD1 WILD-TYPE  262   48
   clus
vv  ANKHD1 MUTATED ANKHD1 WILD-TYPE
  0             23              262
  1              0               48
[1] 2 2
[1] FALSE
D413V7, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    12  17
  ANKHD1 WILD-TYPE 158 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     12   17
  ANKHD1 WILD-TYPE  158  180
        clus
vv       ANKHD1 MUTATED ANKHD1 WILD-TYPE
  FEMALE             12              158
  MALE               17              180
[1] 2 2
[1] FALSE
D413V8, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    24   1
  ANKHD1 WILD-TYPE 276   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     24    1
  ANKHD1 WILD-TYPE  276    7
     clus
vv    ANKHD1 MUTATED ANKHD1 WILD-TYPE
  NO              24              276
  YES              1                7
[1] 2 2
[1] FALSE
D413V9, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    23   5
  ANKHD1 WILD-TYPE 291  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     23    5
  ANKHD1 WILD-TYPE  291   43
                               clus
vv                              ANKHD1 MUTATED ANKHD1 WILD-TYPE
  COLON ADENOCARCINOMA                      23              291
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ANKHD1 MUTATED    21   0   0   1
  ANKHD1 WILD-TYPE 238   3  22  20
D413V10, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  R0             21              238
  R1              0                3
  R2              0               22
  RX              1               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"
D413V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKHD1 MUTATED                                  0     1
  ANKHD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANKHD1 MUTATED                           3    15
  ANKHD1 WILD-TYPE                        16   161
D413V12, multiclass
                                  clus
vv                                 ANKHD1 MUTATED ANKHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        15              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(414) Variable = GAB2 MUTATION ANALYSIS
D414V1, survival
                sevent
clus2              0   1
  GAB2 MUTATED     9   0
  GAB2 WILD-TYPE 268  78
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            346 
  GAB2 MUTATED GAB2 WILD-TYPE 
             0             78 
$`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 
       14.04       139.17        44.68 

$`GAB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GAB2 MUTATED GAB2 WILD-TYPE 
          1.02           0.00 
  GAB2 MUTATED GAB2 WILD-TYPE 
        139.17         148.01 
  GAB2 MUTATED GAB2 WILD-TYPE 
         15.02          22.09 
[1] "1.0 - 139.2 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D414V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAB2 MUTATED         1        0        1         5         0         0
  GAB2 WILD-TYPE      63        1       25       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAB2 MUTATED           0          0          0          1        0         0
  GAB2 WILD-TYPE        18          6         44         32       35        12
                vv
clus             STAGE IVB
  GAB2 MUTATED           0
  GAB2 WILD-TYPE         1
D414V3, multiclass
            clus
vv           GAB2 MUTATED GAB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  GAB2 MUTATED     0   2   6   1
  GAB2 WILD-TYPE   9  65 243  40
D414V4, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            1             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
  GAB2 MUTATED     8   1   0
  GAB2 WILD-TYPE 212  80  66
D414V5, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V6, binary
                cls
clus               0   1
  GAB2 MUTATED     8   0
  GAB2 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      8    0
  GAB2 WILD-TYPE  277   48
   clus
vv  GAB2 MUTATED GAB2 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D414V7, binary
                cls
clus               0   1
  GAB2 MUTATED     4   5
  GAB2 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      4    5
  GAB2 WILD-TYPE  166  192
        clus
vv       GAB2 MUTATED GAB2 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D414V8, binary
                cls
clus               0   1
  GAB2 MUTATED     7   0
  GAB2 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      7    0
  GAB2 WILD-TYPE  293    8
     clus
vv    GAB2 MUTATED GAB2 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D414V9, binary
                cls
clus               0   1
  GAB2 MUTATED     8   1
  GAB2 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      8    1
  GAB2 WILD-TYPE  306   47
                               clus
vv                              GAB2 MUTATED GAB2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAB2 MUTATED     8   0   0   0
  GAB2 WILD-TYPE 251   3  22  21
D414V10, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D414V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAB2 MUTATED                                  0     0
  GAB2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAB2 MUTATED                           2     5
  GAB2 WILD-TYPE                        17   171
D414V12, multiclass
                                  clus
vv                                 GAB2 MUTATED GAB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       5            171
[1] 4 2
[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 = ADAM18 MUTATION ANALYSIS
D415V1, survival
                  sevent
clus2                0   1
  ADAM18 MUTATED    14   4
  ADAM18 WILD-TYPE 263  74
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              18              337 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
               4               74 
$`ADAM18 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-5661 TCGA-A6-6137 TCGA-AA-3812 TCGA-AA-3815 
       19.04        19.04        33.53        27.09        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 

$`ADAM18 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        10.06         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ADAM18 MUTATED ADAM18 WILD-TYPE 
               0                0 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
           58.39           148.01 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
          33.285           21.990 
[1] "0.0 - 58.4 (33.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D415V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM18 MUTATED         1        0        2         9         1         0
  ADAM18 WILD-TYPE      63        1       24        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM18 MUTATED           0          0          4          0        1
  ADAM18 WILD-TYPE        18          6         40         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ADAM18 MUTATED           0         0
  ADAM18 WILD-TYPE        12         1
D415V3, multiclass
            clus
vv           ADAM18 MUTATED ADAM18 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               9               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ADAM18 MUTATED     0   1  16   1
  ADAM18 WILD-TYPE   9  66 233  40
D415V4, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             16              233
  T4              1               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
  ADAM18 MUTATED    14   4   0
  ADAM18 WILD-TYPE 206  77  66
D415V5, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  N0             14              206
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V6, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    15   1
  ADAM18 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     15    1
  ADAM18 WILD-TYPE  270   47
   clus
vv  ADAM18 MUTATED ADAM18 WILD-TYPE
  0             15              270
  1              1               47
[1] 2 2
[1] FALSE
D415V7, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    10   8
  ADAM18 WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     10    8
  ADAM18 WILD-TYPE  160  189
        clus
vv       ADAM18 MUTATED ADAM18 WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D415V8, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    15   1
  ADAM18 WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     15    1
  ADAM18 WILD-TYPE  285    7
     clus
vv    ADAM18 MUTATED ADAM18 WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D415V9, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    16   2
  ADAM18 WILD-TYPE 298  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     16    2
  ADAM18 WILD-TYPE  298   46
                               clus
vv                              ADAM18 MUTATED ADAM18 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ADAM18 MUTATED    12   0   1   2
  ADAM18 WILD-TYPE 247   3  21  19
D415V10, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              1               21
  RX              2               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"
D415V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM18 MUTATED                                  0     1
  ADAM18 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM18 MUTATED                           2     9
  ADAM18 WILD-TYPE                        17   167
D415V12, multiclass
                                  clus
vv                                 ADAM18 MUTATED ADAM18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         9              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(416) Variable = KIT MUTATION ANALYSIS
D416V1, survival
               sevent
clus2             0   1
  KIT MUTATED    73  19
  KIT WILD-TYPE 204  59
  KIT MUTATED KIT WILD-TYPE 
           92           263 
  KIT MUTATED KIT WILD-TYPE 
           19            59 
$`KIT MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A024 TCGA-AZ-6601 TCGA-G4-6310 
        6.05        85.05        19.04        39.06       100.01        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 
       22.09        35.80        26.17        32.75        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6648 
       29.19        33.53        22.06        32.71         8.38        25.18 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-A00N 
       24.69        23.87        19.66         3.02        61.02         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AU-3779 TCGA-AY-6196 
       34.98        12.16        24.53         5.79        14.50         0.20 
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-6605 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 
        5.23        12.59        12.20        12.76        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4752 
       15.62        51.32        21.99        21.14         2.01        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 
       22.03        30.08         5.03        17.03        15.02        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        15.02        14.04        11.01        12.95 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       54.61        55.92        20.19        18.25         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A1D0 
       16.14        15.58         9.44        13.41        13.35       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28C 
       49.91        13.32       140.38         7.50       131.51        81.37 
TCGA-DM-A28E TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6808 
      119.93         8.61        31.96        35.74         6.18        33.67 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       35.31       133.18        53.62        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

$`KIT WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        36.53        32.91 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       23.61        22.09        27.09        22.52        25.08        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       24.39        20.12        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       40.96        83.24        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       16.31         0.95        33.01         1.41         5.13        22.36 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        29.56        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4950 
       12.36        12.39        12.59        10.06        14.30        85.45 
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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.98        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6675 
       12.00        14.04        21.99        12.99        13.02        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       19.59        56.09        25.48        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        11.64        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
       24.43        38.20        92.75        12.59        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 
      139.17        35.97        60.79       117.07        98.24        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        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6626 
       47.41        74.56        65.85        44.68        46.75 

  KIT MUTATED KIT WILD-TYPE 
          0.2           0.0 
  KIT MUTATED KIT WILD-TYPE 
       148.01        139.17 
  KIT MUTATED KIT WILD-TYPE 
       22.045        22.090 
[1] "0.2 - 148.0 (22.0)" "0.0 - 139.2 (22.1)"
[1] "hr=" "1.4"
D416V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIT MUTATED        12        1        7        30         4         1
  KIT WILD-TYPE      52        0       19        78         4         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIT MUTATED           4          0         17          9        6         4
  KIT WILD-TYPE        14          6         27         24       29         8
               vv
clus            STAGE IVB
  KIT MUTATED           0
  KIT WILD-TYPE         1
D416V3, multiclass
            clus
vv           KIT MUTATED KIT WILD-TYPE
  STAGE I             12            52
  STAGE IA             1             0
  STAGE II             7            19
  STAGE IIA           30            78
  STAGE IIB            4             4
  STAGE IIC            1             0
  STAGE III            4            14
  STAGE IIIA           0             6
  STAGE IIIB          17            27
  STAGE IIIC           9            24
  STAGE IV             6            29
  STAGE IVA            4             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
  KIT MUTATED     4  10  68  13
  KIT WILD-TYPE   5  57 181  28
D416V4, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  T1           4             5
  T2          10            57
  T3          68           181
  T4          13            28
[1] 4 2
[1] TRUE
[1] "dimension 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    59  25  12
  KIT WILD-TYPE 161  56  54
D416V5, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  N0          59           161
  N1          25            56
  N2          12            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V6, binary
               cls
clus              0   1
  KIT MUTATED    71  10
  KIT WILD-TYPE 214  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     71   10
  KIT WILD-TYPE  214   38
   clus
vv  KIT MUTATED KIT WILD-TYPE
  0          71           214
  1          10            38
[1] 2 2
[1] FALSE
D416V7, binary
               cls
clus              0   1
  KIT MUTATED    47  49
  KIT WILD-TYPE 123 148
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     47   49
  KIT WILD-TYPE  123  148
        clus
vv       KIT MUTATED KIT WILD-TYPE
  FEMALE          47           123
  MALE            49           148
[1] 2 2
[1] FALSE
D416V8, binary
               cls
clus              0   1
  KIT MUTATED    78   2
  KIT WILD-TYPE 222   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     78    2
  KIT WILD-TYPE  222    6
     clus
vv    KIT MUTATED KIT WILD-TYPE
  NO           78           222
  YES           2             6
[1] 2 2
[1] FALSE
D416V9, binary
               cls
clus              0   1
  KIT MUTATED    81  14
  KIT WILD-TYPE 233  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     81   14
  KIT WILD-TYPE  233   34
                               clus
vv                              KIT MUTATED KIT WILD-TYPE
  COLON ADENOCARCINOMA                   81           233
  COLON MUCINOUS ADENOCARCINOMA          14            34
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  KIT MUTATED    63   0   3   9
  KIT WILD-TYPE 196   3  19  12
D416V10, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  R0          63           196
  R1           0             3
  R2           3            19
  RX           9            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIT MUTATED                                  0     3
  KIT WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  KIT MUTATED                          10    72
  KIT WILD-TYPE                         9   104
D416V12, multiclass
                                  clus
vv                                 KIT MUTATED KIT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             7
  BLACK OR AFRICAN AMERICAN                 10             9
  WHITE                                     72           104
[1] 4 2
[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 = HUWE1 MUTATION ANALYSIS
D417V1, survival
                 sevent
clus2               0   1
  HUWE1 MUTATED    32   9
  HUWE1 WILD-TYPE 245  69
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             41             314 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
              9              69 
$`HUWE1 MUTATED`
TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 TCGA-A6-5665 
        6.05        19.04        24.00        25.08        10.88        22.06 
TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3818 TCGA-AA-3837 
       20.12        29.95        78.08         6.97         0.99        38.99 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       36.03        53.00        24.00        33.01        26.01         2.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02F TCGA-AU-3779 TCGA-AU-6004 
       34.98        38.07         1.02        39.98        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 
        7.50       135.65         8.61         6.18        47.87 

$`HUWE1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 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-A6-6651 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
        5.03        26.99        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
        2.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       24.53         5.79        22.42        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
        5.13        22.36        88.21         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       14.04        16.04        21.99        12.99        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E 
      140.38        44.32       131.51       139.17        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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HUWE1 MUTATED HUWE1 WILD-TYPE 
           0.99            0.00 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
         135.65          148.01 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
          24.00           22.01 
[1] "1.0 - 135.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D417V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HUWE1 MUTATED         3        0        6        16         3         0
  HUWE1 WILD-TYPE      61        1       20        92         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HUWE1 MUTATED           1          0          5          2        3         1
  HUWE1 WILD-TYPE        17          6         39         31       32        11
                 vv
clus              STAGE IVB
  HUWE1 MUTATED           0
  HUWE1 WILD-TYPE         1
D417V3, multiclass
            clus
vv           HUWE1 MUTATED HUWE1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA             16              92
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              1              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
  HUWE1 MUTATED     0   4  32   6
  HUWE1 WILD-TYPE   9  63 217  35
D417V4, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            32             217
  T4             6              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
  HUWE1 MUTATED    29   8   5
  HUWE1 WILD-TYPE 191  73  61
D417V5, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  N0            29             191
  N1             8              73
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V6, binary
                 cls
clus                0   1
  HUWE1 MUTATED    32   4
  HUWE1 WILD-TYPE 253  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     32    4
  HUWE1 WILD-TYPE  253   44
   clus
vv  HUWE1 MUTATED HUWE1 WILD-TYPE
  0            32             253
  1             4              44
[1] 2 2
[1] FALSE
D417V7, binary
                 cls
clus                0   1
  HUWE1 MUTATED    26  16
  HUWE1 WILD-TYPE 144 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     26   16
  HUWE1 WILD-TYPE  144  181
        clus
vv       HUWE1 MUTATED HUWE1 WILD-TYPE
  FEMALE            26             144
  MALE              16             181
[1] 2 2
[1] FALSE
D417V8, binary
                 cls
clus                0   1
  HUWE1 MUTATED    34   1
  HUWE1 WILD-TYPE 266   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     34    1
  HUWE1 WILD-TYPE  266    7
     clus
vv    HUWE1 MUTATED HUWE1 WILD-TYPE
  NO             34             266
  YES             1               7
[1] 2 2
[1] FALSE
D417V9, binary
                 cls
clus                0   1
  HUWE1 MUTATED    31  10
  HUWE1 WILD-TYPE 283  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     31   10
  HUWE1 WILD-TYPE  283   38
                               clus
vv                              HUWE1 MUTATED HUWE1 WILD-TYPE
  COLON ADENOCARCINOMA                     31             283
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HUWE1 MUTATED    30   0   3   1
  HUWE1 WILD-TYPE 229   3  19  20
D417V10, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  R0            30             229
  R1             0               3
  R2             3              19
  RX             1              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"
D417V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HUWE1 MUTATED                                  0     0
  HUWE1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HUWE1 MUTATED                           3    21
  HUWE1 WILD-TYPE                        16   155
D417V12, multiclass
                                  clus
vv                                 HUWE1 MUTATED HUWE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       21             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(418) Variable = NTRK3 MUTATION ANALYSIS
D418V1, survival
                 sevent
clus2               0   1
  NTRK3 MUTATED    19   4
  NTRK3 WILD-TYPE 258  74
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             23             332 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
              4              74 
$`NTRK3 MUTATED`
TCGA-AA-3713 TCGA-G4-6586 TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3664 TCGA-AA-3815 
       19.04        35.80        31.63        19.66        54.02        33.04 
TCGA-AA-3833 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4682 
       15.95        31.00        24.00        34.98        12.16        22.36 
TCGA-AZ-6599 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 
        6.77        10.06        30.08        32.02        15.02        15.02 
TCGA-CM-6166 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-G4-6303 TCGA-G4-6315 
       21.99        12.00       140.38        65.85        61.91 

$`NTRK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        62.79        88.21        49.41 
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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6317 
       74.56        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NTRK3 MUTATED NTRK3 WILD-TYPE 
           6.77            0.00 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
         140.38          148.01 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
          24.00           22.01 
[1] "6.8 - 140.4 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D418V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTRK3 MUTATED         5        0        2         9         1         0
  NTRK3 WILD-TYPE      59        1       24        99         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTRK3 MUTATED           0          0          1          2        3         2
  NTRK3 WILD-TYPE        18          6         43         31       32        10
                 vv
clus              STAGE IVB
  NTRK3 MUTATED           0
  NTRK3 WILD-TYPE         1
D418V3, multiclass
            clus
vv           NTRK3 MUTATED NTRK3 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              9              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              2              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
  NTRK3 MUTATED     1   4  15   5
  NTRK3 WILD-TYPE   8  63 234  36
D418V4, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            15             234
  T4             5              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
  NTRK3 MUTATED    19   5   1
  NTRK3 WILD-TYPE 201  76  65
D418V5, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  N0            19             201
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V6, binary
                 cls
clus                0   1
  NTRK3 MUTATED    17   5
  NTRK3 WILD-TYPE 268  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     17    5
  NTRK3 WILD-TYPE  268   43
   clus
vv  NTRK3 MUTATED NTRK3 WILD-TYPE
  0            17             268
  1             5              43
[1] 2 2
[1] FALSE
D418V7, binary
                 cls
clus                0   1
  NTRK3 MUTATED    15  10
  NTRK3 WILD-TYPE 155 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     15   10
  NTRK3 WILD-TYPE  155  187
        clus
vv       NTRK3 MUTATED NTRK3 WILD-TYPE
  FEMALE            15             155
  MALE              10             187
[1] 2 2
[1] FALSE
D418V8, binary
                 cls
clus                0   1
  NTRK3 MUTATED    21   1
  NTRK3 WILD-TYPE 279   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     21    1
  NTRK3 WILD-TYPE  279    7
     clus
vv    NTRK3 MUTATED NTRK3 WILD-TYPE
  NO             21             279
  YES             1               7
[1] 2 2
[1] FALSE
D418V9, binary
                 cls
clus                0   1
  NTRK3 MUTATED    22   3
  NTRK3 WILD-TYPE 292  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     22    3
  NTRK3 WILD-TYPE  292   45
                               clus
vv                              NTRK3 MUTATED NTRK3 WILD-TYPE
  COLON ADENOCARCINOMA                     22             292
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NTRK3 MUTATED    21   0   1   1
  NTRK3 WILD-TYPE 238   3  21  20
D418V10, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  R0            21             238
  R1             0               3
  R2             1              21
  RX             1              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"
D418V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTRK3 MUTATED                                  0     1
  NTRK3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTRK3 MUTATED                           1    14
  NTRK3 WILD-TYPE                        18   162
D418V12, multiclass
                                  clus
vv                                 NTRK3 MUTATED NTRK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       14             162
[1] 4 2
[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 = EGFR MUTATION ANALYSIS
D419V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    52  21
  EGFR WILD-TYPE 225  57
  EGFR MUTATED EGFR WILD-TYPE 
            73            282 
  EGFR MUTATED EGFR WILD-TYPE 
            21             57 
$`EGFR MUTATED`
TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6588 
       85.05        10.88       100.01         1.94         5.88        26.17 
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-3811 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-A00E TCGA-AA-A00N 
       10.06         2.01        21.99        27.02        30.02         4.01 
TCGA-AA-A00R TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-5900 TCGA-AD-6901 TCGA-AU-3779 
        0.99        35.01        14.01        12.16        22.42        14.50 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       27.09        33.01         0.20        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 
        6.77        12.10        29.56        12.76        51.32        21.99 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6162 
        2.01       124.27        22.03        32.02         5.03        12.00 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 
       21.99        12.99        13.02        15.02        11.08        11.08 
TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       12.03        19.59        56.09        25.48        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6928 
        4.80        17.13        12.49         7.53        12.39        11.64 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6808 
       12.59        44.32       135.65        35.97        31.96        33.67 
TCGA-F4-6809 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 
       13.25        74.56        65.85        44.68        55.04        61.91 
TCGA-G4-6317 
       36.00 

$`EGFR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-CK-5912 
       39.06        21.37        15.52        25.08       106.75        49.08 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       63.62        22.09        35.80        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       33.34        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       34.03        16.08        13.05        34.06        25.02        27.02 
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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        18.05        27.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
       24.53         5.79        27.42        26.47        16.31         0.95 
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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4743 
      148.01        85.45        15.62        21.14        82.95        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-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 
       14.04        29.03        16.04        14.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       12.95        13.05        11.01        10.06        45.40        54.61 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6541 
       55.92        20.19        18.25        15.12        16.14        15.58 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        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-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.50       131.51       139.17        81.37       119.93        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-F4-6854 TCGA-F4-6855 
        1.55        34.42        41.42        43.04         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6626 
       35.31       133.18        53.62        85.48        13.78        46.75 

  EGFR MUTATED EGFR WILD-TYPE 
           0.2            0.0 
  EGFR MUTATED EGFR WILD-TYPE 
        135.65         148.01 
  EGFR MUTATED EGFR WILD-TYPE 
         21.99          22.44 
[1] "0.2 - 135.7 (22.0)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D419V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EGFR MUTATED        14        0        5        17         2         0
  EGFR WILD-TYPE      50        1       21        91         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EGFR MUTATED           3          2         11          5        6         3
  EGFR WILD-TYPE        15          4         33         28       29         9
                vv
clus             STAGE IVB
  EGFR MUTATED           0
  EGFR WILD-TYPE         1
D419V3, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE I              14             50
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA            17             91
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            2              4
  STAGE IIIB           11             33
  STAGE IIIC            5             28
  STAGE IV              6             29
  STAGE IVA             3              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
  EGFR MUTATED     2  15  52   6
  EGFR WILD-TYPE   7  52 197  35
D419V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            2              7
  T2           15             52
  T3           52            197
  T4            6             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
  EGFR MUTATED    42  20  13
  EGFR WILD-TYPE 178  61  53
D419V5, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  N0           42            178
  N1           20             61
  N2           13             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V6, binary
                cls
clus               0   1
  EGFR MUTATED    51   9
  EGFR WILD-TYPE 234  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     51    9
  EGFR WILD-TYPE  234   39
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0           51            234
  1            9             39
[1] 2 2
[1] FALSE
D419V7, binary
                cls
clus               0   1
  EGFR MUTATED    38  37
  EGFR WILD-TYPE 132 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     38   37
  EGFR WILD-TYPE  132  160
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           38            132
  MALE             37            160
[1] 2 2
[1] FALSE
D419V8, binary
                cls
clus               0   1
  EGFR MUTATED    60   1
  EGFR WILD-TYPE 240   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     60    1
  EGFR WILD-TYPE  240    7
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO            60            240
  YES            1              7
[1] 2 2
[1] FALSE
D419V9, binary
                cls
clus               0   1
  EGFR MUTATED    60  14
  EGFR WILD-TYPE 254  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     60   14
  EGFR WILD-TYPE  254   34
                               clus
vv                              EGFR MUTATED EGFR WILD-TYPE
  COLON ADENOCARCINOMA                    60            254
  COLON MUCINOUS ADENOCARCINOMA           14             34
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EGFR MUTATED    50   0   1   6
  EGFR WILD-TYPE 209   3  21  15
D419V10, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           50            209
  R1            0              3
  R2            1             21
  RX            6             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"
D419V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     1
  EGFR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           5    54
  EGFR WILD-TYPE                        14   122
D419V12, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   5             14
  WHITE                                      54            122
[1] 4 2
[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 = GATA3 MUTATION ANALYSIS
D420V1, survival
                 sevent
clus2               0   1
  GATA3 MUTATED     9   4
  GATA3 WILD-TYPE 268  74
  GATA3 MUTATED GATA3 WILD-TYPE 
             13             342 
  GATA3 MUTATED GATA3 WILD-TYPE 
              4              74 
$`GATA3 MUTATED`
TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3821 
       25.08       100.01        22.06         8.38         3.02         1.02 
TCGA-AA-3930 TCGA-AA-A00Q TCGA-AD-6901 TCGA-AY-6197 TCGA-DM-A0X9 TCGA-G4-6293 
        2.01        42.02        22.42        21.44       119.70       133.18 
TCGA-G4-6307 
       55.04 

$`GATA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  GATA3 MUTATED GATA3 WILD-TYPE 
           1.02            0.00 
  GATA3 MUTATED GATA3 WILD-TYPE 
         133.18          148.01 
  GATA3 MUTATED GATA3 WILD-TYPE 
          22.42           22.01 
[1] "1.0 - 133.2 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D420V2, continuous
                 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      62        1       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA3 MUTATED           2          0          3          0        1         0
  GATA3 WILD-TYPE        16          6         41         33       34        12
                 vv
clus              STAGE IVB
  GATA3 MUTATED           0
  GATA3 WILD-TYPE         1
D420V3, multiclass
            clus
vv           GATA3 MUTATED GATA3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GATA3 MUTATED     0   2  12   2
  GATA3 WILD-TYPE   9  65 237  39
D420V4, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            12             237
  T4             2              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
  GATA3 MUTATED    10   4   2
  GATA3 WILD-TYPE 210  77  64
D420V5, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  N0            10             210
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V6, binary
                 cls
clus                0   1
  GATA3 MUTATED    11   1
  GATA3 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     11    1
  GATA3 WILD-TYPE  274   47
   clus
vv  GATA3 MUTATED GATA3 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D420V7, binary
                 cls
clus                0   1
  GATA3 MUTATED     8   8
  GATA3 WILD-TYPE 162 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED      8    8
  GATA3 WILD-TYPE  162  189
        clus
vv       GATA3 MUTATED GATA3 WILD-TYPE
  FEMALE             8             162
  MALE               8             189
[1] 2 2
[1] FALSE
D420V8, binary
                 cls
clus                0   1
  GATA3 MUTATED    12   0
  GATA3 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     12    0
  GATA3 WILD-TYPE  288    8
     clus
vv    GATA3 MUTATED GATA3 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D420V9, binary
                 cls
clus                0   1
  GATA3 MUTATED    15   1
  GATA3 WILD-TYPE 299  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     15    1
  GATA3 WILD-TYPE  299   47
                               clus
vv                              GATA3 MUTATED GATA3 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GATA3 MUTATED     9   0   1   2
  GATA3 WILD-TYPE 250   3  21  19
D420V10, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             2              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"
D420V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GATA3 MUTATED                                  0     0
  GATA3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GATA3 MUTATED                           1    10
  GATA3 WILD-TYPE                        18   166
D420V12, multiclass
                                  clus
vv                                 GATA3 MUTATED GATA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(421) Variable = ATP13A5 MUTATION ANALYSIS
D421V1, survival
                   sevent
clus2                 0   1
  ATP13A5 MUTATED    20   2
  ATP13A5 WILD-TYPE 257  76
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               22               333 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
                2                76 
$`ATP13A5 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 
       19.04        26.17        33.53        25.08        21.76        20.12 
TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6963 
       63.98         2.01        25.02        34.98        12.16        27.42 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-6747 TCGA-CM-6167 
       58.39        12.76        10.06        15.62        82.95        14.99 
TCGA-CM-6168 TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6293 
       12.99       131.51         6.18       133.18 

$`ATP13A5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6169 
       12.00        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50        44.32       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
             2.01              0.00 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
           133.18            148.01 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
            23.39             22.06 
[1] "2.0 - 133.2 (23.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D421V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP13A5 MUTATED         1        0        1        10         1         0
  ATP13A5 WILD-TYPE      63        1       25        98         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP13A5 MUTATED           1          0          1          3        1
  ATP13A5 WILD-TYPE        17          6         43         30       34
                   vv
clus                STAGE IVA STAGE IVB
  ATP13A5 MUTATED           1         0
  ATP13A5 WILD-TYPE        11         1
D421V3, multiclass
            clus
vv           ATP13A5 MUTATED ATP13A5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA               10                98
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               3                30
  STAGE IV                 1                34
  STAGE IVA                1                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
  ATP13A5 MUTATED     0   2  18   2
  ATP13A5 WILD-TYPE   9  65 231  39
D421V4, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              18               231
  T4               2                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
  ATP13A5 MUTATED    16   3   3
  ATP13A5 WILD-TYPE 204  78  63
D421V5, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  N0              16               204
  N1               3                78
  N2               3                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"
D421V6, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    14   2
  ATP13A5 WILD-TYPE 271  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     14    2
  ATP13A5 WILD-TYPE  271   46
   clus
vv  ATP13A5 MUTATED ATP13A5 WILD-TYPE
  0              14               271
  1               2                46
[1] 2 2
[1] FALSE
D421V7, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    12  10
  ATP13A5 WILD-TYPE 158 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     12   10
  ATP13A5 WILD-TYPE  158  187
        clus
vv       ATP13A5 MUTATED ATP13A5 WILD-TYPE
  FEMALE              12               158
  MALE                10               187
[1] 2 2
[1] FALSE
D421V8, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    18   1
  ATP13A5 WILD-TYPE 282   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     18    1
  ATP13A5 WILD-TYPE  282    7
     clus
vv    ATP13A5 MUTATED ATP13A5 WILD-TYPE
  NO               18               282
  YES               1                 7
[1] 2 2
[1] FALSE
D421V9, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    17   5
  ATP13A5 WILD-TYPE 297  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     17    5
  ATP13A5 WILD-TYPE  297   43
                               clus
vv                              ATP13A5 MUTATED ATP13A5 WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ATP13A5 MUTATED    10   0   1   4
  ATP13A5 WILD-TYPE 249   3  21  17
D421V10, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               1                21
  RX               4                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"
D421V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP13A5 MUTATED                                  0     2
  ATP13A5 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATP13A5 MUTATED                           3    12
  ATP13A5 WILD-TYPE                        16   164
D421V12, multiclass
                                  clus
vv                                 ATP13A5 MUTATED ATP13A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      3                16
  WHITE                                         12               164
[1] 4 2
[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 = DKK2 MUTATION ANALYSIS
D422V1, survival
                sevent
clus2              0   1
  DKK2 MUTATED    19   4
  DKK2 WILD-TYPE 258  74
  DKK2 MUTATED DKK2 WILD-TYPE 
            23            332 
  DKK2 MUTATED DKK2 WILD-TYPE 
             4             74 
$`DKK2 MUTATED`
TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AD-6964 TCGA-G4-6310 
       17.95         0.92        85.05        19.04        10.88        63.62 
TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3971 
       26.17        42.90        30.44        33.53        20.28        16.08 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6541 TCGA-D5-6898 
       33.01         0.20        58.39        15.62        15.58         7.53 
TCGA-D5-6930 TCGA-D5-6932 TCGA-F4-6805 TCGA-G4-6309 TCGA-G4-6626 
       13.35        11.38        34.42        85.48        46.75 

$`DKK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       36.53        32.91        31.63        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-A6-6651 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-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        21.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.95        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49        16.14        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
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-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-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 
       36.00        13.78 

  DKK2 MUTATED DKK2 WILD-TYPE 
           0.2            0.0 
  DKK2 MUTATED DKK2 WILD-TYPE 
         85.48         148.01 
  DKK2 MUTATED DKK2 WILD-TYPE 
        20.280         22.075 
[1] "0.2 - 85.5 (20.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D422V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DKK2 MUTATED         2        0        2         9         2         0
  DKK2 WILD-TYPE      62        1       24        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DKK2 MUTATED           2          0          2          2        0         1
  DKK2 WILD-TYPE        16          6         42         31       35        11
                vv
clus             STAGE IVB
  DKK2 MUTATED           0
  DKK2 WILD-TYPE         1
D422V3, multiclass
            clus
vv           DKK2 MUTATED DKK2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             9             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             1             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
  DKK2 MUTATED     0   2  17   4
  DKK2 WILD-TYPE   9  65 232  37
D422V4, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           17            232
  T4            4             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
  DKK2 MUTATED    15   5   3
  DKK2 WILD-TYPE 205  76  63
D422V5, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  N0           15            205
  N1            5             76
  N2            3             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"
D422V6, binary
                cls
clus               0   1
  DKK2 MUTATED    19   1
  DKK2 WILD-TYPE 266  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     19    1
  DKK2 WILD-TYPE  266   47
   clus
vv  DKK2 MUTATED DKK2 WILD-TYPE
  0           19            266
  1            1             47
[1] 2 2
[1] FALSE
D422V7, binary
                cls
clus               0   1
  DKK2 MUTATED    10  13
  DKK2 WILD-TYPE 160 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     10   13
  DKK2 WILD-TYPE  160  184
        clus
vv       DKK2 MUTATED DKK2 WILD-TYPE
  FEMALE           10            160
  MALE             13            184
[1] 2 2
[1] FALSE
D422V8, binary
                cls
clus               0   1
  DKK2 MUTATED    20   1
  DKK2 WILD-TYPE 280   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     20    1
  DKK2 WILD-TYPE  280    7
     clus
vv    DKK2 MUTATED DKK2 WILD-TYPE
  NO            20            280
  YES            1              7
[1] 2 2
[1] FALSE
D422V9, binary
                cls
clus               0   1
  DKK2 MUTATED    20   3
  DKK2 WILD-TYPE 294  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     20    3
  DKK2 WILD-TYPE  294   45
                               clus
vv                              DKK2 MUTATED DKK2 WILD-TYPE
  COLON ADENOCARCINOMA                    20            294
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DKK2 MUTATED    20   0   0   1
  DKK2 WILD-TYPE 239   3  22  20
D422V10, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  R0           20            239
  R1            0              3
  R2            0             22
  RX            1             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"
D422V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DKK2 MUTATED                                  0     0
  DKK2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DKK2 MUTATED                           3    15
  DKK2 WILD-TYPE                        16   161
D422V12, multiclass
                                  clus
vv                                 DKK2 MUTATED DKK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      15            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(423) Variable = PIK3CA MUTATION ANALYSIS
D423V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED   132  41
  PIK3CA WILD-TYPE 145  37
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             173              182 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              41               37 
$`PIK3CA MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 
       14.53        24.16         1.02         6.05        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3939 TCGA-AA-3950 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-6601 
       19.04        12.99        24.00        21.37        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       91.79        79.69        33.34        32.75        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.06        32.71 
TCGA-A6-6141 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
        8.38        24.69        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 
        3.02        35.01        63.98         6.97        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        6.97        50.04         5.03        35.05        33.04         0.99 
TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3861 TCGA-AA-3864 
       38.99        10.06         0.00         0.00        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00N 
       17.03        31.00        33.01        34.03        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01V TCGA-AA-A02O TCGA-AA-A02Y 
       34.98        31.00        31.00         1.02         0.92        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        12.16        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       26.47        14.50        27.09        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        6.77        11.74        12.36        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        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        54.61 
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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
       12.39        12.43         9.04         9.44        13.41        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-A28C TCGA-DM-A28F 
      140.38        44.32       131.51       135.65        81.37        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       47.87        34.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        61.91        36.00        13.78 

$`PIK3CA WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       24.33        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 
       19.99        19.99         0.92        19.00        36.00        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       31.07        24.03        29.98         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        39.06        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-G4-6321 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       25.08       106.75        22.09        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5664 
       42.90        42.28        16.57        34.65        36.53        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       27.09        22.52        25.08        25.18        21.76        24.39 
TCGA-A6-6781 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       19.66         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
        5.98        37.05        26.99        10.06        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3851 
       17.98        15.95        37.02         0.00        17.03        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3875 
       36.03        32.05         0.99        31.07        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
        2.01        24.00        26.01        20.98         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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-A01P 
       14.99        15.02        10.98        32.02        12.00        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-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W 
       51.98        39.98         2.01         5.03        14.01        41.00 
TCGA-AD-6889 TCGA-AD-6901 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4323 
       83.24        22.42        16.31         0.95         0.20         1.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 
       12.10        29.56         5.23         3.19        12.69        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5913 TCGA-CK-6748 TCGA-CK-6751 
       12.59        12.59        12.20        51.32         2.01       124.27 
TCGA-CM-4744 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6163 
       20.02        29.06        22.98        15.02        17.03        14.04 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 
       16.04        14.99        15.02        13.05        11.08        10.06 
TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6924 
       45.40        25.48        15.12        12.49        10.13        14.30 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.64        13.35        11.38       130.65        92.75        49.91 
TCGA-DM-A1DA TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28K TCGA-F4-6704 TCGA-F4-6806 
        7.50       139.17       119.93        98.24         1.55        41.42 
TCGA-G4-6309 TCGA-G4-6626 
       85.48        46.75 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
               0                0 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          148.01           139.17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          23.870           20.995 
[1] "0.0 - 148.0 (23.9)" "0.0 - 139.2 (21.0)"
[1] "hr=" "1.1"
D423V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3CA MUTATED        31        1       16        55         7         1
  PIK3CA WILD-TYPE      33        0       10        53         1         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           4          2         22         13        9
  PIK3CA WILD-TYPE        14          4         22         20       26
                  vv
clus               STAGE IVA STAGE IVB
  PIK3CA MUTATED           8         0
  PIK3CA WILD-TYPE         4         1
D423V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                31               33
  STAGE IA                1                0
  STAGE II               16               10
  STAGE IIA              55               53
  STAGE IIB               7                1
  STAGE IIC               1                0
  STAGE III               4               14
  STAGE IIIA              2                4
  STAGE IIIB             22               22
  STAGE IIIC             13               20
  STAGE IV                9               26
  STAGE IVA               8                4
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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     5  30 119  20
  PIK3CA WILD-TYPE   4  37 130  21
D423V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              5                4
  T2             30               37
  T3            119              130
  T4             20               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"
                  vv
clus                N0  N1  N2
  PIK3CA MUTATED   118  33  24
  PIK3CA WILD-TYPE 102  48  42
D423V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0            118              102
  N1             33               48
  N2             24               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   138  17
  PIK3CA WILD-TYPE 147  31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    138   17
  PIK3CA WILD-TYPE  147   31
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0            138              147
  1             17               31
[1] 2 2
[1] FALSE
D423V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    79  96
  PIK3CA WILD-TYPE  91 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     79   96
  PIK3CA WILD-TYPE   91  101
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             79               91
  MALE               96              101
[1] 2 2
[1] FALSE
D423V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   145   4
  PIK3CA WILD-TYPE 155   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    145    4
  PIK3CA WILD-TYPE  155    4
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO             145              155
  YES              4                4
[1] 2 2
[1] FALSE
D423V9, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   151  21
  PIK3CA WILD-TYPE 163  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    151   21
  PIK3CA WILD-TYPE  163   27
                               clus
vv                              PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON ADENOCARCINOMA                     151              163
  COLON MUCINOUS ADENOCARCINOMA             21               27
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED   121   2   3  11
  PIK3CA WILD-TYPE 138   1  19  10
D423V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0            121              138
  R1              2                1
  R2              3               19
  RX             11               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     4
  PIK3CA WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                          13   117
  PIK3CA WILD-TYPE                         6    59
D423V12, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                    13                6
  WHITE                                       117               59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(424) Variable = CLVS2 MUTATION ANALYSIS
D424V1, survival
                 sevent
clus2               0   1
  CLVS2 MUTATED     7   1
  CLVS2 WILD-TYPE 270  77
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              8             347 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              1              77 
$`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        83.24        22.98        18.25 
TCGA-D5-6533 TCGA-D5-6540 
       25.48        16.14 

$`CLVS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CLVS2 MUTATED CLVS2 WILD-TYPE 
           1.02            0.00 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
          83.24          148.01 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
          21.01           22.06 
[1] "1.0 - 83.2 (21.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D424V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLVS2 MUTATED         2        0        2         2         0         0
  CLVS2 WILD-TYPE      62        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLVS2 MUTATED           0          0          1          0        1         0
  CLVS2 WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  CLVS2 MUTATED           0
  CLVS2 WILD-TYPE         1
D424V3, multiclass
            clus
vv           CLVS2 MUTATED CLVS2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  CLVS2 MUTATED     0   2   6   1
  CLVS2 WILD-TYPE   9  65 243  40
D424V4, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             1              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
  CLVS2 MUTATED     8   1   0
  CLVS2 WILD-TYPE 212  80  66
D424V5, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V6, binary
                 cls
clus                0   1
  CLVS2 MUTATED     7   1
  CLVS2 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      7    1
  CLVS2 WILD-TYPE  278   47
   clus
vv  CLVS2 MUTATED CLVS2 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D424V7, binary
                 cls
clus                0   1
  CLVS2 MUTATED     2   7
  CLVS2 WILD-TYPE 168 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      2    7
  CLVS2 WILD-TYPE  168  190
        clus
vv       CLVS2 MUTATED CLVS2 WILD-TYPE
  FEMALE             2             168
  MALE               7             190
[1] 2 2
[1] FALSE
D424V8, binary
                 cls
clus                0   1
  CLVS2 MUTATED     6   1
  CLVS2 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      6    1
  CLVS2 WILD-TYPE  294    7
     clus
vv    CLVS2 MUTATED CLVS2 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D424V9, binary
                 cls
clus                0   1
  CLVS2 MUTATED     8   1
  CLVS2 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      8    1
  CLVS2 WILD-TYPE  306   47
                               clus
vv                              CLVS2 MUTATED CLVS2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLVS2 MUTATED     7   0   1   1
  CLVS2 WILD-TYPE 252   3  21  20
D424V10, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             1              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"
D424V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLVS2 MUTATED                                  0     1
  CLVS2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLVS2 MUTATED                           0     5
  CLVS2 WILD-TYPE                        19   171
D424V12, multiclass
                                  clus
vv                                 CLVS2 MUTATED CLVS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = EP300 MUTATION ANALYSIS
D425V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    31   4
  EP300 WILD-TYPE 246  74
  EP300 MUTATED EP300 WILD-TYPE 
             35             320 
  EP300 MUTATED EP300 WILD-TYPE 
              4              74 
$`EP300 MUTATED`
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3715 TCGA-G4-6628 TCGA-A6-5659 TCGA-A6-6141 
       17.95         6.05        19.04        79.69        30.44         8.38 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3864 
       24.39        20.12        19.66        29.95        61.02        53.00 
TCGA-AA-3877 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       31.00        18.05         4.01         0.99        34.98        12.00 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-5913 
       83.24        27.09        17.82        12.39        12.76        51.32 
TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-5540 TCGA-D5-6539 
       23.05        13.02        17.03        12.00        56.09        12.49 
TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-G4-6323 
       12.39        12.00       130.65         7.50        13.78 

$`EP300 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.69        23.87        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       42.02        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.36        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
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-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        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        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6626 
       36.00        46.75 

  EP300 MUTATED EP300 WILD-TYPE 
           0.99            0.00 
  EP300 MUTATED EP300 WILD-TYPE 
         130.65          148.01 
  EP300 MUTATED EP300 WILD-TYPE 
          18.05           22.39 
[1] "1.0 - 130.7 (18.1)" "0.0 - 148.0 (22.4)"
[1] "hr=" "2.1"
D425V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EP300 MUTATED         6        1        3        15         2         0
  EP300 WILD-TYPE      58        0       23        93         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP300 MUTATED           0          0          3          3        1         1
  EP300 WILD-TYPE        18          6         41         30       34        11
                 vv
clus              STAGE IVB
  EP300 MUTATED           0
  EP300 WILD-TYPE         1
D425V3, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE I                6              58
  STAGE IA               1               0
  STAGE II               3              23
  STAGE IIA             15              93
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             3              30
  STAGE IV               1              34
  STAGE IVA              1              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
  EP300 MUTATED     1   5  22   7
  EP300 WILD-TYPE   8  62 227  34
D425V4, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  T1             1               8
  T2             5              62
  T3            22             227
  T4             7              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
  EP300 MUTATED    28   5   3
  EP300 WILD-TYPE 192  76  63
D425V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            28             192
  N1             5              76
  N2             3              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"
D425V6, binary
                 cls
clus                0   1
  EP300 MUTATED    30   2
  EP300 WILD-TYPE 255  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     30    2
  EP300 WILD-TYPE  255   46
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            30             255
  1             2              46
[1] 2 2
[1] FALSE
D425V7, binary
                 cls
clus                0   1
  EP300 MUTATED    17  19
  EP300 WILD-TYPE 153 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     17   19
  EP300 WILD-TYPE  153  178
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            17             153
  MALE              19             178
[1] 2 2
[1] FALSE
D425V8, binary
                 cls
clus                0   1
  EP300 MUTATED    30   0
  EP300 WILD-TYPE 270   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     30    0
  EP300 WILD-TYPE  270    8
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             30             270
  YES             0               8
[1] 2 2
[1] FALSE
D425V9, binary
                 cls
clus                0   1
  EP300 MUTATED    26  10
  EP300 WILD-TYPE 288  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     26   10
  EP300 WILD-TYPE  288   38
                               clus
vv                              EP300 MUTATED EP300 WILD-TYPE
  COLON ADENOCARCINOMA                     26             288
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED    28   0   1   2
  EP300 WILD-TYPE 231   3  21  19
D425V10, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0            28             231
  R1             0               3
  R2             1              21
  RX             2              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"
D425V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     3
  EP300 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED                           4    16
  EP300 WILD-TYPE                        15   160
D425V12, multiclass
                                  clus
vv                                 EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       16             160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(426) Variable = ITGAV MUTATION ANALYSIS
D426V1, survival
                 sevent
clus2               0   1
  ITGAV MUTATED    13   2
  ITGAV WILD-TYPE 264  76
  ITGAV MUTATED ITGAV WILD-TYPE 
             15             340 
  ITGAV MUTATED ITGAV WILD-TYPE 
              2              76 
$`ITGAV MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6628 TCGA-AA-3655 TCGA-AA-3663 TCGA-AY-4070 
       24.00       100.01        79.69        61.02         6.97        16.31 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5861 TCGA-CM-6674 
       21.44        58.39        12.76       148.01        15.02        12.95 
TCGA-D5-6923 TCGA-F4-6856 TCGA-G4-6306 
       12.43        35.31        44.68 

$`ITGAV WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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          22.045 
[1] "7.0 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "2.5"
D426V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGAV MUTATED         3        0        3         6         0         0
  ITGAV WILD-TYPE      61        1       23       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGAV MUTATED           1          0          0          1        0         0
  ITGAV WILD-TYPE        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  ITGAV MUTATED           0
  ITGAV WILD-TYPE         1
D426V3, multiclass
            clus
vv           ITGAV MUTATED ITGAV WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ITGAV MUTATED     0   4  11   0
  ITGAV WILD-TYPE   9  63 238  41
D426V4, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  T1             0               9
  T2             4              63
  T3            11             238
  T4             0              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
  ITGAV MUTATED    13   1   1
  ITGAV WILD-TYPE 207  80  65
D426V5, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  N0            13             207
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V6, binary
                 cls
clus                0   1
  ITGAV MUTATED    14   0
  ITGAV WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     14    0
  ITGAV WILD-TYPE  271   48
   clus
vv  ITGAV MUTATED ITGAV WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D426V7, binary
                 cls
clus                0   1
  ITGAV MUTATED     4  11
  ITGAV WILD-TYPE 166 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      4   11
  ITGAV WILD-TYPE  166  186
        clus
vv       ITGAV MUTATED ITGAV WILD-TYPE
  FEMALE             4             166
  MALE              11             186
[1] 2 2
[1] FALSE
D426V8, binary
                 cls
clus                0   1
  ITGAV MUTATED    15   0
  ITGAV WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     15    0
  ITGAV WILD-TYPE  285    8
     clus
vv    ITGAV MUTATED ITGAV WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D426V9, binary
                 cls
clus                0   1
  ITGAV MUTATED    12   3
  ITGAV WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     12    3
  ITGAV WILD-TYPE  302   45
                               clus
vv                              ITGAV MUTATED ITGAV WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITGAV MUTATED    12   1   0   1
  ITGAV WILD-TYPE 247   2  22  20
D426V10, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  R0            12             247
  R1             1               2
  R2             0              22
  RX             1              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"
D426V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGAV MUTATED                                  0     1
  ITGAV WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGAV MUTATED                           1    10
  ITGAV WILD-TYPE                        18   166
D426V12, multiclass
                                  clus
vv                                 ITGAV MUTATED ITGAV WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(427) Variable = PPP1R3A MUTATION ANALYSIS
D427V1, survival
                   sevent
clus2                 0   1
  PPP1R3A MUTATED    22   8
  PPP1R3A WILD-TYPE 255  70
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               30               325 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
                8                70 
$`PPP1R3A MUTATED`
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6964 TCGA-AZ-6608 TCGA-A6-6648 
        6.05         0.92        19.04        10.88         1.94        25.18 
TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3848 
       24.69         3.02        63.98        61.02        78.08        10.06 
TCGA-AA-3852 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6963 
        0.00        25.02         4.01        34.98         1.02        27.42 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6675 
       58.39        12.76        10.06        15.02        14.04        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 

$`PPP1R3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       13.02        17.95        23.01        19.99        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       15.52        25.08       106.75       100.01        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 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-A6-6651 
       32.71        27.09        22.52         8.38        25.08        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-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 
       54.61        19.59        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
      117.07         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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
                0                 0 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
           131.51            148.01 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
           18.085            22.090 
[1] "0.0 - 131.5 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D427V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP1R3A MUTATED         1        0        5        10         3         0
  PPP1R3A WILD-TYPE      63        1       21        98         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R3A MUTATED           1          1          1          2        2
  PPP1R3A WILD-TYPE        17          5         43         31       33
                   vv
clus                STAGE IVA STAGE IVB
  PPP1R3A MUTATED           2         1
  PPP1R3A WILD-TYPE        10         0
D427V3, multiclass
            clus
vv           PPP1R3A MUTATED PPP1R3A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 5                21
  STAGE IIA               10                98
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               1                43
  STAGE IIIC               2                31
  STAGE IV                 2                33
  STAGE IVA                2                10
  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     1   2  24   5
  PPP1R3A WILD-TYPE   8  65 225  36
D427V4, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  T1               1                 8
  T2               2                65
  T3              24               225
  T4               5                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
  PPP1R3A MUTATED    24   2   6
  PPP1R3A WILD-TYPE 196  79  60
D427V5, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  N0              24               196
  N1               2                79
  N2               6                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V6, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    23   5
  PPP1R3A WILD-TYPE 262  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     23    5
  PPP1R3A WILD-TYPE  262   43
   clus
vv  PPP1R3A MUTATED PPP1R3A WILD-TYPE
  0              23               262
  1               5                43
[1] 2 2
[1] FALSE
D427V7, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    12  20
  PPP1R3A WILD-TYPE 158 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     12   20
  PPP1R3A WILD-TYPE  158  177
        clus
vv       PPP1R3A MUTATED PPP1R3A WILD-TYPE
  FEMALE              12               158
  MALE                20               177
[1] 2 2
[1] FALSE
D427V8, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    23   1
  PPP1R3A WILD-TYPE 277   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     23    1
  PPP1R3A WILD-TYPE  277    7
     clus
vv    PPP1R3A MUTATED PPP1R3A WILD-TYPE
  NO               23               277
  YES               1                 7
[1] 2 2
[1] FALSE
D427V9, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    28   4
  PPP1R3A WILD-TYPE 286  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     28    4
  PPP1R3A WILD-TYPE  286   44
                               clus
vv                              PPP1R3A MUTATED PPP1R3A WILD-TYPE
  COLON ADENOCARCINOMA                       28               286
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PPP1R3A MUTATED    18   0   2   3
  PPP1R3A WILD-TYPE 241   3  20  18
D427V10, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               2                20
  RX               3                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"
D427V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP1R3A MUTATED                                  0     2
  PPP1R3A WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP1R3A MUTATED                           2    14
  PPP1R3A WILD-TYPE                        17   162
D427V12, multiclass
                                  clus
vv                                 PPP1R3A MUTATED PPP1R3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         14               162
[1] 4 2
[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 = PTPN11 MUTATION ANALYSIS
D428V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED    19   9
  PTPN11 WILD-TYPE 258  69
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              28              327 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9               69 
$`PTPN11 MUTATED`
TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6588 
       85.05        10.88       100.01         1.94        63.62        26.17 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3977 TCGA-AZ-6598 TCGA-AZ-6599 
       29.95        61.02        78.08        25.02        49.41         6.77 
TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-5862 TCGA-CM-6675 TCGA-CM-6676 
       10.06        21.99        82.95         5.03        13.05        11.08 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-DM-A0X9 TCGA-DM-A1HA TCGA-DM-A28F 
       43.27        15.12        17.13       119.70       131.51        35.97 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       74.56        65.85        44.68        55.04 

$`PTPN11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-CK-5912 
       39.06        21.37        15.52        25.08       106.75        49.08 
TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        22.09        35.80        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       24.00        20.98        13.94         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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 
       54.61        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 
       25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 
       47.41        35.31       133.18        53.62        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PTPN11 MUTATED PTPN11 WILD-TYPE 
            1.94             0.00 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
          131.51           148.01 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           39.62            21.99 
[1] "1.9 - 131.5 (39.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D428V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN11 MUTATED         3        0        5         6         0         0
  PTPN11 WILD-TYPE      61        1       21       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN11 MUTATED           1          1          6          2        1
  PTPN11 WILD-TYPE        17          5         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PTPN11 MUTATED           1         1
  PTPN11 WILD-TYPE        11         0
D428V3, multiclass
            clus
vv           PTPN11 MUTATED PTPN11 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              6               38
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               1               11
  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   6  23   1
  PTPN11 WILD-TYPE   9  61 226  40
D428V4, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  T1              0                9
  T2              6               61
  T3             23              226
  T4              1               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
  PTPN11 MUTATED    16   8   6
  PTPN11 WILD-TYPE 204  73  60
D428V5, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  N0             16              204
  N1              8               73
  N2              6               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V6, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    19   3
  PTPN11 WILD-TYPE 266  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     19    3
  PTPN11 WILD-TYPE  266   45
   clus
vv  PTPN11 MUTATED PTPN11 WILD-TYPE
  0             19              266
  1              3               45
[1] 2 2
[1] FALSE
D428V7, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    12  18
  PTPN11 WILD-TYPE 158 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     12   18
  PTPN11 WILD-TYPE  158  179
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  FEMALE             12              158
  MALE               18              179
[1] 2 2
[1] FALSE
D428V8, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    23   1
  PTPN11 WILD-TYPE 277   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     23    1
  PTPN11 WILD-TYPE  277    7
     clus
vv    PTPN11 MUTATED PTPN11 WILD-TYPE
  NO              23              277
  YES              1                7
[1] 2 2
[1] FALSE
D428V9, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    28   2
  PTPN11 WILD-TYPE 286  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     28    2
  PTPN11 WILD-TYPE  286   46
                               clus
vv                              PTPN11 MUTATED PTPN11 WILD-TYPE
  COLON ADENOCARCINOMA                      28              286
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPN11 MUTATED    16   0   0   5
  PTPN11 WILD-TYPE 243   3  22  16
D428V10, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  R0             16              243
  R1              0                3
  R2              0               22
  RX              5               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"
D428V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN11 MUTATED                                  0     1
  PTPN11 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN11 MUTATED                           1    22
  PTPN11 WILD-TYPE                        18   154
D428V12, multiclass
                                  clus
vv                                 PTPN11 MUTATED PTPN11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        22              154
[1] 4 2
[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 = KIAA1409 MUTATION ANALYSIS
D429V1, survival
                    sevent
clus2                  0   1
  KIAA1409 MUTATED    30   8
  KIAA1409 WILD-TYPE 247  70
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                38                317 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                 8                 70 
$`KIAA1409 MUTATED`
TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3713 TCGA-A6-2672 
        1.02         8.05        23.01         0.92        19.04        46.65 
TCGA-A6-5659 TCGA-A6-5662 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3680 
       30.44        23.61         3.02        63.98        78.08        11.01 
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        12.16        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        13.35        12.00 
TCGA-DM-A1D7 TCGA-G4-6304 
       13.32        53.62 

$`KIAA1409 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        10.06        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.44        13.41        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                 0                  0 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
             78.08             148.01 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
            13.335             22.520 
[1] "0.0 - 78.1 (13.3)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.2"
D429V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1409 MUTATED         5        0        5        10         3         0
  KIAA1409 WILD-TYPE      59        1       21        98         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1409 MUTATED           2          0          6          2        4
  KIAA1409 WILD-TYPE        16          6         38         31       31
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1409 MUTATED           1         0
  KIAA1409 WILD-TYPE        11         1
D429V3, multiclass
            clus
vv           KIAA1409 MUTATED KIAA1409 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  5                 21
  STAGE IIA                10                 98
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                0                  6
  STAGE IIIB                6                 38
  STAGE IIIC                2                 31
  STAGE IV                  4                 31
  STAGE IVA                 1                 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
  KIAA1409 MUTATED     0   6  24   9
  KIAA1409 WILD-TYPE   9  61 225  32
D429V4, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  T1                0                  9
  T2                6                 61
  T3               24                225
  T4                9                 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
  KIAA1409 MUTATED    25   7   7
  KIAA1409 WILD-TYPE 195  74  59
D429V5, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  N0               25                195
  N1                7                 74
  N2                7                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V6, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    32   5
  KIAA1409 WILD-TYPE 253  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     32    5
  KIAA1409 WILD-TYPE  253   43
   clus
vv  KIAA1409 MUTATED KIAA1409 WILD-TYPE
  0               32                253
  1                5                 43
[1] 2 2
[1] FALSE
D429V7, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    17  22
  KIAA1409 WILD-TYPE 153 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     17   22
  KIAA1409 WILD-TYPE  153  175
        clus
vv       KIAA1409 MUTATED KIAA1409 WILD-TYPE
  FEMALE               17                153
  MALE                 22                175
[1] 2 2
[1] FALSE
D429V8, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    30   2
  KIAA1409 WILD-TYPE 270   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     30    2
  KIAA1409 WILD-TYPE  270    6
     clus
vv    KIAA1409 MUTATED KIAA1409 WILD-TYPE
  NO                30                270
  YES                2                  6
[1] 2 2
[1] FALSE
D429V9, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    29   8
  KIAA1409 WILD-TYPE 285  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     29    8
  KIAA1409 WILD-TYPE  285   40
                               clus
vv                              KIAA1409 MUTATED KIAA1409 WILD-TYPE
  COLON ADENOCARCINOMA                        29                285
  COLON MUCINOUS ADENOCARCINOMA                8                 40
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1409 MUTATED    29   0   3   3
  KIAA1409 WILD-TYPE 230   3  19  18
D429V10, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  R0               29                230
  R1                0                  3
  R2                3                 19
  RX                3                 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"
D429V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1409 MUTATED                                  0     2
  KIAA1409 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1409 MUTATED                           1    18
  KIAA1409 WILD-TYPE                        18   158
D429V12, multiclass
                                  clus
vv                                 KIAA1409 MUTATED KIAA1409 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          18                158
[1] 4 2
[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 = EPHA3 MUTATION ANALYSIS
D430V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    39  16
  EPHA3 WILD-TYPE 238  62
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             55             300 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             16              62 
$`EPHA3 MUTATED`
TCGA-AA-3516 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6321 TCGA-G4-6588 
       13.02        19.00        19.04        24.00        22.09        26.17 
TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3544 
       29.19        33.53         3.02        35.01        63.98        14.01 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3811 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3861 
       13.94        61.02        10.06        15.95         0.00        30.05 
TCGA-AA-3869 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6889 
       27.02        26.01         2.01        30.02        34.98        83.24 
TCGA-AD-6899 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-5403 TCGA-AZ-6600 
        5.79        26.47        27.09        33.01        62.79        12.10 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5344 TCGA-CM-6162 
       12.76        15.62        51.32        21.14        22.03        12.00 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6533 TCGA-D5-6540 
       14.04        12.95        12.03        54.61        25.48        16.14 
TCGA-D5-6541 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D7 
       15.58         9.04        11.64        13.35       130.65        13.32 
TCGA-DM-A1HB TCGA-DM-A28G TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 
      135.65        60.79        31.96        65.85        44.68        85.48 
TCGA-G4-6626 
       46.75 

$`EPHA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        63.62        35.80        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3511 
       23.87        20.12        19.66        20.28         7.04         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        12.99        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       24.00        29.95        20.98        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        17.03        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6901 
       39.98        18.05        40.96        12.16        24.53        22.42 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       27.42        14.50        16.31         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        22.36        88.21 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 
       10.06        14.30        17.56       148.01        85.45        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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 
       14.04        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.44        13.41        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-A28C 
      140.38         7.50        44.32       131.51       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
      119.93        35.97       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       74.56        53.62        55.04        61.91        36.00        13.78 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
              0               0 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         135.65          148.01 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
          24.00           21.99 
[1] "0.0 - 135.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D430V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA3 MUTATED         6        0        4        21         2         0
  EPHA3 WILD-TYPE      58        1       22        87         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA3 MUTATED           3          0          9          4        5         1
  EPHA3 WILD-TYPE        15          6         35         29       30        11
                 vv
clus              STAGE IVB
  EPHA3 MUTATED           0
  EPHA3 WILD-TYPE         1
D430V3, multiclass
            clus
vv           EPHA3 MUTATED EPHA3 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             21              87
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             9              35
  STAGE IIIC             4              29
  STAGE IV               5              30
  STAGE IVA              1              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
  EPHA3 MUTATED     1   7  40   9
  EPHA3 WILD-TYPE   8  60 209  32
D430V4, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  T1             1               8
  T2             7              60
  T3            40             209
  T4             9              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
  EPHA3 MUTATED    36  13   8
  EPHA3 WILD-TYPE 184  68  58
D430V5, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0            36             184
  N1            13              68
  N2             8              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"
D430V6, binary
                 cls
clus                0   1
  EPHA3 MUTATED    46   6
  EPHA3 WILD-TYPE 239  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     46    6
  EPHA3 WILD-TYPE  239   42
   clus
vv  EPHA3 MUTATED EPHA3 WILD-TYPE
  0            46             239
  1             6              42
[1] 2 2
[1] FALSE
D430V7, binary
                 cls
clus                0   1
  EPHA3 MUTATED    29  28
  EPHA3 WILD-TYPE 141 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     29   28
  EPHA3 WILD-TYPE  141  169
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE            29             141
  MALE              28             169
[1] 2 2
[1] FALSE
D430V8, binary
                 cls
clus                0   1
  EPHA3 MUTATED    45   2
  EPHA3 WILD-TYPE 255   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     45    2
  EPHA3 WILD-TYPE  255    6
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO             45             255
  YES             2               6
[1] 2 2
[1] FALSE
D430V9, binary
                 cls
clus                0   1
  EPHA3 MUTATED    44  11
  EPHA3 WILD-TYPE 270  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     44   11
  EPHA3 WILD-TYPE  270   37
                               clus
vv                              EPHA3 MUTATED EPHA3 WILD-TYPE
  COLON ADENOCARCINOMA                     44             270
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA3 MUTATED    38   1   3   5
  EPHA3 WILD-TYPE 221   2  19  16
D430V10, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  R0            38             221
  R1             1               2
  R2             3              19
  RX             5              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"
D430V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA3 MUTATED                                  0     2
  EPHA3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA3 MUTATED                           5    30
  EPHA3 WILD-TYPE                        14   146
D430V12, multiclass
                                  clus
vv                                 EPHA3 MUTATED EPHA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       30             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(431) Variable = HFE2 MUTATION ANALYSIS
D431V1, survival
                sevent
clus2              0   1
  HFE2 MUTATED     5   1
  HFE2 WILD-TYPE 272  77
  HFE2 MUTATED HFE2 WILD-TYPE 
             6            349 
  HFE2 MUTATED HFE2 WILD-TYPE 
             1             77 
$`HFE2 MUTATED`
TCGA-AZ-6601 TCGA-AA-3815 TCGA-AA-A03J TCGA-CK-5914 TCGA-G4-6306 TCGA-G4-6315 
      100.01        33.04        40.96        21.99        44.68        61.91 

$`HFE2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-AD-5900 
       14.01         0.92        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6317 TCGA-G4-6323 
       65.85        53.62        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  HFE2 MUTATED HFE2 WILD-TYPE 
         21.99           0.00 
  HFE2 MUTATED HFE2 WILD-TYPE 
        100.01         148.01 
  HFE2 MUTATED HFE2 WILD-TYPE 
         42.82          21.99 
[1] "22.0 - 100.0 (42.8)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.4"
D431V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HFE2 MUTATED         2        0        2         1         0         0
  HFE2 WILD-TYPE      62        1       24       107         8         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  HFE2 MUTATED           0
  HFE2 WILD-TYPE         1
D431V3, multiclass
            clus
vv           HFE2 MUTATED HFE2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  HFE2 MUTATED     0   3   4   1
  HFE2 WILD-TYPE   9  64 245  40
D431V4, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            4            245
  T4            1             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
  HFE2 MUTATED     6   2   0
  HFE2 WILD-TYPE 214  79  66
D431V5, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  N0            6            214
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V6, binary
                cls
clus               0   1
  HFE2 MUTATED     5   1
  HFE2 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      5    1
  HFE2 WILD-TYPE  280   47
   clus
vv  HFE2 MUTATED HFE2 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D431V7, binary
                cls
clus               0   1
  HFE2 MUTATED     3   5
  HFE2 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      3    5
  HFE2 WILD-TYPE  167  192
        clus
vv       HFE2 MUTATED HFE2 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D431V8, binary
                cls
clus               0   1
  HFE2 MUTATED     5   0
  HFE2 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      5    0
  HFE2 WILD-TYPE  295    8
     clus
vv    HFE2 MUTATED HFE2 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D431V9, binary
                cls
clus               0   1
  HFE2 MUTATED     8   0
  HFE2 WILD-TYPE 306  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      8    0
  HFE2 WILD-TYPE  306   48
                               clus
vv                              HFE2 MUTATED HFE2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HFE2 MUTATED     5   0   0   2
  HFE2 WILD-TYPE 254   3  22  19
D431V10, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            2             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"
D431V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HFE2 MUTATED                                  0     0
  HFE2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HFE2 MUTATED                           0     5
  HFE2 WILD-TYPE                        19   171
D431V12, multiclass
                                  clus
vv                                 HFE2 MUTATED HFE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = MYH1 MUTATION ANALYSIS
D432V1, survival
                sevent
clus2              0   1
  MYH1 MUTATED    23   8
  MYH1 WILD-TYPE 254  70
  MYH1 MUTATED MYH1 WILD-TYPE 
            31            324 
  MYH1 MUTATED MYH1 WILD-TYPE 
             8             70 
$`MYH1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5666 
      100.01        35.80        30.44        29.19        33.53        32.71 
TCGA-AA-3492 TCGA-AA-3818 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 
        3.02         0.99         2.01        25.02        18.05        34.98 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-4948 
       83.24        24.53        58.39         5.23        12.76       148.01 
TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6676 
       51.32        23.05        15.02        12.00        14.99        11.08 
TCGA-D5-6535 TCGA-D5-6922 TCGA-D5-6923 TCGA-DM-A1D8 TCGA-DM-A28F TCGA-G4-6306 
       15.12        10.13        12.43        12.59        35.97        44.68 
TCGA-G4-6626 
       46.75 

$`MYH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       36.53        32.91        31.63        23.61        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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6899 TCGA-AD-6901 TCGA-AD-6963 
       18.05        40.96        12.16         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.20        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       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-5864 
       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        14.04        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-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 
       54.61        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 
       25.48        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 
       16.14        15.58         7.53        12.39        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 

  MYH1 MUTATED MYH1 WILD-TYPE 
          0.99           0.00 
  MYH1 MUTATED MYH1 WILD-TYPE 
        148.01         140.38 
  MYH1 MUTATED MYH1 WILD-TYPE 
         24.53          22.01 
[1] "1.0 - 148.0 (24.5)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D432V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH1 MUTATED         3        0        2        11         1         1
  MYH1 WILD-TYPE      61        1       24        97         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH1 MUTATED           1          1          6          2        0         0
  MYH1 WILD-TYPE        17          5         38         31       35        12
                vv
clus             STAGE IVB
  MYH1 MUTATED           0
  MYH1 WILD-TYPE         1
D432V3, multiclass
            clus
vv           MYH1 MUTATED MYH1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            11             97
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            6             38
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  MYH1 MUTATED     1   5  22   4
  MYH1 WILD-TYPE   8  62 227  37
D432V4, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  T1            1              8
  T2            5             62
  T3           22            227
  T4            4             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
  MYH1 MUTATED    21   9   2
  MYH1 WILD-TYPE 199  72  64
D432V5, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  N0           21            199
  N1            9             72
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V6, binary
                cls
clus               0   1
  MYH1 MUTATED    27   0
  MYH1 WILD-TYPE 258  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     27    0
  MYH1 WILD-TYPE  258   48
   clus
vv  MYH1 MUTATED MYH1 WILD-TYPE
  0           27            258
  1            0             48
[1] 2 2
[1] FALSE
D432V7, binary
                cls
clus               0   1
  MYH1 MUTATED    14  18
  MYH1 WILD-TYPE 156 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     14   18
  MYH1 WILD-TYPE  156  179
        clus
vv       MYH1 MUTATED MYH1 WILD-TYPE
  FEMALE           14            156
  MALE             18            179
[1] 2 2
[1] FALSE
D432V8, binary
                cls
clus               0   1
  MYH1 MUTATED    27   0
  MYH1 WILD-TYPE 273   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     27    0
  MYH1 WILD-TYPE  273    8
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  NO            27            273
  YES            0              8
[1] 2 2
[1] FALSE
D432V9, binary
                cls
clus               0   1
  MYH1 MUTATED    27   5
  MYH1 WILD-TYPE 287  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     27    5
  MYH1 WILD-TYPE  287   43
                               clus
vv                              MYH1 MUTATED MYH1 WILD-TYPE
  COLON ADENOCARCINOMA                    27            287
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYH1 MUTATED    20   0   0   3
  MYH1 WILD-TYPE 239   3  22  18
D432V10, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  R0           20            239
  R1            0              3
  R2            0             22
  RX            3             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"
D432V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH1 MUTATED                                  0     2
  MYH1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH1 MUTATED                           3    20
  MYH1 WILD-TYPE                        16   156
D432V12, multiclass
                                  clus
vv                                 MYH1 MUTATED MYH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      20            156
[1] 4 2
[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 = EEA1 MUTATION ANALYSIS
D433V1, survival
                sevent
clus2              0   1
  EEA1 MUTATED    10   3
  EEA1 WILD-TYPE 267  75
  EEA1 MUTATED EEA1 WILD-TYPE 
            13            342 
  EEA1 MUTATED EEA1 WILD-TYPE 
             3             75 
$`EEA1 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3947 TCGA-AA-A010 
       19.04        19.04        22.06        63.98        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 
       35.31 

$`EEA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  EEA1 MUTATED EEA1 WILD-TYPE 
          6.18           0.00 
  EEA1 MUTATED EEA1 WILD-TYPE 
         63.98         148.01 
  EEA1 MUTATED EEA1 WILD-TYPE 
         22.06          22.06 
[1] "6.2 - 64.0 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D433V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EEA1 MUTATED         2        0        2         5         2         0
  EEA1 WILD-TYPE      62        1       24       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EEA1 MUTATED           0          0          0          1        1         0
  EEA1 WILD-TYPE        18          6         44         32       34        12
                vv
clus             STAGE IVB
  EEA1 MUTATED           0
  EEA1 WILD-TYPE         1
D433V3, multiclass
            clus
vv           EEA1 MUTATED EEA1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  EEA1 MUTATED     0   2   9   2
  EEA1 WILD-TYPE   9  65 240  39
D433V4, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            9            240
  T4            2             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
  EEA1 MUTATED    12   0   1
  EEA1 WILD-TYPE 208  81  65
D433V5, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  N0           12            208
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V6, binary
                cls
clus               0   1
  EEA1 MUTATED    12   1
  EEA1 WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     12    1
  EEA1 WILD-TYPE  273   47
   clus
vv  EEA1 MUTATED EEA1 WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D433V7, binary
                cls
clus               0   1
  EEA1 MUTATED     5   8
  EEA1 WILD-TYPE 165 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED      5    8
  EEA1 WILD-TYPE  165  189
        clus
vv       EEA1 MUTATED EEA1 WILD-TYPE
  FEMALE            5            165
  MALE              8            189
[1] 2 2
[1] FALSE
D433V8, binary
                cls
clus               0   1
  EEA1 MUTATED    11   1
  EEA1 WILD-TYPE 289   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     11    1
  EEA1 WILD-TYPE  289    7
     clus
vv    EEA1 MUTATED EEA1 WILD-TYPE
  NO            11            289
  YES            1              7
[1] 2 2
[1] FALSE
D433V9, binary
                cls
clus               0   1
  EEA1 MUTATED    10   3
  EEA1 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     10    3
  EEA1 WILD-TYPE  304   45
                               clus
vv                              EEA1 MUTATED EEA1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EEA1 MUTATED    10   0   1   1
  EEA1 WILD-TYPE 249   3  21  20
D433V10, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            1             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"
D433V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEA1 MUTATED                                  0     1
  EEA1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EEA1 MUTATED                           1     6
  EEA1 WILD-TYPE                        18   170
D433V12, multiclass
                                  clus
vv                                 EEA1 MUTATED EEA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = GRM7 MUTATION ANALYSIS
D434V1, survival
                sevent
clus2              0   1
  GRM7 MUTATED    18   4
  GRM7 WILD-TYPE 259  74
  GRM7 MUTATED GRM7 WILD-TYPE 
            22            333 
  GRM7 MUTATED GRM7 WILD-TYPE 
             4             74 
$`GRM7 MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3844 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-3809 
        6.05        85.05        14.93       100.01        79.69        32.75 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3680 TCGA-AA-3947 
       33.53        22.06         8.38        24.69        11.01        33.01 
TCGA-AA-A00N TCGA-AA-A02W TCGA-AU-6004 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-5913 
        4.01        41.00        27.09         6.77        12.76        51.32 
TCGA-CM-6165 TCGA-CM-6171 TCGA-F4-6807 TCGA-G4-6309 
       16.04        14.04        43.04        85.48 

$`GRM7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        19.04        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-3810 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-A6-5662 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-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GRM7 MUTATED GRM7 WILD-TYPE 
          4.01           0.00 
  GRM7 MUTATED GRM7 WILD-TYPE 
        100.01         148.01 
  GRM7 MUTATED GRM7 WILD-TYPE 
         25.89          21.99 
[1] "4.0 - 100.0 (25.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D434V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM7 MUTATED         6        0        2         8         3         0
  GRM7 WILD-TYPE      58        1       24       100         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRM7 MUTATED           0          0          1          2        2         1
  GRM7 WILD-TYPE        18          6         43         31       33        11
                vv
clus             STAGE IVB
  GRM7 MUTATED           0
  GRM7 WILD-TYPE         1
D434V3, multiclass
            clus
vv           GRM7 MUTATED GRM7 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              2             33
  STAGE IVA             1             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
  GRM7 MUTATED     0   6  14   5
  GRM7 WILD-TYPE   9  61 235  36
D434V4, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  T1            0              9
  T2            6             61
  T3           14            235
  T4            5             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
  GRM7 MUTATED    20   1   4
  GRM7 WILD-TYPE 200  80  62
D434V5, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  N0           20            200
  N1            1             80
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V6, binary
                cls
clus               0   1
  GRM7 MUTATED    19   3
  GRM7 WILD-TYPE 266  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     19    3
  GRM7 WILD-TYPE  266   45
   clus
vv  GRM7 MUTATED GRM7 WILD-TYPE
  0           19            266
  1            3             45
[1] 2 2
[1] FALSE
D434V7, binary
                cls
clus               0   1
  GRM7 MUTATED    15  10
  GRM7 WILD-TYPE 155 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     15   10
  GRM7 WILD-TYPE  155  187
        clus
vv       GRM7 MUTATED GRM7 WILD-TYPE
  FEMALE           15            155
  MALE             10            187
[1] 2 2
[1] FALSE
D434V8, binary
                cls
clus               0   1
  GRM7 MUTATED    19   1
  GRM7 WILD-TYPE 281   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     19    1
  GRM7 WILD-TYPE  281    7
     clus
vv    GRM7 MUTATED GRM7 WILD-TYPE
  NO            19            281
  YES            1              7
[1] 2 2
[1] FALSE
D434V9, binary
                cls
clus               0   1
  GRM7 MUTATED    21   4
  GRM7 WILD-TYPE 293  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     21    4
  GRM7 WILD-TYPE  293   44
                               clus
vv                              GRM7 MUTATED GRM7 WILD-TYPE
  COLON ADENOCARCINOMA                    21            293
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GRM7 MUTATED    16   0   2   3
  GRM7 WILD-TYPE 243   3  20  18
D434V10, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            2             20
  RX            3             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"
D434V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRM7 MUTATED                                  0     1
  GRM7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRM7 MUTATED                           4    11
  GRM7 WILD-TYPE                        15   165
D434V12, multiclass
                                  clus
vv                                 GRM7 MUTATED GRM7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      11            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(435) Variable = GRM8 MUTATION ANALYSIS
D435V1, survival
                sevent
clus2              0   1
  GRM8 MUTATED    13   7
  GRM8 WILD-TYPE 264  71
  GRM8 MUTATED GRM8 WILD-TYPE 
            20            335 
  GRM8 MUTATED GRM8 WILD-TYPE 
             7             71 
$`GRM8 MUTATED`
TCGA-AA-3715 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3489 TCGA-AA-3977 TCGA-AA-A00N 
       19.04        33.53        22.06         7.04        25.02         4.01 
TCGA-AA-A010 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6717 
       34.98         0.20        58.39        62.79        49.41        12.76 
TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-6677 TCGA-D5-6927 TCGA-F4-6805 TCGA-F4-6856 
       10.06        32.02        11.08         9.44        34.42        35.31 
TCGA-G4-6303 TCGA-G4-6309 
       65.85        85.48 

$`GRM8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-4682 
       33.01        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  GRM8 MUTATED GRM8 WILD-TYPE 
           0.2            0.0 
  GRM8 MUTATED GRM8 WILD-TYPE 
         85.48         148.01 
  GRM8 MUTATED GRM8 WILD-TYPE 
         28.52          21.99 
[1] "0.2 - 85.5 (28.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D435V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM8 MUTATED         1        0        4         9         3         0
  GRM8 WILD-TYPE      63        1       22        99         5         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        18          6         43         32       34        12
                vv
clus             STAGE IVB
  GRM8 MUTATED           0
  GRM8 WILD-TYPE         1
D435V3, multiclass
            clus
vv           GRM8 MUTATED GRM8 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             9             99
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  GRM8 MUTATED     0   2  16   3
  GRM8 WILD-TYPE   9  65 233  38
D435V4, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           16            233
  T4            3             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
  GRM8 MUTATED    18   2   1
  GRM8 WILD-TYPE 202  79  65
D435V5, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  N0           18            202
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V6, binary
                cls
clus               0   1
  GRM8 MUTATED    15   1
  GRM8 WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     15    1
  GRM8 WILD-TYPE  270   47
   clus
vv  GRM8 MUTATED GRM8 WILD-TYPE
  0           15            270
  1            1             47
[1] 2 2
[1] FALSE
D435V7, binary
                cls
clus               0   1
  GRM8 MUTATED     9  12
  GRM8 WILD-TYPE 161 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED      9   12
  GRM8 WILD-TYPE  161  185
        clus
vv       GRM8 MUTATED GRM8 WILD-TYPE
  FEMALE            9            161
  MALE             12            185
[1] 2 2
[1] FALSE
D435V8, binary
                cls
clus               0   1
  GRM8 MUTATED    18   0
  GRM8 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     18    0
  GRM8 WILD-TYPE  282    8
     clus
vv    GRM8 MUTATED GRM8 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D435V9, binary
                cls
clus               0   1
  GRM8 MUTATED    17   4
  GRM8 WILD-TYPE 297  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     17    4
  GRM8 WILD-TYPE  297   44
                               clus
vv                              GRM8 MUTATED GRM8 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GRM8 MUTATED    15   0   0   3
  GRM8 WILD-TYPE 244   3  22  18
D435V10, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  R0           15            244
  R1            0              3
  R2            0             22
  RX            3             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"
D435V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRM8 MUTATED                                  0     2
  GRM8 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRM8 MUTATED                           2    12
  GRM8 WILD-TYPE                        17   164
D435V12, multiclass
                                  clus
vv                                 GRM8 MUTATED GRM8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      12            164
[1] 4 2
[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 = TAF1 MUTATION ANALYSIS
D436V1, survival
                sevent
clus2              0   1
  TAF1 MUTATED    15   7
  TAF1 WILD-TYPE 262  71
  TAF1 MUTATED TAF1 WILD-TYPE 
            22            333 
  TAF1 MUTATED TAF1 WILD-TYPE 
             7             71 
$`TAF1 MUTATED`
TCGA-AA-3697 TCGA-A6-2683 TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3864 TCGA-AA-3977 
       85.05        16.57        31.63        22.06        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        10.13        11.64 
TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A28E TCGA-G4-6309 
       24.43         7.50       119.93        85.48 

$`TAF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        42.28        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5863 
       29.06        22.03        22.98        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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       12.39        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28F 
       44.32       131.51       135.65       139.17        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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         22.090 
[1] "4.0 - 119.9 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D436V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF1 MUTATED         2        0        2         8         2         0
  TAF1 WILD-TYPE      62        1       24       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF1 MUTATED           1          1          2          1        1         1
  TAF1 WILD-TYPE        17          5         42         32       34        11
                vv
clus             STAGE IVB
  TAF1 MUTATED           0
  TAF1 WILD-TYPE         1
D436V3, multiclass
            clus
vv           TAF1 MUTATED TAF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  TAF1 MUTATED     0   3  16   3
  TAF1 WILD-TYPE   9  64 233  38
D436V4, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           16            233
  T4            3             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
  TAF1 MUTATED    16   4   2
  TAF1 WILD-TYPE 204  77  64
D436V5, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  N0           16            204
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V6, binary
                cls
clus               0   1
  TAF1 MUTATED    19   2
  TAF1 WILD-TYPE 266  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     19    2
  TAF1 WILD-TYPE  266   46
   clus
vv  TAF1 MUTATED TAF1 WILD-TYPE
  0           19            266
  1            2             46
[1] 2 2
[1] FALSE
D436V7, binary
                cls
clus               0   1
  TAF1 MUTATED     9  13
  TAF1 WILD-TYPE 161 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED      9   13
  TAF1 WILD-TYPE  161  184
        clus
vv       TAF1 MUTATED TAF1 WILD-TYPE
  FEMALE            9            161
  MALE             13            184
[1] 2 2
[1] FALSE
D436V8, binary
                cls
clus               0   1
  TAF1 MUTATED    18   0
  TAF1 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     18    0
  TAF1 WILD-TYPE  282    8
     clus
vv    TAF1 MUTATED TAF1 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D436V9, binary
                cls
clus               0   1
  TAF1 MUTATED    18   4
  TAF1 WILD-TYPE 296  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     18    4
  TAF1 WILD-TYPE  296   44
                               clus
vv                              TAF1 MUTATED TAF1 WILD-TYPE
  COLON ADENOCARCINOMA                    18            296
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAF1 MUTATED    16   0   0   2
  TAF1 WILD-TYPE 243   3  22  19
D436V10, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            2             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"
D436V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF1 MUTATED                                  0     2
  TAF1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF1 MUTATED                           2    12
  TAF1 WILD-TYPE                        17   164
D436V12, multiclass
                                  clus
vv                                 TAF1 MUTATED TAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      12            164
[1] 4 2
[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 = ANKRD30A MUTATION ANALYSIS
D437V1, survival
                    sevent
clus2                  0   1
  ANKRD30A MUTATED    21   6
  ANKRD30A WILD-TYPE 256  72
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                27                328 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 6                 72 
$`ANKRD30A MUTATED`
TCGA-A6-4105 TCGA-G4-6588 TCGA-A6-5656 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       14.53        26.17        32.91        22.52         8.38        25.08 
TCGA-AA-3660 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-5900 TCGA-AU-3779 
       78.08        25.02        34.98        37.02        12.16        14.50 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-5862 
       58.39        12.59        12.76        10.06       124.27         5.03 
TCGA-CM-6164 TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6931 TCGA-DM-A28E TCGA-DM-A28F 
       29.03        12.99        45.40        12.00       119.93        35.97 
TCGA-F4-6703 TCGA-G4-6303 TCGA-G4-6307 
       47.87        65.85        55.04 

$`ANKRD30A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6651 
       22.09        22.06        32.71        27.09        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.36        12.39        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H TCGA-DM-A28K 
      135.65       139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
              5.03               0.00 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
            124.27             148.01 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
             26.17              21.99 
[1] "5.0 - 124.3 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D437V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD30A MUTATED         4        0        2        12         1         0
  ANKRD30A WILD-TYPE      60        1       24        96         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD30A MUTATED           1          0          3          1        1
  ANKRD30A WILD-TYPE        17          6         41         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  ANKRD30A MUTATED           2         0
  ANKRD30A WILD-TYPE        10         1
D437V3, multiclass
            clus
vv           ANKRD30A MUTATED ANKRD30A WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                12                 96
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 2                 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
  ANKRD30A MUTATED     0   5  21   2
  ANKRD30A WILD-TYPE   9  62 228  39
D437V4, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  T1                0                  9
  T2                5                 62
  T3               21                228
  T4                2                 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
  ANKRD30A MUTATED    19   6   3
  ANKRD30A WILD-TYPE 201  75  63
D437V5, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  N0               19                201
  N1                6                 75
  N2                3                 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"
D437V6, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    21   3
  ANKRD30A WILD-TYPE 264  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     21    3
  ANKRD30A WILD-TYPE  264   45
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0               21                264
  1                3                 45
[1] 2 2
[1] FALSE
D437V7, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    11  17
  ANKRD30A WILD-TYPE 159 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     11   17
  ANKRD30A WILD-TYPE  159  180
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  FEMALE               11                159
  MALE                 17                180
[1] 2 2
[1] FALSE
D437V8, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    25   0
  ANKRD30A WILD-TYPE 275   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     25    0
  ANKRD30A WILD-TYPE  275    8
     clus
vv    ANKRD30A MUTATED ANKRD30A WILD-TYPE
  NO                25                275
  YES                0                  8
[1] 2 2
[1] FALSE
D437V9, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    25   3
  ANKRD30A WILD-TYPE 289  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     25    3
  ANKRD30A WILD-TYPE  289   45
                               clus
vv                              ANKRD30A MUTATED ANKRD30A WILD-TYPE
  COLON ADENOCARCINOMA                        25                289
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ANKRD30A MUTATED    15   0   0   5
  ANKRD30A WILD-TYPE 244   3  22  16
D437V10, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  R0               15                244
  R1                0                  3
  R2                0                 22
  RX                5                 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"
D437V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD30A MUTATED                                  0     3
  ANKRD30A WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ANKRD30A MUTATED                           2    18
  ANKRD30A WILD-TYPE                        17   158
D437V12, multiclass
                                  clus
vv                                 ANKRD30A MUTATED ANKRD30A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          18                158
[1] 4 2
[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 = PTPRD MUTATION ANALYSIS
D438V1, survival
                 sevent
clus2               0   1
  PTPRD MUTATED    25   6
  PTPRD WILD-TYPE 252  72
  PTPRD MUTATED PTPRD WILD-TYPE 
             31             324 
  PTPRD MUTATED PTPRD WILD-TYPE 
              6              72 
$`PTPRD MUTATED`
TCGA-A6-2677 TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-5659 TCGA-A6-5660 TCGA-AA-3660 
       24.33        49.08        26.17        30.44        29.19        78.08 
TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       10.06        33.01         2.01        25.02         4.01        34.98 
TCGA-AA-A01P TCGA-AY-6196 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-5913 
       38.07         0.20        62.79        88.21        12.76        51.32 
TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6163 
       23.05        13.02        22.03        32.02        12.00        14.04 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-5540 TCGA-DM-A28E TCGA-DM-A28K 
       14.04        12.95        19.59        56.09       119.93        98.24 
TCGA-G4-6304 
       53.62 

$`PTPRD WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
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        54.61        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        81.37        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PTPRD MUTATED PTPRD WILD-TYPE 
            0.2             0.0 
  PTPRD MUTATED PTPRD WILD-TYPE 
         119.93          148.01 
  PTPRD MUTATED PTPRD WILD-TYPE 
          26.17           21.99 
[1] "0.2 - 119.9 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D438V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRD MUTATED         5        0        2        12         4         0
  PTPRD WILD-TYPE      59        1       24        96         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRD MUTATED           2          1          2          3        0         0
  PTPRD WILD-TYPE        16          5         42         30       35        12
                 vv
clus              STAGE IVB
  PTPRD MUTATED           0
  PTPRD WILD-TYPE         1
D438V3, multiclass
            clus
vv           PTPRD MUTATED PTPRD WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             12              96
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              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
  PTPRD MUTATED     2   4  22   4
  PTPRD WILD-TYPE   7  63 227  37
D438V4, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  T1             2               7
  T2             4              63
  T3            22             227
  T4             4              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
  PTPRD MUTATED    24   4   4
  PTPRD WILD-TYPE 196  77  62
D438V5, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  N0            24             196
  N1             4              77
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V6, binary
                 cls
clus                0   1
  PTPRD MUTATED    27   0
  PTPRD WILD-TYPE 258  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     27    0
  PTPRD WILD-TYPE  258   48
   clus
vv  PTPRD MUTATED PTPRD WILD-TYPE
  0            27             258
  1             0              48
[1] 2 2
[1] FALSE
D438V7, binary
                 cls
clus                0   1
  PTPRD MUTATED    16  16
  PTPRD WILD-TYPE 154 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     16   16
  PTPRD WILD-TYPE  154  181
        clus
vv       PTPRD MUTATED PTPRD WILD-TYPE
  FEMALE            16             154
  MALE              16             181
[1] 2 2
[1] FALSE
D438V8, binary
                 cls
clus                0   1
  PTPRD MUTATED    26   0
  PTPRD WILD-TYPE 274   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     26    0
  PTPRD WILD-TYPE  274    8
     clus
vv    PTPRD MUTATED PTPRD WILD-TYPE
  NO             26             274
  YES             0               8
[1] 2 2
[1] FALSE
D438V9, binary
                 cls
clus                0   1
  PTPRD MUTATED    24   8
  PTPRD WILD-TYPE 290  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     24    8
  PTPRD WILD-TYPE  290   40
                               clus
vv                              PTPRD MUTATED PTPRD WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRD MUTATED    22   0   0   3
  PTPRD WILD-TYPE 237   3  22  18
D438V10, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  R0            22             237
  R1             0               3
  R2             0              22
  RX             3              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"
D438V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRD MUTATED                                  0     1
  PTPRD WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRD MUTATED                           2    20
  PTPRD WILD-TYPE                        17   156
D438V12, multiclass
                                  clus
vv                                 PTPRD MUTATED PTPRD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       20             156
[1] 4 2
[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 = CSMD3 MUTATION ANALYSIS
D439V1, survival
                 sevent
clus2               0   1
  CSMD3 MUTATED    65  19
  CSMD3 WILD-TYPE 212  59
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             84             271 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             19              59 
$`CSMD3 MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       13.02         8.05        17.95        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6586 
       19.04        24.00        25.08       100.01         5.88        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-6137 
       26.17        79.69        42.90        32.75        29.19        27.09 
TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 
        8.38        24.39        23.87        20.12        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3821 TCGA-AA-3861 
       63.98         6.97        29.95        78.08         1.02        30.05 
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-AY-5543 
        4.01        34.98         1.02        37.02        83.24        33.01 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5797 
       58.39        88.21         6.77        29.56        12.69        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-5916 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6167 
       21.14        20.02        13.02        22.98        32.02        14.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6928 
       14.04        12.95        25.48        15.12        16.14        11.64 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1DA 
       13.41        10.26       119.70       130.65        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6807 TCGA-F4-6855 
       44.32       117.07        98.24         8.61        43.04        47.41 
TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6626 
       35.31        65.85        53.62        55.04        36.00        46.75 

$`CSMD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 
       36.03        19.07        34.03         0.99        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3844 
       19.99        19.99         6.05         0.92        19.00        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       63.62        22.09        91.79        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       32.71        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       20.28         7.04        35.01         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       20.98        34.03        16.08        34.06        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 
        5.13        22.36        62.79        49.41        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6719 TCGA-CK-4950 
       11.74         3.19        12.36        12.39        14.30        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       23.05        37.02        25.02        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-6168 
       12.00        14.04        29.03        16.04        21.99        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        54.61        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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
       10.13        12.43        14.30         9.04         9.44        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.00        11.38        24.43        38.20        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       13.32       140.38       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      119.93        35.97        60.79        31.96        35.74         6.18 
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-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
        0.53       133.18        74.56        44.68        85.48        61.91 
TCGA-G4-6323 
       13.78 

  CSMD3 MUTATED CSMD3 WILD-TYPE 
           1.02            0.00 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
         148.01          140.38 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
         23.935          21.990 
[1] "1.0 - 148.0 (23.9)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D439V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSMD3 MUTATED        12        0       10        28         5         0
  CSMD3 WILD-TYPE      52        1       16        80         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CSMD3 MUTATED           2          0         11          7        6         1
  CSMD3 WILD-TYPE        16          6         33         26       29        11
                 vv
clus              STAGE IVB
  CSMD3 MUTATED           0
  CSMD3 WILD-TYPE         1
D439V3, multiclass
            clus
vv           CSMD3 MUTATED CSMD3 WILD-TYPE
  STAGE I               12              52
  STAGE IA               0               1
  STAGE II              10              16
  STAGE IIA             28              80
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB            11              33
  STAGE IIIC             7              26
  STAGE IV               6              29
  STAGE IVA              1              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
  CSMD3 MUTATED     2  12  60  12
  CSMD3 WILD-TYPE   7  55 189  29
D439V4, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  T1             2               7
  T2            12              55
  T3            60             189
  T4            12              29
[1] 4 2
[1] TRUE
[1] "dimension 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    58  18  10
  CSMD3 WILD-TYPE 162  63  56
D439V5, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  N0            58             162
  N1            18              63
  N2            10              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V6, binary
                 cls
clus                0   1
  CSMD3 MUTATED    71   7
  CSMD3 WILD-TYPE 214  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     71    7
  CSMD3 WILD-TYPE  214   41
   clus
vv  CSMD3 MUTATED CSMD3 WILD-TYPE
  0            71             214
  1             7              41
[1] 2 2
[1] FALSE
D439V7, binary
                 cls
clus                0   1
  CSMD3 MUTATED    44  42
  CSMD3 WILD-TYPE 126 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     44   42
  CSMD3 WILD-TYPE  126  155
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  FEMALE            44             126
  MALE              42             155
[1] 2 2
[1] FALSE
D439V8, binary
                 cls
clus                0   1
  CSMD3 MUTATED    71   2
  CSMD3 WILD-TYPE 229   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     71    2
  CSMD3 WILD-TYPE  229    6
     clus
vv    CSMD3 MUTATED CSMD3 WILD-TYPE
  NO             71             229
  YES             2               6
[1] 2 2
[1] FALSE
D439V9, binary
                 cls
clus                0   1
  CSMD3 MUTATED    68  18
  CSMD3 WILD-TYPE 246  30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     68   18
  CSMD3 WILD-TYPE  246   30
                               clus
vv                              CSMD3 MUTATED CSMD3 WILD-TYPE
  COLON ADENOCARCINOMA                     68             246
  COLON MUCINOUS ADENOCARCINOMA            18              30
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CSMD3 MUTATED    54   0   3   8
  CSMD3 WILD-TYPE 205   3  19  13
D439V10, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  R0            54             205
  R1             0               3
  R2             3              19
  RX             8              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"
D439V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSMD3 MUTATED                                  0     7
  CSMD3 WILD-TYPE                                1     3
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSMD3 MUTATED                           5    47
  CSMD3 WILD-TYPE                        14   129
D439V12, multiclass
                                  clus
vv                                 CSMD3 MUTATED CSMD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        7               3
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       47             129
[1] 4 2
[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 = ZCCHC6 MUTATION ANALYSIS
D440V1, survival
                  sevent
clus2                0   1
  ZCCHC6 MUTATED    14   4
  ZCCHC6 WILD-TYPE 263  74
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              18              337 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
               4               74 
$`ZCCHC6 MUTATED`
TCGA-AA-3516 TCGA-AA-3950 TCGA-G4-6628 TCGA-AA-3532 TCGA-AA-3663 TCGA-AA-3681 
       13.02        24.00        79.69        29.00         6.97         5.98 
TCGA-AA-3821 TCGA-AA-A017 TCGA-AA-A02J TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6598 
        1.02        15.02         5.03        83.24        21.44        49.41 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6680 TCGA-DM-A28K TCGA-G4-6309 TCGA-G4-6323 
       12.76        15.62        12.03        98.24        85.48        13.78 

$`ZCCHC6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6626 
       46.75 

  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
            1.02             0.00 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           98.24           148.01 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           15.32            22.09 
[1] "1.0 - 98.2 (15.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D440V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZCCHC6 MUTATED         2        1        2         7         0         0
  ZCCHC6 WILD-TYPE      62        0       24       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC6 MUTATED           2          0          2          1        1
  ZCCHC6 WILD-TYPE        16          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ZCCHC6 MUTATED           0         0
  ZCCHC6 WILD-TYPE        12         1
D440V3, multiclass
            clus
vv           ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  ZCCHC6 MUTATED     0   2  14   1
  ZCCHC6 WILD-TYPE   9  65 235  40
D440V4, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             14              235
  T4              1               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
  ZCCHC6 MUTATED    13   2   3
  ZCCHC6 WILD-TYPE 207  79  63
D440V5, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  N0             13              207
  N1              2               79
  N2              3               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"
D440V6, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    14   1
  ZCCHC6 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     14    1
  ZCCHC6 WILD-TYPE  271   47
   clus
vv  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D440V7, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    10   8
  ZCCHC6 WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     10    8
  ZCCHC6 WILD-TYPE  160  189
        clus
vv       ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D440V8, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    15   0
  ZCCHC6 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     15    0
  ZCCHC6 WILD-TYPE  285    8
     clus
vv    ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D440V9, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    12   6
  ZCCHC6 WILD-TYPE 302  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     12    6
  ZCCHC6 WILD-TYPE  302   42
                               clus
vv                              ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZCCHC6 MUTATED    12   0   1   2
  ZCCHC6 WILD-TYPE 247   3  21  19
D440V10, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              1               21
  RX              2               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"
D440V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZCCHC6 MUTATED                                  0     2
  ZCCHC6 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZCCHC6 MUTATED                           2     6
  ZCCHC6 WILD-TYPE                        17   170
D440V12, multiclass
                                  clus
vv                                 ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         6              170
[1] 4 2
[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 = FUBP3 MUTATION ANALYSIS
D441V1, survival
                 sevent
clus2               0   1
  FUBP3 MUTATED     8   1
  FUBP3 WILD-TYPE 269  77
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             346 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              1              77 
$`FUBP3 MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 
       24.00        25.08         6.97        34.98        12.16        58.39 
TCGA-CM-6162 TCGA-F4-6570 TCGA-F4-6856 
       12.00         6.18        35.31 

$`FUBP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  FUBP3 MUTATED FUBP3 WILD-TYPE 
           6.18            0.00 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
          58.39          148.01 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
         24.000          22.045 
[1] "6.2 - 58.4 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D441V2, continuous
                 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      62        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FUBP3 MUTATED           0          0          2          0        0         0
  FUBP3 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  FUBP3 MUTATED           0
  FUBP3 WILD-TYPE         1
D441V3, multiclass
            clus
vv           FUBP3 MUTATED FUBP3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  FUBP3 MUTATED     0   2   6   1
  FUBP3 WILD-TYPE   9  65 243  40
D441V4, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             1              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
  FUBP3 MUTATED     7   2   0
  FUBP3 WILD-TYPE 213  79  66
D441V5, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V6, binary
                 cls
clus                0   1
  FUBP3 MUTATED     8   0
  FUBP3 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      8    0
  FUBP3 WILD-TYPE  277   48
   clus
vv  FUBP3 MUTATED FUBP3 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D441V7, binary
                 cls
clus                0   1
  FUBP3 MUTATED     4   5
  FUBP3 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      4    5
  FUBP3 WILD-TYPE  166  192
        clus
vv       FUBP3 MUTATED FUBP3 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D441V8, binary
                 cls
clus                0   1
  FUBP3 MUTATED     9   0
  FUBP3 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      9    0
  FUBP3 WILD-TYPE  291    8
     clus
vv    FUBP3 MUTATED FUBP3 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D441V9, binary
                 cls
clus                0   1
  FUBP3 MUTATED     5   4
  FUBP3 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      5    4
  FUBP3 WILD-TYPE  309   44
                               clus
vv                              FUBP3 MUTATED FUBP3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FUBP3 MUTATED     9   0   0   0
  FUBP3 WILD-TYPE 250   3  22  21
D441V10, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D441V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUBP3 MUTATED                                  0     0
  FUBP3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FUBP3 MUTATED                           0     6
  FUBP3 WILD-TYPE                        19   170
D441V12, multiclass
                                  clus
vv                                 FUBP3 MUTATED FUBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = SYT1 MUTATION ANALYSIS
D442V1, survival
                sevent
clus2              0   1
  SYT1 MUTATED    12   1
  SYT1 WILD-TYPE 265  77
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            342 
  SYT1 MUTATED SYT1 WILD-TYPE 
             1             77 
$`SYT1 MUTATED`
TCGA-AA-3697 TCGA-G4-6586 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-A010 TCGA-CA-6717 
       85.05        35.80        29.19        63.98        34.98        12.76 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6680 TCGA-D5-6529 TCGA-G4-6323 
      124.27        23.05        15.02        12.03        20.19        13.78 
TCGA-G4-6626 
       46.75 

$`SYT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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 

  SYT1 MUTATED SYT1 WILD-TYPE 
         12.03           0.00 
  SYT1 MUTATED SYT1 WILD-TYPE 
        124.27         148.01 
  SYT1 MUTATED SYT1 WILD-TYPE 
         29.19          22.01 
[1] "12.0 - 124.3 (29.2)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "4"  
D442V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT1 MUTATED         1        1        2         6         1         0
  SYT1 WILD-TYPE      63        0       24       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT1 MUTATED           0          0          1          1        0         0
  SYT1 WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  SYT1 MUTATED           0
  SYT1 WILD-TYPE         1
D442V3, multiclass
            clus
vv           SYT1 MUTATED SYT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  SYT1 MUTATED     0   1  10   1
  SYT1 WILD-TYPE   9  66 239  40
D442V4, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           10            239
  T4            1             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
  SYT1 MUTATED    11   0   2
  SYT1 WILD-TYPE 209  81  64
D442V5, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  N0           11            209
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V6, binary
                cls
clus               0   1
  SYT1 MUTATED    11   0
  SYT1 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     11    0
  SYT1 WILD-TYPE  274   48
   clus
vv  SYT1 MUTATED SYT1 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D442V7, binary
                cls
clus               0   1
  SYT1 MUTATED     5   8
  SYT1 WILD-TYPE 165 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED      5    8
  SYT1 WILD-TYPE  165  189
        clus
vv       SYT1 MUTATED SYT1 WILD-TYPE
  FEMALE            5            165
  MALE              8            189
[1] 2 2
[1] FALSE
D442V8, binary
                cls
clus               0   1
  SYT1 MUTATED    13   0
  SYT1 WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     13    0
  SYT1 WILD-TYPE  287    8
     clus
vv    SYT1 MUTATED SYT1 WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D442V9, binary
                cls
clus               0   1
  SYT1 MUTATED    11   2
  SYT1 WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     11    2
  SYT1 WILD-TYPE  303   46
                               clus
vv                              SYT1 MUTATED SYT1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SYT1 MUTATED    10   0   0   2
  SYT1 WILD-TYPE 249   3  22  19
D442V10, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            2             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"
D442V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYT1 MUTATED                                  0     1
  SYT1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SYT1 MUTATED                           2     7
  SYT1 WILD-TYPE                        17   169
D442V12, multiclass
                                  clus
vv                                 SYT1 MUTATED SYT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       7            169
[1] 4 2
[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 = OSBPL11 MUTATION ANALYSIS
D443V1, survival
                   sevent
clus2                 0   1
  OSBPL11 MUTATED     8   8
  OSBPL11 WILD-TYPE 269  70
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               16               339 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
                8                70 
$`OSBPL11 MUTATED`
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3715 TCGA-AD-6964 TCGA-AA-3966 TCGA-AA-A00A 
       17.95         6.05        19.04        10.88         2.01        38.04 
TCGA-AA-A00N TCGA-AY-6196 TCGA-CA-6717 TCGA-D5-5537 TCGA-DM-A0XD TCGA-F4-6570 
        4.01         0.20        12.76        45.40        24.43         6.18 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6626 
      133.18        65.85        44.68        46.75 

$`OSBPL11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       61.91        36.00        13.78 

  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
              0.2               0.0 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
           133.18            148.01 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
           18.495            22.090 
[1] "0.2 - 133.2 (18.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D443V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL11 MUTATED         0        0        1         8         1         0
  OSBPL11 WILD-TYPE      64        1       25       100         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL11 MUTATED           1          0          0          1        2
  OSBPL11 WILD-TYPE        17          6         44         32       33
                   vv
clus                STAGE IVA STAGE IVB
  OSBPL11 MUTATED           0         0
  OSBPL11 WILD-TYPE        12         1
D443V3, multiclass
            clus
vv           OSBPL11 MUTATED OSBPL11 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                8               100
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 2                33
  STAGE IVA                0                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
  OSBPL11 MUTATED     0   1  12   3
  OSBPL11 WILD-TYPE   9  66 237  38
D443V4, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              12               237
  T4               3                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
  OSBPL11 MUTATED    10   2   4
  OSBPL11 WILD-TYPE 210  79  62
D443V5, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  N0              10               210
  N1               2                79
  N2               4                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V6, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    11   2
  OSBPL11 WILD-TYPE 274  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     11    2
  OSBPL11 WILD-TYPE  274   46
   clus
vv  OSBPL11 MUTATED OSBPL11 WILD-TYPE
  0              11               274
  1               2                46
[1] 2 2
[1] FALSE
D443V7, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED     6  10
  OSBPL11 WILD-TYPE 164 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED      6   10
  OSBPL11 WILD-TYPE  164  187
        clus
vv       OSBPL11 MUTATED OSBPL11 WILD-TYPE
  FEMALE               6               164
  MALE                10               187
[1] 2 2
[1] FALSE
D443V8, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    12   0
  OSBPL11 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     12    0
  OSBPL11 WILD-TYPE  288    8
     clus
vv    OSBPL11 MUTATED OSBPL11 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D443V9, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    12   4
  OSBPL11 WILD-TYPE 302  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     12    4
  OSBPL11 WILD-TYPE  302   44
                               clus
vv                              OSBPL11 MUTATED OSBPL11 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  OSBPL11 MUTATED    10   0   1   2
  OSBPL11 WILD-TYPE 249   3  21  19
D443V10, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               1                21
  RX               2                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"
D443V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSBPL11 MUTATED                                  0     1
  OSBPL11 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  OSBPL11 MUTATED                           0     9
  OSBPL11 WILD-TYPE                        19   167
D443V12, multiclass
                                  clus
vv                                 OSBPL11 MUTATED OSBPL11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(444) Variable = SFRS18 MUTATION ANALYSIS
D444V1, survival
                  sevent
clus2                0   1
  SFRS18 MUTATED     9   2
  SFRS18 WILD-TYPE 268  76
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              11              344 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
               2               76 
$`SFRS18 MUTATED`
TCGA-AD-6895 TCGA-A6-5661 TCGA-AA-3947 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 
       25.08        33.53        33.01        30.02        34.98        12.16 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 
       83.24        58.39        49.41        12.76        51.32 

$`SFRS18 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SFRS18 MUTATED SFRS18 WILD-TYPE 
           12.16             0.00 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
           83.24           148.01 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
           33.53            21.99 
[1] "12.2 - 83.2 (33.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D444V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS18 MUTATED         1        0        1         7         2         0
  SFRS18 WILD-TYPE      63        1       25       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS18 MUTATED           0          0          1          0        0
  SFRS18 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SFRS18 MUTATED           0         0
  SFRS18 WILD-TYPE        12         1
D444V3, multiclass
            clus
vv           SFRS18 MUTATED SFRS18 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SFRS18 MUTATED     0   1   9   2
  SFRS18 WILD-TYPE   9  66 240  39
D444V4, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              9              240
  T4              2               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
  SFRS18 MUTATED    11   1   0
  SFRS18 WILD-TYPE 209  80  66
D444V5, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  N0             11              209
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V6, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     9   0
  SFRS18 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      9    0
  SFRS18 WILD-TYPE  276   48
   clus
vv  SFRS18 MUTATED SFRS18 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D444V7, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     6   6
  SFRS18 WILD-TYPE 164 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      6    6
  SFRS18 WILD-TYPE  164  191
        clus
vv       SFRS18 MUTATED SFRS18 WILD-TYPE
  FEMALE              6              164
  MALE                6              191
[1] 2 2
[1] FALSE
D444V8, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    11   0
  SFRS18 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     11    0
  SFRS18 WILD-TYPE  289    8
     clus
vv    SFRS18 MUTATED SFRS18 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D444V9, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     9   3
  SFRS18 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      9    3
  SFRS18 WILD-TYPE  305   45
                               clus
vv                              SFRS18 MUTATED SFRS18 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SFRS18 MUTATED     9   0   0   2
  SFRS18 WILD-TYPE 250   3  22  19
D444V10, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              2               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"
D444V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS18 MUTATED                                  0     2
  SFRS18 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SFRS18 MUTATED                           1     5
  SFRS18 WILD-TYPE                        18   171
D444V12, multiclass
                                  clus
vv                                 SFRS18 MUTATED SFRS18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = MAP9 MUTATION ANALYSIS
D445V1, survival
                sevent
clus2              0   1
  MAP9 MUTATED    12   4
  MAP9 WILD-TYPE 265  74
  MAP9 MUTATED MAP9 WILD-TYPE 
            16            339 
  MAP9 MUTATED MAP9 WILD-TYPE 
             4             74 
$`MAP9 MUTATED`
TCGA-AA-3662 TCGA-A6-5665 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3977 TCGA-AU-6004 
        6.05        22.06        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 
        4.80        17.13        10.13        13.41 

$`MAP9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        43.27        15.12        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        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        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP9 MUTATED MAP9 WILD-TYPE 
             0              0 
  MAP9 MUTATED MAP9 WILD-TYPE 
         51.32         148.01 
  MAP9 MUTATED MAP9 WILD-TYPE 
        19.595         22.090 
[1] "0.0 - 51.3 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D445V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP9 MUTATED         1        0        1         7         0         0
  MAP9 WILD-TYPE      63        1       25       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP9 MUTATED           0          1          3          0        2         0
  MAP9 WILD-TYPE        18          5         41         33       33        12
                vv
clus             STAGE IVB
  MAP9 MUTATED           0
  MAP9 WILD-TYPE         1
D445V3, multiclass
            clus
vv           MAP9 MUTATED MAP9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  MAP9 MUTATED     0   2  13   1
  MAP9 WILD-TYPE   9  65 236  40
D445V4, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           13            236
  T4            1             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
  MAP9 MUTATED    10   4   2
  MAP9 WILD-TYPE 210  77  64
D445V5, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  N0           10            210
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V6, binary
                cls
clus               0   1
  MAP9 MUTATED    10   2
  MAP9 WILD-TYPE 275  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     10    2
  MAP9 WILD-TYPE  275   46
   clus
vv  MAP9 MUTATED MAP9 WILD-TYPE
  0           10            275
  1            2             46
[1] 2 2
[1] FALSE
D445V7, binary
                cls
clus               0   1
  MAP9 MUTATED     8   8
  MAP9 WILD-TYPE 162 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      8    8
  MAP9 WILD-TYPE  162  189
        clus
vv       MAP9 MUTATED MAP9 WILD-TYPE
  FEMALE            8            162
  MALE              8            189
[1] 2 2
[1] FALSE
D445V8, binary
                cls
clus               0   1
  MAP9 MUTATED    14   0
  MAP9 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     14    0
  MAP9 WILD-TYPE  286    8
     clus
vv    MAP9 MUTATED MAP9 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D445V9, binary
                cls
clus               0   1
  MAP9 MUTATED    14   2
  MAP9 WILD-TYPE 300  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     14    2
  MAP9 WILD-TYPE  300   46
                               clus
vv                              MAP9 MUTATED MAP9 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAP9 MUTATED    10   0   1   3
  MAP9 WILD-TYPE 249   3  21  18
D445V10, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            3             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"
D445V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP9 MUTATED                                  0     2
  MAP9 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAP9 MUTATED                           0    10
  MAP9 WILD-TYPE                        19   166
D445V12, multiclass
                                  clus
vv                                 MAP9 MUTATED MAP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(446) Variable = TNPO1 MUTATION ANALYSIS
D446V1, survival
                 sevent
clus2               0   1
  TNPO1 MUTATED    13   2
  TNPO1 WILD-TYPE 264  76
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             15             340 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              2              76 
$`TNPO1 MUTATED`
TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3966 
       35.80        32.75         8.38        63.98         1.02         2.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CK-5916 
       25.02        34.98        27.09        49.41        21.99        21.14 
TCGA-CM-6678 TCGA-D5-6929 TCGA-G4-6323 
       11.01        13.41        13.78 

$`TNPO1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6142 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        51.32        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6626 
       85.48        61.91        36.00        46.75 

  TNPO1 MUTATED TNPO1 WILD-TYPE 
           1.02            0.00 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
          63.98          148.01 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
         21.990          22.075 
[1] "1.0 - 64.0 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D446V2, continuous
                 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      62        0       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNPO1 MUTATED           0          0          1          0        1         1
  TNPO1 WILD-TYPE        18          6         43         33       34        11
                 vv
clus              STAGE IVB
  TNPO1 MUTATED           0
  TNPO1 WILD-TYPE         1
D446V3, multiclass
            clus
vv           TNPO1 MUTATED TNPO1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  TNPO1 MUTATED     1   2   9   3
  TNPO1 WILD-TYPE   8  65 240  38
D446V4, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             9             240
  T4             3              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
  TNPO1 MUTATED    13   3   0
  TNPO1 WILD-TYPE 207  78  66
D446V5, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  N0            13             207
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V6, binary
                 cls
clus                0   1
  TNPO1 MUTATED    10   2
  TNPO1 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     10    2
  TNPO1 WILD-TYPE  275   46
   clus
vv  TNPO1 MUTATED TNPO1 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D446V7, binary
                 cls
clus                0   1
  TNPO1 MUTATED    11   5
  TNPO1 WILD-TYPE 159 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     11    5
  TNPO1 WILD-TYPE  159  192
        clus
vv       TNPO1 MUTATED TNPO1 WILD-TYPE
  FEMALE            11             159
  MALE               5             192
[1] 2 2
[1] FALSE
D446V8, binary
                 cls
clus                0   1
  TNPO1 MUTATED    11   0
  TNPO1 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     11    0
  TNPO1 WILD-TYPE  289    8
     clus
vv    TNPO1 MUTATED TNPO1 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D446V9, binary
                 cls
clus                0   1
  TNPO1 MUTATED    14   2
  TNPO1 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     14    2
  TNPO1 WILD-TYPE  300   46
                               clus
vv                              TNPO1 MUTATED TNPO1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TNPO1 MUTATED    10   0   0   2
  TNPO1 WILD-TYPE 249   3  22  19
D446V10, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D446V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNPO1 MUTATED                                  0     0
  TNPO1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TNPO1 MUTATED                           2     8
  TNPO1 WILD-TYPE                        17   168
D446V12, multiclass
                                  clus
vv                                 TNPO1 MUTATED TNPO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = CLCNKA MUTATION ANALYSIS
D447V1, survival
                  sevent
clus2                0   1
  CLCNKA MUTATED     6   3
  CLCNKA WILD-TYPE 271  75
  CLCNKA MUTATED CLCNKA WILD-TYPE 
               9              346 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
               3               75 
$`CLCNKA MUTATED`
TCGA-AA-3672 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3663 TCGA-AY-6197 TCGA-AZ-6598 
        0.92        79.69         3.02         6.97        21.44        49.41 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-F4-6856 
       49.91       140.38        35.31 

$`CLCNKA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-A1DA 
       38.20       130.65        92.75        13.32        12.59         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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.045 
[1] "0.9 - 140.4 (35.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D447V2, continuous
                  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      61        1       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLCNKA MUTATED           1          0          0          0        0
  CLCNKA WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CLCNKA MUTATED           0         0
  CLCNKA WILD-TYPE        12         1
D447V3, multiclass
            clus
vv           CLCNKA MUTATED CLCNKA WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CLCNKA MUTATED     0   3   7   0
  CLCNKA WILD-TYPE   9  64 242  41
D447V4, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  T1              0                9
  T2              3               64
  T3              7              242
  T4              0               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
  CLCNKA MUTATED     9   1   0
  CLCNKA WILD-TYPE 211  80  66
D447V5, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  N0              9              211
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V6, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     7   0
  CLCNKA WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      7    0
  CLCNKA WILD-TYPE  278   48
   clus
vv  CLCNKA MUTATED CLCNKA WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D447V7, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     4   6
  CLCNKA WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      4    6
  CLCNKA WILD-TYPE  166  191
        clus
vv       CLCNKA MUTATED CLCNKA WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D447V8, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     7   0
  CLCNKA WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      7    0
  CLCNKA WILD-TYPE  293    8
     clus
vv    CLCNKA MUTATED CLCNKA WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D447V9, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     8   2
  CLCNKA WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      8    2
  CLCNKA WILD-TYPE  306   46
                               clus
vv                              CLCNKA MUTATED CLCNKA WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLCNKA MUTATED     6   0   0   1
  CLCNKA WILD-TYPE 253   3  22  20
D447V10, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D447V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLCNKA MUTATED                                  0     0
  CLCNKA WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLCNKA MUTATED                           0     7
  CLCNKA WILD-TYPE                        19   169
D447V12, multiclass
                                  clus
vv                                 CLCNKA MUTATED CLCNKA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = CREBBP MUTATION ANALYSIS
D448V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    45  12
  CREBBP WILD-TYPE 232  66
  CREBBP MUTATED CREBBP WILD-TYPE 
              57              298 
  CREBBP MUTATED CREBBP WILD-TYPE 
              12               66 
$`CREBBP MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       13.02         8.05         6.05         0.92        19.04        19.04 
TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-5665 
      100.01        35.80        26.17        91.79        79.69        22.06 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3864 
       63.98         1.02        10.06        33.04         0.99        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-A00E TCGA-AA-A010 
       31.00        33.01         2.01        13.05        30.02        34.98 
TCGA-AA-A029 TCGA-AD-5900 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
       51.98        12.16        27.42        14.50        27.09        33.01 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-5344 
       58.39         6.77        12.76       148.01        23.05        22.03 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6680 
       30.08        15.02        29.03        12.99        14.04        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6923 TCGA-DM-A1D7 
       45.40        54.61        15.12        16.14        12.43        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6808 
       12.59         7.50       131.51       117.07        31.96        33.67 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 
      133.18        53.62        55.04 

$`CREBBP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       23.01        19.99        19.99        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
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-A6-5656 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 
        5.98        37.05         5.03        26.99        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       18.05         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        34.06        25.02        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        37.02        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       40.96        83.24        24.53         5.79        22.42        26.47 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       13.02        29.06        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-6165 
       15.02        17.03        15.02        12.00        14.04        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-D5-5539 
       13.05        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 
       24.43        38.20       130.65        92.75        49.91       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24         8.61        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        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 
       47.41        35.31        74.56        65.85        44.68        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CREBBP MUTATED CREBBP WILD-TYPE 
            0.92             0.00 
  CREBBP MUTATED CREBBP WILD-TYPE 
          148.01           140.38 
  CREBBP MUTATED CREBBP WILD-TYPE 
           26.17            21.99 
[1] "0.9 - 148.0 (26.2)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.3"
D448V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CREBBP MUTATED         9        0        6        20         4         0
  CREBBP WILD-TYPE      55        1       20        88         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CREBBP MUTATED           5          0          7          3        3
  CREBBP WILD-TYPE        13          6         37         30       32
                  vv
clus               STAGE IVA STAGE IVB
  CREBBP MUTATED           1         0
  CREBBP WILD-TYPE        11         1
D448V3, multiclass
            clus
vv           CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                 9               55
  STAGE IA                0                1
  STAGE II                6               20
  STAGE IIA              20               88
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               5               13
  STAGE IIIA              0                6
  STAGE IIIB              7               37
  STAGE IIIC              3               30
  STAGE IV                3               32
  STAGE IVA               1               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
  CREBBP MUTATED     2   7  44   7
  CREBBP WILD-TYPE   7  60 205  34
D448V4, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  T1              2                7
  T2              7               60
  T3             44              205
  T4              7               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
  CREBBP MUTATED    40  12   8
  CREBBP WILD-TYPE 180  69  58
D448V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             40              180
  N1             12               69
  N2              8               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"
D448V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    49   4
  CREBBP WILD-TYPE 236  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     49    4
  CREBBP WILD-TYPE  236   44
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             49              236
  1              4               44
[1] 2 2
[1] FALSE
D448V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED    38  22
  CREBBP WILD-TYPE 132 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     38   22
  CREBBP WILD-TYPE  132  175
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             38              132
  MALE               22              175
[1] 2 2
[1] FALSE
D448V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    47   1
  CREBBP WILD-TYPE 253   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     47    1
  CREBBP WILD-TYPE  253    7
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              47              253
  YES              1                7
[1] 2 2
[1] FALSE
D448V9, binary
                  cls
clus                 0   1
  CREBBP MUTATED    52   7
  CREBBP WILD-TYPE 262  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     52    7
  CREBBP WILD-TYPE  262   41
                               clus
vv                              CREBBP MUTATED CREBBP WILD-TYPE
  COLON ADENOCARCINOMA                      52              262
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CREBBP MUTATED    43   0   3   4
  CREBBP WILD-TYPE 216   3  19  17
D448V10, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  R0             43              216
  R1              0                3
  R2              3               19
  RX              4               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"
D448V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREBBP MUTATED                                  0     1
  CREBBP WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED                           2    36
  CREBBP WILD-TYPE                        17   140
D448V12, multiclass
                                  clus
vv                                 CREBBP MUTATED CREBBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        36              140
[1] 4 2
[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 = INTS4 MUTATION ANALYSIS
D449V1, survival
                 sevent
clus2               0   1
  INTS4 MUTATED    11   6
  INTS4 WILD-TYPE 266  72
  INTS4 MUTATED INTS4 WILD-TYPE 
             17             338 
  INTS4 MUTATED INTS4 WILD-TYPE 
              6              72 
$`INTS4 MUTATED`
TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3672 TCGA-AZ-6601 TCGA-A6-5660 TCGA-A6-5664 
        8.05         6.05         0.92       100.01        29.19        22.09 
TCGA-AA-3663 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-5868 
        6.97        58.39        62.79        49.41        10.06        17.03 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6930 TCGA-F4-6459 TCGA-G4-6306 
       14.04         4.80        13.35         8.61        44.68 

$`INTS4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5665 TCGA-A6-5666 
       31.63        30.44        33.53        23.61        22.06        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-A6-6653 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  INTS4 MUTATED INTS4 WILD-TYPE 
           0.92            0.00 
  INTS4 MUTATED INTS4 WILD-TYPE 
         100.01          148.01 
  INTS4 MUTATED INTS4 WILD-TYPE 
         14.040          22.225 
[1] "0.9 - 100.0 (14.0)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.6"
D449V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INTS4 MUTATED         2        0        4         3         0         0
  INTS4 WILD-TYPE      62        1       22       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INTS4 MUTATED           1          0          3          2        1         1
  INTS4 WILD-TYPE        17          6         41         31       34        11
                 vv
clus              STAGE IVB
  INTS4 MUTATED           0
  INTS4 WILD-TYPE         1
D449V3, multiclass
            clus
vv           INTS4 MUTATED INTS4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  INTS4 MUTATED     0   3  12   3
  INTS4 WILD-TYPE   9  64 237  38
D449V4, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             3              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
  INTS4 MUTATED    10   4   4
  INTS4 WILD-TYPE 210  77  62
D449V5, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  N0            10             210
  N1             4              77
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V6, binary
                 cls
clus                0   1
  INTS4 MUTATED    11   2
  INTS4 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     11    2
  INTS4 WILD-TYPE  274   46
   clus
vv  INTS4 MUTATED INTS4 WILD-TYPE
  0            11             274
  1             2              46
[1] 2 2
[1] FALSE
D449V7, binary
                 cls
clus                0   1
  INTS4 MUTATED     6  12
  INTS4 WILD-TYPE 164 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED      6   12
  INTS4 WILD-TYPE  164  185
        clus
vv       INTS4 MUTATED INTS4 WILD-TYPE
  FEMALE             6             164
  MALE              12             185
[1] 2 2
[1] FALSE
D449V8, binary
                 cls
clus                0   1
  INTS4 MUTATED    17   0
  INTS4 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     17    0
  INTS4 WILD-TYPE  283    8
     clus
vv    INTS4 MUTATED INTS4 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D449V9, binary
                 cls
clus                0   1
  INTS4 MUTATED    17   1
  INTS4 WILD-TYPE 297  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     17    1
  INTS4 WILD-TYPE  297   47
                               clus
vv                              INTS4 MUTATED INTS4 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INTS4 MUTATED    10   0   1   2
  INTS4 WILD-TYPE 249   3  21  19
D449V10, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             1              21
  RX             2              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"
D449V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INTS4 MUTATED                                  0     1
  INTS4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INTS4 MUTATED                           2    11
  INTS4 WILD-TYPE                        17   165
D449V12, multiclass
                                  clus
vv                                 INTS4 MUTATED INTS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       11             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(450) Variable = PRKAA2 MUTATION ANALYSIS
D450V1, survival
                  sevent
clus2                0   1
  PRKAA2 MUTATED     7   4
  PRKAA2 WILD-TYPE 270  74
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              11              344 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
               4               74 
$`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 
       58.39        49.41        12.76        12.95         6.18 

$`PRKAA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
            3.02             0.00 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
           58.39           148.01 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
          20.120           22.075 
[1] "3.0 - 58.4 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D450V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKAA2 MUTATED         1        0        2         8         1         0
  PRKAA2 WILD-TYPE      63        1       24       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAA2 MUTATED           0          0          0          0        0
  PRKAA2 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  PRKAA2 MUTATED           0         0
  PRKAA2 WILD-TYPE        12         1
D450V3, multiclass
            clus
vv           PRKAA2 MUTATED PRKAA2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  PRKAA2 MUTATED     0   1  10   1
  PRKAA2 WILD-TYPE   9  66 239  40
D450V4, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             10              239
  T4              1               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
  PRKAA2 MUTATED    12   0   0
  PRKAA2 WILD-TYPE 208  81  66
D450V5, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  N0             12              208
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V6, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    10   0
  PRKAA2 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     10    0
  PRKAA2 WILD-TYPE  275   48
   clus
vv  PRKAA2 MUTATED PRKAA2 WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D450V7, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     4   8
  PRKAA2 WILD-TYPE 166 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      4    8
  PRKAA2 WILD-TYPE  166  189
        clus
vv       PRKAA2 MUTATED PRKAA2 WILD-TYPE
  FEMALE              4              166
  MALE                8              189
[1] 2 2
[1] FALSE
D450V8, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    10   0
  PRKAA2 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     10    0
  PRKAA2 WILD-TYPE  290    8
     clus
vv    PRKAA2 MUTATED PRKAA2 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D450V9, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     8   4
  PRKAA2 WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      8    4
  PRKAA2 WILD-TYPE  306   44
                               clus
vv                              PRKAA2 MUTATED PRKAA2 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRKAA2 MUTATED     9   0   0   1
  PRKAA2 WILD-TYPE 250   3  22  20
D450V10, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D450V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKAA2 MUTATED                                  0     1
  PRKAA2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRKAA2 MUTATED                           0     5
  PRKAA2 WILD-TYPE                        19   171
D450V12, multiclass
                                  clus
vv                                 PRKAA2 MUTATED PRKAA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = LNX2 MUTATION ANALYSIS
D451V1, survival
                sevent
clus2              0   1
  LNX2 MUTATED    11   5
  LNX2 WILD-TYPE 266  73
  LNX2 MUTATED LNX2 WILD-TYPE 
            16            339 
  LNX2 MUTATED LNX2 WILD-TYPE 
             5             73 
$`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 
       55.92        25.48        13.35        92.75 

$`LNX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        26.99        35.05 
TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       33.04        25.02        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-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        18.05        27.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6167 TCGA-CM-6168 
       12.00        14.04        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-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       54.61        19.59        56.09        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         7.53        12.39        10.13        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        13.41        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LNX2 MUTATED LNX2 WILD-TYPE 
          0.99           0.00 
  LNX2 MUTATED LNX2 WILD-TYPE 
         92.75         148.01 
  LNX2 MUTATED LNX2 WILD-TYPE 
        22.025         22.090 
[1] "1.0 - 92.8 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D451V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LNX2 MUTATED         4        0        0         5         1         0
  LNX2 WILD-TYPE      60        1       26       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LNX2 MUTATED           2          0          3          0        0         0
  LNX2 WILD-TYPE        16          6         41         33       35        12
                vv
clus             STAGE IVB
  LNX2 MUTATED           0
  LNX2 WILD-TYPE         1
D451V3, multiclass
            clus
vv           LNX2 MUTATED LNX2 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  LNX2 MUTATED     0   4  10   2
  LNX2 WILD-TYPE   9  63 239  39
D451V4, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           10            239
  T4            2             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
  LNX2 MUTATED    11   3   2
  LNX2 WILD-TYPE 209  78  64
D451V5, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  N0           11            209
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V6, binary
                cls
clus               0   1
  LNX2 MUTATED    16   0
  LNX2 WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     16    0
  LNX2 WILD-TYPE  269   48
   clus
vv  LNX2 MUTATED LNX2 WILD-TYPE
  0           16            269
  1            0             48
[1] 2 2
[1] FALSE
D451V7, binary
                cls
clus               0   1
  LNX2 MUTATED     9   7
  LNX2 WILD-TYPE 161 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED      9    7
  LNX2 WILD-TYPE  161  190
        clus
vv       LNX2 MUTATED LNX2 WILD-TYPE
  FEMALE            9            161
  MALE              7            190
[1] 2 2
[1] FALSE
D451V8, binary
                cls
clus               0   1
  LNX2 MUTATED    10   1
  LNX2 WILD-TYPE 290   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     10    1
  LNX2 WILD-TYPE  290    7
     clus
vv    LNX2 MUTATED LNX2 WILD-TYPE
  NO            10            290
  YES            1              7
[1] 2 2
[1] FALSE
D451V9, binary
                cls
clus               0   1
  LNX2 MUTATED    11   5
  LNX2 WILD-TYPE 303  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     11    5
  LNX2 WILD-TYPE  303   43
                               clus
vv                              LNX2 MUTATED LNX2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LNX2 MUTATED    14   0   0   1
  LNX2 WILD-TYPE 245   3  22  20
D451V10, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            0             22
  RX            1             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"
D451V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LNX2 MUTATED                                  0     1
  LNX2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LNX2 MUTATED                           0     8
  LNX2 WILD-TYPE                        19   168
D451V12, multiclass
                                  clus
vv                                 LNX2 MUTATED LNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = ATG2B MUTATION ANALYSIS
D452V1, survival
                 sevent
clus2               0   1
  ATG2B MUTATED     9   5
  ATG2B WILD-TYPE 268  73
  ATG2B MUTATED ATG2B WILD-TYPE 
             14             341 
  ATG2B MUTATED ATG2B WILD-TYPE 
              5              73 
$`ATG2B MUTATED`
TCGA-AZ-6608 TCGA-G4-6628 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3681 
        1.94        79.69        20.12         3.02         6.97         5.98 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 
       10.06        25.02         4.01        34.98        12.76        10.06 
TCGA-CM-5861 TCGA-CM-6171 
       15.02        14.04 

$`ATG2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       23.87        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ATG2B MUTATED ATG2B WILD-TYPE 
           1.94            0.00 
  ATG2B MUTATED ATG2B WILD-TYPE 
          79.69          148.01 
  ATG2B MUTATED ATG2B WILD-TYPE 
          11.41           22.42 
[1] "1.9 - 79.7 (11.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.6"
D452V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG2B MUTATED         2        0        2         6         2         0
  ATG2B WILD-TYPE      62        1       24       102         6         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        16          5         44         33       35        12
                 vv
clus              STAGE IVB
  ATG2B MUTATED           0
  ATG2B WILD-TYPE         1
D452V3, multiclass
            clus
vv           ATG2B MUTATED ATG2B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ATG2B MUTATED     0   3  10   2
  ATG2B WILD-TYPE   9  64 239  39
D452V4, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             2              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
  ATG2B MUTATED    12   2   1
  ATG2B WILD-TYPE 208  79  65
D452V5, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  N0            12             208
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V6, binary
                 cls
clus                0   1
  ATG2B MUTATED    14   0
  ATG2B WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     14    0
  ATG2B WILD-TYPE  271   48
   clus
vv  ATG2B MUTATED ATG2B WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D452V7, binary
                 cls
clus                0   1
  ATG2B MUTATED     9   6
  ATG2B WILD-TYPE 161 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      9    6
  ATG2B WILD-TYPE  161  191
        clus
vv       ATG2B MUTATED ATG2B WILD-TYPE
  FEMALE             9             161
  MALE               6             191
[1] 2 2
[1] FALSE
D452V8, binary
                 cls
clus                0   1
  ATG2B MUTATED    13   0
  ATG2B WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     13    0
  ATG2B WILD-TYPE  287    8
     clus
vv    ATG2B MUTATED ATG2B WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D452V9, binary
                 cls
clus                0   1
  ATG2B MUTATED    12   3
  ATG2B WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     12    3
  ATG2B WILD-TYPE  302   45
                               clus
vv                              ATG2B MUTATED ATG2B WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATG2B MUTATED    11   0   0   2
  ATG2B WILD-TYPE 248   3  22  19
D452V10, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             2              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"
D452V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG2B MUTATED                                  0     2
  ATG2B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATG2B MUTATED                           0     5
  ATG2B WILD-TYPE                        19   171
D452V12, multiclass
                                  clus
vv                                 ATG2B MUTATED ATG2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = CHRM2 MUTATION ANALYSIS
D453V1, survival
                 sevent
clus2               0   1
  CHRM2 MUTATED    16   4
  CHRM2 WILD-TYPE 261  74
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             20             335 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
              4              74 
$`CHRM2 MUTATED`
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6651 
       19.00        19.04        19.04        22.09         8.38        21.76 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
        3.02        63.98        26.99         4.01        34.98        83.24 
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 
      133.18        53.62 

$`CHRM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
        0.92        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 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-A6-6652 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CHRM2 MUTATED CHRM2 WILD-TYPE 
           3.02            0.00 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
         133.18          148.01 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
          20.40           22.09 
[1] "3.0 - 133.2 (20.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D453V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRM2 MUTATED         1        0        4         5         3         0
  CHRM2 WILD-TYPE      63        1       22       103         5         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        17          6         42         30       31        12
                 vv
clus              STAGE IVB
  CHRM2 MUTATED           0
  CHRM2 WILD-TYPE         1
D453V3, multiclass
            clus
vv           CHRM2 MUTATED CHRM2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              5             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             3              30
  STAGE IV               4              31
  STAGE IVA              0              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
  CHRM2 MUTATED     0   1  15   7
  CHRM2 WILD-TYPE   9  66 234  34
D453V4, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            15             234
  T4             7              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
  CHRM2 MUTATED    14   4   5
  CHRM2 WILD-TYPE 206  77  61
D453V5, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  N0            14             206
  N1             4              77
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V6, binary
                 cls
clus                0   1
  CHRM2 MUTATED    16   4
  CHRM2 WILD-TYPE 269  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     16    4
  CHRM2 WILD-TYPE  269   44
   clus
vv  CHRM2 MUTATED CHRM2 WILD-TYPE
  0            16             269
  1             4              44
[1] 2 2
[1] FALSE
D453V7, binary
                 cls
clus                0   1
  CHRM2 MUTATED    11  12
  CHRM2 WILD-TYPE 159 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     11   12
  CHRM2 WILD-TYPE  159  185
        clus
vv       CHRM2 MUTATED CHRM2 WILD-TYPE
  FEMALE            11             159
  MALE              12             185
[1] 2 2
[1] FALSE
D453V8, binary
                 cls
clus                0   1
  CHRM2 MUTATED    17   1
  CHRM2 WILD-TYPE 283   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     17    1
  CHRM2 WILD-TYPE  283    7
     clus
vv    CHRM2 MUTATED CHRM2 WILD-TYPE
  NO             17             283
  YES             1               7
[1] 2 2
[1] FALSE
D453V9, binary
                 cls
clus                0   1
  CHRM2 MUTATED    20   3
  CHRM2 WILD-TYPE 294  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     20    3
  CHRM2 WILD-TYPE  294   45
                               clus
vv                              CHRM2 MUTATED CHRM2 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHRM2 MUTATED    13   0   4   2
  CHRM2 WILD-TYPE 246   3  18  19
D453V10, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             4              18
  RX             2              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"
D453V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRM2 MUTATED                                  0     2
  CHRM2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRM2 MUTATED                           2     8
  CHRM2 WILD-TYPE                        17   168
D453V12, multiclass
                                  clus
vv                                 CHRM2 MUTATED CHRM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = NUDCD1 MUTATION ANALYSIS
D454V1, survival
                  sevent
clus2                0   1
  NUDCD1 MUTATED     6   2
  NUDCD1 WILD-TYPE 271  76
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               8              347 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               2               76 
$`NUDCD1 MUTATED`
TCGA-G4-6588 TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-A00N TCGA-CM-5868 TCGA-D5-6536 
       26.17        23.87        26.99         4.01        17.03        17.85 
TCGA-DM-A1D8 TCGA-DM-A1HB 
       12.59       135.65 

$`NUDCD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
            4.01             0.00 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
          135.65           148.01 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
           20.86            22.06 
[1] "4.0 - 135.7 (20.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D454V2, continuous
                  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      64        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDCD1 MUTATED           0          0          2          0        0
  NUDCD1 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  NUDCD1 MUTATED           1         0
  NUDCD1 WILD-TYPE        11         1
D454V3, multiclass
            clus
vv           NUDCD1 MUTATED NUDCD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  NUDCD1 MUTATED     0   0   7   2
  NUDCD1 WILD-TYPE   9  67 242  39
D454V4, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              2               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
  NUDCD1 MUTATED     5   4   0
  NUDCD1 WILD-TYPE 215  77  66
D454V5, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  N0              5              215
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V6, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     7   1
  NUDCD1 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      7    1
  NUDCD1 WILD-TYPE  278   47
   clus
vv  NUDCD1 MUTATED NUDCD1 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D454V7, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     6   3
  NUDCD1 WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      6    3
  NUDCD1 WILD-TYPE  164  194
        clus
vv       NUDCD1 MUTATED NUDCD1 WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D454V8, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     5   0
  NUDCD1 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      5    0
  NUDCD1 WILD-TYPE  295    8
     clus
vv    NUDCD1 MUTATED NUDCD1 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D454V9, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     7   1
  NUDCD1 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      7    1
  NUDCD1 WILD-TYPE  307   47
                               clus
vv                              NUDCD1 MUTATED NUDCD1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUDCD1 MUTATED     6   0   0   0
  NUDCD1 WILD-TYPE 253   3  22  21
D454V10, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D454V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDCD1 MUTATED                                  0     0
  NUDCD1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDCD1 MUTATED                           0     6
  NUDCD1 WILD-TYPE                        19   170
D454V12, multiclass
                                  clus
vv                                 NUDCD1 MUTATED NUDCD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = INSM2 MUTATION ANALYSIS
D455V1, survival
                 sevent
clus2               0   1
  INSM2 MUTATED     9   1
  INSM2 WILD-TYPE 268  77
  INSM2 MUTATED INSM2 WILD-TYPE 
             10             345 
  INSM2 MUTATED INSM2 WILD-TYPE 
              1              77 
$`INSM2 MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-6781 TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6717 
       25.08        79.69        19.66        17.82        49.41        12.76 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4744 TCGA-G4-6299 
       15.62        23.05        20.02        74.56 

$`INSM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  INSM2 MUTATED INSM2 WILD-TYPE 
          12.76            0.00 
  INSM2 MUTATED INSM2 WILD-TYPE 
          79.69          148.01 
  INSM2 MUTATED INSM2 WILD-TYPE 
         21.535          22.060 
[1] "12.8 - 79.7 (21.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D455V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INSM2 MUTATED         2        0        1         2         0         0
  INSM2 WILD-TYPE      62        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSM2 MUTATED           0          0          2          3        0         0
  INSM2 WILD-TYPE        18          6         42         30       35        12
                 vv
clus              STAGE IVB
  INSM2 MUTATED           0
  INSM2 WILD-TYPE         1
D455V3, multiclass
            clus
vv           INSM2 MUTATED INSM2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              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
  INSM2 MUTATED     0   2   6   2
  INSM2 WILD-TYPE   9  65 243  39
D455V4, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  INSM2 MUTATED     5   3   2
  INSM2 WILD-TYPE 215  78  64
D455V5, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  N0             5             215
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V6, binary
                 cls
clus                0   1
  INSM2 MUTATED     8   0
  INSM2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      8    0
  INSM2 WILD-TYPE  277   48
   clus
vv  INSM2 MUTATED INSM2 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D455V7, binary
                 cls
clus                0   1
  INSM2 MUTATED     3   7
  INSM2 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      3    7
  INSM2 WILD-TYPE  167  190
        clus
vv       INSM2 MUTATED INSM2 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D455V8, binary
                 cls
clus                0   1
  INSM2 MUTATED     9   0
  INSM2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      9    0
  INSM2 WILD-TYPE  291    8
     clus
vv    INSM2 MUTATED INSM2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D455V9, binary
                 cls
clus                0   1
  INSM2 MUTATED     7   3
  INSM2 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      7    3
  INSM2 WILD-TYPE  307   45
                               clus
vv                              INSM2 MUTATED INSM2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INSM2 MUTATED     7   0   0   2
  INSM2 WILD-TYPE 252   3  22  19
D455V10, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             2              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"
D455V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INSM2 MUTATED                                  0     1
  INSM2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INSM2 MUTATED                           1     8
  INSM2 WILD-TYPE                        18   168
D455V12, multiclass
                                  clus
vv                                 INSM2 MUTATED INSM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = GOLGB1 MUTATION ANALYSIS
D456V1, survival
                  sevent
clus2                0   1
  GOLGB1 MUTATED    29   8
  GOLGB1 WILD-TYPE 248  70
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              37              318 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
               8               70 
$`GOLGB1 MUTATED`
TCGA-G4-6588 TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3510 
       26.17        30.44         8.38        20.12        35.01        63.98 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J 
       29.95        13.94        26.99        53.00        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 
        4.01        34.98        22.42        58.39        49.41        11.74 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6170 
       12.20        12.76        10.06        37.02        12.00        15.02 
TCGA-CM-6680 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       12.03        17.85        17.13        16.14        15.58         7.53 
TCGA-D5-6927 TCGA-DM-A0XF TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6307 
        9.44        38.20       139.17         6.18        13.25        55.04 
TCGA-G4-6317 
       36.00 

$`GOLGB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6142 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04         3.02         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       24.00        20.98        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       88.21         6.77        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 
       43.27        15.12         4.80        12.49        12.39        10.13 
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        13.41        13.35 
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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       135.65        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       53.62        44.68        85.48        61.91        13.78        46.75 

  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
            4.01             0.00 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
          139.17           148.01 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
           18.05            22.09 
[1] "4.0 - 139.2 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D456V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLGB1 MUTATED         6        0        3        16         2         0
  GOLGB1 WILD-TYPE      58        1       23        92         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLGB1 MUTATED           0          0          5          2        1
  GOLGB1 WILD-TYPE        18          6         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  GOLGB1 MUTATED           1         0
  GOLGB1 WILD-TYPE        11         1
D456V3, multiclass
            clus
vv           GOLGB1 MUTATED GOLGB1 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              16               92
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              5               39
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               1               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
  GOLGB1 MUTATED     0   7  27   4
  GOLGB1 WILD-TYPE   9  60 222  37
D456V4, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  T1              0                9
  T2              7               60
  T3             27              222
  T4              4               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
  GOLGB1 MUTATED    29   4   5
  GOLGB1 WILD-TYPE 191  77  61
D456V5, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  N0             29              191
  N1              4               77
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V6, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    31   2
  GOLGB1 WILD-TYPE 254  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     31    2
  GOLGB1 WILD-TYPE  254   46
   clus
vv  GOLGB1 MUTATED GOLGB1 WILD-TYPE
  0             31              254
  1              2               46
[1] 2 2
[1] FALSE
D456V7, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    17  21
  GOLGB1 WILD-TYPE 153 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     17   21
  GOLGB1 WILD-TYPE  153  176
        clus
vv       GOLGB1 MUTATED GOLGB1 WILD-TYPE
  FEMALE             17              153
  MALE               21              176
[1] 2 2
[1] FALSE
D456V8, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    34   0
  GOLGB1 WILD-TYPE 266   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     34    0
  GOLGB1 WILD-TYPE  266    8
     clus
vv    GOLGB1 MUTATED GOLGB1 WILD-TYPE
  NO              34              266
  YES              0                8
[1] 2 2
[1] FALSE
D456V9, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    30   7
  GOLGB1 WILD-TYPE 284  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     30    7
  GOLGB1 WILD-TYPE  284   41
                               clus
vv                              GOLGB1 MUTATED GOLGB1 WILD-TYPE
  COLON ADENOCARCINOMA                      30              284
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GOLGB1 MUTATED    27   0   0   3
  GOLGB1 WILD-TYPE 232   3  22  18
D456V10, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  R0             27              232
  R1              0                3
  R2              0               22
  RX              3               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"
D456V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLGB1 MUTATED                                  0     3
  GOLGB1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GOLGB1 MUTATED                           2    22
  GOLGB1 WILD-TYPE                        17   154
D456V12, multiclass
                                  clus
vv                                 GOLGB1 MUTATED GOLGB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        22              154
[1] 4 2
[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 = KIAA1804 MUTATION ANALYSIS
D457V1, survival
                    sevent
clus2                  0   1
  KIAA1804 MUTATED    13   3
  KIAA1804 WILD-TYPE 264  75
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                16                339 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 3                 75 
$`KIAA1804 MUTATED`
TCGA-AA-3672 TCGA-AA-3688 TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3510 
        0.92        19.00        10.88        79.69        22.06        63.98 
TCGA-AA-3555 TCGA-AA-3845 TCGA-AA-3966 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-6717 
       29.95         0.00         2.01        34.98        49.41        12.76 
TCGA-CM-4744 TCGA-CM-5861 TCGA-D5-6538 TCGA-G4-6317 
       20.02        15.02        17.13        36.00 

$`KIAA1804 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 0                  0 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             79.69             148.01 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             19.51              22.09 
[1] "0.0 - 79.7 (19.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D457V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1804 MUTATED         2        0        2         6         1         0
  KIAA1804 WILD-TYPE      62        1       24       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1804 MUTATED           1          0          1          1        1
  KIAA1804 WILD-TYPE        17          6         43         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1804 MUTATED           0         0
  KIAA1804 WILD-TYPE        12         1
D457V3, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 6                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  KIAA1804 MUTATED     0   2  12   2
  KIAA1804 WILD-TYPE   9  65 237  39
D457V4, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3               12                237
  T4                2                 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
  KIAA1804 MUTATED    11   2   3
  KIAA1804 WILD-TYPE 209  79  63
D457V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0               11                209
  N1                2                 79
  N2                3                 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"
D457V6, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    12   1
  KIAA1804 WILD-TYPE 273  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     12    1
  KIAA1804 WILD-TYPE  273   47
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0               12                273
  1                1                 47
[1] 2 2
[1] FALSE
D457V7, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    10   6
  KIAA1804 WILD-TYPE 160 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     10    6
  KIAA1804 WILD-TYPE  160  191
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE               10                160
  MALE                  6                191
[1] 2 2
[1] FALSE
D457V8, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    14   0
  KIAA1804 WILD-TYPE 286   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     14    0
  KIAA1804 WILD-TYPE  286    8
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  NO                14                286
  YES                0                  8
[1] 2 2
[1] FALSE
D457V9, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    13   3
  KIAA1804 WILD-TYPE 301  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     13    3
  KIAA1804 WILD-TYPE  301   45
                               clus
vv                              KIAA1804 MUTATED KIAA1804 WILD-TYPE
  COLON ADENOCARCINOMA                        13                301
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1804 MUTATED    11   0   1   1
  KIAA1804 WILD-TYPE 248   3  21  20
D457V10, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0               11                248
  R1                0                  3
  R2                1                 21
  RX                1                 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"
D457V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1804 MUTATED                                  0     1
  KIAA1804 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1804 MUTATED                           0     8
  KIAA1804 WILD-TYPE                        19   168
D457V12, multiclass
                                  clus
vv                                 KIAA1804 MUTATED KIAA1804 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           8                168
[1] 4 2
[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 = C10ORF79 MUTATION ANALYSIS
D458V1, survival
                    sevent
clus2                  0   1
  C10ORF79 MUTATED    21   5
  C10ORF79 WILD-TYPE 256  73
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                26                329 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                 5                 73 
$`C10ORF79 MUTATED`
TCGA-AA-3672 TCGA-AD-6964 TCGA-AZ-4681 TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3555 
        0.92        10.88       106.75        32.91         8.38        29.95 
TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-5900 
       78.08        53.00         4.01        34.98        31.00        12.16 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       83.24        58.39         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        14.04        12.95        18.25        12.43       119.93 
TCGA-F4-6805 TCGA-G4-6306 
       34.42        44.68 

$`C10ORF79 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       21.01        24.00        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17        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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
              0.92               0.00 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
            148.01             140.38 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
             24.10              22.06 
[1] "0.9 - 148.0 (24.1)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.5"
D458V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C10ORF79 MUTATED         5        0        3        12         2         0
  C10ORF79 WILD-TYPE      59        1       23        96         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF79 MUTATED           2          0          0          1        0
  C10ORF79 WILD-TYPE        16          6         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C10ORF79 MUTATED           0         0
  C10ORF79 WILD-TYPE        12         1
D458V3, multiclass
            clus
vv           C10ORF79 MUTATED C10ORF79 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                12                 96
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C10ORF79 MUTATED     1   5  17   4
  C10ORF79 WILD-TYPE   8  62 232  37
D458V4, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  T1                1                  8
  T2                5                 62
  T3               17                232
  T4                4                 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
  C10ORF79 MUTATED    23   2   2
  C10ORF79 WILD-TYPE 197  79  64
D458V5, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  N0               23                197
  N1                2                 79
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V6, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    24   0
  C10ORF79 WILD-TYPE 261  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     24    0
  C10ORF79 WILD-TYPE  261   48
   clus
vv  C10ORF79 MUTATED C10ORF79 WILD-TYPE
  0               24                261
  1                0                 48
[1] 2 2
[1] FALSE
D458V7, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    11  16
  C10ORF79 WILD-TYPE 159 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     11   16
  C10ORF79 WILD-TYPE  159  181
        clus
vv       C10ORF79 MUTATED C10ORF79 WILD-TYPE
  FEMALE               11                159
  MALE                 16                181
[1] 2 2
[1] FALSE
D458V8, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    24   0
  C10ORF79 WILD-TYPE 276   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     24    0
  C10ORF79 WILD-TYPE  276    8
     clus
vv    C10ORF79 MUTATED C10ORF79 WILD-TYPE
  NO                24                276
  YES                0                  8
[1] 2 2
[1] FALSE
D458V9, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    23   4
  C10ORF79 WILD-TYPE 291  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     23    4
  C10ORF79 WILD-TYPE  291   44
                               clus
vv                              C10ORF79 MUTATED C10ORF79 WILD-TYPE
  COLON ADENOCARCINOMA                        23                291
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C10ORF79 MUTATED    20   0   0   2
  C10ORF79 WILD-TYPE 239   3  22  19
D458V10, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  R0               20                239
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D458V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF79 MUTATED                                  0     3
  C10ORF79 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C10ORF79 MUTATED                           1    15
  C10ORF79 WILD-TYPE                        18   161
D458V12, multiclass
                                  clus
vv                                 C10ORF79 MUTATED C10ORF79 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          15                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(459) Variable = DENND4A MUTATION ANALYSIS
D459V1, survival
                   sevent
clus2                 0   1
  DENND4A MUTATED    16   5
  DENND4A WILD-TYPE 261  73
  DENND4A MUTATED DENND4A WILD-TYPE 
               21               334 
  DENND4A MUTATED DENND4A WILD-TYPE 
                5                73 
$`DENND4A MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3663 
        0.92        19.04        35.80        31.63        22.06         6.97 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       53.00        33.01         2.01         4.01        34.98        83.24 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-5864 
        0.20        58.39         5.23        21.99        82.95        15.02 
TCGA-CM-6171 TCGA-DM-A1HB TCGA-G4-6303 
       14.04       135.65        65.85 

$`DENND4A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  DENND4A MUTATED DENND4A WILD-TYPE 
              0.2               0.0 
  DENND4A MUTATED DENND4A WILD-TYPE 
           135.65            148.01 
  DENND4A MUTATED DENND4A WILD-TYPE 
            22.06             22.06 
[1] "0.2 - 135.7 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D459V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DENND4A MUTATED         2        0        3         7         3         0
  DENND4A WILD-TYPE      62        1       23       101         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND4A MUTATED           1          0          4          1        1
  DENND4A WILD-TYPE        17          6         40         32       34
                   vv
clus                STAGE IVA STAGE IVB
  DENND4A MUTATED           0         0
  DENND4A WILD-TYPE        12         1
D459V3, multiclass
            clus
vv           DENND4A MUTATED DENND4A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                7               101
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  DENND4A MUTATED     0   2  16   4
  DENND4A WILD-TYPE   9  65 233  37
D459V4, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              16               233
  T4               4                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
  DENND4A MUTATED    15   6   1
  DENND4A WILD-TYPE 205  75  65
D459V5, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  N0              15               205
  N1               6                75
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V6, binary
                   cls
clus                  0   1
  DENND4A MUTATED    18   1
  DENND4A WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     18    1
  DENND4A WILD-TYPE  267   47
   clus
vv  DENND4A MUTATED DENND4A WILD-TYPE
  0              18               267
  1               1                47
[1] 2 2
[1] FALSE
D459V7, binary
                   cls
clus                  0   1
  DENND4A MUTATED    10  12
  DENND4A WILD-TYPE 160 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     10   12
  DENND4A WILD-TYPE  160  185
        clus
vv       DENND4A MUTATED DENND4A WILD-TYPE
  FEMALE              10               160
  MALE                12               185
[1] 2 2
[1] FALSE
D459V8, binary
                   cls
clus                  0   1
  DENND4A MUTATED    16   0
  DENND4A WILD-TYPE 284   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     16    0
  DENND4A WILD-TYPE  284    8
     clus
vv    DENND4A MUTATED DENND4A WILD-TYPE
  NO               16               284
  YES               0                 8
[1] 2 2
[1] FALSE
D459V9, binary
                   cls
clus                  0   1
  DENND4A MUTATED    17   4
  DENND4A WILD-TYPE 297  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     17    4
  DENND4A WILD-TYPE  297   44
                               clus
vv                              DENND4A MUTATED DENND4A WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DENND4A MUTATED    17   0   0   2
  DENND4A WILD-TYPE 242   3  22  19
D459V10, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  R0              17               242
  R1               0                 3
  R2               0                22
  RX               2                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"
D459V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DENND4A MUTATED                                  0     1
  DENND4A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DENND4A MUTATED                           1    11
  DENND4A WILD-TYPE                        18   165
D459V12, multiclass
                                  clus
vv                                 DENND4A MUTATED DENND4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               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(460) Variable = RBL2 MUTATION ANALYSIS
D460V1, survival
                sevent
clus2              0   1
  RBL2 MUTATED    16   4
  RBL2 WILD-TYPE 261  74
  RBL2 MUTATED RBL2 WILD-TYPE 
            20            335 
  RBL2 MUTATED RBL2 WILD-TYPE 
             4             74 
$`RBL2 MUTATED`
TCGA-AA-3554 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3558 
       17.95        25.08        26.17        32.75        22.06        20.98 
TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-5900 
       10.06        53.00        25.02        34.98         1.02        12.16 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-5864 
       58.39         5.23        12.76        10.06        15.02        15.02 
TCGA-CM-6169 TCGA-D5-5538 
       13.02        54.61 

$`RBL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        29.95        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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-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 
       14.04        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-D5-5539 
       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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RBL2 MUTATED RBL2 WILD-TYPE 
          1.02           0.00 
  RBL2 MUTATED RBL2 WILD-TYPE 
         58.39         148.01 
  RBL2 MUTATED RBL2 WILD-TYPE 
        19.465         22.090 
[1] "1.0 - 58.4 (19.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D460V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBL2 MUTATED         3        0        3         8         2         0
  RBL2 WILD-TYPE      61        1       23       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBL2 MUTATED           1          0          3          0        0         0
  RBL2 WILD-TYPE        17          6         41         33       35        12
                vv
clus             STAGE IVB
  RBL2 MUTATED           0
  RBL2 WILD-TYPE         1
D460V3, multiclass
            clus
vv           RBL2 MUTATED RBL2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RBL2 MUTATED     0   4  13   4
  RBL2 WILD-TYPE   9  63 236  37
D460V4, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           13            236
  T4            4             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
  RBL2 MUTATED    17   3   1
  RBL2 WILD-TYPE 203  78  65
D460V5, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  N0           17            203
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V6, binary
                cls
clus               0   1
  RBL2 MUTATED    19   0
  RBL2 WILD-TYPE 266  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     19    0
  RBL2 WILD-TYPE  266   48
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0           19            266
  1            0             48
[1] 2 2
[1] FALSE
D460V7, binary
                cls
clus               0   1
  RBL2 MUTATED    10  11
  RBL2 WILD-TYPE 160 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     10   11
  RBL2 WILD-TYPE  160  186
        clus
vv       RBL2 MUTATED RBL2 WILD-TYPE
  FEMALE           10            160
  MALE             11            186
[1] 2 2
[1] FALSE
D460V8, binary
                cls
clus               0   1
  RBL2 MUTATED    19   0
  RBL2 WILD-TYPE 281   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     19    0
  RBL2 WILD-TYPE  281    8
     clus
vv    RBL2 MUTATED RBL2 WILD-TYPE
  NO            19            281
  YES            0              8
[1] 2 2
[1] FALSE
D460V9, binary
                cls
clus               0   1
  RBL2 MUTATED    18   3
  RBL2 WILD-TYPE 296  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     18    3
  RBL2 WILD-TYPE  296   45
                               clus
vv                              RBL2 MUTATED RBL2 WILD-TYPE
  COLON ADENOCARCINOMA                    18            296
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBL2 MUTATED    16   0   1   2
  RBL2 WILD-TYPE 243   3  21  19
D460V10, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            1             21
  RX            2             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"
D460V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBL2 MUTATED                                  0     2
  RBL2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBL2 MUTATED                           1    10
  RBL2 WILD-TYPE                        18   166
D460V12, multiclass
                                  clus
vv                                 RBL2 MUTATED RBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(461) Variable = DCAF6 MUTATION ANALYSIS
D461V1, survival
                 sevent
clus2               0   1
  DCAF6 MUTATED    10   4
  DCAF6 WILD-TYPE 267  74
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             14             341 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
              4              74 
$`DCAF6 MUTATED`
TCGA-AD-6895 TCGA-A6-2676 TCGA-A6-5661 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N 
       25.08        42.90        33.53        33.04        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 TCGA-CA-5254 TCGA-CA-6718 TCGA-CM-6163 
       34.98        83.24        21.44        12.69        10.06        14.04 
TCGA-CM-6677 TCGA-D5-6540 
       11.08        16.14 

$`DCAF6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DCAF6 MUTATED DCAF6 WILD-TYPE 
           4.01            0.00 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
          83.24          148.01 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
          23.23           22.06 
[1] "4.0 - 83.2 (23.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D461V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCAF6 MUTATED         2        0        0         8         3         0
  DCAF6 WILD-TYPE      62        1       26       100         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCAF6 MUTATED           0          0          1          0        0         0
  DCAF6 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  DCAF6 MUTATED           0
  DCAF6 WILD-TYPE         1
D461V3, multiclass
            clus
vv           DCAF6 MUTATED DCAF6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DCAF6 MUTATED     1   2   9   3
  DCAF6 WILD-TYPE   8  65 240  38
D461V4, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             9             240
  T4             3              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
  DCAF6 MUTATED    14   1   0
  DCAF6 WILD-TYPE 206  80  66
D461V5, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  N0            14             206
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V6, binary
                 cls
clus                0   1
  DCAF6 MUTATED    13   0
  DCAF6 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     13    0
  DCAF6 WILD-TYPE  272   48
   clus
vv  DCAF6 MUTATED DCAF6 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D461V7, binary
                 cls
clus                0   1
  DCAF6 MUTATED     7   8
  DCAF6 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED      7    8
  DCAF6 WILD-TYPE  163  189
        clus
vv       DCAF6 MUTATED DCAF6 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D461V8, binary
                 cls
clus                0   1
  DCAF6 MUTATED    13   0
  DCAF6 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     13    0
  DCAF6 WILD-TYPE  287    8
     clus
vv    DCAF6 MUTATED DCAF6 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D461V9, binary
                 cls
clus                0   1
  DCAF6 MUTATED    13   2
  DCAF6 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     13    2
  DCAF6 WILD-TYPE  301   46
                               clus
vv                              DCAF6 MUTATED DCAF6 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DCAF6 MUTATED    12   0   0   2
  DCAF6 WILD-TYPE 247   3  22  19
D461V10, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             2              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"
D461V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCAF6 MUTATED                                  0     3
  DCAF6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCAF6 MUTATED                           1     6
  DCAF6 WILD-TYPE                        18   170
D461V12, multiclass
                                  clus
vv                                 DCAF6 MUTATED DCAF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = HIST1H1E MUTATION ANALYSIS
D462V1, survival
                    sevent
clus2                  0   1
  HIST1H1E MUTATED     5   1
  HIST1H1E WILD-TYPE 272  77
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                349 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 1                 77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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              22.09 
[1] "12.8 - 49.4 (18.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D462V2, continuous
                    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      63        1       25       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1E MUTATED           0          0          0          0        0
  HIST1H1E WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1E MUTATED           0         0
  HIST1H1E WILD-TYPE        12         1
D462V3, multiclass
            clus
vv           HIST1H1E MUTATED HIST1H1E WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  HIST1H1E MUTATED     0   1   5   0
  HIST1H1E WILD-TYPE   9  66 244  41
D462V4, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                5                244
  T4                0                 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
  HIST1H1E MUTATED     6   0   0
  HIST1H1E WILD-TYPE 214  81  66
D462V5, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  N0                6                214
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V6, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     5   0
  HIST1H1E WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      5    0
  HIST1H1E WILD-TYPE  280   48
   clus
vv  HIST1H1E MUTATED HIST1H1E WILD-TYPE
  0                5                280
  1                0                 48
[1] 2 2
[1] FALSE
D462V7, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     3   3
  HIST1H1E WILD-TYPE 167 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      3    3
  HIST1H1E WILD-TYPE  167  194
        clus
vv       HIST1H1E MUTATED HIST1H1E WILD-TYPE
  FEMALE                3                167
  MALE                  3                194
[1] 2 2
[1] FALSE
D462V8, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     6   0
  HIST1H1E WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      6    0
  HIST1H1E WILD-TYPE  294    8
     clus
vv    HIST1H1E MUTATED HIST1H1E WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D462V9, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     5   1
  HIST1H1E WILD-TYPE 309  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      5    1
  HIST1H1E WILD-TYPE  309   47
                               clus
vv                              HIST1H1E MUTATED HIST1H1E WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1E MUTATED     4   0   0   1
  HIST1H1E WILD-TYPE 255   3  22  20
D462V10, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  R0                4                255
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D462V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1E MUTATED                                  0     1
  HIST1H1E WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1E MUTATED                           2     3
  HIST1H1E WILD-TYPE                        17   173
D462V12, multiclass
                                  clus
vv                                 HIST1H1E MUTATED HIST1H1E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                           3                173
[1] 4 2
[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 = ADK MUTATION ANALYSIS
D463V1, survival
               sevent
clus2             0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 270  78
  ADK MUTATED ADK WILD-TYPE 
            7           348 
  ADK MUTATED ADK WILD-TYPE 
            0            78 
$`ADK MUTATED`
TCGA-G4-6588 TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-5254 
       26.17        34.98        21.44        17.82        58.39        12.69 
TCGA-CM-5349 
       30.08 

$`ADK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20         1.41         5.13        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-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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        22.045 
[1] "12.7 - 58.4 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D463V2, continuous
               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      64        1       26       103         7         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        18          6         43         33       35        12
               vv
clus            STAGE IVB
  ADK MUTATED           0
  ADK WILD-TYPE         1
D463V3, multiclass
            clus
vv           ADK MUTATED ADK WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            5           103
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  ADK MUTATED     0   0   6   1
  ADK WILD-TYPE   9  67 243  40
D463V4, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  T1           0             9
  T2           0            67
  T3           6           243
  T4           1            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
  ADK MUTATED     6   1   0
  ADK WILD-TYPE 214  80  66
D463V5, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  N0           6           214
  N1           1            80
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V6, binary
               cls
clus              0   1
  ADK MUTATED     6   0
  ADK WILD-TYPE 279  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      6    0
  ADK WILD-TYPE  279   48
   clus
vv  ADK MUTATED ADK WILD-TYPE
  0           6           279
  1           0            48
[1] 2 2
[1] FALSE
D463V7, binary
               cls
clus              0   1
  ADK MUTATED     5   2
  ADK WILD-TYPE 165 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      5    2
  ADK WILD-TYPE  165  195
        clus
vv       ADK MUTATED ADK WILD-TYPE
  FEMALE           5           165
  MALE             2           195
[1] 2 2
[1] FALSE
D463V8, binary
               cls
clus              0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 293   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      7    0
  ADK WILD-TYPE  293    8
     clus
vv    ADK MUTATED ADK WILD-TYPE
  NO            7           293
  YES           0             8
[1] 2 2
[1] FALSE
D463V9, binary
               cls
clus              0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 307  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      7    0
  ADK WILD-TYPE  307   48
                               clus
vv                              ADK MUTATED ADK WILD-TYPE
  COLON ADENOCARCINOMA                    7           307
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ADK MUTATED     6   0   0   1
  ADK WILD-TYPE 253   3  22  20
D463V10, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  R0           6           253
  R1           0             3
  R2           0            22
  RX           1            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"
D463V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADK MUTATED                                  0     1
  ADK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ADK MUTATED                           1     4
  ADK WILD-TYPE                        18   172
D463V12, multiclass
                                  clus
vv                                 ADK MUTATED ADK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      4           172
[1] 4 2
[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 = RPA3 MUTATION ANALYSIS
D464V1, survival
                sevent
clus2              0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 273  78
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            351 
  RPA3 MUTATED RPA3 WILD-TYPE 
             0             78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         22.090 
[1] "1.0 - 85.5 (9.0)"   "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D464V2, continuous
                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      63        1       24       108         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  RPA3 MUTATED           0
  RPA3 WILD-TYPE         1
D464V3, multiclass
            clus
vv           RPA3 MUTATED RPA3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RPA3 MUTATED     0   1   2   1
  RPA3 WILD-TYPE   9  66 247  40
D464V4, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            1             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
  RPA3 MUTATED     3   1   0
  RPA3 WILD-TYPE 217  80  66
D464V5, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  N0            3            217
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V6, binary
                cls
clus               0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      4    0
  RPA3 WILD-TYPE  281   48
   clus
vv  RPA3 MUTATED RPA3 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D464V7, binary
                cls
clus               0   1
  RPA3 MUTATED     2   2
  RPA3 WILD-TYPE 168 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      2    2
  RPA3 WILD-TYPE  168  195
        clus
vv       RPA3 MUTATED RPA3 WILD-TYPE
  FEMALE            2            168
  MALE              2            195
[1] 2 2
[1] FALSE
D464V8, binary
                cls
clus               0   1
  RPA3 MUTATED     3   0
  RPA3 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      3    0
  RPA3 WILD-TYPE  297    8
     clus
vv    RPA3 MUTATED RPA3 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D464V9, binary
                cls
clus               0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      4    0
  RPA3 WILD-TYPE  310   48
                               clus
vv                              RPA3 MUTATED RPA3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RPA3 MUTATED     4   0   0   0
  RPA3 WILD-TYPE 255   3  22  21
D464V10, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D464V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPA3 MUTATED                                  0     0
  RPA3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPA3 MUTATED                           1     1
  RPA3 WILD-TYPE                        18   175
D464V12, multiclass
[1] "Remove cluster labels:" "RPA3 MUTATED"          
clus
  RPA3 MUTATED RPA3 WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6600     TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6607     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-5913     TCGA-CK-5914 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6677 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 

Clustering(465) Variable = NFATC3 MUTATION ANALYSIS
D465V1, survival
                  sevent
clus2                0   1
  NFATC3 MUTATED     9   1
  NFATC3 WILD-TYPE 268  77
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              10              345 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
               1               77 
$`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 
       17.03        18.25        16.14        65.85 

$`NFATC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        3.02         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 
       74.56        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NFATC3 MUTATED NFATC3 WILD-TYPE 
            12.2              0.0 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
           65.85           148.01 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
           21.32            22.06 
[1] "12.2 - 65.8 (21.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D465V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFATC3 MUTATED         3        0        2         3         1         0
  NFATC3 WILD-TYPE      61        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFATC3 MUTATED           0          0          0          0        2
  NFATC3 WILD-TYPE        18          6         44         33       33
                  vv
clus               STAGE IVA STAGE IVB
  NFATC3 MUTATED           1         0
  NFATC3 WILD-TYPE        11         1
D465V3, multiclass
            clus
vv           NFATC3 MUTATED NFATC3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               1               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
  NFATC3 MUTATED     0   3   5   4
  NFATC3 WILD-TYPE   9  64 244  37
D465V4, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              4               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
  NFATC3 MUTATED     9   3   0
  NFATC3 WILD-TYPE 211  78  66
D465V5, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V6, binary
                  cls
clus                 0   1
  NFATC3 MUTATED     9   3
  NFATC3 WILD-TYPE 276  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED      9    3
  NFATC3 WILD-TYPE  276   45
   clus
vv  NFATC3 MUTATED NFATC3 WILD-TYPE
  0              9              276
  1              3               45
[1] 2 2
[1] FALSE
D465V7, binary
                  cls
clus                 0   1
  NFATC3 MUTATED     5   7
  NFATC3 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED      5    7
  NFATC3 WILD-TYPE  165  190
        clus
vv       NFATC3 MUTATED NFATC3 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D465V8, binary
                  cls
clus                 0   1
  NFATC3 MUTATED    10   0
  NFATC3 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED     10    0
  NFATC3 WILD-TYPE  290    8
     clus
vv    NFATC3 MUTATED NFATC3 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D465V9, binary
                  cls
clus                 0   1
  NFATC3 MUTATED    10   2
  NFATC3 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED     10    2
  NFATC3 WILD-TYPE  304   46
                               clus
vv                              NFATC3 MUTATED NFATC3 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NFATC3 MUTATED     8   0   1   2
  NFATC3 WILD-TYPE 251   3  21  19
D465V10, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              1               21
  RX              2               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"
D465V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFATC3 MUTATED                                  0     2
  NFATC3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFATC3 MUTATED                           0     5
  NFATC3 WILD-TYPE                        19   171
D465V12, multiclass
                                  clus
vv                                 NFATC3 MUTATED NFATC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = C9ORF84 MUTATION ANALYSIS
D466V1, survival
                   sevent
clus2                 0   1
  C9ORF84 MUTATED    13   6
  C9ORF84 WILD-TYPE 264  72
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               19               336 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
                6                72 
$`C9ORF84 MUTATED`
TCGA-AA-3715 TCGA-G4-6310 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3845 TCGA-AA-A00J 
       19.04        63.62        19.66         7.04         0.00        18.05 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       34.98        12.16        83.24        12.39        12.76        10.06 
TCGA-CK-6751 TCGA-CM-4746 TCGA-D5-6923 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6304 
      124.27        37.02        12.43        13.25        35.31        53.62 
TCGA-G4-6307 
       55.04 

$`C9ORF84 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        20.28         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.36        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
                0                 0 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
           124.27            148.01 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
            19.04             22.09 
[1] "0.0 - 124.3 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D466V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF84 MUTATED         5        0        2         6         2         0
  C9ORF84 WILD-TYPE      59        1       24       102         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF84 MUTATED           0          0          3          1        0
  C9ORF84 WILD-TYPE        18          6         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF84 MUTATED           1         0
  C9ORF84 WILD-TYPE        11         1
D466V3, multiclass
            clus
vv           C9ORF84 MUTATED C9ORF84 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                6               102
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  C9ORF84 MUTATED     0   5  11   4
  C9ORF84 WILD-TYPE   9  62 238  37
D466V4, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3              11               238
  T4               4                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
  C9ORF84 MUTATED    15   5   0
  C9ORF84 WILD-TYPE 205  76  66
D466V5, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  N0              15               205
  N1               5                76
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V6, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    16   1
  C9ORF84 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     16    1
  C9ORF84 WILD-TYPE  269   47
   clus
vv  C9ORF84 MUTATED C9ORF84 WILD-TYPE
  0              16               269
  1               1                47
[1] 2 2
[1] FALSE
D466V7, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED     8  12
  C9ORF84 WILD-TYPE 162 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED      8   12
  C9ORF84 WILD-TYPE  162  185
        clus
vv       C9ORF84 MUTATED C9ORF84 WILD-TYPE
  FEMALE               8               162
  MALE                12               185
[1] 2 2
[1] FALSE
D466V8, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    17   1
  C9ORF84 WILD-TYPE 283   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     17    1
  C9ORF84 WILD-TYPE  283    7
     clus
vv    C9ORF84 MUTATED C9ORF84 WILD-TYPE
  NO               17               283
  YES               1                 7
[1] 2 2
[1] FALSE
D466V9, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    13   7
  C9ORF84 WILD-TYPE 301  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     13    7
  C9ORF84 WILD-TYPE  301   41
                               clus
vv                              C9ORF84 MUTATED C9ORF84 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C9ORF84 MUTATED    17   0   0   3
  C9ORF84 WILD-TYPE 242   3  22  18
D466V10, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  R0              17               242
  R1               0                 3
  R2               0                22
  RX               3                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"
D466V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF84 MUTATED                                  0     4
  C9ORF84 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C9ORF84 MUTATED                           1     9
  C9ORF84 WILD-TYPE                        18   167
D466V12, multiclass
                                  clus
vv                                 C9ORF84 MUTATED C9ORF84 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 6
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          9               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(467) Variable = IKZF4 MUTATION ANALYSIS
D467V1, survival
                 sevent
clus2               0   1
  IKZF4 MUTATED     9   3
  IKZF4 WILD-TYPE 268  75
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             12             343 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
              3              75 
$`IKZF4 MUTATED`
TCGA-AZ-6601 TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3977 TCGA-AY-6197 TCGA-AY-6386 
      100.01         8.38        23.87        25.02        21.44        17.82 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CK-5914 TCGA-CM-5861 TCGA-D5-6924 TCGA-G4-6306 
       12.10        29.56        21.99        15.02        14.30        44.68 

$`IKZF4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        6.77         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  IKZF4 MUTATED IKZF4 WILD-TYPE 
           8.38            0.00 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
         100.01          148.01 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
         21.715          22.090 
[1] "8.4 - 100.0 (21.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D467V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKZF4 MUTATED         0        0        1         4         0         0
  IKZF4 WILD-TYPE      64        1       25       104         8         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        17          6         41         33       34        12
                 vv
clus              STAGE IVB
  IKZF4 MUTATED           0
  IKZF4 WILD-TYPE         1
D467V3, multiclass
            clus
vv           IKZF4 MUTATED IKZF4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  IKZF4 MUTATED     0   3   9   1
  IKZF4 WILD-TYPE   9  64 240  40
D467V4, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             1              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
  IKZF4 MUTATED     7   5   1
  IKZF4 WILD-TYPE 213  76  65
D467V5, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  N0             7             213
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V6, binary
                 cls
clus                0   1
  IKZF4 MUTATED     8   1
  IKZF4 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED      8    1
  IKZF4 WILD-TYPE  277   47
   clus
vv  IKZF4 MUTATED IKZF4 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D467V7, binary
                 cls
clus                0   1
  IKZF4 MUTATED     4   9
  IKZF4 WILD-TYPE 166 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED      4    9
  IKZF4 WILD-TYPE  166  188
        clus
vv       IKZF4 MUTATED IKZF4 WILD-TYPE
  FEMALE             4             166
  MALE               9             188
[1] 2 2
[1] FALSE
D467V8, binary
                 cls
clus                0   1
  IKZF4 MUTATED    11   0
  IKZF4 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED     11    0
  IKZF4 WILD-TYPE  289    8
     clus
vv    IKZF4 MUTATED IKZF4 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D467V9, binary
                 cls
clus                0   1
  IKZF4 MUTATED    13   0
  IKZF4 WILD-TYPE 301  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED     13    0
  IKZF4 WILD-TYPE  301   48
                               clus
vv                              IKZF4 MUTATED IKZF4 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IKZF4 MUTATED     6   0   0   1
  IKZF4 WILD-TYPE 253   3  22  20
D467V10, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D467V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IKZF4 MUTATED                                  0     0
  IKZF4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IKZF4 MUTATED                           3     8
  IKZF4 WILD-TYPE                        16   168
D467V12, multiclass
                                  clus
vv                                 IKZF4 MUTATED IKZF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        8             168
[1] 4 2
[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 = MAP7D1 MUTATION ANALYSIS
D468V1, survival
                  sevent
clus2                0   1
  MAP7D1 MUTATED    12   2
  MAP7D1 WILD-TYPE 265  76
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              14              341 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
               2               76 
$`MAP7D1 MUTATED`
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-5900 TCGA-AU-6004 
       35.80        79.69        19.66         4.01        12.16        27.09 
TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6930 
       14.30        51.32        30.08        15.02        12.00        13.35 
TCGA-DM-A1D8 TCGA-G4-6309 
       12.59        85.48 

$`MAP7D1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        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-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
            4.01             0.00 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           85.48           148.01 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           17.34            22.09 
[1] "4.0 - 85.5 (17.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D468V2, continuous
                  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      61        1       26       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D1 MUTATED           0          0          2          1        0
  MAP7D1 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  MAP7D1 MUTATED           0         0
  MAP7D1 WILD-TYPE        12         1
D468V3, multiclass
            clus
vv           MAP7D1 MUTATED MAP7D1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  MAP7D1 MUTATED     0   3   9   3
  MAP7D1 WILD-TYPE   9  64 240  38
D468V4, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              9              240
  T4              3               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
  MAP7D1 MUTATED    11   4   0
  MAP7D1 WILD-TYPE 209  77  66
D468V5, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  N0             11              209
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V6, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    10   0
  MAP7D1 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     10    0
  MAP7D1 WILD-TYPE  275   48
   clus
vv  MAP7D1 MUTATED MAP7D1 WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D468V7, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     9   6
  MAP7D1 WILD-TYPE 161 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      9    6
  MAP7D1 WILD-TYPE  161  191
        clus
vv       MAP7D1 MUTATED MAP7D1 WILD-TYPE
  FEMALE              9              161
  MALE                6              191
[1] 2 2
[1] FALSE
D468V8, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    11   0
  MAP7D1 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     11    0
  MAP7D1 WILD-TYPE  289    8
     clus
vv    MAP7D1 MUTATED MAP7D1 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D468V9, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    10   5
  MAP7D1 WILD-TYPE 304  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     10    5
  MAP7D1 WILD-TYPE  304   43
                               clus
vv                              MAP7D1 MUTATED MAP7D1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP7D1 MUTATED    11   0   0   3
  MAP7D1 WILD-TYPE 248   3  22  18
D468V10, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              3               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"
D468V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP7D1 MUTATED                                  0     1
  MAP7D1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP7D1 MUTATED                           1    12
  MAP7D1 WILD-TYPE                        18   164
D468V12, multiclass
                                  clus
vv                                 MAP7D1 MUTATED MAP7D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = LRRC39 MUTATION ANALYSIS
D469V1, survival
                  sevent
clus2                0   1
  LRRC39 MUTATED     7   1
  LRRC39 WILD-TYPE 270  77
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               8              347 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               1               77 
$`LRRC39 MUTATED`
TCGA-G4-6628 TCGA-A6-5662 TCGA-AA-3811 TCGA-AA-3977 TCGA-AU-6004 TCGA-CA-6717 
       79.69        23.61        10.06        25.02        27.09        12.76 
TCGA-CM-4743 TCGA-D5-6540 
       23.05        16.14 

$`LRRC39 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LRRC39 MUTATED LRRC39 WILD-TYPE 
           10.06             0.00 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
           79.69           148.01 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
           23.33            22.03 
[1] "10.1 - 79.7 (23.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D469V2, continuous
                  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      61        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC39 MUTATED           1          0          0          0        0
  LRRC39 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRC39 MUTATED           1         0
  LRRC39 WILD-TYPE        11         1
D469V3, multiclass
            clus
vv           LRRC39 MUTATED LRRC39 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  LRRC39 MUTATED     0   4   4   0
  LRRC39 WILD-TYPE   9  63 245  41
D469V4, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  T1              0                9
  T2              4               63
  T3              4              245
  T4              0               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
  LRRC39 MUTATED     6   0   2
  LRRC39 WILD-TYPE 214  81  64
D469V5, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V6, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     6   1
  LRRC39 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      6    1
  LRRC39 WILD-TYPE  279   47
   clus
vv  LRRC39 MUTATED LRRC39 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D469V7, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     2   6
  LRRC39 WILD-TYPE 168 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      2    6
  LRRC39 WILD-TYPE  168  191
        clus
vv       LRRC39 MUTATED LRRC39 WILD-TYPE
  FEMALE              2              168
  MALE                6              191
[1] 2 2
[1] FALSE
D469V8, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     7   0
  LRRC39 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      7    0
  LRRC39 WILD-TYPE  293    8
     clus
vv    LRRC39 MUTATED LRRC39 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D469V9, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     6   2
  LRRC39 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      6    2
  LRRC39 WILD-TYPE  308   46
                               clus
vv                              LRRC39 MUTATED LRRC39 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LRRC39 MUTATED     5   0   0   1
  LRRC39 WILD-TYPE 254   3  22  20
D469V10, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D469V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC39 MUTATED                                  0     1
  LRRC39 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRC39 MUTATED                           0     5
  LRRC39 WILD-TYPE                        19   171
D469V12, multiclass
                                  clus
vv                                 LRRC39 MUTATED LRRC39 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = RING1 MUTATION ANALYSIS
D470V1, survival
                 sevent
clus2               0   1
  RING1 MUTATED     8   0
  RING1 WILD-TYPE 269  78
  RING1 MUTATED RING1 WILD-TYPE 
              8             347 
  RING1 MUTATED RING1 WILD-TYPE 
              0              78 
$`RING1 MUTATED`
TCGA-AA-3713 TCGA-G4-6586 TCGA-A6-6141 TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-6171 
       19.04        35.80         8.38        58.39        23.05        14.04 
TCGA-D5-6930 TCGA-DM-A1HA 
       13.35       131.51 

$`RING1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50        44.32       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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RING1 MUTATED RING1 WILD-TYPE 
           8.38            0.00 
  RING1 MUTATED RING1 WILD-TYPE 
         131.51          148.01 
  RING1 MUTATED RING1 WILD-TYPE 
         21.045          22.060 
[1] "8.4 - 131.5 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "2.5e+07"
D470V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RING1 MUTATED         1        0        0         6         1         0
  RING1 WILD-TYPE      63        1       26       102         7         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        18          6         44         32       34        12
                 vv
clus              STAGE IVB
  RING1 MUTATED           0
  RING1 WILD-TYPE         1
D470V3, multiclass
            clus
vv           RING1 MUTATED RING1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  RING1 MUTATED     0   1   8   1
  RING1 WILD-TYPE   9  66 241  40
D470V4, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             1              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
  RING1 MUTATED     9   0   1
  RING1 WILD-TYPE 211  81  65
D470V5, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V6, binary
                 cls
clus                0   1
  RING1 MUTATED     8   1
  RING1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      8    1
  RING1 WILD-TYPE  277   47
   clus
vv  RING1 MUTATED RING1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D470V7, binary
                 cls
clus                0   1
  RING1 MUTATED     4   6
  RING1 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      4    6
  RING1 WILD-TYPE  166  191
        clus
vv       RING1 MUTATED RING1 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D470V8, binary
                 cls
clus                0   1
  RING1 MUTATED     6   1
  RING1 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      6    1
  RING1 WILD-TYPE  294    7
     clus
vv    RING1 MUTATED RING1 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D470V9, binary
                 cls
clus                0   1
  RING1 MUTATED     9   1
  RING1 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      9    1
  RING1 WILD-TYPE  305   47
                               clus
vv                              RING1 MUTATED RING1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RING1 MUTATED     6   0   1   1
  RING1 WILD-TYPE 253   3  21  20
D470V10, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             1              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"
D470V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RING1 MUTATED                                  0     0
  RING1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RING1 MUTATED                           1     7
  RING1 WILD-TYPE                        18   169
D470V12, multiclass
                                  clus
vv                                 RING1 MUTATED RING1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = VCX2 MUTATION ANALYSIS
D471V1, survival
                sevent
clus2              0   1
  VCX2 MUTATED     4   2
  VCX2 WILD-TYPE 273  76
  VCX2 MUTATED VCX2 WILD-TYPE 
             6            349 
  VCX2 MUTATED VCX2 WILD-TYPE 
             2             76 
$`VCX2 MUTATED`
TCGA-G4-6586 TCGA-A6-5656 TCGA-A6-5657 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-F4-6460 
       35.80        32.91        31.63        11.38        13.32        31.96 

$`VCX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.75        36.53        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  VCX2 MUTATED VCX2 WILD-TYPE 
         11.38           0.00 
  VCX2 MUTATED VCX2 WILD-TYPE 
         35.80         148.01 
  VCX2 MUTATED VCX2 WILD-TYPE 
        31.795         22.030 
[1] "11.4 - 35.8 (31.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D471V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VCX2 MUTATED         1        0        0         3         0         0
  VCX2 WILD-TYPE      63        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCX2 MUTATED           1          0          2          0        0         0
  VCX2 WILD-TYPE        17          6         42         33       35        12
                vv
clus             STAGE IVB
  VCX2 MUTATED           0
  VCX2 WILD-TYPE         1
D471V3, multiclass
            clus
vv           VCX2 MUTATED VCX2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  VCX2 MUTATED     0   1   6   0
  VCX2 WILD-TYPE   9  66 243  41
D471V4, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            0             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
  VCX2 MUTATED     4   2   1
  VCX2 WILD-TYPE 216  79  65
D471V5, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  N0            4            216
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V6, binary
                cls
clus               0   1
  VCX2 MUTATED     7   0
  VCX2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      7    0
  VCX2 WILD-TYPE  278   48
   clus
vv  VCX2 MUTATED VCX2 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D471V7, binary
                cls
clus               0   1
  VCX2 MUTATED     2   5
  VCX2 WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      2    5
  VCX2 WILD-TYPE  168  192
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D471V8, binary
                cls
clus               0   1
  VCX2 MUTATED     5   0
  VCX2 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      5    0
  VCX2 WILD-TYPE  295    8
     clus
vv    VCX2 MUTATED VCX2 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D471V9, binary
                cls
clus               0   1
  VCX2 MUTATED     6   0
  VCX2 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      6    0
  VCX2 WILD-TYPE  308   48
                               clus
vv                              VCX2 MUTATED VCX2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  VCX2 MUTATED     5   0   0   0
  VCX2 WILD-TYPE 254   3  22  21
D471V10, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D471V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VCX2 MUTATED                                  0     0
  VCX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VCX2 MUTATED                           1     5
  VCX2 WILD-TYPE                        18   171
D471V12, multiclass
                                  clus
vv                                 VCX2 MUTATED VCX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = N4BP2 MUTATION ANALYSIS
D472V1, survival
                 sevent
clus2               0   1
  N4BP2 MUTATED    17   6
  N4BP2 WILD-TYPE 260  72
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             23             332 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              6              72 
$`N4BP2 MUTATED`
TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6651 
       26.17        42.90        32.75        32.71        25.18        21.76 
TCGA-AA-3819 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02        30.02        34.98        12.16        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-6162 TCGA-CM-6171 
       12.76        10.06        21.14        82.95        12.00        14.04 
TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-6538 TCGA-DM-A28C TCGA-F4-6704 
       13.05        45.40        17.13        81.37         1.55 

$`N4BP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       43.76        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-A6-6652 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.99         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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-6676 
       12.99        13.02        15.02        11.01        12.95        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  N4BP2 MUTATED N4BP2 WILD-TYPE 
           1.55            0.00 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          82.95          148.01 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          25.18           22.01 
[1] "1.6 - 83.0 (25.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D472V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  N4BP2 MUTATED         3        0        1        10         3         1
  N4BP2 WILD-TYPE      61        1       25        98         5         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        18          6         41         32       35        11
                 vv
clus              STAGE IVB
  N4BP2 MUTATED           1
  N4BP2 WILD-TYPE         0
D472V3, multiclass
            clus
vv           N4BP2 MUTATED N4BP2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              11
  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     1   2  17   4
  N4BP2 WILD-TYPE   8  65 232  37
D472V4, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            17             232
  T4             4              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
  N4BP2 MUTATED    18   2   4
  N4BP2 WILD-TYPE 202  79  62
D472V5, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  N0            18             202
  N1             2              79
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V6, binary
                 cls
clus                0   1
  N4BP2 MUTATED    16   2
  N4BP2 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     16    2
  N4BP2 WILD-TYPE  269   46
   clus
vv  N4BP2 MUTATED N4BP2 WILD-TYPE
  0            16             269
  1             2              46
[1] 2 2
[1] FALSE
D472V7, binary
                 cls
clus                0   1
  N4BP2 MUTATED    13  11
  N4BP2 WILD-TYPE 157 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     13   11
  N4BP2 WILD-TYPE  157  186
        clus
vv       N4BP2 MUTATED N4BP2 WILD-TYPE
  FEMALE            13             157
  MALE              11             186
[1] 2 2
[1] FALSE
D472V8, binary
                 cls
clus                0   1
  N4BP2 MUTATED    21   0
  N4BP2 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     21    0
  N4BP2 WILD-TYPE  279    8
     clus
vv    N4BP2 MUTATED N4BP2 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D472V9, binary
                 cls
clus                0   1
  N4BP2 MUTATED    19   5
  N4BP2 WILD-TYPE 295  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     19    5
  N4BP2 WILD-TYPE  295   43
                               clus
vv                              N4BP2 MUTATED N4BP2 WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  N4BP2 MUTATED    14   0   0   5
  N4BP2 WILD-TYPE 245   3  22  16
D472V10, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             5              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"
D472V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  N4BP2 MUTATED                                  1     2
  N4BP2 WILD-TYPE                                0     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  N4BP2 MUTATED                           1    16
  N4BP2 WILD-TYPE                        18   160
D472V12, multiclass
                                  clus
vv                                 N4BP2 MUTATED N4BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       16             160
[1] 4 2
[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 = NRK MUTATION ANALYSIS
D473V1, survival
               sevent
clus2             0   1
  NRK MUTATED    18   3
  NRK WILD-TYPE 259  75
  NRK MUTATED NRK WILD-TYPE 
           21           334 
  NRK MUTATED NRK WILD-TYPE 
            3            75 
$`NRK MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6654 TCGA-AA-3511 
        1.02         0.92        33.53        32.71        23.87         6.97 
TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 
        6.97         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 
       15.02        14.04        12.00 

$`NRK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6780 TCGA-A6-6781 
       25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3710 TCGA-AA-3812 TCGA-AA-3815 
       11.01         5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  NRK MUTATED NRK WILD-TYPE 
         0.92          0.00 
  NRK MUTATED NRK WILD-TYPE 
        85.45        148.01 
  NRK MUTATED NRK WILD-TYPE 
        14.04         22.09 
[1] "0.9 - 85.5 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D473V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRK MUTATED         3        0        3         7         1         1
  NRK WILD-TYPE      61        1       23       101         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRK MUTATED           2          0          2          1        2         0
  NRK WILD-TYPE        16          6         42         32       33        12
               vv
clus            STAGE IVB
  NRK MUTATED           0
  NRK WILD-TYPE         1
D473V3, multiclass
            clus
vv           NRK MUTATED NRK WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            7           101
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           1            32
  STAGE IV             2            33
  STAGE IVA            0            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
  NRK MUTATED     0   4  14   5
  NRK WILD-TYPE   9  63 235  36
D473V4, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  T1           0             9
  T2           4            63
  T3          14           235
  T4           5            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
  NRK MUTATED    16   5   2
  NRK WILD-TYPE 204  76  64
D473V5, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0          16           204
  N1           5            76
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V6, binary
               cls
clus              0   1
  NRK MUTATED    18   2
  NRK WILD-TYPE 267  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     18    2
  NRK WILD-TYPE  267   46
   clus
vv  NRK MUTATED NRK WILD-TYPE
  0          18           267
  1           2            46
[1] 2 2
[1] FALSE
D473V7, binary
               cls
clus              0   1
  NRK MUTATED    14   9
  NRK WILD-TYPE 156 188
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     14    9
  NRK WILD-TYPE  156  188
        clus
vv       NRK MUTATED NRK WILD-TYPE
  FEMALE          14           156
  MALE             9           188
[1] 2 2
[1] FALSE
D473V8, binary
               cls
clus              0   1
  NRK MUTATED    18   0
  NRK WILD-TYPE 282   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     18    0
  NRK WILD-TYPE  282    8
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO           18           282
  YES           0             8
[1] 2 2
[1] FALSE
D473V9, binary
               cls
clus              0   1
  NRK MUTATED    20   3
  NRK WILD-TYPE 294  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     20    3
  NRK WILD-TYPE  294   45
                               clus
vv                              NRK MUTATED NRK WILD-TYPE
  COLON ADENOCARCINOMA                   20           294
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NRK MUTATED    13   1   1   3
  NRK WILD-TYPE 246   2  21  18
D473V10, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  R0          13           246
  R1           1             2
  R2           1            21
  RX           3            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"
D473V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRK MUTATED                                  0     1
  NRK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NRK MUTATED                           3     9
  NRK WILD-TYPE                        16   167
D473V12, multiclass
                                  clus
vv                                 NRK MUTATED NRK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  3            16
  WHITE                                      9           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(474) Variable = PTPRK MUTATION ANALYSIS
D474V1, survival
                 sevent
clus2               0   1
  PTPRK MUTATED    28   4
  PTPRK WILD-TYPE 249  74
  PTPRK MUTATED PTPRK WILD-TYPE 
             32             323 
  PTPRK MUTATED PTPRK WILD-TYPE 
              4              74 
$`PTPRK MUTATED`
TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6310 TCGA-G4-6588 
       19.04        24.03        24.00        25.08        63.62        26.17 
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-3815 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R TCGA-AA-A01V 
       33.04        33.01        25.02         4.01        35.01         1.02 
TCGA-AU-6004 TCGA-AY-6197 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5349 
       27.09        21.44        15.62        51.32        23.05        30.08 
TCGA-CM-6165 TCGA-CM-6674 TCGA-D5-6532 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-F4-6854 
       16.04        12.95        18.25        24.43        12.59         0.53 
TCGA-F4-6856 TCGA-G4-6304 
       35.31        53.62 

$`PTPRK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       31.07        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        22.09        35.80        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02        33.04        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56       148.01        85.45        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PTPRK MUTATED PTPRK WILD-TYPE 
           0.53            0.00 
  PTPRK MUTATED PTPRK WILD-TYPE 
          63.98          148.01 
  PTPRK MUTATED PTPRK WILD-TYPE 
          24.23           21.99 
[1] "0.5 - 64.0 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D474V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRK MUTATED         3        0        3        15         4         0
  PTPRK WILD-TYPE      61        1       23        93         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRK MUTATED           1          0          2          1        2         0
  PTPRK WILD-TYPE        17          6         42         32       33        12
                 vv
clus              STAGE IVB
  PTPRK MUTATED           0
  PTPRK WILD-TYPE         1
D474V3, multiclass
            clus
vv           PTPRK MUTATED PTPRK WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             15              93
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  PTPRK MUTATED     0   4  23   6
  PTPRK WILD-TYPE   9  63 226  35
D474V4, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  T1             0               9
  T2             4              63
  T3            23             226
  T4             6              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
  PTPRK MUTATED    26   3   4
  PTPRK WILD-TYPE 194  78  62
D474V5, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  N0            26             194
  N1             3              78
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V6, binary
                 cls
clus                0   1
  PTPRK MUTATED    27   2
  PTPRK WILD-TYPE 258  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     27    2
  PTPRK WILD-TYPE  258   46
   clus
vv  PTPRK MUTATED PTPRK WILD-TYPE
  0            27             258
  1             2              46
[1] 2 2
[1] FALSE
D474V7, binary
                 cls
clus                0   1
  PTPRK MUTATED    15  18
  PTPRK WILD-TYPE 155 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     15   18
  PTPRK WILD-TYPE  155  179
        clus
vv       PTPRK MUTATED PTPRK WILD-TYPE
  FEMALE            15             155
  MALE              18             179
[1] 2 2
[1] FALSE
D474V8, binary
                 cls
clus                0   1
  PTPRK MUTATED    24   2
  PTPRK WILD-TYPE 276   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     24    2
  PTPRK WILD-TYPE  276    6
     clus
vv    PTPRK MUTATED PTPRK WILD-TYPE
  NO             24             276
  YES             2               6
[1] 2 2
[1] FALSE
D474V9, binary
                 cls
clus                0   1
  PTPRK MUTATED    24   9
  PTPRK WILD-TYPE 290  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     24    9
  PTPRK WILD-TYPE  290   39
                               clus
vv                              PTPRK MUTATED PTPRK WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRK MUTATED    25   0   2   2
  PTPRK WILD-TYPE 234   3  20  19
D474V10, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  R0            25             234
  R1             0               3
  R2             2              20
  RX             2              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"
D474V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRK MUTATED                                  0     0
  PTPRK WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRK MUTATED                           1    19
  PTPRK WILD-TYPE                        18   157
D474V12, multiclass
                                  clus
vv                                 PTPRK MUTATED PTPRK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       19             157
[1] 4 2
[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 = HDAC1 MUTATION ANALYSIS
D475V1, survival
                 sevent
clus2               0   1
  HDAC1 MUTATED     4   1
  HDAC1 WILD-TYPE 273  77
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             350 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HDAC1 MUTATED HDAC1 WILD-TYPE 
           1.02            0.00 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
          33.53          148.01 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
          15.12           22.09 
[1] "1.0 - 33.5 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D475V2, continuous
                 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      64        1       25       106         8         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  HDAC1 MUTATED           0
  HDAC1 WILD-TYPE         1
D475V3, multiclass
            clus
vv           HDAC1 MUTATED HDAC1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HDAC1 MUTATED     0   0   4   1
  HDAC1 WILD-TYPE   9  67 245  40
D475V4, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  HDAC1 MUTATED     3   1   1
  HDAC1 WILD-TYPE 217  80  65
D475V5, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V6, binary
                 cls
clus                0   1
  HDAC1 MUTATED     2   1
  HDAC1 WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      2    1
  HDAC1 WILD-TYPE  283   47
   clus
vv  HDAC1 MUTATED HDAC1 WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D475V7, binary
                 cls
clus                0   1
  HDAC1 MUTATED     3   2
  HDAC1 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      3    2
  HDAC1 WILD-TYPE  167  195
        clus
vv       HDAC1 MUTATED HDAC1 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D475V8, binary
                 cls
clus                0   1
  HDAC1 MUTATED     4   0
  HDAC1 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      4    0
  HDAC1 WILD-TYPE  296    8
     clus
vv    HDAC1 MUTATED HDAC1 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D475V9, binary
                 cls
clus                0   1
  HDAC1 MUTATED     4   1
  HDAC1 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      4    1
  HDAC1 WILD-TYPE  310   47
                               clus
vv                              HDAC1 MUTATED HDAC1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HDAC1 MUTATED     2   0   1   1
  HDAC1 WILD-TYPE 257   3  21  20
D475V10, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             1              21
  RX             1              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"
D475V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC1 MUTATED                                  0     0
  HDAC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HDAC1 MUTATED                           1     2
  HDAC1 WILD-TYPE                        18   174
D475V12, multiclass
                                  clus
vv                                 HDAC1 MUTATED HDAC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(476) Variable = E2F7 MUTATION ANALYSIS
D476V1, survival
                sevent
clus2              0   1
  E2F7 MUTATED    13   6
  E2F7 WILD-TYPE 264  72
  E2F7 MUTATED E2F7 WILD-TYPE 
            19            336 
  E2F7 MUTATED E2F7 WILD-TYPE 
             6             72 
$`E2F7 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AD-6964 TCGA-G4-6310 
       13.02         0.92        85.05        19.04        10.88        63.62 
TCGA-G4-6586 TCGA-A6-5659 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-A00N 
       35.80        30.44         1.02         6.97         1.02         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-5862 TCGA-D5-5541 
       34.98        12.16        15.62        21.14         5.03        55.92 
TCGA-D5-6930 
       13.35 

$`E2F7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  E2F7 MUTATED E2F7 WILD-TYPE 
          0.92           0.00 
  E2F7 MUTATED E2F7 WILD-TYPE 
         85.05         148.01 
  E2F7 MUTATED E2F7 WILD-TYPE 
         13.35          22.39 
[1] "0.9 - 85.0 (13.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.8"
D476V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  E2F7 MUTATED         4        0        3         4         3         0
  E2F7 WILD-TYPE      60        1       23       104         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  E2F7 MUTATED           2          0          2          1        0         1
  E2F7 WILD-TYPE        16          6         42         32       35        11
                vv
clus             STAGE IVB
  E2F7 MUTATED           0
  E2F7 WILD-TYPE         1
D476V3, multiclass
            clus
vv           E2F7 MUTATED E2F7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             4            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  E2F7 MUTATED     1   3  12   5
  E2F7 WILD-TYPE   8  64 237  36
D476V4, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  T1            1              8
  T2            3             64
  T3           12            237
  T4            5             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
  E2F7 MUTATED    14   4   3
  E2F7 WILD-TYPE 206  77  63
D476V5, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  N0           14            206
  N1            4             77
  N2            3             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"
D476V6, binary
                cls
clus               0   1
  E2F7 MUTATED    17   1
  E2F7 WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     17    1
  E2F7 WILD-TYPE  268   47
   clus
vv  E2F7 MUTATED E2F7 WILD-TYPE
  0           17            268
  1            1             47
[1] 2 2
[1] FALSE
D476V7, binary
                cls
clus               0   1
  E2F7 MUTATED    10  11
  E2F7 WILD-TYPE 160 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     10   11
  E2F7 WILD-TYPE  160  186
        clus
vv       E2F7 MUTATED E2F7 WILD-TYPE
  FEMALE           10            160
  MALE             11            186
[1] 2 2
[1] FALSE
D476V8, binary
                cls
clus               0   1
  E2F7 MUTATED    15   1
  E2F7 WILD-TYPE 285   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     15    1
  E2F7 WILD-TYPE  285    7
     clus
vv    E2F7 MUTATED E2F7 WILD-TYPE
  NO            15            285
  YES            1              7
[1] 2 2
[1] FALSE
D476V9, binary
                cls
clus               0   1
  E2F7 MUTATED    15   6
  E2F7 WILD-TYPE 299  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     15    6
  E2F7 WILD-TYPE  299   42
                               clus
vv                              E2F7 MUTATED E2F7 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  E2F7 MUTATED    16   0   0   3
  E2F7 WILD-TYPE 243   3  22  18
D476V10, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            3             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"
D476V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  E2F7 MUTATED                                  0     0
  E2F7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  E2F7 MUTATED                           0    11
  E2F7 WILD-TYPE                        19   165
D476V12, multiclass
                                  clus
vv                                 E2F7 MUTATED E2F7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      11            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(477) Variable = SLC11A2 MUTATION ANALYSIS
D477V1, survival
                   sevent
clus2                 0   1
  SLC11A2 MUTATED     6   1
  SLC11A2 WILD-TYPE 271  77
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                7               348 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                1                77 
$`SLC11A2 MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6586 TCGA-AA-3949 TCGA-CM-6171 
       24.00        25.08        10.88        35.80        26.01        14.04 
TCGA-D5-6928 
       11.64 

$`SLC11A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
            10.88              0.00 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
            35.80            148.01 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
           24.000            22.045 
[1] "10.9 - 35.8 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D477V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC11A2 MUTATED         1        0        0         4         0         0
  SLC11A2 WILD-TYPE      63        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC11A2 MUTATED           0          0          2          0        0
  SLC11A2 WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC11A2 MUTATED           0         0
  SLC11A2 WILD-TYPE        12         1
D477V3, multiclass
            clus
vv           SLC11A2 MUTATED SLC11A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC11A2 MUTATED     0   1   6   1
  SLC11A2 WILD-TYPE   9  66 243  40
D477V4, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               1                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
  SLC11A2 MUTATED     5   2   1
  SLC11A2 WILD-TYPE 215  79  65
D477V5, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  N0               5               215
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V6, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     7   0
  SLC11A2 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      7    0
  SLC11A2 WILD-TYPE  278   48
   clus
vv  SLC11A2 MUTATED SLC11A2 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D477V7, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     5   3
  SLC11A2 WILD-TYPE 165 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      5    3
  SLC11A2 WILD-TYPE  165  194
        clus
vv       SLC11A2 MUTATED SLC11A2 WILD-TYPE
  FEMALE               5               165
  MALE                 3               194
[1] 2 2
[1] FALSE
D477V8, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     7   0
  SLC11A2 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      7    0
  SLC11A2 WILD-TYPE  293    8
     clus
vv    SLC11A2 MUTATED SLC11A2 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D477V9, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     5   3
  SLC11A2 WILD-TYPE 309  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      5    3
  SLC11A2 WILD-TYPE  309   45
                               clus
vv                              SLC11A2 MUTATED SLC11A2 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC11A2 MUTATED     7   0   0   0
  SLC11A2 WILD-TYPE 252   3  22  21
D477V10, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D477V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC11A2 MUTATED                                  0     0
  SLC11A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC11A2 MUTATED                           0     5
  SLC11A2 WILD-TYPE                        19   171
D477V12, multiclass
                                  clus
vv                                 SLC11A2 MUTATED SLC11A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = HIF3A MUTATION ANALYSIS
D478V1, survival
                 sevent
clus2               0   1
  HIF3A MUTATED     8   6
  HIF3A WILD-TYPE 269  72
  HIF3A MUTATED HIF3A WILD-TYPE 
             14             341 
  HIF3A MUTATED HIF3A WILD-TYPE 
              6              72 
$`HIF3A MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-6653 
       10.88       100.01        26.17        79.69        42.90        24.39 
TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6606 
       31.00        26.01         4.01        34.98        83.24        11.74 
TCGA-CM-5349 TCGA-CM-5861 
       30.08        15.02 

$`HIF3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        43.76        46.65        43.76        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-A6-6648 
       32.71        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       18.05         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41         6.77        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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          21.990 
[1] "4.0 - 100.0 (28.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D478V2, continuous
                 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      61        1       24       104         5         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  HIF3A MUTATED           0
  HIF3A WILD-TYPE         1
D478V3, multiclass
            clus
vv           HIF3A MUTATED HIF3A WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HIF3A MUTATED     1   2   6   6
  HIF3A WILD-TYPE   8  65 243  35
D478V4, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  T1             1               8
  T2             2              65
  T3             6             243
  T4             6              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
  HIF3A MUTATED    12   1   2
  HIF3A WILD-TYPE 208  80  64
D478V5, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  N0            12             208
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V6, binary
                 cls
clus                0   1
  HIF3A MUTATED    13   1
  HIF3A WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     13    1
  HIF3A WILD-TYPE  272   47
   clus
vv  HIF3A MUTATED HIF3A WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D478V7, binary
                 cls
clus                0   1
  HIF3A MUTATED     8   7
  HIF3A WILD-TYPE 162 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED      8    7
  HIF3A WILD-TYPE  162  190
        clus
vv       HIF3A MUTATED HIF3A WILD-TYPE
  FEMALE             8             162
  MALE               7             190
[1] 2 2
[1] FALSE
D478V8, binary
                 cls
clus                0   1
  HIF3A MUTATED    13   0
  HIF3A WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     13    0
  HIF3A WILD-TYPE  287    8
     clus
vv    HIF3A MUTATED HIF3A WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D478V9, binary
                 cls
clus                0   1
  HIF3A MUTATED    12   3
  HIF3A WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     12    3
  HIF3A WILD-TYPE  302   45
                               clus
vv                              HIF3A MUTATED HIF3A WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HIF3A MUTATED    11   0   0   0
  HIF3A WILD-TYPE 248   3  22  21
D478V10, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D478V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIF3A MUTATED                                  0     1
  HIF3A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIF3A MUTATED                           0     9
  HIF3A WILD-TYPE                        19   167
D478V12, multiclass
                                  clus
vv                                 HIF3A MUTATED HIF3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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 = NOX5 MUTATION ANALYSIS
D479V1, survival
                sevent
clus2              0   1
  NOX5 MUTATED     5   0
  NOX5 WILD-TYPE 272  78
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            350 
  NOX5 MUTATED NOX5 WILD-TYPE 
             0             78 
$`NOX5 MUTATED`
TCGA-AA-3713 TCGA-A6-6781 TCGA-AA-3966 TCGA-CA-6717 TCGA-D5-6930 
       19.04        19.66         2.01        12.76        13.35 

$`NOX5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NOX5 MUTATED NOX5 WILD-TYPE 
          2.01           0.00 
  NOX5 MUTATED NOX5 WILD-TYPE 
         19.66         148.01 
  NOX5 MUTATED NOX5 WILD-TYPE 
        13.350         22.225 
[1] "2.0 - 19.7 (13.3)"  "0.0 - 148.0 (22.2)"
[1] "hr="     "3300000"
D479V2, continuous
                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      64        1       26       105         8         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        18          6         44         32       34        12
                vv
clus             STAGE IVB
  NOX5 MUTATED           0
  NOX5 WILD-TYPE         1
D479V3, multiclass
            clus
vv           NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  NOX5 MUTATED     0   0   4   1
  NOX5 WILD-TYPE   9  67 245  40
D479V4, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            4            245
  T4            1             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
  NOX5 MUTATED     4   1   0
  NOX5 WILD-TYPE 216  80  66
D479V5, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V6, binary
                cls
clus               0   1
  NOX5 MUTATED     3   1
  NOX5 WILD-TYPE 282  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      3    1
  NOX5 WILD-TYPE  282   47
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0            3            282
  1            1             47
[1] 2 2
[1] FALSE
D479V7, binary
                cls
clus               0   1
  NOX5 MUTATED     1   4
  NOX5 WILD-TYPE 169 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      1    4
  NOX5 WILD-TYPE  169  193
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  FEMALE            1            169
  MALE              4            193
[1] 2 2
[1] FALSE
D479V8, binary
                cls
clus               0   1
  NOX5 MUTATED     3   1
  NOX5 WILD-TYPE 297   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      3    1
  NOX5 WILD-TYPE  297    7
     clus
vv    NOX5 MUTATED NOX5 WILD-TYPE
  NO             3            297
  YES            1              7
[1] 2 2
[1] FALSE
D479V9, binary
                cls
clus               0   1
  NOX5 MUTATED     1   4
  NOX5 WILD-TYPE 313  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      1    4
  NOX5 WILD-TYPE  313   44
                               clus
vv                              NOX5 MUTATED NOX5 WILD-TYPE
  COLON ADENOCARCINOMA                     1            313
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOX5 MUTATED     2   0   1   1
  NOX5 WILD-TYPE 257   3  21  20
D479V10, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            1             21
  RX            1             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"
D479V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOX5 MUTATED                                  0     1
  NOX5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOX5 MUTATED                           0     2
  NOX5 WILD-TYPE                        19   174
D479V12, multiclass
                                  clus
vv                                 NOX5 MUTATED NOX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(480) Variable = WWTR1 MUTATION ANALYSIS
D480V1, survival
                 sevent
clus2               0   1
  WWTR1 MUTATED     5   1
  WWTR1 WILD-TYPE 272  77
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              6             349 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              1              77 
$`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 

$`WWTR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  WWTR1 MUTATED WWTR1 WILD-TYPE 
          20.12            0.00 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
          29.95          148.01 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
          21.98           22.06 
[1] "20.1 - 29.9 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D480V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WWTR1 MUTATED         3        0        0         3         0         0
  WWTR1 WILD-TYPE      61        1       26       105         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  WWTR1 MUTATED           0
  WWTR1 WILD-TYPE         1
D480V3, multiclass
            clus
vv           WWTR1 MUTATED WWTR1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  WWTR1 MUTATED     1   2   3   0
  WWTR1 WILD-TYPE   8  65 246  41
D480V4, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             3             246
  T4             0              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
  WWTR1 MUTATED     6   0   0
  WWTR1 WILD-TYPE 214  81  66
D480V5, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  N0             6             214
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V6, binary
                 cls
clus                0   1
  WWTR1 MUTATED     4   0
  WWTR1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      4    0
  WWTR1 WILD-TYPE  281   48
   clus
vv  WWTR1 MUTATED WWTR1 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D480V7, binary
                 cls
clus                0   1
  WWTR1 MUTATED     3   3
  WWTR1 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      3    3
  WWTR1 WILD-TYPE  167  194
        clus
vv       WWTR1 MUTATED WWTR1 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D480V8, binary
                 cls
clus                0   1
  WWTR1 MUTATED     6   0
  WWTR1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      6    0
  WWTR1 WILD-TYPE  294    8
     clus
vv    WWTR1 MUTATED WWTR1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D480V9, binary
                 cls
clus                0   1
  WWTR1 MUTATED     4   2
  WWTR1 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      4    2
  WWTR1 WILD-TYPE  310   46
                               clus
vv                              WWTR1 MUTATED WWTR1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WWTR1 MUTATED     3   0   0   1
  WWTR1 WILD-TYPE 256   3  22  20
D480V10, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D480V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WWTR1 MUTATED                                  0     0
  WWTR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WWTR1 MUTATED                           0     4
  WWTR1 WILD-TYPE                        19   172
D480V12, multiclass
                                  clus
vv                                 WWTR1 MUTATED WWTR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = HGS MUTATION ANALYSIS
D481V1, survival
               sevent
clus2             0   1
  HGS MUTATED     7   3
  HGS WILD-TYPE 270  75
  HGS MUTATED HGS WILD-TYPE 
           10           345 
  HGS MUTATED HGS WILD-TYPE 
            3            75 
$`HGS MUTATED`
TCGA-AA-3496 TCGA-AZ-6601 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CK-6751 
        1.02       100.01        21.44        49.41        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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        22.060 
[1] "1.0 - 124.3 (35.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D481V2, continuous
               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      62        1       23       103         8         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        18          6         44         33       35        12
               vv
clus            STAGE IVB
  HGS MUTATED           0
  HGS WILD-TYPE         1
D481V3, multiclass
            clus
vv           HGS MUTATED HGS WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            5           103
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  HGS MUTATED     0   2   8   0
  HGS WILD-TYPE   9  65 241  41
D481V4, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  T1           0             9
  T2           2            65
  T3           8           241
  T4           0            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
  HGS MUTATED    10   0   0
  HGS WILD-TYPE 210  81  66
D481V5, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  N0          10           210
  N1           0            81
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V6, binary
               cls
clus              0   1
  HGS MUTATED     6   0
  HGS WILD-TYPE 279  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      6    0
  HGS WILD-TYPE  279   48
   clus
vv  HGS MUTATED HGS WILD-TYPE
  0           6           279
  1           0            48
[1] 2 2
[1] FALSE
D481V7, binary
               cls
clus              0   1
  HGS MUTATED     6   4
  HGS WILD-TYPE 164 193
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      6    4
  HGS WILD-TYPE  164  193
        clus
vv       HGS MUTATED HGS WILD-TYPE
  FEMALE           6           164
  MALE             4           193
[1] 2 2
[1] FALSE
D481V8, binary
               cls
clus              0   1
  HGS MUTATED     9   0
  HGS WILD-TYPE 291   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      9    0
  HGS WILD-TYPE  291    8
     clus
vv    HGS MUTATED HGS WILD-TYPE
  NO            9           291
  YES           0             8
[1] 2 2
[1] FALSE
D481V9, binary
               cls
clus              0   1
  HGS MUTATED     8   2
  HGS WILD-TYPE 306  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      8    2
  HGS WILD-TYPE  306   46
                               clus
vv                              HGS MUTATED HGS WILD-TYPE
  COLON ADENOCARCINOMA                    8           306
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  HGS MUTATED     6   0   0   2
  HGS WILD-TYPE 253   3  22  19
D481V10, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  R0           6           253
  R1           0             3
  R2           0            22
  RX           2            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"
D481V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HGS MUTATED                                  0     0
  HGS WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  HGS MUTATED                           0     9
  HGS WILD-TYPE                        19   167
D481V12, multiclass
                                  clus
vv                                 HGS MUTATED HGS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      9           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(482) Variable = NLK MUTATION ANALYSIS
D482V1, survival
               sevent
clus2             0   1
  NLK MUTATED    11   0
  NLK WILD-TYPE 266  78
  NLK MUTATED NLK WILD-TYPE 
           11           344 
  NLK MUTATED NLK WILD-TYPE 
            0            78 
$`NLK MUTATED`
TCGA-AA-3662 TCGA-A6-3807 TCGA-A6-5661 TCGA-AA-3663 TCGA-AU-6004 TCGA-CK-6747 
        6.05        34.65        33.53         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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 
       74.56        65.85        53.62        44.68        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NLK MUTATED NLK WILD-TYPE 
         6.05          0.00 
  NLK MUTATED NLK WILD-TYPE 
        85.48        148.01 
  NLK MUTATED NLK WILD-TYPE 
        33.53         21.99 
[1] "6.0 - 85.5 (33.5)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D482V2, continuous
               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      63        1       25       104         8         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        18          5         42         32       34        12
               vv
clus            STAGE IVB
  NLK MUTATED           0
  NLK WILD-TYPE         1
D482V3, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            4           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           1             5
  STAGE IIIB           2            42
  STAGE IIIC           1            32
  STAGE IV             1            34
  STAGE IVA            0            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
  NLK MUTATED     0   1   9   1
  NLK WILD-TYPE   9  66 240  40
D482V4, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  T1           0             9
  T2           1            66
  T3           9           240
  T4           1            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
  NLK MUTATED     6   3   2
  NLK WILD-TYPE 214  78  64
D482V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           6           214
  N1           3            78
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V6, binary
               cls
clus              0   1
  NLK MUTATED     9   1
  NLK WILD-TYPE 276  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      9    1
  NLK WILD-TYPE  276   47
   clus
vv  NLK MUTATED NLK WILD-TYPE
  0           9           276
  1           1            47
[1] 2 2
[1] FALSE
D482V7, binary
               cls
clus              0   1
  NLK MUTATED     9   2
  NLK WILD-TYPE 161 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      9    2
  NLK WILD-TYPE  161  195
        clus
vv       NLK MUTATED NLK WILD-TYPE
  FEMALE           9           161
  MALE             2           195
[1] 2 2
[1] FALSE
D482V8, binary
               cls
clus              0   1
  NLK MUTATED    10   0
  NLK WILD-TYPE 290   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     10    0
  NLK WILD-TYPE  290    8
     clus
vv    NLK MUTATED NLK WILD-TYPE
  NO           10           290
  YES           0             8
[1] 2 2
[1] FALSE
D482V9, binary
               cls
clus              0   1
  NLK MUTATED    10   1
  NLK WILD-TYPE 304  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     10    1
  NLK WILD-TYPE  304   47
                               clus
vv                              NLK MUTATED NLK WILD-TYPE
  COLON ADENOCARCINOMA                   10           304
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NLK MUTATED     9   0   1   1
  NLK WILD-TYPE 250   3  21  20
D482V10, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  R0           9           250
  R1           0             3
  R2           1            21
  RX           1            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"
D482V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLK MUTATED                                  0     0
  NLK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NLK MUTATED                           2     7
  NLK WILD-TYPE                        17   169
D482V12, multiclass
                                  clus
vv                                 NLK MUTATED NLK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                      7           169
[1] 4 2
[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 = ATP8B1 MUTATION ANALYSIS
D483V1, survival
                  sevent
clus2                0   1
  ATP8B1 MUTATED    18   4
  ATP8B1 WILD-TYPE 259  74
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              22              333 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               4               74 
$`ATP8B1 MUTATED`
TCGA-AA-3554 TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6625 TCGA-A6-5665 TCGA-A6-6780 
       17.95         0.92       100.01        91.79        22.06        20.12 
TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-6598 
       31.00        34.98        31.00        12.16        21.44        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-6165 TCGA-CM-6674 
       12.76        10.06        13.02        30.08        16.04        12.95 
TCGA-D5-6529 TCGA-D5-6534 TCGA-DM-A28H TCGA-G4-6626 
       20.19        43.27       117.07        46.75 

$`ATP8B1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        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        14.04        29.03        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-D5-6532 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
            0.92             0.00 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
          117.07           148.01 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
           21.75            22.09 
[1] "0.9 - 117.1 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D483V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP8B1 MUTATED         2        0        2        15         1         0
  ATP8B1 WILD-TYPE      62        1       24        93         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP8B1 MUTATED           1          0          0          2        0
  ATP8B1 WILD-TYPE        17          6         44         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP8B1 MUTATED           0         0
  ATP8B1 WILD-TYPE        12         1
D483V3, multiclass
            clus
vv           ATP8B1 MUTATED ATP8B1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              15               93
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  ATP8B1 MUTATED     1   1  20   1
  ATP8B1 WILD-TYPE   8  66 229  40
D483V4, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             20              229
  T4              1               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
  ATP8B1 MUTATED    20   1   2
  ATP8B1 WILD-TYPE 200  80  64
D483V5, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  N0             20              200
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V6, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    19   0
  ATP8B1 WILD-TYPE 266  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     19    0
  ATP8B1 WILD-TYPE  266   48
   clus
vv  ATP8B1 MUTATED ATP8B1 WILD-TYPE
  0             19              266
  1              0               48
[1] 2 2
[1] FALSE
D483V7, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    11  12
  ATP8B1 WILD-TYPE 159 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     11   12
  ATP8B1 WILD-TYPE  159  185
        clus
vv       ATP8B1 MUTATED ATP8B1 WILD-TYPE
  FEMALE             11              159
  MALE               12              185
[1] 2 2
[1] FALSE
D483V8, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    21   0
  ATP8B1 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     21    0
  ATP8B1 WILD-TYPE  279    8
     clus
vv    ATP8B1 MUTATED ATP8B1 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D483V9, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    18   5
  ATP8B1 WILD-TYPE 296  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     18    5
  ATP8B1 WILD-TYPE  296   43
                               clus
vv                              ATP8B1 MUTATED ATP8B1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP8B1 MUTATED    17   0   0   2
  ATP8B1 WILD-TYPE 242   3  22  19
D483V10, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              0               22
  RX              2               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"
D483V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP8B1 MUTATED                                  0     2
  ATP8B1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP8B1 MUTATED                           1    14
  ATP8B1 WILD-TYPE                        18   162
D483V12, multiclass
                                  clus
vv                                 ATP8B1 MUTATED ATP8B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        14              162
[1] 4 2
[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 = WDR66 MUTATION ANALYSIS
D484V1, survival
                 sevent
clus2               0   1
  WDR66 MUTATED    14   4
  WDR66 WILD-TYPE 263  74
  WDR66 MUTATED WDR66 WILD-TYPE 
             18             337 
  WDR66 MUTATED WDR66 WILD-TYPE 
              4              74 
$`WDR66 MUTATED`
TCGA-AA-3860 TCGA-AD-6964 TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3710 
       31.07        10.88        35.80        63.98         6.97        26.99 
TCGA-AA-3861 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6196 TCGA-CA-6717 
       30.05        25.02         4.01        34.98         0.20        12.76 
TCGA-CA-6718 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A282 TCGA-F4-6459 TCGA-F4-6808 
       10.06        12.00        13.35       139.17         8.61        33.67 

$`WDR66 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65        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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  WDR66 MUTATED WDR66 WILD-TYPE 
            0.2             0.0 
  WDR66 MUTATED WDR66 WILD-TYPE 
         139.17          148.01 
  WDR66 MUTATED WDR66 WILD-TYPE 
         19.185          22.060 
[1] "0.2 - 139.2 (19.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D484V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR66 MUTATED         1        0        2         8         2         0
  WDR66 WILD-TYPE      63        1       24       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR66 MUTATED           0          0          3          1        0         0
  WDR66 WILD-TYPE        18          6         41         32       35        12
                 vv
clus              STAGE IVB
  WDR66 MUTATED           0
  WDR66 WILD-TYPE         1
D484V3, multiclass
            clus
vv           WDR66 MUTATED WDR66 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  WDR66 MUTATED     1   1  14   3
  WDR66 WILD-TYPE   8  66 235  38
D484V4, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            14             235
  T4             3              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
  WDR66 MUTATED    14   2   3
  WDR66 WILD-TYPE 206  79  63
D484V5, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  N0            14             206
  N1             2              79
  N2             3              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"
D484V6, binary
                 cls
clus                0   1
  WDR66 MUTATED    16   0
  WDR66 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     16    0
  WDR66 WILD-TYPE  269   48
   clus
vv  WDR66 MUTATED WDR66 WILD-TYPE
  0            16             269
  1             0              48
[1] 2 2
[1] FALSE
D484V7, binary
                 cls
clus                0   1
  WDR66 MUTATED     9  10
  WDR66 WILD-TYPE 161 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      9   10
  WDR66 WILD-TYPE  161  187
        clus
vv       WDR66 MUTATED WDR66 WILD-TYPE
  FEMALE             9             161
  MALE              10             187
[1] 2 2
[1] FALSE
D484V8, binary
                 cls
clus                0   1
  WDR66 MUTATED    15   0
  WDR66 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     15    0
  WDR66 WILD-TYPE  285    8
     clus
vv    WDR66 MUTATED WDR66 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D484V9, binary
                 cls
clus                0   1
  WDR66 MUTATED    14   5
  WDR66 WILD-TYPE 300  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     14    5
  WDR66 WILD-TYPE  300   43
                               clus
vv                              WDR66 MUTATED WDR66 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR66 MUTATED    14   0   0   2
  WDR66 WILD-TYPE 245   3  22  19
D484V10, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D484V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR66 MUTATED                                  0     2
  WDR66 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR66 MUTATED                           0     8
  WDR66 WILD-TYPE                        19   168
D484V12, multiclass
                                  clus
vv                                 WDR66 MUTATED WDR66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = GPR141 MUTATION ANALYSIS
D485V1, survival
                  sevent
clus2                0   1
  GPR141 MUTATED     8   3
  GPR141 WILD-TYPE 269  75
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              344 
  GPR141 MUTATED GPR141 WILD-TYPE 
               3               75 
$`GPR141 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-6601 TCGA-AA-3877 TCGA-AA-3947 TCGA-CA-6718 
       19.04        19.04       100.01        31.00        33.01        10.06 
TCGA-D5-5539 TCGA-D5-6930 TCGA-DM-A1HB TCGA-DM-A28E TCGA-G4-6306 
       19.59        13.35       135.65       119.93        44.68 

$`GPR141 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28F TCGA-DM-A28G 
       44.32       131.51       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GPR141 MUTATED GPR141 WILD-TYPE 
           10.06             0.00 
  GPR141 MUTATED GPR141 WILD-TYPE 
          135.65           148.01 
  GPR141 MUTATED GPR141 WILD-TYPE 
          31.000           22.045 
[1] "10.1 - 135.7 (31.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.3"
D485V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR141 MUTATED         1        0        2         3         1         0
  GPR141 WILD-TYPE      63        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR141 MUTATED           0          1          1          0        1
  GPR141 WILD-TYPE        18          5         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  GPR141 MUTATED           0         0
  GPR141 WILD-TYPE        12         1
D485V3, multiclass
            clus
vv           GPR141 MUTATED GPR141 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  GPR141 MUTATED     1   1   8   1
  GPR141 WILD-TYPE   8  66 241  40
D485V4, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              8              241
  T4              1               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
  GPR141 MUTATED     9   2   0
  GPR141 WILD-TYPE 211  79  66
D485V5, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  N0              9              211
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V6, binary
                  cls
clus                 0   1
  GPR141 MUTATED    10   1
  GPR141 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED     10    1
  GPR141 WILD-TYPE  275   47
   clus
vv  GPR141 MUTATED GPR141 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D485V7, binary
                  cls
clus                 0   1
  GPR141 MUTATED     3   8
  GPR141 WILD-TYPE 167 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      3    8
  GPR141 WILD-TYPE  167  189
        clus
vv       GPR141 MUTATED GPR141 WILD-TYPE
  FEMALE              3              167
  MALE                8              189
[1] 2 2
[1] FALSE
D485V8, binary
                  cls
clus                 0   1
  GPR141 MUTATED     8   1
  GPR141 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      8    1
  GPR141 WILD-TYPE  292    7
     clus
vv    GPR141 MUTATED GPR141 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D485V9, binary
                  cls
clus                 0   1
  GPR141 MUTATED     6   4
  GPR141 WILD-TYPE 308  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      6    4
  GPR141 WILD-TYPE  308   44
                               clus
vv                              GPR141 MUTATED GPR141 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR141 MUTATED     6   0   1   1
  GPR141 WILD-TYPE 253   3  21  20
D485V10, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              1               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"
D485V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR141 MUTATED                                  0     1
  GPR141 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR141 MUTATED                           0     6
  GPR141 WILD-TYPE                        19   170
D485V12, multiclass
                                  clus
vv                                 GPR141 MUTATED GPR141 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = ATP6V1D MUTATION ANALYSIS
D486V1, survival
                   sevent
clus2                 0   1
  ATP6V1D MUTATED     5   1
  ATP6V1D WILD-TYPE 272  77
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                6               349 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                1                77 
$`ATP6V1D MUTATED`
TCGA-AA-3713 TCGA-A6-5660 TCGA-AZ-6600 TCGA-CK-5914 TCGA-CM-6164 TCGA-F4-6856 
       19.04        29.19        12.10        21.99        29.03        35.31 

$`ATP6V1D WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
             12.1               0.0 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
            35.31            148.01 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
            25.51             22.06 
[1] "12.1 - 35.3 (25.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D486V2, continuous
                   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      63        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1D MUTATED           0          0          1          1        2
  ATP6V1D WILD-TYPE        18          6         43         32       33
                   vv
clus                STAGE IVA STAGE IVB
  ATP6V1D MUTATED           0         0
  ATP6V1D WILD-TYPE        12         1
D486V3, multiclass
            clus
vv           ATP6V1D MUTATED ATP6V1D WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 2                33
  STAGE IVA                0                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
  ATP6V1D MUTATED     0   1   4   1
  ATP6V1D WILD-TYPE   9  66 245  40
D486V4, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               1                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
  ATP6V1D MUTATED     3   2   1
  ATP6V1D WILD-TYPE 217  79  65
D486V5, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  N0               3               217
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V6, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     3   2
  ATP6V1D WILD-TYPE 282  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      3    2
  ATP6V1D WILD-TYPE  282   46
   clus
vv  ATP6V1D MUTATED ATP6V1D WILD-TYPE
  0               3               282
  1               2                46
[1] 2 2
[1] FALSE
D486V7, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     1   5
  ATP6V1D WILD-TYPE 169 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      1    5
  ATP6V1D WILD-TYPE  169  192
        clus
vv       ATP6V1D MUTATED ATP6V1D WILD-TYPE
  FEMALE               1               169
  MALE                 5               192
[1] 2 2
[1] FALSE
D486V8, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     4   1
  ATP6V1D WILD-TYPE 296   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      4    1
  ATP6V1D WILD-TYPE  296    7
     clus
vv    ATP6V1D MUTATED ATP6V1D WILD-TYPE
  NO                4               296
  YES               1                 7
[1] 2 2
[1] FALSE
D486V9, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     5   1
  ATP6V1D WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      5    1
  ATP6V1D WILD-TYPE  309   47
                               clus
vv                              ATP6V1D MUTATED ATP6V1D WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ATP6V1D MUTATED     2   0   1   1
  ATP6V1D WILD-TYPE 257   3  21  20
D486V10, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  R0               2               257
  R1               0                 3
  R2               1                21
  RX               1                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"
D486V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V1D MUTATED                                  0     0
  ATP6V1D WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1D MUTATED                           2     3
  ATP6V1D WILD-TYPE                        17   173
D486V12, multiclass
                                  clus
vv                                 ATP6V1D MUTATED ATP6V1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          3               173
[1] 4 2
[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 = LPCAT3 MUTATION ANALYSIS
D487V1, survival
                  sevent
clus2                0   1
  LPCAT3 MUTATED     4   1
  LPCAT3 WILD-TYPE 273  77
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              350 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               1               77 
$`LPCAT3 MUTATED`
TCGA-G4-6628 TCGA-AA-3542 TCGA-AA-A01Q TCGA-AZ-6598 TCGA-D5-6536 
       79.69        12.99         1.02        49.41        17.85 

$`LPCAT3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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           22.075 
[1] "1.0 - 79.7 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D487V2, continuous
                  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      63        1       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LPCAT3 MUTATED           0          0          0          1        0
  LPCAT3 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  LPCAT3 MUTATED           0         0
  LPCAT3 WILD-TYPE        12         1
D487V3, multiclass
            clus
vv           LPCAT3 MUTATED LPCAT3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  LPCAT3 MUTATED     0   1   4   0
  LPCAT3 WILD-TYPE   9  66 245  41
D487V4, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              0               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
  LPCAT3 MUTATED     4   0   1
  LPCAT3 WILD-TYPE 216  81  65
D487V5, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  N0              4              216
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V6, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     4   0
  LPCAT3 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      4    0
  LPCAT3 WILD-TYPE  281   48
   clus
vv  LPCAT3 MUTATED LPCAT3 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D487V7, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     2   3
  LPCAT3 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      2    3
  LPCAT3 WILD-TYPE  168  194
        clus
vv       LPCAT3 MUTATED LPCAT3 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D487V8, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     4   0
  LPCAT3 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      4    0
  LPCAT3 WILD-TYPE  296    8
     clus
vv    LPCAT3 MUTATED LPCAT3 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D487V9, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     5   0
  LPCAT3 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      5    0
  LPCAT3 WILD-TYPE  309   48
                               clus
vv                              LPCAT3 MUTATED LPCAT3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LPCAT3 MUTATED     4   0   0   0
  LPCAT3 WILD-TYPE 255   3  22  21
D487V10, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D487V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPCAT3 MUTATED                                  0     0
  LPCAT3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LPCAT3 MUTATED                           0     3
  LPCAT3 WILD-TYPE                        19   173
D487V12, multiclass
                                  clus
vv                                 LPCAT3 MUTATED LPCAT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = SP4 MUTATION ANALYSIS
D488V1, survival
               sevent
clus2             0   1
  SP4 MUTATED     8   4
  SP4 WILD-TYPE 269  74
  SP4 MUTATED SP4 WILD-TYPE 
           12           343 
  SP4 MUTATED SP4 WILD-TYPE 
            4            74 
$`SP4 MUTATED`
TCGA-AD-6964 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-6004 TCGA-AY-6386 
       10.88         2.01        34.98         1.02        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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        22.060 
[1] "1.0 - 85.5 (22.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D488V2, continuous
               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      63        1       24       104         7         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        18          6         42         33       34        12
               vv
clus            STAGE IVB
  SP4 MUTATED           0
  SP4 WILD-TYPE         1
D488V3, multiclass
            clus
vv           SP4 MUTATED SP4 WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  SP4 MUTATED     0   1   8   3
  SP4 WILD-TYPE   9  66 241  38
D488V4, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  T1           0             9
  T2           1            66
  T3           8           241
  T4           3            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
  SP4 MUTATED     8   3   1
  SP4 WILD-TYPE 212  78  65
D488V5, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  N0           8           212
  N1           3            78
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V6, binary
               cls
clus              0   1
  SP4 MUTATED     9   1
  SP4 WILD-TYPE 276  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      9    1
  SP4 WILD-TYPE  276   47
   clus
vv  SP4 MUTATED SP4 WILD-TYPE
  0           9           276
  1           1            47
[1] 2 2
[1] FALSE
D488V7, binary
               cls
clus              0   1
  SP4 MUTATED     7   5
  SP4 WILD-TYPE 163 192
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      7    5
  SP4 WILD-TYPE  163  192
        clus
vv       SP4 MUTATED SP4 WILD-TYPE
  FEMALE           7           163
  MALE             5           192
[1] 2 2
[1] FALSE
D488V8, binary
               cls
clus              0   1
  SP4 MUTATED     8   0
  SP4 WILD-TYPE 292   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      8    0
  SP4 WILD-TYPE  292    8
     clus
vv    SP4 MUTATED SP4 WILD-TYPE
  NO            8           292
  YES           0             8
[1] 2 2
[1] FALSE
D488V9, binary
               cls
clus              0   1
  SP4 MUTATED    10   2
  SP4 WILD-TYPE 304  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED     10    2
  SP4 WILD-TYPE  304   46
                               clus
vv                              SP4 MUTATED SP4 WILD-TYPE
  COLON ADENOCARCINOMA                   10           304
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SP4 MUTATED     6   1   0   0
  SP4 WILD-TYPE 253   2  22  21
D488V10, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  R0           6           253
  R1           1             2
  R2           0            22
  RX           0            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"
D488V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SP4 MUTATED                                  0     0
  SP4 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SP4 MUTATED                           3     6
  SP4 WILD-TYPE                        16   170
D488V12, multiclass
                                  clus
vv                                 SP4 MUTATED SP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  3            16
  WHITE                                      6           170
[1] 4 2
[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 = PLA2G4E MUTATION ANALYSIS
D489V1, survival
                   sevent
clus2                 0   1
  PLA2G4E MUTATED     7   2
  PLA2G4E WILD-TYPE 270  76
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
                9               346 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
                2                76 
$`PLA2G4E MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-G4-6588 TCGA-A6-6780 TCGA-AA-3655 TCGA-AU-6004 
        6.05        85.05        26.17        20.12        61.02        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       49.41        12.76        21.14 

$`PLA2G4E WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
             6.05              0.00 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
            85.05            148.01 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
           26.170            22.045 
[1] "6.0 - 85.0 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D489V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLA2G4E MUTATED         2        0        3         3         0         0
  PLA2G4E WILD-TYPE      62        1       23       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G4E MUTATED           1          0          0          0        1
  PLA2G4E WILD-TYPE        17          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  PLA2G4E MUTATED           0         0
  PLA2G4E WILD-TYPE        12         1
D489V3, multiclass
            clus
vv           PLA2G4E MUTATED PLA2G4E WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  PLA2G4E MUTATED     1   1   7   1
  PLA2G4E WILD-TYPE   8  66 242  40
D489V4, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               7               242
  T4               1                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
  PLA2G4E MUTATED     8   0   2
  PLA2G4E WILD-TYPE 212  81  64
D489V5, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  N0               8               212
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V6, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     7   1
  PLA2G4E WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      7    1
  PLA2G4E WILD-TYPE  278   47
   clus
vv  PLA2G4E MUTATED PLA2G4E WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D489V7, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     5   5
  PLA2G4E WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      5    5
  PLA2G4E WILD-TYPE  165  192
        clus
vv       PLA2G4E MUTATED PLA2G4E WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D489V8, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     8   0
  PLA2G4E WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      8    0
  PLA2G4E WILD-TYPE  292    8
     clus
vv    PLA2G4E MUTATED PLA2G4E WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D489V9, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     8   2
  PLA2G4E WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      8    2
  PLA2G4E WILD-TYPE  306   46
                               clus
vv                              PLA2G4E MUTATED PLA2G4E WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLA2G4E MUTATED     5   0   1   2
  PLA2G4E WILD-TYPE 254   3  21  19
D489V10, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               1                21
  RX               2                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"
D489V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLA2G4E MUTATED                                  0     1
  PLA2G4E WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLA2G4E MUTATED                           0     5
  PLA2G4E WILD-TYPE                        19   171
D489V12, multiclass
                                  clus
vv                                 PLA2G4E MUTATED PLA2G4E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = RAB40C MUTATION ANALYSIS
D490V1, survival
                  sevent
clus2                0   1
  RAB40C MUTATED     5   2
  RAB40C WILD-TYPE 272  76
  RAB40C MUTATED RAB40C WILD-TYPE 
               7              348 
  RAB40C MUTATED RAB40C WILD-TYPE 
               2               76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RAB40C MUTATED RAB40C WILD-TYPE 
            3.02             0.00 
  RAB40C MUTATED RAB40C WILD-TYPE 
           49.41           148.01 
  RAB40C MUTATED RAB40C WILD-TYPE 
           33.04            22.01 
[1] "3.0 - 49.4 (33.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D490V2, continuous
                  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      61        1       24       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB40C MUTATED           0          0          0          1        0
  RAB40C WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  RAB40C MUTATED           0         0
  RAB40C WILD-TYPE        12         1
D490V3, multiclass
            clus
vv           RAB40C MUTATED RAB40C WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  RAB40C MUTATED     0   3   3   2
  RAB40C WILD-TYPE   9  64 246  39
D490V4, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  T1              0                9
  T2              3               64
  T3              3              246
  T4              2               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
  RAB40C MUTATED     7   1   0
  RAB40C WILD-TYPE 213  80  66
D490V5, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  N0              7              213
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V6, binary
                  cls
clus                 0   1
  RAB40C MUTATED     5   0
  RAB40C WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      5    0
  RAB40C WILD-TYPE  280   48
   clus
vv  RAB40C MUTATED RAB40C WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D490V7, binary
                  cls
clus                 0   1
  RAB40C MUTATED     5   3
  RAB40C WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      5    3
  RAB40C WILD-TYPE  165  194
        clus
vv       RAB40C MUTATED RAB40C WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D490V8, binary
                  cls
clus                 0   1
  RAB40C MUTATED     6   0
  RAB40C WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      6    0
  RAB40C WILD-TYPE  294    8
     clus
vv    RAB40C MUTATED RAB40C WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D490V9, binary
                  cls
clus                 0   1
  RAB40C MUTATED     6   2
  RAB40C WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      6    2
  RAB40C WILD-TYPE  308   46
                               clus
vv                              RAB40C MUTATED RAB40C WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RAB40C MUTATED     6   0   0   1
  RAB40C WILD-TYPE 253   3  22  20
D490V10, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D490V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB40C MUTATED                                  0     0
  RAB40C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RAB40C MUTATED                           1     5
  RAB40C WILD-TYPE                        18   171
D490V12, multiclass
                                  clus
vv                                 RAB40C MUTATED RAB40C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = UGT3A2 MUTATION ANALYSIS
D491V1, survival
                  sevent
clus2                0   1
  UGT3A2 MUTATED    15   3
  UGT3A2 WILD-TYPE 262  75
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              18              337 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               75 
$`UGT3A2 MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 
      100.01        35.80        33.53         3.02        63.98        29.95 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 
       25.02        27.02        34.98        12.76        51.32        21.14 
TCGA-CM-4743 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6920 TCGA-G4-6307 
       23.05        12.95        25.48        17.85        12.39        55.04 

$`UGT3A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.99        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
            3.02             0.00 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
          100.01           148.01 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
           26.25            21.99 
[1] "3.0 - 100.0 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D491V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGT3A2 MUTATED         1        0        3         9         1         0
  UGT3A2 WILD-TYPE      63        1       23        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT3A2 MUTATED           0          0          2          0        0
  UGT3A2 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT3A2 MUTATED           0         0
  UGT3A2 WILD-TYPE        12         1
D491V3, multiclass
            clus
vv           UGT3A2 MUTATED UGT3A2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               9               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  UGT3A2 MUTATED     1   1  14   2
  UGT3A2 WILD-TYPE   8  66 235  39
D491V4, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             14              235
  T4              2               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
  UGT3A2 MUTATED    16   2   0
  UGT3A2 WILD-TYPE 204  79  66
D491V5, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  N0             16              204
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V6, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    16   0
  UGT3A2 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     16    0
  UGT3A2 WILD-TYPE  269   48
   clus
vv  UGT3A2 MUTATED UGT3A2 WILD-TYPE
  0             16              269
  1              0               48
[1] 2 2
[1] FALSE
D491V7, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    10   8
  UGT3A2 WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     10    8
  UGT3A2 WILD-TYPE  160  189
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D491V8, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    18   0
  UGT3A2 WILD-TYPE 282   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     18    0
  UGT3A2 WILD-TYPE  282    8
     clus
vv    UGT3A2 MUTATED UGT3A2 WILD-TYPE
  NO              18              282
  YES              0                8
[1] 2 2
[1] FALSE
D491V9, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    16   2
  UGT3A2 WILD-TYPE 298  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     16    2
  UGT3A2 WILD-TYPE  298   46
                               clus
vv                              UGT3A2 MUTATED UGT3A2 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UGT3A2 MUTATED    12   0   0   3
  UGT3A2 WILD-TYPE 247   3  22  18
D491V10, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              3               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"
D491V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT3A2 MUTATED                                  0     1
  UGT3A2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT3A2 MUTATED                           1    10
  UGT3A2 WILD-TYPE                        18   166
D491V12, multiclass
                                  clus
vv                                 UGT3A2 MUTATED UGT3A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(492) Variable = ATAD2B MUTATION ANALYSIS
D492V1, survival
                  sevent
clus2                0   1
  ATAD2B MUTATED    12   3
  ATAD2B WILD-TYPE 265  75
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              15              340 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
               3               75 
$`ATAD2B MUTATED`
TCGA-AZ-6601 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3977 TCGA-AA-A010 
      100.01        32.75        22.06        20.28        25.02        34.98 
TCGA-AA-A01K TCGA-AD-5900 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-5348 
       31.00        12.16         5.23         3.19        12.76        22.98 
TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A1D9 
       14.04        13.35       140.38 

$`ATAD2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3510 
       20.12        19.66         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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       29.56        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ATAD2B MUTATED ATAD2B WILD-TYPE 
            3.19             0.00 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
          140.38           148.01 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
           22.06            22.06 
[1] "3.2 - 140.4 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D492V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD2B MUTATED         2        0        1         4         3         0
  ATAD2B WILD-TYPE      62        1       25       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATAD2B MUTATED           0          0          2          1        1
  ATAD2B WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ATAD2B MUTATED           0         0
  ATAD2B WILD-TYPE        12         1
D492V3, multiclass
            clus
vv           ATAD2B MUTATED ATAD2B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  ATAD2B MUTATED     0   3   7   5
  ATAD2B WILD-TYPE   9  64 242  36
D492V4, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  T1              0                9
  T2              3               64
  T3              7              242
  T4              5               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
  ATAD2B MUTATED    11   2   2
  ATAD2B WILD-TYPE 209  79  64
D492V5, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  N0             11              209
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V6, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    11   1
  ATAD2B WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     11    1
  ATAD2B WILD-TYPE  274   47
   clus
vv  ATAD2B MUTATED ATAD2B WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D492V7, binary
                  cls
clus                 0   1
  ATAD2B MUTATED     6   9
  ATAD2B WILD-TYPE 164 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED      6    9
  ATAD2B WILD-TYPE  164  188
        clus
vv       ATAD2B MUTATED ATAD2B WILD-TYPE
  FEMALE              6              164
  MALE                9              188
[1] 2 2
[1] FALSE
D492V8, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    14   0
  ATAD2B WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     14    0
  ATAD2B WILD-TYPE  286    8
     clus
vv    ATAD2B MUTATED ATAD2B WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D492V9, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    11   4
  ATAD2B WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     11    4
  ATAD2B WILD-TYPE  303   44
                               clus
vv                              ATAD2B MUTATED ATAD2B WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATAD2B MUTATED     8   0   0   1
  ATAD2B WILD-TYPE 251   3  22  20
D492V10, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              1               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"
D492V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD2B MUTATED                                  0     1
  ATAD2B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATAD2B MUTATED                           0    11
  ATAD2B WILD-TYPE                        19   165
D492V12, multiclass
                                  clus
vv                                 ATAD2B MUTATED ATAD2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        11              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(493) Variable = SLC33A1 MUTATION ANALYSIS
D493V1, survival
                   sevent
clus2                 0   1
  SLC33A1 MUTATED     6   2
  SLC33A1 WILD-TYPE 271  76
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                8               347 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                2                76 
$`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 
       12.49        61.91 

$`SLC33A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-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        54.61        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        25.48        43.27        15.12         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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
             6.77              0.00 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
           124.27            148.01 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
           20.135            22.060 
[1] "6.8 - 124.3 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D493V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC33A1 MUTATED         2        0        0         3         0         0
  SLC33A1 WILD-TYPE      62        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC33A1 MUTATED           0          0          1          0        1
  SLC33A1 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC33A1 MUTATED           0         0
  SLC33A1 WILD-TYPE        12         1
D493V3, multiclass
            clus
vv           SLC33A1 MUTATED SLC33A1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC33A1 MUTATED     0   2   7   0
  SLC33A1 WILD-TYPE   9  65 242  41
D493V4, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               7               242
  T4               0                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
  SLC33A1 MUTATED     7   1   1
  SLC33A1 WILD-TYPE 213  80  65
D493V5, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  N0               7               213
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V6, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     5   1
  SLC33A1 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      5    1
  SLC33A1 WILD-TYPE  280   47
   clus
vv  SLC33A1 MUTATED SLC33A1 WILD-TYPE
  0               5               280
  1               1                47
[1] 2 2
[1] FALSE
D493V7, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     4   5
  SLC33A1 WILD-TYPE 166 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      4    5
  SLC33A1 WILD-TYPE  166  192
        clus
vv       SLC33A1 MUTATED SLC33A1 WILD-TYPE
  FEMALE               4               166
  MALE                 5               192
[1] 2 2
[1] FALSE
D493V8, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     8   0
  SLC33A1 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      8    0
  SLC33A1 WILD-TYPE  292    8
     clus
vv    SLC33A1 MUTATED SLC33A1 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D493V9, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     8   1
  SLC33A1 WILD-TYPE 306  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      8    1
  SLC33A1 WILD-TYPE  306   47
                               clus
vv                              SLC33A1 MUTATED SLC33A1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC33A1 MUTATED     6   0   0   1
  SLC33A1 WILD-TYPE 253   3  22  20
D493V10, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D493V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC33A1 MUTATED                                  0     0
  SLC33A1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC33A1 MUTATED                           0     8
  SLC33A1 WILD-TYPE                        19   168
D493V12, multiclass
                                  clus
vv                                 SLC33A1 MUTATED SLC33A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          8               168
[1] 4 2
[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 = ABCB4 MUTATION ANALYSIS
D494V1, survival
                 sevent
clus2               0   1
  ABCB4 MUTATED    16   5
  ABCB4 WILD-TYPE 261  73
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             21             334 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              5              73 
$`ABCB4 MUTATED`
TCGA-AA-3525 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3680 TCGA-AA-3811 
        8.05        32.71        19.66        63.98        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        12.16        83.24        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 
       15.58        11.64        13.35 

$`ABCB4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
        4.01        27.02        42.02        17.03        14.99        15.02 
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         1.02        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-6890 
        0.92        41.00        39.98        18.05        40.96        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ABCB4 MUTATED ABCB4 WILD-TYPE 
           0.99            0.00 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          83.24          148.01 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          14.50           22.39 
[1] "1.0 - 83.2 (14.5)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D494V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCB4 MUTATED         4        0        3         9         1         1
  ABCB4 WILD-TYPE      60        1       23        99         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCB4 MUTATED           1          0          1          1        1         0
  ABCB4 WILD-TYPE        17          6         43         32       34        12
                 vv
clus              STAGE IVB
  ABCB4 MUTATED           0
  ABCB4 WILD-TYPE         1
D494V3, multiclass
            clus
vv           ABCB4 MUTATED ABCB4 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              9              99
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  ABCB4 MUTATED     0   4  13   5
  ABCB4 WILD-TYPE   9  63 236  36
D494V4, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            13             236
  T4             5              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
  ABCB4 MUTATED    18   2   2
  ABCB4 WILD-TYPE 202  79  64
D494V5, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  N0            18             202
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V6, binary
                 cls
clus                0   1
  ABCB4 MUTATED    18   1
  ABCB4 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     18    1
  ABCB4 WILD-TYPE  267   47
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0            18             267
  1             1              47
[1] 2 2
[1] FALSE
D494V7, binary
                 cls
clus                0   1
  ABCB4 MUTATED     7  15
  ABCB4 WILD-TYPE 163 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      7   15
  ABCB4 WILD-TYPE  163  182
        clus
vv       ABCB4 MUTATED ABCB4 WILD-TYPE
  FEMALE             7             163
  MALE              15             182
[1] 2 2
[1] FALSE
D494V8, binary
                 cls
clus                0   1
  ABCB4 MUTATED    20   0
  ABCB4 WILD-TYPE 280   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     20    0
  ABCB4 WILD-TYPE  280    8
     clus
vv    ABCB4 MUTATED ABCB4 WILD-TYPE
  NO             20             280
  YES             0               8
[1] 2 2
[1] FALSE
D494V9, binary
                 cls
clus                0   1
  ABCB4 MUTATED    16   6
  ABCB4 WILD-TYPE 298  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     16    6
  ABCB4 WILD-TYPE  298   42
                               clus
vv                              ABCB4 MUTATED ABCB4 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCB4 MUTATED    17   0   1   2
  ABCB4 WILD-TYPE 242   3  21  19
D494V10, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  R0            17             242
  R1             0               3
  R2             1              21
  RX             2              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"
D494V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCB4 MUTATED                                  0     3
  ABCB4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCB4 MUTATED                           1    10
  ABCB4 WILD-TYPE                        18   166
D494V12, multiclass
                                  clus
vv                                 ABCB4 MUTATED ABCB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(495) Variable = RUFY1 MUTATION ANALYSIS
D495V1, survival
                 sevent
clus2               0   1
  RUFY1 MUTATED    12   1
  RUFY1 WILD-TYPE 265  77
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             13             342 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
              1              77 
$`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 
       85.48 

$`RUFY1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        21.44         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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       12.10        29.56         5.23        11.74         3.19        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  RUFY1 MUTATED RUFY1 WILD-TYPE 
           6.97            0.00 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
          85.48          148.01 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
          22.06           22.06 
[1] "7.0 - 85.5 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.8"
D495V2, continuous
                 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      63        1       23       104         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUFY1 MUTATED           0          0          2          1        0         0
  RUFY1 WILD-TYPE        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  RUFY1 MUTATED           0
  RUFY1 WILD-TYPE         1
D495V3, multiclass
            clus
vv           RUFY1 MUTATED RUFY1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RUFY1 MUTATED     0   1  10   2
  RUFY1 WILD-TYPE   9  66 239  39
D495V4, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             2              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
  RUFY1 MUTATED    10   2   1
  RUFY1 WILD-TYPE 210  79  65
D495V5, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V6, binary
                 cls
clus                0   1
  RUFY1 MUTATED    13   0
  RUFY1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     13    0
  RUFY1 WILD-TYPE  272   48
   clus
vv  RUFY1 MUTATED RUFY1 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D495V7, binary
                 cls
clus                0   1
  RUFY1 MUTATED     6   7
  RUFY1 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED      6    7
  RUFY1 WILD-TYPE  164  190
        clus
vv       RUFY1 MUTATED RUFY1 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D495V8, binary
                 cls
clus                0   1
  RUFY1 MUTATED    12   0
  RUFY1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     12    0
  RUFY1 WILD-TYPE  288    8
     clus
vv    RUFY1 MUTATED RUFY1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D495V9, binary
                 cls
clus                0   1
  RUFY1 MUTATED    12   1
  RUFY1 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     12    1
  RUFY1 WILD-TYPE  302   47
                               clus
vv                              RUFY1 MUTATED RUFY1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUFY1 MUTATED    10   0   0   1
  RUFY1 WILD-TYPE 249   3  22  20
D495V10, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             1              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"
D495V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUFY1 MUTATED                                  0     1
  RUFY1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUFY1 MUTATED                           2     7
  RUFY1 WILD-TYPE                        17   169
D495V12, multiclass
                                  clus
vv                                 RUFY1 MUTATED RUFY1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        7             169
[1] 4 2
[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 = IBTK MUTATION ANALYSIS
D496V1, survival
                sevent
clus2              0   1
  IBTK MUTATED    13   6
  IBTK WILD-TYPE 264  72
  IBTK MUTATED IBTK WILD-TYPE 
            19            336 
  IBTK MUTATED IBTK WILD-TYPE 
             6             72 
$`IBTK MUTATED`
TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3715 TCGA-G4-6321 TCGA-G4-6628 
       13.02         0.99         0.92        19.04        22.09        79.69 
TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       33.53         6.97        33.04        34.98        58.39        49.41 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CK-5913 TCGA-CK-6748 TCGA-DM-A1D0 TCGA-F4-6459 
       29.56         3.19        51.32         2.01       130.65         8.61 
TCGA-F4-6806 
       41.42 

$`IBTK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 
        5.88        63.62        35.80        26.17        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        12.10         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6460 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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IBTK MUTATED IBTK WILD-TYPE 
          0.92           0.00 
  IBTK MUTATED IBTK WILD-TYPE 
        130.65         148.01 
  IBTK MUTATED IBTK WILD-TYPE 
         29.56          22.01 
[1] "0.9 - 130.7 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D496V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IBTK MUTATED         3        0        3         5         1         0
  IBTK WILD-TYPE      61        1       23       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IBTK MUTATED           3          0          1          0        2         0
  IBTK WILD-TYPE        15          6         43         33       33        12
                vv
clus             STAGE IVB
  IBTK MUTATED           0
  IBTK WILD-TYPE         1
D496V3, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  IBTK MUTATED     0   5  12   2
  IBTK WILD-TYPE   9  62 237  39
D496V4, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  T1            0              9
  T2            5             62
  T3           12            237
  T4            2             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
  IBTK MUTATED    12   4   3
  IBTK WILD-TYPE 208  77  63
D496V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0           12            208
  N1            4             77
  N2            3             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"
D496V6, binary
                cls
clus               0   1
  IBTK MUTATED    13   2
  IBTK WILD-TYPE 272  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     13    2
  IBTK WILD-TYPE  272   46
   clus
vv  IBTK MUTATED IBTK WILD-TYPE
  0           13            272
  1            2             46
[1] 2 2
[1] FALSE
D496V7, binary
                cls
clus               0   1
  IBTK MUTATED    13   6
  IBTK WILD-TYPE 157 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     13    6
  IBTK WILD-TYPE  157  191
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  FEMALE           13            157
  MALE              6            191
[1] 2 2
[1] FALSE
D496V8, binary
                cls
clus               0   1
  IBTK MUTATED    18   0
  IBTK WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     18    0
  IBTK WILD-TYPE  282    8
     clus
vv    IBTK MUTATED IBTK WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D496V9, binary
                cls
clus               0   1
  IBTK MUTATED    16   3
  IBTK WILD-TYPE 298  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     16    3
  IBTK WILD-TYPE  298   45
                               clus
vv                              IBTK MUTATED IBTK WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IBTK MUTATED    12   0   0   2
  IBTK WILD-TYPE 247   3  22  19
D496V10, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            2             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"
D496V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IBTK MUTATED                                  0     0
  IBTK WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IBTK MUTATED                           1    11
  IBTK WILD-TYPE                        18   165
D496V12, multiclass
                                  clus
vv                                 IBTK MUTATED IBTK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(497) Variable = PNP MUTATION ANALYSIS
D497V1, survival
               sevent
clus2             0   1
  PNP MUTATED     0   3
  PNP WILD-TYPE 277  75
  PNP MUTATED PNP WILD-TYPE 
            3           352 
  PNP MUTATED PNP WILD-TYPE 
            3            75 
$`PNP MUTATED`
TCGA-AA-3492 TCGA-AA-3845 TCGA-AZ-6598 
        3.02         0.00        49.41 

$`PNP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PNP MUTATED PNP WILD-TYPE 
            0             0 
  PNP MUTATED PNP WILD-TYPE 
        49.41        148.01 
  PNP MUTATED PNP WILD-TYPE 
        3.020        22.075 
[1] "0.0 - 49.4 (3.0)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "6.9"
D497V2, continuous
               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      63        1       24       107         8         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        18          6         44         33       35        12
               vv
clus            STAGE IVB
  PNP MUTATED           0
  PNP WILD-TYPE         1
D497V3, multiclass
            clus
vv           PNP MUTATED PNP WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            1           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  PNP MUTATED     0   1   3   0
  PNP WILD-TYPE   9  66 246  41
D497V4, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  T1           0             9
  T2           1            66
  T3           3           246
  T4           0            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
  PNP MUTATED     4   0   0
  PNP WILD-TYPE 216  81  66
D497V5, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  N0           4           216
  N1           0            81
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V6, binary
               cls
clus              0   1
  PNP MUTATED     2   0
  PNP WILD-TYPE 283  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      2    0
  PNP WILD-TYPE  283   48
   clus
vv  PNP MUTATED PNP WILD-TYPE
  0           2           283
  1           0            48
[1] 2 2
[1] FALSE
D497V7, binary
               cls
clus              0   1
  PNP MUTATED     3   1
  PNP WILD-TYPE 167 196
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      3    1
  PNP WILD-TYPE  167  196
        clus
vv       PNP MUTATED PNP WILD-TYPE
  FEMALE           3           167
  MALE             1           196
[1] 2 2
[1] FALSE
D497V8, binary
               cls
clus              0   1
  PNP MUTATED     2   0
  PNP WILD-TYPE 298   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      2    0
  PNP WILD-TYPE  298    8
     clus
vv    PNP MUTATED PNP WILD-TYPE
  NO            2           298
  YES           0             8
[1] 2 2
[1] FALSE
D497V9, binary
               cls
clus              0   1
  PNP MUTATED     4   0
  PNP WILD-TYPE 310  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      4    0
  PNP WILD-TYPE  310   48
                               clus
vv                              PNP MUTATED PNP WILD-TYPE
  COLON ADENOCARCINOMA                    4           310
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  PNP MUTATED     2   0   0   1
  PNP WILD-TYPE 257   3  22  20
D497V10, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  R0           2           257
  R1           0             3
  R2           0            22
  RX           1            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"
D497V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PNP MUTATED                                  0     0
  PNP WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PNP MUTATED                           0     2
  PNP WILD-TYPE                        19   174
D497V12, multiclass
[1] "Remove cluster labels:" "PNP MUTATED"           
clus
  PNP MUTATED PNP WILD-TYPE 
            2           204 
   TCGA-A6-2677    TCGA-A6-4105    TCGA-A6-6649    TCGA-AD-6548    TCGA-AD-6888 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AD-6895    TCGA-AD-6964    TCGA-AZ-4681    TCGA-AZ-6601    TCGA-AZ-6608 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-5912    TCGA-DM-A285    TCGA-G4-6310    TCGA-G4-6321    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-G4-6628    TCGA-A6-2671    TCGA-A6-2672 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-3808    TCGA-A6-3809    TCGA-A6-3810    TCGA-A6-5656    TCGA-A6-5657 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-5659    TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-5665    TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-6142    TCGA-A6-6648    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-6889    TCGA-AD-6890    TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AD-6965    TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AY-5543    TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-4323    TCGA-AZ-4616    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-6603    TCGA-AZ-6605    TCGA-AZ-6606 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-6607    TCGA-CA-5254    TCGA-CA-5255    TCGA-CA-5796    TCGA-CA-5797 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CA-6715    TCGA-CA-6716    TCGA-CA-6717    TCGA-CA-6718    TCGA-CA-6719 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4950    TCGA-CK-4952    TCGA-CK-5913 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-5914    TCGA-CK-5916    TCGA-CK-6746    TCGA-CK-6747    TCGA-CK-6748 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-6751    TCGA-CM-4743    TCGA-CM-4744    TCGA-CM-4746    TCGA-CM-4747 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-4752    TCGA-CM-5341    TCGA-CM-5344    TCGA-CM-5348    TCGA-CM-5349 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-5860    TCGA-CM-5861    TCGA-CM-5862    TCGA-CM-5863    TCGA-CM-5864 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-5868    TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6165    TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6170    TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6676    TCGA-CM-6677    TCGA-CM-6678    TCGA-CM-6679    TCGA-CM-6680 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-5537    TCGA-D5-5538    TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6529    TCGA-D5-6532    TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6536    TCGA-D5-6537    TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6541    TCGA-D5-6898    TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6924    TCGA-D5-6926    TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6930    TCGA-D5-6931    TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A0XD    TCGA-DM-A0XF    TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A1D7    TCGA-DM-A1D8    TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A1HA    TCGA-DM-A1HB    TCGA-DM-A282    TCGA-DM-A28C    TCGA-DM-A28E 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A28F    TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6460    TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6805    TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6854    TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6303    TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6323    TCGA-G4-6626 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 

Clustering(498) Variable = ACTL8 MUTATION ANALYSIS
D498V1, survival
                 sevent
clus2               0   1
  ACTL8 MUTATED     6   2
  ACTL8 WILD-TYPE 271  76
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              8             347 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  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           22.09 
[1] "11.1 - 85.5 (20.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D498V2, continuous
                 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      63        0       25       106         8         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        18          6         43         33       33        12
                 vv
clus              STAGE IVB
  ACTL8 MUTATED           0
  ACTL8 WILD-TYPE         1
D498V3, multiclass
            clus
vv           ACTL8 MUTATED ACTL8 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  ACTL8 MUTATED     0   1   6   1
  ACTL8 WILD-TYPE   9  66 243  40
D498V4, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             1              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
  ACTL8 MUTATED     6   2   1
  ACTL8 WILD-TYPE 214  79  65
D498V5, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V6, binary
                 cls
clus                0   1
  ACTL8 MUTATED     4   2
  ACTL8 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      4    2
  ACTL8 WILD-TYPE  281   46
   clus
vv  ACTL8 MUTATED ACTL8 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D498V7, binary
                 cls
clus                0   1
  ACTL8 MUTATED     3   6
  ACTL8 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      3    6
  ACTL8 WILD-TYPE  167  191
        clus
vv       ACTL8 MUTATED ACTL8 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D498V8, binary
                 cls
clus                0   1
  ACTL8 MUTATED     7   0
  ACTL8 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      7    0
  ACTL8 WILD-TYPE  293    8
     clus
vv    ACTL8 MUTATED ACTL8 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D498V9, binary
                 cls
clus                0   1
  ACTL8 MUTATED     8   1
  ACTL8 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      8    1
  ACTL8 WILD-TYPE  306   47
                               clus
vv                              ACTL8 MUTATED ACTL8 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACTL8 MUTATED     6   1   0   0
  ACTL8 WILD-TYPE 253   2  22  21
D498V10, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  R0             6             253
  R1             1               2
  R2             0              22
  RX             0              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"
D498V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL8 MUTATED                                  0     0
  ACTL8 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACTL8 MUTATED                           3     3
  ACTL8 WILD-TYPE                        16   173
D498V12, multiclass
                                  clus
vv                                 ACTL8 MUTATED ACTL8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        3             173
[1] 4 2
[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 = CDK14 MUTATION ANALYSIS
D499V1, survival
                 sevent
clus2               0   1
  CDK14 MUTATED    10   5
  CDK14 WILD-TYPE 267  73
  CDK14 MUTATED CDK14 WILD-TYPE 
             15             340 
  CDK14 MUTATED CDK14 WILD-TYPE 
              5              73 
$`CDK14 MUTATED`
TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-3807 TCGA-A6-5665 TCGA-AA-3667 TCGA-AA-3855 
       26.17        42.90        34.65        22.06        14.01        32.05 
TCGA-AA-A00N TCGA-AA-A02H TCGA-AZ-5407 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 
        4.01         2.01        88.21        10.06        15.62        23.05 
TCGA-D5-6532 TCGA-D5-6539 TCGA-G4-6303 
       18.25        12.49        65.85 

$`CDK14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       43.76        42.28        16.57        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 
       61.02        78.08         6.97        54.02         2.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02J 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        20.19        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CDK14 MUTATED CDK14 WILD-TYPE 
           2.01            0.00 
  CDK14 MUTATED CDK14 WILD-TYPE 
          88.21          148.01 
  CDK14 MUTATED CDK14 WILD-TYPE 
          22.06           22.06 
[1] "2.0 - 88.2 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D499V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK14 MUTATED         3        0        0         5         2         0
  CDK14 WILD-TYPE      61        1       26       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK14 MUTATED           0          0          0          2        2         0
  CDK14 WILD-TYPE        18          6         44         31       33        12
                 vv
clus              STAGE IVB
  CDK14 MUTATED           0
  CDK14 WILD-TYPE         1
D499V3, multiclass
            clus
vv           CDK14 MUTATED CDK14 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  CDK14 MUTATED     1   2   9   3
  CDK14 WILD-TYPE   8  65 240  38
D499V4, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             9             240
  T4             3              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
  CDK14 MUTATED    11   1   3
  CDK14 WILD-TYPE 209  80  63
D499V5, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  N0            11             209
  N1             1              80
  N2             3              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"
D499V6, binary
                 cls
clus                0   1
  CDK14 MUTATED    13   2
  CDK14 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     13    2
  CDK14 WILD-TYPE  272   46
   clus
vv  CDK14 MUTATED CDK14 WILD-TYPE
  0            13             272
  1             2              46
[1] 2 2
[1] FALSE
D499V7, binary
                 cls
clus                0   1
  CDK14 MUTATED    10   5
  CDK14 WILD-TYPE 160 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     10    5
  CDK14 WILD-TYPE  160  192
        clus
vv       CDK14 MUTATED CDK14 WILD-TYPE
  FEMALE            10             160
  MALE               5             192
[1] 2 2
[1] FALSE
D499V8, binary
                 cls
clus                0   1
  CDK14 MUTATED    12   0
  CDK14 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     12    0
  CDK14 WILD-TYPE  288    8
     clus
vv    CDK14 MUTATED CDK14 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D499V9, binary
                 cls
clus                0   1
  CDK14 MUTATED    13   2
  CDK14 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     13    2
  CDK14 WILD-TYPE  301   46
                               clus
vv                              CDK14 MUTATED CDK14 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK14 MUTATED    11   0   1   2
  CDK14 WILD-TYPE 248   3  21  19
D499V10, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             2              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"
D499V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK14 MUTATED                                  0     1
  CDK14 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK14 MUTATED                           0    10
  CDK14 WILD-TYPE                        19   166
D499V12, multiclass
                                  clus
vv                                 CDK14 MUTATED CDK14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(500) Variable = AXIN2 MUTATION ANALYSIS
D500V1, survival
                 sevent
clus2               0   1
  AXIN2 MUTATED    13   7
  AXIN2 WILD-TYPE 264  71
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             20             335 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
              7              71 
$`AXIN2 MUTATED`
TCGA-AA-3672 TCGA-AA-3972 TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-5661 
        0.92        50.99        10.88        79.69        42.90        33.53 
TCGA-AA-3492 TCGA-AA-3542 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-CA-5255 
        3.02        12.99        30.02        34.98        12.16        12.36 
TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-6162 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A1D6 
       21.14        30.08        12.00         4.80        13.35        49.91 
TCGA-DM-A1DB TCGA-G4-6304 
       44.32        53.62 

$`AXIN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        43.76        46.65        43.76        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-A6-5662 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        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-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
      140.38         7.50       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  AXIN2 MUTATED AXIN2 WILD-TYPE 
           0.92            0.00 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
          79.69          148.01 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
          25.58           22.06 
[1] "0.9 - 79.7 (25.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D500V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AXIN2 MUTATED         3        0        2         7         3         0
  AXIN2 WILD-TYPE      61        1       24       101         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AXIN2 MUTATED           1          0          2          1        1         0
  AXIN2 WILD-TYPE        17          6         42         32       34        12
                 vv
clus              STAGE IVB
  AXIN2 MUTATED           0
  AXIN2 WILD-TYPE         1
D500V3, multiclass
            clus
vv           AXIN2 MUTATED AXIN2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  AXIN2 MUTATED     1   2  13   5
  AXIN2 WILD-TYPE   8  65 236  36
D500V4, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            13             236
  T4             5              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
  AXIN2 MUTATED    15   4   2
  AXIN2 WILD-TYPE 205  77  64
D500V5, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  N0            15             205
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V6, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   1
  AXIN2 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    1
  AXIN2 WILD-TYPE  268   47
   clus
vv  AXIN2 MUTATED AXIN2 WILD-TYPE
  0            17             268
  1             1              47
[1] 2 2
[1] FALSE
D500V7, binary
                 cls
clus                0   1
  AXIN2 MUTATED    10  11
  AXIN2 WILD-TYPE 160 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     10   11
  AXIN2 WILD-TYPE  160  186
        clus
vv       AXIN2 MUTATED AXIN2 WILD-TYPE
  FEMALE            10             160
  MALE              11             186
[1] 2 2
[1] FALSE
D500V8, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   1
  AXIN2 WILD-TYPE 283   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    1
  AXIN2 WILD-TYPE  283    7
     clus
vv    AXIN2 MUTATED AXIN2 WILD-TYPE
  NO             17             283
  YES             1               7
[1] 2 2
[1] FALSE
D500V9, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   4
  AXIN2 WILD-TYPE 297  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    4
  AXIN2 WILD-TYPE  297   44
                               clus
vv                              AXIN2 MUTATED AXIN2 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AXIN2 MUTATED    15   0   1   2
  AXIN2 WILD-TYPE 244   3  21  19
D500V10, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             1              21
  RX             2              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"
D500V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AXIN2 MUTATED                                  0     1
  AXIN2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AXIN2 MUTATED                           1    12
  AXIN2 WILD-TYPE                        18   164
D500V12, multiclass
                                  clus
vv                                 AXIN2 MUTATED AXIN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = KCNH7 MUTATION ANALYSIS
D501V1, survival
                 sevent
clus2               0   1
  KCNH7 MUTATED    21  10
  KCNH7 WILD-TYPE 256  68
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             31             324 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             10              68 
$`KCNH7 MUTATED`
TCGA-AA-3554 TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-2676 TCGA-AA-3510 TCGA-AA-3845 
       17.95        19.04        35.80        42.90        63.98         0.00 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-3779 TCGA-AY-4071 
       24.00         2.01         4.01        35.01        14.50         0.95 
TCGA-AZ-5403 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-5348 
       62.79        12.76        10.06        85.45        21.14        22.98 
TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-6535 
       30.08        15.02        15.02        12.95        11.01        15.12 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6317 
       13.35       130.65        35.74         6.18        35.31        36.00 
TCGA-G4-6626 
       46.75 

$`KCNH7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        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        14.04        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       11.01        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 

  KCNH7 MUTATED KCNH7 WILD-TYPE 
              0               0 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
         130.65          148.01 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
          19.04           22.09 
[1] "0.0 - 130.7 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D501V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNH7 MUTATED         6        0        3        14         2         0
  KCNH7 WILD-TYPE      58        1       23        94         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNH7 MUTATED           1          0          3          1        0         2
  KCNH7 WILD-TYPE        17          6         41         32       35        10
                 vv
clus              STAGE IVB
  KCNH7 MUTATED           0
  KCNH7 WILD-TYPE         1
D501V3, multiclass
            clus
vv           KCNH7 MUTATED KCNH7 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             14              94
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              2              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
  KCNH7 MUTATED     2   4  22   4
  KCNH7 WILD-TYPE   7  63 227  37
D501V4, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  T1             2               7
  T2             4              63
  T3            22             227
  T4             4              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
  KCNH7 MUTATED    25   5   2
  KCNH7 WILD-TYPE 195  76  64
D501V5, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  N0            25             195
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V6, binary
                 cls
clus                0   1
  KCNH7 MUTATED    26   2
  KCNH7 WILD-TYPE 259  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     26    2
  KCNH7 WILD-TYPE  259   46
   clus
vv  KCNH7 MUTATED KCNH7 WILD-TYPE
  0            26             259
  1             2              46
[1] 2 2
[1] FALSE
D501V7, binary
                 cls
clus                0   1
  KCNH7 MUTATED    19  13
  KCNH7 WILD-TYPE 151 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     19   13
  KCNH7 WILD-TYPE  151  184
        clus
vv       KCNH7 MUTATED KCNH7 WILD-TYPE
  FEMALE            19             151
  MALE              13             184
[1] 2 2
[1] FALSE
D501V8, binary
                 cls
clus                0   1
  KCNH7 MUTATED    26   1
  KCNH7 WILD-TYPE 274   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     26    1
  KCNH7 WILD-TYPE  274    7
     clus
vv    KCNH7 MUTATED KCNH7 WILD-TYPE
  NO             26             274
  YES             1               7
[1] 2 2
[1] FALSE
D501V9, binary
                 cls
clus                0   1
  KCNH7 MUTATED    24   7
  KCNH7 WILD-TYPE 290  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     24    7
  KCNH7 WILD-TYPE  290   41
                               clus
vv                              KCNH7 MUTATED KCNH7 WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNH7 MUTATED    24   1   0   4
  KCNH7 WILD-TYPE 235   2  22  17
D501V10, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  R0            24             235
  R1             1               2
  R2             0              22
  RX             4              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"
D501V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNH7 MUTATED                                  0     2
  KCNH7 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNH7 MUTATED                           1    20
  KCNH7 WILD-TYPE                        18   156
D501V12, multiclass
                                  clus
vv                                 KCNH7 MUTATED KCNH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       20             156
[1] 4 2
[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 = SPCS2 MUTATION ANALYSIS
D502V1, survival
                 sevent
clus2               0   1
  SPCS2 MUTATED     3   2
  SPCS2 WILD-TYPE 274  76
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             350 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              2              76 
$`SPCS2 MUTATED`
TCGA-AA-3697 TCGA-AZ-6608 TCGA-CK-6751 TCGA-D5-6923 TCGA-DM-A28C 
       85.05         1.94       124.27        12.43        81.37 

$`SPCS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95         2.01        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SPCS2 MUTATED SPCS2 WILD-TYPE 
           1.94            0.00 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
         124.27          148.01 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
         81.370          22.045 
[1] "1.9 - 124.3 (81.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D502V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPCS2 MUTATED         2        0        1         1         0         0
  SPCS2 WILD-TYPE      62        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPCS2 MUTATED           0          1          0          0        0         0
  SPCS2 WILD-TYPE        18          5         44         33       35        12
                 vv
clus              STAGE IVB
  SPCS2 MUTATED           0
  SPCS2 WILD-TYPE         1
D502V3, multiclass
            clus
vv           SPCS2 MUTATED SPCS2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  SPCS2 MUTATED     0   3   2   0
  SPCS2 WILD-TYPE   9  64 247  41
D502V4, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             2             247
  T4             0              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
  SPCS2 MUTATED     4   1   0
  SPCS2 WILD-TYPE 216  80  66
D502V5, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V6, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   0
  SPCS2 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    0
  SPCS2 WILD-TYPE  281   48
   clus
vv  SPCS2 MUTATED SPCS2 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D502V7, binary
                 cls
clus                0   1
  SPCS2 MUTATED     2   3
  SPCS2 WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      2    3
  SPCS2 WILD-TYPE  168  194
        clus
vv       SPCS2 MUTATED SPCS2 WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D502V8, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   0
  SPCS2 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    0
  SPCS2 WILD-TYPE  296    8
     clus
vv    SPCS2 MUTATED SPCS2 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D502V9, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   1
  SPCS2 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    1
  SPCS2 WILD-TYPE  310   47
                               clus
vv                              SPCS2 MUTATED SPCS2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPCS2 MUTATED     2   0   0   1
  SPCS2 WILD-TYPE 257   3  22  20
D502V10, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             1              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"
D502V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPCS2 MUTATED                                  0     0
  SPCS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPCS2 MUTATED                           0     4
  SPCS2 WILD-TYPE                        19   172
D502V12, multiclass
                                  clus
vv                                 SPCS2 MUTATED SPCS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = TNRC6C MUTATION ANALYSIS
D503V1, survival
                  sevent
clus2                0   1
  TNRC6C MUTATED    12   4
  TNRC6C WILD-TYPE 265  74
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              16              339 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               4               74 
$`TNRC6C MUTATED`
TCGA-AA-3950 TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3845 
       24.00        32.75        22.06         3.02        33.04         0.00 
TCGA-AA-3966 TCGA-AA-A01P TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 
        2.01        38.07        12.16        27.09        21.44        12.76 
TCGA-CK-5913 TCGA-CM-6171 TCGA-F4-6570 TCGA-F4-6856 
       51.32        14.04         6.18        35.31 

$`TNRC6C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
               0                0 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           51.32           148.01 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           21.75            22.09 
[1] "0.0 - 51.3 (21.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D503V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNRC6C MUTATED         4        0        1        10         2         0
  TNRC6C WILD-TYPE      60        1       25        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNRC6C MUTATED           1          0          0          0        0
  TNRC6C WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TNRC6C MUTATED           0         0
  TNRC6C WILD-TYPE        12         1
D503V3, multiclass
            clus
vv           TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              10               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TNRC6C MUTATED     0   4  12   2
  TNRC6C WILD-TYPE   9  63 237  39
D503V4, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  T1              0                9
  T2              4               63
  T3             12              237
  T4              2               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
  TNRC6C MUTATED    17   1   0
  TNRC6C WILD-TYPE 203  80  66
D503V5, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  N0             17              203
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V6, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    14   0
  TNRC6C WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     14    0
  TNRC6C WILD-TYPE  271   48
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D503V7, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    14   4
  TNRC6C WILD-TYPE 156 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     14    4
  TNRC6C WILD-TYPE  156  193
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE             14              156
  MALE                4              193
[1] 2 2
[1] FALSE
D503V8, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    13   0
  TNRC6C WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     13    0
  TNRC6C WILD-TYPE  287    8
     clus
vv    TNRC6C MUTATED TNRC6C WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D503V9, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    12   6
  TNRC6C WILD-TYPE 302  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     12    6
  TNRC6C WILD-TYPE  302   42
                               clus
vv                              TNRC6C MUTATED TNRC6C WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TNRC6C MUTATED    14   0   0   3
  TNRC6C WILD-TYPE 245   3  22  18
D503V10, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0             14              245
  R1              0                3
  R2              0               22
  RX              3               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"
D503V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNRC6C MUTATED                                  0     1
  TNRC6C WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TNRC6C MUTATED                           0    10
  TNRC6C WILD-TYPE                        19   166
D503V12, multiclass
                                  clus
vv                                 TNRC6C MUTATED TNRC6C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(504) Variable = OR4E2 MUTATION ANALYSIS
D504V1, survival
                 sevent
clus2               0   1
  OR4E2 MUTATED     4   0
  OR4E2 WILD-TYPE 273  78
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              4             351 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              0              78 
$`OR4E2 MUTATED`
TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3510 TCGA-CM-6675 
       35.80        22.06        63.98        13.05 

$`OR4E2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.03 
[1] "13.1 - 64.0 (28.9)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D504V2, continuous
                 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      64        1       25       106         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  OR4E2 MUTATED           1
  OR4E2 WILD-TYPE         0
D504V3, multiclass
            clus
vv           OR4E2 MUTATED OR4E2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              12
  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   9  67 245  40
D504V4, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  OR4E2 MUTATED     4   0   1
  OR4E2 WILD-TYPE 216  81  65
D504V5, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V6, binary
                 cls
clus                0   1
  OR4E2 MUTATED     3   1
  OR4E2 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      3    1
  OR4E2 WILD-TYPE  282   47
   clus
vv  OR4E2 MUTATED OR4E2 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D504V7, binary
                 cls
clus                0   1
  OR4E2 MUTATED     3   2
  OR4E2 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      3    2
  OR4E2 WILD-TYPE  167  195
        clus
vv       OR4E2 MUTATED OR4E2 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D504V8, binary
                 cls
clus                0   1
  OR4E2 MUTATED     4   0
  OR4E2 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      4    0
  OR4E2 WILD-TYPE  296    8
     clus
vv    OR4E2 MUTATED OR4E2 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D504V9, binary
                 cls
clus                0   1
  OR4E2 MUTATED     5   0
  OR4E2 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      5    0
  OR4E2 WILD-TYPE  309   48
                               clus
vv                              OR4E2 MUTATED OR4E2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4E2 MUTATED     4   0   0   1
  OR4E2 WILD-TYPE 255   3  22  20
D504V10, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D504V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4E2 MUTATED                                  0     0
  OR4E2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4E2 MUTATED                           1     3
  OR4E2 WILD-TYPE                        18   173
D504V12, multiclass
                                  clus
vv                                 OR4E2 MUTATED OR4E2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = SULT6B1 MUTATION ANALYSIS
D505V1, survival
                   sevent
clus2                 0   1
  SULT6B1 MUTATED     7   1
  SULT6B1 WILD-TYPE 270  77
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                8               347 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                1                77 
$`SULT6B1 MUTATED`
TCGA-G4-6310 TCGA-AA-3510 TCGA-AA-A010 TCGA-AY-6196 TCGA-AZ-4315 TCGA-CM-4743 
       63.62        63.98        34.98         0.20        58.39        23.05 
TCGA-D5-6539 TCGA-DM-A1DB 
       12.49        44.32 

$`SULT6B1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50       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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
              0.2               0.0 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
            63.98            148.01 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
            39.65             21.99 
[1] "0.2 - 64.0 (39.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D505V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SULT6B1 MUTATED         0        0        1         4         1         0
  SULT6B1 WILD-TYPE      64        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT6B1 MUTATED           0          0          1          1        0
  SULT6B1 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SULT6B1 MUTATED           0         0
  SULT6B1 WILD-TYPE        12         1
D505V3, multiclass
            clus
vv           SULT6B1 MUTATED SULT6B1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SULT6B1 MUTATED     0   0   8   1
  SULT6B1 WILD-TYPE   9  67 241  40
D505V4, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               8               241
  T4               1                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
  SULT6B1 MUTATED     7   1   1
  SULT6B1 WILD-TYPE 213  80  65
D505V5, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  N0               7               213
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V6, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     8   0
  SULT6B1 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      8    0
  SULT6B1 WILD-TYPE  277   48
   clus
vv  SULT6B1 MUTATED SULT6B1 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D505V7, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     3   6
  SULT6B1 WILD-TYPE 167 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      3    6
  SULT6B1 WILD-TYPE  167  191
        clus
vv       SULT6B1 MUTATED SULT6B1 WILD-TYPE
  FEMALE               3               167
  MALE                 6               191
[1] 2 2
[1] FALSE
D505V8, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     5   1
  SULT6B1 WILD-TYPE 295   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      5    1
  SULT6B1 WILD-TYPE  295    7
     clus
vv    SULT6B1 MUTATED SULT6B1 WILD-TYPE
  NO                5               295
  YES               1                 7
[1] 2 2
[1] FALSE
D505V9, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     8   1
  SULT6B1 WILD-TYPE 306  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      8    1
  SULT6B1 WILD-TYPE  306   47
                               clus
vv                              SULT6B1 MUTATED SULT6B1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SULT6B1 MUTATED     8   0   0   0
  SULT6B1 WILD-TYPE 251   3  22  21
D505V10, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               0                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"
D505V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULT6B1 MUTATED                                  0     0
  SULT6B1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SULT6B1 MUTATED                           0     6
  SULT6B1 WILD-TYPE                        19   170
D505V12, multiclass
                                  clus
vv                                 SULT6B1 MUTATED SULT6B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = LDHA MUTATION ANALYSIS
D506V1, survival
                sevent
clus2              0   1
  LDHA MUTATED     7   2
  LDHA WILD-TYPE 270  76
  LDHA MUTATED LDHA WILD-TYPE 
             9            346 
  LDHA MUTATED LDHA WILD-TYPE 
             2             76 
$`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         2.01        17.85 
TCGA-D5-6540 TCGA-DM-A28K TCGA-G4-6293 
       16.14        98.24       133.18 

$`LDHA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        79.69        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
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-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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  LDHA MUTATED LDHA WILD-TYPE 
          1.02           0.00 
  LDHA MUTATED LDHA WILD-TYPE 
        133.18         148.01 
  LDHA MUTATED LDHA WILD-TYPE 
        21.140         22.075 
[1] "1.0 - 133.2 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D506V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LDHA MUTATED         3        0        1         3         0         0
  LDHA WILD-TYPE      61        1       25       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LDHA MUTATED           1          0          0          0        2         0
  LDHA WILD-TYPE        17          6         44         33       33        12
                vv
clus             STAGE IVB
  LDHA MUTATED           0
  LDHA WILD-TYPE         1
D506V3, multiclass
            clus
vv           LDHA MUTATED LDHA WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  LDHA MUTATED     1   2   7   0
  LDHA WILD-TYPE   8  65 242  41
D506V4, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  T1            1              8
  T2            2             65
  T3            7            242
  T4            0             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
  LDHA MUTATED     7   2   1
  LDHA WILD-TYPE 213  79  65
D506V5, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  N0            7            213
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V6, binary
                cls
clus               0   1
  LDHA MUTATED     7   2
  LDHA WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      7    2
  LDHA WILD-TYPE  278   46
   clus
vv  LDHA MUTATED LDHA WILD-TYPE
  0            7            278
  1            2             46
[1] 2 2
[1] FALSE
D506V7, binary
                cls
clus               0   1
  LDHA MUTATED     5   5
  LDHA WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      5    5
  LDHA WILD-TYPE  165  192
        clus
vv       LDHA MUTATED LDHA WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D506V8, binary
                cls
clus               0   1
  LDHA MUTATED     7   0
  LDHA WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      7    0
  LDHA WILD-TYPE  293    8
     clus
vv    LDHA MUTATED LDHA WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D506V9, binary
                cls
clus               0   1
  LDHA MUTATED     7   3
  LDHA WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      7    3
  LDHA WILD-TYPE  307   45
                               clus
vv                              LDHA MUTATED LDHA WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LDHA MUTATED     6   0   0   3
  LDHA WILD-TYPE 253   3  22  18
D506V10, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            3             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"
D506V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LDHA MUTATED                                  0     0
  LDHA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LDHA MUTATED                           0     8
  LDHA WILD-TYPE                        19   168
D506V12, multiclass
                                  clus
vv                                 LDHA MUTATED LDHA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = EIF4A2 MUTATION ANALYSIS
D507V1, survival
                  sevent
clus2                0   1
  EIF4A2 MUTATED     9   0
  EIF4A2 WILD-TYPE 268  78
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               9              346 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               0               78 
$`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        15.02        37.02 
TCGA-CM-6168 TCGA-DM-A1HB TCGA-F4-6704 
       12.99       135.65         1.55 

$`EIF4A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        34.06        25.02        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-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-A010 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
            1.55             0.00 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
          135.65           148.01 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
           15.02            22.09 
[1] "1.6 - 135.7 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D507V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF4A2 MUTATED         2        0        0         3         1         0
  EIF4A2 WILD-TYPE      62        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4A2 MUTATED           0          0          2          1        1
  EIF4A2 WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  EIF4A2 MUTATED           0         0
  EIF4A2 WILD-TYPE        12         1
D507V3, multiclass
            clus
vv           EIF4A2 MUTATED EIF4A2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  EIF4A2 MUTATED     0   2   6   2
  EIF4A2 WILD-TYPE   9  65 243  39
D507V4, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              6              243
  T4              2               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
  EIF4A2 MUTATED     6   3   1
  EIF4A2 WILD-TYPE 214  78  65
D507V5, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  N0              6              214
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V6, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     7   1
  EIF4A2 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      7    1
  EIF4A2 WILD-TYPE  278   47
   clus
vv  EIF4A2 MUTATED EIF4A2 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D507V7, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     5   5
  EIF4A2 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      5    5
  EIF4A2 WILD-TYPE  165  192
        clus
vv       EIF4A2 MUTATED EIF4A2 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D507V8, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     7   0
  EIF4A2 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      7    0
  EIF4A2 WILD-TYPE  293    8
     clus
vv    EIF4A2 MUTATED EIF4A2 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D507V9, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     8   1
  EIF4A2 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      8    1
  EIF4A2 WILD-TYPE  306   47
                               clus
vv                              EIF4A2 MUTATED EIF4A2 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF4A2 MUTATED     6   0   1   1
  EIF4A2 WILD-TYPE 253   3  21  20
D507V10, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              1               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"
D507V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4A2 MUTATED                                  1     0
  EIF4A2 WILD-TYPE                                0    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF4A2 MUTATED                           2     3
  EIF4A2 WILD-TYPE                        17   173
D507V12, multiclass
                                  clus
vv                                 EIF4A2 MUTATED EIF4A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         3              173
[1] 4 2
[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 = RCSD1 MUTATION ANALYSIS
D508V1, survival
                 sevent
clus2               0   1
  RCSD1 MUTATED     9   5
  RCSD1 WILD-TYPE 268  73
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             14             341 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
              5              73 
$`RCSD1 MUTATED`
TCGA-AA-3713 TCGA-A6-2672 TCGA-AA-3542 TCGA-AA-A00J TCGA-AD-6899 TCGA-AU-6004 
       19.04        46.65        12.99        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        21.99 
TCGA-D5-6930 TCGA-G4-6303 
       13.35        65.85 

$`RCSD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       24.53        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        12.76        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RCSD1 MUTATED RCSD1 WILD-TYPE 
           5.79            0.00 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
          65.85          148.01 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
         18.545          22.090 
[1] "5.8 - 65.8 (18.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D508V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RCSD1 MUTATED         1        0        1         4         0         0
  RCSD1 WILD-TYPE      63        1       25       104         8         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        18          6         41         31       32        12
                 vv
clus              STAGE IVB
  RCSD1 MUTATED           0
  RCSD1 WILD-TYPE         1
D508V3, multiclass
            clus
vv           RCSD1 MUTATED RCSD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              0              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
  RCSD1 MUTATED     0   1  10   3
  RCSD1 WILD-TYPE   9  66 239  38
D508V4, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             3              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
  RCSD1 MUTATED     7   5   2
  RCSD1 WILD-TYPE 213  76  64
D508V5, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  N0             7             213
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V6, binary
                 cls
clus                0   1
  RCSD1 MUTATED     7   3
  RCSD1 WILD-TYPE 278  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED      7    3
  RCSD1 WILD-TYPE  278   45
   clus
vv  RCSD1 MUTATED RCSD1 WILD-TYPE
  0             7             278
  1             3              45
[1] 2 2
[1] FALSE
D508V7, binary
                 cls
clus                0   1
  RCSD1 MUTATED     5   9
  RCSD1 WILD-TYPE 165 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED      5    9
  RCSD1 WILD-TYPE  165  188
        clus
vv       RCSD1 MUTATED RCSD1 WILD-TYPE
  FEMALE             5             165
  MALE               9             188
[1] 2 2
[1] FALSE
D508V8, binary
                 cls
clus                0   1
  RCSD1 MUTATED    11   1
  RCSD1 WILD-TYPE 289   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED     11    1
  RCSD1 WILD-TYPE  289    7
     clus
vv    RCSD1 MUTATED RCSD1 WILD-TYPE
  NO             11             289
  YES             1               7
[1] 2 2
[1] FALSE
D508V9, binary
                 cls
clus                0   1
  RCSD1 MUTATED    11   3
  RCSD1 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED     11    3
  RCSD1 WILD-TYPE  303   45
                               clus
vv                              RCSD1 MUTATED RCSD1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RCSD1 MUTATED     6   0   1   4
  RCSD1 WILD-TYPE 253   3  21  17
D508V10, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             4              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"
D508V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RCSD1 MUTATED                                  0     2
  RCSD1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RCSD1 MUTATED                           1     8
  RCSD1 WILD-TYPE                        18   168
D508V12, multiclass
                                  clus
vv                                 RCSD1 MUTATED RCSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = EIF5B MUTATION ANALYSIS
D509V1, survival
                 sevent
clus2               0   1
  EIF5B MUTATED     8   7
  EIF5B WILD-TYPE 269  71
  EIF5B MUTATED EIF5B WILD-TYPE 
             15             340 
  EIF5B MUTATED EIF5B WILD-TYPE 
              7              71 
$`EIF5B MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-G4-6588 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3977 
       19.04        35.80        26.17         3.02        63.98        25.02 
TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5916 TCGA-D5-5538 
       83.24        49.41        12.76        85.45        21.14        54.61 
TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6856 
       98.24         6.18        35.31 

$`EIF5B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  EIF5B MUTATED EIF5B WILD-TYPE 
           3.02            0.00 
  EIF5B MUTATED EIF5B WILD-TYPE 
          98.24          148.01 
  EIF5B MUTATED EIF5B WILD-TYPE 
          35.31           21.99 
[1] "3.0 - 98.2 (35.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D509V2, continuous
                 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      62        1       21       102         8         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  EIF5B MUTATED           0
  EIF5B WILD-TYPE         1
D509V3, multiclass
            clus
vv           EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  EIF5B MUTATED     1   2  12   1
  EIF5B WILD-TYPE   8  65 237  40
D509V4, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  T1             1               8
  T2             2              65
  T3            12             237
  T4             1              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
  EIF5B MUTATED    14   2   0
  EIF5B WILD-TYPE 206  79  66
D509V5, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  N0            14             206
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V6, binary
                 cls
clus                0   1
  EIF5B MUTATED    14   0
  EIF5B WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     14    0
  EIF5B WILD-TYPE  271   48
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D509V7, binary
                 cls
clus                0   1
  EIF5B MUTATED     9   7
  EIF5B WILD-TYPE 161 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      9    7
  EIF5B WILD-TYPE  161  190
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  FEMALE             9             161
  MALE               7             190
[1] 2 2
[1] FALSE
D509V8, binary
                 cls
clus                0   1
  EIF5B MUTATED    14   0
  EIF5B WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     14    0
  EIF5B WILD-TYPE  286    8
     clus
vv    EIF5B MUTATED EIF5B WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D509V9, binary
                 cls
clus                0   1
  EIF5B MUTATED    12   4
  EIF5B WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     12    4
  EIF5B WILD-TYPE  302   44
                               clus
vv                              EIF5B MUTATED EIF5B WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EIF5B MUTATED    10   1   0   2
  EIF5B WILD-TYPE 249   2  22  19
D509V10, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  R0            10             249
  R1             1               2
  R2             0              22
  RX             2              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"
D509V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF5B MUTATED                                  0     2
  EIF5B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EIF5B MUTATED                           1     8
  EIF5B WILD-TYPE                        18   168
D509V12, multiclass
                                  clus
vv                                 EIF5B MUTATED EIF5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = FGFR1 MUTATION ANALYSIS
D510V1, survival
                 sevent
clus2               0   1
  FGFR1 MUTATED    13   2
  FGFR1 WILD-TYPE 264  76
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             15             340 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
              2              76 
$`FGFR1 MUTATED`
TCGA-AA-3715 TCGA-AZ-4681 TCGA-AA-3510 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4744 
       19.04       106.75        63.98        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 
       65.85        85.48        61.91 

$`FGFR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        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        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        36.00        13.78        46.75 

  FGFR1 MUTATED FGFR1 WILD-TYPE 
             12               0 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
         135.65          148.01 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
          61.91           22.01 
[1] "12.0 - 135.7 (61.9)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.5"
D510V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGFR1 MUTATED         3        0        2         4         0         0
  FGFR1 WILD-TYPE      61        1       24       104         8         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        17          6         40         32       33        12
                 vv
clus              STAGE IVB
  FGFR1 MUTATED           0
  FGFR1 WILD-TYPE         1
D510V3, multiclass
            clus
vv           FGFR1 MUTATED FGFR1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  FGFR1 MUTATED     0   3  13   1
  FGFR1 WILD-TYPE   9  64 236  40
D510V4, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            13             236
  T4             1              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
  FGFR1 MUTATED     9   5   3
  FGFR1 WILD-TYPE 211  76  63
D510V5, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  N0             9             211
  N1             5              76
  N2             3              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"
D510V6, binary
                 cls
clus                0   1
  FGFR1 MUTATED    15   2
  FGFR1 WILD-TYPE 270  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     15    2
  FGFR1 WILD-TYPE  270   46
   clus
vv  FGFR1 MUTATED FGFR1 WILD-TYPE
  0            15             270
  1             2              46
[1] 2 2
[1] FALSE
D510V7, binary
                 cls
clus                0   1
  FGFR1 MUTATED     8   9
  FGFR1 WILD-TYPE 162 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED      8    9
  FGFR1 WILD-TYPE  162  188
        clus
vv       FGFR1 MUTATED FGFR1 WILD-TYPE
  FEMALE             8             162
  MALE               9             188
[1] 2 2
[1] FALSE
D510V8, binary
                 cls
clus                0   1
  FGFR1 MUTATED    13   0
  FGFR1 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     13    0
  FGFR1 WILD-TYPE  287    8
     clus
vv    FGFR1 MUTATED FGFR1 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D510V9, binary
                 cls
clus                0   1
  FGFR1 MUTATED    13   3
  FGFR1 WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     13    3
  FGFR1 WILD-TYPE  301   45
                               clus
vv                              FGFR1 MUTATED FGFR1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR1 MUTATED    13   1   0   1
  FGFR1 WILD-TYPE 246   2  22  20
D510V10, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  R0            13             246
  R1             1               2
  R2             0              22
  RX             1              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"
D510V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR1 MUTATED                                  0     1
  FGFR1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FGFR1 MUTATED                           2    10
  FGFR1 WILD-TYPE                        17   166
D510V12, multiclass
                                  clus
vv                                 FGFR1 MUTATED FGFR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       10             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(511) Variable = ADNP2 MUTATION ANALYSIS
D511V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    12   3
  ADNP2 WILD-TYPE 265  75
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             15             340 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              3              75 
$`ADNP2 MUTATED`
TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A01Q 
       79.69        22.06         8.38        63.98        26.99         1.02 
TCGA-AA-A02O TCGA-AY-6197 TCGA-CK-4947 TCGA-D5-6535 TCGA-DM-A1D4 TCGA-DM-A1D6 
        0.92        21.44        17.56        15.12        92.75        49.91 
TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6293 
      135.65         6.18       133.18 

$`ADNP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        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-F4-6703 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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ADNP2 MUTATED ADNP2 WILD-TYPE 
           0.92            0.00 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
         135.65          148.01 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          22.06           22.06 
[1] "0.9 - 135.7 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D511V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADNP2 MUTATED         1        0        3         7         0         0
  ADNP2 WILD-TYPE      63        1       23       101         8         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        17          6         41         33       35        12
                 vv
clus              STAGE IVB
  ADNP2 MUTATED           0
  ADNP2 WILD-TYPE         1
D511V3, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ADNP2 MUTATED     0   1  13   1
  ADNP2 WILD-TYPE   9  66 236  40
D511V4, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            13             236
  T4             1              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
  ADNP2 MUTATED    11   4   0
  ADNP2 WILD-TYPE 209  77  66
D511V5, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  N0            11             209
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V6, binary
                 cls
clus                0   1
  ADNP2 MUTATED    13   0
  ADNP2 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     13    0
  ADNP2 WILD-TYPE  272   48
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D511V7, binary
                 cls
clus                0   1
  ADNP2 MUTATED     7   8
  ADNP2 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      7    8
  ADNP2 WILD-TYPE  163  189
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D511V8, binary
                 cls
clus                0   1
  ADNP2 MUTATED    10   0
  ADNP2 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     10    0
  ADNP2 WILD-TYPE  290    8
     clus
vv    ADNP2 MUTATED ADNP2 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D511V9, binary
                 cls
clus                0   1
  ADNP2 MUTATED    13   1
  ADNP2 WILD-TYPE 301  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     13    1
  ADNP2 WILD-TYPE  301   47
                               clus
vv                              ADNP2 MUTATED ADNP2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ADNP2 MUTATED     9   0   0   2
  ADNP2 WILD-TYPE 250   3  22  19
D511V10, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D511V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADNP2 MUTATED                                  0     0
  ADNP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADNP2 MUTATED                           1    10
  ADNP2 WILD-TYPE                        18   166
D511V12, multiclass
                                  clus
vv                                 ADNP2 MUTATED ADNP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(512) Variable = IRAK3 MUTATION ANALYSIS
D512V1, survival
                 sevent
clus2               0   1
  IRAK3 MUTATED     5   2
  IRAK3 WILD-TYPE 272  76
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              7             348 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              2              76 
$`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 
       85.48 

$`IRAK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  IRAK3 MUTATED IRAK3 WILD-TYPE 
           3.02            0.00 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
          85.48          148.01 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
          15.12           22.09 
[1] "3.0 - 85.5 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D512V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRAK3 MUTATED         2        0        1         2         1         0
  IRAK3 WILD-TYPE      62        1       25       106         7         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  IRAK3 MUTATED           0
  IRAK3 WILD-TYPE         1
D512V3, multiclass
            clus
vv           IRAK3 MUTATED IRAK3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  IRAK3 MUTATED     0   2   5   1
  IRAK3 WILD-TYPE   9  65 244  40
D512V4, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             1              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
  IRAK3 MUTATED     6   2   0
  IRAK3 WILD-TYPE 214  79  66
D512V5, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V6, binary
                 cls
clus                0   1
  IRAK3 MUTATED     6   0
  IRAK3 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      6    0
  IRAK3 WILD-TYPE  279   48
   clus
vv  IRAK3 MUTATED IRAK3 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D512V7, binary
                 cls
clus                0   1
  IRAK3 MUTATED     3   5
  IRAK3 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      3    5
  IRAK3 WILD-TYPE  167  192
        clus
vv       IRAK3 MUTATED IRAK3 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D512V8, binary
                 cls
clus                0   1
  IRAK3 MUTATED     6   0
  IRAK3 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      6    0
  IRAK3 WILD-TYPE  294    8
     clus
vv    IRAK3 MUTATED IRAK3 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D512V9, binary
                 cls
clus                0   1
  IRAK3 MUTATED     5   3
  IRAK3 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      5    3
  IRAK3 WILD-TYPE  309   45
                               clus
vv                              IRAK3 MUTATED IRAK3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IRAK3 MUTATED     5   0   0   3
  IRAK3 WILD-TYPE 254   3  22  18
D512V10, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             3              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"
D512V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRAK3 MUTATED                                  0     1
  IRAK3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IRAK3 MUTATED                           1     4
  IRAK3 WILD-TYPE                        18   172
D512V12, multiclass
                                  clus
vv                                 IRAK3 MUTATED IRAK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = KIAA0195 MUTATION ANALYSIS
D513V1, survival
                    sevent
clus2                  0   1
  KIAA0195 MUTATED    14   2
  KIAA0195 WILD-TYPE 263  76
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                16                339 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 2                 76 
$`KIAA0195 MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6588 TCGA-AA-A00W TCGA-AA-A01K 
        0.92        25.08        10.88        26.17        14.99        31.00 
TCGA-AD-5900 TCGA-AY-6197 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6674 
       12.16        21.44        21.14        23.05        15.02        12.95 
TCGA-D5-6540 TCGA-DM-A1HB TCGA-F4-6808 TCGA-G4-6304 
       16.14       135.65        33.67        53.62 

$`KIAA0195 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99        82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
              0.92               0.00 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
            135.65             148.01 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             21.29              22.09 
[1] "0.9 - 135.7 (21.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D513V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0195 MUTATED         5        0        1         5         1         0
  KIAA0195 WILD-TYPE      59        1       25       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0195 MUTATED           1          0          2          1        0
  KIAA0195 WILD-TYPE        17          6         42         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0195 MUTATED           0         0
  KIAA0195 WILD-TYPE        12         1
D513V3, multiclass
            clus
vv           KIAA0195 MUTATED KIAA0195 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA0195 MUTATED     3   2   9   3
  KIAA0195 WILD-TYPE   6  65 240  38
D513V4, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  T1                3                  6
  T2                2                 65
  T3                9                240
  T4                3                 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
  KIAA0195 MUTATED    12   3   2
  KIAA0195 WILD-TYPE 208  78  64
D513V5, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  N0               12                208
  N1                3                 78
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V6, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    14   0
  KIAA0195 WILD-TYPE 271  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     14    0
  KIAA0195 WILD-TYPE  271   48
   clus
vv  KIAA0195 MUTATED KIAA0195 WILD-TYPE
  0               14                271
  1                0                 48
[1] 2 2
[1] FALSE
D513V7, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED     8   9
  KIAA0195 WILD-TYPE 162 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED      8    9
  KIAA0195 WILD-TYPE  162  188
        clus
vv       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  FEMALE                8                162
  MALE                  9                188
[1] 2 2
[1] FALSE
D513V8, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    15   0
  KIAA0195 WILD-TYPE 285   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     15    0
  KIAA0195 WILD-TYPE  285    8
     clus
vv    KIAA0195 MUTATED KIAA0195 WILD-TYPE
  NO                15                285
  YES                0                  8
[1] 2 2
[1] FALSE
D513V9, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    14   2
  KIAA0195 WILD-TYPE 300  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     14    2
  KIAA0195 WILD-TYPE  300   46
                               clus
vv                              KIAA0195 MUTATED KIAA0195 WILD-TYPE
  COLON ADENOCARCINOMA                        14                300
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0195 MUTATED    14   0   0   1
  KIAA0195 WILD-TYPE 245   3  22  20
D513V10, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  R0               14                245
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D513V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0195 MUTATED                                  0     0
  KIAA0195 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0195 MUTATED                           0    13
  KIAA0195 WILD-TYPE                        19   163
D513V12, multiclass
                                  clus
vv                                 KIAA0195 MUTATED KIAA0195 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          13                163
[1] 4 2
[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 = AGBL2 MUTATION ANALYSIS
D514V1, survival
                 sevent
clus2               0   1
  AGBL2 MUTATED    10   2
  AGBL2 WILD-TYPE 267  76
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             12             343 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
              2              76 
$`AGBL2 MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A00K TCGA-AA-A00N 
       14.53         6.05        22.06         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        12.16        58.39       148.01        15.02        61.91 

$`AGBL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  AGBL2 MUTATED AGBL2 WILD-TYPE 
           4.01            0.00 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
         148.01          140.38 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
         16.535          22.090 
[1] "4.0 - 148.0 (16.5)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.5"
D514V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGBL2 MUTATED         1        0        1         6         3         0
  AGBL2 WILD-TYPE      63        1       25       102         5         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        17          6         44         33       33        12
                 vv
clus              STAGE IVB
  AGBL2 MUTATED           0
  AGBL2 WILD-TYPE         1
D514V3, multiclass
            clus
vv           AGBL2 MUTATED AGBL2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  AGBL2 MUTATED     0   1   9   4
  AGBL2 WILD-TYPE   9  66 240  37
D514V4, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             4              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
  AGBL2 MUTATED    11   2   1
  AGBL2 WILD-TYPE 209  79  65
D514V5, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V6, binary
                 cls
clus                0   1
  AGBL2 MUTATED    10   2
  AGBL2 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     10    2
  AGBL2 WILD-TYPE  275   46
   clus
vv  AGBL2 MUTATED AGBL2 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D514V7, binary
                 cls
clus                0   1
  AGBL2 MUTATED     7   7
  AGBL2 WILD-TYPE 163 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED      7    7
  AGBL2 WILD-TYPE  163  190
        clus
vv       AGBL2 MUTATED AGBL2 WILD-TYPE
  FEMALE             7             163
  MALE               7             190
[1] 2 2
[1] FALSE
D514V8, binary
                 cls
clus                0   1
  AGBL2 MUTATED    10   0
  AGBL2 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     10    0
  AGBL2 WILD-TYPE  290    8
     clus
vv    AGBL2 MUTATED AGBL2 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D514V9, binary
                 cls
clus                0   1
  AGBL2 MUTATED    12   2
  AGBL2 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     12    2
  AGBL2 WILD-TYPE  302   46
                               clus
vv                              AGBL2 MUTATED AGBL2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGBL2 MUTATED    11   0   1   1
  AGBL2 WILD-TYPE 248   3  21  20
D514V10, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             1              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"
D514V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGBL2 MUTATED                                  0     0
  AGBL2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGBL2 MUTATED                           0     8
  AGBL2 WILD-TYPE                        19   168
D514V12, multiclass
                                  clus
vv                                 AGBL2 MUTATED AGBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(515) Variable = OR1J2 MUTATION ANALYSIS
D515V1, survival
                 sevent
clus2               0   1
  OR1J2 MUTATED     9   0
  OR1J2 WILD-TYPE 268  78
  OR1J2 MUTATED OR1J2 WILD-TYPE 
              9             346 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
              0              78 
$`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        12.39        12.59        12.59 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-6170 
       21.99        82.95        15.02 

$`OR1J2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       26.47        14.50        27.09        16.31         0.95         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 
        5.23        11.74         3.19        12.69        12.36        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-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  OR1J2 MUTATED OR1J2 WILD-TYPE 
           6.97            0.00 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
          82.95          148.01 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
         15.020          22.225 
[1] "7.0 - 83.0 (15.0)"  "0.0 - 148.0 (22.2)"
[1] "hr="     "9200000"
D515V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR1J2 MUTATED         1        0        1         4         0         0
  OR1J2 WILD-TYPE      63        1       25       104         8         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        17          6         42         33       35        11
                 vv
clus              STAGE IVB
  OR1J2 MUTATED           0
  OR1J2 WILD-TYPE         1
D515V3, multiclass
            clus
vv           OR1J2 MUTATED OR1J2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  OR1J2 MUTATED     0   1   9   0
  OR1J2 WILD-TYPE   9  66 240  41
D515V4, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             0              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
  OR1J2 MUTATED     6   3   1
  OR1J2 WILD-TYPE 214  78  65
D515V5, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V6, binary
                 cls
clus                0   1
  OR1J2 MUTATED     6   1
  OR1J2 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      6    1
  OR1J2 WILD-TYPE  279   47
   clus
vv  OR1J2 MUTATED OR1J2 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D515V7, binary
                 cls
clus                0   1
  OR1J2 MUTATED     4   6
  OR1J2 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      4    6
  OR1J2 WILD-TYPE  166  191
        clus
vv       OR1J2 MUTATED OR1J2 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D515V8, binary
                 cls
clus                0   1
  OR1J2 MUTATED     8   0
  OR1J2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      8    0
  OR1J2 WILD-TYPE  292    8
     clus
vv    OR1J2 MUTATED OR1J2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D515V9, binary
                 cls
clus                0   1
  OR1J2 MUTATED     8   2
  OR1J2 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      8    2
  OR1J2 WILD-TYPE  306   46
                               clus
vv                              OR1J2 MUTATED OR1J2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR1J2 MUTATED     6   0   0   3
  OR1J2 WILD-TYPE 253   3  22  18
D515V10, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             3              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"
D515V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR1J2 MUTATED                                  0     3
  OR1J2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR1J2 MUTATED                           1     4
  OR1J2 WILD-TYPE                        18   172
D515V12, multiclass
                                  clus
vv                                 OR1J2 MUTATED OR1J2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = PTPRC MUTATION ANALYSIS
D516V1, survival
                 sevent
clus2               0   1
  PTPRC MUTATED    18   6
  PTPRC WILD-TYPE 259  72
  PTPRC MUTATED PTPRC WILD-TYPE 
             24             331 
  PTPRC MUTATED PTPRC WILD-TYPE 
              6              72 
$`PTPRC MUTATED`
TCGA-G4-6628 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3510 
       79.69        31.63        33.53        25.08        20.12        63.98 
TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3956 TCGA-AA-3977 
       78.08        26.99         0.00        31.00        34.03        25.02 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AZ-4315 
       18.05        34.98        12.16        83.24        22.42        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5860 TCGA-DM-A1HB TCGA-F4-6460 TCGA-F4-6570 
       12.76        10.06        32.02       135.65        31.96         6.18 

$`PTPRC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.75        36.53        32.91        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PTPRC MUTATED PTPRC WILD-TYPE 
              0               0 
  PTPRC MUTATED PTPRC WILD-TYPE 
         135.65          148.01 
  PTPRC MUTATED PTPRC WILD-TYPE 
         31.315          21.990 
[1] "0.0 - 135.7 (31.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D516V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRC MUTATED         3        0        3        11         1         0
  PTPRC WILD-TYPE      61        1       23        97         7         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        18          6         40         33       35        11
                 vv
clus              STAGE IVB
  PTPRC MUTATED           0
  PTPRC WILD-TYPE         1
D516V3, multiclass
            clus
vv           PTPRC MUTATED PTPRC WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             11              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  PTPRC MUTATED     1   3  18   3
  PTPRC WILD-TYPE   8  64 231  38
D516V4, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  T1             1               8
  T2             3              64
  T3            18             231
  T4             3              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
  PTPRC MUTATED    20   5   0
  PTPRC WILD-TYPE 200  76  66
D516V5, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  N0            20             200
  N1             5              76
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V6, binary
                 cls
clus                0   1
  PTPRC MUTATED    20   1
  PTPRC WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     20    1
  PTPRC WILD-TYPE  265   47
   clus
vv  PTPRC MUTATED PTPRC WILD-TYPE
  0            20             265
  1             1              47
[1] 2 2
[1] FALSE
D516V7, binary
                 cls
clus                0   1
  PTPRC MUTATED    10  15
  PTPRC WILD-TYPE 160 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     10   15
  PTPRC WILD-TYPE  160  182
        clus
vv       PTPRC MUTATED PTPRC WILD-TYPE
  FEMALE            10             160
  MALE              15             182
[1] 2 2
[1] FALSE
D516V8, binary
                 cls
clus                0   1
  PTPRC MUTATED    22   0
  PTPRC WILD-TYPE 278   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     22    0
  PTPRC WILD-TYPE  278    8
     clus
vv    PTPRC MUTATED PTPRC WILD-TYPE
  NO             22             278
  YES             0               8
[1] 2 2
[1] FALSE
D516V9, binary
                 cls
clus                0   1
  PTPRC MUTATED    19   5
  PTPRC WILD-TYPE 295  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     19    5
  PTPRC WILD-TYPE  295   43
                               clus
vv                              PTPRC MUTATED PTPRC WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRC MUTATED    18   0   0   2
  PTPRC WILD-TYPE 241   3  22  19
D516V10, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  R0            18             241
  R1             0               3
  R2             0              22
  RX             2              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"
D516V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRC MUTATED                                  0     3
  PTPRC WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRC MUTATED                           2    10
  PTPRC WILD-TYPE                        17   166
D516V12, multiclass
                                  clus
vv                                 PTPRC MUTATED PTPRC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       10             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(517) Variable = ARMCX5 MUTATION ANALYSIS
D517V1, survival
                  sevent
clus2                0   1
  ARMCX5 MUTATED     5   2
  ARMCX5 WILD-TYPE 272  76
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               7              348 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               2               76 
$`ARMCX5 MUTATED`
TCGA-G4-6588 TCGA-A6-2672 TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-A00N TCGA-AZ-6598 
       26.17        46.65        78.08        33.04         4.01        49.41 
TCGA-CM-5860 
       32.02 

$`ARMCX5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       22.09        35.80        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
            4.01             0.00 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
           78.08           148.01 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
           33.04            21.99 
[1] "4.0 - 78.1 (33.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D517V2, continuous
                  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      64        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARMCX5 MUTATED           0          0          1          0        1
  ARMCX5 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ARMCX5 MUTATED           0         0
  ARMCX5 WILD-TYPE        12         1
D517V3, multiclass
            clus
vv           ARMCX5 MUTATED ARMCX5 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ARMCX5 MUTATED     0   0   7   1
  ARMCX5 WILD-TYPE   9  67 242  40
D517V4, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              1               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
  ARMCX5 MUTATED     6   1   1
  ARMCX5 WILD-TYPE 214  80  65
D517V5, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V6, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   1
  ARMCX5 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    1
  ARMCX5 WILD-TYPE  279   47
   clus
vv  ARMCX5 MUTATED ARMCX5 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D517V7, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   2
  ARMCX5 WILD-TYPE 164 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    2
  ARMCX5 WILD-TYPE  164  195
        clus
vv       ARMCX5 MUTATED ARMCX5 WILD-TYPE
  FEMALE              6              164
  MALE                2              195
[1] 2 2
[1] FALSE
D517V8, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   0
  ARMCX5 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    0
  ARMCX5 WILD-TYPE  294    8
     clus
vv    ARMCX5 MUTATED ARMCX5 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D517V9, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     7   1
  ARMCX5 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      7    1
  ARMCX5 WILD-TYPE  307   47
                               clus
vv                              ARMCX5 MUTATED ARMCX5 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARMCX5 MUTATED     6   0   1   0
  ARMCX5 WILD-TYPE 253   3  21  21
D517V10, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              0               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"
D517V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARMCX5 MUTATED                                  0     0
  ARMCX5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARMCX5 MUTATED                           0     4
  ARMCX5 WILD-TYPE                        19   172
D517V12, multiclass
                                  clus
vv                                 ARMCX5 MUTATED ARMCX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = PPIG MUTATION ANALYSIS
D518V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    10   2
  PPIG WILD-TYPE 267  76
  PPIG MUTATED PPIG WILD-TYPE 
            12            343 
  PPIG MUTATED PPIG WILD-TYPE 
             2             76 
$`PPIG MUTATED`
TCGA-AA-3525 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-6137 TCGA-AA-3949 TCGA-AA-A00E 
        8.05       100.01        35.80        27.09        26.01        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-D5-6540 TCGA-DM-A282 TCGA-G4-6309 
        4.01        34.98        58.39        16.14       139.17        85.48 

$`PPIG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PPIG MUTATED PPIG WILD-TYPE 
          4.01           0.00 
  PPIG MUTATED PPIG WILD-TYPE 
        139.17         148.01 
  PPIG MUTATED PPIG WILD-TYPE 
         32.50          21.99 
[1] "4.0 - 139.2 (32.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D518V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPIG MUTATED         1        0        1         4         2         0
  PPIG WILD-TYPE      63        1       25       104         6         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        18          6         40         33       35        12
                vv
clus             STAGE IVB
  PPIG MUTATED           0
  PPIG WILD-TYPE         1
D518V3, multiclass
            clus
vv           PPIG MUTATED PPIG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PPIG MUTATED     0   1   9   2
  PPIG WILD-TYPE   9  66 240  39
D518V4, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  T1            0              9
  T2            1             66
  T3            9            240
  T4            2             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
  PPIG MUTATED     8   4   0
  PPIG WILD-TYPE 212  77  66
D518V5, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  N0            8            212
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V6, binary
                cls
clus               0   1
  PPIG MUTATED    12   0
  PPIG WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     12    0
  PPIG WILD-TYPE  273   48
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D518V7, binary
                cls
clus               0   1
  PPIG MUTATED     5   7
  PPIG WILD-TYPE 165 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      5    7
  PPIG WILD-TYPE  165  190
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  FEMALE            5            165
  MALE              7            190
[1] 2 2
[1] FALSE
D518V8, binary
                cls
clus               0   1
  PPIG MUTATED    10   0
  PPIG WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     10    0
  PPIG WILD-TYPE  290    8
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D518V9, binary
                cls
clus               0   1
  PPIG MUTATED     9   3
  PPIG WILD-TYPE 305  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      9    3
  PPIG WILD-TYPE  305   45
                               clus
vv                              PPIG MUTATED PPIG WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PPIG MUTATED     9   0   0   0
  PPIG WILD-TYPE 250   3  22  21
D518V10, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            0             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"
D518V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPIG MUTATED                                  0     0
  PPIG WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PPIG MUTATED                           1     6
  PPIG WILD-TYPE                        18   170
D518V12, multiclass
                                  clus
vv                                 PPIG MUTATED PPIG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = NFASC MUTATION ANALYSIS
D519V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    27   4
  NFASC WILD-TYPE 250  74
  NFASC MUTATED NFASC WILD-TYPE 
             31             324 
  NFASC MUTATED NFASC WILD-TYPE 
              4              74 
$`NFASC MUTATED`
TCGA-AA-3543 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-A6-6653 TCGA-A6-6780 
        0.99        85.05        19.04        14.93        24.39        20.12 
TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       78.08        33.04        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 
       25.48        13.35        92.75       135.65        81.37       117.07 
TCGA-F4-6704 
        1.55 

$`NFASC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.00        36.00        19.04        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       24.00        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      131.51       139.17       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
        8.61        31.96        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NFASC MUTATED NFASC WILD-TYPE 
           0.99            0.00 
  NFASC MUTATED NFASC WILD-TYPE 
         135.65          148.01 
  NFASC MUTATED NFASC WILD-TYPE 
          24.39           22.01 
[1] "1.0 - 135.7 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D519V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFASC MUTATED         3        0        2        12         3         0
  NFASC WILD-TYPE      61        1       24        96         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NFASC MUTATED           1          1          5          3        1         0
  NFASC WILD-TYPE        17          5         39         30       34        12
                 vv
clus              STAGE IVB
  NFASC MUTATED           0
  NFASC WILD-TYPE         1
D519V3, multiclass
            clus
vv           NFASC MUTATED NFASC WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             12              96
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             5              39
  STAGE IIIC             3              30
  STAGE IV               1              34
  STAGE IVA              0              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
  NFASC MUTATED     0   4  23   5
  NFASC WILD-TYPE   9  63 226  36
D519V4, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  T1             0               9
  T2             4              63
  T3            23             226
  T4             5              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
  NFASC MUTATED    22   6   4
  NFASC WILD-TYPE 198  75  62
D519V5, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            22             198
  N1             6              75
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V6, binary
                 cls
clus                0   1
  NFASC MUTATED    28   1
  NFASC WILD-TYPE 257  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     28    1
  NFASC WILD-TYPE  257   47
   clus
vv  NFASC MUTATED NFASC WILD-TYPE
  0            28             257
  1             1              47
[1] 2 2
[1] FALSE
D519V7, binary
                 cls
clus                0   1
  NFASC MUTATED    12  20
  NFASC WILD-TYPE 158 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     12   20
  NFASC WILD-TYPE  158  177
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  FEMALE            12             158
  MALE              20             177
[1] 2 2
[1] FALSE
D519V8, binary
                 cls
clus                0   1
  NFASC MUTATED    21   3
  NFASC WILD-TYPE 279   5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     21    3
  NFASC WILD-TYPE  279    5
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO             21             279
  YES             3               5
[1] 2 2
[1] FALSE
D519V9, binary
                 cls
clus                0   1
  NFASC MUTATED    19  12
  NFASC WILD-TYPE 295  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     19   12
  NFASC WILD-TYPE  295   36
                               clus
vv                              NFASC MUTATED NFASC WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NFASC MUTATED    21   0   1   2
  NFASC WILD-TYPE 238   3  21  19
D519V10, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  R0            21             238
  R1             0               3
  R2             1              21
  RX             2              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"
D519V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFASC MUTATED                                  1     2
  NFASC WILD-TYPE                                0     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NFASC MUTATED                           0    13
  NFASC WILD-TYPE                        19   163
D519V12, multiclass
                                  clus
vv                                 NFASC MUTATED NFASC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       13             163
[1] 4 2
[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 = PLCH2 MUTATION ANALYSIS
D520V1, survival
                 sevent
clus2               0   1
  PLCH2 MUTATED    14   5
  PLCH2 WILD-TYPE 263  73
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             336 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
              5              73 
$`PLCH2 MUTATED`
TCGA-G4-6628 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3994 TCGA-AZ-6599 
       79.69        20.28        35.01         6.97        27.02         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CK-4947 TCGA-CK-4952 TCGA-CM-6167 TCGA-D5-6928 
       12.10        29.56        17.56        15.62        14.99        11.64 
TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6855 TCGA-F4-6856 
      130.65       131.51       135.65        35.97        47.41        35.31 
TCGA-G4-6303 
       65.85 

$`PLCH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        19.66         7.04         3.02 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       49.41         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       14.30       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.50        44.32       139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PLCH2 MUTATED PLCH2 WILD-TYPE 
           6.77            0.00 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
         135.65          148.01 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
          29.56           22.01 
[1] "6.8 - 135.7 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D520V2, continuous
                 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      60        1       25       105         7         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        18          6         40         30       33        12
                 vv
clus              STAGE IVB
  PLCH2 MUTATED           0
  PLCH2 WILD-TYPE         1
D520V3, multiclass
            clus
vv           PLCH2 MUTATED PLCH2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             3              30
  STAGE IV               2              33
  STAGE IVA              0              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
  PLCH2 MUTATED     0   5   9   5
  PLCH2 WILD-TYPE   9  62 240  36
D520V4, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             9             240
  T4             5              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
  PLCH2 MUTATED     9   7   3
  PLCH2 WILD-TYPE 211  74  63
D520V5, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  N0             9             211
  N1             7              74
  N2             3              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"
D520V6, binary
                 cls
clus                0   1
  PLCH2 MUTATED    14   2
  PLCH2 WILD-TYPE 271  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     14    2
  PLCH2 WILD-TYPE  271   46
   clus
vv  PLCH2 MUTATED PLCH2 WILD-TYPE
  0            14             271
  1             2              46
[1] 2 2
[1] FALSE
D520V7, binary
                 cls
clus                0   1
  PLCH2 MUTATED     7  12
  PLCH2 WILD-TYPE 163 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED      7   12
  PLCH2 WILD-TYPE  163  185
        clus
vv       PLCH2 MUTATED PLCH2 WILD-TYPE
  FEMALE             7             163
  MALE              12             185
[1] 2 2
[1] FALSE
D520V8, binary
                 cls
clus                0   1
  PLCH2 MUTATED    14   0
  PLCH2 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     14    0
  PLCH2 WILD-TYPE  286    8
     clus
vv    PLCH2 MUTATED PLCH2 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D520V9, binary
                 cls
clus                0   1
  PLCH2 MUTATED    14   4
  PLCH2 WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     14    4
  PLCH2 WILD-TYPE  300   44
                               clus
vv                              PLCH2 MUTATED PLCH2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PLCH2 MUTATED     9   0   0   2
  PLCH2 WILD-TYPE 250   3  22  19
D520V10, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D520V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCH2 MUTATED                                  0     0
  PLCH2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCH2 MUTATED                           2    14
  PLCH2 WILD-TYPE                        17   162
D520V12, multiclass
                                  clus
vv                                 PLCH2 MUTATED PLCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       14             162
[1] 4 2
[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 = MTDH MUTATION ANALYSIS
D521V1, survival
                sevent
clus2              0   1
  MTDH MUTATED     8   3
  MTDH WILD-TYPE 269  75
  MTDH MUTATED MTDH WILD-TYPE 
            11            344 
  MTDH MUTATED MTDH WILD-TYPE 
             3             75 
$`MTDH MUTATED`
TCGA-AA-3979 TCGA-AD-6895 TCGA-G4-6310 TCGA-A6-2676 TCGA-AA-3511 TCGA-AA-A010 
       24.00        25.08        63.62        42.90         6.97        34.98 
TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4744 
       83.24        12.76        10.06        85.45        20.02 

$`MTDH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MTDH MUTATED MTDH WILD-TYPE 
          6.97           0.00 
  MTDH MUTATED MTDH WILD-TYPE 
         85.45         148.01 
  MTDH MUTATED MTDH WILD-TYPE 
         25.08          22.01 
[1] "7.0 - 85.5 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D521V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTDH MUTATED         1        0        1         4         3         0
  MTDH WILD-TYPE      63        1       25       104         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTDH MUTATED           0          0          3          0        0         0
  MTDH WILD-TYPE        18          6         41         33       35        12
                vv
clus             STAGE IVB
  MTDH MUTATED           0
  MTDH WILD-TYPE         1
D521V3, multiclass
            clus
vv           MTDH MUTATED MTDH WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MTDH MUTATED     0   1   7   4
  MTDH WILD-TYPE   9  66 242  37
D521V4, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            4             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
  MTDH MUTATED     9   3   0
  MTDH WILD-TYPE 211  78  66
D521V5, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  N0            9            211
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V6, binary
                cls
clus               0   1
  MTDH MUTATED    11   0
  MTDH WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     11    0
  MTDH WILD-TYPE  274   48
   clus
vv  MTDH MUTATED MTDH WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D521V7, binary
                cls
clus               0   1
  MTDH MUTATED     4   8
  MTDH WILD-TYPE 166 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED      4    8
  MTDH WILD-TYPE  166  189
        clus
vv       MTDH MUTATED MTDH WILD-TYPE
  FEMALE            4            166
  MALE              8            189
[1] 2 2
[1] FALSE
D521V8, binary
                cls
clus               0   1
  MTDH MUTATED    10   1
  MTDH WILD-TYPE 290   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     10    1
  MTDH WILD-TYPE  290    7
     clus
vv    MTDH MUTATED MTDH WILD-TYPE
  NO            10            290
  YES            1              7
[1] 2 2
[1] FALSE
D521V9, binary
                cls
clus               0   1
  MTDH MUTATED    10   2
  MTDH WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     10    2
  MTDH WILD-TYPE  304   46
                               clus
vv                              MTDH MUTATED MTDH WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTDH MUTATED     8   1   0   3
  MTDH WILD-TYPE 251   2  22  18
D521V10, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  R0            8            251
  R1            1              2
  R2            0             22
  RX            3             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"
D521V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTDH MUTATED                                  0     3
  MTDH WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTDH MUTATED                           1     5
  MTDH WILD-TYPE                        18   171
D521V12, multiclass
                                  clus
vv                                 MTDH MUTATED MTDH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = RGS22 MUTATION ANALYSIS
D522V1, survival
                 sevent
clus2               0   1
  RGS22 MUTATED    19   5
  RGS22 WILD-TYPE 258  73
  RGS22 MUTATED RGS22 WILD-TYPE 
             24             331 
  RGS22 MUTATED RGS22 WILD-TYPE 
              5              73 
$`RGS22 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3510 
       19.04        25.08        35.80        79.69        22.06        63.98 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        4.01        34.98        27.09        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-6172 TCGA-D5-6536 
       10.06        15.62        51.32        22.98        11.01        17.85 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A28G TCGA-F4-6569 TCGA-G4-6309 
       13.35        49.91       131.51        60.79        35.74        85.48 

$`RGS22 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 
       12.20        14.30        17.56       148.01        85.45        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       135.65       139.17        81.37       119.93        35.97 
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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RGS22 MUTATED RGS22 WILD-TYPE 
           4.01            0.00 
  RGS22 MUTATED RGS22 WILD-TYPE 
         131.51          148.01 
  RGS22 MUTATED RGS22 WILD-TYPE 
         31.035          21.990 
[1] "4.0 - 131.5 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D522V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RGS22 MUTATED         3        0        2        10         2         0
  RGS22 WILD-TYPE      61        1       24        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RGS22 MUTATED           0          0          4          2        1         0
  RGS22 WILD-TYPE        18          6         40         31       34        12
                 vv
clus              STAGE IVB
  RGS22 MUTATED           0
  RGS22 WILD-TYPE         1
D522V3, multiclass
            clus
vv           RGS22 MUTATED RGS22 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  RGS22 MUTATED     0   3  18   3
  RGS22 WILD-TYPE   9  64 231  38
D522V4, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            18             231
  T4             3              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
  RGS22 MUTATED    18   4   2
  RGS22 WILD-TYPE 202  77  64
D522V5, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  N0            18             202
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V6, binary
                 cls
clus                0   1
  RGS22 MUTATED    21   1
  RGS22 WILD-TYPE 264  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     21    1
  RGS22 WILD-TYPE  264   47
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0            21             264
  1             1              47
[1] 2 2
[1] FALSE
D522V7, binary
                 cls
clus                0   1
  RGS22 MUTATED     9  15
  RGS22 WILD-TYPE 161 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      9   15
  RGS22 WILD-TYPE  161  182
        clus
vv       RGS22 MUTATED RGS22 WILD-TYPE
  FEMALE             9             161
  MALE              15             182
[1] 2 2
[1] FALSE
D522V8, binary
                 cls
clus                0   1
  RGS22 MUTATED    17   1
  RGS22 WILD-TYPE 283   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     17    1
  RGS22 WILD-TYPE  283    7
     clus
vv    RGS22 MUTATED RGS22 WILD-TYPE
  NO             17             283
  YES             1               7
[1] 2 2
[1] FALSE
D522V9, binary
                 cls
clus                0   1
  RGS22 MUTATED    19   5
  RGS22 WILD-TYPE 295  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     19    5
  RGS22 WILD-TYPE  295   43
                               clus
vv                              RGS22 MUTATED RGS22 WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RGS22 MUTATED    15   0   1   4
  RGS22 WILD-TYPE 244   3  21  17
D522V10, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             1              21
  RX             4              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"
D522V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGS22 MUTATED                                  0     2
  RGS22 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RGS22 MUTATED                           1    17
  RGS22 WILD-TYPE                        18   159
D522V12, multiclass
                                  clus
vv                                 RGS22 MUTATED RGS22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       17             159
[1] 4 2
[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 = DMRTB1 MUTATION ANALYSIS
D523V1, survival
                  sevent
clus2                0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 272  77
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              349 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               1               77 
$`DMRTB1 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-AA-3846 TCGA-CK-5916 TCGA-CM-5341 TCGA-D5-6928 
       19.04        26.17        17.03        21.14        29.06        11.64 

$`DMRTB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.09 
[1] "11.6 - 29.1 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D523V2, continuous
                  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      63        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DMRTB1 MUTATED           0          1          0          0        1
  DMRTB1 WILD-TYPE        18          5         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  DMRTB1 MUTATED           0         0
  DMRTB1 WILD-TYPE        12         1
D523V3, multiclass
            clus
vv           DMRTB1 MUTATED DMRTB1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  DMRTB1 MUTATED     1   1   4   0
  DMRTB1 WILD-TYPE   8  66 245  41
D523V4, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              4              245
  T4              0               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
  DMRTB1 MUTATED     5   1   0
  DMRTB1 WILD-TYPE 215  80  66
D523V5, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V6, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  280   47
   clus
vv  DMRTB1 MUTATED DMRTB1 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D523V7, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     4   2
  DMRTB1 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      4    2
  DMRTB1 WILD-TYPE  166  195
        clus
vv       DMRTB1 MUTATED DMRTB1 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D523V8, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 295   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  295    7
     clus
vv    DMRTB1 MUTATED DMRTB1 WILD-TYPE
  NO               5              295
  YES              1                7
[1] 2 2
[1] FALSE
D523V9, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  309   47
                               clus
vv                              DMRTB1 MUTATED DMRTB1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DMRTB1 MUTATED     4   0   1   1
  DMRTB1 WILD-TYPE 255   3  21  20
D523V10, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              1               21
  RX              1               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"
D523V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DMRTB1 MUTATED                                  0     0
  DMRTB1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DMRTB1 MUTATED                           0     4
  DMRTB1 WILD-TYPE                        19   172
D523V12, multiclass
                                  clus
vv                                 DMRTB1 MUTATED DMRTB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = MAP3K4 MUTATION ANALYSIS
D524V1, survival
                  sevent
clus2                0   1
  MAP3K4 MUTATED    21  13
  MAP3K4 WILD-TYPE 256  65
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              34              321 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              13               65 
$`MAP3K4 MUTATED`
TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3715 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 
       13.02        85.05        19.04        15.52        10.88       100.01 
TCGA-G4-6628 TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3833 
       79.69        42.90         3.02        63.98         1.02        15.95 
TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A01P 
       33.01        21.99        25.02        18.05        18.05        38.07 
TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6598 
       35.01        14.01        83.24        58.39         1.41        49.41 
TCGA-CA-5254 TCGA-CA-6716 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6165 
       12.69        12.20        37.02        30.08         5.03        16.04 
TCGA-D5-6534 TCGA-D5-6927 TCGA-F4-6703 TCGA-F4-6806 
       43.27         9.44        47.87        41.42 

$`MAP3K4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       25.08       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       25.02        17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03         2.01        16.08        13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03         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        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       21.44        17.82         5.13        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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-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-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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 
       54.61        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 
       25.48        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.74         6.18         1.55        34.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
            1.02             0.00 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
          100.01           148.01 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
          23.505           22.060 
[1] "1.0 - 100.0 (23.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D524V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP3K4 MUTATED         5        0        7        12         2         0
  MAP3K4 WILD-TYPE      59        1       19        96         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K4 MUTATED           3          0          2          0        2
  MAP3K4 WILD-TYPE        15          6         42         33       33
                  vv
clus               STAGE IVA STAGE IVB
  MAP3K4 MUTATED           1         0
  MAP3K4 WILD-TYPE        11         1
D524V3, multiclass
            clus
vv           MAP3K4 MUTATED MAP3K4 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                7               19
  STAGE IIA              12               96
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               3               15
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               1               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
  MAP3K4 MUTATED     0   6  23   7
  MAP3K4 WILD-TYPE   9  61 226  34
D524V4, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  T1              0                9
  T2              6               61
  T3             23              226
  T4              7               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
  MAP3K4 MUTATED    27   4   5
  MAP3K4 WILD-TYPE 193  77  61
D524V5, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  N0             27              193
  N1              4               77
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V6, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    30   3
  MAP3K4 WILD-TYPE 255  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     30    3
  MAP3K4 WILD-TYPE  255   45
   clus
vv  MAP3K4 MUTATED MAP3K4 WILD-TYPE
  0             30              255
  1              3               45
[1] 2 2
[1] FALSE
D524V7, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    15  21
  MAP3K4 WILD-TYPE 155 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     15   21
  MAP3K4 WILD-TYPE  155  176
        clus
vv       MAP3K4 MUTATED MAP3K4 WILD-TYPE
  FEMALE             15              155
  MALE               21              176
[1] 2 2
[1] FALSE
D524V8, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    32   1
  MAP3K4 WILD-TYPE 268   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     32    1
  MAP3K4 WILD-TYPE  268    7
     clus
vv    MAP3K4 MUTATED MAP3K4 WILD-TYPE
  NO              32              268
  YES              1                7
[1] 2 2
[1] FALSE
D524V9, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    30   6
  MAP3K4 WILD-TYPE 284  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     30    6
  MAP3K4 WILD-TYPE  284   42
                               clus
vv                              MAP3K4 MUTATED MAP3K4 WILD-TYPE
  COLON ADENOCARCINOMA                      30              284
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP3K4 MUTATED    27   0   1   2
  MAP3K4 WILD-TYPE 232   3  21  19
D524V10, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  R0             27              232
  R1              0                3
  R2              1               21
  RX              2               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"
D524V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP3K4 MUTATED                                  0     3
  MAP3K4 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP3K4 MUTATED                           1    15
  MAP3K4 WILD-TYPE                        18   161
D524V12, multiclass
                                  clus
vv                                 MAP3K4 MUTATED MAP3K4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        15              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(525) Variable = PNPLA8 MUTATION ANALYSIS
D525V1, survival
                  sevent
clus2                0   1
  PNPLA8 MUTATED    13   5
  PNPLA8 WILD-TYPE 264  73
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              18              337 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
               5               73 
$`PNPLA8 MUTATED`
TCGA-AD-6895 TCGA-AZ-6608 TCGA-A6-3809 TCGA-A6-6653 TCGA-AA-3710 TCGA-AA-3977 
       25.08         1.94        32.75        24.39        26.99        25.02 
TCGA-AA-A00N TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
        4.01        17.82        58.39         3.19        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 

$`PNPLA8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5913 
       12.59        12.20        14.30        17.56        15.62        51.32 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.99         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
            1.94             0.00 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
          148.01           140.38 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
           23.21            22.06 
[1] "1.9 - 148.0 (23.2)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D525V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PNPLA8 MUTATED         3        0        0         5         2         0
  PNPLA8 WILD-TYPE      61        1       26       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA8 MUTATED           1          1          4          0        1
  PNPLA8 WILD-TYPE        17          5         40         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PNPLA8 MUTATED           0         0
  PNPLA8 WILD-TYPE        12         1
D525V3, multiclass
            clus
vv           PNPLA8 MUTATED PNPLA8 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              4               40
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  PNPLA8 MUTATED     1   4  10   3
  PNPLA8 WILD-TYPE   8  63 239  38
D525V4, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  T1              1                8
  T2              4               63
  T3             10              239
  T4              3               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
  PNPLA8 MUTATED    11   6   1
  PNPLA8 WILD-TYPE 209  75  65
D525V5, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  N0             11              209
  N1              6               75
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V6, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    15   1
  PNPLA8 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     15    1
  PNPLA8 WILD-TYPE  270   47
   clus
vv  PNPLA8 MUTATED PNPLA8 WILD-TYPE
  0             15              270
  1              1               47
[1] 2 2
[1] FALSE
D525V7, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    10   8
  PNPLA8 WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     10    8
  PNPLA8 WILD-TYPE  160  189
        clus
vv       PNPLA8 MUTATED PNPLA8 WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D525V8, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    17   0
  PNPLA8 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     17    0
  PNPLA8 WILD-TYPE  283    8
     clus
vv    PNPLA8 MUTATED PNPLA8 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D525V9, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    14   4
  PNPLA8 WILD-TYPE 300  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     14    4
  PNPLA8 WILD-TYPE  300   44
                               clus
vv                              PNPLA8 MUTATED PNPLA8 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PNPLA8 MUTATED     9   1   0   4
  PNPLA8 WILD-TYPE 250   2  22  17
D525V10, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  R0              9              250
  R1              1                2
  R2              0               22
  RX              4               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"
D525V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PNPLA8 MUTATED                                  0     2
  PNPLA8 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PNPLA8 MUTATED                           2    11
  PNPLA8 WILD-TYPE                        17   165
D525V12, multiclass
                                  clus
vv                                 PNPLA8 MUTATED PNPLA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        11              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(526) Variable = ALX4 MUTATION ANALYSIS
D526V1, survival
                sevent
clus2              0   1
  ALX4 MUTATED     9   2
  ALX4 WILD-TYPE 268  76
  ALX4 MUTATED ALX4 WILD-TYPE 
            11            344 
  ALX4 MUTATED ALX4 WILD-TYPE 
             2             76 
$`ALX4 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6653 TCGA-AA-3949 TCGA-AY-6197 
       19.04       100.01        26.17        24.39        26.01        21.44 
TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6927 
       49.41        15.02        15.02        16.14         9.44 

$`ALX4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ALX4 MUTATED ALX4 WILD-TYPE 
          9.44           0.00 
  ALX4 MUTATED ALX4 WILD-TYPE 
        100.01         148.01 
  ALX4 MUTATED ALX4 WILD-TYPE 
        21.440         22.075 
[1] "9.4 - 100.0 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D526V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALX4 MUTATED         3        0        2         4         0         0
  ALX4 WILD-TYPE      61        1       24       104         8         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  ALX4 MUTATED           0
  ALX4 WILD-TYPE         1
D526V3, multiclass
            clus
vv           ALX4 MUTATED ALX4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  ALX4 MUTATED     0   3   8   0
  ALX4 WILD-TYPE   9  64 241  41
D526V4, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            8            241
  T4            0             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
  ALX4 MUTATED    10   1   0
  ALX4 WILD-TYPE 210  80  66
D526V5, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V6, binary
                cls
clus               0   1
  ALX4 MUTATED     8   1
  ALX4 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      8    1
  ALX4 WILD-TYPE  277   47
   clus
vv  ALX4 MUTATED ALX4 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D526V7, binary
                cls
clus               0   1
  ALX4 MUTATED     5   6
  ALX4 WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      5    6
  ALX4 WILD-TYPE  165  191
        clus
vv       ALX4 MUTATED ALX4 WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D526V8, binary
                cls
clus               0   1
  ALX4 MUTATED    10   1
  ALX4 WILD-TYPE 290   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED     10    1
  ALX4 WILD-TYPE  290    7
     clus
vv    ALX4 MUTATED ALX4 WILD-TYPE
  NO            10            290
  YES            1              7
[1] 2 2
[1] FALSE
D526V9, binary
                cls
clus               0   1
  ALX4 MUTATED     9   2
  ALX4 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      9    2
  ALX4 WILD-TYPE  305   46
                               clus
vv                              ALX4 MUTATED ALX4 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ALX4 MUTATED     7   0   1   0
  ALX4 WILD-TYPE 252   3  21  21
D526V10, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            0             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"
D526V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALX4 MUTATED                                  0     0
  ALX4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALX4 MUTATED                           0     9
  ALX4 WILD-TYPE                        19   167
D526V12, multiclass
                                  clus
vv                                 ALX4 MUTATED ALX4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(527) Variable = ULK1 MUTATION ANALYSIS
D527V1, survival
                sevent
clus2              0   1
  ULK1 MUTATED     6   3
  ULK1 WILD-TYPE 271  75
  ULK1 MUTATED ULK1 WILD-TYPE 
             9            346 
  ULK1 MUTATED ULK1 WILD-TYPE 
             3             75 
$`ULK1 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6780 TCGA-AY-6197 TCGA-AZ-5403 TCGA-AZ-6598 
       35.80        26.17        20.12        21.44        62.79        49.41 
TCGA-AZ-6599 TCGA-CM-5349 TCGA-D5-6928 
        6.77        30.08        11.64 

$`ULK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        22.36        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ULK1 MUTATED ULK1 WILD-TYPE 
          6.77           0.00 
  ULK1 MUTATED ULK1 WILD-TYPE 
         62.79         148.01 
  ULK1 MUTATED ULK1 WILD-TYPE 
        26.170         22.045 
[1] "6.8 - 62.8 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D527V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ULK1 MUTATED         1        0        2         6         1         0
  ULK1 WILD-TYPE      63        1       24       102         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ULK1 MUTATED           0
  ULK1 WILD-TYPE         1
D527V3, multiclass
            clus
vv           ULK1 MUTATED ULK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ULK1 MUTATED     0   1   8   1
  ULK1 WILD-TYPE   9  66 241  40
D527V4, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            1             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
  ULK1 MUTATED    10   0   0
  ULK1 WILD-TYPE 210  81  66
D527V5, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  N0           10            210
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V6, binary
                cls
clus               0   1
  ULK1 MUTATED     4   0
  ULK1 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      4    0
  ULK1 WILD-TYPE  281   48
   clus
vv  ULK1 MUTATED ULK1 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D527V7, binary
                cls
clus               0   1
  ULK1 MUTATED     5   5
  ULK1 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      5    5
  ULK1 WILD-TYPE  165  192
        clus
vv       ULK1 MUTATED ULK1 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D527V8, binary
                cls
clus               0   1
  ULK1 MUTATED     9   0
  ULK1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      9    0
  ULK1 WILD-TYPE  291    8
     clus
vv    ULK1 MUTATED ULK1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D527V9, binary
                cls
clus               0   1
  ULK1 MUTATED     8   2
  ULK1 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      8    2
  ULK1 WILD-TYPE  306   46
                               clus
vv                              ULK1 MUTATED ULK1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ULK1 MUTATED     5   0   0   1
  ULK1 WILD-TYPE 254   3  22  20
D527V10, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D527V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ULK1 MUTATED                                  0     0
  ULK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ULK1 MUTATED                           0    10
  ULK1 WILD-TYPE                        19   166
D527V12, multiclass
                                  clus
vv                                 ULK1 MUTATED ULK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(528) Variable = POLM MUTATION ANALYSIS
D528V1, survival
                sevent
clus2              0   1
  POLM MUTATED     9   1
  POLM WILD-TYPE 268  77
  POLM MUTATED POLM WILD-TYPE 
            10            345 
  POLM MUTATED POLM WILD-TYPE 
             1             77 
$`POLM MUTATED`
TCGA-AA-3672 TCGA-A6-6781 TCGA-AZ-4682 TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6535 
        0.92        19.66        22.36        51.32        15.02        15.12 
TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A1HB TCGA-G4-6293 
        9.44        13.35       135.65       133.18 

$`POLM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  POLM MUTATED POLM WILD-TYPE 
          0.92           0.00 
  POLM MUTATED POLM WILD-TYPE 
        135.65         148.01 
  POLM MUTATED POLM WILD-TYPE 
         17.39          22.09 
[1] "0.9 - 135.7 (17.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3"  
D528V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLM MUTATED         0        0        0         4         1         0
  POLM WILD-TYPE      64        1       26       104         7         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        16          6         42         32       35        11
                vv
clus             STAGE IVB
  POLM MUTATED           0
  POLM WILD-TYPE         1
D528V3, multiclass
            clus
vv           POLM MUTATED POLM WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  POLM MUTATED     0   0   9   2
  POLM WILD-TYPE   9  67 240  39
D528V4, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  T1            0              9
  T2            0             67
  T3            9            240
  T4            2             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
  POLM MUTATED     6   5   0
  POLM WILD-TYPE 214  76  66
D528V5, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  N0            6            214
  N1            5             76
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V6, binary
                cls
clus               0   1
  POLM MUTATED     6   1
  POLM WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      6    1
  POLM WILD-TYPE  279   47
   clus
vv  POLM MUTATED POLM WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D528V7, binary
                cls
clus               0   1
  POLM MUTATED     6   5
  POLM WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      6    5
  POLM WILD-TYPE  164  192
        clus
vv       POLM MUTATED POLM WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D528V8, binary
                cls
clus               0   1
  POLM MUTATED     9   0
  POLM WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      9    0
  POLM WILD-TYPE  291    8
     clus
vv    POLM MUTATED POLM WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D528V9, binary
                cls
clus               0   1
  POLM MUTATED     8   2
  POLM WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      8    2
  POLM WILD-TYPE  306   46
                               clus
vv                              POLM MUTATED POLM WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POLM MUTATED     7   0   0   3
  POLM WILD-TYPE 252   3  22  18
D528V10, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            3             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"
D528V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLM MUTATED                                  0     0
  POLM WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  POLM MUTATED                           0    10
  POLM WILD-TYPE                        19   166
D528V12, multiclass
                                  clus
vv                                 POLM MUTATED POLM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(529) Variable = HIST1H1C MUTATION ANALYSIS
D529V1, survival
                    sevent
clus2                  0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 273  78
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 4                351 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 0                 78 
$`HIST1H1C MUTATED`
TCGA-AD-6895 TCGA-AA-3510 TCGA-AA-A01V TCGA-DM-A0X9 
       25.08        63.98         1.02       119.70 

$`HIST1H1C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        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-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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
              1.02               0.00 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
            119.70             148.01 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             44.53              22.03 
[1] "1.0 - 119.7 (44.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9400000"
D529V2, continuous
                    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      63        1       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1C MUTATED           0          0          1          0        0
  HIST1H1C WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1C MUTATED           0         0
  HIST1H1C WILD-TYPE        12         1
D529V3, multiclass
            clus
vv           HIST1H1C MUTATED HIST1H1C WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 1                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  HIST1H1C MUTATED     0   1   3   0
  HIST1H1C WILD-TYPE   9  66 246  41
D529V4, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                3                246
  T4                0                 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
  HIST1H1C MUTATED     3   1   0
  HIST1H1C WILD-TYPE 217  80  66
D529V5, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  N0                3                217
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V6, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  281   48
   clus
vv  HIST1H1C MUTATED HIST1H1C WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D529V7, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     1   3
  HIST1H1C WILD-TYPE 169 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      1    3
  HIST1H1C WILD-TYPE  169  194
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FEMALE                1                169
  MALE                  3                194
[1] 2 2
[1] FALSE
D529V8, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     2   0
  HIST1H1C WILD-TYPE 298   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      2    0
  HIST1H1C WILD-TYPE  298    8
     clus
vv    HIST1H1C MUTATED HIST1H1C WILD-TYPE
  NO                 2                298
  YES                0                  8
[1] 2 2
[1] FALSE
D529V9, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 310  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  310   48
                               clus
vv                              HIST1H1C MUTATED HIST1H1C WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1C MUTATED     3   0   0   0
  HIST1H1C WILD-TYPE 256   3  22  21
D529V10, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D529V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1C MUTATED                                  0     0
  HIST1H1C WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1C MUTATED                           0     2
  HIST1H1C WILD-TYPE                        19   174
D529V12, multiclass
[1] "Remove cluster labels:" "HIST1H1C MUTATED"      
clus
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6964 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-6601         TCGA-AZ-6608 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-5912         TCGA-DM-A285         TCGA-G4-6310 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6586         TCGA-G4-6588 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6628         TCGA-A6-2671 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-2672         TCGA-A6-2674         TCGA-A6-2676 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2683         TCGA-A6-3807 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-3808         TCGA-A6-3809         TCGA-A6-3810 
"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-A6-6651 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6652         TCGA-A6-6653         TCGA-A6-6654 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6780         TCGA-A6-6781         TCGA-A6-6782 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AD-5900         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-6965         TCGA-AU-3779         TCGA-AU-6004 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4323         TCGA-AZ-4616 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"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-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-5913 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0XD         TCGA-DM-A0XF 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 

Clustering(530) Variable = TGFBR1 MUTATION ANALYSIS
D530V1, survival
                  sevent
clus2                0   1
  TGFBR1 MUTATED    12   2
  TGFBR1 WILD-TYPE 265  76
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              14              341 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               2               76 
$`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 
        9.44        41.42 

$`TGFBR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.08        25.18        21.76        24.69 
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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       34.03        18.05        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
            0.99             0.00 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          124.27           148.01 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          20.285           22.060 
[1] "1.0 - 124.3 (20.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D530V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGFBR1 MUTATED         5        0        2         3         2         0
  TGFBR1 WILD-TYPE      59        1       24       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR1 MUTATED           0          0          2          0        0
  TGFBR1 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TGFBR1 MUTATED           0         0
  TGFBR1 WILD-TYPE        12         1
D530V3, multiclass
            clus
vv           TGFBR1 MUTATED TGFBR1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TGFBR1 MUTATED     0   5   6   3
  TGFBR1 WILD-TYPE   9  62 243  38
D530V4, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  T1              0                9
  T2              5               62
  T3              6              243
  T4              3               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
  TGFBR1 MUTATED    12   2   0
  TGFBR1 WILD-TYPE 208  79  66
D530V5, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  N0             12              208
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V6, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    13   0
  TGFBR1 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     13    0
  TGFBR1 WILD-TYPE  272   48
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D530V7, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED     5   9
  TGFBR1 WILD-TYPE 165 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      5    9
  TGFBR1 WILD-TYPE  165  188
        clus
vv       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  FEMALE              5              165
  MALE                9              188
[1] 2 2
[1] FALSE
D530V8, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    12   0
  TGFBR1 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     12    0
  TGFBR1 WILD-TYPE  288    8
     clus
vv    TGFBR1 MUTATED TGFBR1 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D530V9, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    10   4
  TGFBR1 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     10    4
  TGFBR1 WILD-TYPE  304   44
                               clus
vv                              TGFBR1 MUTATED TGFBR1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TGFBR1 MUTATED    10   0   0   2
  TGFBR1 WILD-TYPE 249   3  22  19
D530V10, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D530V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR1 MUTATED                                  0     1
  TGFBR1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR1 MUTATED                           0     7
  TGFBR1 WILD-TYPE                        19   169
D530V12, multiclass
                                  clus
vv                                 TGFBR1 MUTATED TGFBR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = CIC MUTATION ANALYSIS
D531V1, survival
               sevent
clus2             0   1
  CIC MUTATED    18   5
  CIC WILD-TYPE 259  73
  CIC MUTATED CIC WILD-TYPE 
           23           332 
  CIC MUTATED CIC WILD-TYPE 
            5            73 
$`CIC MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 
       19.04       100.01        35.80        26.17        79.69        22.06 
TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A01R TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
       31.00         2.01        35.01        83.24        21.44        58.39 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6171 
       10.06        51.32        21.99        23.05        14.04        14.04 
TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A1HB TCGA-G4-6303 TCGA-G4-6304 
       12.95        11.64       135.65        65.85        53.62 

$`CIC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-5656 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-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        12.36        12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       74.56        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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         21.99 
[1] "2.0 - 135.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D531V2, continuous
               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      60        1       24        96         7         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        17          6         42         33       34        12
               vv
clus            STAGE IVB
  CIC MUTATED           0
  CIC WILD-TYPE         1
D531V3, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              4            60
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA           12            96
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  CIC MUTATED     2   2  18   1
  CIC WILD-TYPE   7  65 231  40
D531V4, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  T1           2             7
  T2           2            65
  T3          18           231
  T4           1            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
  CIC MUTATED    19   3   1
  CIC WILD-TYPE 201  78  65
D531V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0          19           201
  N1           3            78
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V6, binary
               cls
clus              0   1
  CIC MUTATED    19   1
  CIC WILD-TYPE 266  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     19    1
  CIC WILD-TYPE  266   47
   clus
vv  CIC MUTATED CIC WILD-TYPE
  0          19           266
  1           1            47
[1] 2 2
[1] FALSE
D531V7, binary
               cls
clus              0   1
  CIC MUTATED     9  14
  CIC WILD-TYPE 161 183
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      9   14
  CIC WILD-TYPE  161  183
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE           9           161
  MALE            14           183
[1] 2 2
[1] FALSE
D531V8, binary
               cls
clus              0   1
  CIC MUTATED    19   1
  CIC WILD-TYPE 281   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     19    1
  CIC WILD-TYPE  281    7
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO           19           281
  YES           1             7
[1] 2 2
[1] FALSE
D531V9, binary
               cls
clus              0   1
  CIC MUTATED    18   4
  CIC WILD-TYPE 296  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     18    4
  CIC WILD-TYPE  296   44
                               clus
vv                              CIC MUTATED CIC WILD-TYPE
  COLON ADENOCARCINOMA                   18           296
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CIC MUTATED    17   0   0   3
  CIC WILD-TYPE 242   3  22  18
D531V10, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  R0          17           242
  R1           0             3
  R2           0            22
  RX           3            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"
D531V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIC MUTATED                                  0     2
  CIC WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CIC MUTATED                           0    17
  CIC WILD-TYPE                        19   159
D531V12, multiclass
                                  clus
vv                                 CIC MUTATED CIC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                     17           159
[1] 4 2
[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 = FBXO21 MUTATION ANALYSIS
D532V1, survival
                  sevent
clus2                0   1
  FBXO21 MUTATED     5   1
  FBXO21 WILD-TYPE 272  77
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               6              349 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               1               77 
$`FBXO21 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-A6-5661 TCGA-AZ-6598 TCGA-CK-4952 TCGA-D5-6928 
        0.92        24.00        33.53        49.41        15.62        11.64 

$`FBXO21 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  FBXO21 MUTATED FBXO21 WILD-TYPE 
            0.92             0.00 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
           49.41           148.01 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
           19.81            22.06 
[1] "0.9 - 49.4 (19.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D532V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO21 MUTATED         0        0        1         3         0         0
  FBXO21 WILD-TYPE      64        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO21 MUTATED           1          0          0          1        0
  FBXO21 WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXO21 MUTATED           0         0
  FBXO21 WILD-TYPE        12         1
D532V3, multiclass
            clus
vv           FBXO21 MUTATED FBXO21 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  FBXO21 MUTATED     0   0   5   1
  FBXO21 WILD-TYPE   9  67 244  40
D532V4, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              5              244
  T4              1               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
  FBXO21 MUTATED     4   1   1
  FBXO21 WILD-TYPE 216  80  65
D532V5, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V6, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     5   0
  FBXO21 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      5    0
  FBXO21 WILD-TYPE  280   48
   clus
vv  FBXO21 MUTATED FBXO21 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D532V7, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     5   1
  FBXO21 WILD-TYPE 165 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      5    1
  FBXO21 WILD-TYPE  165  196
        clus
vv       FBXO21 MUTATED FBXO21 WILD-TYPE
  FEMALE              5              165
  MALE                1              196
[1] 2 2
[1] FALSE
D532V8, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     5   0
  FBXO21 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      5    0
  FBXO21 WILD-TYPE  295    8
     clus
vv    FBXO21 MUTATED FBXO21 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D532V9, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     3   3
  FBXO21 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      3    3
  FBXO21 WILD-TYPE  311   45
                               clus
vv                              FBXO21 MUTATED FBXO21 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXO21 MUTATED     4   0   0   1
  FBXO21 WILD-TYPE 255   3  22  20
D532V10, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D532V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO21 MUTATED                                  0     0
  FBXO21 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO21 MUTATED                           1     3
  FBXO21 WILD-TYPE                        18   173
D532V12, multiclass
                                  clus
vv                                 FBXO21 MUTATED FBXO21 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = PI4K2B MUTATION ANALYSIS
D533V1, survival
                  sevent
clus2                0   1
  PI4K2B MUTATED     8   1
  PI4K2B WILD-TYPE 269  77
  PI4K2B MUTATED PI4K2B WILD-TYPE 
               9              346 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
               1               77 
$`PI4K2B MUTATED`
TCGA-AZ-6608 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6648 TCGA-AA-A00J TCGA-AY-6196 
        1.94        32.91        30.44        25.18        18.05         0.20 
TCGA-CA-6717 TCGA-CK-5913 TCGA-DM-A1HA 
       12.76        51.32       131.51 

$`PI4K2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.75        36.53        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PI4K2B MUTATED PI4K2B WILD-TYPE 
             0.2              0.0 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
          131.51           148.01 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
          25.180           22.045 
[1] "0.2 - 131.5 (25.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D533V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PI4K2B MUTATED         2        0        0         2         0         0
  PI4K2B WILD-TYPE      62        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PI4K2B MUTATED           1          1          1          2        0
  PI4K2B WILD-TYPE        17          5         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PI4K2B MUTATED           1         0
  PI4K2B WILD-TYPE        11         1
D533V3, multiclass
            clus
vv           PI4K2B MUTATED PI4K2B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               1               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
  PI4K2B MUTATED     0   3   6   1
  PI4K2B WILD-TYPE   9  64 243  40
D533V4, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  T1              0                9
  T2              3               64
  T3              6              243
  T4              1               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
  PI4K2B MUTATED     5   2   3
  PI4K2B WILD-TYPE 215  79  63
D533V5, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  N0              5              215
  N1              2               79
  N2              3               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"
D533V6, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     7   1
  PI4K2B WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      7    1
  PI4K2B WILD-TYPE  278   47
   clus
vv  PI4K2B MUTATED PI4K2B WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D533V7, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     2   8
  PI4K2B WILD-TYPE 168 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      2    8
  PI4K2B WILD-TYPE  168  189
        clus
vv       PI4K2B MUTATED PI4K2B WILD-TYPE
  FEMALE              2              168
  MALE                8              189
[1] 2 2
[1] FALSE
D533V8, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     7   0
  PI4K2B WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      7    0
  PI4K2B WILD-TYPE  293    8
     clus
vv    PI4K2B MUTATED PI4K2B WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D533V9, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     7   3
  PI4K2B WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      7    3
  PI4K2B WILD-TYPE  307   45
                               clus
vv                              PI4K2B MUTATED PI4K2B WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PI4K2B MUTATED     4   0   0   2
  PI4K2B WILD-TYPE 255   3  22  19
D533V10, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              2               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"
D533V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PI4K2B MUTATED                                  0     1
  PI4K2B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PI4K2B MUTATED                           0     7
  PI4K2B WILD-TYPE                        19   169
D533V12, multiclass
                                  clus
vv                                 PI4K2B MUTATED PI4K2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = OLR1 MUTATION ANALYSIS
D534V1, survival
                sevent
clus2              0   1
  OLR1 MUTATED     8   1
  OLR1 WILD-TYPE 269  77
  OLR1 MUTATED OLR1 WILD-TYPE 
             9            346 
  OLR1 MUTATED OLR1 WILD-TYPE 
             1             77 
$`OLR1 MUTATED`
TCGA-A6-6649 TCGA-A6-5665 TCGA-AA-A01R TCGA-AD-5900 TCGA-CM-4752 TCGA-D5-5539 
       24.16        22.06        35.01        12.16        13.02        19.59 
TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-G4-6307 
       13.32       131.51        55.04 

$`OLR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  OLR1 MUTATED OLR1 WILD-TYPE 
         12.16           0.00 
  OLR1 MUTATED OLR1 WILD-TYPE 
        131.51         148.01 
  OLR1 MUTATED OLR1 WILD-TYPE 
         22.06          22.06 
[1] "12.2 - 131.5 (22.1)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "2.4"
D534V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OLR1 MUTATED         1        0        0         3         0         0
  OLR1 WILD-TYPE      63        1       26       105         8         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        17          5         42         32       35        12
                vv
clus             STAGE IVB
  OLR1 MUTATED           0
  OLR1 WILD-TYPE         1
D534V3, multiclass
            clus
vv           OLR1 MUTATED OLR1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  OLR1 MUTATED     0   1   8   0
  OLR1 WILD-TYPE   9  66 241  41
D534V4, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            0             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
  OLR1 MUTATED     4   3   2
  OLR1 WILD-TYPE 216  78  64
D534V5, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  N0            4            216
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V6, binary
                cls
clus               0   1
  OLR1 MUTATED     8   0
  OLR1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      8    0
  OLR1 WILD-TYPE  277   48
   clus
vv  OLR1 MUTATED OLR1 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D534V7, binary
                cls
clus               0   1
  OLR1 MUTATED     2   7
  OLR1 WILD-TYPE 168 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      2    7
  OLR1 WILD-TYPE  168  190
        clus
vv       OLR1 MUTATED OLR1 WILD-TYPE
  FEMALE            2            168
  MALE              7            190
[1] 2 2
[1] FALSE
D534V8, binary
                cls
clus               0   1
  OLR1 MUTATED     6   1
  OLR1 WILD-TYPE 294   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      6    1
  OLR1 WILD-TYPE  294    7
     clus
vv    OLR1 MUTATED OLR1 WILD-TYPE
  NO             6            294
  YES            1              7
[1] 2 2
[1] FALSE
D534V9, binary
                cls
clus               0   1
  OLR1 MUTATED     5   3
  OLR1 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      5    3
  OLR1 WILD-TYPE  309   45
                               clus
vv                              OLR1 MUTATED OLR1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OLR1 MUTATED     6   0   0   0
  OLR1 WILD-TYPE 253   3  22  21
D534V10, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D534V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OLR1 MUTATED                                  0     0
  OLR1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OLR1 MUTATED                           1     7
  OLR1 WILD-TYPE                        18   169
D534V12, multiclass
                                  clus
vv                                 OLR1 MUTATED OLR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = CCDC160 MUTATION ANALYSIS
D535V1, survival
                   sevent
clus2                 0   1
  CCDC160 MUTATED     8   0
  CCDC160 WILD-TYPE 269  78
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                8               347 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                0                78 
$`CCDC160 MUTATED`
TCGA-AA-3672 TCGA-AA-3688 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6653 
        0.92        19.00        35.80        26.17        79.69        24.39 
TCGA-AA-A010 TCGA-CK-6751 
       34.98       124.27 

$`CCDC160 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-5656 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-A6-6648 
       32.71        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-CM-4743 
       51.32        21.99        21.14        82.95         2.01        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CCDC160 MUTATED CCDC160 WILD-TYPE 
             0.92              0.00 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           124.27            148.01 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           30.575            21.990 
[1] "0.9 - 124.3 (30.6)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D535V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC160 MUTATED         3        0        1         3         1         0
  CCDC160 WILD-TYPE      61        1       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC160 MUTATED           1          0          0          0        1
  CCDC160 WILD-TYPE        17          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC160 MUTATED           0         0
  CCDC160 WILD-TYPE        12         1
D535V3, multiclass
            clus
vv           CCDC160 MUTATED CCDC160 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  CCDC160 MUTATED     0   3   5   2
  CCDC160 WILD-TYPE   9  64 244  39
D535V4, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               5               244
  T4               2                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
  CCDC160 MUTATED     8   2   0
  CCDC160 WILD-TYPE 212  79  66
D535V5, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  N0               8               212
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V6, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     8   1
  CCDC160 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      8    1
  CCDC160 WILD-TYPE  277   47
   clus
vv  CCDC160 MUTATED CCDC160 WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D535V7, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     7   3
  CCDC160 WILD-TYPE 163 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      7    3
  CCDC160 WILD-TYPE  163  194
        clus
vv       CCDC160 MUTATED CCDC160 WILD-TYPE
  FEMALE               7               163
  MALE                 3               194
[1] 2 2
[1] FALSE
D535V8, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     8   0
  CCDC160 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      8    0
  CCDC160 WILD-TYPE  292    8
     clus
vv    CCDC160 MUTATED CCDC160 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D535V9, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     9   1
  CCDC160 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      9    1
  CCDC160 WILD-TYPE  305   47
                               clus
vv                              CCDC160 MUTATED CCDC160 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC160 MUTATED     7   0   1   1
  CCDC160 WILD-TYPE 252   3  21  20
D535V10, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               1                21
  RX               1                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"
D535V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC160 MUTATED                                  0     0
  CCDC160 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC160 MUTATED                           0     5
  CCDC160 WILD-TYPE                        19   171
D535V12, multiclass
                                  clus
vv                                 CCDC160 MUTATED CCDC160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = RNF111 MUTATION ANALYSIS
D536V1, survival
                  sevent
clus2                0   1
  RNF111 MUTATED    10   3
  RNF111 WILD-TYPE 267  75
  RNF111 MUTATED RNF111 WILD-TYPE 
              13              342 
  RNF111 MUTATED RNF111 WILD-TYPE 
               3               75 
$`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 
       46.75 

$`RNF111 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.39        23.87        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  RNF111 MUTATED RNF111 WILD-TYPE 
               0                0 
  RNF111 MUTATED RNF111 WILD-TYPE 
           58.39           148.01 
  RNF111 MUTATED RNF111 WILD-TYPE 
           19.66            22.09 
[1] "0.0 - 58.4 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D536V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF111 MUTATED         1        0        0        10         1         0
  RNF111 WILD-TYPE      63        1       26        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF111 MUTATED           1          0          0          1        0
  RNF111 WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF111 MUTATED           0         0
  RNF111 WILD-TYPE        12         1
D536V3, multiclass
            clus
vv           RNF111 MUTATED RNF111 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA              10               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  RNF111 MUTATED     0   1  11   2
  RNF111 WILD-TYPE   9  66 238  39
D536V4, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             11              238
  T4              2               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
  RNF111 MUTATED    12   1   1
  RNF111 WILD-TYPE 208  80  65
D536V5, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  N0             12              208
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V6, binary
                  cls
clus                 0   1
  RNF111 MUTATED    12   0
  RNF111 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     12    0
  RNF111 WILD-TYPE  273   48
   clus
vv  RNF111 MUTATED RNF111 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D536V7, binary
                  cls
clus                 0   1
  RNF111 MUTATED     5   9
  RNF111 WILD-TYPE 165 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      5    9
  RNF111 WILD-TYPE  165  188
        clus
vv       RNF111 MUTATED RNF111 WILD-TYPE
  FEMALE              5              165
  MALE                9              188
[1] 2 2
[1] FALSE
D536V8, binary
                  cls
clus                 0   1
  RNF111 MUTATED    11   0
  RNF111 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     11    0
  RNF111 WILD-TYPE  289    8
     clus
vv    RNF111 MUTATED RNF111 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D536V9, binary
                  cls
clus                 0   1
  RNF111 MUTATED     9   5
  RNF111 WILD-TYPE 305  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      9    5
  RNF111 WILD-TYPE  305   43
                               clus
vv                              RNF111 MUTATED RNF111 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF111 MUTATED    11   0   0   2
  RNF111 WILD-TYPE 248   3  22  19
D536V10, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              2               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"
D536V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF111 MUTATED                                  0     2
  RNF111 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF111 MUTATED                           0     7
  RNF111 WILD-TYPE                        19   169
D536V12, multiclass
                                  clus
vv                                 RNF111 MUTATED RNF111 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = RBM19 MUTATION ANALYSIS
D537V1, survival
                 sevent
clus2               0   1
  RBM19 MUTATED    14   7
  RBM19 WILD-TYPE 263  71
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             334 
  RBM19 MUTATED RBM19 WILD-TYPE 
              7              71 
$`RBM19 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6310 TCGA-A6-5660 
       13.02         0.92        10.88       100.01        63.62        29.19 
TCGA-AA-3492 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AU-3779 
        3.02        33.01        25.02        18.05         4.01        14.50 
TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6162 TCGA-D5-5539 
       58.39        21.14        32.02        15.02        12.00        19.59 
TCGA-D5-6537 TCGA-G4-6299 TCGA-G4-6317 
        4.80        74.56        36.00 

$`RBM19 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  RBM19 MUTATED RBM19 WILD-TYPE 
           0.92            0.00 
  RBM19 MUTATED RBM19 WILD-TYPE 
         100.01          148.01 
  RBM19 MUTATED RBM19 WILD-TYPE 
          19.59           22.09 
[1] "0.9 - 100.0 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D537V2, continuous
                 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      62        1       24       105         6         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        16          5         40         30       35        12
                 vv
clus              STAGE IVB
  RBM19 MUTATED           0
  RBM19 WILD-TYPE         1
D537V3, multiclass
            clus
vv           RBM19 MUTATED RBM19 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              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
  RBM19 MUTATED     1   2  14   4
  RBM19 WILD-TYPE   8  65 235  37
D537V4, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            14             235
  T4             4              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
  RBM19 MUTATED    10   6   5
  RBM19 WILD-TYPE 210  75  61
D537V5, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  N0            10             210
  N1             6              75
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V6, binary
                 cls
clus                0   1
  RBM19 MUTATED    17   0
  RBM19 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     17    0
  RBM19 WILD-TYPE  268   48
   clus
vv  RBM19 MUTATED RBM19 WILD-TYPE
  0            17             268
  1             0              48
[1] 2 2
[1] FALSE
D537V7, binary
                 cls
clus                0   1
  RBM19 MUTATED     9  12
  RBM19 WILD-TYPE 161 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED      9   12
  RBM19 WILD-TYPE  161  185
        clus
vv       RBM19 MUTATED RBM19 WILD-TYPE
  FEMALE             9             161
  MALE              12             185
[1] 2 2
[1] FALSE
D537V8, binary
                 cls
clus                0   1
  RBM19 MUTATED    19   1
  RBM19 WILD-TYPE 281   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     19    1
  RBM19 WILD-TYPE  281    7
     clus
vv    RBM19 MUTATED RBM19 WILD-TYPE
  NO             19             281
  YES             1               7
[1] 2 2
[1] FALSE
D537V9, binary
                 cls
clus                0   1
  RBM19 MUTATED    15   6
  RBM19 WILD-TYPE 299  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     15    6
  RBM19 WILD-TYPE  299   42
                               clus
vv                              RBM19 MUTATED RBM19 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBM19 MUTATED    15   0   0   1
  RBM19 WILD-TYPE 244   3  22  20
D537V10, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             1              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"
D537V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM19 MUTATED                                  0     0
  RBM19 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM19 MUTATED                           1    13
  RBM19 WILD-TYPE                        18   163
D537V12, multiclass
                                  clus
vv                                 RBM19 MUTATED RBM19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       13             163
[1] 4 2
[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 = NEUROD1 MUTATION ANALYSIS
D538V1, survival
                   sevent
clus2                 0   1
  NEUROD1 MUTATED     8   0
  NEUROD1 WILD-TYPE 269  78
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                8               347 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                0                78 
$`NEUROD1 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3510 TCGA-AA-A00J TCGA-AZ-4315 TCGA-CM-4752 
       19.04        24.00        63.98        18.05        58.39        13.02 
TCGA-CM-6164 TCGA-CM-6172 
       29.03        11.01 

$`NEUROD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            11.01              0.00 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            63.98            148.01 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            21.52             22.06 
[1] "11.0 - 64.0 (21.5)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D538V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEUROD1 MUTATED         0        0        1         4         0         0
  NEUROD1 WILD-TYPE      64        1       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEUROD1 MUTATED           0          0          2          0        1
  NEUROD1 WILD-TYPE        18          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  NEUROD1 MUTATED           0         0
  NEUROD1 WILD-TYPE        12         1
D538V3, multiclass
            clus
vv           NEUROD1 MUTATED NEUROD1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  NEUROD1 MUTATED     0   0   7   1
  NEUROD1 WILD-TYPE   9  67 242  40
D538V4, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               7               242
  T4               1                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
  NEUROD1 MUTATED     6   2   0
  NEUROD1 WILD-TYPE 214  79  66
D538V5, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  N0               6               214
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V6, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     7   1
  NEUROD1 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      7    1
  NEUROD1 WILD-TYPE  278   47
   clus
vv  NEUROD1 MUTATED NEUROD1 WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D538V7, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     3   5
  NEUROD1 WILD-TYPE 167 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      3    5
  NEUROD1 WILD-TYPE  167  192
        clus
vv       NEUROD1 MUTATED NEUROD1 WILD-TYPE
  FEMALE               3               167
  MALE                 5               192
[1] 2 2
[1] FALSE
D538V8, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     7   1
  NEUROD1 WILD-TYPE 293   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      7    1
  NEUROD1 WILD-TYPE  293    7
     clus
vv    NEUROD1 MUTATED NEUROD1 WILD-TYPE
  NO                7               293
  YES               1                 7
[1] 2 2
[1] FALSE
D538V9, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     6   2
  NEUROD1 WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      6    2
  NEUROD1 WILD-TYPE  308   46
                               clus
vv                              NEUROD1 MUTATED NEUROD1 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  NEUROD1 MUTATED     7   0   1   0
  NEUROD1 WILD-TYPE 252   3  21  21
D538V10, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               1                21
  RX               0                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"
D538V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEUROD1 MUTATED                                  0     0
  NEUROD1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NEUROD1 MUTATED                           1     3
  NEUROD1 WILD-TYPE                        18   173
D538V12, multiclass
                                  clus
vv                                 NEUROD1 MUTATED NEUROD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = SLFN12L MUTATION ANALYSIS
D539V1, survival
                   sevent
clus2                 0   1
  SLFN12L MUTATED     6   2
  SLFN12L WILD-TYPE 271  76
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                8               347 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                2                76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.59        12.20        14.30        17.56        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  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             22.06 
[1] "6.0 - 148.0 (22.9)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.2"
D539V2, continuous
                   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      64        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLFN12L MUTATED           3          0          0          0        1
  SLFN12L WILD-TYPE        15          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLFN12L MUTATED           0         0
  SLFN12L WILD-TYPE        12         1
D539V3, multiclass
            clus
vv           SLFN12L MUTATED SLFN12L WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                3                15
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLFN12L MUTATED     0   0   8   0
  SLFN12L WILD-TYPE   9  67 241  41
D539V4, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               8               241
  T4               0                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
  SLFN12L MUTATED     4   3   1
  SLFN12L WILD-TYPE 216  78  65
D539V5, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  N0               4               216
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V6, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     7   1
  SLFN12L WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      7    1
  SLFN12L WILD-TYPE  278   47
   clus
vv  SLFN12L MUTATED SLFN12L WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D539V7, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     4   4
  SLFN12L WILD-TYPE 166 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      4    4
  SLFN12L WILD-TYPE  166  193
        clus
vv       SLFN12L MUTATED SLFN12L WILD-TYPE
  FEMALE               4               166
  MALE                 4               193
[1] 2 2
[1] FALSE
D539V8, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     8   0
  SLFN12L WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      8    0
  SLFN12L WILD-TYPE  292    8
     clus
vv    SLFN12L MUTATED SLFN12L WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D539V9, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     7   1
  SLFN12L WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      7    1
  SLFN12L WILD-TYPE  307   47
                               clus
vv                              SLFN12L MUTATED SLFN12L WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLFN12L MUTATED     6   0   0   2
  SLFN12L WILD-TYPE 253   3  22  19
D539V10, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               2                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"
D539V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLFN12L MUTATED                                  0     2
  SLFN12L WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLFN12L MUTATED                           0     3
  SLFN12L WILD-TYPE                        19   173
D539V12, multiclass
                                  clus
vv                                 SLFN12L MUTATED SLFN12L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = UPF3A MUTATION ANALYSIS
D540V1, survival
                 sevent
clus2               0   1
  UPF3A MUTATED     6   3
  UPF3A WILD-TYPE 271  75
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             346 
  UPF3A MUTATED UPF3A WILD-TYPE 
              3              75 
$`UPF3A MUTATED`
TCGA-AZ-4681 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3977 
      106.75         3.02        63.98        29.95         6.97        25.02 
TCGA-AD-6889 TCGA-CA-6718 TCGA-CK-5913 
       83.24        10.06        51.32 

$`UPF3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  UPF3A MUTATED UPF3A WILD-TYPE 
           3.02            0.00 
  UPF3A MUTATED UPF3A WILD-TYPE 
         106.75          148.01 
  UPF3A MUTATED UPF3A WILD-TYPE 
          29.95           22.01 
[1] "3.0 - 106.8 (29.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D540V2, continuous
                 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      64        1       23       103         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  UPF3A MUTATED           0
  UPF3A WILD-TYPE         1
D540V3, multiclass
            clus
vv           UPF3A MUTATED UPF3A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  UPF3A MUTATED     0   1   8   0
  UPF3A WILD-TYPE   9  66 241  41
D540V4, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             0              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
  UPF3A MUTATED     9   0   0
  UPF3A WILD-TYPE 211  81  66
D540V5, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  N0             9             211
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V6, binary
                 cls
clus                0   1
  UPF3A MUTATED     7   0
  UPF3A WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      7    0
  UPF3A WILD-TYPE  278   48
   clus
vv  UPF3A MUTATED UPF3A WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D540V7, binary
                 cls
clus                0   1
  UPF3A MUTATED     4   5
  UPF3A WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      4    5
  UPF3A WILD-TYPE  166  192
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D540V8, binary
                 cls
clus                0   1
  UPF3A MUTATED     9   0
  UPF3A WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      9    0
  UPF3A WILD-TYPE  291    8
     clus
vv    UPF3A MUTATED UPF3A WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D540V9, binary
                 cls
clus                0   1
  UPF3A MUTATED     8   1
  UPF3A WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      8    1
  UPF3A WILD-TYPE  306   47
                               clus
vv                              UPF3A MUTATED UPF3A WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UPF3A MUTATED     6   0   0   2
  UPF3A WILD-TYPE 253   3  22  19
D540V10, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D540V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UPF3A MUTATED                                  0     2
  UPF3A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UPF3A MUTATED                           0     2
  UPF3A WILD-TYPE                        19   174
D540V12, multiclass
                                  clus
vv                                 UPF3A MUTATED UPF3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        2             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(541) Variable = KDM3B MUTATION ANALYSIS
D541V1, survival
                 sevent
clus2               0   1
  KDM3B MUTATED    27   3
  KDM3B WILD-TYPE 250  75
  KDM3B MUTATED KDM3B WILD-TYPE 
             30             325 
  KDM3B MUTATED KDM3B WILD-TYPE 
              3              75 
$`KDM3B MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6321 TCGA-A6-5661 TCGA-A6-5665 
        0.92        24.00        25.08        22.09        33.53        22.06 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3555 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 
       19.66        20.28        29.95         2.01        25.02        34.98 
TCGA-AA-A01Q TCGA-AD-6963 TCGA-AY-6196 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6717 
        1.02        27.42         0.20        49.41         5.23        12.76 
TCGA-CA-6719 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6171 
       14.30        29.06        22.03        14.04        12.99        14.04 
TCGA-CM-6676 TCGA-D5-6923 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A28H TCGA-F4-6703 
       11.08        12.43        12.59       140.38       117.07        47.87 

$`KDM3B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.12         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 TCGA-AZ-6606 
       62.79        88.21         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        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        21.99        21.14        82.95         2.01       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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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-F4-6459 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KDM3B MUTATED KDM3B WILD-TYPE 
            0.2             0.0 
  KDM3B MUTATED KDM3B WILD-TYPE 
         140.38          148.01 
  KDM3B MUTATED KDM3B WILD-TYPE 
         21.155          22.360 
[1] "0.2 - 140.4 (21.2)" "0.0 - 148.0 (22.4)"
[1] "hr=" "2.1"
D541V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM3B MUTATED         4        0        2        12         2         0
  KDM3B WILD-TYPE      60        1       24        96         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM3B MUTATED           2          1          3          3        0         0
  KDM3B WILD-TYPE        16          5         41         30       35        12
                 vv
clus              STAGE IVB
  KDM3B MUTATED           0
  KDM3B WILD-TYPE         1
D541V3, multiclass
            clus
vv           KDM3B MUTATED KDM3B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             12              96
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              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
  KDM3B MUTATED     1   6  21   4
  KDM3B WILD-TYPE   8  61 228  37
D541V4, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  T1             1               8
  T2             6              61
  T3            21             228
  T4             4              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
  KDM3B MUTATED    22   8   2
  KDM3B WILD-TYPE 198  73  64
D541V5, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  N0            22             198
  N1             8              73
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V6, binary
                 cls
clus                0   1
  KDM3B MUTATED    24   0
  KDM3B WILD-TYPE 261  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     24    0
  KDM3B WILD-TYPE  261   48
   clus
vv  KDM3B MUTATED KDM3B WILD-TYPE
  0            24             261
  1             0              48
[1] 2 2
[1] FALSE
D541V7, binary
                 cls
clus                0   1
  KDM3B MUTATED    18  14
  KDM3B WILD-TYPE 152 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     18   14
  KDM3B WILD-TYPE  152  183
        clus
vv       KDM3B MUTATED KDM3B WILD-TYPE
  FEMALE            18             152
  MALE              14             183
[1] 2 2
[1] FALSE
D541V8, binary
                 cls
clus                0   1
  KDM3B MUTATED    24   0
  KDM3B WILD-TYPE 276   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     24    0
  KDM3B WILD-TYPE  276    8
     clus
vv    KDM3B MUTATED KDM3B WILD-TYPE
  NO             24             276
  YES             0               8
[1] 2 2
[1] FALSE
D541V9, binary
                 cls
clus                0   1
  KDM3B MUTATED    26   6
  KDM3B WILD-TYPE 288  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     26    6
  KDM3B WILD-TYPE  288   42
                               clus
vv                              KDM3B MUTATED KDM3B WILD-TYPE
  COLON ADENOCARCINOMA                     26             288
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM3B MUTATED    21   0   0   2
  KDM3B WILD-TYPE 238   3  22  19
D541V10, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  R0            21             238
  R1             0               3
  R2             0              22
  RX             2              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"
D541V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM3B MUTATED                                  0     2
  KDM3B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM3B MUTATED                           2    19
  KDM3B WILD-TYPE                        17   157
D541V12, multiclass
                                  clus
vv                                 KDM3B MUTATED KDM3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       19             157
[1] 4 2
[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 = RPGRIP1L MUTATION ANALYSIS
D542V1, survival
                    sevent
clus2                  0   1
  RPGRIP1L MUTATED    12   4
  RPGRIP1L WILD-TYPE 265  74
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                16                339 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                 4                 74 
$`RPGRIP1L MUTATED`
TCGA-AA-3950 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6648 TCGA-AA-3511 TCGA-AA-3680 
       24.00        33.53         8.38        25.18         6.97        11.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 
       26.01         2.01         4.01        34.98        83.24        49.41 
TCGA-CM-4752 TCGA-D5-6536 TCGA-F4-6703 TCGA-F4-6808 
       13.02        17.85        47.87        33.67 

$`RPGRIP1L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6142 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-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
              2.01               0.00 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
             83.24             148.01 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
             24.59              22.03 
[1] "2.0 - 83.2 (24.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D542V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPGRIP1L MUTATED         1        0        2         9         2         0
  RPGRIP1L WILD-TYPE      63        1       24        99         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPGRIP1L MUTATED           0          0          1          0        1
  RPGRIP1L WILD-TYPE        18          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  RPGRIP1L MUTATED           1         0
  RPGRIP1L WILD-TYPE        11         1
D542V3, multiclass
            clus
vv           RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 9                 99
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 1                 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
  RPGRIP1L MUTATED     1   0  12   4
  RPGRIP1L WILD-TYPE   8  67 237  37
D542V4, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  T1                1                  8
  T2                0                 67
  T3               12                237
  T4                4                 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
  RPGRIP1L MUTATED    15   1   1
  RPGRIP1L WILD-TYPE 205  80  65
D542V5, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  N0               15                205
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V6, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    14   2
  RPGRIP1L WILD-TYPE 271  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     14    2
  RPGRIP1L WILD-TYPE  271   46
   clus
vv  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  0               14                271
  1                2                 46
[1] 2 2
[1] FALSE
D542V7, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED     9   8
  RPGRIP1L WILD-TYPE 161 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED      9    8
  RPGRIP1L WILD-TYPE  161  189
        clus
vv       RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  FEMALE                9                161
  MALE                  8                189
[1] 2 2
[1] FALSE
D542V8, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    14   0
  RPGRIP1L WILD-TYPE 286   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     14    0
  RPGRIP1L WILD-TYPE  286    8
     clus
vv    RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  NO                14                286
  YES                0                  8
[1] 2 2
[1] FALSE
D542V9, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    13   4
  RPGRIP1L WILD-TYPE 301  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     13    4
  RPGRIP1L WILD-TYPE  301   44
                               clus
vv                              RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  COLON ADENOCARCINOMA                        13                301
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  RPGRIP1L MUTATED    12   0   1   0
  RPGRIP1L WILD-TYPE 247   3  21  21
D542V10, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  R0               12                247
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D542V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPGRIP1L MUTATED                                  0     1
  RPGRIP1L WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  RPGRIP1L MUTATED                           3     5
  RPGRIP1L WILD-TYPE                        16   171
D542V12, multiclass
                                  clus
vv                                 RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       3                 16
  WHITE                                           5                171
[1] 4 2
[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 = RBM12 MUTATION ANALYSIS
D543V1, survival
                 sevent
clus2               0   1
  RBM12 MUTATED    10   2
  RBM12 WILD-TYPE 267  76
  RBM12 MUTATED RBM12 WILD-TYPE 
             12             343 
  RBM12 MUTATED RBM12 WILD-TYPE 
              2              76 
$`RBM12 MUTATED`
TCGA-AA-3713 TCGA-G4-6625 TCGA-A6-6651 TCGA-AA-3529 TCGA-AA-3663 TCGA-AA-3949 
       19.04        91.79        21.76         0.00         6.97        26.01 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6171 TCGA-DM-A28K TCGA-G4-6315 
       12.16        58.39         6.77        14.04        98.24        61.91 

$`RBM12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RBM12 MUTATED RBM12 WILD-TYPE 
              0               0 
  RBM12 MUTATED RBM12 WILD-TYPE 
          98.24          148.01 
  RBM12 MUTATED RBM12 WILD-TYPE 
          20.40           22.09 
[1] "0.0 - 98.2 (20.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D543V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM12 MUTATED         3        0        1         3         0         0
  RBM12 WILD-TYPE      61        1       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM12 MUTATED           0          0          2          1        2         0
  RBM12 WILD-TYPE        18          6         42         32       33        12
                 vv
clus              STAGE IVB
  RBM12 MUTATED           0
  RBM12 WILD-TYPE         1
D543V3, multiclass
            clus
vv           RBM12 MUTATED RBM12 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  RBM12 MUTATED     0   3   9   0
  RBM12 WILD-TYPE   9  64 240  41
D543V4, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             0              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
  RBM12 MUTATED     8   3   1
  RBM12 WILD-TYPE 212  78  65
D543V5, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V6, binary
                 cls
clus                0   1
  RBM12 MUTATED     7   2
  RBM12 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      7    2
  RBM12 WILD-TYPE  278   46
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D543V7, binary
                 cls
clus                0   1
  RBM12 MUTATED     5   7
  RBM12 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      5    7
  RBM12 WILD-TYPE  165  190
        clus
vv       RBM12 MUTATED RBM12 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D543V8, binary
                 cls
clus                0   1
  RBM12 MUTATED     9   1
  RBM12 WILD-TYPE 291   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      9    1
  RBM12 WILD-TYPE  291    7
     clus
vv    RBM12 MUTATED RBM12 WILD-TYPE
  NO              9             291
  YES             1               7
[1] 2 2
[1] FALSE
D543V9, binary
                 cls
clus                0   1
  RBM12 MUTATED     9   3
  RBM12 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      9    3
  RBM12 WILD-TYPE  305   45
                               clus
vv                              RBM12 MUTATED RBM12 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBM12 MUTATED     8   0   1   0
  RBM12 WILD-TYPE 251   3  21  21
D543V10, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             0              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"
D543V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM12 MUTATED                                  0     0
  RBM12 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM12 MUTATED                           0     8
  RBM12 WILD-TYPE                        19   168
D543V12, multiclass
                                  clus
vv                                 RBM12 MUTATED RBM12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = PALB2 MUTATION ANALYSIS
D544V1, survival
                 sevent
clus2               0   1
  PALB2 MUTATED    17   2
  PALB2 WILD-TYPE 260  76
  PALB2 MUTATED PALB2 WILD-TYPE 
             19             336 
  PALB2 MUTATED PALB2 WILD-TYPE 
              2              76 
$`PALB2 MUTATED`
TCGA-A6-4105 TCGA-AA-3543 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3660 
       14.53         0.99        33.53        24.39        63.98        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 
       35.31 

$`PALB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        17.03        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PALB2 MUTATED PALB2 WILD-TYPE 
           0.99            0.00 
  PALB2 MUTATED PALB2 WILD-TYPE 
         124.27          148.01 
  PALB2 MUTATED PALB2 WILD-TYPE 
         24.390          22.045 
[1] "1.0 - 124.3 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D544V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PALB2 MUTATED         9        0        3         5         1         0
  PALB2 WILD-TYPE      55        1       23       103         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  PALB2 MUTATED           0
  PALB2 WILD-TYPE         1
D544V3, multiclass
            clus
vv           PALB2 MUTATED PALB2 WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PALB2 MUTATED     0   9   9   1
  PALB2 WILD-TYPE   9  58 240  40
D544V4, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  T1             0               9
  T2             9              58
  T3             9             240
  T4             1              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
  PALB2 MUTATED    18   1   0
  PALB2 WILD-TYPE 202  80  66
D544V5, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  N0            18             202
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V6, binary
                 cls
clus                0   1
  PALB2 MUTATED    17   0
  PALB2 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     17    0
  PALB2 WILD-TYPE  268   48
   clus
vv  PALB2 MUTATED PALB2 WILD-TYPE
  0            17             268
  1             0              48
[1] 2 2
[1] FALSE
D544V7, binary
                 cls
clus                0   1
  PALB2 MUTATED    10   9
  PALB2 WILD-TYPE 160 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     10    9
  PALB2 WILD-TYPE  160  188
        clus
vv       PALB2 MUTATED PALB2 WILD-TYPE
  FEMALE            10             160
  MALE               9             188
[1] 2 2
[1] FALSE
D544V8, binary
                 cls
clus                0   1
  PALB2 MUTATED    19   0
  PALB2 WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     19    0
  PALB2 WILD-TYPE  281    8
     clus
vv    PALB2 MUTATED PALB2 WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D544V9, binary
                 cls
clus                0   1
  PALB2 MUTATED    13   6
  PALB2 WILD-TYPE 301  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     13    6
  PALB2 WILD-TYPE  301   42
                               clus
vv                              PALB2 MUTATED PALB2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PALB2 MUTATED    14   0   0   2
  PALB2 WILD-TYPE 245   3  22  19
D544V10, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D544V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PALB2 MUTATED                                  0     1
  PALB2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PALB2 MUTATED                           2     9
  PALB2 WILD-TYPE                        17   167
D544V12, multiclass
                                  clus
vv                                 PALB2 MUTATED PALB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(545) Variable = PCDH12 MUTATION ANALYSIS
D545V1, survival
                  sevent
clus2                0   1
  PCDH12 MUTATED    15   2
  PCDH12 WILD-TYPE 262  76
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              17              338 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
               2               76 
$`PCDH12 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6964 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
        0.92        19.04        10.88        33.53        23.61        22.06 
TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-6715 
        1.02        53.00        31.00        34.98        49.41        12.59 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6927 TCGA-D5-6928 
       12.76        51.32        14.04         9.44        11.64 

$`PCDH12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       31.07        30.05        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        3.19        12.69        12.36        12.39        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PCDH12 MUTATED PCDH12 WILD-TYPE 
            0.92             0.00 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
           53.00           148.01 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
           19.04            22.09 
[1] "0.9 - 53.0 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D545V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH12 MUTATED         3        0        2         6         1         0
  PCDH12 WILD-TYPE      61        1       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH12 MUTATED           1          0          1          0        1
  PCDH12 WILD-TYPE        17          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PCDH12 MUTATED           1         0
  PCDH12 WILD-TYPE        11         1
D545V3, multiclass
            clus
vv           PCDH12 MUTATED PCDH12 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  PCDH12 MUTATED     1   2  12   2
  PCDH12 WILD-TYPE   8  65 237  39
D545V4, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             12              237
  T4              2               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
  PCDH12 MUTATED    13   2   2
  PCDH12 WILD-TYPE 207  79  64
D545V5, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  N0             13              207
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V6, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    12   2
  PCDH12 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     12    2
  PCDH12 WILD-TYPE  273   46
   clus
vv  PCDH12 MUTATED PCDH12 WILD-TYPE
  0             12              273
  1              2               46
[1] 2 2
[1] FALSE
D545V7, binary
                  cls
clus                 0   1
  PCDH12 MUTATED     9   8
  PCDH12 WILD-TYPE 161 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED      9    8
  PCDH12 WILD-TYPE  161  189
        clus
vv       PCDH12 MUTATED PCDH12 WILD-TYPE
  FEMALE              9              161
  MALE                8              189
[1] 2 2
[1] FALSE
D545V8, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    16   1
  PCDH12 WILD-TYPE 284   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     16    1
  PCDH12 WILD-TYPE  284    7
     clus
vv    PCDH12 MUTATED PCDH12 WILD-TYPE
  NO              16              284
  YES              1                7
[1] 2 2
[1] FALSE
D545V9, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    13   4
  PCDH12 WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     13    4
  PCDH12 WILD-TYPE  301   44
                               clus
vv                              PCDH12 MUTATED PCDH12 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PCDH12 MUTATED    10   0   1   3
  PCDH12 WILD-TYPE 249   3  21  18
D545V10, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              3               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"
D545V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH12 MUTATED                                  0     2
  PCDH12 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PCDH12 MUTATED                           1     8
  PCDH12 WILD-TYPE                        18   168
D545V12, multiclass
                                  clus
vv                                 PCDH12 MUTATED PCDH12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = MIER1 MUTATION ANALYSIS
D546V1, survival
                 sevent
clus2               0   1
  MIER1 MUTATED     5   1
  MIER1 WILD-TYPE 272  77
  MIER1 MUTATED MIER1 WILD-TYPE 
              6             349 
  MIER1 MUTATED MIER1 WILD-TYPE 
              1              77 
$`MIER1 MUTATED`
TCGA-G4-6588 TCGA-A6-5659 TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A28E TCGA-DM-A28F 
       26.17        30.44        34.98        12.76       119.93        35.97 

$`MIER1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H TCGA-DM-A28K 
      135.65       139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MIER1 MUTATED MIER1 WILD-TYPE 
          12.76            0.00 
  MIER1 MUTATED MIER1 WILD-TYPE 
         119.93          148.01 
  MIER1 MUTATED MIER1 WILD-TYPE 
          32.71           21.99 
[1] "12.8 - 119.9 (32.7)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.8"
D546V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIER1 MUTATED         1        0        0         3         1         0
  MIER1 WILD-TYPE      63        1       26       105         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  MIER1 MUTATED           0
  MIER1 WILD-TYPE         1
D546V3, multiclass
            clus
vv           MIER1 MUTATED MIER1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MIER1 MUTATED     0   1   4   1
  MIER1 WILD-TYPE   9  66 245  40
D546V4, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             1              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
  MIER1 MUTATED     5   1   0
  MIER1 WILD-TYPE 215  80  66
D546V5, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V6, binary
                 cls
clus                0   1
  MIER1 MUTATED     6   0
  MIER1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      6    0
  MIER1 WILD-TYPE  279   48
   clus
vv  MIER1 MUTATED MIER1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D546V7, binary
                 cls
clus                0   1
  MIER1 MUTATED     3   3
  MIER1 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      3    3
  MIER1 WILD-TYPE  167  194
        clus
vv       MIER1 MUTATED MIER1 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D546V8, binary
                 cls
clus                0   1
  MIER1 MUTATED     4   0
  MIER1 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      4    0
  MIER1 WILD-TYPE  296    8
     clus
vv    MIER1 MUTATED MIER1 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D546V9, binary
                 cls
clus                0   1
  MIER1 MUTATED     5   1
  MIER1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      5    1
  MIER1 WILD-TYPE  309   47
                               clus
vv                              MIER1 MUTATED MIER1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MIER1 MUTATED     3   0   0   1
  MIER1 WILD-TYPE 256   3  22  20
D546V10, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D546V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIER1 MUTATED                                  0     1
  MIER1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MIER1 MUTATED                           0     4
  MIER1 WILD-TYPE                        19   172
D546V12, multiclass
                                  clus
vv                                 MIER1 MUTATED MIER1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = ICOSLG MUTATION ANALYSIS
D547V1, survival
                  sevent
clus2                0   1
  ICOSLG MUTATED     2   2
  ICOSLG WILD-TYPE 275  76
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               4              351 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               2               76 
$`ICOSLG MUTATED`
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-6674 
       83.24        58.39        21.14        12.95 

$`ICOSLG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ICOSLG MUTATED ICOSLG WILD-TYPE 
           12.95             0.00 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
           83.24           148.01 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
          39.765           22.060 
[1] "12.9 - 83.2 (39.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D547V2, continuous
                  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      63        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ICOSLG MUTATED           0          0          0          0        0
  ICOSLG WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ICOSLG MUTATED           0         0
  ICOSLG WILD-TYPE        12         1
D547V3, multiclass
            clus
vv           ICOSLG MUTATED ICOSLG WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ICOSLG MUTATED     1   0   3   0
  ICOSLG WILD-TYPE   8  67 246  41
D547V4, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  T1              1                8
  T2              0               67
  T3              3              246
  T4              0               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
  ICOSLG MUTATED     4   0   0
  ICOSLG WILD-TYPE 216  81  66
D547V5, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  N0              4              216
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V6, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   0
  ICOSLG WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    0
  ICOSLG WILD-TYPE  281   48
   clus
vv  ICOSLG MUTATED ICOSLG WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D547V7, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     1   3
  ICOSLG WILD-TYPE 169 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      1    3
  ICOSLG WILD-TYPE  169  194
        clus
vv       ICOSLG MUTATED ICOSLG WILD-TYPE
  FEMALE              1              169
  MALE                3              194
[1] 2 2
[1] FALSE
D547V8, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   0
  ICOSLG WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    0
  ICOSLG WILD-TYPE  296    8
     clus
vv    ICOSLG MUTATED ICOSLG WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D547V9, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   0
  ICOSLG WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    0
  ICOSLG WILD-TYPE  310   48
                               clus
vv                              ICOSLG MUTATED ICOSLG WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ICOSLG MUTATED     3   0   0   1
  ICOSLG WILD-TYPE 256   3  22  20
D547V10, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              1               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"
D547V11, continuous
[1] "Remove cluster labels:" "ICOSLG MUTATED"        
clus
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               2              344 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527       TCGA-AA-3530 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AD-6964       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-DM-A285 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3655       TCGA-AA-3660 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3977       TCGA-AA-3980 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3982       TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AZ-6607       TCGA-CA-6715       TCGA-CK-4947       TCGA-CK-4948 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806       TCGA-F4-6807 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ICOSLG MUTATED                                  0     1
  ICOSLG WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ICOSLG MUTATED                           0     3
  ICOSLG WILD-TYPE                        19   173
D547V12, multiclass
                                  clus
vv                                 ICOSLG MUTATED ICOSLG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ARNT2 MUTATION ANALYSIS
D548V1, survival
                 sevent
clus2               0   1
  ARNT2 MUTATED     8   3
  ARNT2 WILD-TYPE 269  75
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             11             344 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
              3              75 
$`ARNT2 MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-A00E TCGA-AA-A00J 
      100.01        26.17         6.97        10.06        30.02        18.05 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-6928 TCGA-G4-6299 TCGA-G4-6303 
       88.21        12.76        11.64        74.56        65.85 

$`ARNT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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          22.045 
[1] "7.0 - 100.0 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D548V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARNT2 MUTATED         1        0        2         5         0         0
  ARNT2 WILD-TYPE      63        1       24       103         8         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        17          6         43         32       34        12
                 vv
clus              STAGE IVB
  ARNT2 MUTATED           0
  ARNT2 WILD-TYPE         1
D548V3, multiclass
            clus
vv           ARNT2 MUTATED ARNT2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  ARNT2 MUTATED     1   0  10   1
  ARNT2 WILD-TYPE   8  67 239  40
D548V4, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  T1             1               8
  T2             0              67
  T3            10             239
  T4             1              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
  ARNT2 MUTATED     8   2   2
  ARNT2 WILD-TYPE 212  79  64
D548V5, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V6, binary
                 cls
clus                0   1
  ARNT2 MUTATED    11   1
  ARNT2 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED     11    1
  ARNT2 WILD-TYPE  274   47
   clus
vv  ARNT2 MUTATED ARNT2 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D548V7, binary
                 cls
clus                0   1
  ARNT2 MUTATED     5   7
  ARNT2 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED      5    7
  ARNT2 WILD-TYPE  165  190
        clus
vv       ARNT2 MUTATED ARNT2 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D548V8, binary
                 cls
clus                0   1
  ARNT2 MUTATED    11   0
  ARNT2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED     11    0
  ARNT2 WILD-TYPE  289    8
     clus
vv    ARNT2 MUTATED ARNT2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D548V9, binary
                 cls
clus                0   1
  ARNT2 MUTATED     9   3
  ARNT2 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED      9    3
  ARNT2 WILD-TYPE  305   45
                               clus
vv                              ARNT2 MUTATED ARNT2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ARNT2 MUTATED     9   0   0   1
  ARNT2 WILD-TYPE 250   3  22  20
D548V10, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D548V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARNT2 MUTATED                                  0     1
  ARNT2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARNT2 MUTATED                           0     6
  ARNT2 WILD-TYPE                        19   170
D548V12, multiclass
                                  clus
vv                                 ARNT2 MUTATED ARNT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = MRE11A MUTATION ANALYSIS
D549V1, survival
                  sevent
clus2                0   1
  MRE11A MUTATED     9   2
  MRE11A WILD-TYPE 268  76
  MRE11A MUTATED MRE11A WILD-TYPE 
              11              344 
  MRE11A MUTATED MRE11A WILD-TYPE 
               2               76 
$`MRE11A MUTATED`
TCGA-G4-6588 TCGA-A6-6141 TCGA-AA-A00N TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 
       26.17         8.38         4.01        12.76        23.05        15.02 
TCGA-CM-6161 TCGA-CM-6677 TCGA-D5-6534 TCGA-DM-A0XD TCGA-F4-6856 
       15.02        11.08        43.27        24.43        35.31 

$`MRE11A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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           22.075 
[1] "4.0 - 43.3 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D549V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRE11A MUTATED         2        0        0         8         2         0
  MRE11A WILD-TYPE      62        1       26       100         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRE11A MUTATED           0          0          0          0        0
  MRE11A WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MRE11A MUTATED           0         0
  MRE11A WILD-TYPE        12         1
D549V3, multiclass
            clus
vv           MRE11A MUTATED MRE11A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               8              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MRE11A MUTATED     0   2   8   2
  MRE11A WILD-TYPE   9  65 241  39
D549V4, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  T1              0                9
  T2              2               65
  T3              8              241
  T4              2               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
  MRE11A MUTATED    12   0   0
  MRE11A WILD-TYPE 208  81  66
D549V5, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  N0             12              208
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V6, binary
                  cls
clus                 0   1
  MRE11A MUTATED    11   0
  MRE11A WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED     11    0
  MRE11A WILD-TYPE  274   48
   clus
vv  MRE11A MUTATED MRE11A WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D549V7, binary
                  cls
clus                 0   1
  MRE11A MUTATED     6   6
  MRE11A WILD-TYPE 164 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      6    6
  MRE11A WILD-TYPE  164  191
        clus
vv       MRE11A MUTATED MRE11A WILD-TYPE
  FEMALE              6              164
  MALE                6              191
[1] 2 2
[1] FALSE
D549V8, binary
                  cls
clus                 0   1
  MRE11A MUTATED     9   0
  MRE11A WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      9    0
  MRE11A WILD-TYPE  291    8
     clus
vv    MRE11A MUTATED MRE11A WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D549V9, binary
                  cls
clus                 0   1
  MRE11A MUTATED     8   4
  MRE11A WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      8    4
  MRE11A WILD-TYPE  306   44
                               clus
vv                              MRE11A MUTATED MRE11A WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MRE11A MUTATED     8   0   0   2
  MRE11A WILD-TYPE 251   3  22  19
D549V10, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              2               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"
D549V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRE11A MUTATED                                  0     1
  MRE11A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRE11A MUTATED                           1     9
  MRE11A WILD-TYPE                        18   167
D549V12, multiclass
                                  clus
vv                                 MRE11A MUTATED MRE11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(550) Variable = DUSP1 MUTATION ANALYSIS
D550V1, survival
                 sevent
clus2               0   1
  DUSP1 MUTATED     6   0
  DUSP1 WILD-TYPE 271  78
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              6             349 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              0              78 
$`DUSP1 MUTATED`
TCGA-G4-6628 TCGA-A6-5657 TCGA-AA-3514 TCGA-AA-3655 TCGA-AA-3660 TCGA-CA-5796 
       79.69        31.63         1.02        61.02        78.08        12.39 

$`DUSP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DUSP1 MUTATED DUSP1 WILD-TYPE 
           1.02            0.00 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
          79.69          148.01 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
         46.325          22.030 
[1] "1.0 - 79.7 (46.3)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9500000"
D550V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP1 MUTATED         2        0        2         1         0         0
  DUSP1 WILD-TYPE      62        1       24       107         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  DUSP1 MUTATED           0
  DUSP1 WILD-TYPE         1
D550V3, multiclass
            clus
vv           DUSP1 MUTATED DUSP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DUSP1 MUTATED     0   2   4   0
  DUSP1 WILD-TYPE   9  65 245  41
D550V4, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             0              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
  DUSP1 MUTATED     5   1   0
  DUSP1 WILD-TYPE 215  80  66
D550V5, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V6, binary
                 cls
clus                0   1
  DUSP1 MUTATED     6   0
  DUSP1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      6    0
  DUSP1 WILD-TYPE  279   48
   clus
vv  DUSP1 MUTATED DUSP1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D550V7, binary
                 cls
clus                0   1
  DUSP1 MUTATED     3   3
  DUSP1 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      3    3
  DUSP1 WILD-TYPE  167  194
        clus
vv       DUSP1 MUTATED DUSP1 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D550V8, binary
                 cls
clus                0   1
  DUSP1 MUTATED     6   0
  DUSP1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      6    0
  DUSP1 WILD-TYPE  294    8
     clus
vv    DUSP1 MUTATED DUSP1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D550V9, binary
                 cls
clus                0   1
  DUSP1 MUTATED     5   1
  DUSP1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      5    1
  DUSP1 WILD-TYPE  309   47
                               clus
vv                              DUSP1 MUTATED DUSP1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DUSP1 MUTATED     6   0   0   0
  DUSP1 WILD-TYPE 253   3  22  21
D550V10, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D550V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP1 MUTATED                                  0     1
  DUSP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DUSP1 MUTATED                           1     1
  DUSP1 WILD-TYPE                        18   175
D550V12, multiclass
                                  clus
vv                                 DUSP1 MUTATED DUSP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        1             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(551) Variable = ERGIC1 MUTATION ANALYSIS
D551V1, survival
                  sevent
clus2                0   1
  ERGIC1 MUTATED     4   0
  ERGIC1 WILD-TYPE 273  78
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               4              351 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               0               78 
$`ERGIC1 MUTATED`
TCGA-A6-5660 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-6541 
       29.19        13.05        11.08        15.58 

$`ERGIC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        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-6678 
       15.02        14.04        11.01        12.95        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
           11.08             0.00 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
           29.19           148.01 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
          14.315           22.090 
[1] "11.1 - 29.2 (14.3)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D551V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERGIC1 MUTATED         0        0        0         2         0         0
  ERGIC1 WILD-TYPE      64        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERGIC1 MUTATED           0          0          0          1        0
  ERGIC1 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ERGIC1 MUTATED           0         1
  ERGIC1 WILD-TYPE        12         0
D551V3, multiclass
            clus
vv           ERGIC1 MUTATED ERGIC1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               12
  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   4   0
  ERGIC1 WILD-TYPE   9  67 245  41
D551V4, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              0               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
  ERGIC1 MUTATED     2   0   2
  ERGIC1 WILD-TYPE 218  81  64
D551V5, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  N0              2              218
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V6, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     3   1
  ERGIC1 WILD-TYPE 282  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      3    1
  ERGIC1 WILD-TYPE  282   47
   clus
vv  ERGIC1 MUTATED ERGIC1 WILD-TYPE
  0              3              282
  1              1               47
[1] 2 2
[1] FALSE
D551V7, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     1   3
  ERGIC1 WILD-TYPE 169 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      1    3
  ERGIC1 WILD-TYPE  169  194
        clus
vv       ERGIC1 MUTATED ERGIC1 WILD-TYPE
  FEMALE              1              169
  MALE                3              194
[1] 2 2
[1] FALSE
D551V8, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     4   0
  ERGIC1 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      4    0
  ERGIC1 WILD-TYPE  296    8
     clus
vv    ERGIC1 MUTATED ERGIC1 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D551V9, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     4   0
  ERGIC1 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      4    0
  ERGIC1 WILD-TYPE  310   48
                               clus
vv                              ERGIC1 MUTATED ERGIC1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ERGIC1 MUTATED     3   0   0   0
  ERGIC1 WILD-TYPE 256   3  22  21
D551V10, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D551V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERGIC1 MUTATED                                  0     0
  ERGIC1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ERGIC1 MUTATED                           2     2
  ERGIC1 WILD-TYPE                        17   174
D551V12, multiclass
                                  clus
vv                                 ERGIC1 MUTATED ERGIC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         2              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(552) Variable = SYNRG MUTATION ANALYSIS
D552V1, survival
                 sevent
clus2               0   1
  SYNRG MUTATED    13   3
  SYNRG WILD-TYPE 264  75
  SYNRG MUTATED SYNRG WILD-TYPE 
             16             339 
  SYNRG MUTATED SYNRG WILD-TYPE 
              3              75 
$`SYNRG MUTATED`
TCGA-AA-3525 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3864 
        8.05        24.00       100.01        79.69        19.66        53.00 
TCGA-AA-3949 TCGA-AA-A00J TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-6751 
       26.01        18.05        27.09        49.41        12.76       124.27 
TCGA-CM-4752 TCGA-D5-6539 TCGA-DM-A1D6 TCGA-DM-A1D9 
       13.02        12.49        49.91       140.38 

$`SYNRG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
        2.01        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        13.32        12.59         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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SYNRG MUTATED SYNRG WILD-TYPE 
           8.05            0.00 
  SYNRG MUTATED SYNRG WILD-TYPE 
         140.38          148.01 
  SYNRG MUTATED SYNRG WILD-TYPE 
          26.55           21.99 
[1] "8.1 - 140.4 (26.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D552V2, continuous
                 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      61        1       23       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNRG MUTATED           0          0          3          1        0         0
  SYNRG WILD-TYPE        18          6         41         32       35        12
                 vv
clus              STAGE IVB
  SYNRG MUTATED           0
  SYNRG WILD-TYPE         1
D552V3, multiclass
            clus
vv           SYNRG MUTATED SYNRG WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  SYNRG MUTATED     0   3  11   2
  SYNRG WILD-TYPE   9  64 238  39
D552V4, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  T1             0               9
  T2             3              64
  T3            11             238
  T4             2              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
  SYNRG MUTATED    12   4   0
  SYNRG WILD-TYPE 208  77  66
D552V5, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  N0            12             208
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V6, binary
                 cls
clus                0   1
  SYNRG MUTATED    13   0
  SYNRG WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED     13    0
  SYNRG WILD-TYPE  272   48
   clus
vv  SYNRG MUTATED SYNRG WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D552V7, binary
                 cls
clus                0   1
  SYNRG MUTATED     7   9
  SYNRG WILD-TYPE 163 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED      7    9
  SYNRG WILD-TYPE  163  188
        clus
vv       SYNRG MUTATED SYNRG WILD-TYPE
  FEMALE             7             163
  MALE               9             188
[1] 2 2
[1] FALSE
D552V8, binary
                 cls
clus                0   1
  SYNRG MUTATED    13   0
  SYNRG WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED     13    0
  SYNRG WILD-TYPE  287    8
     clus
vv    SYNRG MUTATED SYNRG WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D552V9, binary
                 cls
clus                0   1
  SYNRG MUTATED     9   7
  SYNRG WILD-TYPE 305  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED      9    7
  SYNRG WILD-TYPE  305   41
                               clus
vv                              SYNRG MUTATED SYNRG WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNRG MUTATED    10   0   0   2
  SYNRG WILD-TYPE 249   3  22  19
D552V10, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D552V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNRG MUTATED                                  0     1
  SYNRG WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYNRG MUTATED                           1     9
  SYNRG WILD-TYPE                        18   167
D552V12, multiclass
                                  clus
vv                                 SYNRG MUTATED SYNRG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(553) Variable = BACE2 MUTATION ANALYSIS
D553V1, survival
                 sevent
clus2               0   1
  BACE2 MUTATED    10   0
  BACE2 WILD-TYPE 267  78
  BACE2 MUTATED BACE2 WILD-TYPE 
             10             345 
  BACE2 MUTATED BACE2 WILD-TYPE 
              0              78 
$`BACE2 MUTATED`
TCGA-AD-6895 TCGA-A6-2672 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3994 TCGA-AA-A010 
       25.08        46.65        25.18        21.76        27.02        34.98 
TCGA-AY-6386 TCGA-CK-4952 TCGA-CM-6679 TCGA-G4-6309 
       17.82        15.62        10.06        85.48 

$`BACE2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        25.08        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  BACE2 MUTATED BACE2 WILD-TYPE 
          10.06            0.00 
  BACE2 MUTATED BACE2 WILD-TYPE 
          85.48          148.01 
  BACE2 MUTATED BACE2 WILD-TYPE 
          25.13           22.03 
[1] "10.1 - 85.5 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.5e+07"
D553V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BACE2 MUTATED         0        0        0         1         1         0
  BACE2 WILD-TYPE      64        1       26       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BACE2 MUTATED           0          0          6          1        0         1
  BACE2 WILD-TYPE        18          6         38         32       35        11
                 vv
clus              STAGE IVB
  BACE2 MUTATED           0
  BACE2 WILD-TYPE         1
D553V3, multiclass
            clus
vv           BACE2 MUTATED BACE2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  BACE2 MUTATED     0   0   8   2
  BACE2 WILD-TYPE   9  67 241  39
D553V4, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             8             241
  T4             2              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
  BACE2 MUTATED     3   6   1
  BACE2 WILD-TYPE 217  75  65
D553V5, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  N0             3             217
  N1             6              75
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V6, binary
                 cls
clus                0   1
  BACE2 MUTATED     8   1
  BACE2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      8    1
  BACE2 WILD-TYPE  277   47
   clus
vv  BACE2 MUTATED BACE2 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D553V7, binary
                 cls
clus                0   1
  BACE2 MUTATED     6   4
  BACE2 WILD-TYPE 164 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      6    4
  BACE2 WILD-TYPE  164  193
        clus
vv       BACE2 MUTATED BACE2 WILD-TYPE
  FEMALE             6             164
  MALE               4             193
[1] 2 2
[1] FALSE
D553V8, binary
                 cls
clus                0   1
  BACE2 MUTATED     9   0
  BACE2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      9    0
  BACE2 WILD-TYPE  291    8
     clus
vv    BACE2 MUTATED BACE2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D553V9, binary
                 cls
clus                0   1
  BACE2 MUTATED     8   2
  BACE2 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      8    2
  BACE2 WILD-TYPE  306   46
                               clus
vv                              BACE2 MUTATED BACE2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BACE2 MUTATED     7   0   0   1
  BACE2 WILD-TYPE 252   3  22  20
D553V10, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D553V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BACE2 MUTATED                                  0     0
  BACE2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BACE2 MUTATED                           2     6
  BACE2 WILD-TYPE                        17   170
D553V12, multiclass
                                  clus
vv                                 BACE2 MUTATED BACE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        6             170
[1] 4 2
[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 = LMTK3 MUTATION ANALYSIS
D554V1, survival
                 sevent
clus2               0   1
  LMTK3 MUTATED     9   6
  LMTK3 WILD-TYPE 268  72
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             15             340 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              6              72 
$`LMTK3 MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-6598 TCGA-CA-6716 
      100.01        79.69        83.24         5.79        49.41        12.20 
TCGA-CA-6717 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6930 
       12.76        12.99        14.04        15.12         4.80        13.35 
TCGA-F4-6459 TCGA-F4-6856 TCGA-G4-6304 
        8.61        35.31        53.62 

$`LMTK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       12.16        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        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        25.48        43.27        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  LMTK3 MUTATED LMTK3 WILD-TYPE 
            4.8             0.0 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
         100.01          148.01 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
          14.04           22.09 
[1] "4.8 - 100.0 (14.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D554V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LMTK3 MUTATED         3        0        2         5         1         0
  LMTK3 WILD-TYPE      61        1       24       103         7         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        18          6         41         32       35        12
                 vv
clus              STAGE IVB
  LMTK3 MUTATED           0
  LMTK3 WILD-TYPE         1
D554V3, multiclass
            clus
vv           LMTK3 MUTATED LMTK3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  LMTK3 MUTATED     0   3  10   2
  LMTK3 WILD-TYPE   9  64 239  39
D554V4, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             2              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
  LMTK3 MUTATED    11   2   2
  LMTK3 WILD-TYPE 209  79  64
D554V5, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V6, binary
                 cls
clus                0   1
  LMTK3 MUTATED    11   0
  LMTK3 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     11    0
  LMTK3 WILD-TYPE  274   48
   clus
vv  LMTK3 MUTATED LMTK3 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D554V7, binary
                 cls
clus                0   1
  LMTK3 MUTATED     6   9
  LMTK3 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      6    9
  LMTK3 WILD-TYPE  164  188
        clus
vv       LMTK3 MUTATED LMTK3 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D554V8, binary
                 cls
clus                0   1
  LMTK3 MUTATED    15   0
  LMTK3 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     15    0
  LMTK3 WILD-TYPE  285    8
     clus
vv    LMTK3 MUTATED LMTK3 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D554V9, binary
                 cls
clus                0   1
  LMTK3 MUTATED    11   4
  LMTK3 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     11    4
  LMTK3 WILD-TYPE  303   44
                               clus
vv                              LMTK3 MUTATED LMTK3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMTK3 MUTATED     9   0   0   3
  LMTK3 WILD-TYPE 250   3  22  18
D554V10, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             3              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"
D554V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LMTK3 MUTATED                                  0     3
  LMTK3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LMTK3 MUTATED                           1    11
  LMTK3 WILD-TYPE                        18   165
D554V12, multiclass
                                  clus
vv                                 LMTK3 MUTATED LMTK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(555) Variable = RTP3 MUTATION ANALYSIS
D555V1, survival
                sevent
clus2              0   1
  RTP3 MUTATED     2   3
  RTP3 WILD-TYPE 275  75
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            350 
  RTP3 MUTATED RTP3 WILD-TYPE 
             3             75 
$`RTP3 MUTATED`
TCGA-AZ-6608 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CK-4948 TCGA-D5-6532 
        1.94        49.41        29.56       148.01        18.25 

$`RTP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RTP3 MUTATED RTP3 WILD-TYPE 
          1.94           0.00 
  RTP3 MUTATED RTP3 WILD-TYPE 
        148.01         140.38 
  RTP3 MUTATED RTP3 WILD-TYPE 
        29.560         22.045 
[1] "1.9 - 148.0 (29.6)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.9"
D555V2, continuous
                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      64        1       25       107         8         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        17          5         44         33       35        12
                vv
clus             STAGE IVB
  RTP3 MUTATED           0
  RTP3 WILD-TYPE         1
D555V3, multiclass
            clus
vv           RTP3 MUTATED RTP3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RTP3 MUTATED     0   2   3   0
  RTP3 WILD-TYPE   9  65 246  41
D555V4, multiclass
    clus
vv   RTP3 MUTATED RTP3 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            3            246
  T4            0             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
  RTP3 MUTATED     2   3   0
  RTP3 WILD-TYPE 218  78  66
D555V5, multiclass
    clus
vv   RTP3 MUTATED RTP3 WILD-TYPE
  N0            2            218
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V6, binary
                cls
clus               0   1
  RTP3 MUTATED     3   0
  RTP3 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      3    0
  RTP3 WILD-TYPE  282   48
   clus
vv  RTP3 MUTATED RTP3 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D555V7, binary
                cls
clus               0   1
  RTP3 MUTATED     4   1
  RTP3 WILD-TYPE 166 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      4    1
  RTP3 WILD-TYPE  166  196
        clus
vv       RTP3 MUTATED RTP3 WILD-TYPE
  FEMALE            4            166
  MALE              1            196
[1] 2 2
[1] FALSE
D555V8, binary
                cls
clus               0   1
  RTP3 MUTATED     5   0
  RTP3 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      5    0
  RTP3 WILD-TYPE  295    8
     clus
vv    RTP3 MUTATED RTP3 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D555V9, binary
                cls
clus               0   1
  RTP3 MUTATED     5   0
  RTP3 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      5    0
  RTP3 WILD-TYPE  309   48
                               clus
vv                              RTP3 MUTATED RTP3 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RTP3 MUTATED     2   0   0   0
  RTP3 WILD-TYPE 257   3  22  21
D555V10, multiclass
[1] "Remove cluster labels:" "RTP3 MUTATED"          
clus
  RTP3 MUTATED RTP3 WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     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-3527 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-2676     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-3502     TCGA-AA-3510 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660 
"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-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     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-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3975     TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00W     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-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4682 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4950     TCGA-CK-4952 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
D555V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RTP3 MUTATED                                  0     0
  RTP3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RTP3 MUTATED                           0     5
  RTP3 WILD-TYPE                        19   171
D555V12, multiclass
                                  clus
vv                                 RTP3 MUTATED RTP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = BCL9L MUTATION ANALYSIS
D556V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    17   2
  BCL9L WILD-TYPE 260  76
  BCL9L MUTATED BCL9L WILD-TYPE 
             19             336 
  BCL9L MUTATED BCL9L WILD-TYPE 
              2              76 
$`BCL9L MUTATED`
TCGA-AA-3713 TCGA-AA-3870 TCGA-AA-3972 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       19.04        29.98        50.99        25.08        10.88       100.01 
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3866 TCGA-AA-A01R TCGA-AD-6890 
       19.66         6.97        15.95        17.03        35.01        24.53 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CM-6161 TCGA-D5-6536 TCGA-DM-A1HB TCGA-F4-6856 
       27.09        58.39        15.02        17.85       135.65        35.31 
TCGA-G4-6304 
       53.62 

$`BCL9L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 
       31.07        24.03        12.99        24.00         2.01        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       15.52       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        83.24         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  BCL9L MUTATED BCL9L WILD-TYPE 
           6.97            0.00 
  BCL9L MUTATED BCL9L WILD-TYPE 
         135.65          148.01 
  BCL9L MUTATED BCL9L WILD-TYPE 
          25.08           22.01 
[1] "7.0 - 135.7 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.8"
D556V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCL9L MUTATED         4        0        2         3         1         0
  BCL9L WILD-TYPE      60        1       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9L MUTATED           1          0          2          1        3         0
  BCL9L WILD-TYPE        17          6         42         32       32        12
                 vv
clus              STAGE IVB
  BCL9L MUTATED           0
  BCL9L WILD-TYPE         1
D556V3, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              0              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
  BCL9L MUTATED     1   4  11   3
  BCL9L WILD-TYPE   8  63 238  38
D556V4, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  T1             1               8
  T2             4              63
  T3            11             238
  T4             3              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
  BCL9L MUTATED    12   4   3
  BCL9L WILD-TYPE 208  77  63
D556V5, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  N0            12             208
  N1             4              77
  N2             3              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"
D556V6, binary
                 cls
clus                0   1
  BCL9L MUTATED    13   3
  BCL9L WILD-TYPE 272  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     13    3
  BCL9L WILD-TYPE  272   45
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0            13             272
  1             3              45
[1] 2 2
[1] FALSE
D556V7, binary
                 cls
clus                0   1
  BCL9L MUTATED     6  13
  BCL9L WILD-TYPE 164 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      6   13
  BCL9L WILD-TYPE  164  184
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             6             164
  MALE              13             184
[1] 2 2
[1] FALSE
D556V8, binary
                 cls
clus                0   1
  BCL9L MUTATED    14   2
  BCL9L WILD-TYPE 286   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     14    2
  BCL9L WILD-TYPE  286    6
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO             14             286
  YES             2               6
[1] 2 2
[1] FALSE
D556V9, binary
                 cls
clus                0   1
  BCL9L MUTATED    15   3
  BCL9L WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     15    3
  BCL9L WILD-TYPE  299   45
                               clus
vv                              BCL9L MUTATED BCL9L WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BCL9L MUTATED    13   0   2   0
  BCL9L WILD-TYPE 246   3  20  21
D556V10, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0            13             246
  R1             0               3
  R2             2              20
  RX             0              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"
D556V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL9L MUTATED                                  0     0
  BCL9L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BCL9L MUTATED                           0    12
  BCL9L WILD-TYPE                        19   164
D556V12, multiclass
                                  clus
vv                                 BCL9L MUTATED BCL9L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = AKAP9 MUTATION ANALYSIS
D557V1, survival
                 sevent
clus2               0   1
  AKAP9 MUTATED    30  11
  AKAP9 WILD-TYPE 247  67
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             41             314 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             11              67 
$`AKAP9 MUTATED`
TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6964 
        0.99         0.92        85.05        19.04        19.04        10.88 
TCGA-AZ-6601 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-5661 
      100.01        63.62        26.17        79.69        42.90        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6142 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3532 
       22.06        22.52        25.08         3.02        63.98        29.00 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
       29.95        78.08        26.99        53.00        31.00        33.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6600 
        4.01        34.98        21.44        58.39         6.77        12.10 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5861 
       12.20        12.76        10.06        17.56        23.05        15.02 
TCGA-D5-6534 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB TCGA-F4-6570 
       43.27        12.43         9.04        44.32         6.18 

$`AKAP9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       36.00        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      106.75         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        43.76        46.65        43.76        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-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        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-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       24.00        20.98        13.94        61.02         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       17.03        27.02        18.05         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        12.59        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  AKAP9 MUTATED AKAP9 WILD-TYPE 
           0.92            0.00 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
         100.01          148.01 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
          23.05           21.99 
[1] "0.9 - 100.0 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D557V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP9 MUTATED         6        0        7        17         4         0
  AKAP9 WILD-TYPE      58        1       19        91         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP9 MUTATED           1          0          3          0        3         1
  AKAP9 WILD-TYPE        17          6         41         33       32        11
                 vv
clus              STAGE IVB
  AKAP9 MUTATED           0
  AKAP9 WILD-TYPE         1
D557V3, multiclass
            clus
vv           AKAP9 MUTATED AKAP9 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               7              19
  STAGE IIA             17              91
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              1              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
  AKAP9 MUTATED     1   5  28   9
  AKAP9 WILD-TYPE   8  62 221  32
D557V4, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  T1             1               8
  T2             5              62
  T3            28             221
  T4             9              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
  AKAP9 MUTATED    35   6   2
  AKAP9 WILD-TYPE 185  75  64
D557V5, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  N0            35             185
  N1             6              75
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V6, binary
                 cls
clus                0   1
  AKAP9 MUTATED    36   4
  AKAP9 WILD-TYPE 249  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     36    4
  AKAP9 WILD-TYPE  249   44
   clus
vv  AKAP9 MUTATED AKAP9 WILD-TYPE
  0            36             249
  1             4              44
[1] 2 2
[1] FALSE
D557V7, binary
                 cls
clus                0   1
  AKAP9 MUTATED    19  24
  AKAP9 WILD-TYPE 151 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     19   24
  AKAP9 WILD-TYPE  151  173
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  FEMALE            19             151
  MALE              24             173
[1] 2 2
[1] FALSE
D557V8, binary
                 cls
clus                0   1
  AKAP9 MUTATED    36   3
  AKAP9 WILD-TYPE 264   5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     36    3
  AKAP9 WILD-TYPE  264    5
     clus
vv    AKAP9 MUTATED AKAP9 WILD-TYPE
  NO             36             264
  YES             3               5
[1] 2 2
[1] FALSE
D557V9, binary
                 cls
clus                0   1
  AKAP9 MUTATED    35   8
  AKAP9 WILD-TYPE 279  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     35    8
  AKAP9 WILD-TYPE  279   40
                               clus
vv                              AKAP9 MUTATED AKAP9 WILD-TYPE
  COLON ADENOCARCINOMA                     35             279
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AKAP9 MUTATED    30   0   2   4
  AKAP9 WILD-TYPE 229   3  20  17
D557V10, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  R0            30             229
  R1             0               3
  R2             2              20
  RX             4              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"
D557V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP9 MUTATED                                  0     3
  AKAP9 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP9 MUTATED                           2    20
  AKAP9 WILD-TYPE                        17   156
D557V12, multiclass
                                  clus
vv                                 AKAP9 MUTATED AKAP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       20             156
[1] 4 2
[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 = ZNF547 MUTATION ANALYSIS
D558V1, survival
                  sevent
clus2                0   1
  ZNF547 MUTATED     7   1
  ZNF547 WILD-TYPE 270  77
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               8              347 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               1               77 
$`ZNF547 MUTATED`
TCGA-AA-3697 TCGA-AZ-6608 TCGA-G4-6588 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-4744 
       85.05         1.94        26.17        27.09        12.76        20.02 
TCGA-CM-6168 TCGA-DM-A1D9 
       12.99       140.38 

$`ZNF547 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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-6169 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF547 MUTATED ZNF547 WILD-TYPE 
            1.94             0.00 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
          140.38           148.01 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
          23.095           22.060 
[1] "1.9 - 140.4 (23.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D558V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF547 MUTATED         2        0        1         4         0         0
  ZNF547 WILD-TYPE      62        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF547 MUTATED           0          1          0          0        0
  ZNF547 WILD-TYPE        18          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF547 MUTATED           0         0
  ZNF547 WILD-TYPE        12         1
D558V3, multiclass
            clus
vv           ZNF547 MUTATED ZNF547 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF547 MUTATED     0   3   5   0
  ZNF547 WILD-TYPE   9  64 244  41
D558V4, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              0               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
  ZNF547 MUTATED     7   1   0
  ZNF547 WILD-TYPE 213  80  66
D558V5, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V6, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     8   0
  ZNF547 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      8    0
  ZNF547 WILD-TYPE  277   48
   clus
vv  ZNF547 MUTATED ZNF547 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D558V7, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     5   3
  ZNF547 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      5    3
  ZNF547 WILD-TYPE  165  194
        clus
vv       ZNF547 MUTATED ZNF547 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D558V8, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     6   0
  ZNF547 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      6    0
  ZNF547 WILD-TYPE  294    8
     clus
vv    ZNF547 MUTATED ZNF547 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D558V9, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     7   1
  ZNF547 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      7    1
  ZNF547 WILD-TYPE  307   47
                               clus
vv                              ZNF547 MUTATED ZNF547 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF547 MUTATED     5   0   0   1
  ZNF547 WILD-TYPE 254   3  22  20
D558V10, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D558V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF547 MUTATED                                  0     1
  ZNF547 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF547 MUTATED                           1     5
  ZNF547 WILD-TYPE                        18   171
D558V12, multiclass
                                  clus
vv                                 ZNF547 MUTATED ZNF547 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = MRAS MUTATION ANALYSIS
D559V1, survival
                sevent
clus2              0   1
  MRAS MUTATED     3   1
  MRAS WILD-TYPE 274  77
  MRAS MUTATED MRAS WILD-TYPE 
             4            351 
  MRAS MUTATED MRAS WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         22.060 
[1] "15.0 - 135.7 (32.5)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.4"
D559V2, continuous
                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      63        1       26       108         7         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        18          6         42         33       35        12
                vv
clus             STAGE IVB
  MRAS MUTATED           0
  MRAS WILD-TYPE         1
D559V3, multiclass
            clus
vv           MRAS MUTATED MRAS WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             0            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MRAS MUTATED     0   1   2   1
  MRAS WILD-TYPE   9  66 247  40
D559V4, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            1             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
  MRAS MUTATED     2   2   0
  MRAS WILD-TYPE 218  79  66
D559V5, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  N0            2            218
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V6, binary
                cls
clus               0   1
  MRAS MUTATED     4   0
  MRAS WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      4    0
  MRAS WILD-TYPE  281   48
   clus
vv  MRAS MUTATED MRAS WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D559V7, binary
                cls
clus               0   1
  MRAS MUTATED     3   1
  MRAS WILD-TYPE 167 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      3    1
  MRAS WILD-TYPE  167  196
        clus
vv       MRAS MUTATED MRAS WILD-TYPE
  FEMALE            3            167
  MALE              1            196
[1] 2 2
[1] FALSE
D559V8, binary
                cls
clus               0   1
  MRAS MUTATED     3   0
  MRAS WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      3    0
  MRAS WILD-TYPE  297    8
     clus
vv    MRAS MUTATED MRAS WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D559V9, binary
                cls
clus               0   1
  MRAS MUTATED     3   0
  MRAS WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      3    0
  MRAS WILD-TYPE  311   48
                               clus
vv                              MRAS MUTATED MRAS WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MRAS MUTATED     3   0   0   0
  MRAS WILD-TYPE 256   3  22  21
D559V10, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D559V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRAS MUTATED                                  0     0
  MRAS WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MRAS MUTATED                           0     4
  MRAS WILD-TYPE                        19   172
D559V12, multiclass
                                  clus
vv                                 MRAS MUTATED MRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = ARFIP1 MUTATION ANALYSIS
D560V1, survival
                  sevent
clus2                0   1
  ARFIP1 MUTATED     9   3
  ARFIP1 WILD-TYPE 268  75
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              343 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
               3               75 
$`ARFIP1 MUTATED`
TCGA-G4-6588 TCGA-A6-5657 TCGA-AA-3518 TCGA-AA-3558 TCGA-AA-3975 TCGA-AA-A00N 
       26.17        31.63         1.02        20.98        34.06         4.01 
TCGA-AA-A01P TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       38.07        17.82        58.39        12.76        10.06        23.05 

$`ARFIP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        29.95        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.060 
[1] "1.0 - 58.4 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D560V2, continuous
                  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      62        1       26       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFIP1 MUTATED           1          0          2          0        0
  ARFIP1 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ARFIP1 MUTATED           0         0
  ARFIP1 WILD-TYPE        12         1
D560V3, multiclass
            clus
vv           ARFIP1 MUTATED ARFIP1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ARFIP1 MUTATED     0   2   9   1
  ARFIP1 WILD-TYPE   9  65 240  40
D560V4, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              9              240
  T4              1               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
  ARFIP1 MUTATED     9   3   0
  ARFIP1 WILD-TYPE 211  78  66
D560V5, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V6, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    12   0
  ARFIP1 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     12    0
  ARFIP1 WILD-TYPE  273   48
   clus
vv  ARFIP1 MUTATED ARFIP1 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D560V7, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED     4   8
  ARFIP1 WILD-TYPE 166 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED      4    8
  ARFIP1 WILD-TYPE  166  189
        clus
vv       ARFIP1 MUTATED ARFIP1 WILD-TYPE
  FEMALE              4              166
  MALE                8              189
[1] 2 2
[1] FALSE
D560V8, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    10   0
  ARFIP1 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     10    0
  ARFIP1 WILD-TYPE  290    8
     clus
vv    ARFIP1 MUTATED ARFIP1 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D560V9, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    10   2
  ARFIP1 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     10    2
  ARFIP1 WILD-TYPE  304   46
                               clus
vv                              ARFIP1 MUTATED ARFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARFIP1 MUTATED     9   0   1   2
  ARFIP1 WILD-TYPE 250   3  21  19
D560V10, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              2               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"
D560V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARFIP1 MUTATED                                  0     2
  ARFIP1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARFIP1 MUTATED                           2     3
  ARFIP1 WILD-TYPE                        17   173
D560V12, multiclass
                                  clus
vv                                 ARFIP1 MUTATED ARFIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         3              173
[1] 4 2
[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 = CNTFR MUTATION ANALYSIS
D561V1, survival
                 sevent
clus2               0   1
  CNTFR MUTATED     6   3
  CNTFR WILD-TYPE 271  75
  CNTFR MUTATED CNTFR WILD-TYPE 
              9             346 
  CNTFR MUTATED CNTFR WILD-TYPE 
              3              75 
$`CNTFR MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-6780 TCGA-AA-3673 TCGA-AZ-6598 TCGA-CA-6715 
      100.01        35.80        20.12        50.04        49.41        12.59 
TCGA-CA-6717 TCGA-CM-5862 TCGA-F4-6808 
       12.76         5.03        33.67 

$`CNTFR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        3.19        12.69        12.36        12.39        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6626 
       61.91        36.00        13.78        46.75 

  CNTFR MUTATED CNTFR WILD-TYPE 
           5.03            0.00 
  CNTFR MUTATED CNTFR WILD-TYPE 
         100.01          148.01 
  CNTFR MUTATED CNTFR WILD-TYPE 
         33.670          22.045 
[1] "5.0 - 100.0 (33.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D561V2, continuous
                 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      63        1       23       104         8         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        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  CNTFR MUTATED           0
  CNTFR WILD-TYPE         1
D561V3, multiclass
            clus
vv           CNTFR MUTATED CNTFR WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  CNTFR MUTATED     1   0   9   0
  CNTFR WILD-TYPE   8  67 240  41
D561V4, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  T1             1               8
  T2             0              67
  T3             9             240
  T4             0              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
  CNTFR MUTATED     8   2   0
  CNTFR WILD-TYPE 212  79  66
D561V5, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  N0             8             212
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V6, binary
                 cls
clus                0   1
  CNTFR MUTATED     7   1
  CNTFR WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      7    1
  CNTFR WILD-TYPE  278   47
   clus
vv  CNTFR MUTATED CNTFR WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D561V7, binary
                 cls
clus                0   1
  CNTFR MUTATED     5   5
  CNTFR WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      5    5
  CNTFR WILD-TYPE  165  192
        clus
vv       CNTFR MUTATED CNTFR WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D561V8, binary
                 cls
clus                0   1
  CNTFR MUTATED     9   0
  CNTFR WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      9    0
  CNTFR WILD-TYPE  291    8
     clus
vv    CNTFR MUTATED CNTFR WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D561V9, binary
                 cls
clus                0   1
  CNTFR MUTATED     8   2
  CNTFR WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      8    2
  CNTFR WILD-TYPE  306   46
                               clus
vv                              CNTFR MUTATED CNTFR WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CNTFR MUTATED     5   0   0   2
  CNTFR WILD-TYPE 254   3  22  19
D561V10, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D561V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNTFR MUTATED                                  0     2
  CNTFR WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNTFR MUTATED                           0     6
  CNTFR WILD-TYPE                        19   170
D561V12, multiclass
                                  clus
vv                                 CNTFR MUTATED CNTFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = RANBP17 MUTATION ANALYSIS
D562V1, survival
                   sevent
clus2                 0   1
  RANBP17 MUTATED     6   4
  RANBP17 WILD-TYPE 271  74
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               10               345 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
                4                74 
$`RANBP17 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-AA-3696 TCGA-AA-A01Q TCGA-AD-6889 TCGA-CA-6717 
       19.04        26.17         5.03         1.02        83.24        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-6163 TCGA-D5-6924 
       10.06        21.14        14.04        14.30 

$`RANBP17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RANBP17 MUTATED RANBP17 WILD-TYPE 
             1.02              0.00 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
            83.24            148.01 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
            14.17             22.36 
[1] "1.0 - 83.2 (14.2)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.4"
D562V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RANBP17 MUTATED         2        0        1         5         0         0
  RANBP17 WILD-TYPE      62        1       25       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP17 MUTATED           0          0          0          0        2
  RANBP17 WILD-TYPE        18          6         44         33       33
                   vv
clus                STAGE IVA STAGE IVB
  RANBP17 MUTATED           0         0
  RANBP17 WILD-TYPE        12         1
D562V3, multiclass
            clus
vv           RANBP17 MUTATED RANBP17 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  RANBP17 MUTATED     2   0   8   0
  RANBP17 WILD-TYPE   7  67 241  41
D562V4, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  T1               2                 7
  T2               0                67
  T3               8               241
  T4               0                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
  RANBP17 MUTATED     9   1   0
  RANBP17 WILD-TYPE 211  80  66
D562V5, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  N0               9               211
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V6, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     8   2
  RANBP17 WILD-TYPE 277  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      8    2
  RANBP17 WILD-TYPE  277   46
   clus
vv  RANBP17 MUTATED RANBP17 WILD-TYPE
  0               8               277
  1               2                46
[1] 2 2
[1] FALSE
D562V7, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     4   6
  RANBP17 WILD-TYPE 166 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      4    6
  RANBP17 WILD-TYPE  166  191
        clus
vv       RANBP17 MUTATED RANBP17 WILD-TYPE
  FEMALE               4               166
  MALE                 6               191
[1] 2 2
[1] FALSE
D562V8, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     8   1
  RANBP17 WILD-TYPE 292   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      8    1
  RANBP17 WILD-TYPE  292    7
     clus
vv    RANBP17 MUTATED RANBP17 WILD-TYPE
  NO                8               292
  YES               1                 7
[1] 2 2
[1] FALSE
D562V9, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     9   1
  RANBP17 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      9    1
  RANBP17 WILD-TYPE  305   47
                               clus
vv                              RANBP17 MUTATED RANBP17 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RANBP17 MUTATED     5   0   2   3
  RANBP17 WILD-TYPE 254   3  20  18
D562V10, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               2                20
  RX               3                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"
D562V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RANBP17 MUTATED                                  0     3
  RANBP17 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RANBP17 MUTATED                           0     4
  RANBP17 WILD-TYPE                        19   172
D562V12, multiclass
                                  clus
vv                                 RANBP17 MUTATED RANBP17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = ZNF280C MUTATION ANALYSIS
D563V1, survival
                   sevent
clus2                 0   1
  ZNF280C MUTATED     8   1
  ZNF280C WILD-TYPE 269  77
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                9               346 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                1                77 
$`ZNF280C MUTATED`
TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3518 TCGA-AA-3866 TCGA-AZ-4315 
       79.69        22.06        32.71         1.02        17.03        58.39 
TCGA-CM-6168 TCGA-CM-6678 TCGA-F4-6460 
       12.99        11.01        31.96 

$`ZNF280C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        23.61        22.09        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-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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6569 
       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF280C MUTATED ZNF280C WILD-TYPE 
             1.02              0.00 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
            79.69            148.01 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
            22.06             22.06 
[1] "1.0 - 79.7 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D563V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF280C MUTATED         2        0        0         4         0         1
  ZNF280C WILD-TYPE      62        1       26       104         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF280C MUTATED           0          0          1          0        0
  ZNF280C WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF280C MUTATED           1         0
  ZNF280C WILD-TYPE        11         1
D563V3, multiclass
            clus
vv           ZNF280C MUTATED ZNF280C WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  ZNF280C MUTATED     0   2   5   2
  ZNF280C WILD-TYPE   9  65 244  39
D563V4, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               2                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
  ZNF280C MUTATED     7   2   0
  ZNF280C WILD-TYPE 213  79  66
D563V5, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  N0               7               213
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V6, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     8   1
  ZNF280C WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      8    1
  ZNF280C WILD-TYPE  277   47
   clus
vv  ZNF280C MUTATED ZNF280C WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D563V7, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     6   3
  ZNF280C WILD-TYPE 164 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      6    3
  ZNF280C WILD-TYPE  164  194
        clus
vv       ZNF280C MUTATED ZNF280C WILD-TYPE
  FEMALE               6               164
  MALE                 3               194
[1] 2 2
[1] FALSE
D563V8, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     8   0
  ZNF280C WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      8    0
  ZNF280C WILD-TYPE  292    8
     clus
vv    ZNF280C MUTATED ZNF280C WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D563V9, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     9   0
  ZNF280C WILD-TYPE 305  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      9    0
  ZNF280C WILD-TYPE  305   48
                               clus
vv                              ZNF280C MUTATED ZNF280C WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF280C MUTATED     8   0   0   0
  ZNF280C WILD-TYPE 251   3  22  21
D563V10, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               0                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"
D563V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF280C MUTATED                                  0     0
  ZNF280C WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF280C MUTATED                           1     6
  ZNF280C WILD-TYPE                        18   170
D563V12, multiclass
                                  clus
vv                                 ZNF280C MUTATED ZNF280C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[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 = SCN2A MUTATION ANALYSIS
D564V1, survival
                 sevent
clus2               0   1
  SCN2A MUTATED    38   6
  SCN2A WILD-TYPE 239  72
  SCN2A MUTATED SCN2A WILD-TYPE 
             44             311 
  SCN2A MUTATED SCN2A WILD-TYPE 
              6              72 
$`SCN2A MUTATED`
TCGA-AA-3496 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-5656 TCGA-A6-5657 
        1.02        79.69        43.76        42.90        32.91        31.63 
TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3663 
       29.19        27.09         8.38        21.76         3.02         6.97 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       18.05        31.00        33.01        25.02        27.02        38.04 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A02K 
        0.99        34.98         1.02        35.01        37.02        14.01 
TCGA-AD-5900 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.16        14.50        58.39        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6163 
       14.30        17.56        21.99        23.05        15.02        14.04 
TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A28G TCGA-DM-A28K 
       21.99        11.08        16.14        13.35        60.79        98.24 
TCGA-G4-6306 TCGA-G4-6315 
       44.68        61.91 

$`SCN2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       35.80        26.17        91.79        46.65        43.76        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5659 
       16.57        34.65        33.34        32.75        36.53        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        27.02        27.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
        7.96        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 
       38.07         1.02        33.04         1.02        26.01        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       12.59        12.59       148.01        85.45        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-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-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  SCN2A MUTATED SCN2A WILD-TYPE 
           0.99            0.00 
  SCN2A MUTATED SCN2A WILD-TYPE 
          98.24          148.01 
  SCN2A MUTATED SCN2A WILD-TYPE 
          21.99           22.09 
[1] "1.0 - 98.2 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D564V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN2A MUTATED        10        0        5        13         4         0
  SCN2A WILD-TYPE      54        1       21        95         4         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        17          6         38         32       32        12
                 vv
clus              STAGE IVB
  SCN2A MUTATED           0
  SCN2A WILD-TYPE         1
D564V3, multiclass
            clus
vv           SCN2A MUTATED SCN2A WILD-TYPE
  STAGE I               10              54
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             13              95
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              0              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
  SCN2A MUTATED     3   9  27   6
  SCN2A WILD-TYPE   6  58 222  35
D564V4, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  T1             3               6
  T2             9              58
  T3            27             222
  T4             6              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
  SCN2A MUTATED    34   7   4
  SCN2A WILD-TYPE 186  74  62
D564V5, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  N0            34             186
  N1             7              74
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V6, binary
                 cls
clus                0   1
  SCN2A MUTATED    37   3
  SCN2A WILD-TYPE 248  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     37    3
  SCN2A WILD-TYPE  248   45
   clus
vv  SCN2A MUTATED SCN2A WILD-TYPE
  0            37             248
  1             3              45
[1] 2 2
[1] FALSE
D564V7, binary
                 cls
clus                0   1
  SCN2A MUTATED    15  30
  SCN2A WILD-TYPE 155 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     15   30
  SCN2A WILD-TYPE  155  167
        clus
vv       SCN2A MUTATED SCN2A WILD-TYPE
  FEMALE            15             155
  MALE              30             167
[1] 2 2
[1] FALSE
D564V8, binary
                 cls
clus                0   1
  SCN2A MUTATED    37   1
  SCN2A WILD-TYPE 263   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     37    1
  SCN2A WILD-TYPE  263    7
     clus
vv    SCN2A MUTATED SCN2A WILD-TYPE
  NO             37             263
  YES             1               7
[1] 2 2
[1] FALSE
D564V9, binary
                 cls
clus                0   1
  SCN2A MUTATED    36   9
  SCN2A WILD-TYPE 278  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     36    9
  SCN2A WILD-TYPE  278   39
                               clus
vv                              SCN2A MUTATED SCN2A WILD-TYPE
  COLON ADENOCARCINOMA                     36             278
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCN2A MUTATED    29   0   1   7
  SCN2A WILD-TYPE 230   3  21  14
D564V10, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  R0            29             230
  R1             0               3
  R2             1              21
  RX             7              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"
D564V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCN2A MUTATED                                  0     4
  SCN2A WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCN2A MUTATED                           3    23
  SCN2A WILD-TYPE                        16   153
D564V12, multiclass
                                  clus
vv                                 SCN2A MUTATED SCN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               6
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       23             153
[1] 4 2
[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 = PLEK MUTATION ANALYSIS
D565V1, survival
                sevent
clus2              0   1
  PLEK MUTATED    11   1
  PLEK WILD-TYPE 266  77
  PLEK MUTATED PLEK WILD-TYPE 
            12            343 
  PLEK MUTATED PLEK WILD-TYPE 
             1             77 
$`PLEK MUTATED`
TCGA-AA-3662 TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-A00N 
        6.05        24.39         1.02        29.95        33.04         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5914 TCGA-D5-6931 
       34.98        12.16        58.39        12.76        21.99        12.00 

$`PLEK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PLEK MUTATED PLEK WILD-TYPE 
          1.02           0.00 
  PLEK MUTATED PLEK WILD-TYPE 
         58.39         148.01 
  PLEK MUTATED PLEK WILD-TYPE 
        17.375         22.090 
[1] "1.0 - 58.4 (17.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D565V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEK MUTATED         2        0        0         5         2         0
  PLEK WILD-TYPE      62        1       26       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLEK MUTATED           0          0          1          1        1         0
  PLEK WILD-TYPE        18          6         43         32       34        12
                vv
clus             STAGE IVB
  PLEK MUTATED           0
  PLEK WILD-TYPE         1
D565V3, multiclass
            clus
vv           PLEK MUTATED PLEK WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  PLEK MUTATED     0   2   6   4
  PLEK WILD-TYPE   9  65 243  37
D565V4, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            4             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
  PLEK MUTATED     9   1   2
  PLEK WILD-TYPE 211  80  64
D565V5, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  N0            9            211
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V6, binary
                cls
clus               0   1
  PLEK MUTATED     9   1
  PLEK WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      9    1
  PLEK WILD-TYPE  276   47
   clus
vv  PLEK MUTATED PLEK WILD-TYPE
  0            9            276
  1            1             47
[1] 2 2
[1] FALSE
D565V7, binary
                cls
clus               0   1
  PLEK MUTATED     5   7
  PLEK WILD-TYPE 165 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      5    7
  PLEK WILD-TYPE  165  190
        clus
vv       PLEK MUTATED PLEK WILD-TYPE
  FEMALE            5            165
  MALE              7            190
[1] 2 2
[1] FALSE
D565V8, binary
                cls
clus               0   1
  PLEK MUTATED     9   0
  PLEK WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      9    0
  PLEK WILD-TYPE  291    8
     clus
vv    PLEK MUTATED PLEK WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D565V9, binary
                cls
clus               0   1
  PLEK MUTATED     8   4
  PLEK WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      8    4
  PLEK WILD-TYPE  306   44
                               clus
vv                              PLEK MUTATED PLEK WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PLEK MUTATED     8   0   1   2
  PLEK WILD-TYPE 251   3  21  19
D565V10, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            2             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"
D565V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEK MUTATED                                  0     1
  PLEK WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PLEK MUTATED                           0     5
  PLEK WILD-TYPE                        19   171
D565V12, multiclass
                                  clus
vv                                 PLEK MUTATED PLEK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = FAHD2A MUTATION ANALYSIS
D566V1, survival
                  sevent
clus2                0   1
  FAHD2A MUTATED     5   1
  FAHD2A WILD-TYPE 272  77
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               6              349 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               1               77 
$`FAHD2A MUTATED`
TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6653 TCGA-CK-5916 TCGA-D5-6533 
       24.00        35.80        22.06        24.39        21.14        25.48 

$`FAHD2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  FAHD2A MUTATED FAHD2A WILD-TYPE 
           21.14             0.00 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
           35.80           148.01 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
          24.195           21.990 
[1] "21.1 - 35.8 (24.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D566V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAHD2A MUTATED         2        0        0         3         0         0
  FAHD2A WILD-TYPE      62        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2A MUTATED           0          0          0          0        0
  FAHD2A WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FAHD2A MUTATED           0         0
  FAHD2A WILD-TYPE        12         1
D566V3, multiclass
            clus
vv           FAHD2A MUTATED FAHD2A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  FAHD2A MUTATED     1   1   3   1
  FAHD2A WILD-TYPE   8  66 246  40
D566V4, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  T1              1                8
  T2              1               66
  T3              3              246
  T4              1               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
  FAHD2A MUTATED     6   0   0
  FAHD2A WILD-TYPE 214  81  66
D566V5, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  N0              6              214
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V6, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   0
  FAHD2A WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    0
  FAHD2A WILD-TYPE  279   48
   clus
vv  FAHD2A MUTATED FAHD2A WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D566V7, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     5   1
  FAHD2A WILD-TYPE 165 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      5    1
  FAHD2A WILD-TYPE  165  196
        clus
vv       FAHD2A MUTATED FAHD2A WILD-TYPE
  FEMALE              5              165
  MALE                1              196
[1] 2 2
[1] FALSE
D566V8, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   0
  FAHD2A WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    0
  FAHD2A WILD-TYPE  294    8
     clus
vv    FAHD2A MUTATED FAHD2A WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D566V9, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     5   1
  FAHD2A WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      5    1
  FAHD2A WILD-TYPE  309   47
                               clus
vv                              FAHD2A MUTATED FAHD2A WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAHD2A MUTATED     4   0   0   1
  FAHD2A WILD-TYPE 255   3  22  20
D566V10, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D566V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAHD2A MUTATED                                  0     0
  FAHD2A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAHD2A MUTATED                           0     5
  FAHD2A WILD-TYPE                        19   171
D566V12, multiclass
                                  clus
vv                                 FAHD2A MUTATED FAHD2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = SPANXN2 MUTATION ANALYSIS
D567V1, survival
                   sevent
clus2                 0   1
  SPANXN2 MUTATED     8   0
  SPANXN2 WILD-TYPE 269  78
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               347 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                0                78 
$`SPANXN2 MUTATED`
TCGA-AA-3950 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3977 TCGA-AZ-4315 TCGA-D5-6535 
       24.00        19.66        33.04        25.02        58.39        15.12 
TCGA-G4-6307 TCGA-G4-6309 
       55.04        85.48 

$`SPANXN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        61.91        36.00        13.78        46.75 

  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             21.99 
[1] "15.1 - 85.5 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D567V2, continuous
                   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      64        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXN2 MUTATED           0          0          3          1        0
  SPANXN2 WILD-TYPE        18          6         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SPANXN2 MUTATED           0         0
  SPANXN2 WILD-TYPE        12         1
D567V3, multiclass
            clus
vv           SPANXN2 MUTATED SPANXN2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SPANXN2 MUTATED     0   1   6   1
  SPANXN2 WILD-TYPE   9  66 243  40
D567V4, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               1                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
  SPANXN2 MUTATED     4   4   0
  SPANXN2 WILD-TYPE 216  77  66
D567V5, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  N0               4               216
  N1               4                77
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V6, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     5   0
  SPANXN2 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      5    0
  SPANXN2 WILD-TYPE  280   48
   clus
vv  SPANXN2 MUTATED SPANXN2 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D567V7, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     5   3
  SPANXN2 WILD-TYPE 165 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      5    3
  SPANXN2 WILD-TYPE  165  194
        clus
vv       SPANXN2 MUTATED SPANXN2 WILD-TYPE
  FEMALE               5               165
  MALE                 3               194
[1] 2 2
[1] FALSE
D567V8, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     8   0
  SPANXN2 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      8    0
  SPANXN2 WILD-TYPE  292    8
     clus
vv    SPANXN2 MUTATED SPANXN2 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D567V9, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     6   2
  SPANXN2 WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      6    2
  SPANXN2 WILD-TYPE  308   46
                               clus
vv                              SPANXN2 MUTATED SPANXN2 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SPANXN2 MUTATED     6   0   0   1
  SPANXN2 WILD-TYPE 253   3  22  20
D567V10, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D567V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPANXN2 MUTATED                                  0     0
  SPANXN2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPANXN2 MUTATED                           1     4
  SPANXN2 WILD-TYPE                        18   172
D567V12, multiclass
                                  clus
vv                                 SPANXN2 MUTATED SPANXN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = KIF21A MUTATION ANALYSIS
D568V1, survival
                  sevent
clus2                0   1
  KIF21A MUTATED    18   5
  KIF21A WILD-TYPE 259  73
  KIF21A MUTATED KIF21A WILD-TYPE 
              23              332 
  KIF21A MUTATED KIF21A WILD-TYPE 
               5               73 
$`KIF21A MUTATED`
TCGA-AA-3867 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 
       24.03        22.06        20.12        19.66         3.02         6.97 
TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6197 
       33.04         0.00        25.02         4.01        24.53        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 
        9.04        11.64         6.18        74.56        85.48 

$`KIF21A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       23.87        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KIF21A MUTATED KIF21A WILD-TYPE 
               0                0 
  KIF21A MUTATED KIF21A WILD-TYPE 
           85.48           148.01 
  KIF21A MUTATED KIF21A WILD-TYPE 
           19.66            22.39 
[1] "0.0 - 85.5 (19.7)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D568V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF21A MUTATED         0        0        3        11         1         0
  KIF21A WILD-TYPE      64        1       23        97         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF21A MUTATED           0          0          3          3        1
  KIF21A WILD-TYPE        18          6         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  KIF21A MUTATED           0         0
  KIF21A WILD-TYPE        12         1
D568V3, multiclass
            clus
vv           KIF21A MUTATED KIF21A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              11               97
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              3               30
  STAGE IV                1               34
  STAGE IVA               0               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
  KIF21A MUTATED     1   1  18   4
  KIF21A WILD-TYPE   8  66 231  37
D568V4, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  T1              1                8
  T2              1               66
  T3             18              231
  T4              4               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
  KIF21A MUTATED    17   4   3
  KIF21A WILD-TYPE 203  77  63
D568V5, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  N0             17              203
  N1              4               77
  N2              3               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"
D568V6, binary
                  cls
clus                 0   1
  KIF21A MUTATED    17   1
  KIF21A WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     17    1
  KIF21A WILD-TYPE  268   47
   clus
vv  KIF21A MUTATED KIF21A WILD-TYPE
  0             17              268
  1              1               47
[1] 2 2
[1] FALSE
D568V7, binary
                  cls
clus                 0   1
  KIF21A MUTATED    10  14
  KIF21A WILD-TYPE 160 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     10   14
  KIF21A WILD-TYPE  160  183
        clus
vv       KIF21A MUTATED KIF21A WILD-TYPE
  FEMALE             10              160
  MALE               14              183
[1] 2 2
[1] FALSE
D568V8, binary
                  cls
clus                 0   1
  KIF21A MUTATED    19   1
  KIF21A WILD-TYPE 281   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     19    1
  KIF21A WILD-TYPE  281    7
     clus
vv    KIF21A MUTATED KIF21A WILD-TYPE
  NO              19              281
  YES              1                7
[1] 2 2
[1] FALSE
D568V9, binary
                  cls
clus                 0   1
  KIF21A MUTATED    17   7
  KIF21A WILD-TYPE 297  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     17    7
  KIF21A WILD-TYPE  297   41
                               clus
vv                              KIF21A MUTATED KIF21A WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIF21A MUTATED    17   0   1   2
  KIF21A WILD-TYPE 242   3  21  19
D568V10, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  R0             17              242
  R1              0                3
  R2              1               21
  RX              2               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"
D568V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF21A MUTATED                                  0     1
  KIF21A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF21A MUTATED                           2    13
  KIF21A WILD-TYPE                        17   163
D568V12, multiclass
                                  clus
vv                                 KIF21A MUTATED KIF21A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        13              163
[1] 4 2
[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 = TAOK3 MUTATION ANALYSIS
D569V1, survival
                 sevent
clus2               0   1
  TAOK3 MUTATED    16   3
  TAOK3 WILD-TYPE 261  75
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             19             336 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
              3              75 
$`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        13.41 
TCGA-G4-6307 
       55.04 

$`TAOK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       23.87        20.12        20.28        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        85.45        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  TAOK3 MUTATED TAOK3 WILD-TYPE 
           3.02            0.00 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
          55.04          148.01 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
          15.62           22.47 
[1] "3.0 - 55.0 (15.6)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.1"
D569V2, continuous
                 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      62        1       24       100         5         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        18          6         43         31       34        12
                 vv
clus              STAGE IVB
  TAOK3 MUTATED           0
  TAOK3 WILD-TYPE         1
D569V3, multiclass
            clus
vv           TAOK3 MUTATED TAOK3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  TAOK3 MUTATED     0   3  12   5
  TAOK3 WILD-TYPE   9  64 237  36
D569V4, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             5              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
  TAOK3 MUTATED    16   3   1
  TAOK3 WILD-TYPE 204  78  65
D569V5, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  N0            16             204
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V6, binary
                 cls
clus                0   1
  TAOK3 MUTATED    16   1
  TAOK3 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     16    1
  TAOK3 WILD-TYPE  269   47
   clus
vv  TAOK3 MUTATED TAOK3 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D569V7, binary
                 cls
clus                0   1
  TAOK3 MUTATED    11   9
  TAOK3 WILD-TYPE 159 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     11    9
  TAOK3 WILD-TYPE  159  188
        clus
vv       TAOK3 MUTATED TAOK3 WILD-TYPE
  FEMALE            11             159
  MALE               9             188
[1] 2 2
[1] FALSE
D569V8, binary
                 cls
clus                0   1
  TAOK3 MUTATED    17   0
  TAOK3 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     17    0
  TAOK3 WILD-TYPE  283    8
     clus
vv    TAOK3 MUTATED TAOK3 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D569V9, binary
                 cls
clus                0   1
  TAOK3 MUTATED    14   6
  TAOK3 WILD-TYPE 300  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     14    6
  TAOK3 WILD-TYPE  300   42
                               clus
vv                              TAOK3 MUTATED TAOK3 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAOK3 MUTATED    16   0   0   3
  TAOK3 WILD-TYPE 243   3  22  18
D569V10, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             3              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"
D569V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAOK3 MUTATED                                  0     1
  TAOK3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAOK3 MUTATED                           1    12
  TAOK3 WILD-TYPE                        18   164
D569V12, multiclass
                                  clus
vv                                 TAOK3 MUTATED TAOK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = ANKRD17 MUTATION ANALYSIS
D570V1, survival
                   sevent
clus2                 0   1
  ANKRD17 MUTATED    22   3
  ANKRD17 WILD-TYPE 255  75
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               25               330 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                3                75 
$`ANKRD17 MUTATED`
TCGA-AA-3525 TCGA-AA-3715 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3510 
        8.05        19.04        33.53        32.71        24.39        63.98 
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 
       12.16        58.39        12.76        10.06        15.62         2.01 
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 
       85.48 

$`ANKRD17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6654 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01         0.92        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
             2.01              0.00 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
            85.48            148.01 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
           19.590            22.075 
[1] "2.0 - 85.5 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D570V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD17 MUTATED         6        0        2         7         3         1
  ANKRD17 WILD-TYPE      58        1       24       101         5         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD17 MUTATED           0          1          3          1        1
  ANKRD17 WILD-TYPE        18          5         41         32       34
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD17 MUTATED           0         0
  ANKRD17 WILD-TYPE        12         1
D570V3, multiclass
            clus
vv           ANKRD17 MUTATED ANKRD17 WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                7               101
  STAGE IIB                3                 5
  STAGE IIC                1                 0
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  ANKRD17 MUTATED     0   7  13   6
  ANKRD17 WILD-TYPE   9  60 236  35
D570V4, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  T1               0                 9
  T2               7                60
  T3              13               236
  T4               6                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
  ANKRD17 MUTATED    20   5   1
  ANKRD17 WILD-TYPE 200  76  65
D570V5, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  N0              20               200
  N1               5                76
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V6, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    22   1
  ANKRD17 WILD-TYPE 263  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     22    1
  ANKRD17 WILD-TYPE  263   47
   clus
vv  ANKRD17 MUTATED ANKRD17 WILD-TYPE
  0              22               263
  1               1                47
[1] 2 2
[1] FALSE
D570V7, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED     9  17
  ANKRD17 WILD-TYPE 161 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED      9   17
  ANKRD17 WILD-TYPE  161  180
        clus
vv       ANKRD17 MUTATED ANKRD17 WILD-TYPE
  FEMALE               9               161
  MALE                17               180
[1] 2 2
[1] FALSE
D570V8, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    23   0
  ANKRD17 WILD-TYPE 277   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     23    0
  ANKRD17 WILD-TYPE  277    8
     clus
vv    ANKRD17 MUTATED ANKRD17 WILD-TYPE
  NO               23               277
  YES               0                 8
[1] 2 2
[1] FALSE
D570V9, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    17   9
  ANKRD17 WILD-TYPE 297  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     17    9
  ANKRD17 WILD-TYPE  297   39
                               clus
vv                              ANKRD17 MUTATED ANKRD17 WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               9                39
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD17 MUTATED    18   0   0   5
  ANKRD17 WILD-TYPE 241   3  22  16
D570V10, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               0                22
  RX               5                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"
D570V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD17 MUTATED                                  0     2
  ANKRD17 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD17 MUTATED                           3    12
  ANKRD17 WILD-TYPE                        16   164
D570V12, multiclass
                                  clus
vv                                 ANKRD17 MUTATED ANKRD17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      3                16
  WHITE                                         12               164
[1] 4 2
[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 = WBP11 MUTATION ANALYSIS
D571V1, survival
                 sevent
clus2               0   1
  WBP11 MUTATED     6   1
  WBP11 WILD-TYPE 271  77
  WBP11 MUTATED WBP11 WILD-TYPE 
              7             348 
  WBP11 MUTATED WBP11 WILD-TYPE 
              1              77 
$`WBP11 MUTATED`
TCGA-AA-3713 TCGA-A6-5665 TCGA-CK-4950 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A28G 
       19.04        22.06        85.45        16.14        15.58        60.79 
TCGA-G4-6309 
       85.48 

$`WBP11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  WBP11 MUTATED WBP11 WILD-TYPE 
          15.58            0.00 
  WBP11 MUTATED WBP11 WILD-TYPE 
          85.48          148.01 
  WBP11 MUTATED WBP11 WILD-TYPE 
          22.06           22.06 
[1] "15.6 - 85.5 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D571V2, continuous
                 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      63        1       26       104         8         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        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  WBP11 MUTATED           0
  WBP11 WILD-TYPE         1
D571V3, multiclass
            clus
vv           WBP11 MUTATED WBP11 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  WBP11 MUTATED     0   1   7   0
  WBP11 WILD-TYPE   9  66 242  41
D571V4, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             0              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
  WBP11 MUTATED     6   2   0
  WBP11 WILD-TYPE 214  79  66
D571V5, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V6, binary
                 cls
clus                0   1
  WBP11 MUTATED     7   1
  WBP11 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      7    1
  WBP11 WILD-TYPE  278   47
   clus
vv  WBP11 MUTATED WBP11 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D571V7, binary
                 cls
clus                0   1
  WBP11 MUTATED     4   4
  WBP11 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      4    4
  WBP11 WILD-TYPE  166  193
        clus
vv       WBP11 MUTATED WBP11 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D571V8, binary
                 cls
clus                0   1
  WBP11 MUTATED     5   1
  WBP11 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      5    1
  WBP11 WILD-TYPE  295    7
     clus
vv    WBP11 MUTATED WBP11 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D571V9, binary
                 cls
clus                0   1
  WBP11 MUTATED     6   2
  WBP11 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      6    2
  WBP11 WILD-TYPE  308   46
                               clus
vv                              WBP11 MUTATED WBP11 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WBP11 MUTATED     5   1   1   0
  WBP11 WILD-TYPE 254   2  21  21
D571V10, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  R0             5             254
  R1             1               2
  R2             1              21
  RX             0              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"
D571V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WBP11 MUTATED                                  0     0
  WBP11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WBP11 MUTATED                           2     4
  WBP11 WILD-TYPE                        17   172
D571V12, multiclass
                                  clus
vv                                 WBP11 MUTATED WBP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = HNRNPH3 MUTATION ANALYSIS
D572V1, survival
                   sevent
clus2                 0   1
  HNRNPH3 MUTATED     3   1
  HNRNPH3 WILD-TYPE 274  77
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                4               351 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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            22.060 
[1] "14.0 - 49.4 (24.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D572V2, continuous
                   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      63        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HNRNPH3 MUTATED           0          0          0          0        0
  HNRNPH3 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  HNRNPH3 MUTATED           0         0
  HNRNPH3 WILD-TYPE        12         1
D572V3, multiclass
            clus
vv           HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  HNRNPH3 MUTATED     0   1   3   0
  HNRNPH3 WILD-TYPE   9  66 246  41
D572V4, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               0                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
  HNRNPH3 MUTATED     4   0   0
  HNRNPH3 WILD-TYPE 216  81  66
D572V5, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  N0               4               216
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V6, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     3   0
  HNRNPH3 WILD-TYPE 282  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      3    0
  HNRNPH3 WILD-TYPE  282   48
   clus
vv  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  0               3               282
  1               0                48
[1] 2 2
[1] FALSE
D572V7, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     3   1
  HNRNPH3 WILD-TYPE 167 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      3    1
  HNRNPH3 WILD-TYPE  167  196
        clus
vv       HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  FEMALE               3               167
  MALE                 1               196
[1] 2 2
[1] FALSE
D572V8, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     4   0
  HNRNPH3 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      4    0
  HNRNPH3 WILD-TYPE  296    8
     clus
vv    HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D572V9, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     4   0
  HNRNPH3 WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      4    0
  HNRNPH3 WILD-TYPE  310   48
                               clus
vv                              HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HNRNPH3 MUTATED     3   0   0   0
  HNRNPH3 WILD-TYPE 256   3  22  21
D572V10, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D572V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPH3 MUTATED                                  0     0
  HNRNPH3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HNRNPH3 MUTATED                           0     3
  HNRNPH3 WILD-TYPE                        19   173
D572V12, multiclass
                                  clus
vv                                 HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = ENTPD4 MUTATION ANALYSIS
D573V1, survival
                  sevent
clus2                0   1
  ENTPD4 MUTATED    12   4
  ENTPD4 WILD-TYPE 265  74
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              16              339 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
               4               74 
$`ENTPD4 MUTATED`
TCGA-A6-6649 TCGA-AA-3715 TCGA-AD-6895 TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3489 
       24.16        19.04        25.08        26.17        79.69         7.04 
TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-CM-6170 TCGA-D5-6929 
       26.01        34.98        38.07        83.24        15.02        13.41 
TCGA-D5-6930 TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6315 
       13.35       135.65        35.31        61.91 

$`ENTPD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
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-A6-5656 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-A6-6648 
       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-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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-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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
            7.04             0.00 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
          135.65           148.01 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
           26.09            21.99 
[1] "7.0 - 135.7 (26.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D573V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENTPD4 MUTATED         3        0        3         3         1         0
  ENTPD4 WILD-TYPE      61        1       23       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTPD4 MUTATED           1          0          4          0        2
  ENTPD4 WILD-TYPE        17          6         40         33       33
                  vv
clus               STAGE IVA STAGE IVB
  ENTPD4 MUTATED           0         0
  ENTPD4 WILD-TYPE        12         1
D573V3, multiclass
            clus
vv           ENTPD4 MUTATED ENTPD4 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  ENTPD4 MUTATED     0   3  12   2
  ENTPD4 WILD-TYPE   9  64 237  39
D573V4, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             12              237
  T4              2               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
  ENTPD4 MUTATED    10   7   0
  ENTPD4 WILD-TYPE 210  74  66
D573V5, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  N0             10              210
  N1              7               74
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V6, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    15   2
  ENTPD4 WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     15    2
  ENTPD4 WILD-TYPE  270   46
   clus
vv  ENTPD4 MUTATED ENTPD4 WILD-TYPE
  0             15              270
  1              2               46
[1] 2 2
[1] FALSE
D573V7, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED     7  10
  ENTPD4 WILD-TYPE 163 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED      7   10
  ENTPD4 WILD-TYPE  163  187
        clus
vv       ENTPD4 MUTATED ENTPD4 WILD-TYPE
  FEMALE              7              163
  MALE               10              187
[1] 2 2
[1] FALSE
D573V8, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    15   0
  ENTPD4 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     15    0
  ENTPD4 WILD-TYPE  285    8
     clus
vv    ENTPD4 MUTATED ENTPD4 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D573V9, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    13   3
  ENTPD4 WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     13    3
  ENTPD4 WILD-TYPE  301   45
                               clus
vv                              ENTPD4 MUTATED ENTPD4 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ENTPD4 MUTATED    15   0   0   0
  ENTPD4 WILD-TYPE 244   3  22  21
D573V10, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              0               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"
D573V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENTPD4 MUTATED                                  0     1
  ENTPD4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ENTPD4 MUTATED                           0    10
  ENTPD4 WILD-TYPE                        19   166
D573V12, multiclass
                                  clus
vv                                 ENTPD4 MUTATED ENTPD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(574) Variable = DDX3X MUTATION ANALYSIS
D574V1, survival
                 sevent
clus2               0   1
  DDX3X MUTATED     6   3
  DDX3X WILD-TYPE 271  75
  DDX3X MUTATED DDX3X WILD-TYPE 
              9             346 
  DDX3X MUTATED DDX3X WILD-TYPE 
              3              75 
$`DDX3X MUTATED`
TCGA-AA-3662 TCGA-AD-6964 TCGA-AA-3492 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 
        6.05        10.88         3.02        34.98        27.09        12.76 
TCGA-CK-4950 TCGA-CM-5344 TCGA-G4-6626 
       85.45        22.03        46.75 

$`DDX3X WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  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          22.075 
[1] "3.0 - 85.5 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D574V2, continuous
                 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      63        1       25       105         7         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        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  DDX3X MUTATED           0
  DDX3X WILD-TYPE         1
D574V3, multiclass
            clus
vv           DDX3X MUTATED DDX3X WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  DDX3X MUTATED     0   1   6   3
  DDX3X WILD-TYPE   9  66 243  38
D574V4, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             3              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
  DDX3X MUTATED     6   2   2
  DDX3X WILD-TYPE 214  79  64
D574V5, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0             6             214
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V6, binary
                 cls
clus                0   1
  DDX3X MUTATED     8   1
  DDX3X WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      8    1
  DDX3X WILD-TYPE  277   47
   clus
vv  DDX3X MUTATED DDX3X WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D574V7, binary
                 cls
clus                0   1
  DDX3X MUTATED     7   3
  DDX3X WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      7    3
  DDX3X WILD-TYPE  163  194
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D574V8, binary
                 cls
clus                0   1
  DDX3X MUTATED     8   0
  DDX3X WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      8    0
  DDX3X WILD-TYPE  292    8
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D574V9, binary
                 cls
clus                0   1
  DDX3X MUTATED     8   2
  DDX3X WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      8    2
  DDX3X WILD-TYPE  306   46
                               clus
vv                              DDX3X MUTATED DDX3X WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX3X MUTATED     6   1   1   1
  DDX3X WILD-TYPE 253   2  21  20
D574V10, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  R0             6             253
  R1             1               2
  R2             1              21
  RX             1              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"
D574V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX3X MUTATED                                  0     1
  DDX3X WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX3X MUTATED                           1     4
  DDX3X WILD-TYPE                        18   172
D574V12, multiclass
                                  clus
vv                                 DDX3X MUTATED DDX3X WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = MCCC1 MUTATION ANALYSIS
D575V1, survival
                 sevent
clus2               0   1
  MCCC1 MUTATED    13   3
  MCCC1 WILD-TYPE 264  75
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             16             339 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
              3              75 
$`MCCC1 MUTATED`
TCGA-AZ-6608 TCGA-A6-2676 TCGA-A6-6652 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3664 
        1.94        42.90        24.69        29.95        78.08        54.02 
TCGA-AA-3877 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6598 
       31.00        30.02        34.98        24.53        58.39        49.41 
TCGA-CM-4743 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 
       23.05       133.18        53.62        55.04 

$`MCCC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02         6.97         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       35.31        74.56        65.85        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MCCC1 MUTATED MCCC1 WILD-TYPE 
           1.94            0.00 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
         133.18          148.01 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
          38.94           21.44 
[1] "1.9 - 133.2 (38.9)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.8"
D575V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCCC1 MUTATED         1        0        4         4         3         0
  MCCC1 WILD-TYPE      63        1       22       104         5         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        17          5         43         33       35        11
                 vv
clus              STAGE IVB
  MCCC1 MUTATED           0
  MCCC1 WILD-TYPE         1
D575V3, multiclass
            clus
vv           MCCC1 MUTATED MCCC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              4             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  MCCC1 MUTATED     2   1  10   4
  MCCC1 WILD-TYPE   7  66 239  37
D575V4, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  T1             2               7
  T2             1              66
  T3            10             239
  T4             4              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
  MCCC1 MUTATED    14   3   0
  MCCC1 WILD-TYPE 206  78  66
D575V5, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  N0            14             206
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V6, binary
                 cls
clus                0   1
  MCCC1 MUTATED    14   1
  MCCC1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     14    1
  MCCC1 WILD-TYPE  271   47
   clus
vv  MCCC1 MUTATED MCCC1 WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D575V7, binary
                 cls
clus                0   1
  MCCC1 MUTATED    12   5
  MCCC1 WILD-TYPE 158 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     12    5
  MCCC1 WILD-TYPE  158  192
        clus
vv       MCCC1 MUTATED MCCC1 WILD-TYPE
  FEMALE            12             158
  MALE               5             192
[1] 2 2
[1] FALSE
D575V8, binary
                 cls
clus                0   1
  MCCC1 MUTATED    16   0
  MCCC1 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     16    0
  MCCC1 WILD-TYPE  284    8
     clus
vv    MCCC1 MUTATED MCCC1 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D575V9, binary
                 cls
clus                0   1
  MCCC1 MUTATED    15   2
  MCCC1 WILD-TYPE 299  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     15    2
  MCCC1 WILD-TYPE  299   46
                               clus
vv                              MCCC1 MUTATED MCCC1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MCCC1 MUTATED    13   0   0   0
  MCCC1 WILD-TYPE 246   3  22  21
D575V10, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             0              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"
D575V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCCC1 MUTATED                                  0     0
  MCCC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MCCC1 MUTATED                           1     9
  MCCC1 WILD-TYPE                        18   167
D575V12, multiclass
                                  clus
vv                                 MCCC1 MUTATED MCCC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(576) Variable = MDH1 MUTATION ANALYSIS
D576V1, survival
                sevent
clus2              0   1
  MDH1 MUTATED     6   2
  MDH1 WILD-TYPE 271  76
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            347 
  MDH1 MUTATED MDH1 WILD-TYPE 
             2             76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44        17.82         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MDH1 MUTATED MDH1 WILD-TYPE 
             0              0 
  MDH1 MUTATED MDH1 WILD-TYPE 
         58.39         148.01 
  MDH1 MUTATED MDH1 WILD-TYPE 
        15.505         22.090 
[1] "0.0 - 58.4 (15.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D576V2, continuous
                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      63        1       26       103         8         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        18          6         44         33       34        11
                vv
clus             STAGE IVB
  MDH1 MUTATED           0
  MDH1 WILD-TYPE         1
D576V3, multiclass
            clus
vv           MDH1 MUTATED MDH1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  MDH1 MUTATED     0   1   7   0
  MDH1 WILD-TYPE   9  66 242  41
D576V4, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            0             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
  MDH1 MUTATED     6   1   1
  MDH1 WILD-TYPE 214  80  65
D576V5, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V6, binary
                cls
clus               0   1
  MDH1 MUTATED     6   2
  MDH1 WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      6    2
  MDH1 WILD-TYPE  279   46
   clus
vv  MDH1 MUTATED MDH1 WILD-TYPE
  0            6            279
  1            2             46
[1] 2 2
[1] FALSE
D576V7, binary
                cls
clus               0   1
  MDH1 MUTATED     3   5
  MDH1 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      3    5
  MDH1 WILD-TYPE  167  192
        clus
vv       MDH1 MUTATED MDH1 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D576V8, binary
                cls
clus               0   1
  MDH1 MUTATED     7   0
  MDH1 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      7    0
  MDH1 WILD-TYPE  293    8
     clus
vv    MDH1 MUTATED MDH1 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D576V9, binary
                cls
clus               0   1
  MDH1 MUTATED     7   1
  MDH1 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      7    1
  MDH1 WILD-TYPE  307   47
                               clus
vv                              MDH1 MUTATED MDH1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MDH1 MUTATED     6   0   0   1
  MDH1 WILD-TYPE 253   3  22  20
D576V10, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D576V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MDH1 MUTATED                                  0     1
  MDH1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MDH1 MUTATED                           1     5
  MDH1 WILD-TYPE                        18   171
D576V12, multiclass
                                  clus
vv                                 MDH1 MUTATED MDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = ARHGAP25 MUTATION ANALYSIS
D577V1, survival
                    sevent
clus2                  0   1
  ARHGAP25 MUTATED     9   1
  ARHGAP25 WILD-TYPE 268  77
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                10                345 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                 1                 77 
$`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 
       25.48        17.85        10.13        38.20 

$`ARHGAP25 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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-D5-6540 
       43.27        15.12         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         7.53        12.39        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
             10.13               0.00 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
             78.08             148.01 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
             30.05              21.99 
[1] "10.1 - 78.1 (30.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D577V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP25 MUTATED         1        0        1         3         1         0
  ARHGAP25 WILD-TYPE      63        1       25       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP25 MUTATED           1          1          0          1        0
  ARHGAP25 WILD-TYPE        17          5         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP25 MUTATED           0         0
  ARHGAP25 WILD-TYPE        12         1
D577V3, multiclass
            clus
vv           ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 3                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                1                  5
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  ARHGAP25 MUTATED     0   1   7   2
  ARHGAP25 WILD-TYPE   9  66 242  39
D577V4, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                7                242
  T4                2                 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
  ARHGAP25 MUTATED     7   1   2
  ARHGAP25 WILD-TYPE 213  80  64
D577V5, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  N0                7                213
  N1                1                 80
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V6, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED    10   0
  ARHGAP25 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED     10    0
  ARHGAP25 WILD-TYPE  275   48
   clus
vv  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  0               10                275
  1                0                 48
[1] 2 2
[1] FALSE
D577V7, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED     5   5
  ARHGAP25 WILD-TYPE 165 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED      5    5
  ARHGAP25 WILD-TYPE  165  192
        clus
vv       ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  FEMALE                5                165
  MALE                  5                192
[1] 2 2
[1] FALSE
D577V8, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED     7   1
  ARHGAP25 WILD-TYPE 293   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED      7    1
  ARHGAP25 WILD-TYPE  293    7
     clus
vv    ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  NO                 7                293
  YES                1                  7
[1] 2 2
[1] FALSE
D577V9, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED     6   3
  ARHGAP25 WILD-TYPE 308  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED      6    3
  ARHGAP25 WILD-TYPE  308   45
                               clus
vv                              ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  COLON ADENOCARCINOMA                         6                308
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP25 MUTATED     8   0   0   1
  ARHGAP25 WILD-TYPE 251   3  22  20
D577V10, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  R0                8                251
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D577V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP25 MUTATED                                  0     1
  ARHGAP25 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP25 MUTATED                           0     6
  ARHGAP25 WILD-TYPE                        19   170
D577V12, multiclass
                                  clus
vv                                 ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = SPEN MUTATION ANALYSIS
D578V1, survival
                sevent
clus2              0   1
  SPEN MUTATED    21   8
  SPEN WILD-TYPE 256  70
  SPEN MUTATED SPEN WILD-TYPE 
            29            326 
  SPEN MUTATED SPEN WILD-TYPE 
             8             70 
$`SPEN MUTATED`
TCGA-AA-3522 TCGA-AA-3543 TCGA-AA-3672 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-5661 
       37.05         0.99         0.92        79.69        32.75        33.53 
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3949 TCGA-AA-3956 
       22.06         3.02        26.99        10.06        26.01        34.03 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 
       25.02         4.01        12.16        27.09        33.01        58.39 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5868 
        6.77        29.56        21.14        23.05        37.02        17.03 
TCGA-CM-6169 TCGA-D5-5538 TCGA-D5-6541 TCGA-DM-A0XD TCGA-DM-A1HB 
       13.02        54.61        15.58        24.43       135.65 

$`SPEN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5662 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       33.01        20.98         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95         0.20        21.44        17.82 
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-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.99        82.95         2.01       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-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 
       14.04        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-D5-5539 
       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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SPEN MUTATED SPEN WILD-TYPE 
          0.92           0.00 
  SPEN MUTATED SPEN WILD-TYPE 
        135.65         148.01 
  SPEN MUTATED SPEN WILD-TYPE 
         25.02          21.99 
[1] "0.9 - 135.7 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D578V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPEN MUTATED         7        0        1        11         3         0
  SPEN WILD-TYPE      57        1       25        97         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPEN MUTATED           2          0          3          0        0         2
  SPEN WILD-TYPE        16          6         41         33       35        10
                vv
clus             STAGE IVB
  SPEN MUTATED           0
  SPEN WILD-TYPE         1
D578V3, multiclass
            clus
vv           SPEN MUTATED SPEN WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA            11             97
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             2             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
  SPEN MUTATED     1   8  18   4
  SPEN WILD-TYPE   8  59 231  37
D578V4, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  T1            1              8
  T2            8             59
  T3           18            231
  T4            4             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
  SPEN MUTATED    23   7   1
  SPEN WILD-TYPE 197  74  65
D578V5, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  N0           23            197
  N1            7             74
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V6, binary
                cls
clus               0   1
  SPEN MUTATED    24   2
  SPEN WILD-TYPE 261  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     24    2
  SPEN WILD-TYPE  261   46
   clus
vv  SPEN MUTATED SPEN WILD-TYPE
  0           24            261
  1            2             46
[1] 2 2
[1] FALSE
D578V7, binary
                cls
clus               0   1
  SPEN MUTATED    16  15
  SPEN WILD-TYPE 154 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     16   15
  SPEN WILD-TYPE  154  182
        clus
vv       SPEN MUTATED SPEN WILD-TYPE
  FEMALE           16            154
  MALE             15            182
[1] 2 2
[1] FALSE
D578V8, binary
                cls
clus               0   1
  SPEN MUTATED    25   0
  SPEN WILD-TYPE 275   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     25    0
  SPEN WILD-TYPE  275    8
     clus
vv    SPEN MUTATED SPEN WILD-TYPE
  NO            25            275
  YES            0              8
[1] 2 2
[1] FALSE
D578V9, binary
                cls
clus               0   1
  SPEN MUTATED    25   5
  SPEN WILD-TYPE 289  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     25    5
  SPEN WILD-TYPE  289   43
                               clus
vv                              SPEN MUTATED SPEN WILD-TYPE
  COLON ADENOCARCINOMA                    25            289
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SPEN MUTATED    24   0   0   2
  SPEN WILD-TYPE 235   3  22  19
D578V10, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  R0           24            235
  R1            0              3
  R2            0             22
  RX            2             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"
D578V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPEN MUTATED                                  0     0
  SPEN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SPEN MUTATED                           4    16
  SPEN WILD-TYPE                        15   160
D578V12, multiclass
                                  clus
vv                                 SPEN MUTATED SPEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      16            160
[1] 4 2
[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 = GPR75 MUTATION ANALYSIS
D579V1, survival
                 sevent
clus2               0   1
  GPR75 MUTATED     6   2
  GPR75 WILD-TYPE 271  76
  GPR75 MUTATED GPR75 WILD-TYPE 
              8             347 
  GPR75 MUTATED GPR75 WILD-TYPE 
              2              76 
$`GPR75 MUTATED`
TCGA-G4-6588 TCGA-AA-3811 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-5861 
       26.17        10.06        49.41        12.76        30.08        15.02 
TCGA-CM-6162 TCGA-G4-6306 
       12.00        44.68 

$`GPR75 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPR75 MUTATED GPR75 WILD-TYPE 
          10.06            0.00 
  GPR75 MUTATED GPR75 WILD-TYPE 
          49.41          148.01 
  GPR75 MUTATED GPR75 WILD-TYPE 
         20.595          22.060 
[1] "10.1 - 49.4 (20.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D579V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR75 MUTATED         0        0        1         4         0         0
  GPR75 WILD-TYPE      64        1       25       104         8         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  GPR75 MUTATED           0
  GPR75 WILD-TYPE         1
D579V3, multiclass
            clus
vv           GPR75 MUTATED GPR75 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GPR75 MUTATED     0   1   7   0
  GPR75 WILD-TYPE   9  66 242  41
D579V4, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             0              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
  GPR75 MUTATED     6   1   1
  GPR75 WILD-TYPE 214  80  65
D579V5, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V6, binary
                 cls
clus                0   1
  GPR75 MUTATED     7   0
  GPR75 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      7    0
  GPR75 WILD-TYPE  278   48
   clus
vv  GPR75 MUTATED GPR75 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D579V7, binary
                 cls
clus                0   1
  GPR75 MUTATED     6   2
  GPR75 WILD-TYPE 164 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      6    2
  GPR75 WILD-TYPE  164  195
        clus
vv       GPR75 MUTATED GPR75 WILD-TYPE
  FEMALE             6             164
  MALE               2             195
[1] 2 2
[1] FALSE
D579V8, binary
                 cls
clus                0   1
  GPR75 MUTATED     8   0
  GPR75 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      8    0
  GPR75 WILD-TYPE  292    8
     clus
vv    GPR75 MUTATED GPR75 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D579V9, binary
                 cls
clus                0   1
  GPR75 MUTATED     6   2
  GPR75 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      6    2
  GPR75 WILD-TYPE  308   46
                               clus
vv                              GPR75 MUTATED GPR75 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR75 MUTATED     6   0   0   1
  GPR75 WILD-TYPE 253   3  22  20
D579V10, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D579V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR75 MUTATED                                  0     1
  GPR75 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR75 MUTATED                           0     6
  GPR75 WILD-TYPE                        19   170
D579V12, multiclass
                                  clus
vv                                 GPR75 MUTATED GPR75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = HERC5 MUTATION ANALYSIS
D580V1, survival
                 sevent
clus2               0   1
  HERC5 MUTATED    15   3
  HERC5 WILD-TYPE 262  75
  HERC5 MUTATED HERC5 WILD-TYPE 
             18             337 
  HERC5 MUTATED HERC5 WILD-TYPE 
              3              75 
$`HERC5 MUTATED`
TCGA-A6-6649 TCGA-AA-3713 TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-5659 TCGA-AA-3510 
       24.16        19.04        19.04        35.80        30.44        63.98 
TCGA-AA-3555 TCGA-AA-3848 TCGA-AA-3982 TCGA-AA-A010 TCGA-AD-6965 TCGA-AZ-4315 
       29.95        10.06        27.02        34.98        26.47        58.39 
TCGA-CK-5914 TCGA-CM-6675 TCGA-D5-6926 TCGA-DM-A1D4 TCGA-F4-6854 TCGA-G4-6307 
       21.99        13.05         9.04        92.75         0.53        55.04 

$`HERC5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3850 
       15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  HERC5 MUTATED HERC5 WILD-TYPE 
           0.53            0.00 
  HERC5 MUTATED HERC5 WILD-TYPE 
          92.75          148.01 
  HERC5 MUTATED HERC5 WILD-TYPE 
         26.745          21.990 
[1] "0.5 - 92.8 (26.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D580V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HERC5 MUTATED         1        0        2         5         1         0
  HERC5 WILD-TYPE      63        1       24       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HERC5 MUTATED           0          0          5          2        1         0
  HERC5 WILD-TYPE        18          6         39         31       34        12
                 vv
clus              STAGE IVB
  HERC5 MUTATED           1
  HERC5 WILD-TYPE         0
D580V3, multiclass
            clus
vv           HERC5 MUTATED HERC5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              12
  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   1  14   3
  HERC5 WILD-TYPE   9  66 235  38
D580V4, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            14             235
  T4             3              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
  HERC5 MUTATED    10   5   3
  HERC5 WILD-TYPE 210  76  63
D580V5, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  N0            10             210
  N1             5              76
  N2             3              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"
D580V6, binary
                 cls
clus                0   1
  HERC5 MUTATED    15   2
  HERC5 WILD-TYPE 270  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     15    2
  HERC5 WILD-TYPE  270   46
   clus
vv  HERC5 MUTATED HERC5 WILD-TYPE
  0            15             270
  1             2              46
[1] 2 2
[1] FALSE
D580V7, binary
                 cls
clus                0   1
  HERC5 MUTATED     6  12
  HERC5 WILD-TYPE 164 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      6   12
  HERC5 WILD-TYPE  164  185
        clus
vv       HERC5 MUTATED HERC5 WILD-TYPE
  FEMALE             6             164
  MALE              12             185
[1] 2 2
[1] FALSE
D580V8, binary
                 cls
clus                0   1
  HERC5 MUTATED    14   2
  HERC5 WILD-TYPE 286   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     14    2
  HERC5 WILD-TYPE  286    6
     clus
vv    HERC5 MUTATED HERC5 WILD-TYPE
  NO             14             286
  YES             2               6
[1] 2 2
[1] FALSE
D580V9, binary
                 cls
clus                0   1
  HERC5 MUTATED    17   1
  HERC5 WILD-TYPE 297  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     17    1
  HERC5 WILD-TYPE  297   47
                               clus
vv                              HERC5 MUTATED HERC5 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HERC5 MUTATED    12   1   1   1
  HERC5 WILD-TYPE 247   2  21  20
D580V10, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  R0            12             247
  R1             1               2
  R2             1              21
  RX             1              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"
D580V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HERC5 MUTATED                                  0     0
  HERC5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HERC5 MUTATED                           1    10
  HERC5 WILD-TYPE                        18   166
D580V12, multiclass
                                  clus
vv                                 HERC5 MUTATED HERC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(581) Variable = AKR1C4 MUTATION ANALYSIS
D581V1, survival
                  sevent
clus2                0   1
  AKR1C4 MUTATED     6   3
  AKR1C4 WILD-TYPE 271  75
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               9              346 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               3               75 
$`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 
       38.20        13.25        44.68 

$`AKR1C4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           10.06             0.00 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           85.45           148.01 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           35.01            22.01 
[1] "10.1 - 85.5 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D581V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKR1C4 MUTATED         0        0        1         1         0         0
  AKR1C4 WILD-TYPE      64        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKR1C4 MUTATED           1          0          2          2        0
  AKR1C4 WILD-TYPE        17          6         42         31       35
                  vv
clus               STAGE IVA STAGE IVB
  AKR1C4 MUTATED           1         0
  AKR1C4 WILD-TYPE        11         1
D581V3, multiclass
            clus
vv           AKR1C4 MUTATED AKR1C4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               1               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
  AKR1C4 MUTATED     0   1   8   0
  AKR1C4 WILD-TYPE   9  66 241  41
D581V4, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              8              241
  T4              0               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
  AKR1C4 MUTATED     3   3   3
  AKR1C4 WILD-TYPE 217  78  63
D581V5, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  N0              3              217
  N1              3               78
  N2              3               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"
D581V6, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     7   1
  AKR1C4 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      7    1
  AKR1C4 WILD-TYPE  278   47
   clus
vv  AKR1C4 MUTATED AKR1C4 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D581V7, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     6   3
  AKR1C4 WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      6    3
  AKR1C4 WILD-TYPE  164  194
        clus
vv       AKR1C4 MUTATED AKR1C4 WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D581V8, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     7   1
  AKR1C4 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      7    1
  AKR1C4 WILD-TYPE  293    7
     clus
vv    AKR1C4 MUTATED AKR1C4 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D581V9, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     6   2
  AKR1C4 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      6    2
  AKR1C4 WILD-TYPE  308   46
                               clus
vv                              AKR1C4 MUTATED AKR1C4 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKR1C4 MUTATED     5   1   0   2
  AKR1C4 WILD-TYPE 254   2  22  19
D581V10, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  R0              5              254
  R1              1                2
  R2              0               22
  RX              2               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"
D581V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKR1C4 MUTATED                                  0     1
  AKR1C4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AKR1C4 MUTATED                           1     4
  AKR1C4 WILD-TYPE                        18   172
D581V12, multiclass
                                  clus
vv                                 AKR1C4 MUTATED AKR1C4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = LIG1 MUTATION ANALYSIS
D582V1, survival
                sevent
clus2              0   1
  LIG1 MUTATED    10   5
  LIG1 WILD-TYPE 267  73
  LIG1 MUTATED LIG1 WILD-TYPE 
            15            340 
  LIG1 MUTATED LIG1 WILD-TYPE 
             5             73 
$`LIG1 MUTATED`
TCGA-AZ-6608 TCGA-A6-5665 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 
        1.94        22.06        30.05        53.00         4.01        34.98 
TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-F4-6460 
       12.10         3.19        14.04        17.85        16.14        31.96 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6306 
       35.31        74.56        44.68 

$`LIG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       47.41       133.18        65.85        53.62        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  LIG1 MUTATED LIG1 WILD-TYPE 
          1.94           0.00 
  LIG1 MUTATED LIG1 WILD-TYPE 
         74.56         148.01 
  LIG1 MUTATED LIG1 WILD-TYPE 
         22.06          22.06 
[1] "1.9 - 74.6 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D582V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIG1 MUTATED         3        0        2         3         2         0
  LIG1 WILD-TYPE      61        1       24       105         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIG1 MUTATED           0          1          1          1        2         0
  LIG1 WILD-TYPE        18          5         43         32       33        12
                vv
clus             STAGE IVB
  LIG1 MUTATED           0
  LIG1 WILD-TYPE         1
D582V3, multiclass
            clus
vv           LIG1 MUTATED LIG1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  LIG1 MUTATED     0   5   6   5
  LIG1 WILD-TYPE   9  62 243  36
D582V4, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  T1            0              9
  T2            5             62
  T3            6            243
  T4            5             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
  LIG1 MUTATED    11   3   2
  LIG1 WILD-TYPE 209  78  64
D582V5, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  N0           11            209
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V6, binary
                cls
clus               0   1
  LIG1 MUTATED    14   2
  LIG1 WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     14    2
  LIG1 WILD-TYPE  271   46
   clus
vv  LIG1 MUTATED LIG1 WILD-TYPE
  0           14            271
  1            2             46
[1] 2 2
[1] FALSE
D582V7, binary
                cls
clus               0   1
  LIG1 MUTATED     6  10
  LIG1 WILD-TYPE 164 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      6   10
  LIG1 WILD-TYPE  164  187
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  FEMALE            6            164
  MALE             10            187
[1] 2 2
[1] FALSE
D582V8, binary
                cls
clus               0   1
  LIG1 MUTATED    14   0
  LIG1 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     14    0
  LIG1 WILD-TYPE  286    8
     clus
vv    LIG1 MUTATED LIG1 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D582V9, binary
                cls
clus               0   1
  LIG1 MUTATED    13   3
  LIG1 WILD-TYPE 301  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     13    3
  LIG1 WILD-TYPE  301   45
                               clus
vv                              LIG1 MUTATED LIG1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LIG1 MUTATED    13   0   0   0
  LIG1 WILD-TYPE 246   3  22  21
D582V10, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            0             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"
D582V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIG1 MUTATED                                  0     0
  LIG1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIG1 MUTATED                           1    10
  LIG1 WILD-TYPE                        18   166
D582V12, multiclass
                                  clus
vv                                 LIG1 MUTATED LIG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(583) Variable = ARHGEF10 MUTATION ANALYSIS
D583V1, survival
                    sevent
clus2                  0   1
  ARHGEF10 MUTATED    20   3
  ARHGEF10 WILD-TYPE 257  75
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                23                332 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                 3                 75 
$`ARHGEF10 MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3950 TCGA-A6-6141 TCGA-A6-6780 
        1.02         0.92        19.04        24.00         8.38        20.12 
TCGA-AA-3518 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A01P 
        1.02        26.99        53.00         2.01        25.02        38.07 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       12.16        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 
       14.04        11.01        17.85        15.58        11.64 

$`ARHGEF10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
              0.92               0.00 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
             58.39             148.01 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
             15.58              22.39 
[1] "0.9 - 58.4 (15.6)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D583V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF10 MUTATED         2        0        2        13         0         0
  ARHGEF10 WILD-TYPE      62        1       24        95         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF10 MUTATED           2          0          1          0        1
  ARHGEF10 WILD-TYPE        16          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGEF10 MUTATED           0         0
  ARHGEF10 WILD-TYPE        12         1
D583V3, multiclass
            clus
vv           ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                13                 95
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  ARHGEF10 MUTATED     0   4  19   0
  ARHGEF10 WILD-TYPE   9  63 230  41
D583V4, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  T1                0                  9
  T2                4                 63
  T3               19                230
  T4                0                 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
  ARHGEF10 MUTATED    19   4   0
  ARHGEF10 WILD-TYPE 201  77  66
D583V5, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  N0               19                201
  N1                4                 77
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V6, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    18   1
  ARHGEF10 WILD-TYPE 267  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     18    1
  ARHGEF10 WILD-TYPE  267   47
   clus
vv  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  0               18                267
  1                1                 47
[1] 2 2
[1] FALSE
D583V7, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    10  13
  ARHGEF10 WILD-TYPE 160 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     10   13
  ARHGEF10 WILD-TYPE  160  184
        clus
vv       ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  FEMALE               10                160
  MALE                 13                184
[1] 2 2
[1] FALSE
D583V8, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    19   1
  ARHGEF10 WILD-TYPE 281   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     19    1
  ARHGEF10 WILD-TYPE  281    7
     clus
vv    ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  NO                19                281
  YES                1                  7
[1] 2 2
[1] FALSE
D583V9, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    17   6
  ARHGEF10 WILD-TYPE 297  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     17    6
  ARHGEF10 WILD-TYPE  297   42
                               clus
vv                              ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  COLON ADENOCARCINOMA                        17                297
  COLON MUCINOUS ADENOCARCINOMA                6                 42
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGEF10 MUTATED    15   0   1   2
  ARHGEF10 WILD-TYPE 244   3  21  19
D583V10, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  R0               15                244
  R1                0                  3
  R2                1                 21
  RX                2                 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"
D583V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF10 MUTATED                                  0     2
  ARHGEF10 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF10 MUTATED                           1    10
  ARHGEF10 WILD-TYPE                        18   166
D583V12, multiclass
                                  clus
vv                                 ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          10                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(584) Variable = OVCH1 MUTATION ANALYSIS
D584V1, survival
                 sevent
clus2               0   1
  OVCH1 MUTATED    14   7
  OVCH1 WILD-TYPE 263  71
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             21             334 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
              7              71 
$`OVCH1 MUTATED`
TCGA-G4-6588 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3680 TCGA-AA-3710 
       26.17        20.12        19.66         3.02        11.01        26.99 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6901 TCGA-AU-3779 TCGA-CA-5796 
       25.02         4.01        34.98        22.42        14.50        12.39 
TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-6923 TCGA-DM-A1DB 
       12.76        15.02        29.03        14.04        12.43        44.32 
TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6303 
      135.65         6.18        65.85 

$`OVCH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       24.39        23.87        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       83.24        24.53         5.79        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-6165 
       15.02        17.03        15.02        12.00        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
       12.59       140.38         7.50       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-F4-6703 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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  OVCH1 MUTATED OVCH1 WILD-TYPE 
           3.02            0.00 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
         135.65          148.01 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
          19.66           22.09 
[1] "3.0 - 135.7 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D584V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OVCH1 MUTATED         3        0        1        10         2         0
  OVCH1 WILD-TYPE      61        1       25        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OVCH1 MUTATED           0          0          1          1        2         0
  OVCH1 WILD-TYPE        18          6         43         32       33        12
                 vv
clus              STAGE IVB
  OVCH1 MUTATED           0
  OVCH1 WILD-TYPE         1
D584V3, multiclass
            clus
vv           OVCH1 MUTATED OVCH1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  OVCH1 MUTATED     0   4  14   4
  OVCH1 WILD-TYPE   9  63 235  37
D584V4, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            14             235
  T4             4              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
  OVCH1 MUTATED    18   3   1
  OVCH1 WILD-TYPE 202  78  65
D584V5, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  N0            18             202
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V6, binary
                 cls
clus                0   1
  OVCH1 MUTATED    16   2
  OVCH1 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     16    2
  OVCH1 WILD-TYPE  269   46
   clus
vv  OVCH1 MUTATED OVCH1 WILD-TYPE
  0            16             269
  1             2              46
[1] 2 2
[1] FALSE
D584V7, binary
                 cls
clus                0   1
  OVCH1 MUTATED    12  10
  OVCH1 WILD-TYPE 158 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     12   10
  OVCH1 WILD-TYPE  158  187
        clus
vv       OVCH1 MUTATED OVCH1 WILD-TYPE
  FEMALE            12             158
  MALE              10             187
[1] 2 2
[1] FALSE
D584V8, binary
                 cls
clus                0   1
  OVCH1 MUTATED    18   0
  OVCH1 WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     18    0
  OVCH1 WILD-TYPE  282    8
     clus
vv    OVCH1 MUTATED OVCH1 WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D584V9, binary
                 cls
clus                0   1
  OVCH1 MUTATED    16   5
  OVCH1 WILD-TYPE 298  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     16    5
  OVCH1 WILD-TYPE  298   43
                               clus
vv                              OVCH1 MUTATED OVCH1 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OVCH1 MUTATED    15   0   1   1
  OVCH1 WILD-TYPE 244   3  21  20
D584V10, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             1              21
  RX             1              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"
D584V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OVCH1 MUTATED                                  0     2
  OVCH1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OVCH1 MUTATED                           0    13
  OVCH1 WILD-TYPE                        19   163
D584V12, multiclass
                                  clus
vv                                 OVCH1 MUTATED OVCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       13             163
[1] 4 2
[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 = RRS1 MUTATION ANALYSIS
D585V1, survival
                sevent
clus2              0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 273  78
  RRS1 MUTATED RRS1 WILD-TYPE 
             4            351 
  RRS1 MUTATED RRS1 WILD-TYPE 
             0             78 
$`RRS1 MUTATED`
TCGA-G4-6588 TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6928 
       26.17        15.02        16.14        11.64 

$`RRS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.09 
[1] "11.6 - 26.2 (15.6)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D585V2, continuous
                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      62        1       26       106         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  RRS1 MUTATED           0
  RRS1 WILD-TYPE         1
D585V3, multiclass
            clus
vv           RRS1 MUTATED RRS1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RRS1 MUTATED     0   2   2   0
  RRS1 WILD-TYPE   9  65 247  41
D585V4, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            2            247
  T4            0             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
  RRS1 MUTATED     4   0   0
  RRS1 WILD-TYPE 216  81  66
D585V5, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V6, binary
                cls
clus               0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    0
  RRS1 WILD-TYPE  281   48
   clus
vv  RRS1 MUTATED RRS1 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D585V7, binary
                cls
clus               0   1
  RRS1 MUTATED     2   2
  RRS1 WILD-TYPE 168 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      2    2
  RRS1 WILD-TYPE  168  195
        clus
vv       RRS1 MUTATED RRS1 WILD-TYPE
  FEMALE            2            168
  MALE              2            195
[1] 2 2
[1] FALSE
D585V8, binary
                cls
clus               0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    0
  RRS1 WILD-TYPE  296    8
     clus
vv    RRS1 MUTATED RRS1 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D585V9, binary
                cls
clus               0   1
  RRS1 MUTATED     2   2
  RRS1 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      2    2
  RRS1 WILD-TYPE  312   46
                               clus
vv                              RRS1 MUTATED RRS1 WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RRS1 MUTATED     4   0   0   0
  RRS1 WILD-TYPE 255   3  22  21
D585V10, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D585V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRS1 MUTATED                                  0     0
  RRS1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RRS1 MUTATED                           0     4
  RRS1 WILD-TYPE                        19   172
D585V12, multiclass
                                  clus
vv                                 RRS1 MUTATED RRS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = RFXAP MUTATION ANALYSIS
D586V1, survival
                 sevent
clus2               0   1
  RFXAP MUTATED     4   2
  RFXAP WILD-TYPE 273  76
  RFXAP MUTATED RFXAP WILD-TYPE 
              6             349 
  RFXAP MUTATED RFXAP WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        9.07        19.07        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RFXAP MUTATED RFXAP WILD-TYPE 
              0               0 
  RFXAP MUTATED RFXAP WILD-TYPE 
          29.19          148.01 
  RFXAP MUTATED RFXAP WILD-TYPE 
          12.43           22.09 
[1] "0.0 - 29.2 (12.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.9"
D586V2, continuous
                 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      64        1       26       106         8         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        18          6         43         31       34        12
                 vv
clus              STAGE IVB
  RFXAP MUTATED           0
  RFXAP WILD-TYPE         1
D586V3, multiclass
            clus
vv           RFXAP MUTATED RFXAP WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  RFXAP MUTATED     0   0   5   1
  RFXAP WILD-TYPE   9  67 244  40
D586V4, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             1              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
  RFXAP MUTATED     2   2   2
  RFXAP WILD-TYPE 218  79  64
D586V5, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  N0             2             218
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V6, binary
                 cls
clus                0   1
  RFXAP MUTATED     5   1
  RFXAP WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      5    1
  RFXAP WILD-TYPE  280   47
   clus
vv  RFXAP MUTATED RFXAP WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D586V7, binary
                 cls
clus                0   1
  RFXAP MUTATED     2   4
  RFXAP WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      2    4
  RFXAP WILD-TYPE  168  193
        clus
vv       RFXAP MUTATED RFXAP WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D586V8, binary
                 cls
clus                0   1
  RFXAP MUTATED     5   0
  RFXAP WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      5    0
  RFXAP WILD-TYPE  295    8
     clus
vv    RFXAP MUTATED RFXAP WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D586V9, binary
                 cls
clus                0   1
  RFXAP MUTATED     5   1
  RFXAP WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      5    1
  RFXAP WILD-TYPE  309   47
                               clus
vv                              RFXAP MUTATED RFXAP WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RFXAP MUTATED     2   0   0   1
  RFXAP WILD-TYPE 257   3  22  20
D586V10, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             1              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"
D586V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RFXAP MUTATED                                  0     1
  RFXAP WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RFXAP MUTATED                           2     2
  RFXAP WILD-TYPE                        17   174
D586V12, multiclass
                                  clus
vv                                 RFXAP MUTATED RFXAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        2             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(587) Variable = RBAK MUTATION ANALYSIS
D587V1, survival
                sevent
clus2              0   1
  RBAK MUTATED    15   2
  RBAK WILD-TYPE 262  76
  RBAK MUTATED RBAK WILD-TYPE 
            17            338 
  RBAK MUTATED RBAK WILD-TYPE 
             2             76 
$`RBAK MUTATED`
TCGA-AA-3525 TCGA-AA-3939 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
        8.05        12.99        78.08        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 
       14.30       131.51        13.25       133.18        53.62 

$`RBAK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
       51.32        21.99        82.95         2.01        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50        44.32       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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       43.04        33.67         0.53        47.41        35.31        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-G4-6626 
       13.78        46.75 

  RBAK MUTATED RBAK WILD-TYPE 
          8.05           0.00 
  RBAK MUTATED RBAK WILD-TYPE 
        133.18         148.01 
  RBAK MUTATED RBAK WILD-TYPE 
         29.03          22.01 
[1] "8.1 - 133.2 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3"  
D587V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBAK MUTATED         3        0        1         6         2         0
  RBAK WILD-TYPE      61        1       25       102         6         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        17          6         43         31       35        11
                vv
clus             STAGE IVB
  RBAK MUTATED           0
  RBAK WILD-TYPE         1
D587V3, multiclass
            clus
vv           RBAK MUTATED RBAK WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             1             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
  RBAK MUTATED     1   2  11   3
  RBAK WILD-TYPE   8  65 238  38
D587V4, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  T1            1              8
  T2            2             65
  T3           11            238
  T4            3             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
  RBAK MUTATED    12   3   2
  RBAK WILD-TYPE 208  78  64
D587V5, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  N0           12            208
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V6, binary
                cls
clus               0   1
  RBAK MUTATED    15   1
  RBAK WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     15    1
  RBAK WILD-TYPE  270   47
   clus
vv  RBAK MUTATED RBAK WILD-TYPE
  0           15            270
  1            1             47
[1] 2 2
[1] FALSE
D587V7, binary
                cls
clus               0   1
  RBAK MUTATED     9   8
  RBAK WILD-TYPE 161 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED      9    8
  RBAK WILD-TYPE  161  189
        clus
vv       RBAK MUTATED RBAK WILD-TYPE
  FEMALE            9            161
  MALE              8            189
[1] 2 2
[1] FALSE
D587V8, binary
                cls
clus               0   1
  RBAK MUTATED    15   0
  RBAK WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     15    0
  RBAK WILD-TYPE  285    8
     clus
vv    RBAK MUTATED RBAK WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D587V9, binary
                cls
clus               0   1
  RBAK MUTATED    14   3
  RBAK WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     14    3
  RBAK WILD-TYPE  300   45
                               clus
vv                              RBAK MUTATED RBAK WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBAK MUTATED    12   0   0   4
  RBAK WILD-TYPE 247   3  22  17
D587V10, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            4             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"
D587V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBAK MUTATED                                  0     1
  RBAK WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBAK MUTATED                           1    11
  RBAK WILD-TYPE                        18   165
D587V12, multiclass
                                  clus
vv                                 RBAK MUTATED RBAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(588) Variable = ZHX1 MUTATION ANALYSIS
D588V1, survival
                sevent
clus2              0   1
  ZHX1 MUTATED     6   3
  ZHX1 WILD-TYPE 271  75
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             9            346 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             3             75 
$`ZHX1 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6678 
       63.98        34.98        12.16        49.41        12.76        11.01 
TCGA-D5-6929 TCGA-F4-6460 TCGA-G4-6626 
       13.41        31.96        46.75 

$`ZHX1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  ZHX1 MUTATED ZHX1 WILD-TYPE 
         11.01           0.00 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
         63.98         148.01 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
        31.960         22.045 
[1] "11.0 - 64.0 (32.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D588V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZHX1 MUTATED         1        0        2         2         1         0
  ZHX1 WILD-TYPE      63        1       24       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX1 MUTATED           0          0          1          0        1         1
  ZHX1 WILD-TYPE        18          6         43         33       34        11
                vv
clus             STAGE IVB
  ZHX1 MUTATED           0
  ZHX1 WILD-TYPE         1
D588V3, multiclass
            clus
vv           ZHX1 MUTATED ZHX1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  ZHX1 MUTATED     0   1   6   2
  ZHX1 WILD-TYPE   9  66 243  39
D588V4, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            2             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
  ZHX1 MUTATED     6   3   0
  ZHX1 WILD-TYPE 214  78  66
D588V5, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  N0            6            214
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V6, binary
                cls
clus               0   1
  ZHX1 MUTATED     5   2
  ZHX1 WILD-TYPE 280  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      5    2
  ZHX1 WILD-TYPE  280   46
   clus
vv  ZHX1 MUTATED ZHX1 WILD-TYPE
  0            5            280
  1            2             46
[1] 2 2
[1] FALSE
D588V7, binary
                cls
clus               0   1
  ZHX1 MUTATED     5   4
  ZHX1 WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      5    4
  ZHX1 WILD-TYPE  165  193
        clus
vv       ZHX1 MUTATED ZHX1 WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D588V8, binary
                cls
clus               0   1
  ZHX1 MUTATED     9   0
  ZHX1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      9    0
  ZHX1 WILD-TYPE  291    8
     clus
vv    ZHX1 MUTATED ZHX1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D588V9, binary
                cls
clus               0   1
  ZHX1 MUTATED     7   2
  ZHX1 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      7    2
  ZHX1 WILD-TYPE  307   46
                               clus
vv                              ZHX1 MUTATED ZHX1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ZHX1 MUTATED     7   0   0   1
  ZHX1 WILD-TYPE 252   3  22  20
D588V10, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D588V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZHX1 MUTATED                                  0     1
  ZHX1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZHX1 MUTATED                           0     6
  ZHX1 WILD-TYPE                        19   170
D588V12, multiclass
                                  clus
vv                                 ZHX1 MUTATED ZHX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = DOCK10 MUTATION ANALYSIS
D589V1, survival
                  sevent
clus2                0   1
  DOCK10 MUTATED    16   7
  DOCK10 WILD-TYPE 261  71
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              23              332 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               7               71 
$`DOCK10 MUTATED`
TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3986 
       24.16         1.02         0.92        85.05        19.04        19.07 
TCGA-A6-3809 TCGA-AA-3667 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       32.75        14.01         1.02        25.02         4.01        34.98 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
       12.16        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 
       92.75        12.59       135.65         6.18        55.04 

$`DOCK10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L 
       24.00         2.01        50.99        26.01        24.00        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DOCK10 MUTATED DOCK10 WILD-TYPE 
            0.92             0.00 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
          135.65           148.01 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
          19.040           22.225 
[1] "0.9 - 135.7 (19.0)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.4"
D589V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK10 MUTATED         4        0        3         6         3         0
  DOCK10 WILD-TYPE      60        1       23       102         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOCK10 MUTATED           1          0          3          0        2
  DOCK10 WILD-TYPE        17          6         41         33       33
                  vv
clus               STAGE IVA STAGE IVB
  DOCK10 MUTATED           0         0
  DOCK10 WILD-TYPE        12         1
D589V3, multiclass
            clus
vv           DOCK10 MUTATED DOCK10 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               6              102
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  DOCK10 MUTATED     0   5  15   5
  DOCK10 WILD-TYPE   9  62 234  36
D589V4, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  T1              0                9
  T2              5               62
  T3             15              234
  T4              5               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
  DOCK10 MUTATED    19   6   0
  DOCK10 WILD-TYPE 201  75  66
D589V5, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  N0             19              201
  N1              6               75
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V6, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    18   2
  DOCK10 WILD-TYPE 267  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     18    2
  DOCK10 WILD-TYPE  267   46
   clus
vv  DOCK10 MUTATED DOCK10 WILD-TYPE
  0             18              267
  1              2               46
[1] 2 2
[1] FALSE
D589V7, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    11  14
  DOCK10 WILD-TYPE 159 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     11   14
  DOCK10 WILD-TYPE  159  183
        clus
vv       DOCK10 MUTATED DOCK10 WILD-TYPE
  FEMALE             11              159
  MALE               14              183
[1] 2 2
[1] FALSE
D589V8, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    17   1
  DOCK10 WILD-TYPE 283   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     17    1
  DOCK10 WILD-TYPE  283    7
     clus
vv    DOCK10 MUTATED DOCK10 WILD-TYPE
  NO              17              283
  YES              1                7
[1] 2 2
[1] FALSE
D589V9, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    19   5
  DOCK10 WILD-TYPE 295  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     19    5
  DOCK10 WILD-TYPE  295   43
                               clus
vv                              DOCK10 MUTATED DOCK10 WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DOCK10 MUTATED    15   0   1   2
  DOCK10 WILD-TYPE 244   3  21  19
D589V10, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              1               21
  RX              2               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"
D589V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK10 MUTATED                                  0     2
  DOCK10 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DOCK10 MUTATED                           1    10
  DOCK10 WILD-TYPE                        18   166
D589V12, multiclass
                                  clus
vv                                 DOCK10 MUTATED DOCK10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(590) Variable = CHEK2 MUTATION ANALYSIS
D590V1, survival
                 sevent
clus2               0   1
  CHEK2 MUTATED     8   2
  CHEK2 WILD-TYPE 269  76
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             345 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
              2              76 
$`CHEK2 MUTATED`
TCGA-AZ-6608 TCGA-A6-6653 TCGA-AA-3815 TCGA-AA-A01Q TCGA-CA-6717 TCGA-CA-6718 
        1.94        24.39        33.04         1.02        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  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          22.090 
[1] "1.0 - 36.0 (16.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D590V2, continuous
                 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      63        1       25       102         8         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        18          5         44         32       35        12
                 vv
clus              STAGE IVB
  CHEK2 MUTATED           0
  CHEK2 WILD-TYPE         1
D590V3, multiclass
            clus
vv           CHEK2 MUTATED CHEK2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CHEK2 MUTATED     0   2   8   0
  CHEK2 WILD-TYPE   9  65 241  41
D590V4, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             0              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
  CHEK2 MUTATED     8   1   1
  CHEK2 WILD-TYPE 212  80  65
D590V5, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V6, binary
                 cls
clus                0   1
  CHEK2 MUTATED     9   0
  CHEK2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      9    0
  CHEK2 WILD-TYPE  276   48
   clus
vv  CHEK2 MUTATED CHEK2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D590V7, binary
                 cls
clus                0   1
  CHEK2 MUTATED     4   6
  CHEK2 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      4    6
  CHEK2 WILD-TYPE  166  191
        clus
vv       CHEK2 MUTATED CHEK2 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D590V8, binary
                 cls
clus                0   1
  CHEK2 MUTATED     9   0
  CHEK2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      9    0
  CHEK2 WILD-TYPE  291    8
     clus
vv    CHEK2 MUTATED CHEK2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D590V9, binary
                 cls
clus                0   1
  CHEK2 MUTATED     8   2
  CHEK2 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      8    2
  CHEK2 WILD-TYPE  306   46
                               clus
vv                              CHEK2 MUTATED CHEK2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHEK2 MUTATED     6   0   0   2
  CHEK2 WILD-TYPE 253   3  22  19
D590V10, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D590V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHEK2 MUTATED                                  0     2
  CHEK2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHEK2 MUTATED                           0     6
  CHEK2 WILD-TYPE                        19   170
D590V12, multiclass
                                  clus
vv                                 CHEK2 MUTATED CHEK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = USP9X MUTATION ANALYSIS
D591V1, survival
                 sevent
clus2               0   1
  USP9X MUTATED    19  11
  USP9X WILD-TYPE 258  67
  USP9X MUTATED USP9X WILD-TYPE 
             30             325 
  USP9X MUTATED USP9X WILD-TYPE 
             11              67 
$`USP9X MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-CK-5912 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5660 
       19.04        19.04        49.08        26.17        79.69        29.19 
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3815 
       22.06         3.02        63.98         6.97        10.06        33.04 
TCGA-AA-3864 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6718 
       53.00         4.01        58.39        22.36        49.41        10.06 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 
       85.45        51.32         5.03        15.02        12.00        16.04 
TCGA-CM-6680 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-F4-6570 TCGA-F4-6856 
       12.03         4.80        17.13         7.53         6.18        35.31 

$`USP9X WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
        1.94         5.88        63.62        22.09        35.80        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  USP9X MUTATED USP9X WILD-TYPE 
           3.02            0.00 
  USP9X MUTATED USP9X WILD-TYPE 
          85.45          148.01 
  USP9X MUTATED USP9X WILD-TYPE 
          19.04           22.09 
[1] "3.0 - 85.5 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D591V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP9X MUTATED         5        0        6         9         1         0
  USP9X WILD-TYPE      59        1       20        99         7         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        17          6         39         32       34        10
                 vv
clus              STAGE IVB
  USP9X MUTATED           0
  USP9X WILD-TYPE         1
D591V3, multiclass
            clus
vv           USP9X MUTATED USP9X WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA              9              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              2              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
  USP9X MUTATED     0   5  25   1
  USP9X WILD-TYPE   9  62 224  40
D591V4, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  T1             0               9
  T2             5              62
  T3            25             224
  T4             1              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
  USP9X MUTATED    23   4   4
  USP9X WILD-TYPE 197  77  62
D591V5, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  N0            23             197
  N1             4              77
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V6, binary
                 cls
clus                0   1
  USP9X MUTATED    24   3
  USP9X WILD-TYPE 261  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     24    3
  USP9X WILD-TYPE  261   45
   clus
vv  USP9X MUTATED USP9X WILD-TYPE
  0            24             261
  1             3              45
[1] 2 2
[1] FALSE
D591V7, binary
                 cls
clus                0   1
  USP9X MUTATED    14  17
  USP9X WILD-TYPE 156 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     14   17
  USP9X WILD-TYPE  156  180
        clus
vv       USP9X MUTATED USP9X WILD-TYPE
  FEMALE            14             156
  MALE              17             180
[1] 2 2
[1] FALSE
D591V8, binary
                 cls
clus                0   1
  USP9X MUTATED    28   1
  USP9X WILD-TYPE 272   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     28    1
  USP9X WILD-TYPE  272    7
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO             28             272
  YES             1               7
[1] 2 2
[1] FALSE
D591V9, binary
                 cls
clus                0   1
  USP9X MUTATED    27   4
  USP9X WILD-TYPE 287  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     27    4
  USP9X WILD-TYPE  287   44
                               clus
vv                              USP9X MUTATED USP9X WILD-TYPE
  COLON ADENOCARCINOMA                     27             287
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP9X MUTATED    24   1   1   3
  USP9X WILD-TYPE 235   2  21  18
D591V10, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  R0            24             235
  R1             1               2
  R2             1              21
  RX             3              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"
D591V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP9X MUTATED                                  0     1
  USP9X WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP9X MUTATED                           2    18
  USP9X WILD-TYPE                        17   158
D591V12, multiclass
                                  clus
vv                                 USP9X MUTATED USP9X WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       18             158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(592) Variable = OR5B2 MUTATION ANALYSIS
D592V1, survival
                 sevent
clus2               0   1
  OR5B2 MUTATED     9   2
  OR5B2 WILD-TYPE 268  76
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             11             344 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
              2              76 
$`OR5B2 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       63.98        25.02        34.98         0.20        21.44        58.39 
TCGA-AZ-6605 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-6537 TCGA-DM-A0X9 
        5.23        21.99        11.08         4.80       119.70 

$`OR5B2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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-6717 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OR5B2 MUTATED OR5B2 WILD-TYPE 
            0.2             0.0 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
         119.70          148.01 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
         21.990          22.075 
[1] "0.2 - 119.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D592V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5B2 MUTATED         2        0        1         3         1         0
  OR5B2 WILD-TYPE      62        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5B2 MUTATED           1          0          2          1        0         0
  OR5B2 WILD-TYPE        17          6         42         32       35        12
                 vv
clus              STAGE IVB
  OR5B2 MUTATED           0
  OR5B2 WILD-TYPE         1
D592V3, multiclass
            clus
vv           OR5B2 MUTATED OR5B2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OR5B2 MUTATED     0   3   7   2
  OR5B2 WILD-TYPE   9  64 242  39
D592V4, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             7             242
  T4             2              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
  OR5B2 MUTATED     8   2   2
  OR5B2 WILD-TYPE 212  79  64
D592V5, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V6, binary
                 cls
clus                0   1
  OR5B2 MUTATED     8   0
  OR5B2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED      8    0
  OR5B2 WILD-TYPE  277   48
   clus
vv  OR5B2 MUTATED OR5B2 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D592V7, binary
                 cls
clus                0   1
  OR5B2 MUTATED     3   9
  OR5B2 WILD-TYPE 167 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED      3    9
  OR5B2 WILD-TYPE  167  188
        clus
vv       OR5B2 MUTATED OR5B2 WILD-TYPE
  FEMALE             3             167
  MALE               9             188
[1] 2 2
[1] FALSE
D592V8, binary
                 cls
clus                0   1
  OR5B2 MUTATED     9   0
  OR5B2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED      9    0
  OR5B2 WILD-TYPE  291    8
     clus
vv    OR5B2 MUTATED OR5B2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D592V9, binary
                 cls
clus                0   1
  OR5B2 MUTATED    11   1
  OR5B2 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED     11    1
  OR5B2 WILD-TYPE  303   47
                               clus
vv                              OR5B2 MUTATED OR5B2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5B2 MUTATED     9   0   0   0
  OR5B2 WILD-TYPE 250   3  22  21
D592V10, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D592V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5B2 MUTATED                                  0     0
  OR5B2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5B2 MUTATED                           0     8
  OR5B2 WILD-TYPE                        19   168
D592V12, multiclass
                                  clus
vv                                 OR5B2 MUTATED OR5B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = IFNAR1 MUTATION ANALYSIS
D593V1, survival
                  sevent
clus2                0   1
  IFNAR1 MUTATED     6   1
  IFNAR1 WILD-TYPE 271  77
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              348 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               1               77 
$`IFNAR1 MUTATED`
TCGA-AA-3672 TCGA-CK-5912 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-A010 TCGA-CM-5860 
        0.92        49.08        33.04        32.05        34.98        32.02 
TCGA-CM-6678 
       11.01 

$`IFNAR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
            0.92             0.00 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
           49.08           148.01 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
           32.05            22.01 
[1] "0.9 - 49.1 (32.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D593V2, continuous
                  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      62        1       26       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFNAR1 MUTATED           1          0          0          0        0
  IFNAR1 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  IFNAR1 MUTATED           1         0
  IFNAR1 WILD-TYPE        11         1
D593V3, multiclass
            clus
vv           IFNAR1 MUTATED IFNAR1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  IFNAR1 MUTATED     0   2   3   2
  IFNAR1 WILD-TYPE   9  65 246  39
D593V4, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              3              246
  T4              2               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
  IFNAR1 MUTATED     5   2   0
  IFNAR1 WILD-TYPE 215  79  66
D593V5, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  N0              5              215
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V6, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     5   1
  IFNAR1 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      5    1
  IFNAR1 WILD-TYPE  280   47
   clus
vv  IFNAR1 MUTATED IFNAR1 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D593V7, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     4   3
  IFNAR1 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      4    3
  IFNAR1 WILD-TYPE  166  194
        clus
vv       IFNAR1 MUTATED IFNAR1 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D593V8, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     7   0
  IFNAR1 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      7    0
  IFNAR1 WILD-TYPE  293    8
     clus
vv    IFNAR1 MUTATED IFNAR1 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D593V9, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     7   0
  IFNAR1 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      7    0
  IFNAR1 WILD-TYPE  307   48
                               clus
vv                              IFNAR1 MUTATED IFNAR1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IFNAR1 MUTATED     6   0   0   1
  IFNAR1 WILD-TYPE 253   3  22  20
D593V10, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D593V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNAR1 MUTATED                                  0     0
  IFNAR1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFNAR1 MUTATED                           0     3
  IFNAR1 WILD-TYPE                        19   173
D593V12, multiclass
                                  clus
vv                                 IFNAR1 MUTATED IFNAR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ALDH2 MUTATION ANALYSIS
D594V1, survival
                 sevent
clus2               0   1
  ALDH2 MUTATED     8   2
  ALDH2 WILD-TYPE 269  76
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             10             345 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              2              76 
$`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 
       49.41        12.59        11.64        53.62 

$`ALDH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95         0.20        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-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-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ALDH2 MUTATED ALDH2 WILD-TYPE 
           1.02            0.00 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          53.62          148.01 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
         20.235          22.060 
[1] "1.0 - 53.6 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D594V2, continuous
                 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      63        1       23       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALDH2 MUTATED           0          0          1          0        0         1
  ALDH2 WILD-TYPE        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  ALDH2 MUTATED           0
  ALDH2 WILD-TYPE         1
D594V3, multiclass
            clus
vv           ALDH2 MUTATED ALDH2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  ALDH2 MUTATED     0   1   7   3
  ALDH2 WILD-TYPE   9  66 242  38
D594V4, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             3              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
  ALDH2 MUTATED     9   2   0
  ALDH2 WILD-TYPE 211  79  66
D594V5, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V6, binary
                 cls
clus                0   1
  ALDH2 MUTATED     8   1
  ALDH2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      8    1
  ALDH2 WILD-TYPE  277   47
   clus
vv  ALDH2 MUTATED ALDH2 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D594V7, binary
                 cls
clus                0   1
  ALDH2 MUTATED     5   6
  ALDH2 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      5    6
  ALDH2 WILD-TYPE  165  191
        clus
vv       ALDH2 MUTATED ALDH2 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D594V8, binary
                 cls
clus                0   1
  ALDH2 MUTATED     9   0
  ALDH2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      9    0
  ALDH2 WILD-TYPE  291    8
     clus
vv    ALDH2 MUTATED ALDH2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D594V9, binary
                 cls
clus                0   1
  ALDH2 MUTATED     9   2
  ALDH2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      9    2
  ALDH2 WILD-TYPE  305   46
                               clus
vv                              ALDH2 MUTATED ALDH2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALDH2 MUTATED     9   0   0   0
  ALDH2 WILD-TYPE 250   3  22  21
D594V10, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D594V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDH2 MUTATED                                  0     1
  ALDH2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALDH2 MUTATED                           1     4
  ALDH2 WILD-TYPE                        18   172
D594V12, multiclass
                                  clus
vv                                 ALDH2 MUTATED ALDH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = ZNF14 MUTATION ANALYSIS
D595V1, survival
                 sevent
clus2               0   1
  ZNF14 MUTATED     9   3
  ZNF14 WILD-TYPE 268  75
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             12             343 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
              3              75 
$`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 

$`ZNF14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A01Z TCGA-AA-A029 
       35.01         1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZNF14 MUTATED ZNF14 WILD-TYPE 
           4.01            0.00 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
          88.21          148.01 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
          18.18           22.09 
[1] "4.0 - 88.2 (18.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D595V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF14 MUTATED         1        0        0         7         2         0
  ZNF14 WILD-TYPE      63        1       26       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF14 MUTATED           1          0          0          0        0         0
  ZNF14 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  ZNF14 MUTATED           0
  ZNF14 WILD-TYPE         1
D595V3, multiclass
            clus
vv           ZNF14 MUTATED ZNF14 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ZNF14 MUTATED     1   1   9   2
  ZNF14 WILD-TYPE   8  66 240  39
D595V4, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             9             240
  T4             2              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
  ZNF14 MUTATED    12   1   0
  ZNF14 WILD-TYPE 208  80  66
D595V5, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V6, binary
                 cls
clus                0   1
  ZNF14 MUTATED    12   0
  ZNF14 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     12    0
  ZNF14 WILD-TYPE  273   48
   clus
vv  ZNF14 MUTATED ZNF14 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D595V7, binary
                 cls
clus                0   1
  ZNF14 MUTATED     6   7
  ZNF14 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED      6    7
  ZNF14 WILD-TYPE  164  190
        clus
vv       ZNF14 MUTATED ZNF14 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D595V8, binary
                 cls
clus                0   1
  ZNF14 MUTATED    11   0
  ZNF14 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     11    0
  ZNF14 WILD-TYPE  289    8
     clus
vv    ZNF14 MUTATED ZNF14 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D595V9, binary
                 cls
clus                0   1
  ZNF14 MUTATED    11   2
  ZNF14 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     11    2
  ZNF14 WILD-TYPE  303   46
                               clus
vv                              ZNF14 MUTATED ZNF14 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZNF14 MUTATED     7   0   0   3
  ZNF14 WILD-TYPE 252   3  22  18
D595V10, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             3              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"
D595V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF14 MUTATED                                  0     2
  ZNF14 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF14 MUTATED                           1     6
  ZNF14 WILD-TYPE                        18   170
D595V12, multiclass
                                  clus
vv                                 ZNF14 MUTATED ZNF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = CYP4A22 MUTATION ANALYSIS
D596V1, survival
                   sevent
clus2                 0   1
  CYP4A22 MUTATED     7   5
  CYP4A22 WILD-TYPE 270  73
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               12               343 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                5                73 
$`CYP4A22 MUTATED`
TCGA-AD-6895 TCGA-AA-3821 TCGA-AD-6889 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-6717 
       25.08         1.02        83.24        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        14.04         4.80        14.30        38.20       139.17 

$`CYP4A22 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        5.23        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6164 
        5.03        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
             1.02              0.00 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
           139.17            148.01 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            14.17             22.09 
[1] "1.0 - 139.2 (14.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D596V2, continuous
                   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      61        1       26       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4A22 MUTATED           0          0          2          1        2
  CYP4A22 WILD-TYPE        18          6         42         32       33
                   vv
clus                STAGE IVA STAGE IVB
  CYP4A22 MUTATED           0         0
  CYP4A22 WILD-TYPE        12         1
D596V3, multiclass
            clus
vv           CYP4A22 MUTATED CYP4A22 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 2                33
  STAGE IVA                0                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
  CYP4A22 MUTATED     1   2   8   2
  CYP4A22 WILD-TYPE   8  65 241  39
D596V4, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               8               241
  T4               2                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
  CYP4A22 MUTATED     8   2   3
  CYP4A22 WILD-TYPE 212  79  63
D596V5, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  N0               8               212
  N1               2                79
  N2               3                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"
D596V6, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED    10   2
  CYP4A22 WILD-TYPE 275  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED     10    2
  CYP4A22 WILD-TYPE  275   46
   clus
vv  CYP4A22 MUTATED CYP4A22 WILD-TYPE
  0              10               275
  1               2                46
[1] 2 2
[1] FALSE
D596V7, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED     4   9
  CYP4A22 WILD-TYPE 166 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      4    9
  CYP4A22 WILD-TYPE  166  188
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  FEMALE               4               166
  MALE                 9               188
[1] 2 2
[1] FALSE
D596V8, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED    10   0
  CYP4A22 WILD-TYPE 290   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED     10    0
  CYP4A22 WILD-TYPE  290    8
     clus
vv    CYP4A22 MUTATED CYP4A22 WILD-TYPE
  NO               10               290
  YES               0                 8
[1] 2 2
[1] FALSE
D596V9, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED    10   2
  CYP4A22 WILD-TYPE 304  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED     10    2
  CYP4A22 WILD-TYPE  304   46
                               clus
vv                              CYP4A22 MUTATED CYP4A22 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP4A22 MUTATED     8   0   0   1
  CYP4A22 WILD-TYPE 251   3  22  20
D596V10, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               1                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"
D596V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4A22 MUTATED                                  0     2
  CYP4A22 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP4A22 MUTATED                           0     9
  CYP4A22 WILD-TYPE                        19   167
D596V12, multiclass
                                  clus
vv                                 CYP4A22 MUTATED CYP4A22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(597) Variable = AIFM1 MUTATION ANALYSIS
D597V1, survival
                 sevent
clus2               0   1
  AIFM1 MUTATED     9   2
  AIFM1 WILD-TYPE 268  76
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             344 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
              2              76 
$`AIFM1 MUTATED`
TCGA-AD-6895 TCGA-G4-6321 TCGA-A6-5659 TCGA-AA-A00J TCGA-CA-6718 TCGA-CM-5348 
       25.08        22.09        30.44        18.05        10.06        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-D5-6931 TCGA-DM-A1HB TCGA-G4-6315 
        5.03        15.02        12.00       135.65        61.91 

$`AIFM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  AIFM1 MUTATED AIFM1 WILD-TYPE 
           5.03            0.00 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         135.65          148.01 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         22.090          22.045 
[1] "5.0 - 135.7 (22.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D597V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AIFM1 MUTATED         1        0        0         1         0         0
  AIFM1 WILD-TYPE      63        1       26       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AIFM1 MUTATED           1          0          5          1        1         1
  AIFM1 WILD-TYPE        17          6         39         32       34        11
                 vv
clus              STAGE IVB
  AIFM1 MUTATED           0
  AIFM1 WILD-TYPE         1
D597V3, multiclass
            clus
vv           AIFM1 MUTATED AIFM1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  AIFM1 MUTATED     0   2   7   2
  AIFM1 WILD-TYPE   9  65 242  39
D597V4, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             2              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
  AIFM1 MUTATED     2   8   1
  AIFM1 WILD-TYPE 218  73  65
D597V5, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  N0             2             218
  N1             8              73
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V6, binary
                 cls
clus                0   1
  AIFM1 MUTATED     8   2
  AIFM1 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      8    2
  AIFM1 WILD-TYPE  277   46
   clus
vv  AIFM1 MUTATED AIFM1 WILD-TYPE
  0             8             277
  1             2              46
[1] 2 2
[1] FALSE
D597V7, binary
                 cls
clus                0   1
  AIFM1 MUTATED     2   9
  AIFM1 WILD-TYPE 168 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      2    9
  AIFM1 WILD-TYPE  168  188
        clus
vv       AIFM1 MUTATED AIFM1 WILD-TYPE
  FEMALE             2             168
  MALE               9             188
[1] 2 2
[1] FALSE
D597V8, binary
                 cls
clus                0   1
  AIFM1 MUTATED    10   0
  AIFM1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED     10    0
  AIFM1 WILD-TYPE  290    8
     clus
vv    AIFM1 MUTATED AIFM1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D597V9, binary
                 cls
clus                0   1
  AIFM1 MUTATED     8   2
  AIFM1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      8    2
  AIFM1 WILD-TYPE  306   46
                               clus
vv                              AIFM1 MUTATED AIFM1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AIFM1 MUTATED     9   0   0   1
  AIFM1 WILD-TYPE 250   3  22  20
D597V10, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D597V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIFM1 MUTATED                                  0     1
  AIFM1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AIFM1 MUTATED                           0     9
  AIFM1 WILD-TYPE                        19   167
D597V12, multiclass
                                  clus
vv                                 AIFM1 MUTATED AIFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(598) Variable = ST3GAL6 MUTATION ANALYSIS
D598V1, survival
                   sevent
clus2                 0   1
  ST3GAL6 MUTATED     6   4
  ST3GAL6 WILD-TYPE 271  74
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               10               345 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
                4                74 
$`ST3GAL6 MUTATED`
TCGA-AA-3715 TCGA-AD-6895 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A00R 
       19.04        25.08         6.97        33.01         4.01         0.99 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5864 
       49.41        12.76        21.14        15.02 

$`ST3GAL6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05        18.05        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
             0.99              0.00 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
            49.41            148.01 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
            17.03             22.09 
[1] "1.0 - 49.4 (17.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D598V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST3GAL6 MUTATED         3        0        3         1         2         0
  ST3GAL6 WILD-TYPE      61        1       23       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST3GAL6 MUTATED           0          0          1          0        0
  ST3GAL6 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ST3GAL6 MUTATED           0         0
  ST3GAL6 WILD-TYPE        12         1
D598V3, multiclass
            clus
vv           ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                1               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ST3GAL6 MUTATED     1   2   5   2
  ST3GAL6 WILD-TYPE   8  65 244  39
D598V4, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               5               244
  T4               2                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
  ST3GAL6 MUTATED     9   1   0
  ST3GAL6 WILD-TYPE 211  80  66
D598V5, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  N0               9               211
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V6, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     9   0
  ST3GAL6 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      9    0
  ST3GAL6 WILD-TYPE  276   48
   clus
vv  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D598V7, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     4   6
  ST3GAL6 WILD-TYPE 166 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      4    6
  ST3GAL6 WILD-TYPE  166  191
        clus
vv       ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  FEMALE               4               166
  MALE                 6               191
[1] 2 2
[1] FALSE
D598V8, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     8   0
  ST3GAL6 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      8    0
  ST3GAL6 WILD-TYPE  292    8
     clus
vv    ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D598V9, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     7   3
  ST3GAL6 WILD-TYPE 307  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      7    3
  ST3GAL6 WILD-TYPE  307   45
                               clus
vv                              ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ST3GAL6 MUTATED     7   0   0   2
  ST3GAL6 WILD-TYPE 252   3  22  19
D598V10, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               2                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"
D598V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST3GAL6 MUTATED                                  0     1
  ST3GAL6 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ST3GAL6 MUTATED                           0     4
  ST3GAL6 WILD-TYPE                        19   172
D598V12, multiclass
                                  clus
vv                                 ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = NOVA1 MUTATION ANALYSIS
D599V1, survival
                 sevent
clus2               0   1
  NOVA1 MUTATED     8   5
  NOVA1 WILD-TYPE 269  73
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             13             342 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
              5              73 
$`NOVA1 MUTATED`
TCGA-A6-2677 TCGA-G4-6310 TCGA-A6-3810 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3877 
       24.33        63.62        36.53        19.66        26.99        31.00 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CK-5916 TCGA-D5-6540 
       34.98        12.16        49.41         6.77        21.14        16.14 
TCGA-G4-6303 
       65.85 

$`NOVA1 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NOVA1 MUTATED NOVA1 WILD-TYPE 
           6.77            0.00 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
          65.85          148.01 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
          26.99           22.01 
[1] "6.8 - 65.8 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D599V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOVA1 MUTATED         5        0        1         2         2         0
  NOVA1 WILD-TYPE      59        1       25       106         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOVA1 MUTATED           0          0          1          2        1         0
  NOVA1 WILD-TYPE        18          6         43         31       34        12
                 vv
clus              STAGE IVB
  NOVA1 MUTATED           0
  NOVA1 WILD-TYPE         1
D599V3, multiclass
            clus
vv           NOVA1 MUTATED NOVA1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  NOVA1 MUTATED     2   3   6   3
  NOVA1 WILD-TYPE   7  64 243  38
D599V4, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  T1             2               7
  T2             3              64
  T3             6             243
  T4             3              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
  NOVA1 MUTATED    10   3   1
  NOVA1 WILD-TYPE 210  78  65
D599V5, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  N0            10             210
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V6, binary
                 cls
clus                0   1
  NOVA1 MUTATED     8   1
  NOVA1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED      8    1
  NOVA1 WILD-TYPE  277   47
   clus
vv  NOVA1 MUTATED NOVA1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D599V7, binary
                 cls
clus                0   1
  NOVA1 MUTATED     8   6
  NOVA1 WILD-TYPE 162 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED      8    6
  NOVA1 WILD-TYPE  162  191
        clus
vv       NOVA1 MUTATED NOVA1 WILD-TYPE
  FEMALE             8             162
  MALE               6             191
[1] 2 2
[1] FALSE
D599V8, binary
                 cls
clus                0   1
  NOVA1 MUTATED    12   1
  NOVA1 WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     12    1
  NOVA1 WILD-TYPE  288    7
     clus
vv    NOVA1 MUTATED NOVA1 WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D599V9, binary
                 cls
clus                0   1
  NOVA1 MUTATED    10   4
  NOVA1 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     10    4
  NOVA1 WILD-TYPE  304   44
                               clus
vv                              NOVA1 MUTATED NOVA1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NOVA1 MUTATED    10   0   0   2
  NOVA1 WILD-TYPE 249   3  22  19
D599V10, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D599V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOVA1 MUTATED                                  0     0
  NOVA1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NOVA1 MUTATED                           0    11
  NOVA1 WILD-TYPE                        19   165
D599V12, multiclass
                                  clus
vv                                 NOVA1 MUTATED NOVA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(600) Variable = CD244 MUTATION ANALYSIS
D600V1, survival
                 sevent
clus2               0   1
  CD244 MUTATED     5   2
  CD244 WILD-TYPE 272  76
  CD244 MUTATED CD244 WILD-TYPE 
              7             348 
  CD244 MUTATED CD244 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CD244 MUTATED CD244 WILD-TYPE 
           4.01            0.00 
  CD244 MUTATED CD244 WILD-TYPE 
          63.98          148.01 
  CD244 MUTATED CD244 WILD-TYPE 
          34.98           21.99 
[1] "4.0 - 64.0 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D600V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD244 MUTATED         0        0        2         0         2         0
  CD244 WILD-TYPE      64        1       24       108         6         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  CD244 MUTATED           0
  CD244 WILD-TYPE         1
D600V3, multiclass
            clus
vv           CD244 MUTATED CD244 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              0             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CD244 MUTATED     0   1   4   2
  CD244 WILD-TYPE   9  66 245  39
D600V4, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             2              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
  CD244 MUTATED     5   2   0
  CD244 WILD-TYPE 215  79  66
D600V5, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V6, binary
                 cls
clus                0   1
  CD244 MUTATED     7   0
  CD244 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      7    0
  CD244 WILD-TYPE  278   48
   clus
vv  CD244 MUTATED CD244 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D600V7, binary
                 cls
clus                0   1
  CD244 MUTATED     2   5
  CD244 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      2    5
  CD244 WILD-TYPE  168  192
        clus
vv       CD244 MUTATED CD244 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D600V8, binary
                 cls
clus                0   1
  CD244 MUTATED     6   0
  CD244 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      6    0
  CD244 WILD-TYPE  294    8
     clus
vv    CD244 MUTATED CD244 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D600V9, binary
                 cls
clus                0   1
  CD244 MUTATED     6   1
  CD244 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      6    1
  CD244 WILD-TYPE  308   47
                               clus
vv                              CD244 MUTATED CD244 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CD244 MUTATED     7   0   0   0
  CD244 WILD-TYPE 252   3  22  21
D600V10, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D600V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD244 MUTATED                                  0     0
  CD244 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD244 MUTATED                           1     2
  CD244 WILD-TYPE                        18   174
D600V12, multiclass
                                  clus
vv                                 CD244 MUTATED CD244 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(601) Variable = ARHGEF3 MUTATION ANALYSIS
D601V1, survival
                   sevent
clus2                 0   1
  ARHGEF3 MUTATED    10   1
  ARHGEF3 WILD-TYPE 267  77
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               11               344 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
                1                77 
$`ARHGEF3 MUTATED`
TCGA-AZ-6601 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q 
      100.01        24.39         6.97        25.02        34.98         1.02 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5868 TCGA-D5-6540 
        0.20        58.39        12.76        17.03        16.14 

$`ARHGEF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
              0.2               0.0 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
           100.01            148.01 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
           17.030            22.075 
[1] "0.2 - 100.0 (17.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D601V2, continuous
                   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      62        1       23       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF3 MUTATED           0          0          0          1        0
  ARHGEF3 WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF3 MUTATED           1         0
  ARHGEF3 WILD-TYPE        11         1
D601V3, multiclass
            clus
vv           ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  ARHGEF3 MUTATED     0   3   6   2
  ARHGEF3 WILD-TYPE   9  64 243  39
D601V4, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               6               243
  T4               2                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
  ARHGEF3 MUTATED     9   1   1
  ARHGEF3 WILD-TYPE 211  80  65
D601V5, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  N0               9               211
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V6, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     8   1
  ARHGEF3 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      8    1
  ARHGEF3 WILD-TYPE  277   47
   clus
vv  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D601V7, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     3   8
  ARHGEF3 WILD-TYPE 167 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      3    8
  ARHGEF3 WILD-TYPE  167  189
        clus
vv       ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  FEMALE               3               167
  MALE                 8               189
[1] 2 2
[1] FALSE
D601V8, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     9   0
  ARHGEF3 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      9    0
  ARHGEF3 WILD-TYPE  291    8
     clus
vv    ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D601V9, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     8   3
  ARHGEF3 WILD-TYPE 306  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      8    3
  ARHGEF3 WILD-TYPE  306   45
                               clus
vv                              ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGEF3 MUTATED     7   0   0   1
  ARHGEF3 WILD-TYPE 252   3  22  20
D601V10, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               1                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"
D601V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF3 MUTATED                                  0     1
  ARHGEF3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF3 MUTATED                           0     6
  ARHGEF3 WILD-TYPE                        19   170
D601V12, multiclass
                                  clus
vv                                 ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = MRPL13 MUTATION ANALYSIS
D602V1, survival
                  sevent
clus2                0   1
  MRPL13 MUTATED     4   2
  MRPL13 WILD-TYPE 273  76
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               6              349 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               2               76 
$`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        54.61 

$`MRPL13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MRPL13 MUTATED MRPL13 WILD-TYPE 
           15.02             0.00 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
           62.79           148.01 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
           40.85            21.99 
[1] "15.0 - 62.8 (40.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D602V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPL13 MUTATED         2        0        1         2         0         0
  MRPL13 WILD-TYPE      62        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL13 MUTATED           0          0          1          0        0
  MRPL13 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MRPL13 MUTATED           0         0
  MRPL13 WILD-TYPE        12         1
D602V3, multiclass
            clus
vv           MRPL13 MUTATED MRPL13 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MRPL13 MUTATED     0   2   4   0
  MRPL13 WILD-TYPE   9  65 245  41
D602V4, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              0               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
  MRPL13 MUTATED     5   1   0
  MRPL13 WILD-TYPE 215  80  66
D602V5, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V6, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     5   0
  MRPL13 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      5    0
  MRPL13 WILD-TYPE  280   48
   clus
vv  MRPL13 MUTATED MRPL13 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D602V7, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     4   2
  MRPL13 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      4    2
  MRPL13 WILD-TYPE  166  195
        clus
vv       MRPL13 MUTATED MRPL13 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D602V8, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     5   0
  MRPL13 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      5    0
  MRPL13 WILD-TYPE  295    8
     clus
vv    MRPL13 MUTATED MRPL13 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D602V9, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     5   1
  MRPL13 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      5    1
  MRPL13 WILD-TYPE  309   47
                               clus
vv                              MRPL13 MUTATED MRPL13 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MRPL13 MUTATED     5   0   0   0
  MRPL13 WILD-TYPE 254   3  22  21
D602V10, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D602V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPL13 MUTATED                                  0     0
  MRPL13 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPL13 MUTATED                           0     5
  MRPL13 WILD-TYPE                        19   171
D602V12, multiclass
                                  clus
vv                                 MRPL13 MUTATED MRPL13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = STK36 MUTATION ANALYSIS
D603V1, survival
                 sevent
clus2               0   1
  STK36 MUTATED    12   2
  STK36 WILD-TYPE 265  76
  STK36 MUTATED STK36 WILD-TYPE 
             14             341 
  STK36 MUTATED STK36 WILD-TYPE 
              2              76 
$`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        12.16        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 
      135.65        13.78 

$`STK36 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  STK36 MUTATED STK36 WILD-TYPE 
           2.01            0.00 
  STK36 MUTATED STK36 WILD-TYPE 
         135.65          148.01 
  STK36 MUTATED STK36 WILD-TYPE 
          20.40           22.06 
[1] "2.0 - 135.7 (20.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D603V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK36 MUTATED         1        1        0         7         0         0
  STK36 WILD-TYPE      63        0       26       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK36 MUTATED           0          0          4          0        1         0
  STK36 WILD-TYPE        18          6         40         33       34        12
                 vv
clus              STAGE IVB
  STK36 MUTATED           0
  STK36 WILD-TYPE         1
D603V3, multiclass
            clus
vv           STK36 MUTATED STK36 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  STK36 MUTATED     0   1  11   1
  STK36 WILD-TYPE   9  66 238  40
D603V4, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             1              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
  STK36 MUTATED     9   5   0
  STK36 WILD-TYPE 211  76  66
D603V5, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  N0             9             211
  N1             5              76
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V6, binary
                 cls
clus                0   1
  STK36 MUTATED    10   1
  STK36 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     10    1
  STK36 WILD-TYPE  275   47
   clus
vv  STK36 MUTATED STK36 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D603V7, binary
                 cls
clus                0   1
  STK36 MUTATED     4  10
  STK36 WILD-TYPE 166 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      4   10
  STK36 WILD-TYPE  166  187
        clus
vv       STK36 MUTATED STK36 WILD-TYPE
  FEMALE             4             166
  MALE              10             187
[1] 2 2
[1] FALSE
D603V8, binary
                 cls
clus                0   1
  STK36 MUTATED    12   0
  STK36 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     12    0
  STK36 WILD-TYPE  288    8
     clus
vv    STK36 MUTATED STK36 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D603V9, binary
                 cls
clus                0   1
  STK36 MUTATED    10   3
  STK36 WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     10    3
  STK36 WILD-TYPE  304   45
                               clus
vv                              STK36 MUTATED STK36 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK36 MUTATED     8   0   0   3
  STK36 WILD-TYPE 251   3  22  18
D603V10, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             3              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"
D603V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK36 MUTATED                                  0     2
  STK36 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK36 MUTATED                           4     6
  STK36 WILD-TYPE                        15   170
D603V12, multiclass
                                  clus
vv                                 STK36 MUTATED STK36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                        6             170
[1] 4 2
[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 = IL13RA2 MUTATION ANALYSIS
D604V1, survival
                   sevent
clus2                 0   1
  IL13RA2 MUTATED    12   2
  IL13RA2 WILD-TYPE 265  76
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               14               341 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
                2                76 
$`IL13RA2 MUTATED`
TCGA-AA-3662 TCGA-AA-3697 TCGA-DM-A285 TCGA-G4-6588 TCGA-A6-5660 TCGA-AA-3510 
        6.05        85.05         5.88        26.17        29.19        63.98 
TCGA-AA-A00E TCGA-AA-A010 TCGA-CM-6165 TCGA-D5-6536 TCGA-D5-6920 TCGA-DM-A1DB 
       30.02        34.98        16.04        17.85        12.39        44.32 
TCGA-DM-A28H TCGA-G4-6315 
      117.07        61.91 

$`IL13RA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
        1.94        49.08        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
             5.88              0.00 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
           117.07            148.01 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
           29.605            21.990 
[1] "5.9 - 117.1 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D604V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL13RA2 MUTATED         0        0        2         6         1         0
  IL13RA2 WILD-TYPE      64        1       24       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL13RA2 MUTATED           0          0          0          2        3
  IL13RA2 WILD-TYPE        18          6         44         31       32
                   vv
clus                STAGE IVA STAGE IVB
  IL13RA2 MUTATED           0         0
  IL13RA2 WILD-TYPE        12         1
D604V3, multiclass
            clus
vv           IL13RA2 MUTATED IL13RA2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                6               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 3                32
  STAGE IVA                0                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
  IL13RA2 MUTATED     0   0  12   2
  IL13RA2 WILD-TYPE   9  67 237  39
D604V4, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3              12               237
  T4               2                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
  IL13RA2 MUTATED     9   1   4
  IL13RA2 WILD-TYPE 211  80  62
D604V5, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  N0               9               211
  N1               1                80
  N2               4                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V6, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    11   3
  IL13RA2 WILD-TYPE 274  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     11    3
  IL13RA2 WILD-TYPE  274   45
   clus
vv  IL13RA2 MUTATED IL13RA2 WILD-TYPE
  0              11               274
  1               3                45
[1] 2 2
[1] FALSE
D604V7, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED     5   9
  IL13RA2 WILD-TYPE 165 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED      5    9
  IL13RA2 WILD-TYPE  165  188
        clus
vv       IL13RA2 MUTATED IL13RA2 WILD-TYPE
  FEMALE               5               165
  MALE                 9               188
[1] 2 2
[1] FALSE
D604V8, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    11   0
  IL13RA2 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     11    0
  IL13RA2 WILD-TYPE  289    8
     clus
vv    IL13RA2 MUTATED IL13RA2 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D604V9, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    13   1
  IL13RA2 WILD-TYPE 301  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     13    1
  IL13RA2 WILD-TYPE  301   47
                               clus
vv                              IL13RA2 MUTATED IL13RA2 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  IL13RA2 MUTATED     9   0   1   0
  IL13RA2 WILD-TYPE 250   3  21  21
D604V10, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               0                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"
D604V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL13RA2 MUTATED                                  0     0
  IL13RA2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  IL13RA2 MUTATED                           1     8
  IL13RA2 WILD-TYPE                        18   168
D604V12, multiclass
                                  clus
vv                                 IL13RA2 MUTATED IL13RA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          8               168
[1] 4 2
[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 = FAM26E MUTATION ANALYSIS
D605V1, survival
                  sevent
clus2                0   1
  FAM26E MUTATED     4   1
  FAM26E WILD-TYPE 273  77
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              350 
  FAM26E MUTATED FAM26E WILD-TYPE 
               1               77 
$`FAM26E MUTATED`
TCGA-A6-5661 TCGA-AA-3977 TCGA-AD-6889 TCGA-D5-6540 TCGA-F4-6856 
       33.53        25.02        83.24        16.14        35.31 

$`FAM26E WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FAM26E MUTATED FAM26E WILD-TYPE 
           16.14             0.00 
  FAM26E MUTATED FAM26E WILD-TYPE 
           83.24           148.01 
  FAM26E MUTATED FAM26E WILD-TYPE 
           33.53            22.01 
[1] "16.1 - 83.2 (33.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D605V2, continuous
                  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      62        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM26E MUTATED           0          0          0          0        0
  FAM26E WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM26E MUTATED           0         0
  FAM26E WILD-TYPE        12         1
D605V3, multiclass
            clus
vv           FAM26E MUTATED FAM26E WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  FAM26E MUTATED     0   3   2   0
  FAM26E WILD-TYPE   9  64 247  41
D605V4, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  T1              0                9
  T2              3               64
  T3              2              247
  T4              0               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
  FAM26E MUTATED     5   0   0
  FAM26E WILD-TYPE 215  81  66
D605V5, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  N0              5              215
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V6, binary
                  cls
clus                 0   1
  FAM26E MUTATED     4   0
  FAM26E WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      4    0
  FAM26E WILD-TYPE  281   48
   clus
vv  FAM26E MUTATED FAM26E WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D605V7, binary
                  cls
clus                 0   1
  FAM26E MUTATED     1   4
  FAM26E WILD-TYPE 169 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      1    4
  FAM26E WILD-TYPE  169  193
        clus
vv       FAM26E MUTATED FAM26E WILD-TYPE
  FEMALE              1              169
  MALE                4              193
[1] 2 2
[1] FALSE
D605V8, binary
                  cls
clus                 0   1
  FAM26E MUTATED     5   0
  FAM26E WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      5    0
  FAM26E WILD-TYPE  295    8
     clus
vv    FAM26E MUTATED FAM26E WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D605V9, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   2
  FAM26E WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    2
  FAM26E WILD-TYPE  311   46
                               clus
vv                              FAM26E MUTATED FAM26E WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM26E MUTATED     4   0   0   0
  FAM26E WILD-TYPE 255   3  22  21
D605V10, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D605V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM26E MUTATED                                  0     1
  FAM26E WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM26E MUTATED                           1     2
  FAM26E WILD-TYPE                        18   174
D605V12, multiclass
                                  clus
vv                                 FAM26E MUTATED FAM26E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(606) Variable = ZNF182 MUTATION ANALYSIS
D606V1, survival
                  sevent
clus2                0   1
  ZNF182 MUTATED    11   1
  ZNF182 WILD-TYPE 266  77
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              12              343 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
               1               77 
$`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 

$`ZNF182 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZNF182 MUTATED ZNF182 WILD-TYPE 
           12.76             0.00 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
          135.65           148.01 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
          31.805           21.990 
[1] "12.8 - 135.7 (31.8)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "4.2"
D606V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF182 MUTATED         1        0        0         6         1         0
  ZNF182 WILD-TYPE      63        1       26       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF182 MUTATED           0          0          3          0        1
  ZNF182 WILD-TYPE        18          6         41         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF182 MUTATED           0         0
  ZNF182 WILD-TYPE        12         1
D606V3, multiclass
            clus
vv           ZNF182 MUTATED ZNF182 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF182 MUTATED     1   1  10   1
  ZNF182 WILD-TYPE   8  66 239  40
D606V4, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             10              239
  T4              1               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
  ZNF182 MUTATED     9   4   0
  ZNF182 WILD-TYPE 211  77  66
D606V5, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  N0              9              211
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V6, binary
                  cls
clus                 0   1
  ZNF182 MUTATED     9   1
  ZNF182 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED      9    1
  ZNF182 WILD-TYPE  276   47
   clus
vv  ZNF182 MUTATED ZNF182 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D606V7, binary
                  cls
clus                 0   1
  ZNF182 MUTATED     9   4
  ZNF182 WILD-TYPE 161 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED      9    4
  ZNF182 WILD-TYPE  161  193
        clus
vv       ZNF182 MUTATED ZNF182 WILD-TYPE
  FEMALE              9              161
  MALE                4              193
[1] 2 2
[1] FALSE
D606V8, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    11   0
  ZNF182 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     11    0
  ZNF182 WILD-TYPE  289    8
     clus
vv    ZNF182 MUTATED ZNF182 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D606V9, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    10   2
  ZNF182 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     10    2
  ZNF182 WILD-TYPE  304   46
                               clus
vv                              ZNF182 MUTATED ZNF182 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF182 MUTATED     7   0   0   2
  ZNF182 WILD-TYPE 252   3  22  19
D606V10, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D606V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF182 MUTATED                                  0     1
  ZNF182 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF182 MUTATED                           1     7
  ZNF182 WILD-TYPE                        18   169
D606V12, multiclass
                                  clus
vv                                 ZNF182 MUTATED ZNF182 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = GNA11 MUTATION ANALYSIS
D607V1, survival
                 sevent
clus2               0   1
  GNA11 MUTATED     7   0
  GNA11 WILD-TYPE 270  78
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             348 
  GNA11 MUTATED GNA11 WILD-TYPE 
              0              78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
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-3529 
        6.97         1.02        38.99         1.02         9.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.075 
[1] "8.4 - 33.5 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D607V2, continuous
                 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      62        1       26       104         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  GNA11 MUTATED           0
  GNA11 WILD-TYPE         1
D607V3, multiclass
            clus
vv           GNA11 MUTATED GNA11 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GNA11 MUTATED     0   2   5   0
  GNA11 WILD-TYPE   9  65 244  41
D607V4, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             0              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
  GNA11 MUTATED     6   1   0
  GNA11 WILD-TYPE 214  80  66
D607V5, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V6, binary
                 cls
clus                0   1
  GNA11 MUTATED     6   0
  GNA11 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    0
  GNA11 WILD-TYPE  279   48
   clus
vv  GNA11 MUTATED GNA11 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D607V7, binary
                 cls
clus                0   1
  GNA11 MUTATED     3   4
  GNA11 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      3    4
  GNA11 WILD-TYPE  167  193
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D607V8, binary
                 cls
clus                0   1
  GNA11 MUTATED     6   0
  GNA11 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    0
  GNA11 WILD-TYPE  294    8
     clus
vv    GNA11 MUTATED GNA11 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D607V9, binary
                 cls
clus                0   1
  GNA11 MUTATED     6   1
  GNA11 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    1
  GNA11 WILD-TYPE  308   47
                               clus
vv                              GNA11 MUTATED GNA11 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GNA11 MUTATED     4   0   0   0
  GNA11 WILD-TYPE 255   3  22  21
D607V10, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D607V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNA11 MUTATED                                  0     0
  GNA11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNA11 MUTATED                           2     4
  GNA11 WILD-TYPE                        17   172
D607V12, multiclass
                                  clus
vv                                 GNA11 MUTATED GNA11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = KDM2B MUTATION ANALYSIS
D608V1, survival
                 sevent
clus2               0   1
  KDM2B MUTATED    14   4
  KDM2B WILD-TYPE 263  74
  KDM2B MUTATED KDM2B WILD-TYPE 
             18             337 
  KDM2B MUTATED KDM2B WILD-TYPE 
              4              74 
$`KDM2B MUTATED`
TCGA-AA-3672 TCGA-AA-3697 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5665 
        0.92        85.05        35.80        26.17        32.75        22.06 
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3848 
       24.39        19.66         3.02         6.97        33.04        10.06 
TCGA-AA-3877 TCGA-AY-4070 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5868 TCGA-CM-6162 
       31.00        16.31        49.41        51.32        17.03        12.00 

$`KDM2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.69        23.87        20.12        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KDM2B MUTATED KDM2B WILD-TYPE 
           0.92            0.00 
  KDM2B MUTATED KDM2B WILD-TYPE 
          85.05          148.01 
  KDM2B MUTATED KDM2B WILD-TYPE 
         23.225          22.030 
[1] "0.9 - 85.0 (23.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D608V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM2B MUTATED         3        0        4         5         2         0
  KDM2B WILD-TYPE      61        1       22       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM2B MUTATED           1          0          1          3        0         1
  KDM2B WILD-TYPE        17          6         43         30       35        11
                 vv
clus              STAGE IVB
  KDM2B MUTATED           0
  KDM2B WILD-TYPE         1
D608V3, multiclass
            clus
vv           KDM2B MUTATED KDM2B WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              1              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
  KDM2B MUTATED     1   2  13   4
  KDM2B WILD-TYPE   8  65 236  37
D608V4, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  T1             1               8
  T2             2              65
  T3            13             236
  T4             4              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
  KDM2B MUTATED    14   4   2
  KDM2B WILD-TYPE 206  77  64
D608V5, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  N0            14             206
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V6, binary
                 cls
clus                0   1
  KDM2B MUTATED    14   1
  KDM2B WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     14    1
  KDM2B WILD-TYPE  271   47
   clus
vv  KDM2B MUTATED KDM2B WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D608V7, binary
                 cls
clus                0   1
  KDM2B MUTATED    15   5
  KDM2B WILD-TYPE 155 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     15    5
  KDM2B WILD-TYPE  155  192
        clus
vv       KDM2B MUTATED KDM2B WILD-TYPE
  FEMALE            15             155
  MALE               5             192
[1] 2 2
[1] FALSE
D608V8, binary
                 cls
clus                0   1
  KDM2B MUTATED    18   0
  KDM2B WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     18    0
  KDM2B WILD-TYPE  282    8
     clus
vv    KDM2B MUTATED KDM2B WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D608V9, binary
                 cls
clus                0   1
  KDM2B MUTATED    16   4
  KDM2B WILD-TYPE 298  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     16    4
  KDM2B WILD-TYPE  298   44
                               clus
vv                              KDM2B MUTATED KDM2B WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM2B MUTATED    14   1   0   3
  KDM2B WILD-TYPE 245   2  22  18
D608V10, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  R0            14             245
  R1             1               2
  R2             0              22
  RX             3              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"
D608V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM2B MUTATED                                  0     0
  KDM2B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM2B MUTATED                           1    12
  KDM2B WILD-TYPE                        18   164
D608V12, multiclass
                                  clus
vv                                 KDM2B MUTATED KDM2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = C17ORF47 MUTATION ANALYSIS
D609V1, survival
                    sevent
clus2                  0   1
  C17ORF47 MUTATED     4   1
  C17ORF47 WILD-TYPE 273  77
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 5                350 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 1                 77 
$`C17ORF47 MUTATED`
TCGA-A6-6649 TCGA-A6-5666 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-5862 
       24.16        32.71        34.98        12.76         5.03 

$`C17ORF47 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
              5.03               0.00 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
             34.98             148.01 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
            24.160             22.045 
[1] "5.0 - 35.0 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D609V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C17ORF47 MUTATED         0        0        0         1         1         1
  C17ORF47 WILD-TYPE      64        1       26       107         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF47 MUTATED           0          0          1          0        0
  C17ORF47 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF47 MUTATED           1         0
  C17ORF47 WILD-TYPE        11         1
D609V3, multiclass
            clus
vv           C17ORF47 MUTATED C17ORF47 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 1                107
  STAGE IIB                 1                  7
  STAGE IIC                 1                  0
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  C17ORF47 MUTATED     0   0   3   2
  C17ORF47 WILD-TYPE   9  67 246  39
D609V4, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                3                246
  T4                2                 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
  C17ORF47 MUTATED     3   2   0
  C17ORF47 WILD-TYPE 217  79  66
D609V5, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  N0                3                217
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V6, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     4   1
  C17ORF47 WILD-TYPE 281  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      4    1
  C17ORF47 WILD-TYPE  281   47
   clus
vv  C17ORF47 MUTATED C17ORF47 WILD-TYPE
  0                4                281
  1                1                 47
[1] 2 2
[1] FALSE
D609V7, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     1   4
  C17ORF47 WILD-TYPE 169 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      1    4
  C17ORF47 WILD-TYPE  169  193
        clus
vv       C17ORF47 MUTATED C17ORF47 WILD-TYPE
  FEMALE                1                169
  MALE                  4                193
[1] 2 2
[1] FALSE
D609V8, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     5   0
  C17ORF47 WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      5    0
  C17ORF47 WILD-TYPE  295    8
     clus
vv    C17ORF47 MUTATED C17ORF47 WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D609V9, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     4   1
  C17ORF47 WILD-TYPE 310  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      4    1
  C17ORF47 WILD-TYPE  310   47
                               clus
vv                              C17ORF47 MUTATED C17ORF47 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C17ORF47 MUTATED     2   0   0   1
  C17ORF47 WILD-TYPE 257   3  22  20
D609V10, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  R0                2                257
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D609V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C17ORF47 MUTATED                                  0     1
  C17ORF47 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C17ORF47 MUTATED                           0     3
  C17ORF47 WILD-TYPE                        19   173
D609V12, multiclass
                                  clus
vv                                 C17ORF47 MUTATED C17ORF47 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[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 = KCTD16 MUTATION ANALYSIS
D610V1, survival
                  sevent
clus2                0   1
  KCTD16 MUTATED     5   7
  KCTD16 WILD-TYPE 272  71
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              12              343 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
               7               71 
$`KCTD16 MUTATED`
TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-2676 TCGA-AA-3549 TCGA-AZ-6605 
       85.05        10.88       100.01        42.90        21.01         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 

$`KCTD16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A1DB 
      130.65        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-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79       117.07         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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KCTD16 MUTATED KCTD16 WILD-TYPE 
            5.23             0.00 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
          100.01           148.01 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
           37.43            22.03 
[1] "5.2 - 100.0 (37.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D610V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCTD16 MUTATED         2        0        2         2         1         0
  KCTD16 WILD-TYPE      62        1       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCTD16 MUTATED           0          0          2          1        0
  KCTD16 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  KCTD16 MUTATED           0         0
  KCTD16 WILD-TYPE        12         1
D610V3, multiclass
            clus
vv           KCTD16 MUTATED KCTD16 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  KCTD16 MUTATED     0   3   6   3
  KCTD16 WILD-TYPE   9  64 243  38
D610V4, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              6              243
  T4              3               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
  KCTD16 MUTATED     8   2   2
  KCTD16 WILD-TYPE 212  79  64
D610V5, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  N0              8              212
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V6, binary
                  cls
clus                 0   1
  KCTD16 MUTATED    11   0
  KCTD16 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED     11    0
  KCTD16 WILD-TYPE  274   48
   clus
vv  KCTD16 MUTATED KCTD16 WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D610V7, binary
                  cls
clus                 0   1
  KCTD16 MUTATED     3   9
  KCTD16 WILD-TYPE 167 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED      3    9
  KCTD16 WILD-TYPE  167  188
        clus
vv       KCTD16 MUTATED KCTD16 WILD-TYPE
  FEMALE              3              167
  MALE                9              188
[1] 2 2
[1] FALSE
D610V8, binary
                  cls
clus                 0   1
  KCTD16 MUTATED     8   1
  KCTD16 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED      8    1
  KCTD16 WILD-TYPE  292    7
     clus
vv    KCTD16 MUTATED KCTD16 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D610V9, binary
                  cls
clus                 0   1
  KCTD16 MUTATED    11   1
  KCTD16 WILD-TYPE 303  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED     11    1
  KCTD16 WILD-TYPE  303   47
                               clus
vv                              KCTD16 MUTATED KCTD16 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KCTD16 MUTATED     6   0   0   0
  KCTD16 WILD-TYPE 253   3  22  21
D610V10, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D610V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD16 MUTATED                                  0     0
  KCTD16 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KCTD16 MUTATED                           0    10
  KCTD16 WILD-TYPE                        19   166
D610V12, multiclass
                                  clus
vv                                 KCTD16 MUTATED KCTD16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(611) Variable = LNPEP MUTATION ANALYSIS
D611V1, survival
                 sevent
clus2               0   1
  LNPEP MUTATED    12   5
  LNPEP WILD-TYPE 265  73
  LNPEP MUTATED LNPEP WILD-TYPE 
             17             338 
  LNPEP MUTATED LNPEP WILD-TYPE 
              5              73 
$`LNPEP MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-G4-6310 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3966 
       19.04        19.04        63.62         3.02         6.97         2.01 
TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
       38.04        18.05        34.98        58.39        88.21        49.41 
TCGA-CA-6718 TCGA-CK-6747 TCGA-D5-6536 TCGA-G4-6309 TCGA-G4-6626 
       10.06        82.95        17.85        85.48        46.75 

$`LNPEP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       13.94        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 
       36.00        13.78 

  LNPEP MUTATED LNPEP WILD-TYPE 
           2.01            0.00 
  LNPEP MUTATED LNPEP WILD-TYPE 
          88.21          148.01 
  LNPEP MUTATED LNPEP WILD-TYPE 
         34.980          22.045 
[1] "2.0 - 88.2 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D611V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LNPEP MUTATED         1        0        4         8         1         0
  LNPEP WILD-TYPE      63        1       22       100         7         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        18          6         41         33       34        12
                 vv
clus              STAGE IVB
  LNPEP MUTATED           0
  LNPEP WILD-TYPE         1
D611V3, multiclass
            clus
vv           LNPEP MUTATED LNPEP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  LNPEP MUTATED     1   0  15   2
  LNPEP WILD-TYPE   8  67 234  39
D611V4, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  T1             1               8
  T2             0              67
  T3            15             234
  T4             2              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
  LNPEP MUTATED    15   3   0
  LNPEP WILD-TYPE 205  78  66
D611V5, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  N0            15             205
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V6, binary
                 cls
clus                0   1
  LNPEP MUTATED    15   1
  LNPEP WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     15    1
  LNPEP WILD-TYPE  270   47
   clus
vv  LNPEP MUTATED LNPEP WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D611V7, binary
                 cls
clus                0   1
  LNPEP MUTATED     8  10
  LNPEP WILD-TYPE 162 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED      8   10
  LNPEP WILD-TYPE  162  187
        clus
vv       LNPEP MUTATED LNPEP WILD-TYPE
  FEMALE             8             162
  MALE              10             187
[1] 2 2
[1] FALSE
D611V8, binary
                 cls
clus                0   1
  LNPEP MUTATED    14   2
  LNPEP WILD-TYPE 286   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     14    2
  LNPEP WILD-TYPE  286    6
     clus
vv    LNPEP MUTATED LNPEP WILD-TYPE
  NO             14             286
  YES             2               6
[1] 2 2
[1] FALSE
D611V9, binary
                 cls
clus                0   1
  LNPEP MUTATED    16   2
  LNPEP WILD-TYPE 298  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     16    2
  LNPEP WILD-TYPE  298   46
                               clus
vv                              LNPEP MUTATED LNPEP WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LNPEP MUTATED    12   0   1   2
  LNPEP WILD-TYPE 247   3  21  19
D611V10, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  R0            12             247
  R1             0               3
  R2             1              21
  RX             2              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"
D611V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LNPEP MUTATED                                  0     1
  LNPEP WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LNPEP MUTATED                           1     7
  LNPEP WILD-TYPE                        18   169
D611V12, multiclass
                                  clus
vv                                 LNPEP MUTATED LNPEP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = RHPN2 MUTATION ANALYSIS
D612V1, survival
                 sevent
clus2               0   1
  RHPN2 MUTATED    11   4
  RHPN2 WILD-TYPE 266  74
  RHPN2 MUTATED RHPN2 WILD-TYPE 
             15             340 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              4              74 
$`RHPN2 MUTATED`
TCGA-A6-4105 TCGA-A6-2676 TCGA-A6-6648 TCGA-AA-3561 TCGA-AA-3949 TCGA-AA-A010 
       14.53        42.90        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        12.39        23.05        21.99         4.80 
TCGA-D5-6541 TCGA-F4-6459 TCGA-G4-6293 
       15.58         8.61       133.18 

$`RHPN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-6167 
       15.02        12.00        14.04        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        54.61        19.59        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        25.48        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6460 
      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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  RHPN2 MUTATED RHPN2 WILD-TYPE 
            4.8             0.0 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         133.18          148.01 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         23.050          22.045 
[1] "4.8 - 133.2 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D612V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RHPN2 MUTATED         2        0        0         5         2         0
  RHPN2 WILD-TYPE      62        1       26       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHPN2 MUTATED           1          0          3          0        0         2
  RHPN2 WILD-TYPE        17          6         41         33       35        10
                 vv
clus              STAGE IVB
  RHPN2 MUTATED           0
  RHPN2 WILD-TYPE         1
D612V3, multiclass
            clus
vv           RHPN2 MUTATED RHPN2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              2              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
  RHPN2 MUTATED     0   2  11   2
  RHPN2 WILD-TYPE   9  65 238  39
D612V4, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            11             238
  T4             2              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
  RHPN2 MUTATED    10   4   1
  RHPN2 WILD-TYPE 210  77  65
D612V5, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  N0            10             210
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V6, binary
                 cls
clus                0   1
  RHPN2 MUTATED    12   2
  RHPN2 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     12    2
  RHPN2 WILD-TYPE  273   46
   clus
vv  RHPN2 MUTATED RHPN2 WILD-TYPE
  0            12             273
  1             2              46
[1] 2 2
[1] FALSE
D612V7, binary
                 cls
clus                0   1
  RHPN2 MUTATED     9   6
  RHPN2 WILD-TYPE 161 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      9    6
  RHPN2 WILD-TYPE  161  191
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  FEMALE             9             161
  MALE               6             191
[1] 2 2
[1] FALSE
D612V8, binary
                 cls
clus                0   1
  RHPN2 MUTATED    14   0
  RHPN2 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     14    0
  RHPN2 WILD-TYPE  286    8
     clus
vv    RHPN2 MUTATED RHPN2 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D612V9, binary
                 cls
clus                0   1
  RHPN2 MUTATED    13   2
  RHPN2 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     13    2
  RHPN2 WILD-TYPE  301   46
                               clus
vv                              RHPN2 MUTATED RHPN2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RHPN2 MUTATED    13   0   0   0
  RHPN2 WILD-TYPE 246   3  22  21
D612V10, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             0              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"
D612V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHPN2 MUTATED                                  0     1
  RHPN2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RHPN2 MUTATED                           1    10
  RHPN2 WILD-TYPE                        18   166
D612V12, multiclass
                                  clus
vv                                 RHPN2 MUTATED RHPN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(613) Variable = FRS3 MUTATION ANALYSIS
D613V1, survival
                sevent
clus2              0   1
  FRS3 MUTATED     8   2
  FRS3 WILD-TYPE 269  76
  FRS3 MUTATED FRS3 WILD-TYPE 
            10            345 
  FRS3 MUTATED FRS3 WILD-TYPE 
             2             76 
$`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 
       30.08        13.35       140.38        98.24 

$`FRS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3514 TCGA-AA-3517 
        7.04         3.02        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FRS3 MUTATED FRS3 WILD-TYPE 
          6.97           0.00 
  FRS3 MUTATED FRS3 WILD-TYPE 
        140.38         148.01 
  FRS3 MUTATED FRS3 WILD-TYPE 
        32.545         22.030 
[1] "7.0 - 140.4 (32.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D613V2, continuous
                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      64        1       24       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRS3 MUTATED           1          0          0          0        1         0
  FRS3 WILD-TYPE        17          6         44         33       34        12
                vv
clus             STAGE IVB
  FRS3 MUTATED           0
  FRS3 WILD-TYPE         1
D613V3, multiclass
            clus
vv           FRS3 MUTATED FRS3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  FRS3 MUTATED     0   0   8   2
  FRS3 WILD-TYPE   9  67 241  39
D613V4, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            8            241
  T4            2             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
  FRS3 MUTATED     8   0   2
  FRS3 WILD-TYPE 212  81  64
D613V5, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V6, binary
                cls
clus               0   1
  FRS3 MUTATED     8   1
  FRS3 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      8    1
  FRS3 WILD-TYPE  277   47
   clus
vv  FRS3 MUTATED FRS3 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D613V7, binary
                cls
clus               0   1
  FRS3 MUTATED     3   7
  FRS3 WILD-TYPE 167 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      3    7
  FRS3 WILD-TYPE  167  190
        clus
vv       FRS3 MUTATED FRS3 WILD-TYPE
  FEMALE            3            167
  MALE              7            190
[1] 2 2
[1] FALSE
D613V8, binary
                cls
clus               0   1
  FRS3 MUTATED     7   1
  FRS3 WILD-TYPE 293   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      7    1
  FRS3 WILD-TYPE  293    7
     clus
vv    FRS3 MUTATED FRS3 WILD-TYPE
  NO             7            293
  YES            1              7
[1] 2 2
[1] FALSE
D613V9, binary
                cls
clus               0   1
  FRS3 MUTATED     6   4
  FRS3 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      6    4
  FRS3 WILD-TYPE  308   44
                               clus
vv                              FRS3 MUTATED FRS3 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FRS3 MUTATED     5   0   1   1
  FRS3 WILD-TYPE 254   3  21  20
D613V10, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            1             21
  RX            1             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"
D613V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRS3 MUTATED                                  0     1
  FRS3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FRS3 MUTATED                           0     6
  FRS3 WILD-TYPE                        19   170
D613V12, multiclass
                                  clus
vv                                 FRS3 MUTATED FRS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = POLE MUTATION ANALYSIS
D614V1, survival
                sevent
clus2              0   1
  POLE MUTATED    22   7
  POLE WILD-TYPE 255  71
  POLE MUTATED POLE WILD-TYPE 
            29            326 
  POLE MUTATED POLE WILD-TYPE 
             7             71 
$`POLE MUTATED`
TCGA-A6-4105 TCGA-AA-3525 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-6141 TCGA-A6-6781 
       14.53         8.05        10.88       100.01         8.38        19.66 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3678 TCGA-AA-3710 
       63.98         1.02        29.95        78.08        47.01        26.99 
TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
       33.04        15.95        53.00        25.02        18.05         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 
       34.98        58.39        49.41        12.76        10.06        15.02 
TCGA-CM-6675 TCGA-CM-6678 TCGA-D5-6540 TCGA-DM-A28K TCGA-G4-6303 
       13.05        11.01        16.14        98.24        65.85 

$`POLE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  POLE MUTATED POLE WILD-TYPE 
          1.02           0.00 
  POLE MUTATED POLE WILD-TYPE 
        100.01         148.01 
  POLE MUTATED POLE WILD-TYPE 
        19.660         22.075 
[1] "1.0 - 100.0 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D614V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLE MUTATED         2        0        5        13         2         0
  POLE WILD-TYPE      62        1       21        95         6         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        17          6         42         32       34        11
                vv
clus             STAGE IVB
  POLE MUTATED           1
  POLE WILD-TYPE         0
D614V3, multiclass
            clus
vv           POLE MUTATED POLE WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA            13             95
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             11
  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     0   4  21   6
  POLE WILD-TYPE   9  63 228  35
D614V4, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  T1            0              9
  T2            4             63
  T3           21            228
  T4            6             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
  POLE MUTATED    23   6   2
  POLE WILD-TYPE 197  75  64
D614V5, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  N0           23            197
  N1            6             75
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V6, binary
                cls
clus               0   1
  POLE MUTATED    23   3
  POLE WILD-TYPE 262  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     23    3
  POLE WILD-TYPE  262   45
   clus
vv  POLE MUTATED POLE WILD-TYPE
  0           23            262
  1            3             45
[1] 2 2
[1] FALSE
D614V7, binary
                cls
clus               0   1
  POLE MUTATED    13  18
  POLE WILD-TYPE 157 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     13   18
  POLE WILD-TYPE  157  179
        clus
vv       POLE MUTATED POLE WILD-TYPE
  FEMALE           13            157
  MALE             18            179
[1] 2 2
[1] FALSE
D614V8, binary
                cls
clus               0   1
  POLE MUTATED    26   0
  POLE WILD-TYPE 274   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     26    0
  POLE WILD-TYPE  274    8
     clus
vv    POLE MUTATED POLE WILD-TYPE
  NO            26            274
  YES            0              8
[1] 2 2
[1] FALSE
D614V9, binary
                cls
clus               0   1
  POLE MUTATED    24   7
  POLE WILD-TYPE 290  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     24    7
  POLE WILD-TYPE  290   41
                               clus
vv                              POLE MUTATED POLE WILD-TYPE
  COLON ADENOCARCINOMA                    24            290
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POLE MUTATED    21   0   0   3
  POLE WILD-TYPE 238   3  22  18
D614V10, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  R0           21            238
  R1            0              3
  R2            0             22
  RX            3             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"
D614V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLE MUTATED                                  0     2
  POLE WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  POLE MUTATED                           2    12
  POLE WILD-TYPE                        17   164
D614V12, multiclass
                                  clus
vv                                 POLE MUTATED POLE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      12            164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(615) Variable = NIPA2 MUTATION ANALYSIS
D615V1, survival
                 sevent
clus2               0   1
  NIPA2 MUTATED     6   1
  NIPA2 WILD-TYPE 271  77
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              7             348 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              1              77 
$`NIPA2 MUTATED`
TCGA-AA-3524 TCGA-AA-3715 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3977 TCGA-CM-4746 
       36.03        19.04         6.97        26.99        25.02        37.02 
TCGA-DM-A1HB 
      135.65 

$`NIPA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NIPA2 MUTATED NIPA2 WILD-TYPE 
           6.97            0.00 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
         135.65          148.01 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          26.99           22.01 
[1] "7.0 - 135.7 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D615V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NIPA2 MUTATED         1        0        3         1         0         0
  NIPA2 WILD-TYPE      63        1       23       107         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  NIPA2 MUTATED           0
  NIPA2 WILD-TYPE         1
D615V3, multiclass
            clus
vv           NIPA2 MUTATED NIPA2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  NIPA2 MUTATED     0   2   5   0
  NIPA2 WILD-TYPE   9  65 244  41
D615V4, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             0              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
  NIPA2 MUTATED     6   1   0
  NIPA2 WILD-TYPE 214  80  66
D615V5, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V6, binary
                 cls
clus                0   1
  NIPA2 MUTATED     6   0
  NIPA2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      6    0
  NIPA2 WILD-TYPE  279   48
   clus
vv  NIPA2 MUTATED NIPA2 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D615V7, binary
                 cls
clus                0   1
  NIPA2 MUTATED     1   6
  NIPA2 WILD-TYPE 169 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      1    6
  NIPA2 WILD-TYPE  169  191
        clus
vv       NIPA2 MUTATED NIPA2 WILD-TYPE
  FEMALE             1             169
  MALE               6             191
[1] 2 2
[1] FALSE
D615V8, binary
                 cls
clus                0   1
  NIPA2 MUTATED     6   0
  NIPA2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      6    0
  NIPA2 WILD-TYPE  294    8
     clus
vv    NIPA2 MUTATED NIPA2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D615V9, binary
                 cls
clus                0   1
  NIPA2 MUTATED     6   0
  NIPA2 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      6    0
  NIPA2 WILD-TYPE  308   48
                               clus
vv                              NIPA2 MUTATED NIPA2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NIPA2 MUTATED     5   0   0   0
  NIPA2 WILD-TYPE 254   3  22  21
D615V10, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D615V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPA2 MUTATED                                  0     0
  NIPA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NIPA2 MUTATED                           1     1
  NIPA2 WILD-TYPE                        18   175
D615V12, multiclass
[1] "Remove cluster labels:" "NIPA2 MUTATED"         
clus
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6607      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-5913      TCGA-CK-5914 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 

Clustering(616) Variable = CDH10 MUTATION ANALYSIS
D616V1, survival
                 sevent
clus2               0   1
  CDH10 MUTATED    32   6
  CDH10 WILD-TYPE 245  72
  CDH10 MUTATED CDH10 WILD-TYPE 
             38             317 
  CDH10 MUTATED CDH10 WILD-TYPE 
              6              72 
$`CDH10 MUTATED`
TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3713 TCGA-G4-6628 TCGA-A6-5662 TCGA-A6-5665 
        8.05         0.92        19.04        79.69        23.61        22.06 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3864 
       29.95        78.08        26.99        33.04         1.02        53.00 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01Z 
       25.02         7.96         4.01        34.98        31.00        37.02 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 
        0.20        58.39        49.41        29.56        12.76        10.06 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6171 
       82.95        23.05        15.02        12.00        29.03        14.04 
TCGA-CM-6674 TCGA-CM-6680 TCGA-D5-6536 TCGA-DM-A282 TCGA-F4-6570 TCGA-G4-6299 
       12.95        12.03        17.85       139.17         6.18        74.56 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

$`CDH10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5664 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       24.00        20.98        13.94        61.02         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        27.02        27.02        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 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-A029 TCGA-AA-A02F 
        1.02        33.04         1.02        26.01        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        62.79        88.21         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       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        14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65        81.37       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        43.04        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-G4-6626 
       44.68        55.04        85.48        61.91        46.75 

  CDH10 MUTATED CDH10 WILD-TYPE 
            0.2             0.0 
  CDH10 MUTATED CDH10 WILD-TYPE 
         139.17          148.01 
  CDH10 MUTATED CDH10 WILD-TYPE 
          23.33           21.99 
[1] "0.2 - 139.2 (23.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D616V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH10 MUTATED         4        1        4        15         2         0
  CDH10 WILD-TYPE      60        0       22        93         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH10 MUTATED           2          0          3          3        2         1
  CDH10 WILD-TYPE        16          6         41         30       33        11
                 vv
clus              STAGE IVB
  CDH10 MUTATED           0
  CDH10 WILD-TYPE         1
D616V3, multiclass
            clus
vv           CDH10 MUTATED CDH10 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               4              22
  STAGE IIA             15              93
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             3              30
  STAGE IV               2              33
  STAGE IVA              1              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
  CDH10 MUTATED     0   6  30   2
  CDH10 WILD-TYPE   9  61 219  39
D616V4, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  T1             0               9
  T2             6              61
  T3            30             219
  T4             2              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
  CDH10 MUTATED    28   4   7
  CDH10 WILD-TYPE 192  77  59
D616V5, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  N0            28             192
  N1             4              77
  N2             7              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V6, binary
                 cls
clus                0   1
  CDH10 MUTATED    29   3
  CDH10 WILD-TYPE 256  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     29    3
  CDH10 WILD-TYPE  256   45
   clus
vv  CDH10 MUTATED CDH10 WILD-TYPE
  0            29             256
  1             3              45
[1] 2 2
[1] FALSE
D616V7, binary
                 cls
clus                0   1
  CDH10 MUTATED    19  20
  CDH10 WILD-TYPE 151 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     19   20
  CDH10 WILD-TYPE  151  177
        clus
vv       CDH10 MUTATED CDH10 WILD-TYPE
  FEMALE            19             151
  MALE              20             177
[1] 2 2
[1] FALSE
D616V8, binary
                 cls
clus                0   1
  CDH10 MUTATED    34   1
  CDH10 WILD-TYPE 266   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     34    1
  CDH10 WILD-TYPE  266    7
     clus
vv    CDH10 MUTATED CDH10 WILD-TYPE
  NO             34             266
  YES             1               7
[1] 2 2
[1] FALSE
D616V9, binary
                 cls
clus                0   1
  CDH10 MUTATED    33   6
  CDH10 WILD-TYPE 281  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     33    6
  CDH10 WILD-TYPE  281   42
                               clus
vv                              CDH10 MUTATED CDH10 WILD-TYPE
  COLON ADENOCARCINOMA                     33             281
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH10 MUTATED    29   0   2   3
  CDH10 WILD-TYPE 230   3  20  18
D616V10, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  R0            29             230
  R1             0               3
  R2             2              20
  RX             3              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"
D616V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH10 MUTATED                                  0     2
  CDH10 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH10 MUTATED                           1    20
  CDH10 WILD-TYPE                        18   156
D616V12, multiclass
                                  clus
vv                                 CDH10 MUTATED CDH10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       20             156
[1] 4 2
[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 = CATSPER1 MUTATION ANALYSIS
D617V1, survival
                    sevent
clus2                  0   1
  CATSPER1 MUTATED    11   4
  CATSPER1 WILD-TYPE 266  74
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                15                340 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                 4                 74 
$`CATSPER1 MUTATED`
TCGA-AA-3530 TCGA-AA-3713 TCGA-AZ-6608 TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3555 
       19.07        19.04         1.94        32.71        20.12        29.95 
TCGA-AA-3710 TCGA-AA-3815 TCGA-AZ-5403 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6171 
       26.99        33.04        62.79        15.02        17.03        14.04 
TCGA-DM-A0XD TCGA-DM-A28F TCGA-F4-6854 
       24.43        35.97         0.53 

$`CATSPER1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6161 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-A28C 
        7.50        44.32       131.51       135.65       139.17        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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
              0.53               0.00 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
             62.79             148.01 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
            20.120             22.075 
[1] "0.5 - 62.8 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D617V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CATSPER1 MUTATED         3        0        1         7         0         1
  CATSPER1 WILD-TYPE      61        1       25       101         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER1 MUTATED           0          1          1          0        1
  CATSPER1 WILD-TYPE        18          5         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER1 MUTATED           1         0
  CATSPER1 WILD-TYPE        11         1
D617V3, multiclass
            clus
vv           CATSPER1 MUTATED CATSPER1 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 7                101
  STAGE IIB                 0                  8
  STAGE IIC                 1                  0
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 1                 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
  CATSPER1 MUTATED     0   4  10   2
  CATSPER1 WILD-TYPE   9  63 239  39
D617V4, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  T1                0                  9
  T2                4                 63
  T3               10                239
  T4                2                 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
  CATSPER1 MUTATED    13   3   0
  CATSPER1 WILD-TYPE 207  78  66
D617V5, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  N0               13                207
  N1                3                 78
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V6, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    12   2
  CATSPER1 WILD-TYPE 273  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     12    2
  CATSPER1 WILD-TYPE  273   46
   clus
vv  CATSPER1 MUTATED CATSPER1 WILD-TYPE
  0               12                273
  1                2                 46
[1] 2 2
[1] FALSE
D617V7, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED     8   8
  CATSPER1 WILD-TYPE 162 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED      8    8
  CATSPER1 WILD-TYPE  162  189
        clus
vv       CATSPER1 MUTATED CATSPER1 WILD-TYPE
  FEMALE                8                162
  MALE                  8                189
[1] 2 2
[1] FALSE
D617V8, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    12   1
  CATSPER1 WILD-TYPE 288   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     12    1
  CATSPER1 WILD-TYPE  288    7
     clus
vv    CATSPER1 MUTATED CATSPER1 WILD-TYPE
  NO                12                288
  YES                1                  7
[1] 2 2
[1] FALSE
D617V9, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    14   2
  CATSPER1 WILD-TYPE 300  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     14    2
  CATSPER1 WILD-TYPE  300   46
                               clus
vv                              CATSPER1 MUTATED CATSPER1 WILD-TYPE
  COLON ADENOCARCINOMA                        14                300
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CATSPER1 MUTATED     9   0   1   0
  CATSPER1 WILD-TYPE 250   3  21  21
D617V10, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D617V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CATSPER1 MUTATED                                  0     0
  CATSPER1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CATSPER1 MUTATED                           0    10
  CATSPER1 WILD-TYPE                        19   166
D617V12, multiclass
                                  clus
vv                                 CATSPER1 MUTATED CATSPER1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          10                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(618) Variable = FOXN3 MUTATION ANALYSIS
D618V1, survival
                 sevent
clus2               0   1
  FOXN3 MUTATED    11   0
  FOXN3 WILD-TYPE 266  78
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             344 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              0              78 
$`FOXN3 MUTATED`
TCGA-AA-3713 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3821 
       19.04        24.39        19.66         6.97        26.99         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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FOXN3 MUTATED FOXN3 WILD-TYPE 
           1.02            0.00 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          53.00          148.01 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          19.04           22.09 
[1] "1.0 - 53.0 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D618V2, continuous
                 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      61        1       24       104         8         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        18          6         44         32       34        12
                 vv
clus              STAGE IVB
  FOXN3 MUTATED           0
  FOXN3 WILD-TYPE         1
D618V3, multiclass
            clus
vv           FOXN3 MUTATED FOXN3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  FOXN3 MUTATED     0   3   7   1
  FOXN3 WILD-TYPE   9  64 242  40
D618V4, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             7             242
  T4             1              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
  FOXN3 MUTATED    10   1   0
  FOXN3 WILD-TYPE 210  80  66
D618V5, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V6, binary
                 cls
clus                0   1
  FOXN3 MUTATED     9   1
  FOXN3 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      9    1
  FOXN3 WILD-TYPE  276   47
   clus
vv  FOXN3 MUTATED FOXN3 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D618V7, binary
                 cls
clus                0   1
  FOXN3 MUTATED     2   9
  FOXN3 WILD-TYPE 168 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      2    9
  FOXN3 WILD-TYPE  168  188
        clus
vv       FOXN3 MUTATED FOXN3 WILD-TYPE
  FEMALE             2             168
  MALE               9             188
[1] 2 2
[1] FALSE
D618V8, binary
                 cls
clus                0   1
  FOXN3 MUTATED    10   1
  FOXN3 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     10    1
  FOXN3 WILD-TYPE  290    7
     clus
vv    FOXN3 MUTATED FOXN3 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D618V9, binary
                 cls
clus                0   1
  FOXN3 MUTATED     8   3
  FOXN3 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      8    3
  FOXN3 WILD-TYPE  306   45
                               clus
vv                              FOXN3 MUTATED FOXN3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXN3 MUTATED     8   0   1   1
  FOXN3 WILD-TYPE 251   3  21  20
D618V10, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             1              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"
D618V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXN3 MUTATED                                  0     1
  FOXN3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXN3 MUTATED                           1     4
  FOXN3 WILD-TYPE                        18   172
D618V12, multiclass
                                  clus
vv                                 FOXN3 MUTATED FOXN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = REXO4 MUTATION ANALYSIS
D619V1, survival
                 sevent
clus2               0   1
  REXO4 MUTATED     3   2
  REXO4 WILD-TYPE 274  76
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             350 
  REXO4 MUTATED REXO4 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  REXO4 MUTATED REXO4 WILD-TYPE 
           6.18            0.00 
  REXO4 MUTATED REXO4 WILD-TYPE 
          82.95          148.01 
  REXO4 MUTATED REXO4 WILD-TYPE 
          18.05           22.09 
[1] "6.2 - 83.0 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D619V2, continuous
                 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      64        1       25       105         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  REXO4 MUTATED           0
  REXO4 WILD-TYPE         1
D619V3, multiclass
            clus
vv           REXO4 MUTATED REXO4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  REXO4 MUTATED     0   0   4   1
  REXO4 WILD-TYPE   9  67 245  40
D619V4, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  REXO4 MUTATED     4   1   0
  REXO4 WILD-TYPE 216  80  66
D619V5, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V6, binary
                 cls
clus                0   1
  REXO4 MUTATED     4   0
  REXO4 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      4    0
  REXO4 WILD-TYPE  281   48
   clus
vv  REXO4 MUTATED REXO4 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D619V7, binary
                 cls
clus                0   1
  REXO4 MUTATED     3   2
  REXO4 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      3    2
  REXO4 WILD-TYPE  167  195
        clus
vv       REXO4 MUTATED REXO4 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D619V8, binary
                 cls
clus                0   1
  REXO4 MUTATED     5   0
  REXO4 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      5    0
  REXO4 WILD-TYPE  295    8
     clus
vv    REXO4 MUTATED REXO4 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D619V9, binary
                 cls
clus                0   1
  REXO4 MUTATED     4   1
  REXO4 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      4    1
  REXO4 WILD-TYPE  310   47
                               clus
vv                              REXO4 MUTATED REXO4 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  REXO4 MUTATED     4   0   0   1
  REXO4 WILD-TYPE 255   3  22  20
D619V10, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D619V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  REXO4 MUTATED                                  0     0
  REXO4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  REXO4 MUTATED                           0     3
  REXO4 WILD-TYPE                        19   173
D619V12, multiclass
                                  clus
vv                                 REXO4 MUTATED REXO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = OTX2 MUTATION ANALYSIS
D620V1, survival
                sevent
clus2              0   1
  OTX2 MUTATED     3   2
  OTX2 WILD-TYPE 274  76
  OTX2 MUTATED OTX2 WILD-TYPE 
             5            350 
  OTX2 MUTATED OTX2 WILD-TYPE 
             2             76 
$`OTX2 MUTATED`
TCGA-AA-3697 TCGA-A6-6780 TCGA-AA-3492 TCGA-AD-6889 TCGA-D5-6540 
       85.05        20.12         3.02        83.24        16.14 

$`OTX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        19.66        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OTX2 MUTATED OTX2 WILD-TYPE 
          3.02           0.00 
  OTX2 MUTATED OTX2 WILD-TYPE 
         85.05         148.01 
  OTX2 MUTATED OTX2 WILD-TYPE 
        20.120         22.075 
[1] "3.0 - 85.0 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D620V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OTX2 MUTATED         1        0        2         3         0         0
  OTX2 WILD-TYPE      63        1       24       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OTX2 MUTATED           0          0          0          0        0         0
  OTX2 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  OTX2 MUTATED           0
  OTX2 WILD-TYPE         1
D620V3, multiclass
            clus
vv           OTX2 MUTATED OTX2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  OTX2 MUTATED     0   1   5   0
  OTX2 WILD-TYPE   9  66 244  41
D620V4, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            0             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
  OTX2 MUTATED     6   0   0
  OTX2 WILD-TYPE 214  81  66
D620V5, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V6, binary
                cls
clus               0   1
  OTX2 MUTATED     5   0
  OTX2 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    0
  OTX2 WILD-TYPE  280   48
   clus
vv  OTX2 MUTATED OTX2 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D620V7, binary
                cls
clus               0   1
  OTX2 MUTATED     2   4
  OTX2 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      2    4
  OTX2 WILD-TYPE  168  193
        clus
vv       OTX2 MUTATED OTX2 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D620V8, binary
                cls
clus               0   1
  OTX2 MUTATED     5   0
  OTX2 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    0
  OTX2 WILD-TYPE  295    8
     clus
vv    OTX2 MUTATED OTX2 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D620V9, binary
                cls
clus               0   1
  OTX2 MUTATED     4   2
  OTX2 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      4    2
  OTX2 WILD-TYPE  310   46
                               clus
vv                              OTX2 MUTATED OTX2 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OTX2 MUTATED     5   0   0   0
  OTX2 WILD-TYPE 254   3  22  21
D620V10, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D620V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OTX2 MUTATED                                  0     1
  OTX2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OTX2 MUTATED                           0     2
  OTX2 WILD-TYPE                        19   174
D620V12, multiclass
                                  clus
vv                                 OTX2 MUTATED OTX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(621) Variable = NGEF MUTATION ANALYSIS
D621V1, survival
                sevent
clus2              0   1
  NGEF MUTATED    12   3
  NGEF WILD-TYPE 265  75
  NGEF MUTATED NGEF WILD-TYPE 
            15            340 
  NGEF MUTATED NGEF WILD-TYPE 
             3             75 
$`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 
       44.32        74.56        36.00 

$`NGEF WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6138 
       29.19        33.53        23.61        22.09        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-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-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  NGEF MUTATED NGEF WILD-TYPE 
             0              0 
  NGEF MUTATED NGEF WILD-TYPE 
         78.08         148.01 
  NGEF MUTATED NGEF WILD-TYPE 
         22.06          22.04 
[1] "0.0 - 78.1 (22.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D621V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NGEF MUTATED         3        0        1         5         0         0
  NGEF WILD-TYPE      61        1       25       103         8         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        17          6         41         30       35        12
                vv
clus             STAGE IVB
  NGEF MUTATED           0
  NGEF WILD-TYPE         1
D621V3, multiclass
            clus
vv           NGEF MUTATED NGEF WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            3             30
  STAGE IV              0             35
  STAGE IVA             0             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
  NGEF MUTATED     0   3  11   2
  NGEF WILD-TYPE   9  64 238  39
D621V4, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  T1            0              9
  T2            3             64
  T3           11            238
  T4            2             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
  NGEF MUTATED     9   3   4
  NGEF WILD-TYPE 211  78  62
D621V5, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  N0            9            211
  N1            3             78
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V6, binary
                cls
clus               0   1
  NGEF MUTATED    14   0
  NGEF WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     14    0
  NGEF WILD-TYPE  271   48
   clus
vv  NGEF MUTATED NGEF WILD-TYPE
  0           14            271
  1            0             48
[1] 2 2
[1] FALSE
D621V7, binary
                cls
clus               0   1
  NGEF MUTATED     5  11
  NGEF WILD-TYPE 165 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED      5   11
  NGEF WILD-TYPE  165  186
        clus
vv       NGEF MUTATED NGEF WILD-TYPE
  FEMALE            5            165
  MALE             11            186
[1] 2 2
[1] FALSE
D621V8, binary
                cls
clus               0   1
  NGEF MUTATED    12   1
  NGEF WILD-TYPE 288   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     12    1
  NGEF WILD-TYPE  288    7
     clus
vv    NGEF MUTATED NGEF WILD-TYPE
  NO            12            288
  YES            1              7
[1] 2 2
[1] FALSE
D621V9, binary
                cls
clus               0   1
  NGEF MUTATED    14   2
  NGEF WILD-TYPE 300  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     14    2
  NGEF WILD-TYPE  300   46
                               clus
vv                              NGEF MUTATED NGEF WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NGEF MUTATED    12   0   0   0
  NGEF WILD-TYPE 247   3  22  21
D621V10, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            0             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"
D621V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NGEF MUTATED                                  0     0
  NGEF WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NGEF MUTATED                           0    13
  NGEF WILD-TYPE                        19   163
D621V12, multiclass
                                  clus
vv                                 NGEF MUTATED NGEF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      13            163
[1] 4 2
[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 = GGT5 MUTATION ANALYSIS
D622V1, survival
                sevent
clus2              0   1
  GGT5 MUTATED     9   4
  GGT5 WILD-TYPE 268  74
  GGT5 MUTATED GGT5 WILD-TYPE 
            13            342 
  GGT5 MUTATED GGT5 WILD-TYPE 
             4             74 
$`GGT5 MUTATED`
TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AA-A00E TCGA-AD-6889 TCGA-AZ-4315 
       85.05        10.88       100.01        30.02        83.24        58.39 
TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6169 TCGA-D5-6535 
       49.41        23.05        15.02        12.99        13.02        15.12 
TCGA-G4-6304 
       53.62 

$`GGT5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GGT5 MUTATED GGT5 WILD-TYPE 
         10.88           0.00 
  GGT5 MUTATED GGT5 WILD-TYPE 
        100.01         148.01 
  GGT5 MUTATED GGT5 WILD-TYPE 
         30.02          22.01 
[1] "10.9 - 100.0 (30.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.1"
D622V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGT5 MUTATED         0        0        4         7         1         0
  GGT5 WILD-TYPE      64        1       22       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GGT5 MUTATED           0          0          1          0        0         0
  GGT5 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  GGT5 MUTATED           0
  GGT5 WILD-TYPE         1
D622V3, multiclass
            clus
vv           GGT5 MUTATED GGT5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GGT5 MUTATED     0   0  11   3
  GGT5 WILD-TYPE   9  67 238  38
D622V4, multiclass
    clus
vv   GGT5 MUTATED GGT5 WILD-TYPE
  T1            0              9
  T2            0             67
  T3           11            238
  T4            3             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
  GGT5 MUTATED    12   1   1
  GGT5 WILD-TYPE 208  80  65
D622V5, multiclass
    clus
vv   GGT5 MUTATED GGT5 WILD-TYPE
  N0           12            208
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V6, binary
                cls
clus               0   1
  GGT5 MUTATED    11   0
  GGT5 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT5 MUTATED     11    0
  GGT5 WILD-TYPE  274   48
   clus
vv  GGT5 MUTATED GGT5 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D622V7, binary
                cls
clus               0   1
  GGT5 MUTATED     6   8
  GGT5 WILD-TYPE 164 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT5 MUTATED      6    8
  GGT5 WILD-TYPE  164  189
        clus
vv       GGT5 MUTATED GGT5 WILD-TYPE
  FEMALE            6            164
  MALE              8            189
[1] 2 2
[1] FALSE
D622V8, binary
                cls
clus               0   1
  GGT5 MUTATED    13   0
  GGT5 WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT5 MUTATED     13    0
  GGT5 WILD-TYPE  287    8
     clus
vv    GGT5 MUTATED GGT5 WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D622V9, binary
                cls
clus               0   1
  GGT5 MUTATED    14   0
  GGT5 WILD-TYPE 300  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT5 MUTATED     14    0
  GGT5 WILD-TYPE  300   48
                               clus
vv                              GGT5 MUTATED GGT5 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GGT5 MUTATED    10   0   0   1
  GGT5 WILD-TYPE 249   3  22  20
D622V10, multiclass
    clus
vv   GGT5 MUTATED GGT5 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D622V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGT5 MUTATED                                  0     1
  GGT5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GGT5 MUTATED                           2     8
  GGT5 WILD-TYPE                        17   168
D622V12, multiclass
                                  clus
vv                                 GGT5 MUTATED GGT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       8            168
[1] 4 2
[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 = CXORF38 MUTATION ANALYSIS
D623V1, survival
                   sevent
clus2                 0   1
  CXORF38 MUTATED     5   0
  CXORF38 WILD-TYPE 272  78
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                5               350 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                0                78 
$`CXORF38 MUTATED`
TCGA-G4-6588 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-5349 TCGA-G4-6309 
       26.17        21.44        58.39        30.08        85.48 

$`CXORF38 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CXORF38 MUTATED CXORF38 WILD-TYPE 
            21.44              0.00 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
            85.48            148.01 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
            30.08             22.01 
[1] "21.4 - 85.5 (30.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D623V2, continuous
                   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      64        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CXORF38 MUTATED           0          0          1          0        0
  CXORF38 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  CXORF38 MUTATED           0         0
  CXORF38 WILD-TYPE        12         1
D623V3, multiclass
            clus
vv           CXORF38 MUTATED CXORF38 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  CXORF38 MUTATED     0   0   5   0
  CXORF38 WILD-TYPE   9  67 244  41
D623V4, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  CXORF38 MUTATED     4   1   0
  CXORF38 WILD-TYPE 216  80  66
D623V5, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V6, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     4   0
  CXORF38 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      4    0
  CXORF38 WILD-TYPE  281   48
   clus
vv  CXORF38 MUTATED CXORF38 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D623V7, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     3   2
  CXORF38 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      3    2
  CXORF38 WILD-TYPE  167  195
        clus
vv       CXORF38 MUTATED CXORF38 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D623V8, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     5   0
  CXORF38 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      5    0
  CXORF38 WILD-TYPE  295    8
     clus
vv    CXORF38 MUTATED CXORF38 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D623V9, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     5   0
  CXORF38 WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      5    0
  CXORF38 WILD-TYPE  309   48
                               clus
vv                              CXORF38 MUTATED CXORF38 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CXORF38 MUTATED     5   0   0   0
  CXORF38 WILD-TYPE 254   3  22  21
D623V10, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D623V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXORF38 MUTATED                                  0     0
  CXORF38 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CXORF38 MUTATED                           1     4
  CXORF38 WILD-TYPE                        18   172
D623V12, multiclass
                                  clus
vv                                 CXORF38 MUTATED CXORF38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = BST2 MUTATION ANALYSIS
D624V1, survival
                sevent
clus2              0   1
  BST2 MUTATED     5   1
  BST2 WILD-TYPE 272  77
  BST2 MUTATED BST2 WILD-TYPE 
             6            349 
  BST2 MUTATED BST2 WILD-TYPE 
             1             77 
$`BST2 MUTATED`
TCGA-AZ-6601 TCGA-AA-3833 TCGA-AY-6386 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6541 
      100.01        15.95        17.82        23.05        15.02        15.58 

$`BST2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.090 
[1] "15.0 - 100.0 (16.9)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.6"
D624V2, continuous
                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      64        1       25       104         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  BST2 MUTATED           0
  BST2 WILD-TYPE         1
D624V3, multiclass
            clus
vv           BST2 MUTATED BST2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  BST2 MUTATED     0   0   6   0
  BST2 WILD-TYPE   9  67 243  41
D624V4, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            0             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
  BST2 MUTATED     5   1   0
  BST2 WILD-TYPE 215  80  66
D624V5, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V6, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  279   48
   clus
vv  BST2 MUTATED BST2 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D624V7, binary
                cls
clus               0   1
  BST2 MUTATED     3   3
  BST2 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      3    3
  BST2 WILD-TYPE  167  194
        clus
vv       BST2 MUTATED BST2 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D624V8, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  294    8
     clus
vv    BST2 MUTATED BST2 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D624V9, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  308   48
                               clus
vv                              BST2 MUTATED BST2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BST2 MUTATED     5   0   0   0
  BST2 WILD-TYPE 254   3  22  21
D624V10, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D624V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BST2 MUTATED                                  0     0
  BST2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BST2 MUTATED                           1     4
  BST2 WILD-TYPE                        18   172
D624V12, multiclass
                                  clus
vv                                 BST2 MUTATED BST2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = SFRS15 MUTATION ANALYSIS
D625V1, survival
                  sevent
clus2                0   1
  SFRS15 MUTATED    15   3
  SFRS15 WILD-TYPE 262  75
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              18              337 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
               3               75 
$`SFRS15 MUTATED`
TCGA-AA-3524 TCGA-AD-6964 TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3710 
       36.03        10.88        32.75        63.98        29.95        26.99 
TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 
       31.00        25.02        34.98        83.24        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 

$`SFRS15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SFRS15 MUTATED SFRS15 WILD-TYPE 
            9.44             0.00 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
          119.70           148.01 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
          31.875           21.990 
[1] "9.4 - 119.7 (31.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D625V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS15 MUTATED         1        0        3         9         2         0
  SFRS15 WILD-TYPE      63        1       23        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS15 MUTATED           0          0          2          0        0
  SFRS15 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SFRS15 MUTATED           0         0
  SFRS15 WILD-TYPE        12         1
D625V3, multiclass
            clus
vv           SFRS15 MUTATED SFRS15 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               9               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SFRS15 MUTATED     1   1  14   3
  SFRS15 WILD-TYPE   8  66 235  38
D625V4, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             14              235
  T4              3               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
  SFRS15 MUTATED    16   1   2
  SFRS15 WILD-TYPE 204  80  64
D625V5, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  N0             16              204
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V6, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    16   0
  SFRS15 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     16    0
  SFRS15 WILD-TYPE  269   48
   clus
vv  SFRS15 MUTATED SFRS15 WILD-TYPE
  0             16              269
  1              0               48
[1] 2 2
[1] FALSE
D625V7, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    10   9
  SFRS15 WILD-TYPE 160 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     10    9
  SFRS15 WILD-TYPE  160  188
        clus
vv       SFRS15 MUTATED SFRS15 WILD-TYPE
  FEMALE             10              160
  MALE                9              188
[1] 2 2
[1] FALSE
D625V8, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    17   0
  SFRS15 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     17    0
  SFRS15 WILD-TYPE  283    8
     clus
vv    SFRS15 MUTATED SFRS15 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D625V9, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    14   5
  SFRS15 WILD-TYPE 300  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     14    5
  SFRS15 WILD-TYPE  300   43
                               clus
vv                              SFRS15 MUTATED SFRS15 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SFRS15 MUTATED    14   0   0   1
  SFRS15 WILD-TYPE 245   3  22  20
D625V10, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              0               22
  RX              1               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"
D625V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS15 MUTATED                                  0     2
  SFRS15 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SFRS15 MUTATED                           1     8
  SFRS15 WILD-TYPE                        18   168
D625V12, multiclass
                                  clus
vv                                 SFRS15 MUTATED SFRS15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = EIF2AK4 MUTATION ANALYSIS
D626V1, survival
                   sevent
clus2                 0   1
  EIF2AK4 MUTATED    16   2
  EIF2AK4 WILD-TYPE 261  76
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               18               337 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
                2                76 
$`EIF2AK4 MUTATED`
TCGA-AA-A024 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 
       39.06        25.08       100.01        32.75        33.53        20.12 
TCGA-AA-3681 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3977 TCGA-CA-6717 TCGA-CM-5349 
        5.98        33.04        53.00        25.02        12.76        30.08 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6169 TCGA-CM-6171 TCGA-D5-6534 TCGA-F4-6856 
       12.00        14.04        13.02        14.04        43.27        35.31 

$`EIF2AK4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.99        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01        37.05         5.03        26.99        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6164 
        5.03        15.02        15.02        17.03        15.02        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        54.61        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        25.48        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
             5.98              0.00 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
           100.01            148.01 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
            27.58             21.99 
[1] "6.0 - 100.0 (27.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D626V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2AK4 MUTATED         3        0        3         7         1         0
  EIF2AK4 WILD-TYPE      61        1       23       101         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2AK4 MUTATED           1          0          2          0        0
  EIF2AK4 WILD-TYPE        17          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  EIF2AK4 MUTATED           0         0
  EIF2AK4 WILD-TYPE        12         1
D626V3, multiclass
            clus
vv           EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                7               101
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  EIF2AK4 MUTATED     1   3  13   1
  EIF2AK4 WILD-TYPE   8  64 236  40
D626V4, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  T1               1                 8
  T2               3                64
  T3              13               236
  T4               1                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
  EIF2AK4 MUTATED    15   3   0
  EIF2AK4 WILD-TYPE 205  78  66
D626V5, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  N0              15               205
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V6, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    16   0
  EIF2AK4 WILD-TYPE 269  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     16    0
  EIF2AK4 WILD-TYPE  269   48
   clus
vv  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  0              16               269
  1               0                48
[1] 2 2
[1] FALSE
D626V7, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED     8  10
  EIF2AK4 WILD-TYPE 162 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED      8   10
  EIF2AK4 WILD-TYPE  162  187
        clus
vv       EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  FEMALE               8               162
  MALE                10               187
[1] 2 2
[1] FALSE
D626V8, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    18   0
  EIF2AK4 WILD-TYPE 282   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     18    0
  EIF2AK4 WILD-TYPE  282    8
     clus
vv    EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  NO               18               282
  YES               0                 8
[1] 2 2
[1] FALSE
D626V9, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    11   7
  EIF2AK4 WILD-TYPE 303  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     11    7
  EIF2AK4 WILD-TYPE  303   41
                               clus
vv                              EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EIF2AK4 MUTATED    14   0   0   1
  EIF2AK4 WILD-TYPE 245   3  22  20
D626V10, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  R0              14               245
  R1               0                 3
  R2               0                22
  RX               1                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"
D626V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2AK4 MUTATED                                  0     1
  EIF2AK4 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EIF2AK4 MUTATED                           2    10
  EIF2AK4 WILD-TYPE                        17   166
D626V12, multiclass
                                  clus
vv                                 EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         10               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(627) Variable = LAS1L MUTATION ANALYSIS
D627V1, survival
                 sevent
clus2               0   1
  LAS1L MUTATED     8   1
  LAS1L WILD-TYPE 269  77
  LAS1L MUTATED LAS1L WILD-TYPE 
              9             346 
  LAS1L MUTATED LAS1L WILD-TYPE 
              1              77 
$`LAS1L MUTATED`
TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2672 TCGA-A6-2676 TCGA-AU-3779 TCGA-AU-6004 
       22.09        91.79        46.65        42.90        14.50        27.09 
TCGA-AZ-5407 TCGA-CM-6680 TCGA-G4-6309 
       88.21        12.03        85.48 

$`LAS1L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 
       35.80        26.17        79.69        43.76        43.76        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       24.53         5.79        22.42        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  LAS1L MUTATED LAS1L WILD-TYPE 
          12.03            0.00 
  LAS1L MUTATED LAS1L WILD-TYPE 
          91.79          148.01 
  LAS1L MUTATED LAS1L WILD-TYPE 
          42.90           21.99 
[1] "12.0 - 91.8 (42.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.4"
D627V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAS1L MUTATED         2        0        0         2         1         0
  LAS1L WILD-TYPE      62        1       26       106         7         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        17          6         41         33       35        12
                 vv
clus              STAGE IVB
  LAS1L MUTATED           0
  LAS1L WILD-TYPE         1
D627V3, multiclass
            clus
vv           LAS1L MUTATED LAS1L WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LAS1L MUTATED     1   2   5   1
  LAS1L WILD-TYPE   8  65 244  40
D627V4, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  T1             1               8
  T2             2              65
  T3             5             244
  T4             1              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
  LAS1L MUTATED     5   3   1
  LAS1L WILD-TYPE 215  78  65
D627V5, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  N0             5             215
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V6, binary
                 cls
clus                0   1
  LAS1L MUTATED     8   0
  LAS1L WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      8    0
  LAS1L WILD-TYPE  277   48
   clus
vv  LAS1L MUTATED LAS1L WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D627V7, binary
                 cls
clus                0   1
  LAS1L MUTATED     9   0
  LAS1L WILD-TYPE 161 197
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      9    0
  LAS1L WILD-TYPE  161  197
        clus
vv       LAS1L MUTATED LAS1L WILD-TYPE
  FEMALE             9             161
  MALE               0             197
[1] 2 2
[1] FALSE
D627V8, binary
                 cls
clus                0   1
  LAS1L MUTATED     8   0
  LAS1L WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      8    0
  LAS1L WILD-TYPE  292    8
     clus
vv    LAS1L MUTATED LAS1L WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D627V9, binary
                 cls
clus                0   1
  LAS1L MUTATED     9   0
  LAS1L WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      9    0
  LAS1L WILD-TYPE  305   48
                               clus
vv                              LAS1L MUTATED LAS1L WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LAS1L MUTATED     8   0   0   0
  LAS1L WILD-TYPE 251   3  22  21
D627V10, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D627V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAS1L MUTATED                                  0     0
  LAS1L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAS1L MUTATED                           1     8
  LAS1L WILD-TYPE                        18   168
D627V12, multiclass
                                  clus
vv                                 LAS1L MUTATED LAS1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = CATSPER4 MUTATION ANALYSIS
D628V1, survival
                    sevent
clus2                  0   1
  CATSPER4 MUTATED     6   3
  CATSPER4 WILD-TYPE 271  75
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                 9                346 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                 3                 75 
$`CATSPER4 MUTATED`
TCGA-AA-3525 TCGA-AD-6895 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3947 TCGA-AD-6901 
        8.05        25.08        23.87        20.12        33.01        22.42 
TCGA-AU-6004 TCGA-AZ-6606 TCGA-CA-6718 
       27.09        11.74        10.06 

$`CATSPER4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
              8.05               0.00 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
             33.01             148.01 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
            22.420             22.045 
[1] "8.1 - 33.0 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D628V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CATSPER4 MUTATED         1        0        0         3         2         0
  CATSPER4 WILD-TYPE      63        1       26       105         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER4 MUTATED           0          0          3          0        1
  CATSPER4 WILD-TYPE        18          6         41         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER4 MUTATED           0         0
  CATSPER4 WILD-TYPE        12         1
D628V3, multiclass
            clus
vv           CATSPER4 MUTATED CATSPER4 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 3                105
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  CATSPER4 MUTATED     0   1   7   3
  CATSPER4 WILD-TYPE   9  66 242  38
D628V4, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                7                242
  T4                3                 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
  CATSPER4 MUTATED     7   3   1
  CATSPER4 WILD-TYPE 213  78  65
D628V5, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  N0                7                213
  N1                3                 78
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V6, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     7   1
  CATSPER4 WILD-TYPE 278  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      7    1
  CATSPER4 WILD-TYPE  278   47
   clus
vv  CATSPER4 MUTATED CATSPER4 WILD-TYPE
  0                7                278
  1                1                 47
[1] 2 2
[1] FALSE
D628V7, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     5   6
  CATSPER4 WILD-TYPE 165 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      5    6
  CATSPER4 WILD-TYPE  165  191
        clus
vv       CATSPER4 MUTATED CATSPER4 WILD-TYPE
  FEMALE                5                165
  MALE                  6                191
[1] 2 2
[1] FALSE
D628V8, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     8   0
  CATSPER4 WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      8    0
  CATSPER4 WILD-TYPE  292    8
     clus
vv    CATSPER4 MUTATED CATSPER4 WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D628V9, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     9   2
  CATSPER4 WILD-TYPE 305  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      9    2
  CATSPER4 WILD-TYPE  305   46
                               clus
vv                              CATSPER4 MUTATED CATSPER4 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CATSPER4 MUTATED     5   0   0   2
  CATSPER4 WILD-TYPE 254   3  22  19
D628V10, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D628V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CATSPER4 MUTATED                                  0     1
  CATSPER4 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CATSPER4 MUTATED                           0     7
  CATSPER4 WILD-TYPE                        19   169
D628V12, multiclass
                                  clus
vv                                 CATSPER4 MUTATED CATSPER4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           7                169
[1] 4 2
[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 = OR4M2 MUTATION ANALYSIS
D629V1, survival
                 sevent
clus2               0   1
  OR4M2 MUTATED     9   4
  OR4M2 WILD-TYPE 268  74
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             13             342 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              4              74 
$`OR4M2 MUTATED`
TCGA-AA-3715 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3864 TCGA-AA-A010 TCGA-AU-6004 
       19.04        22.06        24.39        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 
       13.35 

$`OR4M2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79        88.21        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  OR4M2 MUTATED OR4M2 WILD-TYPE 
           6.77            0.00 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
          53.00          148.01 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
          22.06           22.06 
[1] "6.8 - 53.0 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D629V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4M2 MUTATED         3        0        3         6         2         0
  OR4M2 WILD-TYPE      61        1       23       102         6         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  OR4M2 MUTATED           0
  OR4M2 WILD-TYPE         1
D629V3, multiclass
            clus
vv           OR4M2 MUTATED OR4M2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR4M2 MUTATED     0   3   9   2
  OR4M2 WILD-TYPE   9  64 240  39
D629V4, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             2              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
  OR4M2 MUTATED    14   0   0
  OR4M2 WILD-TYPE 206  81  66
D629V5, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  N0            14             206
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V6, binary
                 cls
clus                0   1
  OR4M2 MUTATED    10   0
  OR4M2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     10    0
  OR4M2 WILD-TYPE  275   48
   clus
vv  OR4M2 MUTATED OR4M2 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D629V7, binary
                 cls
clus                0   1
  OR4M2 MUTATED     6   8
  OR4M2 WILD-TYPE 164 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED      6    8
  OR4M2 WILD-TYPE  164  189
        clus
vv       OR4M2 MUTATED OR4M2 WILD-TYPE
  FEMALE             6             164
  MALE               8             189
[1] 2 2
[1] FALSE
D629V8, binary
                 cls
clus                0   1
  OR4M2 MUTATED    12   0
  OR4M2 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     12    0
  OR4M2 WILD-TYPE  288    8
     clus
vv    OR4M2 MUTATED OR4M2 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D629V9, binary
                 cls
clus                0   1
  OR4M2 MUTATED    12   2
  OR4M2 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     12    2
  OR4M2 WILD-TYPE  302   46
                               clus
vv                              OR4M2 MUTATED OR4M2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4M2 MUTATED     7   0   0   4
  OR4M2 WILD-TYPE 252   3  22  17
D629V10, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             4              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"
D629V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4M2 MUTATED                                  0     2
  OR4M2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4M2 MUTATED                           0     9
  OR4M2 WILD-TYPE                        19   167
D629V12, multiclass
                                  clus
vv                                 OR4M2 MUTATED OR4M2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(630) Variable = HIVEP2 MUTATION ANALYSIS
D630V1, survival
                  sevent
clus2                0   1
  HIVEP2 MUTATED    14   4
  HIVEP2 WILD-TYPE 263  74
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              18              337 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
               4               74 
$`HIVEP2 MUTATED`
TCGA-AA-3950 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3821 
       24.00        19.66        63.98        54.02        26.99         1.02 
TCGA-AA-3877 TCGA-AD-6889 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5344 
       31.00        83.24         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 

$`HIVEP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        23.05        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-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
            1.02             0.00 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          135.65           148.01 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          21.025           22.090 
[1] "1.0 - 135.7 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D630V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIVEP2 MUTATED         4        0        2         7         0         0
  HIVEP2 WILD-TYPE      60        1       24       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP2 MUTATED           0          0          2          1        1
  HIVEP2 WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  HIVEP2 MUTATED           2         0
  HIVEP2 WILD-TYPE        10         1
D630V3, multiclass
            clus
vv           HIVEP2 MUTATED HIVEP2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               2               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
  HIVEP2 MUTATED     1   3  12   3
  HIVEP2 WILD-TYPE   8  64 237  38
D630V4, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             12              237
  T4              3               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
  HIVEP2 MUTATED    13   5   1
  HIVEP2 WILD-TYPE 207  76  65
D630V5, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  N0             13              207
  N1              5               76
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V6, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    15   3
  HIVEP2 WILD-TYPE 270  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     15    3
  HIVEP2 WILD-TYPE  270   45
   clus
vv  HIVEP2 MUTATED HIVEP2 WILD-TYPE
  0             15              270
  1              3               45
[1] 2 2
[1] FALSE
D630V7, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED     8  11
  HIVEP2 WILD-TYPE 162 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED      8   11
  HIVEP2 WILD-TYPE  162  186
        clus
vv       HIVEP2 MUTATED HIVEP2 WILD-TYPE
  FEMALE              8              162
  MALE               11              186
[1] 2 2
[1] FALSE
D630V8, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    17   0
  HIVEP2 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     17    0
  HIVEP2 WILD-TYPE  283    8
     clus
vv    HIVEP2 MUTATED HIVEP2 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D630V9, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    13   5
  HIVEP2 WILD-TYPE 301  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     13    5
  HIVEP2 WILD-TYPE  301   43
                               clus
vv                              HIVEP2 MUTATED HIVEP2 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HIVEP2 MUTATED    16   0   0   1
  HIVEP2 WILD-TYPE 243   3  22  20
D630V10, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  R0             16              243
  R1              0                3
  R2              0               22
  RX              1               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"
D630V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIVEP2 MUTATED                                  0     2
  HIVEP2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HIVEP2 MUTATED                           1     9
  HIVEP2 WILD-TYPE                        18   167
D630V12, multiclass
                                  clus
vv                                 HIVEP2 MUTATED HIVEP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(631) Variable = ZC3H13 MUTATION ANALYSIS
D631V1, survival
                  sevent
clus2                0   1
  ZC3H13 MUTATED    27   7
  ZC3H13 WILD-TYPE 250  71
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              34              321 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               7               71 
$`ZC3H13 MUTATED`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3713 
       24.33        13.02         8.05        17.95        23.01        19.04 
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-3864 
       33.53        22.06        63.98        29.95        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        10.13        38.20        98.24 
TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6626 
       35.74         6.18        53.62        46.75 

$`ZC3H13 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       14.53        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 
       19.07        34.03         0.99        13.02        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       30.02        34.03        18.05        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        15.02        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       38.07         1.02        33.04         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        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        13.41        13.35        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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        31.96        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       61.91        36.00        13.78 

  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            21.99 
[1] "1.0 - 98.2 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D631V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZC3H13 MUTATED         4        0        3        11         4         0
  ZC3H13 WILD-TYPE      60        1       23        97         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H13 MUTATED           2          3          3          2        1
  ZC3H13 WILD-TYPE        16          3         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZC3H13 MUTATED           0         0
  ZC3H13 WILD-TYPE        12         1
D631V3, multiclass
            clus
vv           ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              11               97
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              3                3
  STAGE IIIB              3               41
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  ZC3H13 MUTATED     1   5  23   5
  ZC3H13 WILD-TYPE   8  62 226  36
D631V4, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T1              1                8
  T2              5               62
  T3             23              226
  T4              5               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
  ZC3H13 MUTATED    24   6   4
  ZC3H13 WILD-TYPE 196  75  62
D631V5, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  N0             24              196
  N1              6               75
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V6, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    32   1
  ZC3H13 WILD-TYPE 253  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     32    1
  ZC3H13 WILD-TYPE  253   47
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0             32              253
  1              1               47
[1] 2 2
[1] FALSE
D631V7, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    16  18
  ZC3H13 WILD-TYPE 154 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     16   18
  ZC3H13 WILD-TYPE  154  179
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  FEMALE             16              154
  MALE               18              179
[1] 2 2
[1] FALSE
D631V8, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    27   2
  ZC3H13 WILD-TYPE 273   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     27    2
  ZC3H13 WILD-TYPE  273    6
     clus
vv    ZC3H13 MUTATED ZC3H13 WILD-TYPE
  NO              27              273
  YES              2                6
[1] 2 2
[1] FALSE
D631V9, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    23   9
  ZC3H13 WILD-TYPE 291  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     23    9
  ZC3H13 WILD-TYPE  291   39
                               clus
vv                              ZC3H13 MUTATED ZC3H13 WILD-TYPE
  COLON ADENOCARCINOMA                      23              291
  COLON MUCINOUS ADENOCARCINOMA              9               39
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZC3H13 MUTATED    27   0   1   2
  ZC3H13 WILD-TYPE 232   3  21  19
D631V10, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  R0             27              232
  R1              0                3
  R2              1               21
  RX              2               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"
D631V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H13 MUTATED                                  0     1
  ZC3H13 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZC3H13 MUTATED                           1    13
  ZC3H13 WILD-TYPE                        18   163
D631V12, multiclass
                                  clus
vv                                 ZC3H13 MUTATED ZC3H13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        13              163
[1] 4 2
[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 = GPR115 MUTATION ANALYSIS
D632V1, survival
                  sevent
clus2                0   1
  GPR115 MUTATED    12   6
  GPR115 WILD-TYPE 265  72
  GPR115 MUTATED GPR115 WILD-TYPE 
              18              337 
  GPR115 MUTATED GPR115 WILD-TYPE 
               6               72 
$`GPR115 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6964 TCGA-G4-6321 TCGA-A6-5661 TCGA-A6-5665 
       19.04        19.04        10.88        22.09        33.53        22.06 
TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3815 TCGA-AZ-4315 TCGA-AZ-6603 
       32.71        63.98        10.06        33.04        58.39        29.56 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5341 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6306 
       12.76        21.14        29.06         7.50       117.07        44.68 

$`GPR115 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6137 
       31.63        30.44        29.19        23.61        22.09        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-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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10         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        12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GPR115 MUTATED GPR115 WILD-TYPE 
             7.5              0.0 
  GPR115 MUTATED GPR115 WILD-TYPE 
          117.07           148.01 
  GPR115 MUTATED GPR115 WILD-TYPE 
          25.575           21.990 
[1] "7.5 - 117.1 (25.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D632V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR115 MUTATED         1        0        2         5         0         1
  GPR115 WILD-TYPE      63        1       24       103         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR115 MUTATED           2          1          0          2        1
  GPR115 WILD-TYPE        16          5         44         31       34
                  vv
clus               STAGE IVA STAGE IVB
  GPR115 MUTATED           0         0
  GPR115 WILD-TYPE        12         1
D632V3, multiclass
            clus
vv           GPR115 MUTATED GPR115 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               2               16
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  GPR115 MUTATED     1   4  11   2
  GPR115 WILD-TYPE   8  63 238  39
D632V4, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  T1              1                8
  T2              4               63
  T3             11              238
  T4              2               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
  GPR115 MUTATED    11   3   4
  GPR115 WILD-TYPE 209  78  62
D632V5, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  N0             11              209
  N1              3               78
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V6, binary
                  cls
clus                 0   1
  GPR115 MUTATED    14   1
  GPR115 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     14    1
  GPR115 WILD-TYPE  271   47
   clus
vv  GPR115 MUTATED GPR115 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D632V7, binary
                  cls
clus                 0   1
  GPR115 MUTATED     9   9
  GPR115 WILD-TYPE 161 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      9    9
  GPR115 WILD-TYPE  161  188
        clus
vv       GPR115 MUTATED GPR115 WILD-TYPE
  FEMALE              9              161
  MALE                9              188
[1] 2 2
[1] FALSE
D632V8, binary
                  cls
clus                 0   1
  GPR115 MUTATED    15   1
  GPR115 WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     15    1
  GPR115 WILD-TYPE  285    7
     clus
vv    GPR115 MUTATED GPR115 WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D632V9, binary
                  cls
clus                 0   1
  GPR115 MUTATED    17   1
  GPR115 WILD-TYPE 297  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     17    1
  GPR115 WILD-TYPE  297   47
                               clus
vv                              GPR115 MUTATED GPR115 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR115 MUTATED    10   0   1   2
  GPR115 WILD-TYPE 249   3  21  19
D632V10, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              2               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"
D632V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR115 MUTATED                                  0     1
  GPR115 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR115 MUTATED                           1    11
  GPR115 WILD-TYPE                        18   165
D632V12, multiclass
                                  clus
vv                                 GPR115 MUTATED GPR115 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(633) Variable = NCOA6 MUTATION ANALYSIS
D633V1, survival
                 sevent
clus2               0   1
  NCOA6 MUTATED    17   7
  NCOA6 WILD-TYPE 260  71
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             24             331 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
              7              71 
$`NCOA6 MUTATED`
TCGA-AA-3525 TCGA-AA-3715 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3510 
        8.05        19.04        26.17        79.69        19.66        63.98 
TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6607 
        6.97         2.01        25.02         4.01        34.98         3.19 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-6679 
       12.20        12.76        10.06        51.32        22.03        10.06 
TCGA-D5-5538 TCGA-D5-6927 TCGA-DM-A1DB TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6307 
       54.61         9.44        44.32         6.18        74.56        55.04 

$`NCOA6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        12.59        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  NCOA6 MUTATED NCOA6 WILD-TYPE 
           2.01            0.00 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
          79.69          148.01 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
          19.35           22.09 
[1] "2.0 - 79.7 (19.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D633V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA6 MUTATED         1        0        3        10         2         0
  NCOA6 WILD-TYPE      63        1       23        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA6 MUTATED           0          0          4          2        1         0
  NCOA6 WILD-TYPE        18          6         40         31       34        12
                 vv
clus              STAGE IVB
  NCOA6 MUTATED           0
  NCOA6 WILD-TYPE         1
D633V3, multiclass
            clus
vv           NCOA6 MUTATED NCOA6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  NCOA6 MUTATED     0   2  18   4
  NCOA6 WILD-TYPE   9  65 231  37
D633V4, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            18             231
  T4             4              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
  NCOA6 MUTATED    17   5   2
  NCOA6 WILD-TYPE 203  76  64
D633V5, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  N0            17             203
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V6, binary
                 cls
clus                0   1
  NCOA6 MUTATED    20   1
  NCOA6 WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     20    1
  NCOA6 WILD-TYPE  265   47
   clus
vv  NCOA6 MUTATED NCOA6 WILD-TYPE
  0            20             265
  1             1              47
[1] 2 2
[1] FALSE
D633V7, binary
                 cls
clus                0   1
  NCOA6 MUTATED     8  16
  NCOA6 WILD-TYPE 162 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED      8   16
  NCOA6 WILD-TYPE  162  181
        clus
vv       NCOA6 MUTATED NCOA6 WILD-TYPE
  FEMALE             8             162
  MALE              16             181
[1] 2 2
[1] FALSE
D633V8, binary
                 cls
clus                0   1
  NCOA6 MUTATED    21   0
  NCOA6 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     21    0
  NCOA6 WILD-TYPE  279    8
     clus
vv    NCOA6 MUTATED NCOA6 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D633V9, binary
                 cls
clus                0   1
  NCOA6 MUTATED    20   4
  NCOA6 WILD-TYPE 294  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     20    4
  NCOA6 WILD-TYPE  294   44
                               clus
vv                              NCOA6 MUTATED NCOA6 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NCOA6 MUTATED    16   0   0   4
  NCOA6 WILD-TYPE 243   3  22  17
D633V10, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             4              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"
D633V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA6 MUTATED                                  0     3
  NCOA6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA6 MUTATED                           0    13
  NCOA6 WILD-TYPE                        19   163
D633V12, multiclass
                                  clus
vv                                 NCOA6 MUTATED NCOA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       13             163
[1] 4 2
[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 = LAMC1 MUTATION ANALYSIS
D634V1, survival
                 sevent
clus2               0   1
  LAMC1 MUTATED    16   5
  LAMC1 WILD-TYPE 261  73
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             21             334 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
              5              73 
$`LAMC1 MUTATED`
TCGA-A6-4105 TCGA-AA-3715 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3977 
       14.53        19.04        29.19        63.98        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        15.02        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        12.39 
TCGA-D5-6930 TCGA-DM-A1D7 TCGA-F4-6570 
       13.35        13.32         6.18 

$`LAMC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A01D 
        4.01        27.02        42.02         0.99        14.99        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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10         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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       22.98        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-6167 
       15.02        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        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         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LAMC1 MUTATED LAMC1 WILD-TYPE 
           6.18            0.00 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
          63.98          148.01 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
          21.44           22.09 
[1] "6.2 - 64.0 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D634V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAMC1 MUTATED         1        0        3        10         1         0
  LAMC1 WILD-TYPE      63        1       23        98         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAMC1 MUTATED           0          0          3          1        0         0
  LAMC1 WILD-TYPE        18          6         41         32       35        12
                 vv
clus              STAGE IVB
  LAMC1 MUTATED           0
  LAMC1 WILD-TYPE         1
D634V3, multiclass
            clus
vv           LAMC1 MUTATED LAMC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             10              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  LAMC1 MUTATED     0   3  17   1
  LAMC1 WILD-TYPE   9  64 232  40
D634V4, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            17             232
  T4             1              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
  LAMC1 MUTATED    16   4   1
  LAMC1 WILD-TYPE 204  77  65
D634V5, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  N0            16             204
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V6, binary
                 cls
clus                0   1
  LAMC1 MUTATED    18   0
  LAMC1 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     18    0
  LAMC1 WILD-TYPE  267   48
   clus
vv  LAMC1 MUTATED LAMC1 WILD-TYPE
  0            18             267
  1             0              48
[1] 2 2
[1] FALSE
D634V7, binary
                 cls
clus                0   1
  LAMC1 MUTATED     8  13
  LAMC1 WILD-TYPE 162 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED      8   13
  LAMC1 WILD-TYPE  162  184
        clus
vv       LAMC1 MUTATED LAMC1 WILD-TYPE
  FEMALE             8             162
  MALE              13             184
[1] 2 2
[1] FALSE
D634V8, binary
                 cls
clus                0   1
  LAMC1 MUTATED    20   0
  LAMC1 WILD-TYPE 280   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     20    0
  LAMC1 WILD-TYPE  280    8
     clus
vv    LAMC1 MUTATED LAMC1 WILD-TYPE
  NO             20             280
  YES             0               8
[1] 2 2
[1] FALSE
D634V9, binary
                 cls
clus                0   1
  LAMC1 MUTATED    18   2
  LAMC1 WILD-TYPE 296  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     18    2
  LAMC1 WILD-TYPE  296   46
                               clus
vv                              LAMC1 MUTATED LAMC1 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LAMC1 MUTATED    16   0   0   0
  LAMC1 WILD-TYPE 243   3  22  21
D634V10, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             0              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"
D634V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAMC1 MUTATED                                  0     0
  LAMC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAMC1 MUTATED                           1    12
  LAMC1 WILD-TYPE                        18   164
D634V12, multiclass
                                  clus
vv                                 LAMC1 MUTATED LAMC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(635) Variable = CYP1B1 MUTATION ANALYSIS
D635V1, survival
                  sevent
clus2                0   1
  CYP1B1 MUTATED     8   2
  CYP1B1 WILD-TYPE 269  76
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              10              345 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
               2               76 
$`CYP1B1 MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3861 
       19.04        35.80        26.17        22.06        23.87        30.05 
TCGA-CA-6717 TCGA-CM-5348 TCGA-D5-6533 TCGA-G4-6303 
       12.76        22.98        25.48        65.85 

$`CYP1B1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6780 TCGA-A6-6781 
       25.18        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-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 
       74.56        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
           12.76             0.00 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
           65.85           148.01 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
          24.675           21.990 
[1] "12.8 - 65.8 (24.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D635V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP1B1 MUTATED         0        0        1         6         0         0
  CYP1B1 WILD-TYPE      64        1       25       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP1B1 MUTATED           0          0          2          0        1
  CYP1B1 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CYP1B1 MUTATED           0         0
  CYP1B1 WILD-TYPE        12         1
D635V3, multiclass
            clus
vv           CYP1B1 MUTATED CYP1B1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CYP1B1 MUTATED     0   0  10   1
  CYP1B1 WILD-TYPE   9  67 239  40
D635V4, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             10              239
  T4              1               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
  CYP1B1 MUTATED     8   3   0
  CYP1B1 WILD-TYPE 212  78  66
D635V5, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  N0              8              212
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V6, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    10   1
  CYP1B1 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     10    1
  CYP1B1 WILD-TYPE  275   47
   clus
vv  CYP1B1 MUTATED CYP1B1 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D635V7, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED     7   4
  CYP1B1 WILD-TYPE 163 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED      7    4
  CYP1B1 WILD-TYPE  163  193
        clus
vv       CYP1B1 MUTATED CYP1B1 WILD-TYPE
  FEMALE              7              163
  MALE                4              193
[1] 2 2
[1] FALSE
D635V8, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    10   0
  CYP1B1 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     10    0
  CYP1B1 WILD-TYPE  290    8
     clus
vv    CYP1B1 MUTATED CYP1B1 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D635V9, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    10   1
  CYP1B1 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     10    1
  CYP1B1 WILD-TYPE  304   47
                               clus
vv                              CYP1B1 MUTATED CYP1B1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CYP1B1 MUTATED     9   0   0   1
  CYP1B1 WILD-TYPE 250   3  22  20
D635V10, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D635V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP1B1 MUTATED                                  0     1
  CYP1B1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP1B1 MUTATED                           0     7
  CYP1B1 WILD-TYPE                        19   169
D635V12, multiclass
                                  clus
vv                                 CYP1B1 MUTATED CYP1B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = AFM MUTATION ANALYSIS
D636V1, survival
               sevent
clus2             0   1
  AFM MUTATED    10   3
  AFM WILD-TYPE 267  75
  AFM MUTATED AFM WILD-TYPE 
           13           342 
  AFM MUTATED AFM WILD-TYPE 
            3            75 
$`AFM MUTATED`
TCGA-AA-3713 TCGA-G4-6310 TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-A010 TCGA-AA-A01Q 
       19.04        63.62        32.75         1.02        34.98         1.02 
TCGA-AD-6965 TCGA-AZ-6599 TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-6923 TCGA-DM-A1DB 
       26.47         6.77        10.06        15.02        12.43        44.32 
TCGA-DM-A1HA 
      131.51 

$`AFM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38         7.50       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  AFM MUTATED AFM WILD-TYPE 
         1.02          0.00 
  AFM MUTATED AFM WILD-TYPE 
       131.51        148.01 
  AFM MUTATED AFM WILD-TYPE 
       19.040        22.075 
[1] "1.0 - 131.5 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D636V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AFM MUTATED         2        0        1         4         2         0
  AFM WILD-TYPE      62        1       25       104         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFM MUTATED           0          0          1          2        1         0
  AFM WILD-TYPE        18          6         43         31       34        12
               vv
clus            STAGE IVB
  AFM MUTATED           0
  AFM WILD-TYPE         1
D636V3, multiclass
            clus
vv           AFM MUTATED AFM WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            4           104
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           2            31
  STAGE IV             1            34
  STAGE IVA            0            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
  AFM MUTATED     0   2   8   3
  AFM WILD-TYPE   9  65 241  38
D636V4, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  T1           0             9
  T2           2            65
  T3           8           241
  T4           3            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
  AFM MUTATED    10   1   2
  AFM WILD-TYPE 210  80  64
D636V5, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  N0          10           210
  N1           1            80
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V6, binary
               cls
clus              0   1
  AFM MUTATED    11   1
  AFM WILD-TYPE 274  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     11    1
  AFM WILD-TYPE  274   47
   clus
vv  AFM MUTATED AFM WILD-TYPE
  0          11           274
  1           1            47
[1] 2 2
[1] FALSE
D636V7, binary
               cls
clus              0   1
  AFM MUTATED     5   8
  AFM WILD-TYPE 165 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED      5    8
  AFM WILD-TYPE  165  189
        clus
vv       AFM MUTATED AFM WILD-TYPE
  FEMALE           5           165
  MALE             8           189
[1] 2 2
[1] FALSE
D636V8, binary
               cls
clus              0   1
  AFM MUTATED     7   2
  AFM WILD-TYPE 293   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED      7    2
  AFM WILD-TYPE  293    6
     clus
vv    AFM MUTATED AFM WILD-TYPE
  NO            7           293
  YES           2             6
[1] 2 2
[1] FALSE
D636V9, binary
               cls
clus              0   1
  AFM MUTATED    12   1
  AFM WILD-TYPE 302  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     12    1
  AFM WILD-TYPE  302   47
                               clus
vv                              AFM MUTATED AFM WILD-TYPE
  COLON ADENOCARCINOMA                   12           302
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  AFM MUTATED     7   1   1   1
  AFM WILD-TYPE 252   2  21  20
D636V10, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  R0           7           252
  R1           1             2
  R2           1            21
  RX           1            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"
D636V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AFM MUTATED                                  0     1
  AFM WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  AFM MUTATED                           0     8
  AFM WILD-TYPE                        19   168
D636V12, multiclass
                                  clus
vv                                 AFM MUTATED AFM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      8           168
[1] 4 2
[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 = SLC22A9 MUTATION ANALYSIS
D637V1, survival
                   sevent
clus2                 0   1
  SLC22A9 MUTATED     8   0
  SLC22A9 WILD-TYPE 269  78
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                8               347 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                0                78 
$`SLC22A9 MUTATED`
TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3511 TCGA-AA-3977 TCGA-AY-6196 TCGA-CA-6717 
       25.08        19.66         6.97        25.02         0.20        12.76 
TCGA-CK-5913 TCGA-D5-6541 
       51.32        15.58 

$`SLC22A9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
              0.2               0.0 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            51.32            148.01 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            17.62             22.09 
[1] "0.2 - 51.3 (17.6)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D637V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A9 MUTATED         0        0        1         4         0         0
  SLC22A9 WILD-TYPE      64        1       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A9 MUTATED           0          0          0          2        0
  SLC22A9 WILD-TYPE        18          6         44         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A9 MUTATED           1         0
  SLC22A9 WILD-TYPE        11         1
D637V3, multiclass
            clus
vv           SLC22A9 MUTATED SLC22A9 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                1                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
  SLC22A9 MUTATED     0   1   6   2
  SLC22A9 WILD-TYPE   9  66 243  39
D637V4, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               2                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
  SLC22A9 MUTATED     6   2   1
  SLC22A9 WILD-TYPE 214  79  65
D637V5, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  N0               6               214
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V6, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     4   1
  SLC22A9 WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      4    1
  SLC22A9 WILD-TYPE  281   47
   clus
vv  SLC22A9 MUTATED SLC22A9 WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D637V7, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     3   6
  SLC22A9 WILD-TYPE 167 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      3    6
  SLC22A9 WILD-TYPE  167  191
        clus
vv       SLC22A9 MUTATED SLC22A9 WILD-TYPE
  FEMALE               3               167
  MALE                 6               191
[1] 2 2
[1] FALSE
D637V8, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     7   0
  SLC22A9 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      7    0
  SLC22A9 WILD-TYPE  293    8
     clus
vv    SLC22A9 MUTATED SLC22A9 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D637V9, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     6   3
  SLC22A9 WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      6    3
  SLC22A9 WILD-TYPE  308   45
                               clus
vv                              SLC22A9 MUTATED SLC22A9 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC22A9 MUTATED     5   0   0   2
  SLC22A9 WILD-TYPE 254   3  22  19
D637V10, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               2                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"
D637V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A9 MUTATED                                  0     1
  SLC22A9 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC22A9 MUTATED                           0     5
  SLC22A9 WILD-TYPE                        19   171
D637V12, multiclass
                                  clus
vv                                 SLC22A9 MUTATED SLC22A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = DDX59 MUTATION ANALYSIS
D638V1, survival
                 sevent
clus2               0   1
  DDX59 MUTATED    10   1
  DDX59 WILD-TYPE 267  77
  DDX59 MUTATED DDX59 WILD-TYPE 
             11             344 
  DDX59 MUTATED DDX59 WILD-TYPE 
              1              77 
$`DDX59 MUTATED`
TCGA-AD-6895 TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3510 TCGA-AZ-4315 TCGA-AZ-6600 
       25.08        35.80        22.06        63.98        58.39        12.10 
TCGA-CA-6717 TCGA-CK-4947 TCGA-D5-6540 TCGA-D5-6930 TCGA-G4-6306 
       12.76        17.56        16.14        13.35        44.68 

$`DDX59 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DDX59 MUTATED DDX59 WILD-TYPE 
           12.1             0.0 
  DDX59 MUTATED DDX59 WILD-TYPE 
          63.98          148.01 
  DDX59 MUTATED DDX59 WILD-TYPE 
          22.06           22.06 
[1] "12.1 - 64.0 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D638V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX59 MUTATED         1        0        1         5         0         0
  DDX59 WILD-TYPE      63        1       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX59 MUTATED           0          0          2          0        1         0
  DDX59 WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  DDX59 MUTATED           0
  DDX59 WILD-TYPE         1
D638V3, multiclass
            clus
vv           DDX59 MUTATED DDX59 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  DDX59 MUTATED     0   2   7   2
  DDX59 WILD-TYPE   9  65 242  39
D638V4, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             2              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
  DDX59 MUTATED     8   3   0
  DDX59 WILD-TYPE 212  78  66
D638V5, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V6, binary
                 cls
clus                0   1
  DDX59 MUTATED    10   1
  DDX59 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED     10    1
  DDX59 WILD-TYPE  275   47
   clus
vv  DDX59 MUTATED DDX59 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D638V7, binary
                 cls
clus                0   1
  DDX59 MUTATED     3   8
  DDX59 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED      3    8
  DDX59 WILD-TYPE  167  189
        clus
vv       DDX59 MUTATED DDX59 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D638V8, binary
                 cls
clus                0   1
  DDX59 MUTATED    11   0
  DDX59 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED     11    0
  DDX59 WILD-TYPE  289    8
     clus
vv    DDX59 MUTATED DDX59 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D638V9, binary
                 cls
clus                0   1
  DDX59 MUTATED     8   3
  DDX59 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED      8    3
  DDX59 WILD-TYPE  306   45
                               clus
vv                              DDX59 MUTATED DDX59 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX59 MUTATED     8   0   0   2
  DDX59 WILD-TYPE 251   3  22  19
D638V10, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D638V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX59 MUTATED                                  0     1
  DDX59 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX59 MUTATED                           1     8
  DDX59 WILD-TYPE                        18   168
D638V12, multiclass
                                  clus
vv                                 DDX59 MUTATED DDX59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = SLC25A13 MUTATION ANALYSIS
D639V1, survival
                    sevent
clus2                  0   1
  SLC25A13 MUTATED    11   3
  SLC25A13 WILD-TYPE 266  75
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                14                341 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                 3                 75 
$`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 
       12.43        53.62 

$`SLC25A13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                 0                  0 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
             88.21             148.01 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
             28.21              22.06 
[1] "0.0 - 88.2 (28.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D639V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC25A13 MUTATED         3        0        1         6         3         0
  SLC25A13 WILD-TYPE      61        1       25       102         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A13 MUTATED           0          0          1          0        0
  SLC25A13 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A13 MUTATED           0         0
  SLC25A13 WILD-TYPE        12         1
D639V3, multiclass
            clus
vv           SLC25A13 MUTATED SLC25A13 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 6                102
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SLC25A13 MUTATED     1   3   7   3
  SLC25A13 WILD-TYPE   8  64 242  38
D639V4, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  T1                1                  8
  T2                3                 64
  T3                7                242
  T4                3                 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
  SLC25A13 MUTATED    13   0   1
  SLC25A13 WILD-TYPE 207  81  65
D639V5, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  N0               13                207
  N1                0                 81
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V6, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    11   0
  SLC25A13 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     11    0
  SLC25A13 WILD-TYPE  274   48
   clus
vv  SLC25A13 MUTATED SLC25A13 WILD-TYPE
  0               11                274
  1                0                 48
[1] 2 2
[1] FALSE
D639V7, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED     5   9
  SLC25A13 WILD-TYPE 165 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED      5    9
  SLC25A13 WILD-TYPE  165  188
        clus
vv       SLC25A13 MUTATED SLC25A13 WILD-TYPE
  FEMALE                5                165
  MALE                  9                188
[1] 2 2
[1] FALSE
D639V8, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    12   0
  SLC25A13 WILD-TYPE 288   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     12    0
  SLC25A13 WILD-TYPE  288    8
     clus
vv    SLC25A13 MUTATED SLC25A13 WILD-TYPE
  NO                12                288
  YES                0                  8
[1] 2 2
[1] FALSE
D639V9, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    13   1
  SLC25A13 WILD-TYPE 301  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     13    1
  SLC25A13 WILD-TYPE  301   47
                               clus
vv                              SLC25A13 MUTATED SLC25A13 WILD-TYPE
  COLON ADENOCARCINOMA                        13                301
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC25A13 MUTATED    10   0   0   2
  SLC25A13 WILD-TYPE 249   3  22  19
D639V10, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  R0               10                249
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D639V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A13 MUTATED                                  0     1
  SLC25A13 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A13 MUTATED                           1     8
  SLC25A13 WILD-TYPE                        18   168
D639V12, multiclass
                                  clus
vv                                 SLC25A13 MUTATED SLC25A13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           8                168
[1] 4 2
[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 = EXD2 MUTATION ANALYSIS
D640V1, survival
                sevent
clus2              0   1
  EXD2 MUTATED     7   3
  EXD2 WILD-TYPE 270  75
  EXD2 MUTATED EXD2 WILD-TYPE 
            10            345 
  EXD2 MUTATED EXD2 WILD-TYPE 
             3             75 
$`EXD2 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6964 TCGA-AA-A00N TCGA-CA-6717 TCGA-CM-5864 
       19.04        24.00        10.88         4.01        12.76        15.02 
TCGA-D5-6534 TCGA-D5-6539 TCGA-F4-6459 TCGA-G4-6323 
       43.27        12.49         8.61        13.78 

$`EXD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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-D5-6540 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        46.75 

  EXD2 MUTATED EXD2 WILD-TYPE 
          4.01           0.00 
  EXD2 MUTATED EXD2 WILD-TYPE 
         43.27         148.01 
  EXD2 MUTATED EXD2 WILD-TYPE 
         13.27          22.36 
[1] "4.0 - 43.3 (13.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.2"
D640V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXD2 MUTATED         1        1        0         3         1         0
  EXD2 WILD-TYPE      63        0       26       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXD2 MUTATED           0          0          1          0        1         0
  EXD2 WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  EXD2 MUTATED           0
  EXD2 WILD-TYPE         1
D640V3, multiclass
            clus
vv           EXD2 MUTATED EXD2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  EXD2 MUTATED     0   1   6   2
  EXD2 WILD-TYPE   9  66 243  39
D640V4, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            2             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
  EXD2 MUTATED     8   0   2
  EXD2 WILD-TYPE 212  81  64
D640V5, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V6, binary
                cls
clus               0   1
  EXD2 MUTATED     7   1
  EXD2 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      7    1
  EXD2 WILD-TYPE  278   47
   clus
vv  EXD2 MUTATED EXD2 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D640V7, binary
                cls
clus               0   1
  EXD2 MUTATED     4   6
  EXD2 WILD-TYPE 166 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      4    6
  EXD2 WILD-TYPE  166  191
        clus
vv       EXD2 MUTATED EXD2 WILD-TYPE
  FEMALE            4            166
  MALE              6            191
[1] 2 2
[1] FALSE
D640V8, binary
                cls
clus               0   1
  EXD2 MUTATED     8   1
  EXD2 WILD-TYPE 292   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      8    1
  EXD2 WILD-TYPE  292    7
     clus
vv    EXD2 MUTATED EXD2 WILD-TYPE
  NO             8            292
  YES            1              7
[1] 2 2
[1] FALSE
D640V9, binary
                cls
clus               0   1
  EXD2 MUTATED     6   4
  EXD2 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      6    4
  EXD2 WILD-TYPE  308   44
                               clus
vv                              EXD2 MUTATED EXD2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EXD2 MUTATED     7   0   1   1
  EXD2 WILD-TYPE 252   3  21  20
D640V10, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            1             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"
D640V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXD2 MUTATED                                  0     1
  EXD2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EXD2 MUTATED                           1     5
  EXD2 WILD-TYPE                        18   171
D640V12, multiclass
                                  clus
vv                                 EXD2 MUTATED EXD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = ATP8B2 MUTATION ANALYSIS
D641V1, survival
                  sevent
clus2                0   1
  ATP8B2 MUTATED    13   4
  ATP8B2 WILD-TYPE 264  74
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
              17              338 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
               4               74 
$`ATP8B2 MUTATED`
TCGA-AA-3950 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3966 TCGA-AA-A010 
       24.00        22.06         6.97        15.95         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 
       13.35        12.00       139.17        35.97         6.18 

$`ATP8B2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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-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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28G 
       44.32       131.51       135.65        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
            2.01             0.00 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
          139.17           148.01 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
           15.02            22.39 
[1] "2.0 - 139.2 (15.0)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.3"
D641V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP8B2 MUTATED         2        0        1        10         1         0
  ATP8B2 WILD-TYPE      62        1       25        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP8B2 MUTATED           0          0          2          1        0
  ATP8B2 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP8B2 MUTATED           0         0
  ATP8B2 WILD-TYPE        12         1
D641V3, multiclass
            clus
vv           ATP8B2 MUTATED ATP8B2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              10               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ATP8B2 MUTATED     1   1  13   2
  ATP8B2 WILD-TYPE   8  66 236  39
D641V4, multiclass
    clus
vv   ATP8B2 MUTATED ATP8B2 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             13              236
  T4              2               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
  ATP8B2 MUTATED    14   2   1
  ATP8B2 WILD-TYPE 206  79  65
D641V5, multiclass
    clus
vv   ATP8B2 MUTATED ATP8B2 WILD-TYPE
  N0             14              206
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V6, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED    16   0
  ATP8B2 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED     16    0
  ATP8B2 WILD-TYPE  269   48
   clus
vv  ATP8B2 MUTATED ATP8B2 WILD-TYPE
  0             16              269
  1              0               48
[1] 2 2
[1] FALSE
D641V7, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED     9   8
  ATP8B2 WILD-TYPE 161 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED      9    8
  ATP8B2 WILD-TYPE  161  189
        clus
vv       ATP8B2 MUTATED ATP8B2 WILD-TYPE
  FEMALE              9              161
  MALE                8              189
[1] 2 2
[1] FALSE
D641V8, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED    14   0
  ATP8B2 WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED     14    0
  ATP8B2 WILD-TYPE  286    8
     clus
vv    ATP8B2 MUTATED ATP8B2 WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D641V9, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED    13   4
  ATP8B2 WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED     13    4
  ATP8B2 WILD-TYPE  301   44
                               clus
vv                              ATP8B2 MUTATED ATP8B2 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP8B2 MUTATED    12   0   0   2
  ATP8B2 WILD-TYPE 247   3  22  19
D641V10, multiclass
    clus
vv   ATP8B2 MUTATED ATP8B2 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              2               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"
D641V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP8B2 MUTATED                                  0     1
  ATP8B2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP8B2 MUTATED                           2     9
  ATP8B2 WILD-TYPE                        17   167
D641V12, multiclass
                                  clus
vv                                 ATP8B2 MUTATED ATP8B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         9              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(642) Variable = TBL1XR1 MUTATION ANALYSIS
D642V1, survival
                   sevent
clus2                 0   1
  TBL1XR1 MUTATED    10   1
  TBL1XR1 WILD-TYPE 267  77
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               11               344 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                1                77 
$`TBL1XR1 MUTATED`
TCGA-AA-3713 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N 
       19.04        23.87        63.98        31.00        25.02         4.01 
TCGA-AA-A010 TCGA-CK-6748 TCGA-D5-6927 TCGA-D5-6928 TCGA-F4-6856 
       34.98         2.01         9.44        11.64        35.31 

$`TBL1XR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6780 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6751 TCGA-CM-4743 
       51.32        21.99        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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
             2.01              0.00 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            63.98            148.01 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
           23.870            22.045 
[1] "2.0 - 64.0 (23.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D642V2, continuous
                   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      62        1       24       105         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBL1XR1 MUTATED           0          0          1          0        2
  TBL1XR1 WILD-TYPE        18          6         43         33       33
                   vv
clus                STAGE IVA STAGE IVB
  TBL1XR1 MUTATED           0         0
  TBL1XR1 WILD-TYPE        12         1
D642V3, multiclass
            clus
vv           TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                3               105
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  TBL1XR1 MUTATED     1   2   7   3
  TBL1XR1 WILD-TYPE   8  65 242  38
D642V4, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               7               242
  T4               3                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
  TBL1XR1 MUTATED    11   2   0
  TBL1XR1 WILD-TYPE 209  79  66
D642V5, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  N0              11               209
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V6, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED    10   2
  TBL1XR1 WILD-TYPE 275  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED     10    2
  TBL1XR1 WILD-TYPE  275   46
   clus
vv  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  0              10               275
  1               2                46
[1] 2 2
[1] FALSE
D642V7, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     6   7
  TBL1XR1 WILD-TYPE 164 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      6    7
  TBL1XR1 WILD-TYPE  164  190
        clus
vv       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  FEMALE               6               164
  MALE                 7               190
[1] 2 2
[1] FALSE
D642V8, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     9   1
  TBL1XR1 WILD-TYPE 291   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      9    1
  TBL1XR1 WILD-TYPE  291    7
     clus
vv    TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  NO                9               291
  YES               1                 7
[1] 2 2
[1] FALSE
D642V9, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     8   5
  TBL1XR1 WILD-TYPE 306  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      8    5
  TBL1XR1 WILD-TYPE  306   43
                               clus
vv                              TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TBL1XR1 MUTATED     9   0   1   1
  TBL1XR1 WILD-TYPE 250   3  21  20
D642V10, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               1                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"
D642V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBL1XR1 MUTATED                                  0     0
  TBL1XR1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TBL1XR1 MUTATED                           0     5
  TBL1XR1 WILD-TYPE                        19   171
D642V12, multiclass
                                  clus
vv                                 TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(643) Variable = SPANXC MUTATION ANALYSIS
D643V1, survival
                  sevent
clus2                0   1
  SPANXC MUTATED     3   0
  SPANXC WILD-TYPE 274  78
  SPANXC MUTATED SPANXC WILD-TYPE 
               3              352 
  SPANXC MUTATED SPANXC WILD-TYPE 
               0               78 
$`SPANXC MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-CK-5913 
       33.53        24.39        51.32 

$`SPANXC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SPANXC MUTATED SPANXC WILD-TYPE 
           24.39             0.00 
  SPANXC MUTATED SPANXC WILD-TYPE 
           51.32           148.01 
  SPANXC MUTATED SPANXC WILD-TYPE 
           33.53            22.01 
[1] "24.4 - 51.3 (33.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D643V2, continuous
                  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      63        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXC MUTATED           0          0          0          0        1
  SPANXC WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  SPANXC MUTATED           0         0
  SPANXC WILD-TYPE        12         1
D643V3, multiclass
            clus
vv           SPANXC MUTATED SPANXC WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  SPANXC MUTATED     0   1   2   1
  SPANXC WILD-TYPE   9  66 247  40
D643V4, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  T1              0                9
  T2              1               66
  T3              2              247
  T4              1               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
  SPANXC MUTATED     3   0   1
  SPANXC WILD-TYPE 217  81  65
D643V5, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  N0              3              217
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V6, binary
                  cls
clus                 0   1
  SPANXC MUTATED     2   1
  SPANXC WILD-TYPE 283  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      2    1
  SPANXC WILD-TYPE  283   47
   clus
vv  SPANXC MUTATED SPANXC WILD-TYPE
  0              2              283
  1              1               47
[1] 2 2
[1] FALSE
D643V7, binary
                  cls
clus                 0   1
  SPANXC MUTATED     2   2
  SPANXC WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      2    2
  SPANXC WILD-TYPE  168  195
        clus
vv       SPANXC MUTATED SPANXC WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D643V8, binary
                  cls
clus                 0   1
  SPANXC MUTATED     3   0
  SPANXC WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      3    0
  SPANXC WILD-TYPE  297    8
     clus
vv    SPANXC MUTATED SPANXC WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D643V9, binary
                  cls
clus                 0   1
  SPANXC MUTATED     4   0
  SPANXC WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      4    0
  SPANXC WILD-TYPE  310   48
                               clus
vv                              SPANXC MUTATED SPANXC WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SPANXC MUTATED     1   0   1   1
  SPANXC WILD-TYPE 258   3  21  20
D643V10, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  R0              1              258
  R1              0                3
  R2              1               21
  RX              1               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"
D643V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPANXC MUTATED                                  0     0
  SPANXC WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SPANXC MUTATED                           1     2
  SPANXC WILD-TYPE                        18   174
D643V12, multiclass
                                  clus
vv                                 SPANXC MUTATED SPANXC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(644) Variable = HORMAD1 MUTATION ANALYSIS
D644V1, survival
                   sevent
clus2                 0   1
  HORMAD1 MUTATED     9   4
  HORMAD1 WILD-TYPE 268  74
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               13               342 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                4                74 
$`HORMAD1 MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6607 
       25.08        79.69        24.39         4.01        34.98         3.19 
TCGA-CK-4950 TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6806 
       85.45       130.65       131.51        35.97         6.18        41.42 
TCGA-G4-6309 
       85.48 

$`HORMAD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 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-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
       44.32       135.65       139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
             3.19              0.00 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
           131.51            148.01 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
            35.97             21.99 
[1] "3.2 - 131.5 (36.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D644V2, continuous
                   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      61        1       26       106         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HORMAD1 MUTATED           0          0          4          1        1
  HORMAD1 WILD-TYPE        18          6         40         32       34
                   vv
clus                STAGE IVA STAGE IVB
  HORMAD1 MUTATED           0         0
  HORMAD1 WILD-TYPE        12         1
D644V3, multiclass
            clus
vv           HORMAD1 MUTATED HORMAD1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  HORMAD1 MUTATED     0   3   7   3
  HORMAD1 WILD-TYPE   9  64 242  38
D644V4, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               7               242
  T4               3                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
  HORMAD1 MUTATED     7   4   2
  HORMAD1 WILD-TYPE 213  77  64
D644V5, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  N0               7               213
  N1               4                77
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V6, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED    12   1
  HORMAD1 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED     12    1
  HORMAD1 WILD-TYPE  273   47
   clus
vv  HORMAD1 MUTATED HORMAD1 WILD-TYPE
  0              12               273
  1               1                47
[1] 2 2
[1] FALSE
D644V7, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     6   7
  HORMAD1 WILD-TYPE 164 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      6    7
  HORMAD1 WILD-TYPE  164  190
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  FEMALE               6               164
  MALE                 7               190
[1] 2 2
[1] FALSE
D644V8, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     9   0
  HORMAD1 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      9    0
  HORMAD1 WILD-TYPE  291    8
     clus
vv    HORMAD1 MUTATED HORMAD1 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D644V9, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED    11   2
  HORMAD1 WILD-TYPE 303  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED     11    2
  HORMAD1 WILD-TYPE  303   46
                               clus
vv                              HORMAD1 MUTATED HORMAD1 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HORMAD1 MUTATED     7   1   0   0
  HORMAD1 WILD-TYPE 252   2  22  21
D644V10, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  R0               7               252
  R1               1                 2
  R2               0                22
  RX               0                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"
D644V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HORMAD1 MUTATED                                  0     0
  HORMAD1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HORMAD1 MUTATED                           2     9
  HORMAD1 WILD-TYPE                        17   167
D644V12, multiclass
                                  clus
vv                                 HORMAD1 MUTATED HORMAD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          9               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(645) Variable = TMEM131 MUTATION ANALYSIS
D645V1, survival
                   sevent
clus2                 0   1
  TMEM131 MUTATED    16   4
  TMEM131 WILD-TYPE 261  74
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               20               335 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
                4                74 
$`TMEM131 MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3845 
        1.02         0.92        32.71        35.01        63.98         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 
       35.31        85.48 

$`TMEM131 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        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-3511 
       20.12        19.66        20.28         7.04         3.02         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  TMEM131 MUTATED TMEM131 WILD-TYPE 
                0                 0 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
           119.93            148.01 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
           22.705            22.030 
[1] "0.0 - 119.9 (22.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D645V2, continuous
                   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      61        1       24        99         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM131 MUTATED           1          0          2          2        0
  TMEM131 WILD-TYPE        17          6         42         31       35
                   vv
clus                STAGE IVA STAGE IVB
  TMEM131 MUTATED           1         0
  TMEM131 WILD-TYPE        11         1
D645V3, multiclass
            clus
vv           TMEM131 MUTATED TMEM131 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                9                99
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                1                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
  TMEM131 MUTATED     0   3  16   2
  TMEM131 WILD-TYPE   9  64 233  39
D645V4, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              16               233
  T4               2                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
  TMEM131 MUTATED    16   3   2
  TMEM131 WILD-TYPE 204  78  64
D645V5, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  N0              16               204
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V6, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    18   1
  TMEM131 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     18    1
  TMEM131 WILD-TYPE  267   47
   clus
vv  TMEM131 MUTATED TMEM131 WILD-TYPE
  0              18               267
  1               1                47
[1] 2 2
[1] FALSE
D645V7, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    11  10
  TMEM131 WILD-TYPE 159 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     11   10
  TMEM131 WILD-TYPE  159  187
        clus
vv       TMEM131 MUTATED TMEM131 WILD-TYPE
  FEMALE              11               159
  MALE                10               187
[1] 2 2
[1] FALSE
D645V8, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    15   0
  TMEM131 WILD-TYPE 285   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     15    0
  TMEM131 WILD-TYPE  285    8
     clus
vv    TMEM131 MUTATED TMEM131 WILD-TYPE
  NO               15               285
  YES               0                 8
[1] 2 2
[1] FALSE
D645V9, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    16   4
  TMEM131 WILD-TYPE 298  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     16    4
  TMEM131 WILD-TYPE  298   44
                               clus
vv                              TMEM131 MUTATED TMEM131 WILD-TYPE
  COLON ADENOCARCINOMA                       16               298
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM131 MUTATED    15   0   0   3
  TMEM131 WILD-TYPE 244   3  22  18
D645V10, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  R0              15               244
  R1               0                 3
  R2               0                22
  RX               3                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"
D645V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM131 MUTATED                                  0     1
  TMEM131 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM131 MUTATED                           1    12
  TMEM131 WILD-TYPE                        18   164
D645V12, multiclass
                                  clus
vv                                 TMEM131 MUTATED TMEM131 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         12               164
[1] 4 2
[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 = PVRL4 MUTATION ANALYSIS
D646V1, survival
                 sevent
clus2               0   1
  PVRL4 MUTATED     8   1
  PVRL4 WILD-TYPE 269  77
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              9             346 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              1              77 
$`PVRL4 MUTATED`
TCGA-AA-3715 TCGA-A6-6141 TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A00J TCGA-CM-5349 
       19.04         8.38        31.00         2.01        18.05        30.08 
TCGA-CM-5868 TCGA-DM-A1HB TCGA-G4-6293 
       17.03       135.65       133.18 

$`PVRL4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PVRL4 MUTATED PVRL4 WILD-TYPE 
           2.01            0.00 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         135.65          148.01 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         19.040          22.075 
[1] "2.0 - 135.7 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D646V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PVRL4 MUTATED         1        0        1         3         0         0
  PVRL4 WILD-TYPE      63        1       25       105         8         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        17          6         42         33       35        11
                 vv
clus              STAGE IVB
  PVRL4 MUTATED           0
  PVRL4 WILD-TYPE         1
D646V3, multiclass
            clus
vv           PVRL4 MUTATED PVRL4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  PVRL4 MUTATED     1   0   6   2
  PVRL4 WILD-TYPE   8  67 243  39
D646V4, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             6             243
  T4             2              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
  PVRL4 MUTATED     5   4   0
  PVRL4 WILD-TYPE 215  77  66
D646V5, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  N0             5             215
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V6, binary
                 cls
clus                0   1
  PVRL4 MUTATED     8   1
  PVRL4 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      8    1
  PVRL4 WILD-TYPE  277   47
   clus
vv  PVRL4 MUTATED PVRL4 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D646V7, binary
                 cls
clus                0   1
  PVRL4 MUTATED     5   4
  PVRL4 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      5    4
  PVRL4 WILD-TYPE  165  193
        clus
vv       PVRL4 MUTATED PVRL4 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D646V8, binary
                 cls
clus                0   1
  PVRL4 MUTATED     7   0
  PVRL4 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      7    0
  PVRL4 WILD-TYPE  293    8
     clus
vv    PVRL4 MUTATED PVRL4 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D646V9, binary
                 cls
clus                0   1
  PVRL4 MUTATED     5   3
  PVRL4 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      5    3
  PVRL4 WILD-TYPE  309   45
                               clus
vv                              PVRL4 MUTATED PVRL4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PVRL4 MUTATED     6   0   0   0
  PVRL4 WILD-TYPE 253   3  22  21
D646V10, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D646V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PVRL4 MUTATED                                  0     0
  PVRL4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PVRL4 MUTATED                           1     4
  PVRL4 WILD-TYPE                        18   172
D646V12, multiclass
                                  clus
vv                                 PVRL4 MUTATED PVRL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = C12ORF49 MUTATION ANALYSIS
D647V1, survival
                    sevent
clus2                  0   1
  C12ORF49 MUTATED     1   3
  C12ORF49 WILD-TYPE 276  75
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                351 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 3                 75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-F4-6459 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  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             22.060 
[1] "7.0 - 49.4 (27.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.3"
D647V2, continuous
                    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      64        1       24       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF49 MUTATED           0          0          0          1        0
  C12ORF49 WILD-TYPE        18          6         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF49 MUTATED           0         0
  C12ORF49 WILD-TYPE        12         1
D647V3, multiclass
            clus
vv           C12ORF49 MUTATED C12ORF49 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 1                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C12ORF49 MUTATED     0   0   4   0
  C12ORF49 WILD-TYPE   9  67 245  41
D647V4, multiclass
    clus
vv   C12ORF49 MUTATED C12ORF49 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                4                245
  T4                0                 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
  C12ORF49 MUTATED     3   0   1
  C12ORF49 WILD-TYPE 217  81  65
D647V5, multiclass
    clus
vv   C12ORF49 MUTATED C12ORF49 WILD-TYPE
  N0                3                217
  N1                0                 81
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V6, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     3   0
  C12ORF49 WILD-TYPE 282  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      3    0
  C12ORF49 WILD-TYPE  282   48
   clus
vv  C12ORF49 MUTATED C12ORF49 WILD-TYPE
  0                3                282
  1                0                 48
[1] 2 2
[1] FALSE
D647V7, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     2   2
  C12ORF49 WILD-TYPE 168 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      2    2
  C12ORF49 WILD-TYPE  168  195
        clus
vv       C12ORF49 MUTATED C12ORF49 WILD-TYPE
  FEMALE                2                168
  MALE                  2                195
[1] 2 2
[1] FALSE
D647V8, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     3   0
  C12ORF49 WILD-TYPE 297   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      3    0
  C12ORF49 WILD-TYPE  297    8
     clus
vv    C12ORF49 MUTATED C12ORF49 WILD-TYPE
  NO                 3                297
  YES                0                  8
[1] 2 2
[1] FALSE
D647V9, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     4   0
  C12ORF49 WILD-TYPE 310  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      4    0
  C12ORF49 WILD-TYPE  310   48
                               clus
vv                              C12ORF49 MUTATED C12ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF49 MUTATED     2   0   0   0
  C12ORF49 WILD-TYPE 257   3  22  21
D647V10, multiclass
[1] "Remove cluster labels:" "C12ORF49 MUTATED"      
clus
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 2                303 
        TCGA-A6-2677         TCGA-AA-3496         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-3527         TCGA-AA-3530 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3662         TCGA-AA-3672 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3697 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3814 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3860         TCGA-AA-3867 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3939         TCGA-AA-3950 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3972         TCGA-AA-3976 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3986         TCGA-AA-A00L 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A024         TCGA-AD-6548 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AZ-4681 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-5912         TCGA-G4-6310         TCGA-G4-6321 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6586         TCGA-G4-6588         TCGA-G4-6625 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6628         TCGA-A6-2671         TCGA-A6-2672 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         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-3502         TCGA-AA-3510         TCGA-AA-3511 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3517         TCGA-AA-3518 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3526         TCGA-AA-3529 
"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-3544         TCGA-AA-3548 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3553         TCGA-AA-3555 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3561         TCGA-AA-3655 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3664         TCGA-AA-3666 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3673         TCGA-AA-3678 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3693 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3811         TCGA-AA-3812 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         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-3861         TCGA-AA-3864         TCGA-AA-3866 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3872         TCGA-AA-3875 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3941 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         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-3973         TCGA-AA-3975         TCGA-AA-3984 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"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-A029         TCGA-AA-A02F 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02K 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02O         TCGA-AA-A02W         TCGA-AA-A02Y 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A03F         TCGA-AA-A03J         TCGA-AD-5900 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6965         TCGA-AU-3779 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4682 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-4952         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-G4-6315         TCGA-G4-6317         TCGA-G4-6323 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
D647V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF49 MUTATED                                  0     0
  C12ORF49 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF49 MUTATED                           0     3
  C12ORF49 WILD-TYPE                        19   173
D647V12, multiclass
                                  clus
vv                                 C12ORF49 MUTATED C12ORF49 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[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 = CWF19L2 MUTATION ANALYSIS
D648V1, survival
                   sevent
clus2                 0   1
  CWF19L2 MUTATED    13   1
  CWF19L2 WILD-TYPE 264  77
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               14               341 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
                1                77 
$`CWF19L2 MUTATED`
TCGA-AA-3543 TCGA-A6-5659 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3977 
        0.99        30.44        24.39        19.66         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 
       23.05        17.03 

$`CWF19L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        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        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
             0.99              0.00 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            51.32            148.01 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
           21.355            22.060 
[1] "1.0 - 51.3 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D648V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CWF19L2 MUTATED         4        0        1         5         1         0
  CWF19L2 WILD-TYPE      60        1       25       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CWF19L2 MUTATED           0          0          1          1        0
  CWF19L2 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  CWF19L2 MUTATED           1         0
  CWF19L2 WILD-TYPE        11         1
D648V3, multiclass
            clus
vv           CWF19L2 MUTATED CWF19L2 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  CWF19L2 MUTATED     0   5   6   4
  CWF19L2 WILD-TYPE   9  62 243  37
D648V4, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3               6               243
  T4               4                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
  CWF19L2 MUTATED    12   3   0
  CWF19L2 WILD-TYPE 208  78  66
D648V5, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  N0              12               208
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V6, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    11   1
  CWF19L2 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     11    1
  CWF19L2 WILD-TYPE  274   47
   clus
vv  CWF19L2 MUTATED CWF19L2 WILD-TYPE
  0              11               274
  1               1                47
[1] 2 2
[1] FALSE
D648V7, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED     5  10
  CWF19L2 WILD-TYPE 165 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED      5   10
  CWF19L2 WILD-TYPE  165  187
        clus
vv       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  FEMALE               5               165
  MALE                10               187
[1] 2 2
[1] FALSE
D648V8, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    13   0
  CWF19L2 WILD-TYPE 287   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     13    0
  CWF19L2 WILD-TYPE  287    8
     clus
vv    CWF19L2 MUTATED CWF19L2 WILD-TYPE
  NO               13               287
  YES               0                 8
[1] 2 2
[1] FALSE
D648V9, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    11   4
  CWF19L2 WILD-TYPE 303  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     11    4
  CWF19L2 WILD-TYPE  303   44
                               clus
vv                              CWF19L2 MUTATED CWF19L2 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CWF19L2 MUTATED    10   0   0   3
  CWF19L2 WILD-TYPE 249   3  22  18
D648V10, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               3                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"
D648V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CWF19L2 MUTATED                                  0     2
  CWF19L2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CWF19L2 MUTATED                           0     7
  CWF19L2 WILD-TYPE                        19   169
D648V12, multiclass
                                  clus
vv                                 CWF19L2 MUTATED CWF19L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = ATAD5 MUTATION ANALYSIS
D649V1, survival
                 sevent
clus2               0   1
  ATAD5 MUTATED    14   6
  ATAD5 WILD-TYPE 263  72
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             20             335 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
              6              72 
$`ATAD5 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3864 
       26.17        79.69        33.53        29.95         6.97        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AZ-5407 
       33.01         2.01        34.98        38.07        83.24        88.21 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-F4-6570 TCGA-F4-6854 TCGA-F4-6856 
       49.41        12.76        10.06         6.18         0.53        35.31 
TCGA-G4-6309 TCGA-G4-6626 
       85.48        46.75 

$`ATAD5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
       58.39         1.41         5.13        22.36        62.79         6.77 
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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       13.25        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        61.91        36.00        13.78 

  ATAD5 MUTATED ATAD5 WILD-TYPE 
           0.53            0.00 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
          88.21          148.01 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
         34.255          21.990 
[1] "0.5 - 88.2 (34.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D649V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD5 MUTATED         3        0        3        11         2         0
  ATAD5 WILD-TYPE      61        1       23        97         6         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  ATAD5 MUTATED           0
  ATAD5 WILD-TYPE         1
D649V3, multiclass
            clus
vv           ATAD5 MUTATED ATAD5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             11              97
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ATAD5 MUTATED     1   2  16   2
  ATAD5 WILD-TYPE   8  65 233  39
D649V4, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            16             233
  T4             2              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
  ATAD5 MUTATED    19   2   0
  ATAD5 WILD-TYPE 201  79  66
D649V5, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  N0            19             201
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V6, binary
                 cls
clus                0   1
  ATAD5 MUTATED    20   0
  ATAD5 WILD-TYPE 265  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     20    0
  ATAD5 WILD-TYPE  265   48
   clus
vv  ATAD5 MUTATED ATAD5 WILD-TYPE
  0            20             265
  1             0              48
[1] 2 2
[1] FALSE
D649V7, binary
                 cls
clus                0   1
  ATAD5 MUTATED    13   8
  ATAD5 WILD-TYPE 157 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     13    8
  ATAD5 WILD-TYPE  157  189
        clus
vv       ATAD5 MUTATED ATAD5 WILD-TYPE
  FEMALE            13             157
  MALE               8             189
[1] 2 2
[1] FALSE
D649V8, binary
                 cls
clus                0   1
  ATAD5 MUTATED    19   0
  ATAD5 WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     19    0
  ATAD5 WILD-TYPE  281    8
     clus
vv    ATAD5 MUTATED ATAD5 WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D649V9, binary
                 cls
clus                0   1
  ATAD5 MUTATED    16   5
  ATAD5 WILD-TYPE 298  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     16    5
  ATAD5 WILD-TYPE  298   43
                               clus
vv                              ATAD5 MUTATED ATAD5 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATAD5 MUTATED    16   0   0   2
  ATAD5 WILD-TYPE 243   3  22  19
D649V10, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             2              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"
D649V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD5 MUTATED                                  0     3
  ATAD5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD5 MUTATED                           2     8
  ATAD5 WILD-TYPE                        17   168
D649V12, multiclass
                                  clus
vv                                 ATAD5 MUTATED ATAD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = PHF21A MUTATION ANALYSIS
D650V1, survival
                  sevent
clus2                0   1
  PHF21A MUTATED     8   3
  PHF21A WILD-TYPE 269  75
  PHF21A MUTATED PHF21A WILD-TYPE 
              11              344 
  PHF21A MUTATED PHF21A WILD-TYPE 
               3               75 
$`PHF21A MUTATED`
TCGA-AA-3525 TCGA-AA-3672 TCGA-AD-6964 TCGA-AZ-4681 TCGA-G4-6588 TCGA-AA-3492 
        8.05         0.92        10.88       106.75        26.17         3.02 
TCGA-AA-3947 TCGA-AA-3949 TCGA-CK-5916 TCGA-D5-6930 TCGA-G4-6304 
       33.01        26.01        21.14        13.35        53.62 

$`PHF21A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  PHF21A MUTATED PHF21A WILD-TYPE 
            0.92             0.00 
  PHF21A MUTATED PHF21A WILD-TYPE 
          106.75           148.01 
  PHF21A MUTATED PHF21A WILD-TYPE 
          21.140           22.075 
[1] "0.9 - 106.8 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D650V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF21A MUTATED         1        0        1         3         2         0
  PHF21A WILD-TYPE      63        1       25       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHF21A MUTATED           1          0          2          0        0
  PHF21A WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  PHF21A MUTATED           0         0
  PHF21A WILD-TYPE        12         1
D650V3, multiclass
            clus
vv           PHF21A MUTATED PHF21A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  PHF21A MUTATED     1   0   7   3
  PHF21A WILD-TYPE   8  67 242  38
D650V4, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  T1              1                8
  T2              0               67
  T3              7              242
  T4              3               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
  PHF21A MUTATED     7   3   1
  PHF21A WILD-TYPE 213  78  65
D650V5, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  N0              7              213
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V6, binary
                  cls
clus                 0   1
  PHF21A MUTATED    10   0
  PHF21A WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED     10    0
  PHF21A WILD-TYPE  275   48
   clus
vv  PHF21A MUTATED PHF21A WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D650V7, binary
                  cls
clus                 0   1
  PHF21A MUTATED     8   3
  PHF21A WILD-TYPE 162 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      8    3
  PHF21A WILD-TYPE  162  194
        clus
vv       PHF21A MUTATED PHF21A WILD-TYPE
  FEMALE              8              162
  MALE                3              194
[1] 2 2
[1] FALSE
D650V8, binary
                  cls
clus                 0   1
  PHF21A MUTATED    11   0
  PHF21A WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED     11    0
  PHF21A WILD-TYPE  289    8
     clus
vv    PHF21A MUTATED PHF21A WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D650V9, binary
                  cls
clus                 0   1
  PHF21A MUTATED     8   3
  PHF21A WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      8    3
  PHF21A WILD-TYPE  306   45
                               clus
vv                              PHF21A MUTATED PHF21A WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PHF21A MUTATED     9   0   0   1
  PHF21A WILD-TYPE 250   3  22  20
D650V10, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D650V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF21A MUTATED                                  0     0
  PHF21A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PHF21A MUTATED                           0     6
  PHF21A WILD-TYPE                        19   170
D650V12, multiclass
                                  clus
vv                                 PHF21A MUTATED PHF21A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = BMPR1A MUTATION ANALYSIS
D651V1, survival
                  sevent
clus2                0   1
  BMPR1A MUTATED    16   2
  BMPR1A WILD-TYPE 261  76
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              337 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
               2               76 
$`BMPR1A MUTATED`
TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3664 
       24.00        10.88       100.01        63.98         6.97        54.02 
TCGA-AA-3833 TCGA-AA-3966 TCGA-AA-A00J TCGA-AY-6386 TCGA-CM-4743 TCGA-CM-5344 
       15.95         2.01        18.05        17.82        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        78.08         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  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            22.09 
[1] "1.6 - 140.4 (20.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D651V2, continuous
                  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      64        1       22       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BMPR1A MUTATED           0          0          4          2        0
  BMPR1A WILD-TYPE        18          6         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  BMPR1A MUTATED           0         0
  BMPR1A WILD-TYPE        12         1
D651V3, multiclass
            clus
vv           BMPR1A MUTATED BMPR1A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  BMPR1A MUTATED     0   0  16   2
  BMPR1A WILD-TYPE   9  67 233  39
D651V4, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  T1              0                9
  T2              0               67
  T3             16              233
  T4              2               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
  BMPR1A MUTATED    11   4   3
  BMPR1A WILD-TYPE 209  77  63
D651V5, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  N0             11              209
  N1              4               77
  N2              3               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"
D651V6, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    15   0
  BMPR1A WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     15    0
  BMPR1A WILD-TYPE  270   48
   clus
vv  BMPR1A MUTATED BMPR1A WILD-TYPE
  0             15              270
  1              0               48
[1] 2 2
[1] FALSE
D651V7, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    10   8
  BMPR1A WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     10    8
  BMPR1A WILD-TYPE  160  189
        clus
vv       BMPR1A MUTATED BMPR1A WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D651V8, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    14   0
  BMPR1A WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     14    0
  BMPR1A WILD-TYPE  286    8
     clus
vv    BMPR1A MUTATED BMPR1A WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D651V9, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    12   6
  BMPR1A WILD-TYPE 302  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     12    6
  BMPR1A WILD-TYPE  302   42
                               clus
vv                              BMPR1A MUTATED BMPR1A WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BMPR1A MUTATED    13   0   0   0
  BMPR1A WILD-TYPE 246   3  22  21
D651V10, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              0               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"
D651V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMPR1A MUTATED                                  1     0
  BMPR1A WILD-TYPE                                0    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BMPR1A MUTATED                           1     9
  BMPR1A WILD-TYPE                        18   167
D651V12, multiclass
                                  clus
vv                                 BMPR1A MUTATED BMPR1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(652) Variable = C14ORF39 MUTATION ANALYSIS
D652V1, survival
                    sevent
clus2                  0   1
  C14ORF39 MUTATED     9   3
  C14ORF39 WILD-TYPE 268  75
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                12                343 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                 3                 75 
$`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        54.61        13.35       119.93 

$`C14ORF39 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        10.06        12.03        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
             10.06               0.00 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
            119.93             148.01 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
            33.995             21.990 
[1] "10.1 - 119.9 (34.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.3"
D652V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF39 MUTATED         1        0        1         6         2         0
  C14ORF39 WILD-TYPE      63        1       25       102         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF39 MUTATED           0          0          1          0        0
  C14ORF39 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF39 MUTATED           1         0
  C14ORF39 WILD-TYPE        11         1
D652V3, multiclass
            clus
vv           C14ORF39 MUTATED C14ORF39 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 6                102
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  C14ORF39 MUTATED     0   2   9   2
  C14ORF39 WILD-TYPE   9  65 240  39
D652V4, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                9                240
  T4                2                 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
  C14ORF39 MUTATED    10   2   1
  C14ORF39 WILD-TYPE 210  79  65
D652V5, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  N0               10                210
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V6, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED     9   1
  C14ORF39 WILD-TYPE 276  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED      9    1
  C14ORF39 WILD-TYPE  276   47
   clus
vv  C14ORF39 MUTATED C14ORF39 WILD-TYPE
  0                9                276
  1                1                 47
[1] 2 2
[1] FALSE
D652V7, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED     6   7
  C14ORF39 WILD-TYPE 164 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED      6    7
  C14ORF39 WILD-TYPE  164  190
        clus
vv       C14ORF39 MUTATED C14ORF39 WILD-TYPE
  FEMALE                6                164
  MALE                  7                190
[1] 2 2
[1] FALSE
D652V8, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED    10   0
  C14ORF39 WILD-TYPE 290   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED     10    0
  C14ORF39 WILD-TYPE  290    8
     clus
vv    C14ORF39 MUTATED C14ORF39 WILD-TYPE
  NO                10                290
  YES                0                  8
[1] 2 2
[1] FALSE
D652V9, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED    11   2
  C14ORF39 WILD-TYPE 303  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED     11    2
  C14ORF39 WILD-TYPE  303   46
                               clus
vv                              C14ORF39 MUTATED C14ORF39 WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C14ORF39 MUTATED     7   0   0   4
  C14ORF39 WILD-TYPE 252   3  22  17
D652V10, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                4                 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"
D652V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF39 MUTATED                                  0     2
  C14ORF39 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF39 MUTATED                           1     7
  C14ORF39 WILD-TYPE                        18   169
D652V12, multiclass
                                  clus
vv                                 C14ORF39 MUTATED C14ORF39 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           7                169
[1] 4 2
[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 = TAT MUTATION ANALYSIS
D653V1, survival
               sevent
clus2             0   1
  TAT MUTATED    10   3
  TAT WILD-TYPE 267  75
  TAT MUTATED TAT WILD-TYPE 
           13           342 
  TAT MUTATED TAT WILD-TYPE 
            3            75 
$`TAT MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3977 TCGA-AA-A00R 
       19.04        24.00       100.01        26.17        25.02         0.99 
TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-5348 TCGA-CM-6161 TCGA-D5-7000 
       49.41        10.06        85.45        22.98        15.02        10.26 
TCGA-G4-6304 
       53.62 

$`TAT WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TAT MUTATED TAT WILD-TYPE 
         0.99          0.00 
  TAT MUTATED TAT WILD-TYPE 
       100.01        148.01 
  TAT MUTATED TAT WILD-TYPE 
        24.00         22.01 
[1] "1.0 - 100.0 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D653V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAT MUTATED         3        0        2         4         1         0
  TAT WILD-TYPE      61        1       24       104         7         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        18          6         42         33       34        12
               vv
clus            STAGE IVB
  TAT MUTATED           0
  TAT WILD-TYPE         1
D653V3, multiclass
            clus
vv           TAT MUTATED TAT WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  TAT MUTATED     0   4   9   1
  TAT WILD-TYPE   9  63 240  40
D653V4, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  T1           0             9
  T2           4            63
  T3           9           240
  T4           1            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
  TAT MUTATED    12   2   0
  TAT WILD-TYPE 208  79  66
D653V5, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  N0          12           208
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V6, binary
               cls
clus              0   1
  TAT MUTATED    11   1
  TAT WILD-TYPE 274  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     11    1
  TAT WILD-TYPE  274   47
   clus
vv  TAT MUTATED TAT WILD-TYPE
  0          11           274
  1           1            47
[1] 2 2
[1] FALSE
D653V7, binary
               cls
clus              0   1
  TAT MUTATED     9   5
  TAT WILD-TYPE 161 192
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED      9    5
  TAT WILD-TYPE  161  192
        clus
vv       TAT MUTATED TAT WILD-TYPE
  FEMALE           9           161
  MALE             5           192
[1] 2 2
[1] FALSE
D653V8, binary
               cls
clus              0   1
  TAT MUTATED    11   1
  TAT WILD-TYPE 289   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     11    1
  TAT WILD-TYPE  289    7
     clus
vv    TAT MUTATED TAT WILD-TYPE
  NO           11           289
  YES           1             7
[1] 2 2
[1] FALSE
D653V9, binary
               cls
clus              0   1
  TAT MUTATED    11   3
  TAT WILD-TYPE 303  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     11    3
  TAT WILD-TYPE  303   45
                               clus
vv                              TAT MUTATED TAT WILD-TYPE
  COLON ADENOCARCINOMA                   11           303
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TAT MUTATED     8   1   1   1
  TAT WILD-TYPE 251   2  21  20
D653V10, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  R0           8           251
  R1           1             2
  R2           1            21
  RX           1            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"
D653V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAT MUTATED                                  0     1
  TAT WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TAT MUTATED                           1     7
  TAT WILD-TYPE                        18   169
D653V12, multiclass
                                  clus
vv                                 TAT MUTATED TAT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      7           169
[1] 4 2
[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 = FAS MUTATION ANALYSIS
D654V1, survival
               sevent
clus2             0   1
  FAS MUTATED     5   2
  FAS WILD-TYPE 272  76
  FAS MUTATED FAS WILD-TYPE 
            7           348 
  FAS MUTATED FAS WILD-TYPE 
            2            76 
$`FAS MUTATED`
TCGA-A6-6780 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-5862 
       20.12        83.24        58.39        12.76        17.56         5.03 
TCGA-D5-6927 
        9.44 

$`FAS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.59        12.20        10.06        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  FAS MUTATED FAS WILD-TYPE 
         5.03          0.00 
  FAS MUTATED FAS WILD-TYPE 
        83.24        148.01 
  FAS MUTATED FAS WILD-TYPE 
        17.56         22.09 
[1] "5.0 - 83.2 (17.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D654V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAS MUTATED         0        0        0         5         0         0
  FAS WILD-TYPE      64        1       26       103         8         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        18          6         43         33       35        11
               vv
clus            STAGE IVB
  FAS MUTATED           0
  FAS WILD-TYPE         1
D654V3, multiclass
            clus
vv           FAS MUTATED FAS WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            5           103
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            1            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
  FAS MUTATED     0   0   6   1
  FAS WILD-TYPE   9  67 243  40
D654V4, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  T1           0             9
  T2           0            67
  T3           6           243
  T4           1            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
  FAS MUTATED     5   2   0
  FAS WILD-TYPE 215  79  66
D654V5, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  N0           5           215
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V6, binary
               cls
clus              0   1
  FAS MUTATED     5   1
  FAS WILD-TYPE 280  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      5    1
  FAS WILD-TYPE  280   47
   clus
vv  FAS MUTATED FAS WILD-TYPE
  0           5           280
  1           1            47
[1] 2 2
[1] FALSE
D654V7, binary
               cls
clus              0   1
  FAS MUTATED     1   6
  FAS WILD-TYPE 169 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      1    6
  FAS WILD-TYPE  169  191
        clus
vv       FAS MUTATED FAS WILD-TYPE
  FEMALE           1           169
  MALE             6           191
[1] 2 2
[1] FALSE
D654V8, binary
               cls
clus              0   1
  FAS MUTATED     7   0
  FAS WILD-TYPE 293   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      7    0
  FAS WILD-TYPE  293    8
     clus
vv    FAS MUTATED FAS WILD-TYPE
  NO            7           293
  YES           0             8
[1] 2 2
[1] FALSE
D654V9, binary
               cls
clus              0   1
  FAS MUTATED     5   2
  FAS WILD-TYPE 309  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      5    2
  FAS WILD-TYPE  309   46
                               clus
vv                              FAS MUTATED FAS WILD-TYPE
  COLON ADENOCARCINOMA                    5           309
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FAS MUTATED     4   0   0   2
  FAS WILD-TYPE 255   3  22  19
D654V10, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  R0           4           255
  R1           0             3
  R2           0            22
  RX           2            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"
D654V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAS MUTATED                                  0     2
  FAS WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FAS MUTATED                           0     5
  FAS WILD-TYPE                        19   171
D654V12, multiclass
                                  clus
vv                                 FAS MUTATED FAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      5           171
[1] 4 2
[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 = TXNDC17 MUTATION ANALYSIS
D655V1, survival
                   sevent
clus2                 0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 272  78
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               350 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                0                78 
$`TXNDC17 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-CM-5861 TCGA-D5-6533 TCGA-D5-6923 
       22.06         6.97        15.02        25.48        12.43 

$`TXNDC17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
             6.97              0.00 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
            25.48            148.01 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
            15.02             22.09 
[1] "7.0 - 25.5 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D655V2, continuous
                   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      63        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC17 MUTATED           0          0          0          0        0
  TXNDC17 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  TXNDC17 MUTATED           0         0
  TXNDC17 WILD-TYPE        12         1
D655V3, multiclass
            clus
vv           TXNDC17 MUTATED TXNDC17 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  TXNDC17 MUTATED     0   1   3   1
  TXNDC17 WILD-TYPE   9  66 246  40
D655V4, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               1                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
  TXNDC17 MUTATED     5   0   0
  TXNDC17 WILD-TYPE 215  81  66
D655V5, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  N0               5               215
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V6, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  280   48
   clus
vv  TXNDC17 MUTATED TXNDC17 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D655V7, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     3   2
  TXNDC17 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      3    2
  TXNDC17 WILD-TYPE  167  195
        clus
vv       TXNDC17 MUTATED TXNDC17 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D655V8, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  295    8
     clus
vv    TXNDC17 MUTATED TXNDC17 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D655V9, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  309   48
                               clus
vv                              TXNDC17 MUTATED TXNDC17 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TXNDC17 MUTATED     5   0   0   0
  TXNDC17 WILD-TYPE 254   3  22  21
D655V10, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D655V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC17 MUTATED                                  0     0
  TXNDC17 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TXNDC17 MUTATED                           0     4
  TXNDC17 WILD-TYPE                        19   172
D655V12, multiclass
                                  clus
vv                                 TXNDC17 MUTATED TXNDC17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = SMTN MUTATION ANALYSIS
D656V1, survival
                sevent
clus2              0   1
  SMTN MUTATED    10   3
  SMTN WILD-TYPE 267  75
  SMTN MUTATED SMTN WILD-TYPE 
            13            342 
  SMTN MUTATED SMTN WILD-TYPE 
             3             75 
$`SMTN MUTATED`
TCGA-AD-6964 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3845 
       10.88        26.17        79.69        22.06         3.02         0.00 
TCGA-AA-A00A TCGA-AU-6004 TCGA-CM-6674 TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6930 
       38.04        27.09        12.95        12.39        11.64        13.35 
TCGA-G4-6304 
       53.62 

$`SMTN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SMTN MUTATED SMTN WILD-TYPE 
             0              0 
  SMTN MUTATED SMTN WILD-TYPE 
         79.69         148.01 
  SMTN MUTATED SMTN WILD-TYPE 
         13.35          22.09 
[1] "0.0 - 79.7 (13.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D656V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMTN MUTATED         2        0        2         8         1         0
  SMTN WILD-TYPE      62        1       24       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMTN MUTATED           0          0          0          0        0         0
  SMTN WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  SMTN MUTATED           0
  SMTN WILD-TYPE         1
D656V3, multiclass
            clus
vv           SMTN MUTATED SMTN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  SMTN MUTATED     0   2   9   3
  SMTN WILD-TYPE   9  65 240  38
D656V4, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  T1            0              9
  T2            2             65
  T3            9            240
  T4            3             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
  SMTN MUTATED    13   0   1
  SMTN WILD-TYPE 207  81  65
D656V5, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  N0           13            207
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V6, binary
                cls
clus               0   1
  SMTN MUTATED    13   0
  SMTN WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     13    0
  SMTN WILD-TYPE  272   48
   clus
vv  SMTN MUTATED SMTN WILD-TYPE
  0           13            272
  1            0             48
[1] 2 2
[1] FALSE
D656V7, binary
                cls
clus               0   1
  SMTN MUTATED     8   6
  SMTN WILD-TYPE 162 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED      8    6
  SMTN WILD-TYPE  162  191
        clus
vv       SMTN MUTATED SMTN WILD-TYPE
  FEMALE            8            162
  MALE              6            191
[1] 2 2
[1] FALSE
D656V8, binary
                cls
clus               0   1
  SMTN MUTATED    11   0
  SMTN WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     11    0
  SMTN WILD-TYPE  289    8
     clus
vv    SMTN MUTATED SMTN WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D656V9, binary
                cls
clus               0   1
  SMTN MUTATED    12   2
  SMTN WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     12    2
  SMTN WILD-TYPE  302   46
                               clus
vv                              SMTN MUTATED SMTN WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMTN MUTATED    13   0   0   0
  SMTN WILD-TYPE 246   3  22  21
D656V10, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            0             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"
D656V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMTN MUTATED                                  0     0
  SMTN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMTN MUTATED                           0    10
  SMTN WILD-TYPE                        19   166
D656V12, multiclass
                                  clus
vv                                 SMTN MUTATED SMTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(657) Variable = STRADB MUTATION ANALYSIS
D657V1, survival
                  sevent
clus2                0   1
  STRADB MUTATED     3   2
  STRADB WILD-TYPE 274  76
  STRADB MUTATED STRADB WILD-TYPE 
               5              350 
  STRADB MUTATED STRADB WILD-TYPE 
               2               76 
$`STRADB MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-AA-3492 TCGA-AY-6196 TCGA-DM-A28H 
       19.04        10.88         3.02         0.20       117.07 

$`STRADB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  STRADB MUTATED STRADB WILD-TYPE 
             0.2              0.0 
  STRADB MUTATED STRADB WILD-TYPE 
          117.07           148.01 
  STRADB MUTATED STRADB WILD-TYPE 
           10.88            22.09 
[1] "0.2 - 117.1 (10.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D657V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STRADB MUTATED         0        0        1         0         0         0
  STRADB WILD-TYPE      64        1       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STRADB MUTATED           0          0          0          2        1
  STRADB WILD-TYPE        18          6         44         31       34
                  vv
clus               STAGE IVA STAGE IVB
  STRADB MUTATED           0         0
  STRADB WILD-TYPE        12         1
D657V3, multiclass
            clus
vv           STRADB MUTATED STRADB WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  STRADB MUTATED     0   0   4   1
  STRADB WILD-TYPE   9  67 245  40
D657V4, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              1               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
  STRADB MUTATED     2   0   3
  STRADB WILD-TYPE 218  81  63
D657V5, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  N0              2              218
  N1              0               81
  N2              3               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"
D657V6, binary
                  cls
clus                 0   1
  STRADB MUTATED     2   1
  STRADB WILD-TYPE 283  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      2    1
  STRADB WILD-TYPE  283   47
   clus
vv  STRADB MUTATED STRADB WILD-TYPE
  0              2              283
  1              1               47
[1] 2 2
[1] FALSE
D657V7, binary
                  cls
clus                 0   1
  STRADB MUTATED     1   4
  STRADB WILD-TYPE 169 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      1    4
  STRADB WILD-TYPE  169  193
        clus
vv       STRADB MUTATED STRADB WILD-TYPE
  FEMALE              1              169
  MALE                4              193
[1] 2 2
[1] FALSE
D657V8, binary
                  cls
clus                 0   1
  STRADB MUTATED     2   1
  STRADB WILD-TYPE 298   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      2    1
  STRADB WILD-TYPE  298    7
     clus
vv    STRADB MUTATED STRADB WILD-TYPE
  NO               2              298
  YES              1                7
[1] 2 2
[1] FALSE
D657V9, binary
                  cls
clus                 0   1
  STRADB MUTATED     4   1
  STRADB WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      4    1
  STRADB WILD-TYPE  310   47
                               clus
vv                              STRADB MUTATED STRADB WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  STRADB MUTATED     2   0   1   0
  STRADB WILD-TYPE 257   3  21  21
D657V10, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  R0              2              257
  R1              0                3
  R2              1               21
  RX              0               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"
D657V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STRADB MUTATED                                  0     0
  STRADB WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STRADB MUTATED                           0     3
  STRADB WILD-TYPE                        19   173
D657V12, multiclass
                                  clus
vv                                 STRADB MUTATED STRADB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ACVR2A MUTATION ANALYSIS
D658V1, survival
                  sevent
clus2                0   1
  ACVR2A MUTATED    11   5
  ACVR2A WILD-TYPE 266  73
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              16              339 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               5               73 
$`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 
        1.02        39.98        22.42        88.21        49.41        12.76 
TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-6677 TCGA-DM-A1DA 
       10.06       124.27        11.08         7.50 

$`ACVR2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-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-A029 TCGA-AA-A02H TCGA-AA-A02J 
       33.04        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-CM-4743 
       51.32        21.99        21.14        82.95         2.01        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ACVR2A MUTATED ACVR2A WILD-TYPE 
            1.02             0.00 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
          124.27           148.01 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
          24.705           21.990 
[1] "1.0 - 124.3 (24.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D658V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACVR2A MUTATED         3        0        3         6         1         0
  ACVR2A WILD-TYPE      61        1       23       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR2A MUTATED           0          0          1          1        1
  ACVR2A WILD-TYPE        18          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ACVR2A MUTATED           0         0
  ACVR2A WILD-TYPE        12         1
D658V3, multiclass
            clus
vv           ACVR2A MUTATED ACVR2A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  ACVR2A MUTATED     1   2  13   1
  ACVR2A WILD-TYPE   8  65 236  40
D658V4, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  T1              1                8
  T2              2               65
  T3             13              236
  T4              1               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
  ACVR2A MUTATED    14   2   1
  ACVR2A WILD-TYPE 206  79  65
D658V5, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  N0             14              206
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V6, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    13   1
  ACVR2A WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     13    1
  ACVR2A WILD-TYPE  272   47
   clus
vv  ACVR2A MUTATED ACVR2A WILD-TYPE
  0             13              272
  1              1               47
[1] 2 2
[1] FALSE
D658V7, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    12   5
  ACVR2A WILD-TYPE 158 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     12    5
  ACVR2A WILD-TYPE  158  192
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  FEMALE             12              158
  MALE                5              192
[1] 2 2
[1] FALSE
D658V8, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    14   0
  ACVR2A WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     14    0
  ACVR2A WILD-TYPE  286    8
     clus
vv    ACVR2A MUTATED ACVR2A WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D658V9, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    15   2
  ACVR2A WILD-TYPE 299  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     15    2
  ACVR2A WILD-TYPE  299   46
                               clus
vv                              ACVR2A MUTATED ACVR2A WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACVR2A MUTATED     9   0   1   3
  ACVR2A WILD-TYPE 250   3  21  18
D658V10, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              3               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"
D658V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACVR2A MUTATED                                  0     2
  ACVR2A WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACVR2A MUTATED                           0     8
  ACVR2A WILD-TYPE                        19   168
D658V12, multiclass
                                  clus
vv                                 ACVR2A MUTATED ACVR2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = WT1 MUTATION ANALYSIS
D659V1, survival
               sevent
clus2             0   1
  WT1 MUTATED    20   6
  WT1 WILD-TYPE 257  72
  WT1 MUTATED WT1 WILD-TYPE 
           26           329 
  WT1 MUTATED WT1 WILD-TYPE 
            6            72 
$`WT1 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-2672 TCGA-A6-5657 
        6.05        19.04        25.08       100.01        46.65        31.63 
TCGA-A6-5662 TCGA-AA-3544 TCGA-AA-3930 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6600 
       23.61        14.01         2.01        21.44         1.41        12.10 
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        21.99        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        54.61        18.25        12.43 
TCGA-F4-6806 TCGA-G4-6306 
       41.42        44.68 

$`WT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        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-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        12.99        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         5.13        22.36        62.79        88.21 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       10.06        14.30        85.45        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  WT1 MUTATED WT1 WILD-TYPE 
         1.41          0.00 
  WT1 MUTATED WT1 WILD-TYPE 
       148.01        140.38 
  WT1 MUTATED WT1 WILD-TYPE 
       18.645        22.360 
[1] "1.4 - 148.0 (18.6)" "0.0 - 140.4 (22.4)"
[1] "hr=" "1"  
D659V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WT1 MUTATED         5        0        2         4         0         0
  WT1 WILD-TYPE      59        1       24       104         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WT1 MUTATED           1          0          6          1        4         1
  WT1 WILD-TYPE        17          6         38         32       31        11
               vv
clus            STAGE IVB
  WT1 MUTATED           1
  WT1 WILD-TYPE         0
D659V3, multiclass
            clus
vv           WT1 MUTATED WT1 WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            4           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           6            38
  STAGE IIIC           1            32
  STAGE IV             4            31
  STAGE IVA            1            11
  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   6  15   5
  WT1 WILD-TYPE   9  61 234  36
D659V4, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  T1           0             9
  T2           6            61
  T3          15           234
  T4           5            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
  WT1 MUTATED    12   8   6
  WT1 WILD-TYPE 208  73  60
D659V5, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  N0          12           208
  N1           8            73
  N2           6            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V6, binary
               cls
clus              0   1
  WT1 MUTATED    18   6
  WT1 WILD-TYPE 267  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     18    6
  WT1 WILD-TYPE  267   42
   clus
vv  WT1 MUTATED WT1 WILD-TYPE
  0          18           267
  1           6            42
[1] 2 2
[1] FALSE
D659V7, binary
               cls
clus              0   1
  WT1 MUTATED     8  18
  WT1 WILD-TYPE 162 179
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      8   18
  WT1 WILD-TYPE  162  179
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  FEMALE           8           162
  MALE            18           179
[1] 2 2
[1] FALSE
D659V8, binary
               cls
clus              0   1
  WT1 MUTATED    24   0
  WT1 WILD-TYPE 276   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     24    0
  WT1 WILD-TYPE  276    8
     clus
vv    WT1 MUTATED WT1 WILD-TYPE
  NO           24           276
  YES           0             8
[1] 2 2
[1] FALSE
D659V9, binary
               cls
clus              0   1
  WT1 MUTATED    24   2
  WT1 WILD-TYPE 290  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     24    2
  WT1 WILD-TYPE  290   46
                               clus
vv                              WT1 MUTATED WT1 WILD-TYPE
  COLON ADENOCARCINOMA                   24           290
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  WT1 MUTATED    16   0   2   4
  WT1 WILD-TYPE 243   3  20  17
D659V10, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  R0          16           243
  R1           0             3
  R2           2            20
  RX           4            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"
D659V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WT1 MUTATED                                  0     1
  WT1 WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  WT1 MUTATED                           3    18
  WT1 WILD-TYPE                        16   158
D659V12, multiclass
                                  clus
vv                                 WT1 MUTATED WT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  3            16
  WHITE                                     18           158
[1] 4 2
[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 = EFHC1 MUTATION ANALYSIS
D660V1, survival
                 sevent
clus2               0   1
  EFHC1 MUTATED     8   1
  EFHC1 WILD-TYPE 269  77
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              9             346 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              1              77 
$`EFHC1 MUTATED`
TCGA-G4-6628 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 
       79.69        20.98        34.03        25.02        34.98        27.09 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-6163 
       10.06        14.30        14.04 

$`EFHC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       31.00         2.01        24.00        33.01        26.01         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       12.76        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 
       21.99        21.14        82.95         2.01       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-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  EFHC1 MUTATED EFHC1 WILD-TYPE 
          10.06            0.00 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
          79.69          148.01 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
         25.020          22.045 
[1] "10.1 - 79.7 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D660V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFHC1 MUTATED         3        0        0         3         2         0
  EFHC1 WILD-TYPE      61        1       26       105         6         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  EFHC1 MUTATED           0
  EFHC1 WILD-TYPE         1
D660V3, multiclass
            clus
vv           EFHC1 MUTATED EFHC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  EFHC1 MUTATED     1   4   4   2
  EFHC1 WILD-TYPE   8  63 245  39
D660V4, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  T1             1               8
  T2             4              63
  T3             4             245
  T4             2              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
  EFHC1 MUTATED     9   0   2
  EFHC1 WILD-TYPE 211  81  64
D660V5, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V6, binary
                 cls
clus                0   1
  EFHC1 MUTATED     9   0
  EFHC1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      9    0
  EFHC1 WILD-TYPE  276   48
   clus
vv  EFHC1 MUTATED EFHC1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D660V7, binary
                 cls
clus                0   1
  EFHC1 MUTATED     3   8
  EFHC1 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      3    8
  EFHC1 WILD-TYPE  167  189
        clus
vv       EFHC1 MUTATED EFHC1 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D660V8, binary
                 cls
clus                0   1
  EFHC1 MUTATED     8   0
  EFHC1 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      8    0
  EFHC1 WILD-TYPE  292    8
     clus
vv    EFHC1 MUTATED EFHC1 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D660V9, binary
                 cls
clus                0   1
  EFHC1 MUTATED    11   0
  EFHC1 WILD-TYPE 303  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     11    0
  EFHC1 WILD-TYPE  303   48
                               clus
vv                              EFHC1 MUTATED EFHC1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EFHC1 MUTATED     7   0   0   3
  EFHC1 WILD-TYPE 252   3  22  18
D660V10, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             3              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"
D660V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFHC1 MUTATED                                  0     2
  EFHC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFHC1 MUTATED                           0     4
  EFHC1 WILD-TYPE                        19   172
D660V12, multiclass
                                  clus
vv                                 EFHC1 MUTATED EFHC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = MTMR8 MUTATION ANALYSIS
D661V1, survival
                 sevent
clus2               0   1
  MTMR8 MUTATED     8   3
  MTMR8 WILD-TYPE 269  75
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             11             344 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
              3              75 
$`MTMR8 MUTATED`
TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-A01D TCGA-AU-3779 
       35.80        22.06        26.99        33.01        10.98        14.50 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CM-5344 TCGA-CM-6163 TCGA-D5-6541 
       62.79        29.56        22.03        14.04        15.58 

$`MTMR8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MTMR8 MUTATED MTMR8 WILD-TYPE 
          10.98            0.00 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
          62.79          148.01 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
          22.06           22.04 
[1] "11.0 - 62.8 (22.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D661V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTMR8 MUTATED         1        0        1         5         1         0
  MTMR8 WILD-TYPE      63        1       25       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTMR8 MUTATED           0          0          1          1        0         0
  MTMR8 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  MTMR8 MUTATED           0
  MTMR8 WILD-TYPE         1
D661V3, multiclass
            clus
vv           MTMR8 MUTATED MTMR8 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  MTMR8 MUTATED     1   1   8   1
  MTMR8 WILD-TYPE   8  66 241  40
D661V4, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             8             241
  T4             1              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
  MTMR8 MUTATED     8   2   1
  MTMR8 WILD-TYPE 212  79  65
D661V5, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V6, binary
                 cls
clus                0   1
  MTMR8 MUTATED     9   0
  MTMR8 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED      9    0
  MTMR8 WILD-TYPE  276   48
   clus
vv  MTMR8 MUTATED MTMR8 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D661V7, binary
                 cls
clus                0   1
  MTMR8 MUTATED     8   3
  MTMR8 WILD-TYPE 162 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED      8    3
  MTMR8 WILD-TYPE  162  194
        clus
vv       MTMR8 MUTATED MTMR8 WILD-TYPE
  FEMALE             8             162
  MALE               3             194
[1] 2 2
[1] FALSE
D661V8, binary
                 cls
clus                0   1
  MTMR8 MUTATED    11   0
  MTMR8 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED     11    0
  MTMR8 WILD-TYPE  289    8
     clus
vv    MTMR8 MUTATED MTMR8 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D661V9, binary
                 cls
clus                0   1
  MTMR8 MUTATED     9   2
  MTMR8 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED      9    2
  MTMR8 WILD-TYPE  305   46
                               clus
vv                              MTMR8 MUTATED MTMR8 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MTMR8 MUTATED     9   0   0   0
  MTMR8 WILD-TYPE 250   3  22  21
D661V10, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D661V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTMR8 MUTATED                                  0     0
  MTMR8 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MTMR8 MUTATED                           0     8
  MTMR8 WILD-TYPE                        19   168
D661V12, multiclass
                                  clus
vv                                 MTMR8 MUTATED MTMR8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = ACTL6A MUTATION ANALYSIS
D662V1, survival
                  sevent
clus2                0   1
  ACTL6A MUTATED     4   2
  ACTL6A WILD-TYPE 273  76
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               6              349 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               2               76 
$`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 

$`ACTL6A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ACTL6A MUTATED ACTL6A WILD-TYPE 
            4.01             0.00 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
           46.65           148.01 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
          27.075           22.060 
[1] "4.0 - 46.6 (27.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D662V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTL6A MUTATED         1        0        0         1         2         0
  ACTL6A WILD-TYPE      63        1       26       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6A MUTATED           0          0          1          1        0
  ACTL6A WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ACTL6A MUTATED           0         0
  ACTL6A WILD-TYPE        12         1
D662V3, multiclass
            clus
vv           ACTL6A MUTATED ACTL6A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ACTL6A MUTATED     1   0   2   3
  ACTL6A WILD-TYPE   8  67 247  38
D662V4, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  T1              1                8
  T2              0               67
  T3              2              247
  T4              3               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
  ACTL6A MUTATED     4   2   0
  ACTL6A WILD-TYPE 216  79  66
D662V5, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  N0              4              216
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V6, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     5   0
  ACTL6A WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      5    0
  ACTL6A WILD-TYPE  280   48
   clus
vv  ACTL6A MUTATED ACTL6A WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D662V7, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     4   2
  ACTL6A WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      4    2
  ACTL6A WILD-TYPE  166  195
        clus
vv       ACTL6A MUTATED ACTL6A WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D662V8, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     5   0
  ACTL6A WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      5    0
  ACTL6A WILD-TYPE  295    8
     clus
vv    ACTL6A MUTATED ACTL6A WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D662V9, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     3   3
  ACTL6A WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      3    3
  ACTL6A WILD-TYPE  311   45
                               clus
vv                              ACTL6A MUTATED ACTL6A WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACTL6A MUTATED     5   0   0   1
  ACTL6A WILD-TYPE 254   3  22  20
D662V10, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D662V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL6A MUTATED                                  0     0
  ACTL6A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTL6A MUTATED                           0     3
  ACTL6A WILD-TYPE                        19   173
D662V12, multiclass
                                  clus
vv                                 ACTL6A MUTATED ACTL6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = FAM163B MUTATION ANALYSIS
D663V1, survival
                   sevent
clus2                 0   1
  FAM163B MUTATED     2   2
  FAM163B WILD-TYPE 275  76
  FAM163B MUTATED FAM163B WILD-TYPE 
                4               351 
  FAM163B MUTATED FAM163B WILD-TYPE 
                2                76 
$`FAM163B MUTATED`
TCGA-AZ-6601 TCGA-A6-5661 TCGA-AA-3855 TCGA-DM-A28C 
      100.01        33.53        32.05        81.37 

$`FAM163B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07         0.00        36.03         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FAM163B MUTATED FAM163B WILD-TYPE 
            32.05              0.00 
  FAM163B MUTATED FAM163B WILD-TYPE 
           100.01            148.01 
  FAM163B MUTATED FAM163B WILD-TYPE 
            57.45             21.99 
[1] "32.0 - 100.0 (57.5)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.1"
D663V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM163B MUTATED         1        0        1         2         0         0
  FAM163B WILD-TYPE      63        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM163B MUTATED           0          0          0          0        0
  FAM163B WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM163B MUTATED           0         0
  FAM163B WILD-TYPE        12         1
D663V3, multiclass
            clus
vv           FAM163B MUTATED FAM163B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM163B MUTATED     0   1   3   0
  FAM163B WILD-TYPE   9  66 246  41
D663V4, multiclass
    clus
vv   FAM163B MUTATED FAM163B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               0                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
  FAM163B MUTATED     4   0   0
  FAM163B WILD-TYPE 216  81  66
D663V5, multiclass
    clus
vv   FAM163B MUTATED FAM163B WILD-TYPE
  N0               4               216
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V6, binary
                   cls
clus                  0   1
  FAM163B MUTATED     4   0
  FAM163B WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163B MUTATED      4    0
  FAM163B WILD-TYPE  281   48
   clus
vv  FAM163B MUTATED FAM163B WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D663V7, binary
                   cls
clus                  0   1
  FAM163B MUTATED     1   3
  FAM163B WILD-TYPE 169 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163B MUTATED      1    3
  FAM163B WILD-TYPE  169  194
        clus
vv       FAM163B MUTATED FAM163B WILD-TYPE
  FEMALE               1               169
  MALE                 3               194
[1] 2 2
[1] FALSE
D663V8, binary
                   cls
clus                  0   1
  FAM163B MUTATED     3   0
  FAM163B WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163B MUTATED      3    0
  FAM163B WILD-TYPE  297    8
     clus
vv    FAM163B MUTATED FAM163B WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D663V9, binary
                   cls
clus                  0   1
  FAM163B MUTATED     4   0
  FAM163B WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163B MUTATED      4    0
  FAM163B WILD-TYPE  310   48
                               clus
vv                              FAM163B MUTATED FAM163B WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM163B MUTATED     2   0   0   0
  FAM163B WILD-TYPE 257   3  22  21
D663V10, multiclass
[1] "Remove cluster labels:" "FAM163B MUTATED"       
clus
  FAM163B MUTATED FAM163B WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        TCGA-AA-3520        TCGA-AA-3521 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3527 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3662        TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AD-6895        TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5665        TCGA-A6-6781        TCGA-AA-3489 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3492        TCGA-AA-3502        TCGA-AA-3510        TCGA-AA-3511 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532        TCGA-AA-3534 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544        TCGA-AA-3548 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555        TCGA-AA-3558 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3561        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3663 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3673 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693        TCGA-AA-3695 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3811 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3812        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3861        TCGA-AA-3864 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3872        TCGA-AA-3875 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3941        TCGA-AA-3947 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3984 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A010 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A029 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6965 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5913 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6315 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
D663V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM163B MUTATED                                  0     0
  FAM163B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM163B MUTATED                           1     2
  FAM163B WILD-TYPE                        18   174
D663V12, multiclass
                                  clus
vv                                 FAM163B MUTATED FAM163B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          2               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(664) Variable = GPR22 MUTATION ANALYSIS
D664V1, survival
                 sevent
clus2               0   1
  GPR22 MUTATED     6   3
  GPR22 WILD-TYPE 271  75
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             346 
  GPR22 MUTATED GPR22 WILD-TYPE 
              3              75 
$`GPR22 MUTATED`
TCGA-AA-3713 TCGA-AA-3492 TCGA-AA-3833 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 
       19.04         3.02        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GPR22 MUTATED GPR22 WILD-TYPE 
           3.02            0.00 
  GPR22 MUTATED GPR22 WILD-TYPE 
          44.68          148.01 
  GPR22 MUTATED GPR22 WILD-TYPE 
          19.04           22.09 
[1] "3.0 - 44.7 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D664V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR22 MUTATED         3        0        1         2         1         0
  GPR22 WILD-TYPE      61        1       25       106         7         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  GPR22 MUTATED           0
  GPR22 WILD-TYPE         1
D664V3, multiclass
            clus
vv           GPR22 MUTATED GPR22 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GPR22 MUTATED     1   3   4   1
  GPR22 WILD-TYPE   8  64 245  40
D664V4, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  T1             1               8
  T2             3              64
  T3             4             245
  T4             1              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
  GPR22 MUTATED     9   0   0
  GPR22 WILD-TYPE 211  81  66
D664V5, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V6, binary
                 cls
clus                0   1
  GPR22 MUTATED     8   1
  GPR22 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      8    1
  GPR22 WILD-TYPE  277   47
   clus
vv  GPR22 MUTATED GPR22 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D664V7, binary
                 cls
clus                0   1
  GPR22 MUTATED     4   5
  GPR22 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      4    5
  GPR22 WILD-TYPE  166  192
        clus
vv       GPR22 MUTATED GPR22 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D664V8, binary
                 cls
clus                0   1
  GPR22 MUTATED     6   1
  GPR22 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      6    1
  GPR22 WILD-TYPE  294    7
     clus
vv    GPR22 MUTATED GPR22 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D664V9, binary
                 cls
clus                0   1
  GPR22 MUTATED     6   3
  GPR22 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      6    3
  GPR22 WILD-TYPE  308   45
                               clus
vv                              GPR22 MUTATED GPR22 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR22 MUTATED     6   0   1   2
  GPR22 WILD-TYPE 253   3  21  19
D664V10, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             2              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"
D664V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR22 MUTATED                                  0     1
  GPR22 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR22 MUTATED                           0     4
  GPR22 WILD-TYPE                        19   172
D664V12, multiclass
                                  clus
vv                                 GPR22 MUTATED GPR22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = MAPK9 MUTATION ANALYSIS
D665V1, survival
                 sevent
clus2               0   1
  MAPK9 MUTATED     6   3
  MAPK9 WILD-TYPE 271  75
  MAPK9 MUTATED MAPK9 WILD-TYPE 
              9             346 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
              3              75 
$`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 
       13.41         6.18        44.68 

$`MAPK9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02H TCGA-AA-A02J 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  MAPK9 MUTATED MAPK9 WILD-TYPE 
           6.18            0.00 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
          49.41          148.01 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
         17.820          22.075 
[1] "6.2 - 49.4 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D665V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAPK9 MUTATED         0        0        1         4         1         0
  MAPK9 WILD-TYPE      64        1       25       104         7         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        18          6         43         33       33        12
                 vv
clus              STAGE IVB
  MAPK9 MUTATED           0
  MAPK9 WILD-TYPE         1
D665V3, multiclass
            clus
vv           MAPK9 MUTATED MAPK9 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  MAPK9 MUTATED     0   1   8   1
  MAPK9 WILD-TYPE   9  66 241  40
D665V4, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             1              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
  MAPK9 MUTATED     7   3   0
  MAPK9 WILD-TYPE 213  78  66
D665V5, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V6, binary
                 cls
clus                0   1
  MAPK9 MUTATED     7   2
  MAPK9 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED      7    2
  MAPK9 WILD-TYPE  278   46
   clus
vv  MAPK9 MUTATED MAPK9 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D665V7, binary
                 cls
clus                0   1
  MAPK9 MUTATED     8   2
  MAPK9 WILD-TYPE 162 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED      8    2
  MAPK9 WILD-TYPE  162  195
        clus
vv       MAPK9 MUTATED MAPK9 WILD-TYPE
  FEMALE             8             162
  MALE               2             195
[1] 2 2
[1] FALSE
D665V8, binary
                 cls
clus                0   1
  MAPK9 MUTATED     9   0
  MAPK9 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED      9    0
  MAPK9 WILD-TYPE  291    8
     clus
vv    MAPK9 MUTATED MAPK9 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D665V9, binary
                 cls
clus                0   1
  MAPK9 MUTATED    10   0
  MAPK9 WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED     10    0
  MAPK9 WILD-TYPE  304   48
                               clus
vv                              MAPK9 MUTATED MAPK9 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MAPK9 MUTATED     7   0   1   1
  MAPK9 WILD-TYPE 252   3  21  20
D665V10, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             1              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"
D665V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK9 MUTATED                                  0     1
  MAPK9 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAPK9 MUTATED                           2     4
  MAPK9 WILD-TYPE                        17   172
D665V12, multiclass
                                  clus
vv                                 MAPK9 MUTATED MAPK9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = APOB MUTATION ANALYSIS
D666V1, survival
                sevent
clus2              0   1
  APOB MUTATED    42   9
  APOB WILD-TYPE 235  69
  APOB MUTATED APOB WILD-TYPE 
            51            304 
  APOB MUTATED APOB WILD-TYPE 
             9             69 
$`APOB MUTATED`
TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6964 TCGA-G4-6586 
        8.05        23.01        19.04        24.00        10.88        35.80 
TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 
       79.69        46.65        32.75        29.19        23.61        22.06 
TCGA-AA-3489 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-A00J TCGA-AA-A00N 
        7.04        21.01        29.95        26.99        18.05         4.01 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02F TCGA-AU-6004 
       17.03        34.98        38.07         1.02        39.98        27.09 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5797 
        0.20        58.39        62.79        49.41         3.19        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5913 TCGA-CK-5914 
       12.20        12.76        14.30        17.56        51.32        21.99 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-5538 
       23.05        22.98        32.02        15.02        12.99        54.61 
TCGA-D5-5541 TCGA-D5-6538 TCGA-D5-6927 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D0 
       55.92        17.13         9.44        12.00       119.70       130.65 
TCGA-F4-6460 TCGA-F4-6854 TCGA-F4-6855 
       31.96         0.53        47.41 

$`APOB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2674 
       63.62        22.09        26.17        91.79        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 
       32.91        31.63        30.44        33.53        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-A6-6653 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-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3558 
       26.01        12.99        14.01        33.99        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       34.03        18.05        27.02        42.02         0.99        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        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-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 
       11.74        12.69        12.36        12.39        12.59        10.06 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.14        82.95         2.01 
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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.03        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        14.04        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-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       45.40        19.59        56.09        20.19        18.25        25.48 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64        13.41        13.35        11.38        10.26 
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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-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-F4-6856 TCGA-G4-6293 
       41.42        43.04        33.67        13.25        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-G4-6626 
       61.91        36.00        13.78        46.75 

  APOB MUTATED APOB WILD-TYPE 
           0.2            0.0 
  APOB MUTATED APOB WILD-TYPE 
        130.65         148.01 
  APOB MUTATED APOB WILD-TYPE 
         23.01          21.99 
[1] "0.2 - 130.7 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D666V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APOB MUTATED         4        0        5        21         4         0
  APOB WILD-TYPE      60        1       21        87         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APOB MUTATED           1          0         11          3        3         1
  APOB WILD-TYPE        17          6         33         30       32        11
                vv
clus             STAGE IVB
  APOB MUTATED           0
  APOB WILD-TYPE         1
D666V3, multiclass
            clus
vv           APOB MUTATED APOB WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA            21             87
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB           11             33
  STAGE IIIC            3             30
  STAGE IV              3             32
  STAGE IVA             1             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
  APOB MUTATED     0   4  40  10
  APOB WILD-TYPE   9  63 209  31
D666V4, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  T1            0              9
  T2            4             63
  T3           40            209
  T4           10             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
  APOB MUTATED    35  12   7
  APOB WILD-TYPE 185  69  59
D666V5, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  N0           35            185
  N1           12             69
  N2            7             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V6, binary
                cls
clus               0   1
  APOB MUTATED    43   4
  APOB WILD-TYPE 242  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     43    4
  APOB WILD-TYPE  242   44
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           43            242
  1            4             44
[1] 2 2
[1] FALSE
D666V7, binary
                cls
clus               0   1
  APOB MUTATED    27  27
  APOB WILD-TYPE 143 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     27   27
  APOB WILD-TYPE  143  170
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE           27            143
  MALE             27            170
[1] 2 2
[1] FALSE
D666V8, binary
                cls
clus               0   1
  APOB MUTATED    42   2
  APOB WILD-TYPE 258   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     42    2
  APOB WILD-TYPE  258    6
     clus
vv    APOB MUTATED APOB WILD-TYPE
  NO            42            258
  YES            2              6
[1] 2 2
[1] FALSE
D666V9, binary
                cls
clus               0   1
  APOB MUTATED    46   7
  APOB WILD-TYPE 268  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     46    7
  APOB WILD-TYPE  268   41
                               clus
vv                              APOB MUTATED APOB WILD-TYPE
  COLON ADENOCARCINOMA                    46            268
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  APOB MUTATED    37   0   2   7
  APOB WILD-TYPE 222   3  20  14
D666V10, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  R0           37            222
  R1            0              3
  R2            2             20
  RX            7             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"
D666V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOB MUTATED                                  0     4
  APOB WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  APOB MUTATED                           2    31
  APOB WILD-TYPE                        17   145
D666V12, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      31            145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(667) Variable = OR4D2 MUTATION ANALYSIS
D667V1, survival
                 sevent
clus2               0   1
  OR4D2 MUTATED     3   1
  OR4D2 WILD-TYPE 274  77
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             351 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              1              77 
$`OR4D2 MUTATED`
TCGA-AA-3496 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6653 
        1.02       100.01        26.17        24.39 

$`OR4D2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.03 
[1] "1.0 - 100.0 (25.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D667V2, continuous
                 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      63        1       24       107         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  OR4D2 MUTATED           0
  OR4D2 WILD-TYPE         1
D667V3, multiclass
            clus
vv           OR4D2 MUTATED OR4D2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR4D2 MUTATED     0   1   3   0
  OR4D2 WILD-TYPE   9  66 246  41
D667V4, multiclass
    clus
vv   OR4D2 MUTATED OR4D2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             0              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
  OR4D2 MUTATED     4   0   0
  OR4D2 WILD-TYPE 216  81  66
D667V5, multiclass
    clus
vv   OR4D2 MUTATED OR4D2 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V6, binary
                 cls
clus                0   1
  OR4D2 MUTATED     4   0
  OR4D2 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      4    0
  OR4D2 WILD-TYPE  281   48
   clus
vv  OR4D2 MUTATED OR4D2 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D667V7, binary
                 cls
clus                0   1
  OR4D2 MUTATED     2   2
  OR4D2 WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      2    2
  OR4D2 WILD-TYPE  168  195
        clus
vv       OR4D2 MUTATED OR4D2 WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D667V8, binary
                 cls
clus                0   1
  OR4D2 MUTATED     3   0
  OR4D2 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      3    0
  OR4D2 WILD-TYPE  297    8
     clus
vv    OR4D2 MUTATED OR4D2 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D667V9, binary
                 cls
clus                0   1
  OR4D2 MUTATED     4   0
  OR4D2 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      4    0
  OR4D2 WILD-TYPE  310   48
                               clus
vv                              OR4D2 MUTATED OR4D2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4D2 MUTATED     2   0   0   0
  OR4D2 WILD-TYPE 257   3  22  21
D667V10, multiclass
[1] "Remove cluster labels:" "OR4D2 MUTATED"         
clus
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              2             303 
     TCGA-A6-2677      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-3527      TCGA-AA-3530 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552      TCGA-AA-3554 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3662 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3697 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814      TCGA-AA-3844 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870      TCGA-AA-3939 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972      TCGA-AA-3976 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L      TCGA-AA-A00Z 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6895 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-CK-5912      TCGA-G4-6310      TCGA-G4-6321 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-3810      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5661 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-5665      TCGA-A6-6781      TCGA-AA-3489      TCGA-AA-3492 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3526 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3542      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3561 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3663      TCGA-AA-3664 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3673      TCGA-AA-3678 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3811      TCGA-AA-3812 
"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-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861      TCGA-AA-3864 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3869      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-3941      TCGA-AA-3947 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3984 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00K      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-A010 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A029 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6965 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      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-G4-6315 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
D667V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4D2 MUTATED                                  0     0
  OR4D2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4D2 MUTATED                           0     3
  OR4D2 WILD-TYPE                        19   173
D667V12, multiclass
                                  clus
vv                                 OR4D2 MUTATED OR4D2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = DSG4 MUTATION ANALYSIS
D668V1, survival
                sevent
clus2              0   1
  DSG4 MUTATED    19   2
  DSG4 WILD-TYPE 258  76
  DSG4 MUTATED DSG4 WILD-TYPE 
            21            334 
  DSG4 MUTATED DSG4 WILD-TYPE 
             2             76 
$`DSG4 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-G4-6321 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 
        0.92        24.00        22.09        20.12        19.66        63.98 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A00J TCGA-AY-6196 TCGA-AY-6386 
       29.95        78.08        53.00        18.05         0.20        17.82 
TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6929 
       10.06        85.45        25.48        16.14        12.39        13.41 
TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6703 
      139.17         6.18        47.87 

$`DSG4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       24.00        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       12.76        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  DSG4 MUTATED DSG4 WILD-TYPE 
           0.2            0.0 
  DSG4 MUTATED DSG4 WILD-TYPE 
        139.17         148.01 
  DSG4 MUTATED DSG4 WILD-TYPE 
        20.120         22.075 
[1] "0.2 - 139.2 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D668V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSG4 MUTATED         1        0        3         8         0         0
  DSG4 WILD-TYPE      63        1       23       100         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSG4 MUTATED           2          0          3          2        1         0
  DSG4 WILD-TYPE        16          6         41         31       34        12
                vv
clus             STAGE IVB
  DSG4 MUTATED           0
  DSG4 WILD-TYPE         1
D668V3, multiclass
            clus
vv           DSG4 MUTATED DSG4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             8            100
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             0             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
  DSG4 MUTATED     0   2  16   3
  DSG4 WILD-TYPE   9  65 233  38
D668V4, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           16            233
  T4            3             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
  DSG4 MUTATED    13   7   1
  DSG4 WILD-TYPE 207  74  65
D668V5, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  N0           13            207
  N1            7             74
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V6, binary
                cls
clus               0   1
  DSG4 MUTATED    16   1
  DSG4 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     16    1
  DSG4 WILD-TYPE  269   47
   clus
vv  DSG4 MUTATED DSG4 WILD-TYPE
  0           16            269
  1            1             47
[1] 2 2
[1] FALSE
D668V7, binary
                cls
clus               0   1
  DSG4 MUTATED    12   9
  DSG4 WILD-TYPE 158 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     12    9
  DSG4 WILD-TYPE  158  188
        clus
vv       DSG4 MUTATED DSG4 WILD-TYPE
  FEMALE           12            158
  MALE              9            188
[1] 2 2
[1] FALSE
D668V8, binary
                cls
clus               0   1
  DSG4 MUTATED    19   0
  DSG4 WILD-TYPE 281   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     19    0
  DSG4 WILD-TYPE  281    8
     clus
vv    DSG4 MUTATED DSG4 WILD-TYPE
  NO            19            281
  YES            0              8
[1] 2 2
[1] FALSE
D668V9, binary
                cls
clus               0   1
  DSG4 MUTATED    13   8
  DSG4 WILD-TYPE 301  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     13    8
  DSG4 WILD-TYPE  301   40
                               clus
vv                              DSG4 MUTATED DSG4 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DSG4 MUTATED    17   1   0   1
  DSG4 WILD-TYPE 242   2  22  20
D668V10, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  R0           17            242
  R1            1              2
  R2            0             22
  RX            1             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"
D668V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSG4 MUTATED                                  0     1
  DSG4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSG4 MUTATED                           2    11
  DSG4 WILD-TYPE                        17   165
D668V12, multiclass
                                  clus
vv                                 DSG4 MUTATED DSG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      11            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(669) Variable = KIAA0319L MUTATION ANALYSIS
D669V1, survival
                     sevent
clus2                   0   1
  KIAA0319L MUTATED    15   4
  KIAA0319L WILD-TYPE 262  74
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 19                 336 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                  4                  74 
$`KIAA0319L MUTATED`
TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3819 
       26.17        42.90        30.44        19.66         3.02        25.02 
TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-6598 
       31.00        25.02        34.98         1.02        58.39        49.41 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6570 
       12.76        17.56        37.02         9.44       135.65         6.18 
TCGA-G4-6307 
       55.04 

$`KIAA0319L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.12        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        10.06        35.05        33.04         0.99         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
               1.02                0.00 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
             135.65              148.01 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
              26.17               21.99 
[1] "1.0 - 135.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D669V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0319L MUTATED         3        0        3         6         2         0
  KIAA0319L WILD-TYPE      61        1       23       102         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0319L MUTATED           0          0          3          1        0
  KIAA0319L WILD-TYPE        18          6         41         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  KIAA0319L MUTATED           0         0
  KIAA0319L WILD-TYPE        12         1
D669V3, multiclass
            clus
vv           KIAA0319L MUTATED KIAA0319L WILD-TYPE
  STAGE I                    3                  61
  STAGE IA                   0                   1
  STAGE II                   3                  23
  STAGE IIA                  6                 102
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 3                  41
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  KIAA0319L MUTATED     1   3  11   4
  KIAA0319L WILD-TYPE   8  64 238  37
D669V4, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  T1                 1                   8
  T2                 3                  64
  T3                11                 238
  T4                 4                  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
  KIAA0319L MUTATED    15   4   0
  KIAA0319L WILD-TYPE 205  77  66
D669V5, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  N0                15                 205
  N1                 4                  77
  N2                 0                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V6, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    16   0
  KIAA0319L WILD-TYPE 269  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     16    0
  KIAA0319L WILD-TYPE  269   48
   clus
vv  KIAA0319L MUTATED KIAA0319L WILD-TYPE
  0                16                 269
  1                 0                  48
[1] 2 2
[1] FALSE
D669V7, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    11   8
  KIAA0319L WILD-TYPE 159 189
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     11    8
  KIAA0319L WILD-TYPE  159  189
        clus
vv       KIAA0319L MUTATED KIAA0319L WILD-TYPE
  FEMALE                11                 159
  MALE                   8                 189
[1] 2 2
[1] FALSE
D669V8, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    17   0
  KIAA0319L WILD-TYPE 283   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     17    0
  KIAA0319L WILD-TYPE  283    8
     clus
vv    KIAA0319L MUTATED KIAA0319L WILD-TYPE
  NO                 17                 283
  YES                 0                   8
[1] 2 2
[1] FALSE
D669V9, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    15   3
  KIAA0319L WILD-TYPE 299  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     15    3
  KIAA0319L WILD-TYPE  299   45
                               clus
vv                              KIAA0319L MUTATED KIAA0319L WILD-TYPE
  COLON ADENOCARCINOMA                         15                 299
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  KIAA0319L MUTATED    14   0   0   2
  KIAA0319L WILD-TYPE 245   3  22  19
D669V10, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  R0                14                 245
  R1                 0                   3
  R2                 0                  22
  RX                 2                  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"
D669V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0319L MUTATED                                  0     1
  KIAA0319L WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KIAA0319L MUTATED                           1    11
  KIAA0319L WILD-TYPE                        18   165
D669V12, multiclass
                                  clus
vv                                 KIAA0319L MUTATED KIAA0319L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                   9
  BLACK OR AFRICAN AMERICAN                        1                  18
  WHITE                                           11                 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(670) Variable = TXNDC6 MUTATION ANALYSIS
D670V1, survival
                  sevent
clus2                0   1
  TXNDC6 MUTATED     6   2
  TXNDC6 WILD-TYPE 271  76
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               8              347 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               2               76 
$`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 
        7.50       135.65 

$`TXNDC6 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E 
      140.38        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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
            1.02             0.00 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
          135.65           148.01 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
           21.09            22.06 
[1] "1.0 - 135.7 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D670V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC6 MUTATED         2        0        1         2         0         0
  TXNDC6 WILD-TYPE      62        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC6 MUTATED           0          0          1          2        0
  TXNDC6 WILD-TYPE        18          6         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TXNDC6 MUTATED           0         0
  TXNDC6 WILD-TYPE        12         1
D670V3, multiclass
            clus
vv           TXNDC6 MUTATED TXNDC6 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  TXNDC6 MUTATED     1   1   6   0
  TXNDC6 WILD-TYPE   8  66 243  41
D670V4, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              6              243
  T4              0               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
  TXNDC6 MUTATED     5   1   2
  TXNDC6 WILD-TYPE 215  80  64
D670V5, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V6, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     8   0
  TXNDC6 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      8    0
  TXNDC6 WILD-TYPE  277   48
   clus
vv  TXNDC6 MUTATED TXNDC6 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D670V7, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     4   4
  TXNDC6 WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      4    4
  TXNDC6 WILD-TYPE  166  193
        clus
vv       TXNDC6 MUTATED TXNDC6 WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D670V8, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     6   0
  TXNDC6 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      6    0
  TXNDC6 WILD-TYPE  294    8
     clus
vv    TXNDC6 MUTATED TXNDC6 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D670V9, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     6   1
  TXNDC6 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      6    1
  TXNDC6 WILD-TYPE  308   47
                               clus
vv                              TXNDC6 MUTATED TXNDC6 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TXNDC6 MUTATED     5   0   0   0
  TXNDC6 WILD-TYPE 254   3  22  21
D670V10, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D670V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC6 MUTATED                                  0     0
  TXNDC6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TXNDC6 MUTATED                           1     5
  TXNDC6 WILD-TYPE                        18   171
D670V12, multiclass
                                  clus
vv                                 TXNDC6 MUTATED TXNDC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = PFN4 MUTATION ANALYSIS
D671V1, survival
                sevent
clus2              0   1
  PFN4 MUTATED     5   1
  PFN4 WILD-TYPE 272  77
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            349 
  PFN4 MUTATED PFN4 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.09 
[1] "3.0 - 30.1 (18.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D671V2, continuous
                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      64        1       24       105         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  PFN4 MUTATED           0
  PFN4 WILD-TYPE         1
D671V3, multiclass
            clus
vv           PFN4 MUTATED PFN4 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PFN4 MUTATED     0   1   5   0
  PFN4 WILD-TYPE   9  66 244  41
D671V4, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            0             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
  PFN4 MUTATED     6   0   0
  PFN4 WILD-TYPE 214  81  66
D671V5, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V6, binary
                cls
clus               0   1
  PFN4 MUTATED     4   0
  PFN4 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      4    0
  PFN4 WILD-TYPE  281   48
   clus
vv  PFN4 MUTATED PFN4 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D671V7, binary
                cls
clus               0   1
  PFN4 MUTATED     3   3
  PFN4 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      3    3
  PFN4 WILD-TYPE  167  194
        clus
vv       PFN4 MUTATED PFN4 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D671V8, binary
                cls
clus               0   1
  PFN4 MUTATED     6   0
  PFN4 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      6    0
  PFN4 WILD-TYPE  294    8
     clus
vv    PFN4 MUTATED PFN4 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D671V9, binary
                cls
clus               0   1
  PFN4 MUTATED     6   0
  PFN4 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      6    0
  PFN4 WILD-TYPE  308   48
                               clus
vv                              PFN4 MUTATED PFN4 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PFN4 MUTATED     5   0   0   0
  PFN4 WILD-TYPE 254   3  22  21
D671V10, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D671V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PFN4 MUTATED                                  0     0
  PFN4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PFN4 MUTATED                           0     3
  PFN4 WILD-TYPE                        19   173
D671V12, multiclass
                                  clus
vv                                 PFN4 MUTATED PFN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = NOS3 MUTATION ANALYSIS
D672V1, survival
                sevent
clus2              0   1
  NOS3 MUTATED    14   4
  NOS3 WILD-TYPE 263  74
  NOS3 MUTATED NOS3 WILD-TYPE 
            18            337 
  NOS3 MUTATED NOS3 WILD-TYPE 
             4             74 
$`NOS3 MUTATED`
TCGA-AA-3662 TCGA-AA-3976 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3977 TCGA-AD-6889 
        6.05        26.01        19.66         6.97        25.02        83.24 
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 

$`NOS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        17.82        58.39         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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74         3.19        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  NOS3 MUTATED NOS3 WILD-TYPE 
          6.05           0.00 
  NOS3 MUTATED NOS3 WILD-TYPE 
         83.24         148.01 
  NOS3 MUTATED NOS3 WILD-TYPE 
         20.40          22.09 
[1] "6.0 - 83.2 (20.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D672V2, continuous
                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      61        1       24       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOS3 MUTATED           0          1          2          1        1         0
  NOS3 WILD-TYPE        18          5         42         32       34        12
                vv
clus             STAGE IVB
  NOS3 MUTATED           0
  NOS3 WILD-TYPE         1
D672V3, multiclass
            clus
vv           NOS3 MUTATED NOS3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  NOS3 MUTATED     1   4  11   2
  NOS3 WILD-TYPE   8  63 238  39
D672V4, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  T1            1              8
  T2            4             63
  T3           11            238
  T4            2             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
  NOS3 MUTATED    13   4   1
  NOS3 WILD-TYPE 207  77  65
D672V5, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  N0           13            207
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V6, binary
                cls
clus               0   1
  NOS3 MUTATED    12   1
  NOS3 WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     12    1
  NOS3 WILD-TYPE  273   47
   clus
vv  NOS3 MUTATED NOS3 WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D672V7, binary
                cls
clus               0   1
  NOS3 MUTATED     8  10
  NOS3 WILD-TYPE 162 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      8   10
  NOS3 WILD-TYPE  162  187
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  FEMALE            8            162
  MALE             10            187
[1] 2 2
[1] FALSE
D672V8, binary
                cls
clus               0   1
  NOS3 MUTATED    18   0
  NOS3 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     18    0
  NOS3 WILD-TYPE  282    8
     clus
vv    NOS3 MUTATED NOS3 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D672V9, binary
                cls
clus               0   1
  NOS3 MUTATED    15   3
  NOS3 WILD-TYPE 299  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     15    3
  NOS3 WILD-TYPE  299   45
                               clus
vv                              NOS3 MUTATED NOS3 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOS3 MUTATED    11   0   1   4
  NOS3 WILD-TYPE 248   3  21  17
D672V10, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            1             21
  RX            4             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"
D672V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOS3 MUTATED                                  0     3
  NOS3 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOS3 MUTATED                           1    10
  NOS3 WILD-TYPE                        18   166
D672V12, multiclass
                                  clus
vv                                 NOS3 MUTATED NOS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(673) Variable = MUC7 MUTATION ANALYSIS
D673V1, survival
                sevent
clus2              0   1
  MUC7 MUTATED     6   3
  MUC7 WILD-TYPE 271  75
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            346 
  MUC7 MUTATED MUC7 WILD-TYPE 
             3             75 
$`MUC7 MUTATED`
TCGA-AA-3715 TCGA-A6-6141 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6603 
       19.04         8.38         0.20        58.39        88.21        29.56 
TCGA-D5-6536 TCGA-DM-A1DA TCGA-G4-6309 
       17.85         7.50        85.48 

$`MUC7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  MUC7 MUTATED MUC7 WILD-TYPE 
           0.2            0.0 
  MUC7 MUTATED MUC7 WILD-TYPE 
         88.21         148.01 
  MUC7 MUTATED MUC7 WILD-TYPE 
        19.040         22.075 
[1] "0.2 - 88.2 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D673V2, continuous
                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      63        1       25       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC7 MUTATED           0          0          1          2        0         0
  MUC7 WILD-TYPE        18          6         43         31       35        12
                vv
clus             STAGE IVB
  MUC7 MUTATED           0
  MUC7 WILD-TYPE         1
D673V3, multiclass
            clus
vv           MUC7 MUTATED MUC7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  MUC7 MUTATED     1   1   7   0
  MUC7 WILD-TYPE   8  66 242  41
D673V4, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            7            242
  T4            0             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
  MUC7 MUTATED     5   2   2
  MUC7 WILD-TYPE 215  79  64
D673V5, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  N0            5            215
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V6, binary
                cls
clus               0   1
  MUC7 MUTATED     7   0
  MUC7 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      7    0
  MUC7 WILD-TYPE  278   48
   clus
vv  MUC7 MUTATED MUC7 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D673V7, binary
                cls
clus               0   1
  MUC7 MUTATED     4   5
  MUC7 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      4    5
  MUC7 WILD-TYPE  166  192
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D673V8, binary
                cls
clus               0   1
  MUC7 MUTATED     7   0
  MUC7 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      7    0
  MUC7 WILD-TYPE  293    8
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D673V9, binary
                cls
clus               0   1
  MUC7 MUTATED     8   1
  MUC7 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      8    1
  MUC7 WILD-TYPE  306   47
                               clus
vv                              MUC7 MUTATED MUC7 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MUC7 MUTATED     5   0   0   0
  MUC7 WILD-TYPE 254   3  22  21
D673V10, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D673V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC7 MUTATED                                  0     0
  MUC7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MUC7 MUTATED                           2     6
  MUC7 WILD-TYPE                        17   170
D673V12, multiclass
                                  clus
vv                                 MUC7 MUTATED MUC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       6            170
[1] 4 2
[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 = BCHE MUTATION ANALYSIS
D674V1, survival
                sevent
clus2              0   1
  BCHE MUTATED    17   7
  BCHE WILD-TYPE 260  71
  BCHE MUTATED BCHE WILD-TYPE 
            24            331 
  BCHE MUTATED BCHE WILD-TYPE 
             7             71 
$`BCHE MUTATED`
TCGA-AA-3516 TCGA-AD-6964 TCGA-AA-3492 TCGA-AA-3517 TCGA-AA-3544 TCGA-AA-3811 
       13.02        10.88         3.02        38.99        14.01        10.06 
TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A01V TCGA-AD-6889 TCGA-AU-6004 
       33.04        25.02        30.02         1.02        83.24        27.09 
TCGA-AZ-4315 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6748 TCGA-CM-5860 
       58.39        12.39        12.76        15.62         2.01        32.02 
TCGA-CM-5861 TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A0XF TCGA-G4-6303 
       15.02        25.48         9.44        13.35        38.20        65.85 

$`BCHE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        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-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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         7.53        12.39        10.13        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        13.41        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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  BCHE MUTATED BCHE WILD-TYPE 
          1.02           0.00 
  BCHE MUTATED BCHE WILD-TYPE 
         83.24         148.01 
  BCHE MUTATED BCHE WILD-TYPE 
         15.32          22.09 
[1] "1.0 - 83.2 (15.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D674V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCHE MUTATED         3        0        1        11         0         0
  BCHE WILD-TYPE      61        1       25        97         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCHE MUTATED           3          0          0          2        2         0
  BCHE WILD-TYPE        15          6         44         31       33        12
                vv
clus             STAGE IVB
  BCHE MUTATED           0
  BCHE WILD-TYPE         1
D674V3, multiclass
            clus
vv           BCHE MUTATED BCHE WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA            11             97
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            2             31
  STAGE IV              2             33
  STAGE IVA             0             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
  BCHE MUTATED     0   4  18   3
  BCHE WILD-TYPE   9  63 231  38
D674V4, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  T1            0              9
  T2            4             63
  T3           18            231
  T4            3             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
  BCHE MUTATED    17   2   6
  BCHE WILD-TYPE 203  79  60
D674V5, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  N0           17            203
  N1            2             79
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V6, binary
                cls
clus               0   1
  BCHE MUTATED    21   2
  BCHE WILD-TYPE 264  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     21    2
  BCHE WILD-TYPE  264   46
   clus
vv  BCHE MUTATED BCHE WILD-TYPE
  0           21            264
  1            2             46
[1] 2 2
[1] FALSE
D674V7, binary
                cls
clus               0   1
  BCHE MUTATED    12  13
  BCHE WILD-TYPE 158 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     12   13
  BCHE WILD-TYPE  158  184
        clus
vv       BCHE MUTATED BCHE WILD-TYPE
  FEMALE           12            158
  MALE             13            184
[1] 2 2
[1] FALSE
D674V8, binary
                cls
clus               0   1
  BCHE MUTATED    20   0
  BCHE WILD-TYPE 280   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     20    0
  BCHE WILD-TYPE  280    8
     clus
vv    BCHE MUTATED BCHE WILD-TYPE
  NO            20            280
  YES            0              8
[1] 2 2
[1] FALSE
D674V9, binary
                cls
clus               0   1
  BCHE MUTATED    18   6
  BCHE WILD-TYPE 296  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     18    6
  BCHE WILD-TYPE  296   42
                               clus
vv                              BCHE MUTATED BCHE WILD-TYPE
  COLON ADENOCARCINOMA                    18            296
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCHE MUTATED    18   0   0   3
  BCHE WILD-TYPE 241   3  22  18
D674V10, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  R0           18            241
  R1            0              3
  R2            0             22
  RX            3             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"
D674V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCHE MUTATED                                  0     3
  BCHE WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BCHE MUTATED                           0    12
  BCHE WILD-TYPE                        19   164
D674V12, multiclass
                                  clus
vv                                 BCHE MUTATED BCHE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      12            164
[1] 4 2
[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 = SLC27A2 MUTATION ANALYSIS
D675V1, survival
                   sevent
clus2                 0   1
  SLC27A2 MUTATED     4   1
  SLC27A2 WILD-TYPE 273  77
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                5               350 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                1                77 
$`SLC27A2 MUTATED`
TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-A01D TCGA-D5-6533 TCGA-F4-6856 
       31.63        63.98        10.98        25.48        35.31 

$`SLC27A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
            10.98              0.00 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
            63.98            148.01 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
            31.63             22.01 
[1] "11.0 - 64.0 (31.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D675V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC27A2 MUTATED         1        0        1         1         0         0
  SLC27A2 WILD-TYPE      63        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A2 MUTATED           0          0          1          1        0
  SLC27A2 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC27A2 MUTATED           0         0
  SLC27A2 WILD-TYPE        12         1
D675V3, multiclass
            clus
vv           SLC27A2 MUTATED SLC27A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC27A2 MUTATED     0   1   4   1
  SLC27A2 WILD-TYPE   9  66 245  40
D675V4, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               1                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
  SLC27A2 MUTATED     4   1   1
  SLC27A2 WILD-TYPE 216  80  65
D675V5, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V6, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     6   0
  SLC27A2 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      6    0
  SLC27A2 WILD-TYPE  279   48
   clus
vv  SLC27A2 MUTATED SLC27A2 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D675V7, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     3   3
  SLC27A2 WILD-TYPE 167 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      3    3
  SLC27A2 WILD-TYPE  167  194
        clus
vv       SLC27A2 MUTATED SLC27A2 WILD-TYPE
  FEMALE               3               167
  MALE                 3               194
[1] 2 2
[1] FALSE
D675V8, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     5   0
  SLC27A2 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      5    0
  SLC27A2 WILD-TYPE  295    8
     clus
vv    SLC27A2 MUTATED SLC27A2 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D675V9, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     4   2
  SLC27A2 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      4    2
  SLC27A2 WILD-TYPE  310   46
                               clus
vv                              SLC27A2 MUTATED SLC27A2 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC27A2 MUTATED     6   0   0   0
  SLC27A2 WILD-TYPE 253   3  22  21
D675V10, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               0                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"
D675V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC27A2 MUTATED                                  0     0
  SLC27A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC27A2 MUTATED                           1     2
  SLC27A2 WILD-TYPE                        18   174
D675V12, multiclass
                                  clus
vv                                 SLC27A2 MUTATED SLC27A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          2               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(676) Variable = KRT19 MUTATION ANALYSIS
D676V1, survival
                 sevent
clus2               0   1
  KRT19 MUTATED     3   1
  KRT19 WILD-TYPE 274  77
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             351 
  KRT19 MUTATED KRT19 WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.030 
[1] "0.9 - 49.4 (29.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D676V2, continuous
                 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      64        1       25       107         7         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  KRT19 MUTATED           0
  KRT19 WILD-TYPE         1
D676V3, multiclass
            clus
vv           KRT19 MUTATED KRT19 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  KRT19 MUTATED     0   0   3   1
  KRT19 WILD-TYPE   9  67 246  40
D676V4, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             1              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
  KRT19 MUTATED     3   1   0
  KRT19 WILD-TYPE 217  80  66
D676V5, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V6, binary
                 cls
clus                0   1
  KRT19 MUTATED     3   0
  KRT19 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      3    0
  KRT19 WILD-TYPE  282   48
   clus
vv  KRT19 MUTATED KRT19 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D676V7, binary
                 cls
clus                0   1
  KRT19 MUTATED     3   1
  KRT19 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      3    1
  KRT19 WILD-TYPE  167  196
        clus
vv       KRT19 MUTATED KRT19 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D676V8, binary
                 cls
clus                0   1
  KRT19 MUTATED     4   0
  KRT19 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      4    0
  KRT19 WILD-TYPE  296    8
     clus
vv    KRT19 MUTATED KRT19 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D676V9, binary
                 cls
clus                0   1
  KRT19 MUTATED     4   0
  KRT19 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      4    0
  KRT19 WILD-TYPE  310   48
                               clus
vv                              KRT19 MUTATED KRT19 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KRT19 MUTATED     3   0   0   0
  KRT19 WILD-TYPE 256   3  22  21
D676V10, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D676V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT19 MUTATED                                  0     0
  KRT19 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT19 MUTATED                           0     2
  KRT19 WILD-TYPE                        19   174
D676V12, multiclass
[1] "Remove cluster labels:" "KRT19 MUTATED"         
clus
  KRT19 MUTATED KRT19 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6599      TCGA-AZ-6600 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"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-5913      TCGA-CK-5914      TCGA-CK-5915 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 

Clustering(677) Variable = LASS3 MUTATION ANALYSIS
D677V1, survival
                 sevent
clus2               0   1
  LASS3 MUTATED    13   1
  LASS3 WILD-TYPE 264  77
  LASS3 MUTATED LASS3 WILD-TYPE 
             14             341 
  LASS3 MUTATED LASS3 WILD-TYPE 
              1              77 
$`LASS3 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3977 
        0.92        19.04        63.98        54.02        26.99        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        25.48        15.12 
TCGA-D5-6538 TCGA-F4-6459 
       17.13         8.61 

$`LASS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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-A01K 
       14.99        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       20.19        18.25        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6460 
      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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LASS3 MUTATED LASS3 WILD-TYPE 
           0.92            0.00 
  LASS3 MUTATED LASS3 WILD-TYPE 
          63.98          148.01 
  LASS3 MUTATED LASS3 WILD-TYPE 
          24.00           22.03 
[1] "0.9 - 64.0 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3"  
D677V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LASS3 MUTATED         1        0        2         1         1         0
  LASS3 WILD-TYPE      63        1       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LASS3 MUTATED           1          0          5          0        1         0
  LASS3 WILD-TYPE        17          6         39         33       34        12
                 vv
clus              STAGE IVB
  LASS3 MUTATED           0
  LASS3 WILD-TYPE         1
D677V3, multiclass
            clus
vv           LASS3 MUTATED LASS3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  LASS3 MUTATED     0   2  10   2
  LASS3 WILD-TYPE   9  65 239  39
D677V4, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             2              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
  LASS3 MUTATED     8   4   2
  LASS3 WILD-TYPE 212  77  64
D677V5, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V6, binary
                 cls
clus                0   1
  LASS3 MUTATED    11   1
  LASS3 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     11    1
  LASS3 WILD-TYPE  274   47
   clus
vv  LASS3 MUTATED LASS3 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D677V7, binary
                 cls
clus                0   1
  LASS3 MUTATED     9   5
  LASS3 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED      9    5
  LASS3 WILD-TYPE  161  192
        clus
vv       LASS3 MUTATED LASS3 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D677V8, binary
                 cls
clus                0   1
  LASS3 MUTATED    13   1
  LASS3 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     13    1
  LASS3 WILD-TYPE  287    7
     clus
vv    LASS3 MUTATED LASS3 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D677V9, binary
                 cls
clus                0   1
  LASS3 MUTATED    14   0
  LASS3 WILD-TYPE 300  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     14    0
  LASS3 WILD-TYPE  300   48
                               clus
vv                              LASS3 MUTATED LASS3 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LASS3 MUTATED    11   0   1   1
  LASS3 WILD-TYPE 248   3  21  20
D677V10, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             1              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"
D677V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LASS3 MUTATED                                  0     0
  LASS3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LASS3 MUTATED                           1     5
  LASS3 WILD-TYPE                        18   171
D677V12, multiclass
                                  clus
vv                                 LASS3 MUTATED LASS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = GAB1 MUTATION ANALYSIS
D678V1, survival
                sevent
clus2              0   1
  GAB1 MUTATED     7   7
  GAB1 WILD-TYPE 270  71
  GAB1 MUTATED GAB1 WILD-TYPE 
            14            341 
  GAB1 MUTATED GAB1 WILD-TYPE 
             7             71 
$`GAB1 MUTATED`
TCGA-AA-3715 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3854 
       19.04        26.17        42.90        22.06         3.02        36.03 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6605 TCGA-CM-5349 TCGA-CM-5860 
        4.01        34.98        83.24         5.23        30.08        32.02 
TCGA-CM-6679 TCGA-DM-A28C 
       10.06        81.37 

$`GAB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 
       25.02        13.02        29.06        22.03        22.98        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E 
        7.50        44.32       131.51       135.65       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GAB1 MUTATED GAB1 WILD-TYPE 
          3.02           0.00 
  GAB1 MUTATED GAB1 WILD-TYPE 
         83.24         148.01 
  GAB1 MUTATED GAB1 WILD-TYPE 
        28.125         21.990 
[1] "3.0 - 83.2 (28.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D678V2, continuous
                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      63        1       24       100         5         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  GAB1 MUTATED           0
  GAB1 WILD-TYPE         1
D678V3, multiclass
            clus
vv           GAB1 MUTATED GAB1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GAB1 MUTATED     0   1  10   4
  GAB1 WILD-TYPE   9  66 239  37
D678V4, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           10            239
  T4            4             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
  GAB1 MUTATED    14   1   0
  GAB1 WILD-TYPE 206  80  66
D678V5, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  N0           14            206
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V6, binary
                cls
clus               0   1
  GAB1 MUTATED    15   0
  GAB1 WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     15    0
  GAB1 WILD-TYPE  270   48
   clus
vv  GAB1 MUTATED GAB1 WILD-TYPE
  0           15            270
  1            0             48
[1] 2 2
[1] FALSE
D678V7, binary
                cls
clus               0   1
  GAB1 MUTATED     8   7
  GAB1 WILD-TYPE 162 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED      8    7
  GAB1 WILD-TYPE  162  190
        clus
vv       GAB1 MUTATED GAB1 WILD-TYPE
  FEMALE            8            162
  MALE              7            190
[1] 2 2
[1] FALSE
D678V8, binary
                cls
clus               0   1
  GAB1 MUTATED    12   0
  GAB1 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     12    0
  GAB1 WILD-TYPE  288    8
     clus
vv    GAB1 MUTATED GAB1 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D678V9, binary
                cls
clus               0   1
  GAB1 MUTATED    13   2
  GAB1 WILD-TYPE 301  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     13    2
  GAB1 WILD-TYPE  301   46
                               clus
vv                              GAB1 MUTATED GAB1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAB1 MUTATED    13   0   0   0
  GAB1 WILD-TYPE 246   3  22  21
D678V10, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            0             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"
D678V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAB1 MUTATED                                  0     1
  GAB1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAB1 MUTATED                           0     8
  GAB1 WILD-TYPE                        19   168
D678V12, multiclass
                                  clus
vv                                 GAB1 MUTATED GAB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = ZNF518B MUTATION ANALYSIS
D679V1, survival
                   sevent
clus2                 0   1
  ZNF518B MUTATED     7   2
  ZNF518B WILD-TYPE 270  76
  ZNF518B MUTATED ZNF518B WILD-TYPE 
                9               346 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
                2                76 
$`ZNF518B MUTATED`
TCGA-A6-6781 TCGA-AD-6889 TCGA-AD-6901 TCGA-CA-6717 TCGA-CM-6163 TCGA-CM-6171 
       19.66        83.24        22.42        12.76        14.04        14.04 
TCGA-CM-6172 TCGA-D5-6929 TCGA-G4-6306 
       11.01        13.41        44.68 

$`ZNF518B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       40.96        12.16        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF518B MUTATED ZNF518B WILD-TYPE 
            11.01              0.00 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
            83.24            148.01 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
            14.04             22.09 
[1] "11.0 - 83.2 (14.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D679V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF518B MUTATED         3        0        0         2         0         0
  ZNF518B WILD-TYPE      61        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF518B MUTATED           0          0          1          1        1
  ZNF518B WILD-TYPE        18          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  ZNF518B MUTATED           0         0
  ZNF518B WILD-TYPE        12         1
D679V3, multiclass
            clus
vv           ZNF518B MUTATED ZNF518B WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  ZNF518B MUTATED     1   3   5   1
  ZNF518B WILD-TYPE   8  64 244  40
D679V4, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  T1               1                 8
  T2               3                64
  T3               5               244
  T4               1                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
  ZNF518B MUTATED     7   3   0
  ZNF518B WILD-TYPE 213  78  66
D679V5, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  N0               7               213
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V6, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     6   1
  ZNF518B WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      6    1
  ZNF518B WILD-TYPE  279   47
   clus
vv  ZNF518B MUTATED ZNF518B WILD-TYPE
  0               6               279
  1               1                47
[1] 2 2
[1] FALSE
D679V7, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     3   7
  ZNF518B WILD-TYPE 167 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      3    7
  ZNF518B WILD-TYPE  167  190
        clus
vv       ZNF518B MUTATED ZNF518B WILD-TYPE
  FEMALE               3               167
  MALE                 7               190
[1] 2 2
[1] FALSE
D679V8, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     9   0
  ZNF518B WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      9    0
  ZNF518B WILD-TYPE  291    8
     clus
vv    ZNF518B MUTATED ZNF518B WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D679V9, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     8   2
  ZNF518B WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      8    2
  ZNF518B WILD-TYPE  306   46
                               clus
vv                              ZNF518B MUTATED ZNF518B WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF518B MUTATED     7   0   0   2
  ZNF518B WILD-TYPE 252   3  22  19
D679V10, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               2                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"
D679V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF518B MUTATED                                  0     2
  ZNF518B WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF518B MUTATED                           0     8
  ZNF518B WILD-TYPE                        19   168
D679V12, multiclass
                                  clus
vv                                 ZNF518B MUTATED ZNF518B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          8               168
[1] 4 2
[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 = C14ORF159 MUTATION ANALYSIS
D680V1, survival
                     sevent
clus2                   0   1
  C14ORF159 MUTATED     7   1
  C14ORF159 WILD-TYPE 270  77
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  8                 347 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  1                  77 
$`C14ORF159 MUTATED`
TCGA-AZ-6601 TCGA-A6-5660 TCGA-AA-A010 TCGA-AU-3779 TCGA-D5-6927 TCGA-DM-A1D9 
      100.01        29.19        34.98        14.50         9.44       140.38 
TCGA-DM-A1HB TCGA-F4-6808 
      135.65        33.67 

$`C14ORF159 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C 
       12.59         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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
               9.44                0.00 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
             140.38              148.01 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
             34.325              21.990 
[1] "9.4 - 140.4 (34.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.5"
D680V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF159 MUTATED         2        0        1         3         1         0
  C14ORF159 WILD-TYPE      62        1       25       105         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF159 MUTATED           0          0          1          1        0
  C14ORF159 WILD-TYPE        18          6         43         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF159 MUTATED           0         0
  C14ORF159 WILD-TYPE        12         1
D680V3, multiclass
            clus
vv           C14ORF159 MUTATED C14ORF159 WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  3                 105
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 1                  43
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C14ORF159 MUTATED     1   1   6   1
  C14ORF159 WILD-TYPE   8  66 243  40
D680V4, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  T1                 1                   8
  T2                 1                  66
  T3                 6                 243
  T4                 1                  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
  C14ORF159 MUTATED     7   1   1
  C14ORF159 WILD-TYPE 213  80  65
D680V5, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  N0                 7                 213
  N1                 1                  80
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V6, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     8   0
  C14ORF159 WILD-TYPE 277  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      8    0
  C14ORF159 WILD-TYPE  277   48
   clus
vv  C14ORF159 MUTATED C14ORF159 WILD-TYPE
  0                 8                 277
  1                 0                  48
[1] 2 2
[1] FALSE
D680V7, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     4   5
  C14ORF159 WILD-TYPE 166 192
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      4    5
  C14ORF159 WILD-TYPE  166  192
        clus
vv       C14ORF159 MUTATED C14ORF159 WILD-TYPE
  FEMALE                 4                 166
  MALE                   5                 192
[1] 2 2
[1] FALSE
D680V8, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     6   0
  C14ORF159 WILD-TYPE 294   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      6    0
  C14ORF159 WILD-TYPE  294    8
     clus
vv    C14ORF159 MUTATED C14ORF159 WILD-TYPE
  NO                  6                 294
  YES                 0                   8
[1] 2 2
[1] FALSE
D680V9, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     8   0
  C14ORF159 WILD-TYPE 306  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      8    0
  C14ORF159 WILD-TYPE  306   48
                               clus
vv                              C14ORF159 MUTATED C14ORF159 WILD-TYPE
  COLON ADENOCARCINOMA                          8                 306
  COLON MUCINOUS ADENOCARCINOMA                 0                  48
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF159 MUTATED     4   0   0   1
  C14ORF159 WILD-TYPE 255   3  22  20
D680V10, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  R0                 4                 255
  R1                 0                   3
  R2                 0                  22
  RX                 1                  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"
D680V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF159 MUTATED                                  0     0
  C14ORF159 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF159 MUTATED                           1     7
  C14ORF159 WILD-TYPE                        18   169
D680V12, multiclass
                                  clus
vv                                 C14ORF159 MUTATED C14ORF159 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        1                  18
  WHITE                                            7                 169
[1] 4 2
[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 = EFEMP1 MUTATION ANALYSIS
D681V1, survival
                  sevent
clus2                0   1
  EFEMP1 MUTATED    15   5
  EFEMP1 WILD-TYPE 262  73
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              335 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               5               73 
$`EFEMP1 MUTATED`
TCGA-AA-3672 TCGA-AA-3844 TCGA-AA-3950 TCGA-AZ-6601 TCGA-AD-6965 TCGA-CA-6718 
        0.92        14.93        24.00       100.01        26.47        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 
       54.61        56.09        20.19       140.38       135.65        81.37 
TCGA-F4-6569 TCGA-F4-6807 
       35.74        43.04 

$`EFEMP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        19.04        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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-5861 TCGA-CM-5862 TCGA-CM-5864 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        14.04        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-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        55.92        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17       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-F4-6808 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
            0.92             0.00 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
          140.38           148.01 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
          25.235           22.030 
[1] "0.9 - 140.4 (25.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D681V2, continuous
                  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      62        1       25        99         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFEMP1 MUTATED           1          0          4          3        0
  EFEMP1 WILD-TYPE        17          6         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  EFEMP1 MUTATED           0         0
  EFEMP1 WILD-TYPE        12         1
D681V3, multiclass
            clus
vv           EFEMP1 MUTATED EFEMP1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               9               99
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              3               30
  STAGE IV                0               35
  STAGE IVA               0               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
  EFEMP1 MUTATED     1   1  17   1
  EFEMP1 WILD-TYPE   8  66 232  40
D681V4, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             17              232
  T4              1               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
  EFEMP1 MUTATED    12   5   3
  EFEMP1 WILD-TYPE 208  76  63
D681V5, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  N0             12              208
  N1              5               76
  N2              3               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"
D681V6, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    20   0
  EFEMP1 WILD-TYPE 265  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     20    0
  EFEMP1 WILD-TYPE  265   48
   clus
vv  EFEMP1 MUTATED EFEMP1 WILD-TYPE
  0             20              265
  1              0               48
[1] 2 2
[1] FALSE
D681V7, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    10  10
  EFEMP1 WILD-TYPE 160 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     10   10
  EFEMP1 WILD-TYPE  160  187
        clus
vv       EFEMP1 MUTATED EFEMP1 WILD-TYPE
  FEMALE             10              160
  MALE               10              187
[1] 2 2
[1] FALSE
D681V8, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    16   1
  EFEMP1 WILD-TYPE 284   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     16    1
  EFEMP1 WILD-TYPE  284    7
     clus
vv    EFEMP1 MUTATED EFEMP1 WILD-TYPE
  NO              16              284
  YES              1                7
[1] 2 2
[1] FALSE
D681V9, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    17   2
  EFEMP1 WILD-TYPE 297  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     17    2
  EFEMP1 WILD-TYPE  297   46
                               clus
vv                              EFEMP1 MUTATED EFEMP1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EFEMP1 MUTATED    13   1   0   2
  EFEMP1 WILD-TYPE 246   2  22  19
D681V10, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  R0             13              246
  R1              1                2
  R2              0               22
  RX              2               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"
D681V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFEMP1 MUTATED                                  0     1
  EFEMP1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EFEMP1 MUTATED                           2    14
  EFEMP1 WILD-TYPE                        17   162
D681V12, multiclass
                                  clus
vv                                 EFEMP1 MUTATED EFEMP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        14              162
[1] 4 2
[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 = PDP2 MUTATION ANALYSIS
D682V1, survival
                sevent
clus2              0   1
  PDP2 MUTATED     4   1
  PDP2 WILD-TYPE 273  77
  PDP2 MUTATED PDP2 WILD-TYPE 
             5            350 
  PDP2 MUTATED PDP2 WILD-TYPE 
             1             77 
$`PDP2 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6165 
       19.04        25.08        83.24        12.76        16.04 

$`PDP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PDP2 MUTATED PDP2 WILD-TYPE 
         12.76           0.00 
  PDP2 MUTATED PDP2 WILD-TYPE 
         83.24         148.01 
  PDP2 MUTATED PDP2 WILD-TYPE 
        19.040         22.075 
[1] "12.8 - 83.2 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D682V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDP2 MUTATED         0        0        0         3         0         0
  PDP2 WILD-TYPE      64        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDP2 MUTATED           0          0          1          0        1         0
  PDP2 WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  PDP2 MUTATED           0
  PDP2 WILD-TYPE         1
D682V3, multiclass
            clus
vv           PDP2 MUTATED PDP2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  PDP2 MUTATED     0   0   5   0
  PDP2 WILD-TYPE   9  67 244  41
D682V4, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            0             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
  PDP2 MUTATED     4   1   0
  PDP2 WILD-TYPE 216  80  66
D682V5, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V6, binary
                cls
clus               0   1
  PDP2 MUTATED     4   1
  PDP2 WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      4    1
  PDP2 WILD-TYPE  281   47
   clus
vv  PDP2 MUTATED PDP2 WILD-TYPE
  0            4            281
  1            1             47
[1] 2 2
[1] FALSE
D682V7, binary
                cls
clus               0   1
  PDP2 MUTATED     0   5
  PDP2 WILD-TYPE 170 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      0    5
  PDP2 WILD-TYPE  170  192
        clus
vv       PDP2 MUTATED PDP2 WILD-TYPE
  FEMALE            0            170
  MALE              5            192
[1] 2 2
[1] FALSE
D682V8, binary
                cls
clus               0   1
  PDP2 MUTATED     4   1
  PDP2 WILD-TYPE 296   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      4    1
  PDP2 WILD-TYPE  296    7
     clus
vv    PDP2 MUTATED PDP2 WILD-TYPE
  NO             4            296
  YES            1              7
[1] 2 2
[1] FALSE
D682V9, binary
                cls
clus               0   1
  PDP2 MUTATED     4   1
  PDP2 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      4    1
  PDP2 WILD-TYPE  310   47
                               clus
vv                              PDP2 MUTATED PDP2 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PDP2 MUTATED     3   0   1   1
  PDP2 WILD-TYPE 256   3  21  20
D682V10, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            1             21
  RX            1             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"
D682V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDP2 MUTATED                                  0     2
  PDP2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PDP2 MUTATED                           0     2
  PDP2 WILD-TYPE                        19   174
D682V12, multiclass
                                  clus
vv                                 PDP2 MUTATED PDP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(683) Variable = ENSA MUTATION ANALYSIS
D683V1, survival
                sevent
clus2              0   1
  ENSA MUTATED     2   3
  ENSA WILD-TYPE 275  75
  ENSA MUTATED ENSA WILD-TYPE 
             5            350 
  ENSA MUTATED ENSA WILD-TYPE 
             3             75 
$`ENSA MUTATED`
TCGA-AA-3492 TCGA-CA-6718 TCGA-D5-5537 TCGA-D5-6532 TCGA-G4-6309 
        3.02        10.06        45.40        18.25        85.48 

$`ENSA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ENSA MUTATED ENSA WILD-TYPE 
          3.02           0.00 
  ENSA MUTATED ENSA WILD-TYPE 
         85.48         148.01 
  ENSA MUTATED ENSA WILD-TYPE 
        18.250         22.075 
[1] "3.0 - 85.5 (18.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D683V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENSA MUTATED         0        0        1         3         0         0
  ENSA WILD-TYPE      64        1       25       105         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  ENSA MUTATED           0
  ENSA WILD-TYPE         1
D683V3, multiclass
            clus
vv           ENSA MUTATED ENSA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ENSA MUTATED     0   0   5   0
  ENSA WILD-TYPE   9  67 244  41
D683V4, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            0             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
  ENSA MUTATED     3   1   1
  ENSA WILD-TYPE 217  80  65
D683V5, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  N0            3            217
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V6, binary
                cls
clus               0   1
  ENSA MUTATED     4   0
  ENSA WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      4    0
  ENSA WILD-TYPE  281   48
   clus
vv  ENSA MUTATED ENSA WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D683V7, binary
                cls
clus               0   1
  ENSA MUTATED     2   3
  ENSA WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      2    3
  ENSA WILD-TYPE  168  194
        clus
vv       ENSA MUTATED ENSA WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D683V8, binary
                cls
clus               0   1
  ENSA MUTATED     5   0
  ENSA WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      5    0
  ENSA WILD-TYPE  295    8
     clus
vv    ENSA MUTATED ENSA WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D683V9, binary
                cls
clus               0   1
  ENSA MUTATED     5   0
  ENSA WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      5    0
  ENSA WILD-TYPE  309   48
                               clus
vv                              ENSA MUTATED ENSA WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ENSA MUTATED     3   0   0   2
  ENSA WILD-TYPE 256   3  22  19
D683V10, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            2             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"
D683V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENSA MUTATED                                  0     1
  ENSA WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ENSA MUTATED                           1     2
  ENSA WILD-TYPE                        18   174
D683V12, multiclass
                                  clus
vv                                 ENSA MUTATED ENSA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(684) Variable = C20ORF177 MUTATION ANALYSIS
D684V1, survival
                     sevent
clus2                   0   1
  C20ORF177 MUTATED     7   2
  C20ORF177 WILD-TYPE 270  76
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  9                 346 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  2                  76 
$`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 
      130.65         1.55        53.62 

$`C20ORF177 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6805 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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
               1.55                0.00 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
             130.65              148.01 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
              14.30               22.09 
[1] "1.6 - 130.7 (14.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D684V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF177 MUTATED         1        0        0         4         2         0
  C20ORF177 WILD-TYPE      63        1       26       104         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF177 MUTATED           1          0          0          1        0
  C20ORF177 WILD-TYPE        17          6         44         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  C20ORF177 MUTATED           0         0
  C20ORF177 WILD-TYPE        12         1
D684V3, multiclass
            clus
vv           C20ORF177 MUTATED C20ORF177 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  26
  STAGE IIA                  4                 104
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  1                  17
  STAGE IIIA                 0                   6
  STAGE IIIB                 0                  44
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C20ORF177 MUTATED     0   1   6   2
  C20ORF177 WILD-TYPE   9  66 243  39
D684V4, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 6                 243
  T4                 2                  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
  C20ORF177 MUTATED     7   0   2
  C20ORF177 WILD-TYPE 213  81  64
D684V5, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  N0                 7                 213
  N1                 0                  81
  N2                 2                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V6, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     8   0
  C20ORF177 WILD-TYPE 277  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      8    0
  C20ORF177 WILD-TYPE  277   48
   clus
vv  C20ORF177 MUTATED C20ORF177 WILD-TYPE
  0                 8                 277
  1                 0                  48
[1] 2 2
[1] FALSE
D684V7, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     3   6
  C20ORF177 WILD-TYPE 167 191
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      3    6
  C20ORF177 WILD-TYPE  167  191
        clus
vv       C20ORF177 MUTATED C20ORF177 WILD-TYPE
  FEMALE                 3                 167
  MALE                   6                 191
[1] 2 2
[1] FALSE
D684V8, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     5   1
  C20ORF177 WILD-TYPE 295   7
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      5    1
  C20ORF177 WILD-TYPE  295    7
     clus
vv    C20ORF177 MUTATED C20ORF177 WILD-TYPE
  NO                  5                 295
  YES                 1                   7
[1] 2 2
[1] FALSE
D684V9, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     6   3
  C20ORF177 WILD-TYPE 308  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      6    3
  C20ORF177 WILD-TYPE  308   45
                               clus
vv                              C20ORF177 MUTATED C20ORF177 WILD-TYPE
  COLON ADENOCARCINOMA                          6                 308
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C20ORF177 MUTATED     6   0   0   2
  C20ORF177 WILD-TYPE 253   3  22  19
D684V10, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  R0                 6                 253
  R1                 0                   3
  R2                 0                  22
  RX                 2                  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"
D684V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF177 MUTATED                                  1     2
  C20ORF177 WILD-TYPE                                0     8
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C20ORF177 MUTATED                           0     4
  C20ORF177 WILD-TYPE                        19   172
D684V12, multiclass
                                  clus
vv                                 C20ORF177 MUTATED C20ORF177 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   0
  ASIAN                                            2                   8
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            4                 172
[1] 4 2
[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 = POMGNT1 MUTATION ANALYSIS
D685V1, survival
                   sevent
clus2                 0   1
  POMGNT1 MUTATED     6   2
  POMGNT1 WILD-TYPE 271  76
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               347 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                2                76 
$`POMGNT1 MUTATED`
TCGA-AA-3715 TCGA-G4-6588 TCGA-AA-3966 TCGA-CM-4743 TCGA-CM-5349 TCGA-D5-6537 
       19.04        26.17         2.01        23.05        30.08         4.80 
TCGA-D5-6540 TCGA-D5-6930 
       16.14        13.35 

$`POMGNT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
             2.01              0.00 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            30.08            148.01 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            17.59             22.09 
[1] "2.0 - 30.1 (17.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D685V2, continuous
                   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      63        1       25       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POMGNT1 MUTATED           0          0          1          0        0
  POMGNT1 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  POMGNT1 MUTATED           0         0
  POMGNT1 WILD-TYPE        12         1
D685V3, multiclass
            clus
vv           POMGNT1 MUTATED POMGNT1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  POMGNT1 MUTATED     0   1   7   0
  POMGNT1 WILD-TYPE   9  66 242  41
D685V4, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               7               242
  T4               0                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
  POMGNT1 MUTATED     7   1   0
  POMGNT1 WILD-TYPE 213  80  66
D685V5, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  N0               7               213
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V6, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     7   0
  POMGNT1 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      7    0
  POMGNT1 WILD-TYPE  278   48
   clus
vv  POMGNT1 MUTATED POMGNT1 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D685V7, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     3   5
  POMGNT1 WILD-TYPE 167 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      3    5
  POMGNT1 WILD-TYPE  167  192
        clus
vv       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  FEMALE               3               167
  MALE                 5               192
[1] 2 2
[1] FALSE
D685V8, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     7   0
  POMGNT1 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      7    0
  POMGNT1 WILD-TYPE  293    8
     clus
vv    POMGNT1 MUTATED POMGNT1 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D685V9, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     5   3
  POMGNT1 WILD-TYPE 309  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      5    3
  POMGNT1 WILD-TYPE  309   45
                               clus
vv                              POMGNT1 MUTATED POMGNT1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  POMGNT1 MUTATED     7   0   0   0
  POMGNT1 WILD-TYPE 252   3  22  21
D685V10, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D685V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POMGNT1 MUTATED                                  0     0
  POMGNT1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  POMGNT1 MUTATED                           0     6
  POMGNT1 WILD-TYPE                        19   170
D685V12, multiclass
                                  clus
vv                                 POMGNT1 MUTATED POMGNT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(686) Variable = SMG1 MUTATION ANALYSIS
D686V1, survival
                sevent
clus2              0   1
  SMG1 MUTATED    16   9
  SMG1 WILD-TYPE 261  69
  SMG1 MUTATED SMG1 WILD-TYPE 
            25            330 
  SMG1 MUTATED SMG1 WILD-TYPE 
             9             69 
$`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        54.61        38.20        60.79        31.96 
TCGA-G4-6626 
       46.75 

$`SMG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       14.30        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       124.27        23.05        20.02        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-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  SMG1 MUTATED SMG1 WILD-TYPE 
          3.02           0.00 
  SMG1 MUTATED SMG1 WILD-TYPE 
        148.01         140.38 
  SMG1 MUTATED SMG1 WILD-TYPE 
         33.01          21.99 
[1] "3.0 - 148.0 (33.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.4"
D686V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMG1 MUTATED         2        0        4         5         3         0
  SMG1 WILD-TYPE      62        1       22       103         5         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        16          6         38         31       35        11
                vv
clus             STAGE IVB
  SMG1 MUTATED           0
  SMG1 WILD-TYPE         1
D686V3, multiclass
            clus
vv           SMG1 MUTATED SMG1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             5            103
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            6             38
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             1             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
  SMG1 MUTATED     0   2  18   5
  SMG1 WILD-TYPE   9  65 231  36
D686V4, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           18            231
  T4            5             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
  SMG1 MUTATED    14   9   2
  SMG1 WILD-TYPE 206  72  64
D686V5, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  N0           14            206
  N1            9             72
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V6, binary
                cls
clus               0   1
  SMG1 MUTATED    22   1
  SMG1 WILD-TYPE 263  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     22    1
  SMG1 WILD-TYPE  263   47
   clus
vv  SMG1 MUTATED SMG1 WILD-TYPE
  0           22            263
  1            1             47
[1] 2 2
[1] FALSE
D686V7, binary
                cls
clus               0   1
  SMG1 MUTATED    13  12
  SMG1 WILD-TYPE 157 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     13   12
  SMG1 WILD-TYPE  157  185
        clus
vv       SMG1 MUTATED SMG1 WILD-TYPE
  FEMALE           13            157
  MALE             12            185
[1] 2 2
[1] FALSE
D686V8, binary
                cls
clus               0   1
  SMG1 MUTATED    21   1
  SMG1 WILD-TYPE 279   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     21    1
  SMG1 WILD-TYPE  279    7
     clus
vv    SMG1 MUTATED SMG1 WILD-TYPE
  NO            21            279
  YES            1              7
[1] 2 2
[1] FALSE
D686V9, binary
                cls
clus               0   1
  SMG1 MUTATED    18   6
  SMG1 WILD-TYPE 296  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     18    6
  SMG1 WILD-TYPE  296   42
                               clus
vv                              SMG1 MUTATED SMG1 WILD-TYPE
  COLON ADENOCARCINOMA                    18            296
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMG1 MUTATED    18   1   0   3
  SMG1 WILD-TYPE 241   2  22  18
D686V10, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  R0           18            241
  R1            1              2
  R2            0             22
  RX            3             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"
D686V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMG1 MUTATED                                  0     2
  SMG1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMG1 MUTATED                           3    11
  SMG1 WILD-TYPE                        16   165
D686V12, multiclass
                                  clus
vv                                 SMG1 MUTATED SMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      11            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(687) Variable = HMCN1 MUTATION ANALYSIS
D687V1, survival
                 sevent
clus2               0   1
  HMCN1 MUTATED    57  12
  HMCN1 WILD-TYPE 220  66
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             69             286 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             12              66 
$`HMCN1 MUTATED`
TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-A024 TCGA-AD-6895 
        8.05        17.95         0.92        19.04        39.06        25.08 
TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2674 TCGA-A6-3809 
      100.01        22.09        35.80        26.17        43.76        32.75 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6781 TCGA-AA-3510 
       29.19        33.53        22.06        21.76        19.66        63.98 
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-A03J TCGA-AU-6004 TCGA-AY-6197 
       18.05         4.01        34.98        40.96        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       58.39        88.21        12.59        12.76        10.06        15.62 
TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       21.99       124.27        23.05        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6674 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       15.02         5.03        12.95        10.06        12.03        45.40 
TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6930 
       20.19        17.85        15.58        10.13        12.43        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6460 
       12.00        11.38        44.32       135.65         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6307 
        6.18        47.87        55.04 

$`HMCN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       19.07        38.04        21.99        21.37        15.52        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 
      106.75         1.94        49.08         5.88        63.62        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        46.65        42.90        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-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.69        24.39        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3861 
       33.07         0.00        36.03        32.05         0.99        30.05 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        27.02        27.02        19.00        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-AD-5900 TCGA-AD-6889 
        0.92        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.39        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       85.45        51.32        21.14        82.95         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 
       37.02        25.02        13.02        29.06        22.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        18.25        25.48 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        7.53        12.39        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       13.41        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
      117.07        98.24        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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  HMCN1 MUTATED HMCN1 WILD-TYPE 
              0               0 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
         135.65          148.01 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
          22.98           21.99 
[1] "0.0 - 135.7 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D687V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMCN1 MUTATED         6        0        4        32         5         0
  HMCN1 WILD-TYPE      58        1       22        76         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMCN1 MUTATED           3          1         12          4        3         1
  HMCN1 WILD-TYPE        15          5         32         29       32        11
                 vv
clus              STAGE IVB
  HMCN1 MUTATED           0
  HMCN1 WILD-TYPE         1
D687V3, multiclass
            clus
vv           HMCN1 MUTATED HMCN1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             32              76
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             1               5
  STAGE IIIB            12              32
  STAGE IIIC             4              29
  STAGE IV               3              32
  STAGE IVA              1              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
  HMCN1 MUTATED     1   7  55   9
  HMCN1 WILD-TYPE   8  60 194  32
D687V4, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  T1             1               8
  T2             7              60
  T3            55             194
  T4             9              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
  HMCN1 MUTATED    48  15   9
  HMCN1 WILD-TYPE 172  66  57
D687V5, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  N0            48             172
  N1            15              66
  N2             9              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V6, binary
                 cls
clus                0   1
  HMCN1 MUTATED    59   4
  HMCN1 WILD-TYPE 226  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     59    4
  HMCN1 WILD-TYPE  226   44
   clus
vv  HMCN1 MUTATED HMCN1 WILD-TYPE
  0            59             226
  1             4              44
[1] 2 2
[1] FALSE
D687V7, binary
                 cls
clus                0   1
  HMCN1 MUTATED    28  44
  HMCN1 WILD-TYPE 142 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     28   44
  HMCN1 WILD-TYPE  142  153
        clus
vv       HMCN1 MUTATED HMCN1 WILD-TYPE
  FEMALE            28             142
  MALE              44             153
[1] 2 2
[1] FALSE
D687V8, binary
                 cls
clus                0   1
  HMCN1 MUTATED    61   1
  HMCN1 WILD-TYPE 239   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     61    1
  HMCN1 WILD-TYPE  239    7
     clus
vv    HMCN1 MUTATED HMCN1 WILD-TYPE
  NO             61             239
  YES             1               7
[1] 2 2
[1] FALSE
D687V9, binary
                 cls
clus                0   1
  HMCN1 MUTATED    59  12
  HMCN1 WILD-TYPE 255  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     59   12
  HMCN1 WILD-TYPE  255   36
                               clus
vv                              HMCN1 MUTATED HMCN1 WILD-TYPE
  COLON ADENOCARCINOMA                     59             255
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HMCN1 MUTATED    56   0   2   7
  HMCN1 WILD-TYPE 203   3  20  14
D687V10, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  R0            56             203
  R1             0               3
  R2             2              20
  RX             7              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"
D687V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HMCN1 MUTATED                                  0     3
  HMCN1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HMCN1 MUTATED                           2    43
  HMCN1 WILD-TYPE                        17   133
D687V12, multiclass
                                  clus
vv                                 HMCN1 MUTATED HMCN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       43             133
[1] 4 2
[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 = CHUK MUTATION ANALYSIS
D688V1, survival
                sevent
clus2              0   1
  CHUK MUTATED    15   6
  CHUK WILD-TYPE 262  72
  CHUK MUTATED CHUK WILD-TYPE 
            21            334 
  CHUK MUTATED CHUK WILD-TYPE 
             6             72 
$`CHUK MUTATED`
TCGA-AA-3662 TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-A00A TCGA-AA-A010 
        6.05        30.44        63.98        29.95        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 
       12.59        35.31        53.62 

$`CHUK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        22.36        62.79        12.10        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CHUK MUTATED CHUK WILD-TYPE 
          3.19           0.00 
  CHUK MUTATED CHUK WILD-TYPE 
         88.21         148.01 
  CHUK MUTATED CHUK WILD-TYPE 
         29.95          22.01 
[1] "3.2 - 88.2 (29.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D688V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHUK MUTATED         5        0        2         8         2         0
  CHUK WILD-TYPE      59        1       24       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHUK MUTATED           0          0          0          0        3         0
  CHUK WILD-TYPE        18          6         44         33       32        12
                vv
clus             STAGE IVB
  CHUK MUTATED           0
  CHUK WILD-TYPE         1
D688V3, multiclass
            clus
vv           CHUK MUTATED CHUK WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              3             32
  STAGE IVA             0             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
  CHUK MUTATED     1   4  11   5
  CHUK WILD-TYPE   8  63 238  36
D688V4, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  T1            1              8
  T2            4             63
  T3           11            238
  T4            5             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
  CHUK MUTATED    17   1   3
  CHUK WILD-TYPE 203  80  63
D688V5, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  N0           17            203
  N1            1             80
  N2            3             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"
D688V6, binary
                cls
clus               0   1
  CHUK MUTATED    15   3
  CHUK WILD-TYPE 270  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     15    3
  CHUK WILD-TYPE  270   45
   clus
vv  CHUK MUTATED CHUK WILD-TYPE
  0           15            270
  1            3             45
[1] 2 2
[1] FALSE
D688V7, binary
                cls
clus               0   1
  CHUK MUTATED    11  10
  CHUK WILD-TYPE 159 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     11   10
  CHUK WILD-TYPE  159  187
        clus
vv       CHUK MUTATED CHUK WILD-TYPE
  FEMALE           11            159
  MALE             10            187
[1] 2 2
[1] FALSE
D688V8, binary
                cls
clus               0   1
  CHUK MUTATED    20   0
  CHUK WILD-TYPE 280   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     20    0
  CHUK WILD-TYPE  280    8
     clus
vv    CHUK MUTATED CHUK WILD-TYPE
  NO            20            280
  YES            0              8
[1] 2 2
[1] FALSE
D688V9, binary
                cls
clus               0   1
  CHUK MUTATED    18   3
  CHUK WILD-TYPE 296  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     18    3
  CHUK WILD-TYPE  296   45
                               clus
vv                              CHUK MUTATED CHUK WILD-TYPE
  COLON ADENOCARCINOMA                    18            296
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHUK MUTATED    12   0   2   2
  CHUK WILD-TYPE 247   3  20  19
D688V10, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  R0           12            247
  R1            0              3
  R2            2             20
  RX            2             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"
D688V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHUK MUTATED                                  0     2
  CHUK WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHUK MUTATED                           0    13
  CHUK WILD-TYPE                        19   163
D688V12, multiclass
                                  clus
vv                                 CHUK MUTATED CHUK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      13            163
[1] 4 2
[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 = MYH3 MUTATION ANALYSIS
D689V1, survival
                sevent
clus2              0   1
  MYH3 MUTATED    21   9
  MYH3 WILD-TYPE 256  69
  MYH3 MUTATED MYH3 WILD-TYPE 
            30            325 
  MYH3 MUTATED MYH3 WILD-TYPE 
             9             69 
$`MYH3 MUTATED`
TCGA-AA-3516 TCGA-AA-3662 TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       13.02         6.05        24.00        25.08        10.88       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-A6-3809 TCGA-AA-3555 TCGA-AA-A00N TCGA-AD-6889 
       22.09        35.80        32.75        29.95         4.01        83.24 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CK-4947 
       58.39         5.13        12.10        11.74        12.76        17.56 
TCGA-CK-6751 TCGA-CM-4747 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6529 
      124.27        25.02        13.02        11.01        12.95        20.19 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6539 TCGA-DM-A28G TCGA-F4-6808 TCGA-G4-6306 
       25.48        15.12        12.49        60.79        33.67        44.68 

$`MYH3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       15.52       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        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        54.61        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        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        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYH3 MUTATED MYH3 WILD-TYPE 
          4.01           0.00 
  MYH3 MUTATED MYH3 WILD-TYPE 
        124.27         148.01 
  MYH3 MUTATED MYH3 WILD-TYPE 
         21.14          22.06 
[1] "4.0 - 124.3 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D689V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH3 MUTATED         3        0        2        11         2         0
  MYH3 WILD-TYPE      61        1       24        97         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH3 MUTATED           2          0          4          0        4         1
  MYH3 WILD-TYPE        16          6         40         33       31        11
                vv
clus             STAGE IVB
  MYH3 MUTATED           0
  MYH3 WILD-TYPE         1
D689V3, multiclass
            clus
vv           MYH3 MUTATED MYH3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            11             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              4             31
  STAGE IVA             1             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
  MYH3 MUTATED     1   4  18  10
  MYH3 WILD-TYPE   8  63 231  31
D689V4, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  T1            1              8
  T2            4             63
  T3           18            231
  T4           10             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
  MYH3 MUTATED    21   7   5
  MYH3 WILD-TYPE 199  74  61
D689V5, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  N0           21            199
  N1            7             74
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V6, binary
                cls
clus               0   1
  MYH3 MUTATED    23   5
  MYH3 WILD-TYPE 262  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     23    5
  MYH3 WILD-TYPE  262   43
   clus
vv  MYH3 MUTATED MYH3 WILD-TYPE
  0           23            262
  1            5             43
[1] 2 2
[1] FALSE
D689V7, binary
                cls
clus               0   1
  MYH3 MUTATED    17  16
  MYH3 WILD-TYPE 153 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     17   16
  MYH3 WILD-TYPE  153  181
        clus
vv       MYH3 MUTATED MYH3 WILD-TYPE
  FEMALE           17            153
  MALE             16            181
[1] 2 2
[1] FALSE
D689V8, binary
                cls
clus               0   1
  MYH3 MUTATED    28   0
  MYH3 WILD-TYPE 272   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     28    0
  MYH3 WILD-TYPE  272    8
     clus
vv    MYH3 MUTATED MYH3 WILD-TYPE
  NO            28            272
  YES            0              8
[1] 2 2
[1] FALSE
D689V9, binary
                cls
clus               0   1
  MYH3 MUTATED    26   7
  MYH3 WILD-TYPE 288  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     26    7
  MYH3 WILD-TYPE  288   41
                               clus
vv                              MYH3 MUTATED MYH3 WILD-TYPE
  COLON ADENOCARCINOMA                    26            288
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYH3 MUTATED    20   0   1   5
  MYH3 WILD-TYPE 239   3  21  16
D689V10, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  R0           20            239
  R1            0              3
  R2            1             21
  RX            5             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"
D689V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH3 MUTATED                                  0     2
  MYH3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH3 MUTATED                           2    22
  MYH3 WILD-TYPE                        17   154
D689V12, multiclass
                                  clus
vv                                 MYH3 MUTATED MYH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      22            154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(690) Variable = ING2 MUTATION ANALYSIS
D690V1, survival
                sevent
clus2              0   1
  ING2 MUTATED     6   0
  ING2 WILD-TYPE 271  78
  ING2 MUTATED ING2 WILD-TYPE 
             6            349 
  ING2 MUTATED ING2 WILD-TYPE 
             0             78 
$`ING2 MUTATED`
TCGA-G4-6586 TCGA-AA-3663 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-F4-6703 
       35.80         6.97        12.16        58.39        88.21        47.87 

$`ING2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ING2 MUTATED ING2 WILD-TYPE 
          6.97           0.00 
  ING2 MUTATED ING2 WILD-TYPE 
         88.21         148.01 
  ING2 MUTATED ING2 WILD-TYPE 
        41.835         22.030 
[1] "7.0 - 88.2 (41.8)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D690V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ING2 MUTATED         2        0        1         3         0         0
  ING2 WILD-TYPE      62        1       25       105         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ING2 MUTATED           0
  ING2 WILD-TYPE         1
D690V3, multiclass
            clus
vv           ING2 MUTATED ING2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ING2 MUTATED     1   1   4   0
  ING2 WILD-TYPE   8  66 245  41
D690V4, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            4            245
  T4            0             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
  ING2 MUTATED     6   0   0
  ING2 WILD-TYPE 214  81  66
D690V5, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V6, binary
                cls
clus               0   1
  ING2 MUTATED     5   0
  ING2 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      5    0
  ING2 WILD-TYPE  280   48
   clus
vv  ING2 MUTATED ING2 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D690V7, binary
                cls
clus               0   1
  ING2 MUTATED     2   4
  ING2 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      2    4
  ING2 WILD-TYPE  168  193
        clus
vv       ING2 MUTATED ING2 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D690V8, binary
                cls
clus               0   1
  ING2 MUTATED     6   0
  ING2 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      6    0
  ING2 WILD-TYPE  294    8
     clus
vv    ING2 MUTATED ING2 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D690V9, binary
                cls
clus               0   1
  ING2 MUTATED     5   1
  ING2 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      5    1
  ING2 WILD-TYPE  309   47
                               clus
vv                              ING2 MUTATED ING2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ING2 MUTATED     5   0   0   0
  ING2 WILD-TYPE 254   3  22  21
D690V10, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D690V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ING2 MUTATED                                  0     0
  ING2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ING2 MUTATED                           0     5
  ING2 WILD-TYPE                        19   171
D690V12, multiclass
                                  clus
vv                                 ING2 MUTATED ING2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = VAV3 MUTATION ANALYSIS
D691V1, survival
                sevent
clus2              0   1
  VAV3 MUTATED    20   3
  VAV3 WILD-TYPE 257  75
  VAV3 MUTATED VAV3 WILD-TYPE 
            23            332 
  VAV3 MUTATED VAV3 WILD-TYPE 
             3             75 
$`VAV3 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3867 TCGA-G4-6321 TCGA-A6-2672 TCGA-A6-6141 
        0.92        19.04        24.03        22.09        46.65         8.38 
TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 
       26.01        34.98        35.01        58.39        29.56        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5868 TCGA-CM-6171 TCGA-CM-6677 
       10.06        17.56        23.05        17.03        14.04        11.08 
TCGA-D5-5539 TCGA-D5-6539 TCGA-D5-6540 TCGA-DM-A1DB TCGA-G4-6304 
       19.59        12.49        16.14        44.32        53.62 

$`VAV3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       12.20        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 
       43.27        15.12        17.85         4.80        17.13        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  VAV3 MUTATED VAV3 WILD-TYPE 
          0.92           0.00 
  VAV3 MUTATED VAV3 WILD-TYPE 
         58.39         148.01 
  VAV3 MUTATED VAV3 WILD-TYPE 
        19.590         22.075 
[1] "0.9 - 58.4 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D691V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VAV3 MUTATED         2        0        0         8         2         0
  VAV3 WILD-TYPE      62        1       26       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VAV3 MUTATED           3          1          3          0        2         1
  VAV3 WILD-TYPE        15          5         41         33       33        11
                vv
clus             STAGE IVB
  VAV3 MUTATED           0
  VAV3 WILD-TYPE         1
D691V3, multiclass
            clus
vv           VAV3 MUTATED VAV3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             1             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
  VAV3 MUTATED     0   4  16   4
  VAV3 WILD-TYPE   9  63 233  37
D691V4, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           16            233
  T4            4             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
  VAV3 MUTATED    14   8   2
  VAV3 WILD-TYPE 206  73  64
D691V5, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  N0           14            206
  N1            8             73
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V6, binary
                cls
clus               0   1
  VAV3 MUTATED    19   3
  VAV3 WILD-TYPE 266  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     19    3
  VAV3 WILD-TYPE  266   45
   clus
vv  VAV3 MUTATED VAV3 WILD-TYPE
  0           19            266
  1            3             45
[1] 2 2
[1] FALSE
D691V7, binary
                cls
clus               0   1
  VAV3 MUTATED    13  11
  VAV3 WILD-TYPE 157 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     13   11
  VAV3 WILD-TYPE  157  186
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  FEMALE           13            157
  MALE             11            186
[1] 2 2
[1] FALSE
D691V8, binary
                cls
clus               0   1
  VAV3 MUTATED    20   2
  VAV3 WILD-TYPE 280   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     20    2
  VAV3 WILD-TYPE  280    6
     clus
vv    VAV3 MUTATED VAV3 WILD-TYPE
  NO            20            280
  YES            2              6
[1] 2 2
[1] FALSE
D691V9, binary
                cls
clus               0   1
  VAV3 MUTATED    19   5
  VAV3 WILD-TYPE 295  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     19    5
  VAV3 WILD-TYPE  295   43
                               clus
vv                              VAV3 MUTATED VAV3 WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  VAV3 MUTATED    16   0   2   3
  VAV3 WILD-TYPE 243   3  20  18
D691V10, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            2             20
  RX            3             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"
D691V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VAV3 MUTATED                                  0     2
  VAV3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VAV3 MUTATED                           1    14
  VAV3 WILD-TYPE                        18   162
D691V12, multiclass
                                  clus
vv                                 VAV3 MUTATED VAV3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      14            162
[1] 4 2
[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 = UIMC1 MUTATION ANALYSIS
D692V1, survival
                 sevent
clus2               0   1
  UIMC1 MUTATED     4   2
  UIMC1 WILD-TYPE 273  76
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              6             349 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              2              76 
$`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 

$`UIMC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6626 
       46.75 

  UIMC1 MUTATED UIMC1 WILD-TYPE 
           5.03            0.00 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
         148.01          140.38 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
          13.27           22.09 
[1] "5.0 - 148.0 (13.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.4"
D692V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UIMC1 MUTATED         0        1        0         2         0         0
  UIMC1 WILD-TYPE      64        0       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UIMC1 MUTATED           2          0          0          0        0         1
  UIMC1 WILD-TYPE        16          6         44         33       35        11
                 vv
clus              STAGE IVB
  UIMC1 MUTATED           0
  UIMC1 WILD-TYPE         1
D692V3, multiclass
            clus
vv           UIMC1 MUTATED UIMC1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  UIMC1 MUTATED     0   0   5   0
  UIMC1 WILD-TYPE   9  67 244  41
D692V4, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             0              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
  UIMC1 MUTATED     3   3   0
  UIMC1 WILD-TYPE 217  78  66
D692V5, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  N0             3             217
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V6, binary
                 cls
clus                0   1
  UIMC1 MUTATED     4   1
  UIMC1 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      4    1
  UIMC1 WILD-TYPE  281   47
   clus
vv  UIMC1 MUTATED UIMC1 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D692V7, binary
                 cls
clus                0   1
  UIMC1 MUTATED     2   4
  UIMC1 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      2    4
  UIMC1 WILD-TYPE  168  193
        clus
vv       UIMC1 MUTATED UIMC1 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D692V8, binary
                 cls
clus                0   1
  UIMC1 MUTATED     6   0
  UIMC1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      6    0
  UIMC1 WILD-TYPE  294    8
     clus
vv    UIMC1 MUTATED UIMC1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D692V9, binary
                 cls
clus                0   1
  UIMC1 MUTATED     5   1
  UIMC1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      5    1
  UIMC1 WILD-TYPE  309   47
                               clus
vv                              UIMC1 MUTATED UIMC1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UIMC1 MUTATED     5   0   0   1
  UIMC1 WILD-TYPE 254   3  22  20
D692V10, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D692V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UIMC1 MUTATED                                  0     1
  UIMC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UIMC1 MUTATED                           1     3
  UIMC1 WILD-TYPE                        18   173
D692V12, multiclass
                                  clus
vv                                 UIMC1 MUTATED UIMC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = LAMB4 MUTATION ANALYSIS
D693V1, survival
                 sevent
clus2               0   1
  LAMB4 MUTATED    18   7
  LAMB4 WILD-TYPE 259  71
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             25             330 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
              7              71 
$`LAMB4 MUTATED`
TCGA-AA-3950 TCGA-AA-A024 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3655 
       24.00        39.06        79.69         3.02        29.95        61.02 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3968 
        5.98        26.99        33.04        53.00        31.00        21.99 
TCGA-AA-A00N TCGA-AD-6963 TCGA-AY-6386 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
        4.01        27.42        17.82        12.10        12.76        10.06 
TCGA-CM-5344 TCGA-D5-5539 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A0XF TCGA-F4-6459 
       22.03        19.59         9.04        13.41        38.20         8.61 
TCGA-F4-6807 
       43.04 

$`LAMB4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       15.02        11.01        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        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-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-F4-6460 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  LAMB4 MUTATED LAMB4 WILD-TYPE 
           3.02            0.00 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
          79.69          148.01 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
         22.030          22.075 
[1] "3.0 - 79.7 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D693V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAMB4 MUTATED         3        0        4         7         1         0
  LAMB4 WILD-TYPE      61        1       22       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAMB4 MUTATED           1          1          4          2        2         0
  LAMB4 WILD-TYPE        17          5         40         31       33        12
                 vv
clus              STAGE IVB
  LAMB4 MUTATED           0
  LAMB4 WILD-TYPE         1
D693V3, multiclass
            clus
vv           LAMB4 MUTATED LAMB4 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  LAMB4 MUTATED     1   2  20   3
  LAMB4 WILD-TYPE   8  65 229  38
D693V4, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            20             229
  T4             3              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
  LAMB4 MUTATED    16   7   3
  LAMB4 WILD-TYPE 204  74  63
D693V5, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  N0            16             204
  N1             7              74
  N2             3              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"
D693V6, binary
                 cls
clus                0   1
  LAMB4 MUTATED    23   2
  LAMB4 WILD-TYPE 262  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     23    2
  LAMB4 WILD-TYPE  262   46
   clus
vv  LAMB4 MUTATED LAMB4 WILD-TYPE
  0            23             262
  1             2              46
[1] 2 2
[1] FALSE
D693V7, binary
                 cls
clus                0   1
  LAMB4 MUTATED    15  11
  LAMB4 WILD-TYPE 155 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     15   11
  LAMB4 WILD-TYPE  155  186
        clus
vv       LAMB4 MUTATED LAMB4 WILD-TYPE
  FEMALE            15             155
  MALE              11             186
[1] 2 2
[1] FALSE
D693V8, binary
                 cls
clus                0   1
  LAMB4 MUTATED    22   1
  LAMB4 WILD-TYPE 278   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     22    1
  LAMB4 WILD-TYPE  278    7
     clus
vv    LAMB4 MUTATED LAMB4 WILD-TYPE
  NO             22             278
  YES             1               7
[1] 2 2
[1] FALSE
D693V9, binary
                 cls
clus                0   1
  LAMB4 MUTATED    18   7
  LAMB4 WILD-TYPE 296  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     18    7
  LAMB4 WILD-TYPE  296   41
                               clus
vv                              LAMB4 MUTATED LAMB4 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LAMB4 MUTATED    21   0   0   2
  LAMB4 WILD-TYPE 238   3  22  19
D693V10, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  R0            21             238
  R1             0               3
  R2             0              22
  RX             2              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"
D693V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAMB4 MUTATED                                  0     2
  LAMB4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAMB4 MUTATED                           2     9
  LAMB4 WILD-TYPE                        17   167
D693V12, multiclass
                                  clus
vv                                 LAMB4 MUTATED LAMB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(694) Variable = MOV10L1 MUTATION ANALYSIS
D694V1, survival
                   sevent
clus2                 0   1
  MOV10L1 MUTATED    12   3
  MOV10L1 WILD-TYPE 265  75
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               15               340 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
                3                75 
$`MOV10L1 MUTATED`
TCGA-AA-3672 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3947 TCGA-AA-3977 
        0.92        34.65        32.75        33.53        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 
       15.58        24.43        55.04 

$`MOV10L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 
       43.76        42.90        42.28        16.57        33.34        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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        54.61        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        25.48        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
             0.92              0.00 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
            55.04            148.01 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
            25.02             22.01 
[1] "0.9 - 55.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D694V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOV10L1 MUTATED         1        0        0         5         3         0
  MOV10L1 WILD-TYPE      63        1       26       103         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOV10L1 MUTATED           1          0          3          1        0
  MOV10L1 WILD-TYPE        17          6         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  MOV10L1 MUTATED           0         0
  MOV10L1 WILD-TYPE        12         1
D694V3, multiclass
            clus
vv           MOV10L1 MUTATED MOV10L1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  MOV10L1 MUTATED     0   2  10   3
  MOV10L1 WILD-TYPE   9  65 239  38
D694V4, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              10               239
  T4               3                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
  MOV10L1 MUTATED    10   4   1
  MOV10L1 WILD-TYPE 210  77  65
D694V5, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  N0              10               210
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V6, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    13   0
  MOV10L1 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     13    0
  MOV10L1 WILD-TYPE  272   48
   clus
vv  MOV10L1 MUTATED MOV10L1 WILD-TYPE
  0              13               272
  1               0                48
[1] 2 2
[1] FALSE
D694V7, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED     8   7
  MOV10L1 WILD-TYPE 162 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED      8    7
  MOV10L1 WILD-TYPE  162  190
        clus
vv       MOV10L1 MUTATED MOV10L1 WILD-TYPE
  FEMALE               8               162
  MALE                 7               190
[1] 2 2
[1] FALSE
D694V8, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    12   0
  MOV10L1 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     12    0
  MOV10L1 WILD-TYPE  288    8
     clus
vv    MOV10L1 MUTATED MOV10L1 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D694V9, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    12   3
  MOV10L1 WILD-TYPE 302  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     12    3
  MOV10L1 WILD-TYPE  302   45
                               clus
vv                              MOV10L1 MUTATED MOV10L1 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  MOV10L1 MUTATED    13   0   0   0
  MOV10L1 WILD-TYPE 246   3  22  21
D694V10, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               0                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"
D694V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOV10L1 MUTATED                                  0     0
  MOV10L1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MOV10L1 MUTATED                           1    10
  MOV10L1 WILD-TYPE                        18   166
D694V12, multiclass
                                  clus
vv                                 MOV10L1 MUTATED MOV10L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         10               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(695) Variable = CTBP2 MUTATION ANALYSIS
D695V1, survival
                 sevent
clus2               0   1
  CTBP2 MUTATED     4   1
  CTBP2 WILD-TYPE 273  77
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              5             350 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              1              77 
$`CTBP2 MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-CM-6168 TCGA-D5-6931 TCGA-DM-A1HB 
       19.04        10.88        12.99        12.00       135.65 

$`CTBP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CTBP2 MUTATED CTBP2 WILD-TYPE 
          10.88            0.00 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
         135.65          148.01 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
          12.99           22.09 
[1] "10.9 - 135.7 (13.0)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.3"
D695V2, continuous
                 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      64        1       26       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTBP2 MUTATED           0          0          1          1        1         0
  CTBP2 WILD-TYPE        18          6         43         32       34        12
                 vv
clus              STAGE IVB
  CTBP2 MUTATED           0
  CTBP2 WILD-TYPE         1
D695V3, multiclass
            clus
vv           CTBP2 MUTATED CTBP2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  CTBP2 MUTATED     0   0   3   3
  CTBP2 WILD-TYPE   9  67 246  38
D695V4, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             3              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
  CTBP2 MUTATED     3   1   2
  CTBP2 WILD-TYPE 217  80  64
D695V5, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V6, binary
                 cls
clus                0   1
  CTBP2 MUTATED     3   1
  CTBP2 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      3    1
  CTBP2 WILD-TYPE  282   47
   clus
vv  CTBP2 MUTATED CTBP2 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D695V7, binary
                 cls
clus                0   1
  CTBP2 MUTATED     2   4
  CTBP2 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      2    4
  CTBP2 WILD-TYPE  168  193
        clus
vv       CTBP2 MUTATED CTBP2 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D695V8, binary
                 cls
clus                0   1
  CTBP2 MUTATED     3   1
  CTBP2 WILD-TYPE 297   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      3    1
  CTBP2 WILD-TYPE  297    7
     clus
vv    CTBP2 MUTATED CTBP2 WILD-TYPE
  NO              3             297
  YES             1               7
[1] 2 2
[1] FALSE
D695V9, binary
                 cls
clus                0   1
  CTBP2 MUTATED     5   0
  CTBP2 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      5    0
  CTBP2 WILD-TYPE  309   48
                               clus
vv                              CTBP2 MUTATED CTBP2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CTBP2 MUTATED     2   0   1   1
  CTBP2 WILD-TYPE 257   3  21  20
D695V10, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             1              21
  RX             1              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"
D695V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTBP2 MUTATED                                  0     0
  CTBP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CTBP2 MUTATED                           1     4
  CTBP2 WILD-TYPE                        18   172
D695V12, multiclass
                                  clus
vv                                 CTBP2 MUTATED CTBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = TM9SF2 MUTATION ANALYSIS
D696V1, survival
                  sevent
clus2                0   1
  TM9SF2 MUTATED     8   2
  TM9SF2 WILD-TYPE 269  76
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              10              345 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
               2               76 
$`TM9SF2 MUTATED`
TCGA-AD-6548 TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00R TCGA-AA-A01R 
       21.37        10.88        22.06        63.98         0.99        35.01 
TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-6680 
       14.50        21.44        49.41        12.03 

$`TM9SF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
            0.99             0.00 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
           63.98           148.01 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
          21.405           22.090 
[1] "1.0 - 64.0 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D696V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TM9SF2 MUTATED         2        0        2         3         0         0
  TM9SF2 WILD-TYPE      62        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM9SF2 MUTATED           1          0          1          0        0
  TM9SF2 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TM9SF2 MUTATED           0         0
  TM9SF2 WILD-TYPE        12         1
D696V3, multiclass
            clus
vv           TM9SF2 MUTATED TM9SF2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TM9SF2 MUTATED     0   2   7   1
  TM9SF2 WILD-TYPE   9  65 242  40
D696V4, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              1               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
  TM9SF2 MUTATED     7   0   3
  TM9SF2 WILD-TYPE 213  81  63
D696V5, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              3               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"
D696V6, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     7   0
  TM9SF2 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      7    0
  TM9SF2 WILD-TYPE  278   48
   clus
vv  TM9SF2 MUTATED TM9SF2 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D696V7, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     6   4
  TM9SF2 WILD-TYPE 164 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      6    4
  TM9SF2 WILD-TYPE  164  193
        clus
vv       TM9SF2 MUTATED TM9SF2 WILD-TYPE
  FEMALE              6              164
  MALE                4              193
[1] 2 2
[1] FALSE
D696V8, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     8   1
  TM9SF2 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      8    1
  TM9SF2 WILD-TYPE  292    7
     clus
vv    TM9SF2 MUTATED TM9SF2 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D696V9, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     9   1
  TM9SF2 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      9    1
  TM9SF2 WILD-TYPE  305   47
                               clus
vv                              TM9SF2 MUTATED TM9SF2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TM9SF2 MUTATED     8   0   0   0
  TM9SF2 WILD-TYPE 251   3  22  21
D696V10, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              0               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"
D696V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TM9SF2 MUTATED                                  0     0
  TM9SF2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TM9SF2 MUTATED                           0     7
  TM9SF2 WILD-TYPE                        19   169
D696V12, multiclass
                                  clus
vv                                 TM9SF2 MUTATED TM9SF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = CCDC88A MUTATION ANALYSIS
D697V1, survival
                   sevent
clus2                 0   1
  CCDC88A MUTATED    21   6
  CCDC88A WILD-TYPE 256  72
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               27               328 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                6                72 
$`CCDC88A MUTATED`
TCGA-AA-3516 TCGA-AA-3524 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-3809 
       13.02        36.03        35.80        79.69        42.90        32.75 
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       22.06        24.39        19.66        63.98         1.02        29.95 
TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00U TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-4323 
        6.97        25.02        17.03        34.98        58.39         1.41 
TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5348 TCGA-D5-5540 
       29.56        12.76        10.06        37.02        22.98        56.09 
TCGA-DM-A0XD TCGA-DM-A1HA TCGA-DM-A28K 
       24.43       131.51        98.24 

$`CCDC88A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        43.76        46.65        43.76        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-A6-5666 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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       27.02        42.02         0.99        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       17.82         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10         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 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-A28C TCGA-DM-A28E 
        7.50        44.32       135.65       139.17        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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
             1.02              0.00 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
           131.51            148.01 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
           29.560            21.875 
[1] "1.0 - 131.5 (29.6)" "0.0 - 148.0 (21.9)"
[1] "hr=" "1.2"
D697V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC88A MUTATED         3        0        3        11         4         0
  CCDC88A WILD-TYPE      61        1       23        97         4         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC88A MUTATED           1          0          2          2        2
  CCDC88A WILD-TYPE        17          6         42         31       33
                   vv
clus                STAGE IVA STAGE IVB
  CCDC88A MUTATED           0         0
  CCDC88A WILD-TYPE        12         1
D697V3, multiclass
            clus
vv           CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA               11                97
  STAGE IIB                4                 4
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               2                31
  STAGE IV                 2                33
  STAGE IVA                0                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
  CCDC88A MUTATED     0   5  19   6
  CCDC88A WILD-TYPE   9  62 230  35
D697V4, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  T1               0                 9
  T2               5                62
  T3              19               230
  T4               6                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
  CCDC88A MUTATED    22   4   4
  CCDC88A WILD-TYPE 198  77  62
D697V5, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  N0              22               198
  N1               4                77
  N2               4                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V6, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    24   2
  CCDC88A WILD-TYPE 261  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     24    2
  CCDC88A WILD-TYPE  261   46
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0              24               261
  1               2                46
[1] 2 2
[1] FALSE
D697V7, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    12  18
  CCDC88A WILD-TYPE 158 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     12   18
  CCDC88A WILD-TYPE  158  179
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  FEMALE              12               158
  MALE                18               179
[1] 2 2
[1] FALSE
D697V8, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    23   0
  CCDC88A WILD-TYPE 277   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     23    0
  CCDC88A WILD-TYPE  277    8
     clus
vv    CCDC88A MUTATED CCDC88A WILD-TYPE
  NO               23               277
  YES               0                 8
[1] 2 2
[1] FALSE
D697V9, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    24   6
  CCDC88A WILD-TYPE 290  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     24    6
  CCDC88A WILD-TYPE  290   42
                               clus
vv                              CCDC88A MUTATED CCDC88A WILD-TYPE
  COLON ADENOCARCINOMA                       24               290
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC88A MUTATED    18   0   1   3
  CCDC88A WILD-TYPE 241   3  21  18
D697V10, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               1                21
  RX               3                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"
D697V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC88A MUTATED                                  0     2
  CCDC88A WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC88A MUTATED                           1    16
  CCDC88A WILD-TYPE                        18   160
D697V12, multiclass
                                  clus
vv                                 CCDC88A MUTATED CCDC88A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         16               160
[1] 4 2
[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 = ART5 MUTATION ANALYSIS
D698V1, survival
                sevent
clus2              0   1
  ART5 MUTATED     6   3
  ART5 WILD-TYPE 271  75
  ART5 MUTATED ART5 WILD-TYPE 
             9            346 
  ART5 MUTATED ART5 WILD-TYPE 
             3             75 
$`ART5 MUTATED`
TCGA-AD-6964 TCGA-A6-6780 TCGA-AA-3864 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
       10.88        20.12        53.00        83.24        21.44        58.39 
TCGA-AZ-6598 TCGA-CM-4752 TCGA-D5-6928 
       49.41        13.02        11.64 

$`ART5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ART5 MUTATED ART5 WILD-TYPE 
         10.88           0.00 
  ART5 MUTATED ART5 WILD-TYPE 
         83.24         148.01 
  ART5 MUTATED ART5 WILD-TYPE 
        21.440         22.075 
[1] "10.9 - 83.2 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D698V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ART5 MUTATED         0        0        2         6         0         0
  ART5 WILD-TYPE      64        1       24       102         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ART5 MUTATED           0
  ART5 WILD-TYPE         1
D698V3, multiclass
            clus
vv           ART5 MUTATED ART5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ART5 MUTATED     0   0   8   1
  ART5 WILD-TYPE   9  67 241  40
D698V4, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            8            241
  T4            1             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
  ART5 MUTATED     8   0   1
  ART5 WILD-TYPE 212  81  65
D698V5, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V6, binary
                cls
clus               0   1
  ART5 MUTATED     5   0
  ART5 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      5    0
  ART5 WILD-TYPE  280   48
   clus
vv  ART5 MUTATED ART5 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D698V7, binary
                cls
clus               0   1
  ART5 MUTATED     1   8
  ART5 WILD-TYPE 169 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      1    8
  ART5 WILD-TYPE  169  189
        clus
vv       ART5 MUTATED ART5 WILD-TYPE
  FEMALE            1            169
  MALE              8            189
[1] 2 2
[1] FALSE
D698V8, binary
                cls
clus               0   1
  ART5 MUTATED     9   0
  ART5 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      9    0
  ART5 WILD-TYPE  291    8
     clus
vv    ART5 MUTATED ART5 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D698V9, binary
                cls
clus               0   1
  ART5 MUTATED     7   2
  ART5 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      7    2
  ART5 WILD-TYPE  307   46
                               clus
vv                              ART5 MUTATED ART5 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ART5 MUTATED     6   0   0   0
  ART5 WILD-TYPE 253   3  22  21
D698V10, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D698V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ART5 MUTATED                                  0     1
  ART5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ART5 MUTATED                           1     6
  ART5 WILD-TYPE                        18   170
D698V12, multiclass
                                  clus
vv                                 ART5 MUTATED ART5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = ASPG MUTATION ANALYSIS
D699V1, survival
                sevent
clus2              0   1
  ASPG MUTATED     6   1
  ASPG WILD-TYPE 271  77
  ASPG MUTATED ASPG WILD-TYPE 
             7            348 
  ASPG MUTATED ASPG WILD-TYPE 
             1             77 
$`ASPG MUTATED`
TCGA-AZ-6601 TCGA-A6-5661 TCGA-AA-3877 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CM-5861 
      100.01        33.53        31.00        14.50        58.39        15.02 
TCGA-CM-6674 
       12.95 

$`ASPG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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         22.045 
[1] "12.9 - 100.0 (31.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.1"
D699V2, continuous
                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      63        1       25       103         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ASPG MUTATED           0
  ASPG WILD-TYPE         1
D699V3, multiclass
            clus
vv           ASPG MUTATED ASPG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ASPG MUTATED     1   0   6   0
  ASPG WILD-TYPE   8  67 243  41
D699V4, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  T1            1              8
  T2            0             67
  T3            6            243
  T4            0             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
  ASPG MUTATED     7   0   0
  ASPG WILD-TYPE 213  81  66
D699V5, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  N0            7            213
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V6, binary
                cls
clus               0   1
  ASPG MUTATED     7   0
  ASPG WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      7    0
  ASPG WILD-TYPE  278   48
   clus
vv  ASPG MUTATED ASPG WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D699V7, binary
                cls
clus               0   1
  ASPG MUTATED     4   3
  ASPG WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      4    3
  ASPG WILD-TYPE  166  194
        clus
vv       ASPG MUTATED ASPG WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D699V8, binary
                cls
clus               0   1
  ASPG MUTATED     7   0
  ASPG WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      7    0
  ASPG WILD-TYPE  293    8
     clus
vv    ASPG MUTATED ASPG WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D699V9, binary
                cls
clus               0   1
  ASPG MUTATED     6   1
  ASPG WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      6    1
  ASPG WILD-TYPE  308   47
                               clus
vv                              ASPG MUTATED ASPG WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ASPG MUTATED     6   0   0   0
  ASPG WILD-TYPE 253   3  22  21
D699V10, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D699V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASPG MUTATED                                  0     0
  ASPG WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ASPG MUTATED                           1     5
  ASPG WILD-TYPE                        18   171
D699V12, multiclass
                                  clus
vv                                 ASPG MUTATED ASPG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = PLEKHB2 MUTATION ANALYSIS
D700V1, survival
                   sevent
clus2                 0   1
  PLEKHB2 MUTATED     3   2
  PLEKHB2 WILD-TYPE 274  76
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                5               350 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2                76 
$`PLEKHB2 MUTATED`
TCGA-AA-3662 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-5666 TCGA-AA-3977 
        6.05        10.88       100.01        32.71        25.02 

$`PLEKHB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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            22.045 
[1] "6.0 - 100.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D700V2, continuous
                   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      64        1       25       108         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHB2 MUTATED           1          0          0          0        1
  PLEKHB2 WILD-TYPE        17          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHB2 MUTATED           0         0
  PLEKHB2 WILD-TYPE        12         1
D700V3, multiclass
            clus
vv           PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                0               108
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  PLEKHB2 MUTATED     0   1   2   3
  PLEKHB2 WILD-TYPE   9  66 247  38
D700V4, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               2               247
  T4               3                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
  PLEKHB2 MUTATED     3   0   3
  PLEKHB2 WILD-TYPE 217  81  63
D700V5, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  N0               3               217
  N1               0                81
  N2               3                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"
D700V6, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     3   1
  PLEKHB2 WILD-TYPE 282  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      3    1
  PLEKHB2 WILD-TYPE  282   47
   clus
vv  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  0               3               282
  1               1                47
[1] 2 2
[1] FALSE
D700V7, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     1   5
  PLEKHB2 WILD-TYPE 169 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      1    5
  PLEKHB2 WILD-TYPE  169  192
        clus
vv       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  FEMALE               1               169
  MALE                 5               192
[1] 2 2
[1] FALSE
D700V8, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     5   0
  PLEKHB2 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      5    0
  PLEKHB2 WILD-TYPE  295    8
     clus
vv    PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D700V9, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     6   0
  PLEKHB2 WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      6    0
  PLEKHB2 WILD-TYPE  308   48
                               clus
vv                              PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHB2 MUTATED     1   0   1   0
  PLEKHB2 WILD-TYPE 258   3  21  21
D700V10, multiclass
[1] "Remove cluster labels:" "PLEKHB2 MUTATED"       
clus
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        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-3527 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3697 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814        TCGA-AA-3844 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870        TCGA-AA-3939 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972        TCGA-AA-3976 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L        TCGA-AA-A00Z 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6895 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310        TCGA-G4-6321 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6628 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       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-A6-2678        TCGA-A6-2683        TCGA-A6-3807        TCGA-A6-3808 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657        TCGA-A6-5659 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781        TCGA-AA-3489 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3492        TCGA-AA-3502        TCGA-AA-3510        TCGA-AA-3511 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532        TCGA-AA-3534 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544        TCGA-AA-3548 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555        TCGA-AA-3558 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3561        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-3673 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693        TCGA-AA-3695 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3811        TCGA-AA-3812 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3842 
"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-3861        TCGA-AA-3864 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3872        TCGA-AA-3875 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3941        TCGA-AA-3947 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3984 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W        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-A029 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6965 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5913 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6315 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
D700V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHB2 MUTATED                                  0     0
  PLEKHB2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHB2 MUTATED                           0     3
  PLEKHB2 WILD-TYPE                        19   173
D700V12, multiclass
                                  clus
vv                                 PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = TMTC4 MUTATION ANALYSIS
D701V1, survival
                 sevent
clus2               0   1
  TMTC4 MUTATED    10   3
  TMTC4 WILD-TYPE 267  75
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             13             342 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
              3              75 
$`TMTC4 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-A6-6138 TCGA-A6-6141 TCGA-AA-3542 TCGA-AA-3864 
       24.00       100.01        22.52         8.38        12.99        53.00 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6386 TCGA-CM-5348 TCGA-CM-5860 TCGA-D5-5537 
       83.24        27.09        17.82        22.98        32.02        45.40 
TCGA-DM-A1D0 
      130.65 

$`TMTC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 
       23.61        22.09        22.06        32.71        27.09        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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           21.99 
[1] "8.4 - 130.7 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D701V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMTC4 MUTATED         2        0        2         6         0         0
  TMTC4 WILD-TYPE      62        1       24       102         8         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        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  TMTC4 MUTATED           0
  TMTC4 WILD-TYPE         1
D701V3, multiclass
            clus
vv           TMTC4 MUTATED TMTC4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TMTC4 MUTATED     0   2  11   0
  TMTC4 WILD-TYPE   9  65 238  41
D701V4, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            11             238
  T4             0              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
  TMTC4 MUTATED     9   2   2
  TMTC4 WILD-TYPE 211  79  64
D701V5, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V6, binary
                 cls
clus                0   1
  TMTC4 MUTATED    12   0
  TMTC4 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     12    0
  TMTC4 WILD-TYPE  273   48
   clus
vv  TMTC4 MUTATED TMTC4 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D701V7, binary
                 cls
clus                0   1
  TMTC4 MUTATED     4   9
  TMTC4 WILD-TYPE 166 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED      4    9
  TMTC4 WILD-TYPE  166  188
        clus
vv       TMTC4 MUTATED TMTC4 WILD-TYPE
  FEMALE             4             166
  MALE               9             188
[1] 2 2
[1] FALSE
D701V8, binary
                 cls
clus                0   1
  TMTC4 MUTATED    11   0
  TMTC4 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     11    0
  TMTC4 WILD-TYPE  289    8
     clus
vv    TMTC4 MUTATED TMTC4 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D701V9, binary
                 cls
clus                0   1
  TMTC4 MUTATED    12   1
  TMTC4 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     12    1
  TMTC4 WILD-TYPE  302   47
                               clus
vv                              TMTC4 MUTATED TMTC4 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TMTC4 MUTATED     8   0   0   1
  TMTC4 WILD-TYPE 251   3  22  20
D701V10, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D701V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMTC4 MUTATED                                  0     1
  TMTC4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMTC4 MUTATED                           2     7
  TMTC4 WILD-TYPE                        17   169
D701V12, multiclass
                                  clus
vv                                 TMTC4 MUTATED TMTC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        7             169
[1] 4 2
[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 = DOCK5 MUTATION ANALYSIS
D702V1, survival
                 sevent
clus2               0   1
  DOCK5 MUTATED    20   6
  DOCK5 WILD-TYPE 257  72
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             26             329 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              6              72 
$`DOCK5 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6601 
        0.92        19.04        19.04        24.00        10.88       100.01 
TCGA-G4-6628 TCGA-A6-5660 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3864 TCGA-AA-3877 
       79.69        29.19        20.12        29.95        53.00        31.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6197 
       30.02        18.05         4.01        34.98        12.16        21.44 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6161 TCGA-DM-A0XF 
       58.39         6.77        12.76        15.02        15.02        38.20 
TCGA-F4-6856 TCGA-G4-6304 
       35.31        53.62 

$`DOCK5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       25.08       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       13.94        38.04        19.00        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DOCK5 MUTATED DOCK5 WILD-TYPE 
           0.92            0.00 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
         100.01          148.01 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          22.72           22.06 
[1] "0.9 - 100.0 (22.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D702V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK5 MUTATED         6        0        3         8         3         0
  DOCK5 WILD-TYPE      58        1       23       100         5         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        17          6         43         31       34        12
                 vv
clus              STAGE IVB
  DOCK5 MUTATED           0
  DOCK5 WILD-TYPE         1
D702V3, multiclass
            clus
vv           DOCK5 MUTATED DOCK5 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  DOCK5 MUTATED     1   5  15   5
  DOCK5 WILD-TYPE   8  62 234  36
D702V4, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  T1             1               8
  T2             5              62
  T3            15             234
  T4             5              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
  DOCK5 MUTATED    21   2   3
  DOCK5 WILD-TYPE 199  79  63
D702V5, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  N0            21             199
  N1             2              79
  N2             3              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"
D702V6, binary
                 cls
clus                0   1
  DOCK5 MUTATED    20   1
  DOCK5 WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     20    1
  DOCK5 WILD-TYPE  265   47
   clus
vv  DOCK5 MUTATED DOCK5 WILD-TYPE
  0            20             265
  1             1              47
[1] 2 2
[1] FALSE
D702V7, binary
                 cls
clus                0   1
  DOCK5 MUTATED     9  17
  DOCK5 WILD-TYPE 161 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED      9   17
  DOCK5 WILD-TYPE  161  180
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  FEMALE             9             161
  MALE              17             180
[1] 2 2
[1] FALSE
D702V8, binary
                 cls
clus                0   1
  DOCK5 MUTATED    23   1
  DOCK5 WILD-TYPE 277   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     23    1
  DOCK5 WILD-TYPE  277    7
     clus
vv    DOCK5 MUTATED DOCK5 WILD-TYPE
  NO             23             277
  YES             1               7
[1] 2 2
[1] FALSE
D702V9, binary
                 cls
clus                0   1
  DOCK5 MUTATED    16   9
  DOCK5 WILD-TYPE 298  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     16    9
  DOCK5 WILD-TYPE  298   39
                               clus
vv                              DOCK5 MUTATED DOCK5 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK5 MUTATED    18   0   1   1
  DOCK5 WILD-TYPE 241   3  21  20
D702V10, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  R0            18             241
  R1             0               3
  R2             1              21
  RX             1              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"
D702V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK5 MUTATED                                  0     1
  DOCK5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK5 MUTATED                           1    13
  DOCK5 WILD-TYPE                        18   163
D702V12, multiclass
                                  clus
vv                                 DOCK5 MUTATED DOCK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       13             163
[1] 4 2
[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 = DNAJC16 MUTATION ANALYSIS
D703V1, survival
                   sevent
clus2                 0   1
  DNAJC16 MUTATED     7   2
  DNAJC16 WILD-TYPE 270  76
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                9               346 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                2                76 
$`DNAJC16 MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-3809 TCGA-AA-3553 TCGA-AA-3663 TCGA-AA-A010 
      100.01        79.69        32.75        24.00         6.97        34.98 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6600 
       58.39        88.21        12.10 

$`DNAJC16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
        5.13        22.36        62.79        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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             21.99 
[1] "7.0 - 100.0 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D703V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC16 MUTATED         3        0        2         1         2         0
  DNAJC16 WILD-TYPE      61        1       24       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC16 MUTATED           0          0          0          0        1
  DNAJC16 WILD-TYPE        18          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC16 MUTATED           0         0
  DNAJC16 WILD-TYPE        12         1
D703V3, multiclass
            clus
vv           DNAJC16 MUTATED DNAJC16 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                1               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  DNAJC16 MUTATED     1   2   3   3
  DNAJC16 WILD-TYPE   8  65 246  38
D703V4, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               3               246
  T4               3                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
  DNAJC16 MUTATED     8   1   0
  DNAJC16 WILD-TYPE 212  80  66
D703V5, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  N0               8               212
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V6, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     8   1
  DNAJC16 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      8    1
  DNAJC16 WILD-TYPE  277   47
   clus
vv  DNAJC16 MUTATED DNAJC16 WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D703V7, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     4   5
  DNAJC16 WILD-TYPE 166 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      4    5
  DNAJC16 WILD-TYPE  166  192
        clus
vv       DNAJC16 MUTATED DNAJC16 WILD-TYPE
  FEMALE               4               166
  MALE                 5               192
[1] 2 2
[1] FALSE
D703V8, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     9   0
  DNAJC16 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      9    0
  DNAJC16 WILD-TYPE  291    8
     clus
vv    DNAJC16 MUTATED DNAJC16 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D703V9, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     8   1
  DNAJC16 WILD-TYPE 306  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      8    1
  DNAJC16 WILD-TYPE  306   47
                               clus
vv                              DNAJC16 MUTATED DNAJC16 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DNAJC16 MUTATED     6   0   0   0
  DNAJC16 WILD-TYPE 253   3  22  21
D703V10, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               0                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"
D703V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC16 MUTATED                                  0     0
  DNAJC16 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJC16 MUTATED                           1     5
  DNAJC16 WILD-TYPE                        18   171
D703V12, multiclass
                                  clus
vv                                 DNAJC16 MUTATED DNAJC16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = PHF1 MUTATION ANALYSIS
D704V1, survival
                sevent
clus2              0   1
  PHF1 MUTATED     4   2
  PHF1 WILD-TYPE 273  76
  PHF1 MUTATED PHF1 WILD-TYPE 
             6            349 
  PHF1 MUTATED PHF1 WILD-TYPE 
             2             76 
$`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 

$`PHF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PHF1 MUTATED PHF1 WILD-TYPE 
          6.18           0.00 
  PHF1 MUTATED PHF1 WILD-TYPE 
         61.91         148.01 
  PHF1 MUTATED PHF1 WILD-TYPE 
         20.86          22.09 
[1] "6.2 - 61.9 (20.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D704V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF1 MUTATED         0        0        1         3         0         0
  PHF1 WILD-TYPE      64        1       25       105         8         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        18          6         44         32       34        12
                vv
clus             STAGE IVB
  PHF1 MUTATED           0
  PHF1 WILD-TYPE         1
D704V3, multiclass
            clus
vv           PHF1 MUTATED PHF1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  PHF1 MUTATED     0   0   5   1
  PHF1 WILD-TYPE   9  67 244  40
D704V4, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            1             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
  PHF1 MUTATED     4   2   0
  PHF1 WILD-TYPE 216  79  66
D704V5, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  N0            4            216
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V6, binary
                cls
clus               0   1
  PHF1 MUTATED     3   1
  PHF1 WILD-TYPE 282  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      3    1
  PHF1 WILD-TYPE  282   47
   clus
vv  PHF1 MUTATED PHF1 WILD-TYPE
  0            3            282
  1            1             47
[1] 2 2
[1] FALSE
D704V7, binary
                cls
clus               0   1
  PHF1 MUTATED     3   3
  PHF1 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      3    3
  PHF1 WILD-TYPE  167  194
        clus
vv       PHF1 MUTATED PHF1 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D704V8, binary
                cls
clus               0   1
  PHF1 MUTATED     6   0
  PHF1 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      6    0
  PHF1 WILD-TYPE  294    8
     clus
vv    PHF1 MUTATED PHF1 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D704V9, binary
                cls
clus               0   1
  PHF1 MUTATED     4   2
  PHF1 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      4    2
  PHF1 WILD-TYPE  310   46
                               clus
vv                              PHF1 MUTATED PHF1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PHF1 MUTATED     4   0   0   1
  PHF1 WILD-TYPE 255   3  22  20
D704V10, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            1             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"
D704V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF1 MUTATED                                  0     1
  PHF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PHF1 MUTATED                           0     5
  PHF1 WILD-TYPE                        19   171
D704V12, multiclass
                                  clus
vv                                 PHF1 MUTATED PHF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = OR2V2 MUTATION ANALYSIS
D705V1, survival
                 sevent
clus2               0   1
  OR2V2 MUTATED     4   2
  OR2V2 WILD-TYPE 273  76
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             349 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          21.990 
[1] "13.2 - 49.4 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D705V2, continuous
                 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      64        1       25       107         7         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        18          6         44         33       35         9
                 vv
clus              STAGE IVB
  OR2V2 MUTATED           0
  OR2V2 WILD-TYPE         1
D705V3, multiclass
            clus
vv           OR2V2 MUTATED OR2V2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              3               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
  OR2V2 MUTATED     0   0   5   1
  OR2V2 WILD-TYPE   9  67 244  40
D705V4, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             1              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
  OR2V2 MUTATED     4   2   0
  OR2V2 WILD-TYPE 216  79  66
D705V5, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V6, binary
                 cls
clus                0   1
  OR2V2 MUTATED     2   3
  OR2V2 WILD-TYPE 283  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      2    3
  OR2V2 WILD-TYPE  283   45
   clus
vv  OR2V2 MUTATED OR2V2 WILD-TYPE
  0             2             283
  1             3              45
[1] 2 2
[1] FALSE
D705V7, binary
                 cls
clus                0   1
  OR2V2 MUTATED     5   1
  OR2V2 WILD-TYPE 165 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      5    1
  OR2V2 WILD-TYPE  165  196
        clus
vv       OR2V2 MUTATED OR2V2 WILD-TYPE
  FEMALE             5             165
  MALE               1             196
[1] 2 2
[1] FALSE
D705V8, binary
                 cls
clus                0   1
  OR2V2 MUTATED     6   0
  OR2V2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      6    0
  OR2V2 WILD-TYPE  294    8
     clus
vv    OR2V2 MUTATED OR2V2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D705V9, binary
                 cls
clus                0   1
  OR2V2 MUTATED     5   1
  OR2V2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      5    1
  OR2V2 WILD-TYPE  309   47
                               clus
vv                              OR2V2 MUTATED OR2V2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2V2 MUTATED     3   0   0   0
  OR2V2 WILD-TYPE 256   3  22  21
D705V10, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D705V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2V2 MUTATED                                  0     0
  OR2V2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2V2 MUTATED                           1     5
  OR2V2 WILD-TYPE                        18   171
D705V12, multiclass
                                  clus
vv                                 OR2V2 MUTATED OR2V2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = EIF2B5 MUTATION ANALYSIS
D706V1, survival
                  sevent
clus2                0   1
  EIF2B5 MUTATED    12   3
  EIF2B5 WILD-TYPE 265  75
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              15              340 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
               3               75 
$`EIF2B5 MUTATED`
TCGA-AA-3525 TCGA-AA-3713 TCGA-G4-6321 TCGA-AA-3542 TCGA-AA-3811 TCGA-AA-A00J 
        8.05        19.04        22.09        12.99        10.06        18.05 
TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CM-6170 
       34.98        33.01        58.39        49.41        12.10        15.02 
TCGA-CM-6675 TCGA-D5-6536 TCGA-G4-6307 
       13.05        17.85        55.04 

$`EIF2B5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6676 
       12.99        13.02        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
            8.05             0.00 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
           58.39           148.01 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
          18.050           22.225 
[1] "8.1 - 58.4 (18.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1"  
D706V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2B5 MUTATED         1        0        1         2         1         0
  EIF2B5 WILD-TYPE      63        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2B5 MUTATED           2          0          3          1        2
  EIF2B5 WILD-TYPE        16          6         41         32       33
                  vv
clus               STAGE IVA STAGE IVB
  EIF2B5 MUTATED           1         1
  EIF2B5 WILD-TYPE        11         0
D706V3, multiclass
            clus
vv           EIF2B5 MUTATED EIF2B5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               1               11
  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  10   3
  EIF2B5 WILD-TYPE   9  65 239  38
D706V4, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              3               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
  EIF2B5 MUTATED     6   6   3
  EIF2B5 WILD-TYPE 214  75  63
D706V5, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  N0              6              214
  N1              6               75
  N2              3               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"
D706V6, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED     9   4
  EIF2B5 WILD-TYPE 276  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED      9    4
  EIF2B5 WILD-TYPE  276   44
   clus
vv  EIF2B5 MUTATED EIF2B5 WILD-TYPE
  0              9              276
  1              4               44
[1] 2 2
[1] FALSE
D706V7, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED     7   8
  EIF2B5 WILD-TYPE 163 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED      7    8
  EIF2B5 WILD-TYPE  163  189
        clus
vv       EIF2B5 MUTATED EIF2B5 WILD-TYPE
  FEMALE              7              163
  MALE                8              189
[1] 2 2
[1] FALSE
D706V8, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED    14   1
  EIF2B5 WILD-TYPE 286   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED     14    1
  EIF2B5 WILD-TYPE  286    7
     clus
vv    EIF2B5 MUTATED EIF2B5 WILD-TYPE
  NO              14              286
  YES              1                7
[1] 2 2
[1] FALSE
D706V9, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED    14   1
  EIF2B5 WILD-TYPE 300  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED     14    1
  EIF2B5 WILD-TYPE  300   47
                               clus
vv                              EIF2B5 MUTATED EIF2B5 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF2B5 MUTATED    12   0   1   0
  EIF2B5 WILD-TYPE 247   3  21  21
D706V10, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              1               21
  RX              0               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"
D706V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2B5 MUTATED                                  0     0
  EIF2B5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF2B5 MUTATED                           3     6
  EIF2B5 WILD-TYPE                        16   170
D706V12, multiclass
                                  clus
vv                                 EIF2B5 MUTATED EIF2B5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         6              170
[1] 4 2
[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 = SR140 MUTATION ANALYSIS
D707V1, survival
                 sevent
clus2               0   1
  SR140 MUTATED     7   3
  SR140 WILD-TYPE 270  75
  SR140 MUTATED SR140 WILD-TYPE 
             10             345 
  SR140 MUTATED SR140 WILD-TYPE 
              3              75 
$`SR140 MUTATED`
TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-2671 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-A00N 
       25.08       100.01        43.76        24.39        19.66         4.01 
TCGA-AZ-4315 TCGA-CK-6747 TCGA-CM-6674 TCGA-DM-A1HB 
       58.39        82.95        12.95       135.65 

$`SR140 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SR140 MUTATED SR140 WILD-TYPE 
           4.01            0.00 
  SR140 MUTATED SR140 WILD-TYPE 
         135.65          148.01 
  SR140 MUTATED SR140 WILD-TYPE 
          34.42           21.99 
[1] "4.0 - 135.7 (34.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D707V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SR140 MUTATED         1        0        1         4         1         0
  SR140 WILD-TYPE      63        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SR140 MUTATED           0          0          2          1        1         0
  SR140 WILD-TYPE        18          6         42         32       34        12
                 vv
clus              STAGE IVB
  SR140 MUTATED           0
  SR140 WILD-TYPE         1
D707V3, multiclass
            clus
vv           SR140 MUTATED SR140 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  SR140 MUTATED     0   1   8   2
  SR140 WILD-TYPE   9  66 241  39
D707V4, multiclass
    clus
vv   SR140 MUTATED SR140 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             2              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
  SR140 MUTATED     7   3   1
  SR140 WILD-TYPE 213  78  65
D707V5, multiclass
    clus
vv   SR140 MUTATED SR140 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V6, binary
                 cls
clus                0   1
  SR140 MUTATED     8   1
  SR140 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SR140 MUTATED      8    1
  SR140 WILD-TYPE  277   47
   clus
vv  SR140 MUTATED SR140 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D707V7, binary
                 cls
clus                0   1
  SR140 MUTATED     2   9
  SR140 WILD-TYPE 168 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SR140 MUTATED      2    9
  SR140 WILD-TYPE  168  188
        clus
vv       SR140 MUTATED SR140 WILD-TYPE
  FEMALE             2             168
  MALE               9             188
[1] 2 2
[1] FALSE
D707V8, binary
                 cls
clus                0   1
  SR140 MUTATED     8   0
  SR140 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SR140 MUTATED      8    0
  SR140 WILD-TYPE  292    8
     clus
vv    SR140 MUTATED SR140 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D707V9, binary
                 cls
clus                0   1
  SR140 MUTATED     8   2
  SR140 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SR140 MUTATED      8    2
  SR140 WILD-TYPE  306   46
                               clus
vv                              SR140 MUTATED SR140 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SR140 MUTATED     7   0   0   1
  SR140 WILD-TYPE 252   3  22  20
D707V10, multiclass
    clus
vv   SR140 MUTATED SR140 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D707V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SR140 MUTATED                                  0     0
  SR140 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SR140 MUTATED                           0     9
  SR140 WILD-TYPE                        19   167
D707V12, multiclass
                                  clus
vv                                 SR140 MUTATED SR140 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(708) Variable = ABI3BP MUTATION ANALYSIS
D708V1, survival
                  sevent
clus2                0   1
  ABI3BP MUTATED    14   6
  ABI3BP WILD-TYPE 263  72
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              20              335 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
               6               72 
$`ABI3BP MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-6654 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
      100.01        35.80        23.87        25.02         4.01        34.98 
TCGA-AA-A01R TCGA-AY-4071 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5344 
       35.01         0.95        49.41        12.76        13.02        22.03 
TCGA-CM-6164 TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A0XF TCGA-F4-6570 
       29.03        17.85         9.04        13.41        38.20         6.18 
TCGA-G4-6307 TCGA-G4-6317 
       55.04        36.00 

$`ABI3BP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       27.42        26.47        14.50        27.09        16.31        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       25.02        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        13.78        46.75 

  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           21.990 
[1] "0.9 - 100.0 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D708V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABI3BP MUTATED         1        0        2         7         2         0
  ABI3BP WILD-TYPE      63        1       24       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABI3BP MUTATED           1          0          4          2        1
  ABI3BP WILD-TYPE        17          6         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ABI3BP MUTATED           0         0
  ABI3BP WILD-TYPE        12         1
D708V3, multiclass
            clus
vv           ABI3BP MUTATED ABI3BP WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  ABI3BP MUTATED     1   1  16   3
  ABI3BP WILD-TYPE   8  66 233  38
D708V4, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  T1              1                8
  T2              1               66
  T3             16              233
  T4              3               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
  ABI3BP MUTATED    13   5   3
  ABI3BP WILD-TYPE 207  76  63
D708V5, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  N0             13              207
  N1              5               76
  N2              3               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"
D708V6, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    16   1
  ABI3BP WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     16    1
  ABI3BP WILD-TYPE  269   47
   clus
vv  ABI3BP MUTATED ABI3BP WILD-TYPE
  0             16              269
  1              1               47
[1] 2 2
[1] FALSE
D708V7, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    13   8
  ABI3BP WILD-TYPE 157 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     13    8
  ABI3BP WILD-TYPE  157  189
        clus
vv       ABI3BP MUTATED ABI3BP WILD-TYPE
  FEMALE             13              157
  MALE                8              189
[1] 2 2
[1] FALSE
D708V8, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    16   2
  ABI3BP WILD-TYPE 284   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     16    2
  ABI3BP WILD-TYPE  284    6
     clus
vv    ABI3BP MUTATED ABI3BP WILD-TYPE
  NO              16              284
  YES              2                6
[1] 2 2
[1] FALSE
D708V9, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    16   3
  ABI3BP WILD-TYPE 298  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     16    3
  ABI3BP WILD-TYPE  298   45
                               clus
vv                              ABI3BP MUTATED ABI3BP WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ABI3BP MUTATED    15   0   0   1
  ABI3BP WILD-TYPE 244   3  22  20
D708V10, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              1               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"
D708V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABI3BP MUTATED                                  0     1
  ABI3BP WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ABI3BP MUTATED                           1    14
  ABI3BP WILD-TYPE                        18   162
D708V12, multiclass
                                  clus
vv                                 ABI3BP MUTATED ABI3BP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        14              162
[1] 4 2
[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 = FBN2 MUTATION ANALYSIS
D709V1, survival
                sevent
clus2              0   1
  FBN2 MUTATED    30  12
  FBN2 WILD-TYPE 247  66
  FBN2 MUTATED FBN2 WILD-TYPE 
            42            313 
  FBN2 MUTATED FBN2 WILD-TYPE 
            12             66 
$`FBN2 MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       14.53        24.16        13.02         0.99        13.02        17.95 
TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 
      100.01        22.09        26.17        32.75        22.06        24.39 
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 
       63.98        29.95        53.00        33.01         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01Q TCGA-AA-A01V TCGA-AA-A03F 
        4.01        34.98        12.00         1.02         1.02        18.05 
TCGA-AD-5900 TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       12.16         0.95         0.20        58.39        12.76        10.06 
TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-6169 TCGA-CM-6674 TCGA-D5-6898 TCGA-D5-6928 
       21.99       124.27        13.02        12.95         7.53        11.64 
TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6315 
       38.20        35.97        31.96         6.18         1.55        61.91 

$`FBN2 WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       24.33         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       19.07        34.03        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      106.75         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02        33.04        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-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       27.42        26.47        14.50        27.09        16.31        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       15.62        51.32        21.14        82.95         2.01        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        14.04        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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-A28C 
        7.50        44.32       131.51       135.65       139.17        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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  FBN2 MUTATED FBN2 WILD-TYPE 
           0.2            0.0 
  FBN2 MUTATED FBN2 WILD-TYPE 
        124.27         148.01 
  FBN2 MUTATED FBN2 WILD-TYPE 
         18.00          22.42 
[1] "0.2 - 124.3 (18.0)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.5"
D709V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBN2 MUTATED         7        0        4        15         4         0
  FBN2 WILD-TYPE      57        1       22        93         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBN2 MUTATED           3          0          4          4        1         0
  FBN2 WILD-TYPE        15          6         40         29       34        12
                vv
clus             STAGE IVB
  FBN2 MUTATED           0
  FBN2 WILD-TYPE         1
D709V3, multiclass
            clus
vv           FBN2 MUTATED FBN2 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            15             93
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            4             29
  STAGE IV              1             34
  STAGE IVA             0             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
  FBN2 MUTATED     1   8  30   4
  FBN2 WILD-TYPE   8  59 219  37
D709V4, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  T1            1              8
  T2            8             59
  T3           30            219
  T4            4             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
  FBN2 MUTATED    31   6   6
  FBN2 WILD-TYPE 189  75  60
D709V5, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  N0           31            189
  N1            6             75
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V6, binary
                cls
clus               0   1
  FBN2 MUTATED    34   1
  FBN2 WILD-TYPE 251  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     34    1
  FBN2 WILD-TYPE  251   47
   clus
vv  FBN2 MUTATED FBN2 WILD-TYPE
  0           34            251
  1            1             47
[1] 2 2
[1] FALSE
D709V7, binary
                cls
clus               0   1
  FBN2 MUTATED    19  24
  FBN2 WILD-TYPE 151 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     19   24
  FBN2 WILD-TYPE  151  173
        clus
vv       FBN2 MUTATED FBN2 WILD-TYPE
  FEMALE           19            151
  MALE             24            173
[1] 2 2
[1] FALSE
D709V8, binary
                cls
clus               0   1
  FBN2 MUTATED    33   0
  FBN2 WILD-TYPE 267   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     33    0
  FBN2 WILD-TYPE  267    8
     clus
vv    FBN2 MUTATED FBN2 WILD-TYPE
  NO            33            267
  YES            0              8
[1] 2 2
[1] FALSE
D709V9, binary
                cls
clus               0   1
  FBN2 MUTATED    26  15
  FBN2 WILD-TYPE 288  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     26   15
  FBN2 WILD-TYPE  288   33
                               clus
vv                              FBN2 MUTATED FBN2 WILD-TYPE
  COLON ADENOCARCINOMA                    26            288
  COLON MUCINOUS ADENOCARCINOMA           15             33
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FBN2 MUTATED    30   0   0   4
  FBN2 WILD-TYPE 229   3  22  17
D709V10, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  R0           30            229
  R1            0              3
  R2            0             22
  RX            4             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"
D709V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBN2 MUTATED                                  1     2
  FBN2 WILD-TYPE                                0     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FBN2 MUTATED                           1    22
  FBN2 WILD-TYPE                        18   154
D709V12, multiclass
                                  clus
vv                                 FBN2 MUTATED FBN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      22            154
[1] 4 2
[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 = FAM98B MUTATION ANALYSIS
D710V1, survival
                  sevent
clus2                0   1
  FAM98B MUTATED     4   0
  FAM98B WILD-TYPE 273  78
  FAM98B MUTATED FAM98B WILD-TYPE 
               4              351 
  FAM98B MUTATED FAM98B WILD-TYPE 
               0               78 
$`FAM98B MUTATED`
TCGA-AA-3977 TCGA-CK-4947 TCGA-CM-6674 TCGA-D5-6923 
       25.02        17.56        12.95        12.43 

$`FAM98B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FAM98B MUTATED FAM98B WILD-TYPE 
           12.43             0.00 
  FAM98B MUTATED FAM98B WILD-TYPE 
           25.02           148.01 
  FAM98B MUTATED FAM98B WILD-TYPE 
          15.255           22.090 
[1] "12.4 - 25.0 (15.3)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D710V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM98B MUTATED         1        0        0         1         0         0
  FAM98B WILD-TYPE      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM98B MUTATED           0          0          1          0        0
  FAM98B WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM98B MUTATED           0         0
  FAM98B WILD-TYPE        12         1
D710V3, multiclass
            clus
vv           FAM98B MUTATED FAM98B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  FAM98B MUTATED     0   2   1   1
  FAM98B WILD-TYPE   9  65 248  40
D710V4, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  T1              0                9
  T2              2               65
  T3              1              248
  T4              1               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
  FAM98B MUTATED     3   1   0
  FAM98B WILD-TYPE 217  80  66
D710V5, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  N0              3              217
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V6, binary
                  cls
clus                 0   1
  FAM98B MUTATED     3   0
  FAM98B WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      3    0
  FAM98B WILD-TYPE  282   48
   clus
vv  FAM98B MUTATED FAM98B WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D710V7, binary
                  cls
clus                 0   1
  FAM98B MUTATED     1   3
  FAM98B WILD-TYPE 169 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      1    3
  FAM98B WILD-TYPE  169  194
        clus
vv       FAM98B MUTATED FAM98B WILD-TYPE
  FEMALE              1              169
  MALE                3              194
[1] 2 2
[1] FALSE
D710V8, binary
                  cls
clus                 0   1
  FAM98B MUTATED     4   0
  FAM98B WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      4    0
  FAM98B WILD-TYPE  296    8
     clus
vv    FAM98B MUTATED FAM98B WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D710V9, binary
                  cls
clus                 0   1
  FAM98B MUTATED     4   0
  FAM98B WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      4    0
  FAM98B WILD-TYPE  310   48
                               clus
vv                              FAM98B MUTATED FAM98B WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM98B MUTATED     2   0   0   1
  FAM98B WILD-TYPE 257   3  22  20
D710V10, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              1               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"
D710V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM98B MUTATED                                  0     0
  FAM98B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM98B MUTATED                           0     3
  FAM98B WILD-TYPE                        19   173
D710V12, multiclass
                                  clus
vv                                 FAM98B MUTATED FAM98B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = KDM5C MUTATION ANALYSIS
D711V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    16   4
  KDM5C WILD-TYPE 261  74
  KDM5C MUTATED KDM5C WILD-TYPE 
             20             335 
  KDM5C MUTATED KDM5C WILD-TYPE 
              4              74 
$`KDM5C MUTATED`
TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3979 TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3555 
       13.02        85.05        24.00        46.65        42.90        29.95 
TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-3977 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5861 
       26.99        33.01        25.02        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 
      133.18        53.62 

$`KDM5C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        79.69        43.76        43.76        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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       37.02        25.02        29.06        22.03        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38       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-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-F4-6854 
        1.55        34.42        41.42        43.04        33.67         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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KDM5C MUTATED KDM5C WILD-TYPE 
          10.26            0.00 
  KDM5C MUTATED KDM5C WILD-TYPE 
         133.18          148.01 
  KDM5C MUTATED KDM5C WILD-TYPE 
         26.005          21.990 
[1] "10.3 - 133.2 (26.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.6"
D711V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM5C MUTATED         1        0        1         7         4         0
  KDM5C WILD-TYPE      63        1       25       101         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM5C MUTATED           2          0          3          0        0         2
  KDM5C WILD-TYPE        16          6         41         33       35        10
                 vv
clus              STAGE IVB
  KDM5C MUTATED           0
  KDM5C WILD-TYPE         1
D711V3, multiclass
            clus
vv           KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              2              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
  KDM5C MUTATED     0   2  14   5
  KDM5C WILD-TYPE   9  65 235  36
D711V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1             0               9
  T2             2              65
  T3            14             235
  T4             5              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
  KDM5C MUTATED    14   6   1
  KDM5C WILD-TYPE 206  75  65
D711V5, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  N0            14             206
  N1             6              75
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    17   2
  KDM5C WILD-TYPE 268  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     17    2
  KDM5C WILD-TYPE  268   46
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            17             268
  1             2              46
[1] 2 2
[1] FALSE
D711V7, binary
                 cls
clus                0   1
  KDM5C MUTATED    15   6
  KDM5C WILD-TYPE 155 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     15    6
  KDM5C WILD-TYPE  155  191
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE            15             155
  MALE               6             191
[1] 2 2
[1] FALSE
D711V8, binary
                 cls
clus                0   1
  KDM5C MUTATED    18   0
  KDM5C WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     18    0
  KDM5C WILD-TYPE  282    8
     clus
vv    KDM5C MUTATED KDM5C WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D711V9, binary
                 cls
clus                0   1
  KDM5C MUTATED    16   5
  KDM5C WILD-TYPE 298  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     16    5
  KDM5C WILD-TYPE  298   43
                               clus
vv                              KDM5C MUTATED KDM5C WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM5C MUTATED    16   0   0   1
  KDM5C WILD-TYPE 243   3  22  20
D711V10, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             1              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"
D711V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5C MUTATED                                  0     0
  KDM5C WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED                           1    13
  KDM5C WILD-TYPE                        18   163
D711V12, multiclass
                                  clus
vv                                 KDM5C MUTATED KDM5C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       13             163
[1] 4 2
[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 = ARAP3 MUTATION ANALYSIS
D712V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED    13   6
  ARAP3 WILD-TYPE 264  72
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             19             336 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              6              72 
$`ARAP3 MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3518 
       19.04       100.01        35.80        26.17        79.69         1.02 
TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-3779 
        6.97        33.04        15.95         4.01        35.01        14.50 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6162 
       27.09        58.39        62.79        21.14        32.02        12.00 
TCGA-F4-6460 
       31.96 

$`ARAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        27.42        26.47        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6569 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           1.02            0.00 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
         100.01          148.01 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          27.09           22.01 
[1] "1.0 - 100.0 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D712V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARAP3 MUTATED         4        0        4         8         2         0
  ARAP3 WILD-TYPE      60        1       22       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARAP3 MUTATED           1          0          2          0        0         0
  ARAP3 WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  ARAP3 MUTATED           0
  ARAP3 WILD-TYPE         1
D712V3, multiclass
            clus
vv           ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ARAP3 MUTATED     1   3  15   2
  ARAP3 WILD-TYPE   8  64 234  39
D712V4, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            15             234
  T4             2              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
  ARAP3 MUTATED    18   2   1
  ARAP3 WILD-TYPE 202  79  65
D712V5, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  N0            18             202
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V6, binary
                 cls
clus                0   1
  ARAP3 MUTATED    18   0
  ARAP3 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     18    0
  ARAP3 WILD-TYPE  267   48
   clus
vv  ARAP3 MUTATED ARAP3 WILD-TYPE
  0            18             267
  1             0              48
[1] 2 2
[1] FALSE
D712V7, binary
                 cls
clus                0   1
  ARAP3 MUTATED    11  10
  ARAP3 WILD-TYPE 159 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     11   10
  ARAP3 WILD-TYPE  159  187
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  FEMALE            11             159
  MALE              10             187
[1] 2 2
[1] FALSE
D712V8, binary
                 cls
clus                0   1
  ARAP3 MUTATED    15   1
  ARAP3 WILD-TYPE 285   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     15    1
  ARAP3 WILD-TYPE  285    7
     clus
vv    ARAP3 MUTATED ARAP3 WILD-TYPE
  NO             15             285
  YES             1               7
[1] 2 2
[1] FALSE
D712V9, binary
                 cls
clus                0   1
  ARAP3 MUTATED    18   3
  ARAP3 WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     18    3
  ARAP3 WILD-TYPE  296   45
                               clus
vv                              ARAP3 MUTATED ARAP3 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ARAP3 MUTATED    16   0   0   3
  ARAP3 WILD-TYPE 243   3  22  18
D712V10, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             3              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"
D712V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARAP3 MUTATED                                  0     0
  ARAP3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARAP3 MUTATED                           0    14
  ARAP3 WILD-TYPE                        19   162
D712V12, multiclass
                                  clus
vv                                 ARAP3 MUTATED ARAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       14             162
[1] 4 2
[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 = CHRNA3 MUTATION ANALYSIS
D713V1, survival
                  sevent
clus2                0   1
  CHRNA3 MUTATED     6   4
  CHRNA3 WILD-TYPE 271  74
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              10              345 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
               4               74 
$`CHRNA3 MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-5659 TCGA-AA-3655 TCGA-AA-3811 TCGA-AZ-6598 
       10.88       100.01        30.44        61.02        10.06        49.41 
TCGA-CK-4952 TCGA-CM-5348 TCGA-F4-6808 TCGA-F4-6856 
       15.62        22.98        33.67        35.31 

$`CHRNA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       43.04        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
           10.06             0.00 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
          100.01           148.01 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
          32.055           21.990 
[1] "10.1 - 100.0 (32.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.4"
D713V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRNA3 MUTATED         3        0        3         0         0         0
  CHRNA3 WILD-TYPE      61        1       23       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNA3 MUTATED           1          0          1          1        0
  CHRNA3 WILD-TYPE        17          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  CHRNA3 MUTATED           0         0
  CHRNA3 WILD-TYPE        12         1
D713V3, multiclass
            clus
vv           CHRNA3 MUTATED CHRNA3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  CHRNA3 MUTATED     1   2   5   2
  CHRNA3 WILD-TYPE   8  65 244  39
D713V4, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              5              244
  T4              2               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
  CHRNA3 MUTATED     6   1   3
  CHRNA3 WILD-TYPE 214  80  63
D713V5, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              3               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"
D713V6, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     8   0
  CHRNA3 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      8    0
  CHRNA3 WILD-TYPE  277   48
   clus
vv  CHRNA3 MUTATED CHRNA3 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D713V7, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     4   6
  CHRNA3 WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      4    6
  CHRNA3 WILD-TYPE  166  191
        clus
vv       CHRNA3 MUTATED CHRNA3 WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D713V8, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     9   0
  CHRNA3 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      9    0
  CHRNA3 WILD-TYPE  291    8
     clus
vv    CHRNA3 MUTATED CHRNA3 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D713V9, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     8   2
  CHRNA3 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      8    2
  CHRNA3 WILD-TYPE  306   46
                               clus
vv                              CHRNA3 MUTATED CHRNA3 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHRNA3 MUTATED     6   0   0   1
  CHRNA3 WILD-TYPE 253   3  22  20
D713V10, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D713V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRNA3 MUTATED                                  0     0
  CHRNA3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHRNA3 MUTATED                           0     8
  CHRNA3 WILD-TYPE                        19   168
D713V12, multiclass
                                  clus
vv                                 CHRNA3 MUTATED CHRNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = FLT3 MUTATION ANALYSIS
D714V1, survival
                sevent
clus2              0   1
  FLT3 MUTATED    18   5
  FLT3 WILD-TYPE 259  73
  FLT3 MUTATED FLT3 WILD-TYPE 
            23            332 
  FLT3 MUTATED FLT3 WILD-TYPE 
             5             73 
$`FLT3 MUTATED`
TCGA-AA-3950 TCGA-AZ-6608 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3864 
       24.00         1.94        32.91        32.71         8.38        53.00 
TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6899 TCGA-AU-6004 TCGA-AY-5543 TCGA-CA-6717 
       34.98        14.01         5.79        27.09        33.01        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        10.13        12.43 
TCGA-D5-6927 TCGA-DM-A1D7 TCGA-G4-6293 TCGA-G4-6315 TCGA-G4-6323 
        9.44        13.32       133.18        61.91        13.78 

$`FLT3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39        14.30         9.04        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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 
       43.04        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-G4-6317 TCGA-G4-6626 
       36.00        46.75 

  FLT3 MUTATED FLT3 WILD-TYPE 
          1.94           0.00 
  FLT3 MUTATED FLT3 WILD-TYPE 
        133.18         148.01 
  FLT3 MUTATED FLT3 WILD-TYPE 
         14.04          22.09 
[1] "1.9 - 133.2 (14.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D714V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLT3 MUTATED         5        1        1         7         1         1
  FLT3 WILD-TYPE      59        0       25       101         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLT3 MUTATED           1          2          1          1        2         1
  FLT3 WILD-TYPE        17          4         43         32       33        11
                vv
clus             STAGE IVB
  FLT3 MUTATED           0
  FLT3 WILD-TYPE         1
D714V3, multiclass
            clus
vv           FLT3 MUTATED FLT3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              1              0
  STAGE II              1             25
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             1             17
  STAGE IIIA            2              4
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             1             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
  FLT3 MUTATED     0   6  13   4
  FLT3 WILD-TYPE   9  61 236  37
D714V4, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  T1            0              9
  T2            6             61
  T3           13            236
  T4            4             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
  FLT3 MUTATED    16   6   2
  FLT3 WILD-TYPE 204  75  64
D714V5, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  N0           16            204
  N1            6             75
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V6, binary
                cls
clus               0   1
  FLT3 MUTATED    18   3
  FLT3 WILD-TYPE 267  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     18    3
  FLT3 WILD-TYPE  267   45
   clus
vv  FLT3 MUTATED FLT3 WILD-TYPE
  0           18            267
  1            3             45
[1] 2 2
[1] FALSE
D714V7, binary
                cls
clus               0   1
  FLT3 MUTATED     8  16
  FLT3 WILD-TYPE 162 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED      8   16
  FLT3 WILD-TYPE  162  181
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  FEMALE            8            162
  MALE             16            181
[1] 2 2
[1] FALSE
D714V8, binary
                cls
clus               0   1
  FLT3 MUTATED    21   0
  FLT3 WILD-TYPE 279   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     21    0
  FLT3 WILD-TYPE  279    8
     clus
vv    FLT3 MUTATED FLT3 WILD-TYPE
  NO            21            279
  YES            0              8
[1] 2 2
[1] FALSE
D714V9, binary
                cls
clus               0   1
  FLT3 MUTATED    20   3
  FLT3 WILD-TYPE 294  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     20    3
  FLT3 WILD-TYPE  294   45
                               clus
vv                              FLT3 MUTATED FLT3 WILD-TYPE
  COLON ADENOCARCINOMA                    20            294
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FLT3 MUTATED    16   0   1   1
  FLT3 WILD-TYPE 243   3  21  20
D714V10, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            1             21
  RX            1             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"
D714V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLT3 MUTATED                                  0     1
  FLT3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLT3 MUTATED                           3    15
  FLT3 WILD-TYPE                        16   161
D714V12, multiclass
                                  clus
vv                                 FLT3 MUTATED FLT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      15            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(715) Variable = STX16 MUTATION ANALYSIS
D715V1, survival
                 sevent
clus2               0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 272  76
  STX16 MUTATED STX16 WILD-TYPE 
              7             348 
  STX16 MUTATED STX16 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        61.91        13.78        46.75 

  STX16 MUTATED STX16 WILD-TYPE 
             12               0 
  STX16 MUTATED STX16 WILD-TYPE 
          42.90          148.01 
  STX16 MUTATED STX16 WILD-TYPE 
         31.630          22.045 
[1] "12.0 - 42.9 (31.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D715V2, continuous
                 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      64        1       26       108         6         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        18          6         42         32       34        11
                 vv
clus              STAGE IVB
  STX16 MUTATED           0
  STX16 WILD-TYPE         1
D715V3, multiclass
            clus
vv           STX16 MUTATED STX16 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  STX16 MUTATED     0   0   5   2
  STX16 WILD-TYPE   9  67 244  39
D715V4, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             2              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
  STX16 MUTATED     2   3   2
  STX16 WILD-TYPE 218  78  64
D715V5, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  N0             2             218
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V6, binary
                 cls
clus                0   1
  STX16 MUTATED     4   2
  STX16 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      4    2
  STX16 WILD-TYPE  281   46
   clus
vv  STX16 MUTATED STX16 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D715V7, binary
                 cls
clus                0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 165 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      5    2
  STX16 WILD-TYPE  165  195
        clus
vv       STX16 MUTATED STX16 WILD-TYPE
  FEMALE             5             165
  MALE               2             195
[1] 2 2
[1] FALSE
D715V8, binary
                 cls
clus                0   1
  STX16 MUTATED     7   0
  STX16 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      7    0
  STX16 WILD-TYPE  293    8
     clus
vv    STX16 MUTATED STX16 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D715V9, binary
                 cls
clus                0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      5    2
  STX16 WILD-TYPE  309   46
                               clus
vv                              STX16 MUTATED STX16 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STX16 MUTATED     6   0   1   0
  STX16 WILD-TYPE 253   3  21  21
D715V10, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             0              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"
D715V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STX16 MUTATED                                  0     0
  STX16 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STX16 MUTATED                           1     4
  STX16 WILD-TYPE                        18   172
D715V12, multiclass
                                  clus
vv                                 STX16 MUTATED STX16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = ERBB2IP MUTATION ANALYSIS
D716V1, survival
                   sevent
clus2                 0   1
  ERBB2IP MUTATED    13   1
  ERBB2IP WILD-TYPE 264  77
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               14               341 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                1                77 
$`ERBB2IP MUTATED`
TCGA-G4-6628 TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3864 TCGA-AA-3977 
       79.69        25.08        63.98        61.02        53.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-6674 TCGA-CM-6677 
        4.01        34.98        27.09        12.76        12.95        11.08 
TCGA-DM-A1HA TCGA-F4-6856 
      131.51        35.31 

$`ERBB2IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C 
      140.38         7.50        44.32       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
             4.01              0.00 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           131.51            148.01 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           31.035            21.990 
[1] "4.0 - 131.5 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "4.5"
D716V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB2IP MUTATED         3        0        3         3         3         0
  ERBB2IP WILD-TYPE      61        1       23       105         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB2IP MUTATED           0          0          0          1        0
  ERBB2IP WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ERBB2IP MUTATED           1         0
  ERBB2IP WILD-TYPE        11         1
D716V3, multiclass
            clus
vv           ERBB2IP MUTATED ERBB2IP WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                3               105
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  ERBB2IP MUTATED     0   4   8   3
  ERBB2IP WILD-TYPE   9  63 241  38
D716V4, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               8               241
  T4               3                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
  ERBB2IP MUTATED    13   1   1
  ERBB2IP WILD-TYPE 207  80  65
D716V5, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  N0              13               207
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V6, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    12   1
  ERBB2IP WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     12    1
  ERBB2IP WILD-TYPE  273   47
   clus
vv  ERBB2IP MUTATED ERBB2IP WILD-TYPE
  0              12               273
  1               1                47
[1] 2 2
[1] FALSE
D716V7, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED     5  10
  ERBB2IP WILD-TYPE 165 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      5   10
  ERBB2IP WILD-TYPE  165  187
        clus
vv       ERBB2IP MUTATED ERBB2IP WILD-TYPE
  FEMALE               5               165
  MALE                10               187
[1] 2 2
[1] FALSE
D716V8, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    11   0
  ERBB2IP WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     11    0
  ERBB2IP WILD-TYPE  289    8
     clus
vv    ERBB2IP MUTATED ERBB2IP WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D716V9, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    12   3
  ERBB2IP WILD-TYPE 302  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     12    3
  ERBB2IP WILD-TYPE  302   45
                               clus
vv                              ERBB2IP MUTATED ERBB2IP WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ERBB2IP MUTATED    10   0   0   2
  ERBB2IP WILD-TYPE 249   3  22  19
D716V10, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               2                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"
D716V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2IP MUTATED                                  0     1
  ERBB2IP WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ERBB2IP MUTATED                           0     8
  ERBB2IP WILD-TYPE                        19   168
D716V12, multiclass
                                  clus
vv                                 ERBB2IP MUTATED ERBB2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          8               168
[1] 4 2
[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 = RNF145 MUTATION ANALYSIS
D717V1, survival
                  sevent
clus2                0   1
  RNF145 MUTATED    10   3
  RNF145 WILD-TYPE 267  75
  RNF145 MUTATED RNF145 WILD-TYPE 
              13              342 
  RNF145 MUTATED RNF145 WILD-TYPE 
               3               75 
$`RNF145 MUTATED`
TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6628 TCGA-AA-3510 TCGA-AZ-4315 
       24.00        10.88       100.01        79.69        63.98        58.39 
TCGA-AZ-6598 TCGA-CM-5348 TCGA-CM-6162 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-F4-6569 
       49.41        22.98        12.00       140.38       131.51        35.74 
TCGA-F4-6856 
       35.31 

$`RNF145 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A1HB 
       49.91        13.32        12.59         7.50        44.32       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RNF145 MUTATED RNF145 WILD-TYPE 
           10.88             0.00 
  RNF145 MUTATED RNF145 WILD-TYPE 
          140.38           148.01 
  RNF145 MUTATED RNF145 WILD-TYPE 
           49.41            21.99 
[1] "10.9 - 140.4 (49.4)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.9"
D717V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF145 MUTATED         3        0        4         3         0         0
  RNF145 WILD-TYPE      61        1       22       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF145 MUTATED           0          0          2          1        0
  RNF145 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF145 MUTATED           0         0
  RNF145 WILD-TYPE        12         1
D717V3, multiclass
            clus
vv           RNF145 MUTATED RNF145 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  RNF145 MUTATED     0   3   9   2
  RNF145 WILD-TYPE   9  64 240  39
D717V4, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              9              240
  T4              2               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
  RNF145 MUTATED    10   2   2
  RNF145 WILD-TYPE 210  79  64
D717V5, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  N0             10              210
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V6, binary
                  cls
clus                 0   1
  RNF145 MUTATED    12   0
  RNF145 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     12    0
  RNF145 WILD-TYPE  273   48
   clus
vv  RNF145 MUTATED RNF145 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D717V7, binary
                  cls
clus                 0   1
  RNF145 MUTATED     5   9
  RNF145 WILD-TYPE 165 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED      5    9
  RNF145 WILD-TYPE  165  188
        clus
vv       RNF145 MUTATED RNF145 WILD-TYPE
  FEMALE              5              165
  MALE                9              188
[1] 2 2
[1] FALSE
D717V8, binary
                  cls
clus                 0   1
  RNF145 MUTATED    11   0
  RNF145 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     11    0
  RNF145 WILD-TYPE  289    8
     clus
vv    RNF145 MUTATED RNF145 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D717V9, binary
                  cls
clus                 0   1
  RNF145 MUTATED    11   3
  RNF145 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     11    3
  RNF145 WILD-TYPE  303   45
                               clus
vv                              RNF145 MUTATED RNF145 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF145 MUTATED     9   0   0   0
  RNF145 WILD-TYPE 250   3  22  21
D717V10, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D717V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF145 MUTATED                                  0     0
  RNF145 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF145 MUTATED                           0    11
  RNF145 WILD-TYPE                        19   165
D717V12, multiclass
                                  clus
vv                                 RNF145 MUTATED RNF145 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        11              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(718) Variable = KTN1 MUTATION ANALYSIS
D718V1, survival
                sevent
clus2              0   1
  KTN1 MUTATED    14   3
  KTN1 WILD-TYPE 263  75
  KTN1 MUTATED KTN1 WILD-TYPE 
            17            338 
  KTN1 MUTATED KTN1 WILD-TYPE 
             3             75 
$`KTN1 MUTATED`
TCGA-AD-6895 TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3518 
       25.08        46.65        33.53        23.61        22.06         1.02 
TCGA-AA-3947 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-4315 
       33.01        30.02         4.01        35.01        83.24        58.39 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6540 TCGA-F4-6703 TCGA-G4-6303 
       12.00        14.04        16.14        47.87        65.85 

$`KTN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        29.19        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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KTN1 MUTATED KTN1 WILD-TYPE 
          1.02           0.00 
  KTN1 MUTATED KTN1 WILD-TYPE 
         83.24         148.01 
  KTN1 MUTATED KTN1 WILD-TYPE 
         30.02          21.99 
[1] "1.0 - 83.2 (30.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D718V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KTN1 MUTATED         2        0        0         7         2         0
  KTN1 WILD-TYPE      62        1       26       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KTN1 MUTATED           2          0          3          0        1         1
  KTN1 WILD-TYPE        16          6         41         33       34        11
                vv
clus             STAGE IVB
  KTN1 MUTATED           0
  KTN1 WILD-TYPE         1
D718V3, multiclass
            clus
vv           KTN1 MUTATED KTN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  KTN1 MUTATED     0   2  14   2
  KTN1 WILD-TYPE   9  65 235  39
D718V4, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           14            235
  T4            2             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
  KTN1 MUTATED    11   4   3
  KTN1 WILD-TYPE 209  77  63
D718V5, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  N0           11            209
  N1            4             77
  N2            3             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"
D718V6, binary
                cls
clus               0   1
  KTN1 MUTATED    16   2
  KTN1 WILD-TYPE 269  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     16    2
  KTN1 WILD-TYPE  269   46
   clus
vv  KTN1 MUTATED KTN1 WILD-TYPE
  0           16            269
  1            2             46
[1] 2 2
[1] FALSE
D718V7, binary
                cls
clus               0   1
  KTN1 MUTATED     8  10
  KTN1 WILD-TYPE 162 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED      8   10
  KTN1 WILD-TYPE  162  187
        clus
vv       KTN1 MUTATED KTN1 WILD-TYPE
  FEMALE            8            162
  MALE             10            187
[1] 2 2
[1] FALSE
D718V8, binary
                cls
clus               0   1
  KTN1 MUTATED    14   1
  KTN1 WILD-TYPE 286   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     14    1
  KTN1 WILD-TYPE  286    7
     clus
vv    KTN1 MUTATED KTN1 WILD-TYPE
  NO            14            286
  YES            1              7
[1] 2 2
[1] FALSE
D718V9, binary
                cls
clus               0   1
  KTN1 MUTATED    13   5
  KTN1 WILD-TYPE 301  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     13    5
  KTN1 WILD-TYPE  301   43
                               clus
vv                              KTN1 MUTATED KTN1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KTN1 MUTATED    17   0   0   0
  KTN1 WILD-TYPE 242   3  22  21
D718V10, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  R0           17            242
  R1            0              3
  R2            0             22
  RX            0             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"
D718V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KTN1 MUTATED                                  0     1
  KTN1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KTN1 MUTATED                           1    10
  KTN1 WILD-TYPE                        18   166
D718V12, multiclass
                                  clus
vv                                 KTN1 MUTATED KTN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(719) Variable = NIPBL MUTATION ANALYSIS
D719V1, survival
                 sevent
clus2               0   1
  NIPBL MUTATED    24   7
  NIPBL WILD-TYPE 253  71
  NIPBL MUTATED NIPBL WILD-TYPE 
             31             324 
  NIPBL MUTATED NIPBL WILD-TYPE 
              7              71 
$`NIPBL MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-2672 TCGA-A6-5659 
        0.92        19.04        25.08       100.01        46.65        30.44 
TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 
       29.19        22.06        20.12        19.66        63.98         6.97 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01R 
       26.99        10.06        31.00        33.01        34.98        35.01 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5868 
       58.39         5.13        12.10        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        12.39        35.97        53.62        85.48 
TCGA-G4-6315 
       61.91 

$`NIPBL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        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-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3812 
       15.02        11.01         5.98        37.05         5.03        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6163 
       15.02         5.03        15.02        15.02        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       65.85        44.68        55.04        36.00        13.78        46.75 

  NIPBL MUTATED NIPBL WILD-TYPE 
           0.92            0.00 
  NIPBL MUTATED NIPBL WILD-TYPE 
         100.01          148.01 
  NIPBL MUTATED NIPBL WILD-TYPE 
          25.08           22.01 
[1] "0.9 - 100.0 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D719V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NIPBL MUTATED         2        0        4         8         3         0
  NIPBL WILD-TYPE      62        1       22       100         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NIPBL MUTATED           3          0          5          2        3         1
  NIPBL WILD-TYPE        15          6         39         31       32        11
                 vv
clus              STAGE IVB
  NIPBL MUTATED           0
  NIPBL WILD-TYPE         1
D719V3, multiclass
            clus
vv           NIPBL MUTATED NIPBL WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              1              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
  NIPBL MUTATED     1   1  24   6
  NIPBL WILD-TYPE   8  66 225  35
D719V4, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  T1             1               8
  T2             1              66
  T3            24             225
  T4             6              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
  NIPBL MUTATED    18  10   4
  NIPBL WILD-TYPE 202  71  62
D719V5, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  N0            18             202
  N1            10              71
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V6, binary
                 cls
clus                0   1
  NIPBL MUTATED    26   4
  NIPBL WILD-TYPE 259  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     26    4
  NIPBL WILD-TYPE  259   44
   clus
vv  NIPBL MUTATED NIPBL WILD-TYPE
  0            26             259
  1             4              44
[1] 2 2
[1] FALSE
D719V7, binary
                 cls
clus                0   1
  NIPBL MUTATED    16  16
  NIPBL WILD-TYPE 154 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     16   16
  NIPBL WILD-TYPE  154  181
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  FEMALE            16             154
  MALE              16             181
[1] 2 2
[1] FALSE
D719V8, binary
                 cls
clus                0   1
  NIPBL MUTATED    29   1
  NIPBL WILD-TYPE 271   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     29    1
  NIPBL WILD-TYPE  271    7
     clus
vv    NIPBL MUTATED NIPBL WILD-TYPE
  NO             29             271
  YES             1               7
[1] 2 2
[1] FALSE
D719V9, binary
                 cls
clus                0   1
  NIPBL MUTATED    25   7
  NIPBL WILD-TYPE 289  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     25    7
  NIPBL WILD-TYPE  289   41
                               clus
vv                              NIPBL MUTATED NIPBL WILD-TYPE
  COLON ADENOCARCINOMA                     25             289
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NIPBL MUTATED    24   0   0   2
  NIPBL WILD-TYPE 235   3  22  19
D719V10, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  R0            24             235
  R1             0               3
  R2             0              22
  RX             2              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"
D719V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPBL MUTATED                                  0     2
  NIPBL WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NIPBL MUTATED                           3    16
  NIPBL WILD-TYPE                        16   160
D719V12, multiclass
                                  clus
vv                                 NIPBL MUTATED NIPBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       16             160
[1] 4 2
[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 = DOCK1 MUTATION ANALYSIS
D720V1, survival
                 sevent
clus2               0   1
  DOCK1 MUTATED    18   5
  DOCK1 WILD-TYPE 259  73
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             23             332 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
              5              73 
$`DOCK1 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3660 TCGA-AA-3664 
       19.04        24.00        26.17        33.53        78.08        54.02 
TCGA-AA-A004 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 TCGA-AY-6196 
       13.94        34.98        12.16        83.24        14.50         0.20 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6166 
       58.39        12.76       148.01        23.05        37.02        21.99 
TCGA-CM-6171 TCGA-D5-6537 TCGA-DM-A0XD TCGA-F4-6570 TCGA-G4-6307 
       14.04         4.80        24.43         6.18        55.04 

$`DOCK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02         6.97         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14        82.95         2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DOCK1 MUTATED DOCK1 WILD-TYPE 
            0.2             0.0 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
         148.01          140.38 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
          24.00           22.01 
[1] "0.2 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D720V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK1 MUTATED         4        0        3        12         1         0
  DOCK1 WILD-TYPE      60        1       23        96         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK1 MUTATED           1          0          2          1        0         0
  DOCK1 WILD-TYPE        17          6         42         32       35        12
                 vv
clus              STAGE IVB
  DOCK1 MUTATED           0
  DOCK1 WILD-TYPE         1
D720V3, multiclass
            clus
vv           DOCK1 MUTATED DOCK1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             12              96
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  DOCK1 MUTATED     0   4  19   1
  DOCK1 WILD-TYPE   9  63 230  40
D720V4, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            19             230
  T4             1              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
  DOCK1 MUTATED    20   3   1
  DOCK1 WILD-TYPE 200  78  65
D720V5, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  N0            20             200
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V6, binary
                 cls
clus                0   1
  DOCK1 MUTATED    21   0
  DOCK1 WILD-TYPE 264  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     21    0
  DOCK1 WILD-TYPE  264   48
   clus
vv  DOCK1 MUTATED DOCK1 WILD-TYPE
  0            21             264
  1             0              48
[1] 2 2
[1] FALSE
D720V7, binary
                 cls
clus                0   1
  DOCK1 MUTATED    13  11
  DOCK1 WILD-TYPE 157 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     13   11
  DOCK1 WILD-TYPE  157  186
        clus
vv       DOCK1 MUTATED DOCK1 WILD-TYPE
  FEMALE            13             157
  MALE              11             186
[1] 2 2
[1] FALSE
D720V8, binary
                 cls
clus                0   1
  DOCK1 MUTATED    21   0
  DOCK1 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     21    0
  DOCK1 WILD-TYPE  279    8
     clus
vv    DOCK1 MUTATED DOCK1 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D720V9, binary
                 cls
clus                0   1
  DOCK1 MUTATED    20   4
  DOCK1 WILD-TYPE 294  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     20    4
  DOCK1 WILD-TYPE  294   44
                               clus
vv                              DOCK1 MUTATED DOCK1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK1 MUTATED    22   0   0   1
  DOCK1 WILD-TYPE 237   3  22  20
D720V10, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  R0            22             237
  R1             0               3
  R2             0              22
  RX             1              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"
D720V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK1 MUTATED                                  0     2
  DOCK1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK1 MUTATED                           2    13
  DOCK1 WILD-TYPE                        17   163
D720V12, multiclass
                                  clus
vv                                 DOCK1 MUTATED DOCK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       13             163
[1] 4 2
[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 = CDH8 MUTATION ANALYSIS
D721V1, survival
                sevent
clus2              0   1
  CDH8 MUTATED    27   4
  CDH8 WILD-TYPE 250  74
  CDH8 MUTATED CDH8 WILD-TYPE 
            31            324 
  CDH8 MUTATED CDH8 WILD-TYPE 
             4             74 
$`CDH8 MUTATED`
TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AZ-6608 TCGA-G4-6628 
        8.05         6.05         0.92        85.05         1.94        79.69 
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3664 TCGA-AA-3864 
       24.39        63.98         6.97         1.02        54.02        53.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-4315 
       25.02         4.01         0.99         1.02        27.09        58.39 
TCGA-AZ-4682 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-4743 
       22.36        12.76        17.56       148.01        15.62        23.05 
TCGA-CM-5861 TCGA-CM-6679 TCGA-CM-6680 TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6703 
       15.02        10.06        12.03       117.07         6.18        47.87 
TCGA-G4-6315 
       61.91 

$`CDH8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75       100.01        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 
       63.62        22.09        35.80        26.17        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        3.02        35.01        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        62.79        88.21        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       14.30        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  CDH8 MUTATED CDH8 WILD-TYPE 
          0.92           0.00 
  CDH8 MUTATED CDH8 WILD-TYPE 
        148.01         140.38 
  CDH8 MUTATED CDH8 WILD-TYPE 
        17.560         22.075 
[1] "0.9 - 148.0 (17.6)" "0.0 - 140.4 (22.1)"
[1] "hr=" "2.1"
D721V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH8 MUTATED         5        0        6         7         2         0
  CDH8 WILD-TYPE      59        1       20       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH8 MUTATED           2          1          3          2        3         1
  CDH8 WILD-TYPE        16          5         41         31       32        11
                vv
clus             STAGE IVB
  CDH8 MUTATED           0
  CDH8 WILD-TYPE         1
D721V3, multiclass
            clus
vv           CDH8 MUTATED CDH8 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            2             31
  STAGE IV              3             32
  STAGE IVA             1             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
  CDH8 MUTATED     0   7  20   6
  CDH8 WILD-TYPE   9  60 229  35
D721V4, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  T1            0              9
  T2            7             60
  T3           20            229
  T4            6             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
  CDH8 MUTATED    22   6   5
  CDH8 WILD-TYPE 198  75  61
D721V5, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  N0           22            198
  N1            6             75
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V6, binary
                cls
clus               0   1
  CDH8 MUTATED    27   4
  CDH8 WILD-TYPE 258  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     27    4
  CDH8 WILD-TYPE  258   44
   clus
vv  CDH8 MUTATED CDH8 WILD-TYPE
  0           27            258
  1            4             44
[1] 2 2
[1] FALSE
D721V7, binary
                cls
clus               0   1
  CDH8 MUTATED    16  17
  CDH8 WILD-TYPE 154 180
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     16   17
  CDH8 WILD-TYPE  154  180
        clus
vv       CDH8 MUTATED CDH8 WILD-TYPE
  FEMALE           16            154
  MALE             17            180
[1] 2 2
[1] FALSE
D721V8, binary
                cls
clus               0   1
  CDH8 MUTATED    25   0
  CDH8 WILD-TYPE 275   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     25    0
  CDH8 WILD-TYPE  275    8
     clus
vv    CDH8 MUTATED CDH8 WILD-TYPE
  NO            25            275
  YES            0              8
[1] 2 2
[1] FALSE
D721V9, binary
                cls
clus               0   1
  CDH8 MUTATED    30   3
  CDH8 WILD-TYPE 284  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     30    3
  CDH8 WILD-TYPE  284   45
                               clus
vv                              CDH8 MUTATED CDH8 WILD-TYPE
  COLON ADENOCARCINOMA                    30            284
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDH8 MUTATED    23   0   2   4
  CDH8 WILD-TYPE 236   3  20  17
D721V10, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  R0           23            236
  R1            0              3
  R2            2             20
  RX            4             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"
D721V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH8 MUTATED                                  0     1
  CDH8 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDH8 MUTATED                           0    18
  CDH8 WILD-TYPE                        19   158
D721V12, multiclass
                                  clus
vv                                 CDH8 MUTATED CDH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      18            158
[1] 4 2
[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 = POLDIP3 MUTATION ANALYSIS
D722V1, survival
                   sevent
clus2                 0   1
  POLDIP3 MUTATED     2   3
  POLDIP3 WILD-TYPE 275  75
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                5               350 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                3                75 
$`POLDIP3 MUTATED`
TCGA-AA-3811 TCGA-AA-3949 TCGA-AA-A01R TCGA-AD-6889 TCGA-F4-6570 
       10.06        26.01        35.01        83.24         6.18 

$`POLDIP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
             6.18              0.00 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
            83.24            148.01 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
           26.010            22.045 
[1] "6.2 - 83.2 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D722V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLDIP3 MUTATED         0        0        0         2         0         0
  POLDIP3 WILD-TYPE      64        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POLDIP3 MUTATED           2          0          1          0        0
  POLDIP3 WILD-TYPE        16          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  POLDIP3 MUTATED           0         0
  POLDIP3 WILD-TYPE        12         1
D722V3, multiclass
            clus
vv           POLDIP3 MUTATED POLDIP3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  POLDIP3 MUTATED     0   0   5   0
  POLDIP3 WILD-TYPE   9  67 244  41
D722V4, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  POLDIP3 MUTATED     2   1   2
  POLDIP3 WILD-TYPE 218  80  64
D722V5, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  N0               2               218
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V6, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     5   0
  POLDIP3 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      5    0
  POLDIP3 WILD-TYPE  280   48
   clus
vv  POLDIP3 MUTATED POLDIP3 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D722V7, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     3   2
  POLDIP3 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      3    2
  POLDIP3 WILD-TYPE  167  195
        clus
vv       POLDIP3 MUTATED POLDIP3 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D722V8, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     4   1
  POLDIP3 WILD-TYPE 296   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      4    1
  POLDIP3 WILD-TYPE  296    7
     clus
vv    POLDIP3 MUTATED POLDIP3 WILD-TYPE
  NO                4               296
  YES               1                 7
[1] 2 2
[1] FALSE
D722V9, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     3   2
  POLDIP3 WILD-TYPE 311  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      3    2
  POLDIP3 WILD-TYPE  311   46
                               clus
vv                              POLDIP3 MUTATED POLDIP3 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  POLDIP3 MUTATED     5   0   0   0
  POLDIP3 WILD-TYPE 254   3  22  21
D722V10, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D722V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLDIP3 MUTATED                                  0     1
  POLDIP3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  POLDIP3 MUTATED                           0     1
  POLDIP3 WILD-TYPE                        19   175
D722V12, multiclass
[1] "Remove cluster labels:" "POLDIP3 MUTATED"       
clus
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6890        TCGA-AD-6899 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965        TCGA-AU-3779 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"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-5913        TCGA-CK-5914        TCGA-CK-5915 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6703 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 

Clustering(723) Variable = KLRC3 MUTATION ANALYSIS
D723V1, survival
                 sevent
clus2               0   1
  KLRC3 MUTATED     4   1
  KLRC3 WILD-TYPE 273  77
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              5             350 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              1              77 
$`KLRC3 MUTATED`
TCGA-AA-3845 TCGA-D5-6931 TCGA-DM-A28K TCGA-F4-6704 TCGA-G4-6309 
        0.00        12.00        98.24         1.55        85.48 

$`KLRC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KLRC3 MUTATED KLRC3 WILD-TYPE 
              0               0 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
          98.24          148.01 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
         12.000          22.075 
[1] "0.0 - 98.2 (12.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D723V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLRC3 MUTATED         0        0        0         2         0         0
  KLRC3 WILD-TYPE      64        1       26       106         8         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        18          6         43         31       35        12
                 vv
clus              STAGE IVB
  KLRC3 MUTATED           0
  KLRC3 WILD-TYPE         1
D723V3, multiclass
            clus
vv           KLRC3 MUTATED KLRC3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  KLRC3 MUTATED     0   0   4   1
  KLRC3 WILD-TYPE   9  67 245  40
D723V4, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  KLRC3 MUTATED     2   1   2
  KLRC3 WILD-TYPE 218  80  64
D723V5, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  N0             2             218
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V6, binary
                 cls
clus                0   1
  KLRC3 MUTATED     4   0
  KLRC3 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      4    0
  KLRC3 WILD-TYPE  281   48
   clus
vv  KLRC3 MUTATED KLRC3 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D723V7, binary
                 cls
clus                0   1
  KLRC3 MUTATED     2   3
  KLRC3 WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      2    3
  KLRC3 WILD-TYPE  168  194
        clus
vv       KLRC3 MUTATED KLRC3 WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D723V8, binary
                 cls
clus                0   1
  KLRC3 MUTATED     2   0
  KLRC3 WILD-TYPE 298   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      2    0
  KLRC3 WILD-TYPE  298    8
     clus
vv    KLRC3 MUTATED KLRC3 WILD-TYPE
  NO              2             298
  YES             0               8
[1] 2 2
[1] FALSE
D723V9, binary
                 cls
clus                0   1
  KLRC3 MUTATED     3   2
  KLRC3 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      3    2
  KLRC3 WILD-TYPE  311   46
                               clus
vv                              KLRC3 MUTATED KLRC3 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLRC3 MUTATED     4   0   0   0
  KLRC3 WILD-TYPE 255   3  22  21
D723V10, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D723V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLRC3 MUTATED                                  1     0
  KLRC3 WILD-TYPE                                0    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLRC3 MUTATED                           1     2
  KLRC3 WILD-TYPE                        18   174
D723V12, multiclass
                                  clus
vv                                 KLRC3 MUTATED KLRC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(724) Variable = ARMC9 MUTATION ANALYSIS
D724V1, survival
                 sevent
clus2               0   1
  ARMC9 MUTATED     4   3
  ARMC9 WILD-TYPE 273  75
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              7             348 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              3              75 
$`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 
       65.85 

$`ARMC9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       24.00        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        85.45        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARMC9 MUTATED ARMC9 WILD-TYPE 
           4.01            0.00 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
          65.85          148.01 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
         21.140          22.075 
[1] "4.0 - 65.8 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D724V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARMC9 MUTATED         2        0        1         1         1         0
  ARMC9 WILD-TYPE      62        1       25       107         7         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        18          6         44         32       34        12
                 vv
clus              STAGE IVB
  ARMC9 MUTATED           0
  ARMC9 WILD-TYPE         1
D724V3, multiclass
            clus
vv           ARMC9 MUTATED ARMC9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  ARMC9 MUTATED     1   1   3   2
  ARMC9 WILD-TYPE   8  66 246  39
D724V4, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             3             246
  T4             2              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
  ARMC9 MUTATED     5   1   1
  ARMC9 WILD-TYPE 215  80  65
D724V5, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V6, binary
                 cls
clus                0   1
  ARMC9 MUTATED     6   1
  ARMC9 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      6    1
  ARMC9 WILD-TYPE  279   47
   clus
vv  ARMC9 MUTATED ARMC9 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D724V7, binary
                 cls
clus                0   1
  ARMC9 MUTATED     4   3
  ARMC9 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      4    3
  ARMC9 WILD-TYPE  166  194
        clus
vv       ARMC9 MUTATED ARMC9 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D724V8, binary
                 cls
clus                0   1
  ARMC9 MUTATED     5   0
  ARMC9 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      5    0
  ARMC9 WILD-TYPE  295    8
     clus
vv    ARMC9 MUTATED ARMC9 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D724V9, binary
                 cls
clus                0   1
  ARMC9 MUTATED     3   4
  ARMC9 WILD-TYPE 311  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      3    4
  ARMC9 WILD-TYPE  311   44
                               clus
vv                              ARMC9 MUTATED ARMC9 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ARMC9 MUTATED     5   0   0   2
  ARMC9 WILD-TYPE 254   3  22  19
D724V10, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D724V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARMC9 MUTATED                                  0     0
  ARMC9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARMC9 MUTATED                           0     4
  ARMC9 WILD-TYPE                        19   172
D724V12, multiclass
                                  clus
vv                                 ARMC9 MUTATED ARMC9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = MAGEB2 MUTATION ANALYSIS
D725V1, survival
                  sevent
clus2                0   1
  MAGEB2 MUTATED     6   4
  MAGEB2 WILD-TYPE 271  74
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              10              345 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
               4               74 
$`MAGEB2 MUTATED`
TCGA-AA-3950 TCGA-AZ-6608 TCGA-G4-6588 TCGA-AA-A02H TCGA-AZ-4315 TCGA-CM-5349 
       24.00         1.94        26.17         2.01        58.39        30.08 
TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A0XF TCGA-F4-6809 
       12.49        14.30        38.20        13.25 

$`MAGEB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
            1.94             0.00 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
           58.39           148.01 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
           19.15            22.06 
[1] "1.9 - 58.4 (19.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D725V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEB2 MUTATED         0        0        0         6         0         0
  MAGEB2 WILD-TYPE      64        1       26       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEB2 MUTATED           0          1          0          1        1
  MAGEB2 WILD-TYPE        18          5         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  MAGEB2 MUTATED           1         0
  MAGEB2 WILD-TYPE        11         1
D725V3, multiclass
            clus
vv           MAGEB2 MUTATED MAGEB2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  MAGEB2 MUTATED     0   1  10   0
  MAGEB2 WILD-TYPE   9  66 239  41
D725V4, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             10              239
  T4              0               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
  MAGEB2 MUTATED     7   2   2
  MAGEB2 WILD-TYPE 213  79  64
D725V5, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V6, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED     9   2
  MAGEB2 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED      9    2
  MAGEB2 WILD-TYPE  276   46
   clus
vv  MAGEB2 MUTATED MAGEB2 WILD-TYPE
  0              9              276
  1              2               46
[1] 2 2
[1] FALSE
D725V7, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED     9   2
  MAGEB2 WILD-TYPE 161 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED      9    2
  MAGEB2 WILD-TYPE  161  195
        clus
vv       MAGEB2 MUTATED MAGEB2 WILD-TYPE
  FEMALE              9              161
  MALE                2              195
[1] 2 2
[1] FALSE
D725V8, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED     8   0
  MAGEB2 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED      8    0
  MAGEB2 WILD-TYPE  292    8
     clus
vv    MAGEB2 MUTATED MAGEB2 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D725V9, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED     9   1
  MAGEB2 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED      9    1
  MAGEB2 WILD-TYPE  305   47
                               clus
vv                              MAGEB2 MUTATED MAGEB2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGEB2 MUTATED     8   0   1   0
  MAGEB2 WILD-TYPE 251   3  21  21
D725V10, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              1               21
  RX              0               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"
D725V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEB2 MUTATED                                  0     0
  MAGEB2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEB2 MUTATED                           0     8
  MAGEB2 WILD-TYPE                        19   168
D725V12, multiclass
                                  clus
vv                                 MAGEB2 MUTATED MAGEB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = ZNF83 MUTATION ANALYSIS
D726V1, survival
                 sevent
clus2               0   1
  ZNF83 MUTATED    12   4
  ZNF83 WILD-TYPE 265  74
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             16             339 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
              4              74 
$`ZNF83 MUTATED`
TCGA-AA-3525 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3492 
        8.05       100.01        35.80        32.75        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AZ-4315 
       63.98        53.00         4.01        34.98        14.01        58.39 
TCGA-CM-4752 TCGA-CM-6674 TCGA-D5-6923 TCGA-DM-A28K 
       13.02        12.95        12.43        98.24 

$`ZNF83 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF83 MUTATED ZNF83 WILD-TYPE 
           3.02            0.00 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
         100.01          148.01 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
         26.205          22.060 
[1] "3.0 - 100.0 (26.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D726V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF83 MUTATED         1        0        4         6         3         0
  ZNF83 WILD-TYPE      63        1       22       102         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF83 MUTATED           0          0          1          1        1         0
  ZNF83 WILD-TYPE        18          6         43         32       34        12
                 vv
clus              STAGE IVB
  ZNF83 MUTATED           0
  ZNF83 WILD-TYPE         1
D726V3, multiclass
            clus
vv           ZNF83 MUTATED ZNF83 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              6             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  ZNF83 MUTATED     0   1  11   5
  ZNF83 WILD-TYPE   9  66 238  36
D726V4, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             5              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
  ZNF83 MUTATED    14   2   1
  ZNF83 WILD-TYPE 206  79  65
D726V5, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  N0            14             206
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V6, binary
                 cls
clus                0   1
  ZNF83 MUTATED    15   1
  ZNF83 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     15    1
  ZNF83 WILD-TYPE  270   47
   clus
vv  ZNF83 MUTATED ZNF83 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D726V7, binary
                 cls
clus                0   1
  ZNF83 MUTATED     5  12
  ZNF83 WILD-TYPE 165 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED      5   12
  ZNF83 WILD-TYPE  165  185
        clus
vv       ZNF83 MUTATED ZNF83 WILD-TYPE
  FEMALE             5             165
  MALE              12             185
[1] 2 2
[1] FALSE
D726V8, binary
                 cls
clus                0   1
  ZNF83 MUTATED    14   0
  ZNF83 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     14    0
  ZNF83 WILD-TYPE  286    8
     clus
vv    ZNF83 MUTATED ZNF83 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D726V9, binary
                 cls
clus                0   1
  ZNF83 MUTATED    13   4
  ZNF83 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     13    4
  ZNF83 WILD-TYPE  301   44
                               clus
vv                              ZNF83 MUTATED ZNF83 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZNF83 MUTATED    14   0   1   0
  ZNF83 WILD-TYPE 245   3  21  21
D726V10, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             1              21
  RX             0              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"
D726V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF83 MUTATED                                  0     0
  ZNF83 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF83 MUTATED                           1     8
  ZNF83 WILD-TYPE                        18   168
D726V12, multiclass
                                  clus
vv                                 ZNF83 MUTATED ZNF83 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(727) Variable = ADAMTS4 MUTATION ANALYSIS
D727V1, survival
                   sevent
clus2                 0   1
  ADAMTS4 MUTATED    11   3
  ADAMTS4 WILD-TYPE 266  75
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               14               341 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
                3                75 
$`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 
       24.43        35.31 

$`ADAMTS4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32        21.99        82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            14.04              0.00 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            78.08            148.01 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
           22.555            22.030 
[1] "14.0 - 78.1 (22.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D727V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTS4 MUTATED         3        0        2         6         1         0
  ADAMTS4 WILD-TYPE      61        1       24       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS4 MUTATED           0          0          1          1        0
  ADAMTS4 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ADAMTS4 MUTATED           0         0
  ADAMTS4 WILD-TYPE        12         1
D727V3, multiclass
            clus
vv           ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                6               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  ADAMTS4 MUTATED     1   2   9   2
  ADAMTS4 WILD-TYPE   8  65 240  39
D727V4, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               9               240
  T4               2                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
  ADAMTS4 MUTATED    12   0   2
  ADAMTS4 WILD-TYPE 208  81  64
D727V5, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  N0              12               208
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V6, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    12   0
  ADAMTS4 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     12    0
  ADAMTS4 WILD-TYPE  273   48
   clus
vv  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  0              12               273
  1               0                48
[1] 2 2
[1] FALSE
D727V7, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    10   4
  ADAMTS4 WILD-TYPE 160 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     10    4
  ADAMTS4 WILD-TYPE  160  193
        clus
vv       ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  FEMALE              10               160
  MALE                 4               193
[1] 2 2
[1] FALSE
D727V8, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    12   0
  ADAMTS4 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     12    0
  ADAMTS4 WILD-TYPE  288    8
     clus
vv    ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D727V9, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    11   3
  ADAMTS4 WILD-TYPE 303  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     11    3
  ADAMTS4 WILD-TYPE  303   45
                               clus
vv                              ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ADAMTS4 MUTATED     9   0   0   2
  ADAMTS4 WILD-TYPE 250   3  22  19
D727V10, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               0                22
  RX               2                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"
D727V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS4 MUTATED                                  0     0
  ADAMTS4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS4 MUTATED                           1    11
  ADAMTS4 WILD-TYPE                        18   165
D727V12, multiclass
                                  clus
vv                                 ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               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(728) Variable = TMEM50B MUTATION ANALYSIS
D728V1, survival
                   sevent
clus2                 0   1
  TMEM50B MUTATED     4   2
  TMEM50B WILD-TYPE 273  76
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                6               349 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                2                76 
$`TMEM50B MUTATED`
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CM-4743 TCGA-CM-5348 TCGA-D5-6922 TCGA-F4-6809 
       58.39        12.10        23.05        22.98        10.13        13.25 

$`TMEM50B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TMEM50B MUTATED TMEM50B WILD-TYPE 
            10.13              0.00 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
            58.39            148.01 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
           18.115            22.060 
[1] "10.1 - 58.4 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D728V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM50B MUTATED         0        0        0         2         0         0
  TMEM50B WILD-TYPE      64        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM50B MUTATED           0          1          1          0        1
  TMEM50B WILD-TYPE        18          5         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  TMEM50B MUTATED           1         0
  TMEM50B WILD-TYPE        11         1
D728V3, multiclass
            clus
vv           TMEM50B MUTATED TMEM50B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                1                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
  TMEM50B MUTATED     0   0   5   1
  TMEM50B WILD-TYPE   9  67 244  40
D728V4, multiclass
    clus
vv   TMEM50B MUTATED TMEM50B WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               1                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
  TMEM50B MUTATED     2   4   0
  TMEM50B WILD-TYPE 218  77  66
D728V5, multiclass
    clus
vv   TMEM50B MUTATED TMEM50B WILD-TYPE
  N0               2               218
  N1               4                77
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V6, binary
                   cls
clus                  0   1
  TMEM50B MUTATED     4   2
  TMEM50B WILD-TYPE 281  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM50B MUTATED      4    2
  TMEM50B WILD-TYPE  281   46
   clus
vv  TMEM50B MUTATED TMEM50B WILD-TYPE
  0               4               281
  1               2                46
[1] 2 2
[1] FALSE
D728V7, binary
                   cls
clus                  0   1
  TMEM50B MUTATED     1   5
  TMEM50B WILD-TYPE 169 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM50B MUTATED      1    5
  TMEM50B WILD-TYPE  169  192
        clus
vv       TMEM50B MUTATED TMEM50B WILD-TYPE
  FEMALE               1               169
  MALE                 5               192
[1] 2 2
[1] FALSE
D728V8, binary
                   cls
clus                  0   1
  TMEM50B MUTATED     6   0
  TMEM50B WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM50B MUTATED      6    0
  TMEM50B WILD-TYPE  294    8
     clus
vv    TMEM50B MUTATED TMEM50B WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D728V9, binary
                   cls
clus                  0   1
  TMEM50B MUTATED     6   0
  TMEM50B WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM50B MUTATED      6    0
  TMEM50B WILD-TYPE  308   48
                               clus
vv                              TMEM50B MUTATED TMEM50B WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM50B MUTATED     5   0   0   0
  TMEM50B WILD-TYPE 254   3  22  21
D728V10, multiclass
    clus
vv   TMEM50B MUTATED TMEM50B WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D728V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM50B MUTATED                                  0     0
  TMEM50B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM50B MUTATED                           1     5
  TMEM50B WILD-TYPE                        18   171
D728V12, multiclass
                                  clus
vv                                 TMEM50B MUTATED TMEM50B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = CDH22 MUTATION ANALYSIS
D729V1, survival
                 sevent
clus2               0   1
  CDH22 MUTATED    11   4
  CDH22 WILD-TYPE 266  74
  CDH22 MUTATED CDH22 WILD-TYPE 
             15             340 
  CDH22 MUTATED CDH22 WILD-TYPE 
              4              74 
$`CDH22 MUTATED`
TCGA-AA-3516 TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3681 TCGA-AA-3837 
       13.02        24.00        35.80        22.06         5.98        38.99 
TCGA-AY-6196 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CM-6677 TCGA-D5-6540 TCGA-DM-A1HA 
        0.20         6.77        11.74        11.08        16.14       131.51 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6315 
       65.85        44.68        61.91 

$`CDH22 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02        11.01        37.05         5.03 
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-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  CDH22 MUTATED CDH22 WILD-TYPE 
            0.2             0.0 
  CDH22 MUTATED CDH22 WILD-TYPE 
         131.51          148.01 
  CDH22 MUTATED CDH22 WILD-TYPE 
          22.06           22.06 
[1] "0.2 - 131.5 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D729V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH22 MUTATED         2        0        0         6         0         0
  CDH22 WILD-TYPE      62        1       26       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH22 MUTATED           2          0          0          2        3         0
  CDH22 WILD-TYPE        16          6         44         31       32        12
                 vv
clus              STAGE IVB
  CDH22 MUTATED           0
  CDH22 WILD-TYPE         1
D729V3, multiclass
            clus
vv           CDH22 MUTATED CDH22 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              0              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
  CDH22 MUTATED     0   3  12   1
  CDH22 WILD-TYPE   9  64 237  40
D729V4, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             1              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
  CDH22 MUTATED     9   3   4
  CDH22 WILD-TYPE 211  78  62
D729V5, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  N0             9             211
  N1             3              78
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V6, binary
                 cls
clus                0   1
  CDH22 MUTATED    11   3
  CDH22 WILD-TYPE 274  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     11    3
  CDH22 WILD-TYPE  274   45
   clus
vv  CDH22 MUTATED CDH22 WILD-TYPE
  0            11             274
  1             3              45
[1] 2 2
[1] FALSE
D729V7, binary
                 cls
clus                0   1
  CDH22 MUTATED     8   8
  CDH22 WILD-TYPE 162 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED      8    8
  CDH22 WILD-TYPE  162  189
        clus
vv       CDH22 MUTATED CDH22 WILD-TYPE
  FEMALE             8             162
  MALE               8             189
[1] 2 2
[1] FALSE
D729V8, binary
                 cls
clus                0   1
  CDH22 MUTATED    13   0
  CDH22 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     13    0
  CDH22 WILD-TYPE  287    8
     clus
vv    CDH22 MUTATED CDH22 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D729V9, binary
                 cls
clus                0   1
  CDH22 MUTATED    11   5
  CDH22 WILD-TYPE 303  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     11    5
  CDH22 WILD-TYPE  303   43
                               clus
vv                              CDH22 MUTATED CDH22 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH22 MUTATED    12   0   0   0
  CDH22 WILD-TYPE 247   3  22  21
D729V10, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             0              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"
D729V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH22 MUTATED                                  0     0
  CDH22 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH22 MUTATED                           0    11
  CDH22 WILD-TYPE                        19   165
D729V12, multiclass
                                  clus
vv                                 CDH22 MUTATED CDH22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(730) Variable = LRRC37B MUTATION ANALYSIS
D730V1, survival
                   sevent
clus2                 0   1
  LRRC37B MUTATED     3   3
  LRRC37B WILD-TYPE 274  75
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                6               349 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                3                75 
$`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 

$`LRRC37B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  LRRC37B MUTATED LRRC37B WILD-TYPE 
            11.38              0.00 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           148.01            140.38 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           22.045            22.060 
[1] "11.4 - 148.0 (22.0)" "0.0 - 140.4 (22.1)" 
[1] "hr=" "1.9"
D730V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC37B MUTATED         0        0        0         3         0         0
  LRRC37B WILD-TYPE      64        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC37B MUTATED           1          0          1          0        0
  LRRC37B WILD-TYPE        17          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  LRRC37B MUTATED           0         0
  LRRC37B WILD-TYPE        12         1
D730V3, multiclass
            clus
vv           LRRC37B MUTATED LRRC37B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  LRRC37B MUTATED     0   1   5   0
  LRRC37B WILD-TYPE   9  66 244  41
D730V4, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               0                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
  LRRC37B MUTATED     3   3   0
  LRRC37B WILD-TYPE 217  78  66
D730V5, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  N0               3               217
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V6, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     5   0
  LRRC37B WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      5    0
  LRRC37B WILD-TYPE  280   48
   clus
vv  LRRC37B MUTATED LRRC37B WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D730V7, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     3   3
  LRRC37B WILD-TYPE 167 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      3    3
  LRRC37B WILD-TYPE  167  194
        clus
vv       LRRC37B MUTATED LRRC37B WILD-TYPE
  FEMALE               3               167
  MALE                 3               194
[1] 2 2
[1] FALSE
D730V8, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     6   0
  LRRC37B WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      6    0
  LRRC37B WILD-TYPE  294    8
     clus
vv    LRRC37B MUTATED LRRC37B WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D730V9, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     5   1
  LRRC37B WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      5    1
  LRRC37B WILD-TYPE  309   47
                               clus
vv                              LRRC37B MUTATED LRRC37B WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  LRRC37B MUTATED     3   0   0   1
  LRRC37B WILD-TYPE 256   3  22  20
D730V10, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               1                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"
D730V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC37B MUTATED                                  0     1
  LRRC37B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LRRC37B MUTATED                           0     5
  LRRC37B WILD-TYPE                        19   171
D730V12, multiclass
                                  clus
vv                                 LRRC37B MUTATED LRRC37B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = C19ORF66 MUTATION ANALYSIS
D731V1, survival
                    sevent
clus2                  0   1
  C19ORF66 MUTATED     4   0
  C19ORF66 WILD-TYPE 273  78
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                351 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 0                 78 
$`C19ORF66 MUTATED`
TCGA-AA-3713 TCGA-AA-3663 TCGA-AA-3949 TCGA-D5-6540 
       19.04         6.97        26.01        16.14 

$`C19ORF66 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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              22.09 
[1] "7.0 - 26.0 (17.6)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D731V2, continuous
                    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      63        1       25       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF66 MUTATED           0          0          1          0        1
  C19ORF66 WILD-TYPE        18          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  C19ORF66 MUTATED           0         0
  C19ORF66 WILD-TYPE        12         1
D731V3, multiclass
            clus
vv           C19ORF66 MUTATED C19ORF66 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 0                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  C19ORF66 MUTATED     0   1   3   0
  C19ORF66 WILD-TYPE   9  66 246  41
D731V4, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                3                246
  T4                0                 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
  C19ORF66 MUTATED     3   1   0
  C19ORF66 WILD-TYPE 217  80  66
D731V5, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  N0                3                217
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V6, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     3   1
  C19ORF66 WILD-TYPE 282  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      3    1
  C19ORF66 WILD-TYPE  282   47
   clus
vv  C19ORF66 MUTATED C19ORF66 WILD-TYPE
  0                3                282
  1                1                 47
[1] 2 2
[1] FALSE
D731V7, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     1   3
  C19ORF66 WILD-TYPE 169 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      1    3
  C19ORF66 WILD-TYPE  169  194
        clus
vv       C19ORF66 MUTATED C19ORF66 WILD-TYPE
  FEMALE                1                169
  MALE                  3                194
[1] 2 2
[1] FALSE
D731V8, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     3   1
  C19ORF66 WILD-TYPE 297   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      3    1
  C19ORF66 WILD-TYPE  297    7
     clus
vv    C19ORF66 MUTATED C19ORF66 WILD-TYPE
  NO                 3                297
  YES                1                  7
[1] 2 2
[1] FALSE
D731V9, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     2   2
  C19ORF66 WILD-TYPE 312  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      2    2
  C19ORF66 WILD-TYPE  312   46
                               clus
vv                              C19ORF66 MUTATED C19ORF66 WILD-TYPE
  COLON ADENOCARCINOMA                         2                312
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C19ORF66 MUTATED     3   0   1   0
  C19ORF66 WILD-TYPE 256   3  21  21
D731V10, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D731V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C19ORF66 MUTATED                                  0     0
  C19ORF66 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C19ORF66 MUTATED                           0     1
  C19ORF66 WILD-TYPE                        19   175
D731V12, multiclass
[1] "Remove cluster labels:" "C19ORF66 MUTATED"      
clus
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 1                205 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6541 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0X9         TCGA-DM-A0XD 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A0XF         TCGA-DM-A1D0         TCGA-DM-A1D4 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1D6         TCGA-DM-A1D7         TCGA-DM-A1D8 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1DB 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1HA         TCGA-DM-A1HB         TCGA-DM-A282 
"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-G4-6315         TCGA-G4-6317         TCGA-G4-6323 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6626 
"C19ORF66 WILD-TYPE" 

Clustering(732) Variable = WWC3 MUTATION ANALYSIS
D732V1, survival
                sevent
clus2              0   1
  WWC3 MUTATED    16   5
  WWC3 WILD-TYPE 261  73
  WWC3 MUTATED WWC3 WILD-TYPE 
            21            334 
  WWC3 MUTATED WWC3 WILD-TYPE 
             5             73 
$`WWC3 MUTATED`
TCGA-AA-3950 TCGA-AZ-6608 TCGA-G4-6586 TCGA-G4-6588 TCGA-AA-3510 TCGA-AA-3833 
       24.00         1.94        35.80        26.17        63.98        15.95 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-5797 TCGA-CK-4947 
       53.00        31.00         4.01        12.16        12.59        17.56 
TCGA-CK-5913 TCGA-CM-6171 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6808 
       51.32        14.04         7.50       135.65         6.18        33.67 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6626 
       53.62        85.48        46.75 

$`WWC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
      100.01        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        61.91        36.00        13.78 

  WWC3 MUTATED WWC3 WILD-TYPE 
          1.94           0.00 
  WWC3 MUTATED WWC3 WILD-TYPE 
        135.65         148.01 
  WWC3 MUTATED WWC3 WILD-TYPE 
         26.17          22.01 
[1] "1.9 - 135.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D732V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WWC3 MUTATED         4        0        2         9         2         0
  WWC3 WILD-TYPE      60        1       24        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WWC3 MUTATED           0          1          3          1        0         0
  WWC3 WILD-TYPE        18          5         41         32       35        12
                vv
clus             STAGE IVB
  WWC3 MUTATED           0
  WWC3 WILD-TYPE         1
D732V3, multiclass
            clus
vv           WWC3 MUTATED WWC3 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             9             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  WWC3 MUTATED     2   3  14   3
  WWC3 WILD-TYPE   7  64 235  38
D732V4, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  T1            2              7
  T2            3             64
  T3           14            235
  T4            3             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
  WWC3 MUTATED    17   4   1
  WWC3 WILD-TYPE 203  77  65
D732V5, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  N0           17            203
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V6, binary
                cls
clus               0   1
  WWC3 MUTATED    20   0
  WWC3 WILD-TYPE 265  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     20    0
  WWC3 WILD-TYPE  265   48
   clus
vv  WWC3 MUTATED WWC3 WILD-TYPE
  0           20            265
  1            0             48
[1] 2 2
[1] FALSE
D732V7, binary
                cls
clus               0   1
  WWC3 MUTATED    15   7
  WWC3 WILD-TYPE 155 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     15    7
  WWC3 WILD-TYPE  155  190
        clus
vv       WWC3 MUTATED WWC3 WILD-TYPE
  FEMALE           15            155
  MALE              7            190
[1] 2 2
[1] FALSE
D732V8, binary
                cls
clus               0   1
  WWC3 MUTATED    18   0
  WWC3 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     18    0
  WWC3 WILD-TYPE  282    8
     clus
vv    WWC3 MUTATED WWC3 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D732V9, binary
                cls
clus               0   1
  WWC3 MUTATED    17   4
  WWC3 WILD-TYPE 297  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     17    4
  WWC3 WILD-TYPE  297   44
                               clus
vv                              WWC3 MUTATED WWC3 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WWC3 MUTATED    17   0   0   2
  WWC3 WILD-TYPE 242   3  22  19
D732V10, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  R0           17            242
  R1            0              3
  R2            0             22
  RX            2             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"
D732V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WWC3 MUTATED                                  0     1
  WWC3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WWC3 MUTATED                           1    13
  WWC3 WILD-TYPE                        18   163
D732V12, multiclass
                                  clus
vv                                 WWC3 MUTATED WWC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      13            163
[1] 4 2
[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 = ZBTB24 MUTATION ANALYSIS
D733V1, survival
                  sevent
clus2                0   1
  ZBTB24 MUTATED     6   2
  ZBTB24 WILD-TYPE 271  76
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               8              347 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               2               76 
$`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 
       38.20       135.65 

$`ZBTB24 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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-6680 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
           10.06             0.00 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
          135.65           148.01 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
           29.57            22.03 
[1] "10.1 - 135.7 (29.6)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.1"
D733V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB24 MUTATED         1        0        1         2         1         0
  ZBTB24 WILD-TYPE      63        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB24 MUTATED           0          0          2          1        0
  ZBTB24 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB24 MUTATED           0         0
  ZBTB24 WILD-TYPE        12         1
D733V3, multiclass
            clus
vv           ZBTB24 MUTATED ZBTB24 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZBTB24 MUTATED     0   1   6   1
  ZBTB24 WILD-TYPE   9  66 243  40
D733V4, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              6              243
  T4              1               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
  ZBTB24 MUTATED     5   2   1
  ZBTB24 WILD-TYPE 215  79  65
D733V5, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  N0              5              215
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V6, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     8   0
  ZBTB24 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      8    0
  ZBTB24 WILD-TYPE  277   48
   clus
vv  ZBTB24 MUTATED ZBTB24 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D733V7, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     3   5
  ZBTB24 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      3    5
  ZBTB24 WILD-TYPE  167  192
        clus
vv       ZBTB24 MUTATED ZBTB24 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D733V8, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     6   0
  ZBTB24 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      6    0
  ZBTB24 WILD-TYPE  294    8
     clus
vv    ZBTB24 MUTATED ZBTB24 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D733V9, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     6   0
  ZBTB24 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      6    0
  ZBTB24 WILD-TYPE  308   48
                               clus
vv                              ZBTB24 MUTATED ZBTB24 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB24 MUTATED     4   0   0   1
  ZBTB24 WILD-TYPE 255   3  22  20
D733V10, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D733V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB24 MUTATED                                  0     1
  ZBTB24 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB24 MUTATED                           0     5
  ZBTB24 WILD-TYPE                        19   171
D733V12, multiclass
                                  clus
vv                                 ZBTB24 MUTATED ZBTB24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = TMEM48 MUTATION ANALYSIS
D734V1, survival
                  sevent
clus2                0   1
  TMEM48 MUTATED     6   3
  TMEM48 WILD-TYPE 271  75
  TMEM48 MUTATED TMEM48 WILD-TYPE 
               9              346 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
               3               75 
$`TMEM48 MUTATED`
TCGA-AA-3525 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AZ-4315 TCGA-AZ-6598 
        8.05        33.53         3.02        63.98        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-G4-6317 
       12.76        10.06        36.00 

$`TMEM48 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  TMEM48 MUTATED TMEM48 WILD-TYPE 
            3.02             0.00 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
           63.98           148.01 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
          33.530           22.045 
[1] "3.0 - 64.0 (33.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D734V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM48 MUTATED         0        0        3         5         0         0
  TMEM48 WILD-TYPE      64        1       23       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM48 MUTATED           0          0          1          1        0
  TMEM48 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM48 MUTATED           0         0
  TMEM48 WILD-TYPE        12         1
D734V3, multiclass
            clus
vv           TMEM48 MUTATED TMEM48 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  TMEM48 MUTATED     0   0  10   0
  TMEM48 WILD-TYPE   9  67 239  41
D734V4, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             10              239
  T4              0               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
  TMEM48 MUTATED     8   1   1
  TMEM48 WILD-TYPE 212  80  65
D734V5, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V6, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     8   0
  TMEM48 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      8    0
  TMEM48 WILD-TYPE  277   48
   clus
vv  TMEM48 MUTATED TMEM48 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D734V7, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     5   5
  TMEM48 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      5    5
  TMEM48 WILD-TYPE  165  192
        clus
vv       TMEM48 MUTATED TMEM48 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D734V8, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     9   0
  TMEM48 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      9    0
  TMEM48 WILD-TYPE  291    8
     clus
vv    TMEM48 MUTATED TMEM48 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D734V9, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     9   1
  TMEM48 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      9    1
  TMEM48 WILD-TYPE  305   47
                               clus
vv                              TMEM48 MUTATED TMEM48 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM48 MUTATED     7   0   0   2
  TMEM48 WILD-TYPE 252   3  22  19
D734V10, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D734V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM48 MUTATED                                  0     2
  TMEM48 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM48 MUTATED                           1     3
  TMEM48 WILD-TYPE                        18   173
D734V12, multiclass
                                  clus
vv                                 TMEM48 MUTATED TMEM48 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = EXPH5 MUTATION ANALYSIS
D735V1, survival
                 sevent
clus2               0   1
  EXPH5 MUTATED    14   6
  EXPH5 WILD-TYPE 263  72
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             20             335 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
              6              72 
$`EXPH5 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6781 
       26.17        79.69        22.06         8.38        25.08        19.66 
TCGA-AA-3555 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A01R 
       29.95        31.00        26.01        18.05         4.01        35.01 
TCGA-AZ-5403 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5862 
       62.79         5.23        12.76        10.06        23.05         5.03 
TCGA-D5-5539 TCGA-DM-A28F 
       19.59        35.97 

$`EXPH5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       23.61        22.09        32.71        27.09        22.52        25.18 
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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        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        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  EXPH5 MUTATED EXPH5 WILD-TYPE 
           4.01            0.00 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
          79.69          148.01 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
         22.555          22.030 
[1] "4.0 - 79.7 (22.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D735V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXPH5 MUTATED         2        0        1         8         1         0
  EXPH5 WILD-TYPE      62        1       25       100         7         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        17          5         40         32       35        10
                 vv
clus              STAGE IVB
  EXPH5 MUTATED           0
  EXPH5 WILD-TYPE         1
D735V3, multiclass
            clus
vv           EXPH5 MUTATED EXPH5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              2              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
  EXPH5 MUTATED     1   1  15   4
  EXPH5 WILD-TYPE   8  66 234  37
D735V4, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            15             234
  T4             4              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
  EXPH5 MUTATED    12   8   1
  EXPH5 WILD-TYPE 208  73  65
D735V5, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  N0            12             208
  N1             8              73
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V6, binary
                 cls
clus                0   1
  EXPH5 MUTATED    17   2
  EXPH5 WILD-TYPE 268  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     17    2
  EXPH5 WILD-TYPE  268   46
   clus
vv  EXPH5 MUTATED EXPH5 WILD-TYPE
  0            17             268
  1             2              46
[1] 2 2
[1] FALSE
D735V7, binary
                 cls
clus                0   1
  EXPH5 MUTATED     7  14
  EXPH5 WILD-TYPE 163 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED      7   14
  EXPH5 WILD-TYPE  163  183
        clus
vv       EXPH5 MUTATED EXPH5 WILD-TYPE
  FEMALE             7             163
  MALE              14             183
[1] 2 2
[1] FALSE
D735V8, binary
                 cls
clus                0   1
  EXPH5 MUTATED    17   1
  EXPH5 WILD-TYPE 283   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     17    1
  EXPH5 WILD-TYPE  283    7
     clus
vv    EXPH5 MUTATED EXPH5 WILD-TYPE
  NO             17             283
  YES             1               7
[1] 2 2
[1] FALSE
D735V9, binary
                 cls
clus                0   1
  EXPH5 MUTATED    12   9
  EXPH5 WILD-TYPE 302  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     12    9
  EXPH5 WILD-TYPE  302   39
                               clus
vv                              EXPH5 MUTATED EXPH5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EXPH5 MUTATED    14   0   0   2
  EXPH5 WILD-TYPE 245   3  22  19
D735V10, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D735V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXPH5 MUTATED                                  0     2
  EXPH5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EXPH5 MUTATED                           1    11
  EXPH5 WILD-TYPE                        18   165
D735V12, multiclass
                                  clus
vv                                 EXPH5 MUTATED EXPH5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(736) Variable = MARVELD2 MUTATION ANALYSIS
D736V1, survival
                    sevent
clus2                  0   1
  MARVELD2 MUTATED     8   2
  MARVELD2 WILD-TYPE 269  76
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                10                345 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                 2                 76 
$`MARVELD2 MUTATED`
TCGA-AZ-6601 TCGA-A6-5661 TCGA-AA-3852 TCGA-AA-A00E TCGA-AU-6004 TCGA-AZ-4315 
      100.01        33.53         0.00        30.02        27.09        58.39 
TCGA-CK-5913 TCGA-CM-4743 TCGA-F4-6856 TCGA-G4-6309 
       51.32        23.05        35.31        85.48 

$`MARVELD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-G4-6293 
       43.04        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                 0                  0 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
            100.01             148.01 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
             34.42              21.99 
[1] "0.0 - 100.0 (34.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D736V2, continuous
                    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      62        1       25       102         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARVELD2 MUTATED           0          0          1          0        0
  MARVELD2 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  MARVELD2 MUTATED           0         0
  MARVELD2 WILD-TYPE        12         1
D736V3, multiclass
            clus
vv           MARVELD2 MUTATED MARVELD2 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 6                102
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  MARVELD2 MUTATED     0   2   8   0
  MARVELD2 WILD-TYPE   9  65 241  41
D736V4, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                8                241
  T4                0                 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
  MARVELD2 MUTATED     9   1   0
  MARVELD2 WILD-TYPE 211  80  66
D736V5, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  N0                9                211
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V6, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     9   0
  MARVELD2 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      9    0
  MARVELD2 WILD-TYPE  276   48
   clus
vv  MARVELD2 MUTATED MARVELD2 WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D736V7, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     4   6
  MARVELD2 WILD-TYPE 166 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      4    6
  MARVELD2 WILD-TYPE  166  191
        clus
vv       MARVELD2 MUTATED MARVELD2 WILD-TYPE
  FEMALE                4                166
  MALE                  6                191
[1] 2 2
[1] FALSE
D736V8, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     8   0
  MARVELD2 WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      8    0
  MARVELD2 WILD-TYPE  292    8
     clus
vv    MARVELD2 MUTATED MARVELD2 WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D736V9, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     8   2
  MARVELD2 WILD-TYPE 306  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      8    2
  MARVELD2 WILD-TYPE  306   46
                               clus
vv                              MARVELD2 MUTATED MARVELD2 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  MARVELD2 MUTATED     8   0   0   1
  MARVELD2 WILD-TYPE 251   3  22  20
D736V10, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  R0                8                251
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D736V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARVELD2 MUTATED                                  0     0
  MARVELD2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  MARVELD2 MUTATED                           2     6
  MARVELD2 WILD-TYPE                        17   170
D736V12, multiclass
                                  clus
vv                                 MARVELD2 MUTATED MARVELD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                           6                170
[1] 4 2
[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 = GDE1 MUTATION ANALYSIS
D737V1, survival
                sevent
clus2              0   1
  GDE1 MUTATED     5   0
  GDE1 WILD-TYPE 272  78
  GDE1 MUTATED GDE1 WILD-TYPE 
             5            350 
  GDE1 MUTATED GDE1 WILD-TYPE 
             0             78 
$`GDE1 MUTATED`
TCGA-A6-5656 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4950 TCGA-D5-6898 
       32.91        58.39        12.76        85.45         7.53 

$`GDE1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GDE1 MUTATED GDE1 WILD-TYPE 
          7.53           0.00 
  GDE1 MUTATED GDE1 WILD-TYPE 
         85.45         148.01 
  GDE1 MUTATED GDE1 WILD-TYPE 
        32.910         22.045 
[1] "7.5 - 85.5 (32.9)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D737V2, continuous
                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      62        1       26       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GDE1 MUTATED           0          0          1          0        0         0
  GDE1 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  GDE1 MUTATED           0
  GDE1 WILD-TYPE         1
D737V3, multiclass
            clus
vv           GDE1 MUTATED GDE1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GDE1 MUTATED     0   2   3   0
  GDE1 WILD-TYPE   9  65 246  41
D737V4, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            3            246
  T4            0             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
  GDE1 MUTATED     4   1   0
  GDE1 WILD-TYPE 216  80  66
D737V5, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V6, binary
                cls
clus               0   1
  GDE1 MUTATED     5   0
  GDE1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      5    0
  GDE1 WILD-TYPE  280   48
   clus
vv  GDE1 MUTATED GDE1 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D737V7, binary
                cls
clus               0   1
  GDE1 MUTATED     2   3
  GDE1 WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      2    3
  GDE1 WILD-TYPE  168  194
        clus
vv       GDE1 MUTATED GDE1 WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D737V8, binary
                cls
clus               0   1
  GDE1 MUTATED     5   0
  GDE1 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      5    0
  GDE1 WILD-TYPE  295    8
     clus
vv    GDE1 MUTATED GDE1 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D737V9, binary
                cls
clus               0   1
  GDE1 MUTATED     3   2
  GDE1 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      3    2
  GDE1 WILD-TYPE  311   46
                               clus
vv                              GDE1 MUTATED GDE1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GDE1 MUTATED     2   1   0   1
  GDE1 WILD-TYPE 257   2  22  20
D737V10, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  R0            2            257
  R1            1              2
  R2            0             22
  RX            1             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"
D737V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GDE1 MUTATED                                  0     1
  GDE1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GDE1 MUTATED                           1     3
  GDE1 WILD-TYPE                        18   173
D737V12, multiclass
                                  clus
vv                                 GDE1 MUTATED GDE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = ZNF721 MUTATION ANALYSIS
D738V1, survival
                  sevent
clus2                0   1
  ZNF721 MUTATED    10   4
  ZNF721 WILD-TYPE 267  74
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              14              341 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
               4               74 
$`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 
       10.06         5.03 

$`ZNF721 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF721 MUTATED ZNF721 WILD-TYPE 
            4.01             0.00 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           63.98           148.01 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
          24.705           22.030 
[1] "4.0 - 64.0 (24.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D738V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF721 MUTATED         2        0        1         7         2         0
  ZNF721 WILD-TYPE      62        1       25       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF721 MUTATED           1          0          0          0        0
  ZNF721 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF721 MUTATED           1         0
  ZNF721 WILD-TYPE        11         1
D738V3, multiclass
            clus
vv           ZNF721 MUTATED ZNF721 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF721 MUTATED     0   3  10   2
  ZNF721 WILD-TYPE   9  64 239  39
D738V4, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             10              239
  T4              2               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
  ZNF721 MUTATED    13   1   1
  ZNF721 WILD-TYPE 207  80  65
D738V5, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  N0             13              207
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V6, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    13   1
  ZNF721 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     13    1
  ZNF721 WILD-TYPE  272   47
   clus
vv  ZNF721 MUTATED ZNF721 WILD-TYPE
  0             13              272
  1              1               47
[1] 2 2
[1] FALSE
D738V7, binary
                  cls
clus                 0   1
  ZNF721 MUTATED     6   9
  ZNF721 WILD-TYPE 164 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED      6    9
  ZNF721 WILD-TYPE  164  188
        clus
vv       ZNF721 MUTATED ZNF721 WILD-TYPE
  FEMALE              6              164
  MALE                9              188
[1] 2 2
[1] FALSE
D738V8, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    12   0
  ZNF721 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     12    0
  ZNF721 WILD-TYPE  288    8
     clus
vv    ZNF721 MUTATED ZNF721 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D738V9, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    12   3
  ZNF721 WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     12    3
  ZNF721 WILD-TYPE  302   45
                               clus
vv                              ZNF721 MUTATED ZNF721 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF721 MUTATED    10   0   0   2
  ZNF721 WILD-TYPE 249   3  22  19
D738V10, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D738V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF721 MUTATED                                  0     2
  ZNF721 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF721 MUTATED                           1     4
  ZNF721 WILD-TYPE                        18   172
D738V12, multiclass
                                  clus
vv                                 ZNF721 MUTATED ZNF721 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = PAX6 MUTATION ANALYSIS
D739V1, survival
                sevent
clus2              0   1
  PAX6 MUTATED    12   2
  PAX6 WILD-TYPE 265  76
  PAX6 MUTATED PAX6 WILD-TYPE 
            14            341 
  PAX6 MUTATED PAX6 WILD-TYPE 
             2             76 
$`PAX6 MUTATED`
TCGA-AA-3950 TCGA-A6-6138 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-A00J TCGA-AA-A00R 
       24.00        22.52        19.66        10.06        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 
       35.97        98.24 

$`PAX6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PAX6 MUTATED PAX6 WILD-TYPE 
          0.99           0.00 
  PAX6 MUTATED PAX6 WILD-TYPE 
         98.24         148.01 
  PAX6 MUTATED PAX6 WILD-TYPE 
         21.09          22.06 
[1] "1.0 - 98.2 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D739V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAX6 MUTATED         4        0        0         5         0         0
  PAX6 WILD-TYPE      60        1       26       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX6 MUTATED           1          0          2          1        0         0
  PAX6 WILD-TYPE        17          6         42         32       35        12
                vv
clus             STAGE IVB
  PAX6 MUTATED           0
  PAX6 WILD-TYPE         1
D739V3, multiclass
            clus
vv           PAX6 MUTATED PAX6 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  PAX6 MUTATED     0   4   8   2
  PAX6 WILD-TYPE   9  63 241  39
D739V4, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  T1            0              9
  T2            4             63
  T3            8            241
  T4            2             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
  PAX6 MUTATED    10   3   1
  PAX6 WILD-TYPE 210  78  65
D739V5, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  N0           10            210
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V6, binary
                cls
clus               0   1
  PAX6 MUTATED    13   0
  PAX6 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     13    0
  PAX6 WILD-TYPE  272   48
   clus
vv  PAX6 MUTATED PAX6 WILD-TYPE
  0           13            272
  1            0             48
[1] 2 2
[1] FALSE
D739V7, binary
                cls
clus               0   1
  PAX6 MUTATED     5   9
  PAX6 WILD-TYPE 165 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      5    9
  PAX6 WILD-TYPE  165  188
        clus
vv       PAX6 MUTATED PAX6 WILD-TYPE
  FEMALE            5            165
  MALE              9            188
[1] 2 2
[1] FALSE
D739V8, binary
                cls
clus               0   1
  PAX6 MUTATED    11   0
  PAX6 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     11    0
  PAX6 WILD-TYPE  289    8
     clus
vv    PAX6 MUTATED PAX6 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D739V9, binary
                cls
clus               0   1
  PAX6 MUTATED     9   5
  PAX6 WILD-TYPE 305  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      9    5
  PAX6 WILD-TYPE  305   43
                               clus
vv                              PAX6 MUTATED PAX6 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAX6 MUTATED    10   0   0   1
  PAX6 WILD-TYPE 249   3  22  20
D739V10, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D739V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAX6 MUTATED                                  0     1
  PAX6 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAX6 MUTATED                           1     8
  PAX6 WILD-TYPE                        18   168
D739V12, multiclass
                                  clus
vv                                 PAX6 MUTATED PAX6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = ENPP1 MUTATION ANALYSIS
D740V1, survival
                 sevent
clus2               0   1
  ENPP1 MUTATED     9   4
  ENPP1 WILD-TYPE 268  74
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             13             342 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
              4              74 
$`ENPP1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3848 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-5254 
      100.01        26.17        10.06         4.01        58.39        12.69 
TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6538 TCGA-F4-6570 
       12.76        15.02        11.01        55.92        17.13         6.18 
TCGA-G4-6306 
       44.68 

$`ENPP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ENPP1 MUTATED ENPP1 WILD-TYPE 
           4.01            0.00 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
         100.01          148.01 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
          15.02           22.09 
[1] "4.0 - 100.0 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D740V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPP1 MUTATED         0        0        1         7         1         0
  ENPP1 WILD-TYPE      64        1       25       101         7         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        18          6         41         32       35        12
                 vv
clus              STAGE IVB
  ENPP1 MUTATED           0
  ENPP1 WILD-TYPE         1
D740V3, multiclass
            clus
vv           ENPP1 MUTATED ENPP1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ENPP1 MUTATED     0   1  12   1
  ENPP1 WILD-TYPE   9  66 237  40
D740V4, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            12             237
  T4             1              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
  ENPP1 MUTATED    10   2   2
  ENPP1 WILD-TYPE 210  79  64
D740V5, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V6, binary
                 cls
clus                0   1
  ENPP1 MUTATED    14   0
  ENPP1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     14    0
  ENPP1 WILD-TYPE  271   48
   clus
vv  ENPP1 MUTATED ENPP1 WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D740V7, binary
                 cls
clus                0   1
  ENPP1 MUTATED     8   6
  ENPP1 WILD-TYPE 162 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED      8    6
  ENPP1 WILD-TYPE  162  191
        clus
vv       ENPP1 MUTATED ENPP1 WILD-TYPE
  FEMALE             8             162
  MALE               6             191
[1] 2 2
[1] FALSE
D740V8, binary
                 cls
clus                0   1
  ENPP1 MUTATED    12   0
  ENPP1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     12    0
  ENPP1 WILD-TYPE  288    8
     clus
vv    ENPP1 MUTATED ENPP1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D740V9, binary
                 cls
clus                0   1
  ENPP1 MUTATED    12   2
  ENPP1 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     12    2
  ENPP1 WILD-TYPE  302   46
                               clus
vv                              ENPP1 MUTATED ENPP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ENPP1 MUTATED    11   0   0   2
  ENPP1 WILD-TYPE 248   3  22  19
D740V10, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             2              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"
D740V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENPP1 MUTATED                                  0     2
  ENPP1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ENPP1 MUTATED                           0     9
  ENPP1 WILD-TYPE                        19   167
D740V12, multiclass
                                  clus
vv                                 ENPP1 MUTATED ENPP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(741) Variable = CHM MUTATION ANALYSIS
D741V1, survival
               sevent
clus2             0   1
  CHM MUTATED     2   2
  CHM WILD-TYPE 275  76
  CHM MUTATED CHM WILD-TYPE 
            4           351 
  CHM MUTATED CHM WILD-TYPE 
            2            76 
$`CHM MUTATED`
TCGA-DM-A285 TCGA-AZ-6600 TCGA-CM-5863 TCGA-CM-6678 
        5.88        12.10        15.02        11.01 

$`CHM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-5864 
       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CHM MUTATED CHM WILD-TYPE 
         5.88          0.00 
  CHM MUTATED CHM WILD-TYPE 
        15.02        148.01 
  CHM MUTATED CHM WILD-TYPE 
       11.555        22.090 
[1] "5.9 - 15.0 (11.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "4.7"
D741V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHM MUTATED         0        0        0         0         0         0
  CHM WILD-TYPE      64        1       26       108         8         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        18          6         43         33       33        11
               vv
clus            STAGE IVB
  CHM MUTATED           0
  CHM WILD-TYPE         1
D741V3, multiclass
            clus
vv           CHM MUTATED CHM WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            0           108
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             2            33
  STAGE IVA            1            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
  CHM MUTATED     0   0   2   2
  CHM WILD-TYPE   9  67 247  39
D741V4, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  T1           0             9
  T2           0            67
  T3           2           247
  T4           2            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
  CHM MUTATED     0   3   1
  CHM WILD-TYPE 220  78  65
D741V5, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  N0           0           220
  N1           3            78
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V6, binary
               cls
clus              0   1
  CHM MUTATED     1   3
  CHM WILD-TYPE 284  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      1    3
  CHM WILD-TYPE  284   45
   clus
vv  CHM MUTATED CHM WILD-TYPE
  0           1           284
  1           3            45
[1] 2 2
[1] FALSE
D741V7, binary
               cls
clus              0   1
  CHM MUTATED     3   1
  CHM WILD-TYPE 167 196
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      3    1
  CHM WILD-TYPE  167  196
        clus
vv       CHM MUTATED CHM WILD-TYPE
  FEMALE           3           167
  MALE             1           196
[1] 2 2
[1] FALSE
D741V8, binary
               cls
clus              0   1
  CHM MUTATED     3   0
  CHM WILD-TYPE 297   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      3    0
  CHM WILD-TYPE  297    8
     clus
vv    CHM MUTATED CHM WILD-TYPE
  NO            3           297
  YES           0             8
[1] 2 2
[1] FALSE
D741V9, binary
               cls
clus              0   1
  CHM MUTATED     2   2
  CHM WILD-TYPE 312  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      2    2
  CHM WILD-TYPE  312   46
                               clus
vv                              CHM MUTATED CHM WILD-TYPE
  COLON ADENOCARCINOMA                    2           312
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CHM MUTATED     2   0   0   0
  CHM WILD-TYPE 257   3  22  21
D741V10, multiclass
[1] "Remove cluster labels:" "CHM MUTATED"           
clus
  CHM MUTATED CHM WILD-TYPE 
            2           303 
   TCGA-A6-2677    TCGA-AA-3496    TCGA-AA-3520    TCGA-AA-3521    TCGA-AA-3522 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3524    TCGA-AA-3525    TCGA-AA-3527    TCGA-AA-3530    TCGA-AA-3531 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3543    TCGA-AA-3552    TCGA-AA-3554    TCGA-AA-3556    TCGA-AA-3560 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3562    TCGA-AA-3662    TCGA-AA-3672    TCGA-AA-3688    TCGA-AA-3692 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3697    TCGA-AA-3713    TCGA-AA-3715    TCGA-AA-3814    TCGA-AA-3844 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3860    TCGA-AA-3867    TCGA-AA-3870    TCGA-AA-3939    TCGA-AA-3950 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3952    TCGA-AA-3972    TCGA-AA-3976    TCGA-AA-3979    TCGA-AA-3986 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A00L    TCGA-AA-A00Z    TCGA-AA-A024    TCGA-AD-6548    TCGA-AD-6888 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AD-6895    TCGA-AZ-4681    TCGA-CK-5912    TCGA-G4-6310    TCGA-G4-6321 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-G4-6586    TCGA-G4-6588    TCGA-G4-6625    TCGA-G4-6628    TCGA-A6-2671 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2678    TCGA-A6-2683 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809    TCGA-A6-3810    TCGA-A6-5657 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-A6-5659    TCGA-A6-5661    TCGA-A6-5665    TCGA-A6-6781    TCGA-AA-3489 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3492    TCGA-AA-3502    TCGA-AA-3510    TCGA-AA-3511    TCGA-AA-3514 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3517    TCGA-AA-3518    TCGA-AA-3519    TCGA-AA-3526    TCGA-AA-3529 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3532    TCGA-AA-3534    TCGA-AA-3538    TCGA-AA-3542    TCGA-AA-3544 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3548    TCGA-AA-3549    TCGA-AA-3553    TCGA-AA-3555    TCGA-AA-3558 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3561    TCGA-AA-3655    TCGA-AA-3660    TCGA-AA-3663    TCGA-AA-3664 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3666    TCGA-AA-3667    TCGA-AA-3673    TCGA-AA-3678    TCGA-AA-3679 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3680    TCGA-AA-3681    TCGA-AA-3684    TCGA-AA-3685    TCGA-AA-3693 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3695    TCGA-AA-3696    TCGA-AA-3710    TCGA-AA-3712    TCGA-AA-3811 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3812    TCGA-AA-3815    TCGA-AA-3818    TCGA-AA-3819    TCGA-AA-3821 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3831    TCGA-AA-3833    TCGA-AA-3837    TCGA-AA-3842    TCGA-AA-3845 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3846    TCGA-AA-3848    TCGA-AA-3850    TCGA-AA-3851    TCGA-AA-3852 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3854    TCGA-AA-3855    TCGA-AA-3856    TCGA-AA-3858    TCGA-AA-3861 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3864    TCGA-AA-3866    TCGA-AA-3869    TCGA-AA-3872    TCGA-AA-3875 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3877    TCGA-AA-3930    TCGA-AA-3941    TCGA-AA-3947    TCGA-AA-3949 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3955    TCGA-AA-3956    TCGA-AA-3968    TCGA-AA-3971    TCGA-AA-3973 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3975    TCGA-AA-3984    TCGA-AA-3989    TCGA-AA-3994    TCGA-AA-A004 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A00A    TCGA-AA-A00D    TCGA-AA-A00E    TCGA-AA-A00F    TCGA-AA-A00J 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A00K    TCGA-AA-A00N    TCGA-AA-A00O    TCGA-AA-A00Q    TCGA-AA-A00R 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A00U    TCGA-AA-A00W    TCGA-AA-A010    TCGA-AA-A017    TCGA-AA-A01D 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A01F    TCGA-AA-A01G    TCGA-AA-A01I    TCGA-AA-A01K    TCGA-AA-A01P 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A01Q    TCGA-AA-A01R    TCGA-AA-A01S    TCGA-AA-A01T    TCGA-AA-A01V 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A01X    TCGA-AA-A01Z    TCGA-AA-A022    TCGA-AA-A029    TCGA-AA-A02F 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A02H    TCGA-AA-A02J    TCGA-AA-A02K    TCGA-AA-A02O    TCGA-AA-A02W 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A02Y    TCGA-AA-A03F    TCGA-AA-A03J    TCGA-AD-5900    TCGA-AD-6889 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AD-6965    TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AY-5543    TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AZ-4682    TCGA-CA-5254    TCGA-CA-5255    TCGA-CA-5796    TCGA-CA-5797 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CA-6715    TCGA-CA-6716    TCGA-CA-6717    TCGA-CA-6718    TCGA-CA-6719 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4950    TCGA-CK-4952    TCGA-CK-5913 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CK-5914    TCGA-CK-5915    TCGA-CK-5916    TCGA-CK-6746    TCGA-CK-6747 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CK-6748    TCGA-CK-6751    TCGA-CM-4743    TCGA-CM-4744    TCGA-CM-4746 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-4747    TCGA-CM-4752    TCGA-CM-5341    TCGA-CM-5344    TCGA-CM-5348 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-5349    TCGA-CM-5860    TCGA-CM-5861    TCGA-CM-5862    TCGA-CM-5864 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-5868    TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-6165    TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-6170    TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-6676    TCGA-CM-6677    TCGA-CM-6679    TCGA-CM-6680    TCGA-D5-5537 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-5538    TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541    TCGA-D5-6529 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6532    TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535    TCGA-D5-6536 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6537    TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540    TCGA-D5-6541 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6898    TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923    TCGA-D5-6924 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6926    TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929    TCGA-D5-6930 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6931    TCGA-D5-6932    TCGA-D5-7000    TCGA-F4-6459    TCGA-F4-6460 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704    TCGA-F4-6805 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809    TCGA-F4-6854 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299    TCGA-G4-6303 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309    TCGA-G4-6315 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-G4-6317    TCGA-G4-6323    TCGA-G4-6626 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
D741V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHM MUTATED                                  0     0
  CHM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CHM MUTATED                           1     3
  CHM WILD-TYPE                        18   173
D741V12, multiclass
                                  clus
vv                                 CHM MUTATED CHM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      3           173
[1] 4 2
[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 = THAP9 MUTATION ANALYSIS
D742V1, survival
                 sevent
clus2               0   1
  THAP9 MUTATED     9   3
  THAP9 WILD-TYPE 268  75
  THAP9 MUTATED THAP9 WILD-TYPE 
             12             343 
  THAP9 MUTATED THAP9 WILD-TYPE 
              3              75 
$`THAP9 MUTATED`
TCGA-AA-3713 TCGA-A6-5666 TCGA-AA-3848 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00N 
       19.04        32.71        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        13.41         7.50 

$`THAP9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  THAP9 MUTATED THAP9 WILD-TYPE 
           1.02            0.00 
  THAP9 MUTATED THAP9 WILD-TYPE 
          88.21          148.01 
  THAP9 MUTATED THAP9 WILD-TYPE 
          18.43           22.09 
[1] "1.0 - 88.2 (18.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D742V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THAP9 MUTATED         2        0        1         0         3         1
  THAP9 WILD-TYPE      62        1       25       108         5         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THAP9 MUTATED           0          0          1          2        2         0
  THAP9 WILD-TYPE        18          6         43         31       33        12
                 vv
clus              STAGE IVB
  THAP9 MUTATED           0
  THAP9 WILD-TYPE         1
D742V3, multiclass
            clus
vv           THAP9 MUTATED THAP9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  THAP9 MUTATED     2   0   6   4
  THAP9 WILD-TYPE   7  67 243  37
D742V4, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  T1             2               7
  T2             0              67
  T3             6             243
  T4             4              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
  THAP9 MUTATED     8   2   2
  THAP9 WILD-TYPE 212  79  64
D742V5, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V6, binary
                 cls
clus                0   1
  THAP9 MUTATED    10   2
  THAP9 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED     10    2
  THAP9 WILD-TYPE  275   46
   clus
vv  THAP9 MUTATED THAP9 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D742V7, binary
                 cls
clus                0   1
  THAP9 MUTATED     9   3
  THAP9 WILD-TYPE 161 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED      9    3
  THAP9 WILD-TYPE  161  194
        clus
vv       THAP9 MUTATED THAP9 WILD-TYPE
  FEMALE             9             161
  MALE               3             194
[1] 2 2
[1] FALSE
D742V8, binary
                 cls
clus                0   1
  THAP9 MUTATED     8   1
  THAP9 WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED      8    1
  THAP9 WILD-TYPE  292    7
     clus
vv    THAP9 MUTATED THAP9 WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D742V9, binary
                 cls
clus                0   1
  THAP9 MUTATED     9   3
  THAP9 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED      9    3
  THAP9 WILD-TYPE  305   45
                               clus
vv                              THAP9 MUTATED THAP9 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  THAP9 MUTATED     8   0   1   0
  THAP9 WILD-TYPE 251   3  21  21
D742V10, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             0              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"
D742V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THAP9 MUTATED                                  0     0
  THAP9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THAP9 MUTATED                           1     4
  THAP9 WILD-TYPE                        18   172
D742V12, multiclass
                                  clus
vv                                 THAP9 MUTATED THAP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = C1QL3 MUTATION ANALYSIS
D743V1, survival
                 sevent
clus2               0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 273  78
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             351 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              0              78 
$`C1QL3 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-CM-6166 TCGA-D5-6533 
       22.06        22.52        21.99        25.48 

$`C1QL3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  C1QL3 MUTATED C1QL3 WILD-TYPE 
          21.99            0.00 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
          25.48          148.01 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
          22.29           22.03 
[1] "22.0 - 25.5 (22.3)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D743V2, continuous
                 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      62        1       26       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C1QL3 MUTATED           0          0          0          0        0         0
  C1QL3 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  C1QL3 MUTATED           0
  C1QL3 WILD-TYPE         1
D743V3, multiclass
            clus
vv           C1QL3 MUTATED C1QL3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  C1QL3 MUTATED     0   2   1   1
  C1QL3 WILD-TYPE   9  65 248  40
D743V4, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             1             248
  T4             1              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
  C1QL3 MUTATED     4   0   0
  C1QL3 WILD-TYPE 216  81  66
D743V5, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V6, binary
                 cls
clus                0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  281   48
   clus
vv  C1QL3 MUTATED C1QL3 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D743V7, binary
                 cls
clus                0   1
  C1QL3 MUTATED     3   1
  C1QL3 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      3    1
  C1QL3 WILD-TYPE  167  196
        clus
vv       C1QL3 MUTATED C1QL3 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D743V8, binary
                 cls
clus                0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  296    8
     clus
vv    C1QL3 MUTATED C1QL3 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D743V9, binary
                 cls
clus                0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  310   48
                               clus
vv                              C1QL3 MUTATED C1QL3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  C1QL3 MUTATED     3   0   0   0
  C1QL3 WILD-TYPE 256   3  22  21
D743V10, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D743V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1QL3 MUTATED                                  0     0
  C1QL3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  C1QL3 MUTATED                           0     4
  C1QL3 WILD-TYPE                        19   172
D743V12, multiclass
                                  clus
vv                                 C1QL3 MUTATED C1QL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = HCRTR2 MUTATION ANALYSIS
D744V1, survival
                  sevent
clus2                0   1
  HCRTR2 MUTATED     6   1
  HCRTR2 WILD-TYPE 271  77
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              348 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               1               77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
             7.5              0.0 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           88.21           148.01 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           30.05            22.01 
[1] "7.5 - 88.2 (30.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D744V2, continuous
                  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      62        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR2 MUTATED           0          0          0          1        0
  HCRTR2 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  HCRTR2 MUTATED           0         0
  HCRTR2 WILD-TYPE        12         1
D744V3, multiclass
            clus
vv           HCRTR2 MUTATED HCRTR2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  HCRTR2 MUTATED     1   2   4   0
  HCRTR2 WILD-TYPE   8  65 245  41
D744V4, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              4              245
  T4              0               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
  HCRTR2 MUTATED     6   0   1
  HCRTR2 WILD-TYPE 214  81  65
D744V5, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V6, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     6   0
  HCRTR2 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      6    0
  HCRTR2 WILD-TYPE  279   48
   clus
vv  HCRTR2 MUTATED HCRTR2 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D744V7, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     4   3
  HCRTR2 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      4    3
  HCRTR2 WILD-TYPE  166  194
        clus
vv       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D744V8, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     6   0
  HCRTR2 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      6    0
  HCRTR2 WILD-TYPE  294    8
     clus
vv    HCRTR2 MUTATED HCRTR2 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D744V9, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     7   0
  HCRTR2 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      7    0
  HCRTR2 WILD-TYPE  307   48
                               clus
vv                              HCRTR2 MUTATED HCRTR2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HCRTR2 MUTATED     4   0   0   0
  HCRTR2 WILD-TYPE 255   3  22  21
D744V10, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D744V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCRTR2 MUTATED                                  0     0
  HCRTR2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HCRTR2 MUTATED                           1     3
  HCRTR2 WILD-TYPE                        18   173
D744V12, multiclass
                                  clus
vv                                 HCRTR2 MUTATED HCRTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = C9ORF71 MUTATION ANALYSIS
D745V1, survival
                   sevent
clus2                 0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 273  78
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               351 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                0                78 
$`C9ORF71 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-CA-6717 
       35.80        26.17        79.69        12.76 

$`C9ORF71 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       22.09        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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            22.030 
[1] "12.8 - 79.7 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D745V2, continuous
                   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      63        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF71 MUTATED           0          0          0          0        0
  C9ORF71 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF71 MUTATED           0         0
  C9ORF71 WILD-TYPE        12         1
D745V3, multiclass
            clus
vv           C9ORF71 MUTATED C9ORF71 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C9ORF71 MUTATED     0   1   3   0
  C9ORF71 WILD-TYPE   9  66 246  41
D745V4, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               0                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
  C9ORF71 MUTATED     4   0   0
  C9ORF71 WILD-TYPE 216  81  66
D745V5, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  N0               4               216
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D745V6, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      4    0
  C9ORF71 WILD-TYPE  281   48
   clus
vv  C9ORF71 MUTATED C9ORF71 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D745V7, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     2   2
  C9ORF71 WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      2    2
  C9ORF71 WILD-TYPE  168  195
        clus
vv       C9ORF71 MUTATED C9ORF71 WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D745V8, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      4    0
  C9ORF71 WILD-TYPE  296    8
     clus
vv    C9ORF71 MUTATED C9ORF71 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D745V9, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     3   1
  C9ORF71 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      3    1
  C9ORF71 WILD-TYPE  311   47
                               clus
vv                              C9ORF71 MUTATED C9ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C9ORF71 MUTATED     3   0   0   1
  C9ORF71 WILD-TYPE 256   3  22  20
D745V10, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               1                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"
D745V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF71 MUTATED                                  0     1
  C9ORF71 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C9ORF71 MUTATED                           0     3
  C9ORF71 WILD-TYPE                        19   173
D745V12, multiclass
                                  clus
vv                                 C9ORF71 MUTATED C9ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = RIMBP3 MUTATION ANALYSIS
D746V1, survival
                  sevent
clus2                0   1
  RIMBP3 MUTATED     6   0
  RIMBP3 WILD-TYPE 271  78
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              349 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               0               78 
$`RIMBP3 MUTATED`
TCGA-G4-6310 TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6928 TCGA-G4-6293 
       63.62        34.98        12.16        14.50        11.64       133.18 

$`RIMBP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           11.64             0.00 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
          133.18           148.01 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           24.74            22.06 
[1] "11.6 - 133.2 (24.7)" "0.0 - 148.0 (22.1)" 
[1] "hr="     "9400000"
D746V2, continuous
                  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      63        1       26       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RIMBP3 MUTATED           1          0          1          0        0
  RIMBP3 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  RIMBP3 MUTATED           0         0
  RIMBP3 WILD-TYPE        12         1
D746V3, multiclass
            clus
vv           RIMBP3 MUTATED RIMBP3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  RIMBP3 MUTATED     0   1   4   1
  RIMBP3 WILD-TYPE   9  66 245  40
D746V4, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              1               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
  RIMBP3 MUTATED     4   2   0
  RIMBP3 WILD-TYPE 216  79  66
D746V5, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  N0              4              216
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V6, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     5   0
  RIMBP3 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      5    0
  RIMBP3 WILD-TYPE  280   48
   clus
vv  RIMBP3 MUTATED RIMBP3 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D746V7, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     3   3
  RIMBP3 WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      3    3
  RIMBP3 WILD-TYPE  167  194
        clus
vv       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D746V8, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     5   1
  RIMBP3 WILD-TYPE 295   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      5    1
  RIMBP3 WILD-TYPE  295    7
     clus
vv    RIMBP3 MUTATED RIMBP3 WILD-TYPE
  NO               5              295
  YES              1                7
[1] 2 2
[1] FALSE
D746V9, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     4   2
  RIMBP3 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      4    2
  RIMBP3 WILD-TYPE  310   46
                               clus
vv                              RIMBP3 MUTATED RIMBP3 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RIMBP3 MUTATED     6   0   0   0
  RIMBP3 WILD-TYPE 253   3  22  21
D746V10, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D746V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMBP3 MUTATED                                  0     0
  RIMBP3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RIMBP3 MUTATED                           0     5
  RIMBP3 WILD-TYPE                        19   171
D746V12, multiclass
                                  clus
vv                                 RIMBP3 MUTATED RIMBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = HELQ MUTATION ANALYSIS
D747V1, survival
                sevent
clus2              0   1
  HELQ MUTATED    12   4
  HELQ WILD-TYPE 265  74
  HELQ MUTATED HELQ WILD-TYPE 
            16            339 
  HELQ MUTATED HELQ WILD-TYPE 
             4             74 
$`HELQ MUTATED`
TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00N 
       79.69        63.98        78.08         1.02         2.01         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6598 
       34.98        12.16        83.24        24.53        58.39        49.41 
TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6165 TCGA-F4-6459 
       12.76        15.02        16.04         8.61 

$`HELQ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       40.96         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  HELQ MUTATED HELQ WILD-TYPE 
          1.02           0.00 
  HELQ MUTATED HELQ WILD-TYPE 
         83.24         148.01 
  HELQ MUTATED HELQ WILD-TYPE 
        20.285         22.060 
[1] "1.0 - 83.2 (20.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D747V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HELQ MUTATED         3        0        3         6         3         0
  HELQ WILD-TYPE      61        1       23       102         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HELQ MUTATED           1          0          1          0        0         0
  HELQ WILD-TYPE        17          6         43         33       35        12
                vv
clus             STAGE IVB
  HELQ MUTATED           0
  HELQ WILD-TYPE         1
D747V3, multiclass
            clus
vv           HELQ MUTATED HELQ WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             6            102
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  HELQ MUTATED     1   3  11   3
  HELQ WILD-TYPE   8  64 238  38
D747V4, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  T1            1              8
  T2            3             64
  T3           11            238
  T4            3             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
  HELQ MUTATED    16   0   2
  HELQ WILD-TYPE 204  81  64
D747V5, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  N0           16            204
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V6, binary
                cls
clus               0   1
  HELQ MUTATED    14   0
  HELQ WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     14    0
  HELQ WILD-TYPE  271   48
   clus
vv  HELQ MUTATED HELQ WILD-TYPE
  0           14            271
  1            0             48
[1] 2 2
[1] FALSE
D747V7, binary
                cls
clus               0   1
  HELQ MUTATED     8  10
  HELQ WILD-TYPE 162 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED      8   10
  HELQ WILD-TYPE  162  187
        clus
vv       HELQ MUTATED HELQ WILD-TYPE
  FEMALE            8            162
  MALE             10            187
[1] 2 2
[1] FALSE
D747V8, binary
                cls
clus               0   1
  HELQ MUTATED    14   0
  HELQ WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     14    0
  HELQ WILD-TYPE  286    8
     clus
vv    HELQ MUTATED HELQ WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D747V9, binary
                cls
clus               0   1
  HELQ MUTATED    13   5
  HELQ WILD-TYPE 301  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     13    5
  HELQ WILD-TYPE  301   43
                               clus
vv                              HELQ MUTATED HELQ WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HELQ MUTATED    13   0   0   2
  HELQ WILD-TYPE 246   3  22  19
D747V10, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            2             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"
D747V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HELQ MUTATED                                  0     2
  HELQ WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HELQ MUTATED                           0     9
  HELQ WILD-TYPE                        19   167
D747V12, multiclass
                                  clus
vv                                 HELQ MUTATED HELQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(748) Variable = VPS13B MUTATION ANALYSIS
D748V1, survival
                  sevent
clus2                0   1
  VPS13B MUTATED    39  11
  VPS13B WILD-TYPE 238  67
  VPS13B MUTATED VPS13B WILD-TYPE 
              50              305 
  VPS13B MUTATED VPS13B WILD-TYPE 
              11               67 
$`VPS13B MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6964 
        1.02        13.02         0.92        19.04        19.04        10.88 
TCGA-G4-6628 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 
       79.69        29.19        33.53        24.39        19.66         3.02 
TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3667 TCGA-AA-3864 TCGA-AA-3956 TCGA-AA-3977 
        0.00        29.95        14.01        53.00        34.03        25.02 
TCGA-AA-3980 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-4071 TCGA-AY-6197 
       27.02         4.01        34.98        35.01         0.95        21.44 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CA-6717 
       58.39        62.79        49.41        12.10        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5860 
       10.06        14.30        51.32        37.02        30.08        32.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-5541 
       12.00        29.03        14.04        12.95        19.59        55.92 
TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       15.12        16.14        15.58         9.44        13.35        12.00 
TCGA-F4-6805 TCGA-G4-6293 
       34.42       133.18 

$`VPS13B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       85.05        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       32.75        36.53        32.91        31.63        30.44        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02         9.07        19.07        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31        33.01         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        22.36        88.21         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 
       12.59        17.56       148.01        85.45        15.62        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 
       25.02        13.02        29.06        22.03        22.98        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        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       12.03        45.40        54.61        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.41        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  VPS13B MUTATED VPS13B WILD-TYPE 
               0                0 
  VPS13B MUTATED VPS13B WILD-TYPE 
          133.18           148.01 
  VPS13B MUTATED VPS13B WILD-TYPE 
          19.315           22.360 
[1] "0.0 - 133.2 (19.3)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D748V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS13B MUTATED         8        0        7        18         3         0
  VPS13B WILD-TYPE      56        1       19        90         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13B MUTATED           4          1          3          4        2
  VPS13B WILD-TYPE        14          5         41         29       33
                  vv
clus               STAGE IVA STAGE IVB
  VPS13B MUTATED           0         0
  VPS13B WILD-TYPE        12         1
D748V3, multiclass
            clus
vv           VPS13B MUTATED VPS13B WILD-TYPE
  STAGE I                 8               56
  STAGE IA                0                1
  STAGE II                7               19
  STAGE IIA              18               90
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               4               14
  STAGE IIIA              1                5
  STAGE IIIB              3               41
  STAGE IIIC              4               29
  STAGE IV                2               33
  STAGE IVA               0               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
  VPS13B MUTATED     1   8  35   8
  VPS13B WILD-TYPE   8  59 214  33
D748V4, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  T1              1                8
  T2              8               59
  T3             35              214
  T4              8               33
[1] 4 2
[1] TRUE
[1] "dimension 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    38   8   6
  VPS13B WILD-TYPE 182  73  60
D748V5, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  N0             38              182
  N1              8               73
  N2              6               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V6, binary
                  cls
clus                 0   1
  VPS13B MUTATED    40   2
  VPS13B WILD-TYPE 245  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     40    2
  VPS13B WILD-TYPE  245   46
   clus
vv  VPS13B MUTATED VPS13B WILD-TYPE
  0             40              245
  1              2               46
[1] 2 2
[1] FALSE
D748V7, binary
                  cls
clus                 0   1
  VPS13B MUTATED    22  30
  VPS13B WILD-TYPE 148 167
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     22   30
  VPS13B WILD-TYPE  148  167
        clus
vv       VPS13B MUTATED VPS13B WILD-TYPE
  FEMALE             22              148
  MALE               30              167
[1] 2 2
[1] FALSE
D748V8, binary
                  cls
clus                 0   1
  VPS13B MUTATED    45   2
  VPS13B WILD-TYPE 255   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     45    2
  VPS13B WILD-TYPE  255    6
     clus
vv    VPS13B MUTATED VPS13B WILD-TYPE
  NO              45              255
  YES              2                6
[1] 2 2
[1] FALSE
D748V9, binary
                  cls
clus                 0   1
  VPS13B MUTATED    41  10
  VPS13B WILD-TYPE 273  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     41   10
  VPS13B WILD-TYPE  273   38
                               clus
vv                              VPS13B MUTATED VPS13B WILD-TYPE
  COLON ADENOCARCINOMA                      41              273
  COLON MUCINOUS ADENOCARCINOMA             10               38
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  VPS13B MUTATED    35   0   1   7
  VPS13B WILD-TYPE 224   3  21  14
D748V10, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  R0             35              224
  R1              0                3
  R2              1               21
  RX              7               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"
D748V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS13B MUTATED                                  0     4
  VPS13B WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS13B MUTATED                           4    27
  VPS13B WILD-TYPE                        15   149
D748V12, multiclass
                                  clus
vv                                 VPS13B MUTATED VPS13B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                        27              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(749) Variable = ZNF620 MUTATION ANALYSIS
D749V1, survival
                  sevent
clus2                0   1
  ZNF620 MUTATED     7   1
  ZNF620 WILD-TYPE 270  77
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               8              347 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               1               77 
$`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 
       12.76       135.65 

$`ZNF620 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
        0.92        41.00        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF620 MUTATED ZNF620 WILD-TYPE 
            12.1              0.0 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
          135.65           148.01 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
          19.745           22.090 
[1] "12.1 - 135.7 (19.7)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "2.4"
D749V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF620 MUTATED         1        0        1         3         0         0
  ZNF620 WILD-TYPE      63        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF620 MUTATED           0          0          2          0        1
  ZNF620 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF620 MUTATED           0         0
  ZNF620 WILD-TYPE        12         1
D749V3, multiclass
            clus
vv           ZNF620 MUTATED ZNF620 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF620 MUTATED     0   1   5   2
  ZNF620 WILD-TYPE   9  66 244  39
D749V4, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              2               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
  ZNF620 MUTATED     5   3   0
  ZNF620 WILD-TYPE 215  78  66
D749V5, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  N0              5              215
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V6, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     6   1
  ZNF620 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      6    1
  ZNF620 WILD-TYPE  279   47
   clus
vv  ZNF620 MUTATED ZNF620 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D749V7, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     1   7
  ZNF620 WILD-TYPE 169 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      1    7
  ZNF620 WILD-TYPE  169  190
        clus
vv       ZNF620 MUTATED ZNF620 WILD-TYPE
  FEMALE              1              169
  MALE                7              190
[1] 2 2
[1] FALSE
D749V8, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     7   0
  ZNF620 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      7    0
  ZNF620 WILD-TYPE  293    8
     clus
vv    ZNF620 MUTATED ZNF620 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D749V9, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     5   2
  ZNF620 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      5    2
  ZNF620 WILD-TYPE  309   46
                               clus
vv                              ZNF620 MUTATED ZNF620 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF620 MUTATED     5   0   0   1
  ZNF620 WILD-TYPE 254   3  22  20
D749V10, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D749V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF620 MUTATED                                  0     1
  ZNF620 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF620 MUTATED                           1     2
  ZNF620 WILD-TYPE                        18   174
D749V12, multiclass
                                  clus
vv                                 ZNF620 MUTATED ZNF620 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(750) Variable = ZNF570 MUTATION ANALYSIS
D750V1, survival
                  sevent
clus2                0   1
  ZNF570 MUTATED     7   1
  ZNF570 WILD-TYPE 270  77
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               8              347 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               1               77 
$`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 
       16.14        85.48 

$`ZNF570 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  ZNF570 MUTATED ZNF570 WILD-TYPE 
           15.95             0.00 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
          124.27           148.01 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
           27.09            22.06 
[1] "15.9 - 124.3 (27.1)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "2.6"
D750V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF570 MUTATED         3        0        0         3         1         0
  ZNF570 WILD-TYPE      61        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF570 MUTATED           0          0          1          0        0
  ZNF570 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF570 MUTATED           1         0
  ZNF570 WILD-TYPE        11         1
D750V3, multiclass
            clus
vv           ZNF570 MUTATED ZNF570 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF570 MUTATED     1   2   4   2
  ZNF570 WILD-TYPE   8  65 245  39
D750V4, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              4              245
  T4              2               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
  ZNF570 MUTATED     7   2   0
  ZNF570 WILD-TYPE 213  79  66
D750V5, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V6, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     6   1
  ZNF570 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      6    1
  ZNF570 WILD-TYPE  279   47
   clus
vv  ZNF570 MUTATED ZNF570 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D750V7, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     7   2
  ZNF570 WILD-TYPE 163 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      7    2
  ZNF570 WILD-TYPE  163  195
        clus
vv       ZNF570 MUTATED ZNF570 WILD-TYPE
  FEMALE              7              163
  MALE                2              195
[1] 2 2
[1] FALSE
D750V8, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     8   0
  ZNF570 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      8    0
  ZNF570 WILD-TYPE  292    8
     clus
vv    ZNF570 MUTATED ZNF570 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D750V9, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     7   2
  ZNF570 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      7    2
  ZNF570 WILD-TYPE  307   46
                               clus
vv                              ZNF570 MUTATED ZNF570 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF570 MUTATED     6   0   0   3
  ZNF570 WILD-TYPE 253   3  22  18
D750V10, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              3               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"
D750V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF570 MUTATED                                  0     0
  ZNF570 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF570 MUTATED                           1     6
  ZNF570 WILD-TYPE                        18   170
D750V12, multiclass
                                  clus
vv                                 ZNF570 MUTATED ZNF570 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = AP1G2 MUTATION ANALYSIS
D751V1, survival
                 sevent
clus2               0   1
  AP1G2 MUTATED    12   1
  AP1G2 WILD-TYPE 265  77
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             13             342 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
              1              77 
$`AP1G2 MUTATED`
TCGA-AA-3554 TCGA-AA-3672 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3966 
       17.95         0.92        20.12        19.66         1.02         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 
       74.56 

$`AP1G2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  AP1G2 MUTATED AP1G2 WILD-TYPE 
           0.92            0.00 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
          74.56          148.01 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
          19.66           22.09 
[1] "0.9 - 74.6 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D751V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP1G2 MUTATED         0        0        0         7         0         0
  AP1G2 WILD-TYPE      64        1       26       101         8         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        16          6         43         31       35        12
                 vv
clus              STAGE IVB
  AP1G2 MUTATED           0
  AP1G2 WILD-TYPE         1
D751V3, multiclass
            clus
vv           AP1G2 MUTATED AP1G2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  AP1G2 MUTATED     0   1  11   1
  AP1G2 WILD-TYPE   9  66 238  40
D751V4, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             1              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
  AP1G2 MUTATED     8   4   1
  AP1G2 WILD-TYPE 212  77  65
D751V5, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V6, binary
                 cls
clus                0   1
  AP1G2 MUTATED    10   0
  AP1G2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     10    0
  AP1G2 WILD-TYPE  275   48
   clus
vv  AP1G2 MUTATED AP1G2 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D751V7, binary
                 cls
clus                0   1
  AP1G2 MUTATED     6   7
  AP1G2 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED      6    7
  AP1G2 WILD-TYPE  164  190
        clus
vv       AP1G2 MUTATED AP1G2 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D751V8, binary
                 cls
clus                0   1
  AP1G2 MUTATED    11   0
  AP1G2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     11    0
  AP1G2 WILD-TYPE  289    8
     clus
vv    AP1G2 MUTATED AP1G2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D751V9, binary
                 cls
clus                0   1
  AP1G2 MUTATED    10   3
  AP1G2 WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     10    3
  AP1G2 WILD-TYPE  304   45
                               clus
vv                              AP1G2 MUTATED AP1G2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AP1G2 MUTATED    10   0   0   0
  AP1G2 WILD-TYPE 249   3  22  21
D751V10, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D751V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP1G2 MUTATED                                  0     0
  AP1G2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP1G2 MUTATED                           0     6
  AP1G2 WILD-TYPE                        19   170
D751V12, multiclass
                                  clus
vv                                 AP1G2 MUTATED AP1G2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = SLC22A16 MUTATION ANALYSIS
D752V1, survival
                    sevent
clus2                  0   1
  SLC22A16 MUTATED     9   3
  SLC22A16 WILD-TYPE 268  75
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                12                343 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 75 
$`SLC22A16 MUTATED`
TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-A00R 
       10.88        26.17        22.06        19.66         3.02         0.99 
TCGA-AA-A01T TCGA-AU-6004 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-6171 
       33.04        27.09        10.06        51.32        37.02        14.04 

$`SLC22A16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.12        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
              0.99               0.00 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             51.32             148.01 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             20.86              22.09 
[1] "1.0 - 51.3 (20.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D752V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A16 MUTATED         4        0        1         5         0         0
  SLC22A16 WILD-TYPE      60        1       25       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A16 MUTATED           1          0          0          1        0
  SLC22A16 WILD-TYPE        17          6         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC22A16 MUTATED           0         0
  SLC22A16 WILD-TYPE        12         1
D752V3, multiclass
            clus
vv           SLC22A16 MUTATED SLC22A16 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SLC22A16 MUTATED     0   4   7   2
  SLC22A16 WILD-TYPE   9  63 242  39
D752V4, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  T1                0                  9
  T2                4                 63
  T3                7                242
  T4                2                 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
  SLC22A16 MUTATED    10   2   1
  SLC22A16 WILD-TYPE 210  79  65
D752V5, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  N0               10                210
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V6, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    10   0
  SLC22A16 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     10    0
  SLC22A16 WILD-TYPE  275   48
   clus
vv  SLC22A16 MUTATED SLC22A16 WILD-TYPE
  0               10                275
  1                0                 48
[1] 2 2
[1] FALSE
D752V7, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     9   4
  SLC22A16 WILD-TYPE 161 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      9    4
  SLC22A16 WILD-TYPE  161  193
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  FEMALE                9                161
  MALE                  4                193
[1] 2 2
[1] FALSE
D752V8, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    10   0
  SLC22A16 WILD-TYPE 290   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     10    0
  SLC22A16 WILD-TYPE  290    8
     clus
vv    SLC22A16 MUTATED SLC22A16 WILD-TYPE
  NO                10                290
  YES                0                  8
[1] 2 2
[1] FALSE
D752V9, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    12   1
  SLC22A16 WILD-TYPE 302  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     12    1
  SLC22A16 WILD-TYPE  302   47
                               clus
vv                              SLC22A16 MUTATED SLC22A16 WILD-TYPE
  COLON ADENOCARCINOMA                        12                302
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC22A16 MUTATED    10   0   0   2
  SLC22A16 WILD-TYPE 249   3  22  19
D752V10, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  R0               10                249
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D752V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A16 MUTATED                                  0     1
  SLC22A16 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC22A16 MUTATED                           1     7
  SLC22A16 WILD-TYPE                        18   169
D752V12, multiclass
                                  clus
vv                                 SLC22A16 MUTATED SLC22A16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           7                169
[1] 4 2
[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 = FER MUTATION ANALYSIS
D753V1, survival
               sevent
clus2             0   1
  FER MUTATED    12   2
  FER WILD-TYPE 265  76
  FER MUTATED FER WILD-TYPE 
           14           341 
  FER MUTATED FER WILD-TYPE 
            2            76 
$`FER MUTATED`
TCGA-AA-3867 TCGA-AA-3950 TCGA-G4-6586 TCGA-G4-6628 TCGA-AA-3947 TCGA-AA-A010 
       24.03        24.00        35.80        79.69        33.01        34.98 
TCGA-AZ-4315 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6172 TCGA-CM-6674 
       58.39        21.99        21.14         5.03        11.01        12.95 
TCGA-D5-6930 TCGA-G4-6306 
       13.35        44.68 

$`FER WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  FER MUTATED FER WILD-TYPE 
         5.03          0.00 
  FER MUTATED FER WILD-TYPE 
        79.69        148.01 
  FER MUTATED FER WILD-TYPE 
       24.015        22.030 
[1] "5.0 - 79.7 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D753V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FER MUTATED         2        0        0         6         2         0
  FER WILD-TYPE      62        1       26       102         6         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        18          6         42         33       34        11
               vv
clus            STAGE IVB
  FER MUTATED           0
  FER WILD-TYPE         1
D753V3, multiclass
            clus
vv           FER MUTATED FER WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            6           102
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            1            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
  FER MUTATED     1   2  10   2
  FER WILD-TYPE   8  65 239  39
D753V4, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  T1           1             8
  T2           2            65
  T3          10           239
  T4           2            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
  FER MUTATED    11   3   1
  FER WILD-TYPE 209  78  65
D753V5, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  N0          11           209
  N1           3            78
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V6, binary
               cls
clus              0   1
  FER MUTATED    12   2
  FER WILD-TYPE 273  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     12    2
  FER WILD-TYPE  273   46
   clus
vv  FER MUTATED FER WILD-TYPE
  0          12           273
  1           2            46
[1] 2 2
[1] FALSE
D753V7, binary
               cls
clus              0   1
  FER MUTATED     7   8
  FER WILD-TYPE 163 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      7    8
  FER WILD-TYPE  163  189
        clus
vv       FER MUTATED FER WILD-TYPE
  FEMALE           7           163
  MALE             8           189
[1] 2 2
[1] FALSE
D753V8, binary
               cls
clus              0   1
  FER MUTATED    13   0
  FER WILD-TYPE 287   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     13    0
  FER WILD-TYPE  287    8
     clus
vv    FER MUTATED FER WILD-TYPE
  NO           13           287
  YES           0             8
[1] 2 2
[1] FALSE
D753V9, binary
               cls
clus              0   1
  FER MUTATED    12   3
  FER WILD-TYPE 302  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     12    3
  FER WILD-TYPE  302   45
                               clus
vv                              FER MUTATED FER WILD-TYPE
  COLON ADENOCARCINOMA                   12           302
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FER MUTATED    12   0   1   2
  FER WILD-TYPE 247   3  21  19
D753V10, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  R0          12           247
  R1           0             3
  R2           1            21
  RX           2            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"
D753V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FER MUTATED                                  0     0
  FER WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FER MUTATED                           0    10
  FER WILD-TYPE                        19   166
D753V12, multiclass
                                  clus
vv                                 FER MUTATED FER WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                     10           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(754) Variable = SCN3A MUTATION ANALYSIS
D754V1, survival
                 sevent
clus2               0   1
  SCN3A MUTATED    31   8
  SCN3A WILD-TYPE 246  70
  SCN3A MUTATED SCN3A WILD-TYPE 
             39             316 
  SCN3A MUTATED SCN3A WILD-TYPE 
              8              70 
$`SCN3A MUTATED`
TCGA-AA-3556 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6321 TCGA-A6-2671 
       23.01        19.04        19.04        24.00        22.09        43.76 
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6652 TCGA-A6-6781 
       32.75        33.53        22.06        32.71        24.69        19.66 
TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       63.98        31.00        33.01        25.02         4.01        34.98 
TCGA-AA-A02F TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       39.98        17.82        58.39        62.79        49.41         6.77 
TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5541 
       12.76        22.03        12.95        11.01        10.06        55.92 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 
       25.48        15.12         4.80        13.35        12.00       140.38 
TCGA-DM-A1HB TCGA-F4-6459 TCGA-G4-6323 
      135.65         8.61        13.78 

$`SCN3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        35.80        26.17        91.79        79.69 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       23.61        22.09        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       25.18        21.76        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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-A02H 
       33.04         1.02        26.01        37.02        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        21.44         1.41         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-6680 
       14.04        11.01        13.05        11.08        11.08        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       45.40        54.61        19.59        56.09        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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C 
       12.59         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-F4-6460 
      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 
       43.04        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-G4-6626 
       85.48        61.91        36.00        46.75 

  SCN3A MUTATED SCN3A WILD-TYPE 
           4.01            0.00 
  SCN3A MUTATED SCN3A WILD-TYPE 
         140.38          148.01 
  SCN3A MUTATED SCN3A WILD-TYPE 
          23.01           21.99 
[1] "4.0 - 140.4 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D754V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN3A MUTATED         3        1        5        10         4         1
  SCN3A WILD-TYPE      61        0       21        98         4         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN3A MUTATED           2          0          7          2        3         2
  SCN3A WILD-TYPE        16          6         37         31       32        10
                 vv
clus              STAGE IVB
  SCN3A MUTATED           0
  SCN3A WILD-TYPE         1
D754V3, multiclass
            clus
vv           SCN3A MUTATED SCN3A WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               5              21
  STAGE IIA             10              98
  STAGE IIB              4               4
  STAGE IIC              1               0
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             7              37
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              2              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
  SCN3A MUTATED     1   4  26  10
  SCN3A WILD-TYPE   8  63 223  31
D754V4, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  T1             1               8
  T2             4              63
  T3            26             223
  T4            10              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
  SCN3A MUTATED    28  10   4
  SCN3A WILD-TYPE 192  71  62
D754V5, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  N0            28             192
  N1            10              71
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V6, binary
                 cls
clus                0   1
  SCN3A MUTATED    28   5
  SCN3A WILD-TYPE 257  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     28    5
  SCN3A WILD-TYPE  257   43
   clus
vv  SCN3A MUTATED SCN3A WILD-TYPE
  0            28             257
  1             5              43
[1] 2 2
[1] FALSE
D754V7, binary
                 cls
clus                0   1
  SCN3A MUTATED    19  23
  SCN3A WILD-TYPE 151 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     19   23
  SCN3A WILD-TYPE  151  174
        clus
vv       SCN3A MUTATED SCN3A WILD-TYPE
  FEMALE            19             151
  MALE              23             174
[1] 2 2
[1] FALSE
D754V8, binary
                 cls
clus                0   1
  SCN3A MUTATED    35   1
  SCN3A WILD-TYPE 265   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     35    1
  SCN3A WILD-TYPE  265    7
     clus
vv    SCN3A MUTATED SCN3A WILD-TYPE
  NO             35             265
  YES             1               7
[1] 2 2
[1] FALSE
D754V9, binary
                 cls
clus                0   1
  SCN3A MUTATED    32   8
  SCN3A WILD-TYPE 282  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     32    8
  SCN3A WILD-TYPE  282   40
                               clus
vv                              SCN3A MUTATED SCN3A WILD-TYPE
  COLON ADENOCARCINOMA                     32             282
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCN3A MUTATED    30   0   2   2
  SCN3A WILD-TYPE 229   3  20  19
D754V10, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  R0            30             229
  R1             0               3
  R2             2              20
  RX             2              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"
D754V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCN3A MUTATED                                  0     1
  SCN3A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCN3A MUTATED                           4    23
  SCN3A WILD-TYPE                        15   153
D754V12, multiclass
                                  clus
vv                                 SCN3A MUTATED SCN3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       23             153
[1] 4 2
[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 = IQGAP2 MUTATION ANALYSIS
D755V1, survival
                  sevent
clus2                0   1
  IQGAP2 MUTATED    13   7
  IQGAP2 WILD-TYPE 264  71
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              20              335 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
               7               71 
$`IQGAP2 MUTATED`
TCGA-AA-3543 TCGA-AA-3950 TCGA-AA-A00L TCGA-A6-2676 TCGA-AA-3549 TCGA-AA-3977 
        0.99        24.00        38.04        42.90        21.01        25.02 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6606 
       30.02         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 
        6.18        47.87 

$`IQGAP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        19.07        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       88.21         6.77        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28H TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
            0.99             0.00 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
           62.79           148.01 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
           24.51            22.03 
[1] "1.0 - 62.8 (24.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D755V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQGAP2 MUTATED         2        0        2        11         2         0
  IQGAP2 WILD-TYPE      62        1       24        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQGAP2 MUTATED           0          0          0          1        2
  IQGAP2 WILD-TYPE        18          6         44         32       33
                  vv
clus               STAGE IVA STAGE IVB
  IQGAP2 MUTATED           0         0
  IQGAP2 WILD-TYPE        12         1
D755V3, multiclass
            clus
vv           IQGAP2 MUTATED IQGAP2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              11               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               0               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
  IQGAP2 MUTATED     0   3  14   4
  IQGAP2 WILD-TYPE   9  64 235  37
D755V4, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             14              235
  T4              4               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
  IQGAP2 MUTATED    18   0   3
  IQGAP2 WILD-TYPE 202  81  63
D755V5, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  N0             18              202
  N1              0               81
  N2              3               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"
D755V6, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    15   2
  IQGAP2 WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     15    2
  IQGAP2 WILD-TYPE  270   46
   clus
vv  IQGAP2 MUTATED IQGAP2 WILD-TYPE
  0             15              270
  1              2               46
[1] 2 2
[1] FALSE
D755V7, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED     6  15
  IQGAP2 WILD-TYPE 164 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED      6   15
  IQGAP2 WILD-TYPE  164  182
        clus
vv       IQGAP2 MUTATED IQGAP2 WILD-TYPE
  FEMALE              6              164
  MALE               15              182
[1] 2 2
[1] FALSE
D755V8, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    17   1
  IQGAP2 WILD-TYPE 283   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     17    1
  IQGAP2 WILD-TYPE  283    7
     clus
vv    IQGAP2 MUTATED IQGAP2 WILD-TYPE
  NO              17              283
  YES              1                7
[1] 2 2
[1] FALSE
D755V9, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    17   4
  IQGAP2 WILD-TYPE 297  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     17    4
  IQGAP2 WILD-TYPE  297   44
                               clus
vv                              IQGAP2 MUTATED IQGAP2 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IQGAP2 MUTATED    13   0   1   2
  IQGAP2 WILD-TYPE 246   3  21  19
D755V10, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              1               21
  RX              2               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"
D755V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQGAP2 MUTATED                                  0     1
  IQGAP2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IQGAP2 MUTATED                           1    11
  IQGAP2 WILD-TYPE                        18   165
D755V12, multiclass
                                  clus
vv                                 IQGAP2 MUTATED IQGAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(756) Variable = CD3D MUTATION ANALYSIS
D756V1, survival
                sevent
clus2              0   1
  CD3D MUTATED     2   2
  CD3D WILD-TYPE 275  76
  CD3D MUTATED CD3D WILD-TYPE 
             4            351 
  CD3D MUTATED CD3D WILD-TYPE 
             2             76 
$`CD3D MUTATED`
TCGA-AZ-6608 TCGA-A6-5657 TCGA-AA-A00N TCGA-CA-5254 
        1.94        31.63         4.01        12.69 

$`CD3D WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CD3D MUTATED CD3D WILD-TYPE 
          1.94           0.00 
  CD3D MUTATED CD3D WILD-TYPE 
         31.63         148.01 
  CD3D MUTATED CD3D WILD-TYPE 
          8.35          22.09 
[1] "1.9 - 31.6 (8.3)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "5.2"
D756V2, continuous
                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      64        1       26       107         7         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        18          5         43         33       35        12
                vv
clus             STAGE IVB
  CD3D MUTATED           0
  CD3D WILD-TYPE         1
D756V3, multiclass
            clus
vv           CD3D MUTATED CD3D WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CD3D MUTATED     0   1   2   1
  CD3D WILD-TYPE   9  66 247  40
D756V4, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            1             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
  CD3D MUTATED     2   2   0
  CD3D WILD-TYPE 218  79  66
D756V5, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  N0            2            218
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V6, binary
                cls
clus               0   1
  CD3D MUTATED     4   0
  CD3D WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      4    0
  CD3D WILD-TYPE  281   48
   clus
vv  CD3D MUTATED CD3D WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D756V7, binary
                cls
clus               0   1
  CD3D MUTATED     2   2
  CD3D WILD-TYPE 168 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      2    2
  CD3D WILD-TYPE  168  195
        clus
vv       CD3D MUTATED CD3D WILD-TYPE
  FEMALE            2            168
  MALE              2            195
[1] 2 2
[1] FALSE
D756V8, binary
                cls
clus               0   1
  CD3D MUTATED     3   0
  CD3D WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      3    0
  CD3D WILD-TYPE  297    8
     clus
vv    CD3D MUTATED CD3D WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D756V9, binary
                cls
clus               0   1
  CD3D MUTATED     3   1
  CD3D WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      3    1
  CD3D WILD-TYPE  311   47
                               clus
vv                              CD3D MUTATED CD3D WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD3D MUTATED     2   0   0   1
  CD3D WILD-TYPE 257   3  22  20
D756V10, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  R0            2            257
  R1            0              3
  R2            0             22
  RX            1             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"
D756V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD3D MUTATED                                  0     1
  CD3D WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD3D MUTATED                           1     1
  CD3D WILD-TYPE                        18   175
D756V12, multiclass
                                  clus
vv                                 CD3D MUTATED CD3D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       1            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(757) Variable = ADORA3 MUTATION ANALYSIS
D757V1, survival
                  sevent
clus2                0   1
  ADORA3 MUTATED     9   5
  ADORA3 WILD-TYPE 268  73
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              14              341 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5               73 
$`ADORA3 MUTATED`
TCGA-G4-6588 TCGA-A6-3807 TCGA-AA-3864 TCGA-AA-3955 TCGA-AU-3779 TCGA-CA-6718 
       26.17        34.65        53.00        20.98        14.50        10.06 
TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-6676 TCGA-DM-A1D8 TCGA-F4-6570 
       21.14       124.27        22.98        11.08        12.59         6.18 
TCGA-F4-6809 TCGA-F4-6855 
       13.25        47.41 

$`ADORA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        26.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       15.62        51.32        21.99        82.95         2.01        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ADORA3 MUTATED ADORA3 WILD-TYPE 
            6.18             0.00 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
          124.27           148.01 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
           21.06            22.09 
[1] "6.2 - 124.3 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D757V2, continuous
                  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      61        1       25       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADORA3 MUTATED           0          0          2          1        0
  ADORA3 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ADORA3 MUTATED           1         0
  ADORA3 WILD-TYPE        11         1
D757V3, multiclass
            clus
vv           ADORA3 MUTATED ADORA3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  ADORA3 MUTATED     1   3  10   0
  ADORA3 WILD-TYPE   8  64 239  41
D757V4, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             10              239
  T4              0               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
  ADORA3 MUTATED     9   3   2
  ADORA3 WILD-TYPE 211  78  64
D757V5, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V6, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    11   1
  ADORA3 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     11    1
  ADORA3 WILD-TYPE  274   47
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D757V7, binary
                  cls
clus                 0   1
  ADORA3 MUTATED     9   5
  ADORA3 WILD-TYPE 161 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      9    5
  ADORA3 WILD-TYPE  161  192
        clus
vv       ADORA3 MUTATED ADORA3 WILD-TYPE
  FEMALE              9              161
  MALE                5              192
[1] 2 2
[1] FALSE
D757V8, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    13   0
  ADORA3 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     13    0
  ADORA3 WILD-TYPE  287    8
     clus
vv    ADORA3 MUTATED ADORA3 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D757V9, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    13   1
  ADORA3 WILD-TYPE 301  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     13    1
  ADORA3 WILD-TYPE  301   47
                               clus
vv                              ADORA3 MUTATED ADORA3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ADORA3 MUTATED    10   0   0   3
  ADORA3 WILD-TYPE 249   3  22  18
D757V10, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              3               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"
D757V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADORA3 MUTATED                                  0     1
  ADORA3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADORA3 MUTATED                           0    11
  ADORA3 WILD-TYPE                        19   165
D757V12, multiclass
                                  clus
vv                                 ADORA3 MUTATED ADORA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        11              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(758) Variable = ALDOB MUTATION ANALYSIS
D758V1, survival
                 sevent
clus2               0   1
  ALDOB MUTATED    12   3
  ALDOB WILD-TYPE 265  75
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             340 
  ALDOB MUTATED ALDOB WILD-TYPE 
              3              75 
$`ALDOB MUTATED`
TCGA-AD-6895 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3821 
       25.08        35.80        79.69        42.90         8.38         1.02 
TCGA-AA-3845 TCGA-AA-3949 TCGA-AA-A01Q TCGA-AZ-6599 TCGA-CK-4948 TCGA-CK-6747 
        0.00        26.01         1.02         6.77       148.01        82.95 
TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6928 
       43.27        16.14        11.64 

$`ALDOB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       26.17        91.79        43.76        46.65        43.76        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ALDOB MUTATED ALDOB WILD-TYPE 
              0               0 
  ALDOB MUTATED ALDOB WILD-TYPE 
         148.01          140.38 
  ALDOB MUTATED ALDOB WILD-TYPE 
         25.080          22.045 
[1] "0.0 - 148.0 (25.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D758V2, continuous
                 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      60        1       25       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALDOB MUTATED           1          0          2          0        0         0
  ALDOB WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  ALDOB MUTATED           0
  ALDOB WILD-TYPE         1
D758V3, multiclass
            clus
vv           ALDOB MUTATED ALDOB WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ALDOB MUTATED     0   4  10   1
  ALDOB WILD-TYPE   9  63 239  40
D758V4, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  T1             0               9
  T2             4              63
  T3            10             239
  T4             1              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
  ALDOB MUTATED    12   3   0
  ALDOB WILD-TYPE 208  78  66
D758V5, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  N0            12             208
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D758V6, binary
                 cls
clus                0   1
  ALDOB MUTATED    13   0
  ALDOB WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     13    0
  ALDOB WILD-TYPE  272   48
   clus
vv  ALDOB MUTATED ALDOB WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D758V7, binary
                 cls
clus                0   1
  ALDOB MUTATED     9   6
  ALDOB WILD-TYPE 161 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED      9    6
  ALDOB WILD-TYPE  161  191
        clus
vv       ALDOB MUTATED ALDOB WILD-TYPE
  FEMALE             9             161
  MALE               6             191
[1] 2 2
[1] FALSE
D758V8, binary
                 cls
clus                0   1
  ALDOB MUTATED    13   0
  ALDOB WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     13    0
  ALDOB WILD-TYPE  287    8
     clus
vv    ALDOB MUTATED ALDOB WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D758V9, binary
                 cls
clus                0   1
  ALDOB MUTATED    10   5
  ALDOB WILD-TYPE 304  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     10    5
  ALDOB WILD-TYPE  304   43
                               clus
vv                              ALDOB MUTATED ALDOB WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALDOB MUTATED    12   0   0   1
  ALDOB WILD-TYPE 247   3  22  20
D758V10, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D758V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDOB MUTATED                                  0     0
  ALDOB WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALDOB MUTATED                           1    10
  ALDOB WILD-TYPE                        18   166
D758V12, multiclass
                                  clus
vv                                 ALDOB MUTATED ALDOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(759) Variable = ELFN2 MUTATION ANALYSIS
D759V1, survival
                 sevent
clus2               0   1
  ELFN2 MUTATED     8   1
  ELFN2 WILD-TYPE 269  77
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             346 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              1              77 
$`ELFN2 MUTATED`
TCGA-AA-3979 TCGA-AD-6895 TCGA-CK-4947 TCGA-CM-5860 TCGA-D5-6533 TCGA-D5-6535 
       24.00        25.08        17.56        32.02        25.48        15.12 
TCGA-D5-6537 TCGA-D5-6927 TCGA-G4-6315 
        4.80         9.44        61.91 

$`ELFN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25        43.27        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  ELFN2 MUTATED ELFN2 WILD-TYPE 
            4.8             0.0 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
          61.91          148.01 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
         24.000          22.045 
[1] "4.8 - 61.9 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D759V2, continuous
                 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      64        1       26       105         8         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        18          6         40         33       34        12
                 vv
clus              STAGE IVB
  ELFN2 MUTATED           0
  ELFN2 WILD-TYPE         1
D759V3, multiclass
            clus
vv           ELFN2 MUTATED ELFN2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ELFN2 MUTATED     0   0   7   2
  ELFN2 WILD-TYPE   9  67 242  39
D759V4, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             2              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
  ELFN2 MUTATED     4   5   0
  ELFN2 WILD-TYPE 216  76  66
D759V5, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  N0             4             216
  N1             5              76
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V6, binary
                 cls
clus                0   1
  ELFN2 MUTATED     6   1
  ELFN2 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      6    1
  ELFN2 WILD-TYPE  279   47
   clus
vv  ELFN2 MUTATED ELFN2 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D759V7, binary
                 cls
clus                0   1
  ELFN2 MUTATED     3   6
  ELFN2 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      3    6
  ELFN2 WILD-TYPE  167  191
        clus
vv       ELFN2 MUTATED ELFN2 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D759V8, binary
                 cls
clus                0   1
  ELFN2 MUTATED     9   0
  ELFN2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      9    0
  ELFN2 WILD-TYPE  291    8
     clus
vv    ELFN2 MUTATED ELFN2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D759V9, binary
                 cls
clus                0   1
  ELFN2 MUTATED     9   0
  ELFN2 WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      9    0
  ELFN2 WILD-TYPE  305   48
                               clus
vv                              ELFN2 MUTATED ELFN2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ELFN2 MUTATED     7   0   0   2
  ELFN2 WILD-TYPE 252   3  22  19
D759V10, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             2              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"
D759V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELFN2 MUTATED                                  0     0
  ELFN2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ELFN2 MUTATED                           0     8
  ELFN2 WILD-TYPE                        19   168
D759V12, multiclass
                                  clus
vv                                 ELFN2 MUTATED ELFN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = AWAT1 MUTATION ANALYSIS
D760V1, survival
                 sevent
clus2               0   1
  AWAT1 MUTATED     7   1
  AWAT1 WILD-TYPE 270  77
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              8             347 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              1              77 
$`AWAT1 MUTATED`
TCGA-AA-A024 TCGA-G4-6588 TCGA-AA-3947 TCGA-AA-3949 TCGA-CA-6717 TCGA-D5-5540 
       39.06        26.17        33.01        26.01        12.76        56.09 
TCGA-D5-6536 TCGA-D5-6538 
       17.85        17.13 

$`AWAT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
        2.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  AWAT1 MUTATED AWAT1 WILD-TYPE 
          12.76            0.00 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
          56.09          148.01 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
          26.09           22.03 
[1] "12.8 - 56.1 (26.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D760V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AWAT1 MUTATED         0        0        1         4         1         0
  AWAT1 WILD-TYPE      64        1       25       104         7         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  AWAT1 MUTATED           0
  AWAT1 WILD-TYPE         1
D760V3, multiclass
            clus
vv           AWAT1 MUTATED AWAT1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  AWAT1 MUTATED     0   0   7   1
  AWAT1 WILD-TYPE   9  67 242  40
D760V4, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  AWAT1 MUTATED     6   1   1
  AWAT1 WILD-TYPE 214  80  65
D760V5, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V6, binary
                 cls
clus                0   1
  AWAT1 MUTATED     8   0
  AWAT1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      8    0
  AWAT1 WILD-TYPE  277   48
   clus
vv  AWAT1 MUTATED AWAT1 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D760V7, binary
                 cls
clus                0   1
  AWAT1 MUTATED     4   4
  AWAT1 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      4    4
  AWAT1 WILD-TYPE  166  193
        clus
vv       AWAT1 MUTATED AWAT1 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D760V8, binary
                 cls
clus                0   1
  AWAT1 MUTATED     8   0
  AWAT1 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      8    0
  AWAT1 WILD-TYPE  292    8
     clus
vv    AWAT1 MUTATED AWAT1 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D760V9, binary
                 cls
clus                0   1
  AWAT1 MUTATED     4   4
  AWAT1 WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      4    4
  AWAT1 WILD-TYPE  310   44
                               clus
vv                              AWAT1 MUTATED AWAT1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AWAT1 MUTATED     7   0   0   1
  AWAT1 WILD-TYPE 252   3  22  20
D760V10, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D760V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AWAT1 MUTATED                                  0     1
  AWAT1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AWAT1 MUTATED                           0     4
  AWAT1 WILD-TYPE                        19   172
D760V12, multiclass
                                  clus
vv                                 AWAT1 MUTATED AWAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = EXT1 MUTATION ANALYSIS
D761V1, survival
                sevent
clus2              0   1
  EXT1 MUTATED    14   4
  EXT1 WILD-TYPE 263  74
  EXT1 MUTATED EXT1 WILD-TYPE 
            18            337 
  EXT1 MUTATED EXT1 WILD-TYPE 
             4             74 
$`EXT1 MUTATED`
TCGA-AA-3715 TCGA-CK-5912 TCGA-A6-5656 TCGA-AA-3517 TCGA-AA-3555 TCGA-AA-3666 
       19.04        49.08        32.91        38.99        29.95         2.01 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 
       25.02        38.04         4.01        34.98        35.01        12.16 
TCGA-AD-6963 TCGA-AY-6197 TCGA-AY-6386 TCGA-CK-6751 TCGA-CM-6676 TCGA-D5-6536 
       27.42        21.44        17.82       124.27        11.08        17.85 

$`EXT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  EXT1 MUTATED EXT1 WILD-TYPE 
          2.01           0.00 
  EXT1 MUTATED EXT1 WILD-TYPE 
        124.27         148.01 
  EXT1 MUTATED EXT1 WILD-TYPE 
         26.22          22.03 
[1] "2.0 - 124.3 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D761V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXT1 MUTATED         5        0        1         5         2         0
  EXT1 WILD-TYPE      59        1       25       103         6         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        16          6         43         33       35        12
                vv
clus             STAGE IVB
  EXT1 MUTATED           0
  EXT1 WILD-TYPE         1
D761V3, multiclass
            clus
vv           EXT1 MUTATED EXT1 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  EXT1 MUTATED     0   6  10   2
  EXT1 WILD-TYPE   9  61 239  39
D761V4, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  T1            0              9
  T2            6             61
  T3           10            239
  T4            2             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
  EXT1 MUTATED    15   2   1
  EXT1 WILD-TYPE 205  79  65
D761V5, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  N0           15            205
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V6, binary
                cls
clus               0   1
  EXT1 MUTATED    12   0
  EXT1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     12    0
  EXT1 WILD-TYPE  273   48
   clus
vv  EXT1 MUTATED EXT1 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D761V7, binary
                cls
clus               0   1
  EXT1 MUTATED     4  14
  EXT1 WILD-TYPE 166 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED      4   14
  EXT1 WILD-TYPE  166  183
        clus
vv       EXT1 MUTATED EXT1 WILD-TYPE
  FEMALE            4            166
  MALE             14            183
[1] 2 2
[1] FALSE
D761V8, binary
                cls
clus               0   1
  EXT1 MUTATED    15   1
  EXT1 WILD-TYPE 285   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     15    1
  EXT1 WILD-TYPE  285    7
     clus
vv    EXT1 MUTATED EXT1 WILD-TYPE
  NO            15            285
  YES            1              7
[1] 2 2
[1] FALSE
D761V9, binary
                cls
clus               0   1
  EXT1 MUTATED    13   5
  EXT1 WILD-TYPE 301  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     13    5
  EXT1 WILD-TYPE  301   43
                               clus
vv                              EXT1 MUTATED EXT1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EXT1 MUTATED    13   0   0   2
  EXT1 WILD-TYPE 246   3  22  19
D761V10, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            2             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"
D761V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXT1 MUTATED                                  0     0
  EXT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EXT1 MUTATED                           1     8
  EXT1 WILD-TYPE                        18   168
D761V12, multiclass
                                  clus
vv                                 EXT1 MUTATED EXT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = DNAH17 MUTATION ANALYSIS
D762V1, survival
                  sevent
clus2                0   1
  DNAH17 MUTATED    23   7
  DNAH17 WILD-TYPE 254  71
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              30              325 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
               7               71 
$`DNAH17 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6628 TCGA-A6-5660 TCGA-A6-5662 
       19.04       100.01        49.08        79.69        29.19        23.61 
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 
        8.38        20.12         3.02        63.98        78.08         6.97 
TCGA-AA-3968 TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       21.99        12.16        83.24        17.82        58.39         1.41 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5868 
       12.20        12.76        10.06        13.02        15.02        17.03 
TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1HB TCGA-G4-6293 
       12.99        45.40        16.14        15.58       135.65       133.18 

$`DNAH17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        19.66        20.28         7.04        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       21.44         5.13        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-6719 
       12.69        12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       14.04        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-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DNAH17 MUTATED DNAH17 WILD-TYPE 
            1.41             0.00 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
          135.65           148.01 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
           18.43            22.36 
[1] "1.4 - 135.7 (18.4)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D762V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH17 MUTATED         5        0        5        12         0         0
  DNAH17 WILD-TYPE      59        1       21        96         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH17 MUTATED           1          0          2          1        2
  DNAH17 WILD-TYPE        17          6         42         32       33
                  vv
clus               STAGE IVA STAGE IVB
  DNAH17 MUTATED           2         0
  DNAH17 WILD-TYPE        10         1
D762V3, multiclass
            clus
vv           DNAH17 MUTATED DNAH17 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA              12               96
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               2               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
  DNAH17 MUTATED     0   5  23   2
  DNAH17 WILD-TYPE   9  62 226  39
D762V4, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  T1              0                9
  T2              5               62
  T3             23              226
  T4              2               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
  DNAH17 MUTATED    22   4   4
  DNAH17 WILD-TYPE 198  77  62
D762V5, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  N0             22              198
  N1              4               77
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V6, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    22   4
  DNAH17 WILD-TYPE 263  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     22    4
  DNAH17 WILD-TYPE  263   44
   clus
vv  DNAH17 MUTATED DNAH17 WILD-TYPE
  0             22              263
  1              4               44
[1] 2 2
[1] FALSE
D762V7, binary
                  cls
clus                 0   1
  DNAH17 MUTATED     8  22
  DNAH17 WILD-TYPE 162 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED      8   22
  DNAH17 WILD-TYPE  162  175
        clus
vv       DNAH17 MUTATED DNAH17 WILD-TYPE
  FEMALE              8              162
  MALE               22              175
[1] 2 2
[1] FALSE
D762V8, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    28   1
  DNAH17 WILD-TYPE 272   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     28    1
  DNAH17 WILD-TYPE  272    7
     clus
vv    DNAH17 MUTATED DNAH17 WILD-TYPE
  NO              28              272
  YES              1                7
[1] 2 2
[1] FALSE
D762V9, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    25   4
  DNAH17 WILD-TYPE 289  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     25    4
  DNAH17 WILD-TYPE  289   44
                               clus
vv                              DNAH17 MUTATED DNAH17 WILD-TYPE
  COLON ADENOCARCINOMA                      25              289
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAH17 MUTATED    17   0   1   5
  DNAH17 WILD-TYPE 242   3  21  16
D762V10, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              1               21
  RX              5               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"
D762V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH17 MUTATED                                  0     4
  DNAH17 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAH17 MUTATED                           5    15
  DNAH17 WILD-TYPE                        14   161
D762V12, multiclass
                                  clus
vv                                 DNAH17 MUTATED DNAH17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                     5               14
  WHITE                                        15              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(763) Variable = SYNE1 MUTATION ANALYSIS
D763V1, survival
                 sevent
clus2               0   1
  SYNE1 MUTATED    86  29
  SYNE1 WILD-TYPE 191  49
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            115             240 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             29              49 
$`SYNE1 MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 
       24.33        14.53        24.16        13.02        37.05         8.05 
TCGA-AA-3543 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3950 
        0.99        19.99         0.92        85.05        19.04        24.00 
TCGA-AD-6888 TCGA-AD-6895 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
       15.52        25.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2683 
       26.17        79.69        43.76        46.65        42.90        16.57 
TCGA-A6-3808 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       33.34        29.19        33.53        22.06        32.71         8.38 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 
       25.18        21.76        19.66        20.28         3.02        63.98 
TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
        1.02        29.95        20.98         6.97        54.02         2.01 
TCGA-AA-3710 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3875 
       26.99        15.95         0.00         0.00        36.03        18.05 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00E 
       26.01        25.02        27.02         7.96        27.02        30.02 
TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02K TCGA-AA-A02W 
        4.01        17.03        34.98         1.02        14.01        41.00 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 
       12.16        83.24        24.53        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        12.59 
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        54.61        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        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XF TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB 
       13.35        12.00        38.20       140.38        44.32       135.65 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6809 TCGA-G4-6309 
       35.97        31.96         6.18        47.87        13.25        85.48 
TCGA-G4-6626 
       46.75 

$`SYNE1 WILD-TYPE`
TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
        1.02        24.03        36.03        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99         6.05        19.00        36.00 
TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        21.37        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6625 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-3807 
        1.94        49.08        91.79        43.76        42.28        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       32.75        36.53        32.91        31.63        30.44        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6653 
       22.09        27.09        22.52        25.08        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       23.87        20.12         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        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-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       13.94        61.02        78.08        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        17.03        10.06         0.00        33.07 
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-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       27.02        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 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-A00W TCGA-AA-A017 
       18.05        27.02        42.02         0.99        14.99        15.02 
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         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       51.98        39.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       18.05        40.96         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4616 
       14.50        16.31         0.95         0.20        17.82         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       22.36        62.79        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CK-4947 
        3.19        12.69        12.36        12.39        12.59        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
        2.01        20.02        25.02        30.08        32.02         5.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        14.04        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-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6532 
       11.08        11.08        45.40        19.59        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       25.48        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         7.53        12.39        10.13        12.43         9.04 
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-A1DA TCGA-DM-A1HA TCGA-DM-A282 
       49.91        13.32        12.59         7.50       131.51       139.17 
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-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 

  SYNE1 MUTATED SYNE1 WILD-TYPE 
              0               0 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         140.38          148.01 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         22.030          22.225 
[1] "0.0 - 140.4 (22.0)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D763V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNE1 MUTATED        15        0        8        40         5         1
  SYNE1 WILD-TYPE      49        1       18        68         3         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNE1 MUTATED           4          1         22          7        8         4
  SYNE1 WILD-TYPE        14          5         22         26       27         8
                 vv
clus              STAGE IVB
  SYNE1 MUTATED           0
  SYNE1 WILD-TYPE         1
D763V3, multiclass
            clus
vv           SYNE1 MUTATED SYNE1 WILD-TYPE
  STAGE I               15              49
  STAGE IA               0               1
  STAGE II               8              18
  STAGE IIA             40              68
  STAGE IIB              5               3
  STAGE IIC              1               0
  STAGE III              4              14
  STAGE IIIA             1               5
  STAGE IIIB            22              22
  STAGE IIIC             7              26
  STAGE IV               8              27
  STAGE IVA              4               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
  SYNE1 MUTATED     3  16  85  14
  SYNE1 WILD-TYPE   6  51 164  27
D763V4, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  T1             3               6
  T2            16              51
  T3            85             164
  T4            14              27
[1] 4 2
[1] TRUE
[1] "dimension 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    74  31  13
  SYNE1 WILD-TYPE 146  50  53
D763V5, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  N0            74             146
  N1            31              50
  N2            13              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V6, binary
                 cls
clus                0   1
  SYNE1 MUTATED    94  12
  SYNE1 WILD-TYPE 191  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     94   12
  SYNE1 WILD-TYPE  191   36
   clus
vv  SYNE1 MUTATED SYNE1 WILD-TYPE
  0            94             191
  1            12              36
[1] 2 2
[1] FALSE
D763V7, binary
                 cls
clus                0   1
  SYNE1 MUTATED    55  63
  SYNE1 WILD-TYPE 115 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     55   63
  SYNE1 WILD-TYPE  115  134
        clus
vv       SYNE1 MUTATED SYNE1 WILD-TYPE
  FEMALE            55             115
  MALE              63             134
[1] 2 2
[1] FALSE
D763V8, binary
                 cls
clus                0   1
  SYNE1 MUTATED   100   1
  SYNE1 WILD-TYPE 200   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED    100    1
  SYNE1 WILD-TYPE  200    7
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  NO            100             200
  YES             1               7
[1] 2 2
[1] FALSE
D763V9, binary
                 cls
clus                0   1
  SYNE1 MUTATED    96  20
  SYNE1 WILD-TYPE 218  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     96   20
  SYNE1 WILD-TYPE  218   28
                               clus
vv                              SYNE1 MUTATED SYNE1 WILD-TYPE
  COLON ADENOCARCINOMA                     96             218
  COLON MUCINOUS ADENOCARCINOMA            20              28
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNE1 MUTATED    85   0   4   7
  SYNE1 WILD-TYPE 174   3  18  14
D763V10, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  R0            85             174
  R1             0               3
  R2             4              18
  RX             7              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"
D763V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNE1 MUTATED                                  0     6
  SYNE1 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYNE1 MUTATED                           7    68
  SYNE1 WILD-TYPE                        12   108
D763V12, multiclass
                                  clus
vv                                 SYNE1 MUTATED SYNE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        6               4
  BLACK OR AFRICAN AMERICAN                    7              12
  WHITE                                       68             108
[1] 4 2
[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 = C1ORF35 MUTATION ANALYSIS
D764V1, survival
                   sevent
clus2                 0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 274  77
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                4               351 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                1                77 
$`C1ORF35 MUTATED`
TCGA-AA-3713 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 
       19.04        12.76        51.32        21.14 

$`C1ORF35 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
            12.76              0.00 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
            51.32            148.01 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
            20.09             22.09 
[1] "12.8 - 51.3 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D764V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF35 MUTATED         1        0        0         2         0         0
  C1ORF35 WILD-TYPE      63        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF35 MUTATED           0          0          0          0        1
  C1ORF35 WILD-TYPE        18          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF35 MUTATED           0         0
  C1ORF35 WILD-TYPE        12         1
D764V3, multiclass
            clus
vv           C1ORF35 MUTATED C1ORF35 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  C1ORF35 MUTATED     1   0   3   0
  C1ORF35 WILD-TYPE   8  67 246  41
D764V4, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  T1               1                 8
  T2               0                67
  T3               3               246
  T4               0                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
  C1ORF35 MUTATED     4   0   0
  C1ORF35 WILD-TYPE 216  81  66
D764V5, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  N0               4               216
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V6, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     2   1
  C1ORF35 WILD-TYPE 283  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      2    1
  C1ORF35 WILD-TYPE  283   47
   clus
vv  C1ORF35 MUTATED C1ORF35 WILD-TYPE
  0               2               283
  1               1                47
[1] 2 2
[1] FALSE
D764V7, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     2   2
  C1ORF35 WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      2    2
  C1ORF35 WILD-TYPE  168  195
        clus
vv       C1ORF35 MUTATED C1ORF35 WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D764V8, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 297   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      3    1
  C1ORF35 WILD-TYPE  297    7
     clus
vv    C1ORF35 MUTATED C1ORF35 WILD-TYPE
  NO                3               297
  YES               1                 7
[1] 2 2
[1] FALSE
D764V9, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      3    1
  C1ORF35 WILD-TYPE  311   47
                               clus
vv                              C1ORF35 MUTATED C1ORF35 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C1ORF35 MUTATED     0   0   1   3
  C1ORF35 WILD-TYPE 259   3  21  18
D764V10, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  R0               0               259
  R1               0                 3
  R2               1                21
  RX               3                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"
D764V11, continuous
[1] "Remove cluster labels:" "C1ORF35 MUTATED"       
clus
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                1               345 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AA-3496 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3516        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-3527        TCGA-AA-3530 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552        TCGA-AA-3554 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562        TCGA-AA-3662 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3697 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3715        TCGA-AA-3814        TCGA-AA-3844        TCGA-AA-3860 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3870        TCGA-AA-3939        TCGA-AA-3950 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3972        TCGA-AA-3976        TCGA-AA-3979 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-A00L        TCGA-AA-A00Z        TCGA-AA-A024 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-DM-A285        TCGA-G4-6310 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-2676        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-A6-5656 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660        TCGA-A6-5661 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665        TCGA-A6-5666 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141        TCGA-A6-6142 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6651        TCGA-A6-6652        TCGA-A6-6653 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781        TCGA-A6-6782 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3502        TCGA-AA-3510 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3526        TCGA-AA-3529        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-3544 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3663 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667        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-3693        TCGA-AA-3695 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3811 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3812        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3861 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3872 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3941 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3947        TCGA-AA-3949        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-3973 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3975        TCGA-AA-3977        TCGA-AA-3980        TCGA-AA-3982 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3984        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-A00N        TCGA-AA-A00O 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6889 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6890        TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-6600        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-CA-6715        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-A28C 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6806 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6309        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6626 
"C1ORF35 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF35 MUTATED                                  0     1
  C1ORF35 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF35 MUTATED                           0     2
  C1ORF35 WILD-TYPE                        19   174
D764V12, multiclass
                                  clus
vv                                 C1ORF35 MUTATED C1ORF35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          2               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(765) Variable = POLQ MUTATION ANALYSIS
D765V1, survival
                sevent
clus2              0   1
  POLQ MUTATED    22   7
  POLQ WILD-TYPE 255  71
  POLQ MUTATED POLQ WILD-TYPE 
            29            326 
  POLQ MUTATED POLQ WILD-TYPE 
             7             71 
$`POLQ MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6780 TCGA-A6-6781 
        0.92        19.04        26.17        79.69        20.12        19.66 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3947 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-A010 
       63.98         1.02        33.01        16.08        25.02        34.98 
TCGA-AD-6889 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 
       83.24        62.79        49.41        12.76        10.06       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6675 TCGA-D5-6537 
       23.05        37.02        15.02        12.00        13.05         4.80 
TCGA-D5-6540 TCGA-DM-A1D4 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 
       16.14        92.75        47.41        35.31        65.85 

$`POLQ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        21.76        24.69        24.39        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       21.99        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 
        5.13        22.36        88.21         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        2.01        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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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-G4-6293 TCGA-G4-6299 
       43.04        33.67        13.25         0.53       133.18        74.56 
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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  POLQ MUTATED POLQ WILD-TYPE 
          0.92           0.00 
  POLQ MUTATED POLQ WILD-TYPE 
        124.27         148.01 
  POLQ MUTATED POLQ WILD-TYPE 
         25.02          22.01 
[1] "0.9 - 124.3 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D765V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLQ MUTATED         5        0        3        11         2         0
  POLQ WILD-TYPE      59        1       23        97         6         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        16          6         42         32       33        12
                vv
clus             STAGE IVB
  POLQ MUTATED           1
  POLQ WILD-TYPE         0
D765V3, multiclass
            clus
vv           POLQ MUTATED POLQ WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            11             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             12
  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     0   6  21   3
  POLQ WILD-TYPE   9  61 228  38
D765V4, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  T1            0              9
  T2            6             61
  T3           21            228
  T4            3             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
  POLQ MUTATED    23   6   1
  POLQ WILD-TYPE 197  75  65
D765V5, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  N0           23            197
  N1            6             75
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V6, binary
                cls
clus               0   1
  POLQ MUTATED    20   3
  POLQ WILD-TYPE 265  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     20    3
  POLQ WILD-TYPE  265   45
   clus
vv  POLQ MUTATED POLQ WILD-TYPE
  0           20            265
  1            3             45
[1] 2 2
[1] FALSE
D765V7, binary
                cls
clus               0   1
  POLQ MUTATED    12  18
  POLQ WILD-TYPE 158 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     12   18
  POLQ WILD-TYPE  158  179
        clus
vv       POLQ MUTATED POLQ WILD-TYPE
  FEMALE           12            158
  MALE             18            179
[1] 2 2
[1] FALSE
D765V8, binary
                cls
clus               0   1
  POLQ MUTATED    26   1
  POLQ WILD-TYPE 274   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     26    1
  POLQ WILD-TYPE  274    7
     clus
vv    POLQ MUTATED POLQ WILD-TYPE
  NO            26            274
  YES            1              7
[1] 2 2
[1] FALSE
D765V9, binary
                cls
clus               0   1
  POLQ MUTATED    22   8
  POLQ WILD-TYPE 292  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     22    8
  POLQ WILD-TYPE  292   40
                               clus
vv                              POLQ MUTATED POLQ WILD-TYPE
  COLON ADENOCARCINOMA                    22            292
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POLQ MUTATED    21   0   1   3
  POLQ WILD-TYPE 238   3  21  18
D765V10, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  R0           21            238
  R1            0              3
  R2            1             21
  RX            3             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"
D765V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLQ MUTATED                                  0     3
  POLQ WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  POLQ MUTATED                           2    16
  POLQ WILD-TYPE                        17   160
D765V12, multiclass
                                  clus
vv                                 POLQ MUTATED POLQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      16            160
[1] 4 2
[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 = BAI3 MUTATION ANALYSIS
D766V1, survival
                sevent
clus2              0   1
  BAI3 MUTATED    30   9
  BAI3 WILD-TYPE 247  69
  BAI3 MUTATED BAI3 WILD-TYPE 
            39            316 
  BAI3 MUTATED BAI3 WILD-TYPE 
             9             69 
$`BAI3 MUTATED`
TCGA-AA-3516 TCGA-AA-3554 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-5656 
       13.02        17.95        22.09        91.79        79.69        32.91 
TCGA-AA-3510 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3679 TCGA-AA-3815 
       63.98        19.07        29.95         6.97        15.02        33.04 
TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01G TCGA-AU-6004 
        1.02        33.01         4.01        34.98        12.00        27.09 
TCGA-AY-6196 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
        0.20        49.41        11.74        12.76        10.06        15.62 
TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6166 TCGA-CM-6170 TCGA-D5-5537 
       51.32        15.02        17.03        21.99        15.02        45.40 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6541 TCGA-DM-A1D4 TCGA-DM-A1D8 
       25.48        17.85        17.13        15.58        92.75        12.59 
TCGA-DM-A28G TCGA-G4-6306 TCGA-G4-6315 
       60.79        44.68        61.91 

$`BAI3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
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-A6-5657 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        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-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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       85.45        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       43.27        15.12         4.80        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  BAI3 MUTATED BAI3 WILD-TYPE 
           0.2            0.0 
  BAI3 MUTATED BAI3 WILD-TYPE 
         92.75         148.01 
  BAI3 MUTATED BAI3 WILD-TYPE 
        19.070         22.225 
[1] "0.2 - 92.8 (19.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1"  
D766V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAI3 MUTATED         8        0        4        15         3         0
  BAI3 WILD-TYPE      56        1       22        93         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAI3 MUTATED           2          0          1          2        4         1
  BAI3 WILD-TYPE        16          6         43         31       31        11
                vv
clus             STAGE IVB
  BAI3 MUTATED           0
  BAI3 WILD-TYPE         1
D766V3, multiclass
            clus
vv           BAI3 MUTATED BAI3 WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            15             93
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              4             31
  STAGE IVA             1             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
  BAI3 MUTATED     0  10  25   8
  BAI3 WILD-TYPE   9  57 224  33
D766V4, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  T1            0              9
  T2           10             57
  T3           25            224
  T4            8             33
[1] 4 2
[1] TRUE
[1] "dimension 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    31   4   8
  BAI3 WILD-TYPE 189  77  58
D766V5, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  N0           31            189
  N1            4             77
  N2            8             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"
D766V6, binary
                cls
clus               0   1
  BAI3 MUTATED    31   5
  BAI3 WILD-TYPE 254  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     31    5
  BAI3 WILD-TYPE  254   43
   clus
vv  BAI3 MUTATED BAI3 WILD-TYPE
  0           31            254
  1            5             43
[1] 2 2
[1] FALSE
D766V7, binary
                cls
clus               0   1
  BAI3 MUTATED    21  22
  BAI3 WILD-TYPE 149 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     21   22
  BAI3 WILD-TYPE  149  175
        clus
vv       BAI3 MUTATED BAI3 WILD-TYPE
  FEMALE           21            149
  MALE             22            175
[1] 2 2
[1] FALSE
D766V8, binary
                cls
clus               0   1
  BAI3 MUTATED    32   0
  BAI3 WILD-TYPE 268   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     32    0
  BAI3 WILD-TYPE  268    8
     clus
vv    BAI3 MUTATED BAI3 WILD-TYPE
  NO            32            268
  YES            0              8
[1] 2 2
[1] FALSE
D766V9, binary
                cls
clus               0   1
  BAI3 MUTATED    34   9
  BAI3 WILD-TYPE 280  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     34    9
  BAI3 WILD-TYPE  280   39
                               clus
vv                              BAI3 MUTATED BAI3 WILD-TYPE
  COLON ADENOCARCINOMA                    34            280
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BAI3 MUTATED    28   0   2   6
  BAI3 WILD-TYPE 231   3  20  15
D766V10, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  R0           28            231
  R1            0              3
  R2            2             20
  RX            6             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"
D766V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAI3 MUTATED                                  0     2
  BAI3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAI3 MUTATED                           0    25
  BAI3 WILD-TYPE                        19   151
D766V12, multiclass
                                  clus
vv                                 BAI3 MUTATED BAI3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      25            151
[1] 4 2
[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 = WNK3 MUTATION ANALYSIS
D767V1, survival
                sevent
clus2              0   1
  WNK3 MUTATED    20   2
  WNK3 WILD-TYPE 257  76
  WNK3 MUTATED WNK3 WILD-TYPE 
            22            333 
  WNK3 MUTATED WNK3 WILD-TYPE 
             2             76 
$`WNK3 MUTATED`
TCGA-AD-6895 TCGA-G4-6310 TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6781 
       25.08        63.62        31.63        22.06        32.71        19.66 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3710 TCGA-AA-3875 
       29.95        78.08         6.97        14.01        26.99        18.05 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6168 
       18.05         4.01        58.39        49.41        12.76        12.99 
TCGA-D5-6928 TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6309 
       11.64        43.04        35.31        85.48 

$`WNK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       24.00        20.98        13.94        61.02        54.02         2.01 
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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        31.00         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6808 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  WNK3 MUTATED WNK3 WILD-TYPE 
          4.01           0.00 
  WNK3 MUTATED WNK3 WILD-TYPE 
         85.48         148.01 
  WNK3 MUTATED WNK3 WILD-TYPE 
        26.035         21.990 
[1] "4.0 - 85.5 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.9"
D767V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNK3 MUTATED         3        0        3         8         1         1
  WNK3 WILD-TYPE      61        1       23       100         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK3 MUTATED           0          0          5          2        1         0
  WNK3 WILD-TYPE        18          6         39         31       34        12
                vv
clus             STAGE IVB
  WNK3 MUTATED           0
  WNK3 WILD-TYPE         1
D767V3, multiclass
            clus
vv           WNK3 MUTATED WNK3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            5             39
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             0             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
  WNK3 MUTATED     1   2  16   5
  WNK3 WILD-TYPE   8  65 233  36
D767V4, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  T1            1              8
  T2            2             65
  T3           16            233
  T4            5             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
  WNK3 MUTATED    16   7   1
  WNK3 WILD-TYPE 204  74  65
D767V5, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  N0           16            204
  N1            7             74
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V6, binary
                cls
clus               0   1
  WNK3 MUTATED    21   1
  WNK3 WILD-TYPE 264  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     21    1
  WNK3 WILD-TYPE  264   47
   clus
vv  WNK3 MUTATED WNK3 WILD-TYPE
  0           21            264
  1            1             47
[1] 2 2
[1] FALSE
D767V7, binary
                cls
clus               0   1
  WNK3 MUTATED    12  12
  WNK3 WILD-TYPE 158 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     12   12
  WNK3 WILD-TYPE  158  185
        clus
vv       WNK3 MUTATED WNK3 WILD-TYPE
  FEMALE           12            158
  MALE             12            185
[1] 2 2
[1] FALSE
D767V8, binary
                cls
clus               0   1
  WNK3 MUTATED    20   1
  WNK3 WILD-TYPE 280   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     20    1
  WNK3 WILD-TYPE  280    7
     clus
vv    WNK3 MUTATED WNK3 WILD-TYPE
  NO            20            280
  YES            1              7
[1] 2 2
[1] FALSE
D767V9, binary
                cls
clus               0   1
  WNK3 MUTATED    17   7
  WNK3 WILD-TYPE 297  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     17    7
  WNK3 WILD-TYPE  297   41
                               clus
vv                              WNK3 MUTATED WNK3 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNK3 MUTATED    20   0   1   1
  WNK3 WILD-TYPE 239   3  21  20
D767V10, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  R0           20            239
  R1            0              3
  R2            1             21
  RX            1             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"
D767V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK3 MUTATED                                  0     1
  WNK3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK3 MUTATED                           3    10
  WNK3 WILD-TYPE                        16   166
D767V12, multiclass
                                  clus
vv                                 WNK3 MUTATED WNK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      10            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(768) Variable = CASC1 MUTATION ANALYSIS
D768V1, survival
                 sevent
clus2               0   1
  CASC1 MUTATED    10   2
  CASC1 WILD-TYPE 267  76
  CASC1 MUTATED CASC1 WILD-TYPE 
             12             343 
  CASC1 MUTATED CASC1 WILD-TYPE 
              2              76 
$`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 

$`CASC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41        12.10         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
       12.69        12.36        12.39        12.59        12.59        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CASC1 MUTATED CASC1 WILD-TYPE 
           2.01            0.00 
  CASC1 MUTATED CASC1 WILD-TYPE 
          35.31          148.01 
  CASC1 MUTATED CASC1 WILD-TYPE 
          14.19           22.09 
[1] "2.0 - 35.3 (14.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D768V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASC1 MUTATED         3        0        1         3         1         0
  CASC1 WILD-TYPE      61        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC1 MUTATED           0          0          0          1        0         0
  CASC1 WILD-TYPE        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  CASC1 MUTATED           0
  CASC1 WILD-TYPE         1
D768V3, multiclass
            clus
vv           CASC1 MUTATED CASC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CASC1 MUTATED     0   5   5   2
  CASC1 WILD-TYPE   9  62 244  39
D768V4, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             5             244
  T4             2              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
  CASC1 MUTATED    10   1   1
  CASC1 WILD-TYPE 210  80  65
D768V5, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V6, binary
                 cls
clus                0   1
  CASC1 MUTATED     9   0
  CASC1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED      9    0
  CASC1 WILD-TYPE  276   48
   clus
vv  CASC1 MUTATED CASC1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D768V7, binary
                 cls
clus                0   1
  CASC1 MUTATED     6   6
  CASC1 WILD-TYPE 164 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED      6    6
  CASC1 WILD-TYPE  164  191
        clus
vv       CASC1 MUTATED CASC1 WILD-TYPE
  FEMALE             6             164
  MALE               6             191
[1] 2 2
[1] FALSE
D768V8, binary
                 cls
clus                0   1
  CASC1 MUTATED    10   0
  CASC1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED     10    0
  CASC1 WILD-TYPE  290    8
     clus
vv    CASC1 MUTATED CASC1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D768V9, binary
                 cls
clus                0   1
  CASC1 MUTATED     8   4
  CASC1 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED      8    4
  CASC1 WILD-TYPE  306   44
                               clus
vv                              CASC1 MUTATED CASC1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASC1 MUTATED     5   0   0   3
  CASC1 WILD-TYPE 254   3  22  18
D768V10, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             3              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"
D768V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASC1 MUTATED                                  0     2
  CASC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASC1 MUTATED                           0     6
  CASC1 WILD-TYPE                        19   170
D768V12, multiclass
                                  clus
vv                                 CASC1 MUTATED CASC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = IL2RG MUTATION ANALYSIS
D769V1, survival
                 sevent
clus2               0   1
  IL2RG MUTATED     5   2
  IL2RG WILD-TYPE 272  76
  IL2RG MUTATED IL2RG WILD-TYPE 
              7             348 
  IL2RG MUTATED IL2RG WILD-TYPE 
              2              76 
$`IL2RG MUTATED`
TCGA-G4-6586 TCGA-A6-6781 TCGA-AA-3492 TCGA-AY-6386 TCGA-CA-6717 TCGA-F4-6570 
       35.80        19.66         3.02        17.82        12.76         6.18 
TCGA-G4-6309 
       85.48 

$`IL2RG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        20.12        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  IL2RG MUTATED IL2RG WILD-TYPE 
           3.02            0.00 
  IL2RG MUTATED IL2RG WILD-TYPE 
          85.48          148.01 
  IL2RG MUTATED IL2RG WILD-TYPE 
          17.82           22.09 
[1] "3.0 - 85.5 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D769V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL2RG MUTATED         0        0        1         3         0         0
  IL2RG WILD-TYPE      64        1       25       105         8         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        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  IL2RG MUTATED           0
  IL2RG WILD-TYPE         1
D769V3, multiclass
            clus
vv           IL2RG MUTATED IL2RG WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  IL2RG MUTATED     0   0   6   1
  IL2RG WILD-TYPE   9  67 243  40
D769V4, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  IL2RG MUTATED     4   3   0
  IL2RG WILD-TYPE 216  78  66
D769V5, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  N0             4             216
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V6, binary
                 cls
clus                0   1
  IL2RG MUTATED     6   0
  IL2RG WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      6    0
  IL2RG WILD-TYPE  279   48
   clus
vv  IL2RG MUTATED IL2RG WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D769V7, binary
                 cls
clus                0   1
  IL2RG MUTATED     5   2
  IL2RG WILD-TYPE 165 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      5    2
  IL2RG WILD-TYPE  165  195
        clus
vv       IL2RG MUTATED IL2RG WILD-TYPE
  FEMALE             5             165
  MALE               2             195
[1] 2 2
[1] FALSE
D769V8, binary
                 cls
clus                0   1
  IL2RG MUTATED     7   0
  IL2RG WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      7    0
  IL2RG WILD-TYPE  293    8
     clus
vv    IL2RG MUTATED IL2RG WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D769V9, binary
                 cls
clus                0   1
  IL2RG MUTATED     5   2
  IL2RG WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      5    2
  IL2RG WILD-TYPE  309   46
                               clus
vv                              IL2RG MUTATED IL2RG WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IL2RG MUTATED     6   0   0   1
  IL2RG WILD-TYPE 253   3  22  20
D769V10, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D769V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL2RG MUTATED                                  0     1
  IL2RG WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL2RG MUTATED                           2     3
  IL2RG WILD-TYPE                        17   173
D769V12, multiclass
                                  clus
vv                                 IL2RG MUTATED IL2RG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        3             173
[1] 4 2
[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 = ACOT9 MUTATION ANALYSIS
D770V1, survival
                 sevent
clus2               0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 273  78
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              4             351 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              0              78 
$`ACOT9 MUTATED`
TCGA-AA-3697 TCGA-A6-5665 TCGA-AA-3864 TCGA-CK-4948 
       85.05        22.06        53.00       148.01 

$`ACOT9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ACOT9 MUTATED ACOT9 WILD-TYPE 
          22.06            0.00 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
         148.01          140.38 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
         69.025          21.990 
[1] "22.1 - 148.0 (69.0)" "0.0 - 140.4 (22.0)" 
[1] "hr="     "9500000"
D770V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACOT9 MUTATED         0        0        2         1         0         0
  ACOT9 WILD-TYPE      64        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACOT9 MUTATED           1          0          0          0        0         0
  ACOT9 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  ACOT9 MUTATED           0
  ACOT9 WILD-TYPE         1
D770V3, multiclass
            clus
vv           ACOT9 MUTATED ACOT9 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ACOT9 MUTATED     0   0   4   0
  ACOT9 WILD-TYPE   9  67 245  41
D770V4, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             0              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
  ACOT9 MUTATED     3   1   0
  ACOT9 WILD-TYPE 217  80  66
D770V5, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V6, binary
                 cls
clus                0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      4    0
  ACOT9 WILD-TYPE  281   48
   clus
vv  ACOT9 MUTATED ACOT9 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D770V7, binary
                 cls
clus                0   1
  ACOT9 MUTATED     2   2
  ACOT9 WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      2    2
  ACOT9 WILD-TYPE  168  195
        clus
vv       ACOT9 MUTATED ACOT9 WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D770V8, binary
                 cls
clus                0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      4    0
  ACOT9 WILD-TYPE  296    8
     clus
vv    ACOT9 MUTATED ACOT9 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D770V9, binary
                 cls
clus                0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      4    0
  ACOT9 WILD-TYPE  310   48
                               clus
vv                              ACOT9 MUTATED ACOT9 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACOT9 MUTATED     4   0   0   0
  ACOT9 WILD-TYPE 255   3  22  21
D770V10, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D770V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACOT9 MUTATED                                  0     0
  ACOT9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACOT9 MUTATED                           0     2
  ACOT9 WILD-TYPE                        19   174
D770V12, multiclass
[1] "Remove cluster labels:" "ACOT9 MUTATED"         
clus
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"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-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 

Clustering(771) Variable = DCTN5 MUTATION ANALYSIS
D771V1, survival
                 sevent
clus2               0   1
  DCTN5 MUTATED     5   1
  DCTN5 WILD-TYPE 272  77
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             349 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              1              77 
$`DCTN5 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-3809 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6164 
       19.04        26.17        32.75        49.41        21.99        29.03 

$`DCTN5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DCTN5 MUTATED DCTN5 WILD-TYPE 
          19.04            0.00 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
          49.41          148.01 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
          27.60           22.03 
[1] "19.0 - 49.4 (27.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D771V2, continuous
                 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      64        1       25       106         7         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  DCTN5 MUTATED           0
  DCTN5 WILD-TYPE         1
D771V3, multiclass
            clus
vv           DCTN5 MUTATED DCTN5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  DCTN5 MUTATED     0   0   5   1
  DCTN5 WILD-TYPE   9  67 244  40
D771V4, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             1              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
  DCTN5 MUTATED     5   1   0
  DCTN5 WILD-TYPE 215  80  66
D771V5, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V6, binary
                 cls
clus                0   1
  DCTN5 MUTATED     3   1
  DCTN5 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      3    1
  DCTN5 WILD-TYPE  282   47
   clus
vv  DCTN5 MUTATED DCTN5 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D771V7, binary
                 cls
clus                0   1
  DCTN5 MUTATED     4   2
  DCTN5 WILD-TYPE 166 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      4    2
  DCTN5 WILD-TYPE  166  195
        clus
vv       DCTN5 MUTATED DCTN5 WILD-TYPE
  FEMALE             4             166
  MALE               2             195
[1] 2 2
[1] FALSE
D771V8, binary
                 cls
clus                0   1
  DCTN5 MUTATED     4   1
  DCTN5 WILD-TYPE 296   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      4    1
  DCTN5 WILD-TYPE  296    7
     clus
vv    DCTN5 MUTATED DCTN5 WILD-TYPE
  NO              4             296
  YES             1               7
[1] 2 2
[1] FALSE
D771V9, binary
                 cls
clus                0   1
  DCTN5 MUTATED     5   1
  DCTN5 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      5    1
  DCTN5 WILD-TYPE  309   47
                               clus
vv                              DCTN5 MUTATED DCTN5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DCTN5 MUTATED     3   0   1   1
  DCTN5 WILD-TYPE 256   3  21  20
D771V10, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             1              21
  RX             1              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"
D771V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCTN5 MUTATED                                  0     0
  DCTN5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCTN5 MUTATED                           0     5
  DCTN5 WILD-TYPE                        19   171
D771V12, multiclass
                                  clus
vv                                 DCTN5 MUTATED DCTN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = USH2A MUTATION ANALYSIS
D772V1, survival
                 sevent
clus2               0   1
  USH2A MUTATED    57  15
  USH2A WILD-TYPE 220  63
  USH2A MUTATED USH2A WILD-TYPE 
             72             283 
  USH2A MUTATED USH2A WILD-TYPE 
             15              63 
$`USH2A MUTATED`
TCGA-A6-6649 TCGA-AA-3525 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3715 
       24.16         8.05        19.99         6.05         0.92        19.04 
TCGA-AA-3952 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5660 
        2.01        25.08        10.88        35.80        79.69        29.19 
TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 
        8.38        23.87        19.66         7.04         3.02        63.98 
TCGA-AA-3511 TCGA-AA-3526 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3821 
        6.97        19.07        61.02         6.97        26.99         1.02 
TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3966 
       17.03        32.05        30.05        53.00        31.00         2.01 
TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 
       25.02        13.94         4.01         0.99        17.03        34.98 
TCGA-AA-A01Q TCGA-AA-A02H TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6600 
        1.02         2.01         0.20        58.39        88.21        12.10 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6751 
        3.19        12.76        10.06        15.62        21.14       124.27 
TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 
       37.02        30.08        15.02        15.02        15.02        29.03 
TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6536 
       14.04        54.61        19.59        56.09        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A282 
        4.80        17.13        15.58        12.59       135.65       139.17 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6315 
        6.18         1.55        43.04        47.41       133.18        61.91 

$`USH2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       23.01        19.99        19.00        36.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3517 
       24.39        20.12        20.28        35.01         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3848 
       17.98        15.95        38.99        37.02         0.00        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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        27.02        27.02         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       42.02        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02J 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
       49.41         6.77        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 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        85.45        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        2.01        23.05        20.02        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-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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-D5-5541 
       11.08        11.01        10.06        12.03        45.40        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6540 
       20.19        18.25        25.48        43.27        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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-F4-6805 TCGA-F4-6806 
        8.61        31.96        35.74        47.87        34.42        41.42 
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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  USH2A MUTATED USH2A WILD-TYPE 
            0.2             0.0 
  USH2A MUTATED USH2A WILD-TYPE 
         139.17          148.01 
  USH2A MUTATED USH2A WILD-TYPE 
          17.49           23.01 
[1] "0.2 - 139.2 (17.5)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1"  
D772V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USH2A MUTATED        13        0        9        20         2         0
  USH2A WILD-TYPE      51        1       17        88         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USH2A MUTATED           3          1         10          8        5         0
  USH2A WILD-TYPE        15          5         34         25       30        12
                 vv
clus              STAGE IVB
  USH2A MUTATED           0
  USH2A WILD-TYPE         1
D772V3, multiclass
            clus
vv           USH2A MUTATED USH2A WILD-TYPE
  STAGE I               13              51
  STAGE IA               0               1
  STAGE II               9              17
  STAGE IIA             20              88
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             1               5
  STAGE IIIB            10              34
  STAGE IIIC             8              25
  STAGE IV               5              30
  STAGE IVA              0              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
  USH2A MUTATED     3  11  51   9
  USH2A WILD-TYPE   6  56 198  32
D772V4, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  T1             3               6
  T2            11              56
  T3            51             198
  T4             9              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
  USH2A MUTATED    45  16  13
  USH2A WILD-TYPE 175  65  53
D772V5, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  N0            45             175
  N1            16              65
  N2            13              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V6, binary
                 cls
clus                0   1
  USH2A MUTATED    60   5
  USH2A WILD-TYPE 225  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     60    5
  USH2A WILD-TYPE  225   43
   clus
vv  USH2A MUTATED USH2A WILD-TYPE
  0            60             225
  1             5              43
[1] 2 2
[1] FALSE
D772V7, binary
                 cls
clus                0   1
  USH2A MUTATED    34  40
  USH2A WILD-TYPE 136 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     34   40
  USH2A WILD-TYPE  136  157
        clus
vv       USH2A MUTATED USH2A WILD-TYPE
  FEMALE            34             136
  MALE              40             157
[1] 2 2
[1] FALSE
D772V8, binary
                 cls
clus                0   1
  USH2A MUTATED    60   0
  USH2A WILD-TYPE 240   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     60    0
  USH2A WILD-TYPE  240    8
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             60             240
  YES             0               8
[1] 2 2
[1] FALSE
D772V9, binary
                 cls
clus                0   1
  USH2A MUTATED    62  11
  USH2A WILD-TYPE 252  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     62   11
  USH2A WILD-TYPE  252   37
                               clus
vv                              USH2A MUTATED USH2A WILD-TYPE
  COLON ADENOCARCINOMA                     62             252
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USH2A MUTATED    53   0   2   6
  USH2A WILD-TYPE 206   3  20  15
D772V10, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  R0            53             206
  R1             0               3
  R2             2              20
  RX             6              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"
D772V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USH2A MUTATED                                  1     2
  USH2A WILD-TYPE                                0     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USH2A MUTATED                           4    36
  USH2A WILD-TYPE                        15   140
D772V12, multiclass
                                  clus
vv                                 USH2A MUTATED USH2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       36             140
[1] 4 2
[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 = PARP1 MUTATION ANALYSIS
D773V1, survival
                 sevent
clus2               0   1
  PARP1 MUTATED    13   1
  PARP1 WILD-TYPE 264  77
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             341 
  PARP1 MUTATED PARP1 WILD-TYPE 
              1              77 
$`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-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-5861 TCGA-CM-6676 
        0.20        58.39        12.76        17.56        15.02        11.08 
TCGA-DM-A1HB TCGA-F4-6704 
      135.65         1.55 

$`PARP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        33.53        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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-F4-6805 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PARP1 MUTATED PARP1 WILD-TYPE 
            0.2             0.0 
  PARP1 MUTATED PARP1 WILD-TYPE 
         135.65          148.01 
  PARP1 MUTATED PARP1 WILD-TYPE 
         20.055          22.090 
[1] "0.2 - 135.7 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D773V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARP1 MUTATED         1        0        0         4         1         0
  PARP1 WILD-TYPE      63        1       26       104         7         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        16          6         41         31       35        11
                 vv
clus              STAGE IVB
  PARP1 MUTATED           0
  PARP1 WILD-TYPE         1
D773V3, multiclass
            clus
vv           PARP1 MUTATED PARP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              1              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
  PARP1 MUTATED     0   1  11   2
  PARP1 WILD-TYPE   9  66 238  39
D773V4, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             2              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
  PARP1 MUTATED     6   3   5
  PARP1 WILD-TYPE 214  78  61
D773V5, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V6, binary
                 cls
clus                0   1
  PARP1 MUTATED    11   1
  PARP1 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED     11    1
  PARP1 WILD-TYPE  274   47
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D773V7, binary
                 cls
clus                0   1
  PARP1 MUTATED     6   8
  PARP1 WILD-TYPE 164 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      6    8
  PARP1 WILD-TYPE  164  189
        clus
vv       PARP1 MUTATED PARP1 WILD-TYPE
  FEMALE             6             164
  MALE               8             189
[1] 2 2
[1] FALSE
D773V8, binary
                 cls
clus                0   1
  PARP1 MUTATED    10   1
  PARP1 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED     10    1
  PARP1 WILD-TYPE  290    7
     clus
vv    PARP1 MUTATED PARP1 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D773V9, binary
                 cls
clus                0   1
  PARP1 MUTATED     7   6
  PARP1 WILD-TYPE 307  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      7    6
  PARP1 WILD-TYPE  307   42
                               clus
vv                              PARP1 MUTATED PARP1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PARP1 MUTATED    10   0   0   2
  PARP1 WILD-TYPE 249   3  22  19
D773V10, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D773V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARP1 MUTATED                                  1     1
  PARP1 WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PARP1 MUTATED                           0     8
  PARP1 WILD-TYPE                        19   168
D773V12, multiclass
                                  clus
vv                                 PARP1 MUTATED PARP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = CCDC141 MUTATION ANALYSIS
D774V1, survival
                   sevent
clus2                 0   1
  CCDC141 MUTATED    18   3
  CCDC141 WILD-TYPE 259  75
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               21               334 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
                3                75 
$`CCDC141 MUTATED`
TCGA-AA-3496 TCGA-CK-5912 TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3941 
        1.02        49.08        79.69        63.98        53.00        24.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 
       25.02         4.01        34.98        35.01        58.39        12.76 
TCGA-CM-5348 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6541 TCGA-D5-6929 
       22.98        15.02        21.99        14.04        15.58        13.41 
TCGA-D5-6932 TCGA-F4-6459 TCGA-G4-6304 
       11.38         8.61        53.62 

$`CCDC141 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00        14.04        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-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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-F4-6460 
      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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CCDC141 MUTATED CCDC141 WILD-TYPE 
             1.02              0.00 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
            79.69            148.01 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
           22.980            22.045 
[1] "1.0 - 79.7 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D774V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC141 MUTATED         5        0        3         4         3         0
  CCDC141 WILD-TYPE      59        1       23       104         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC141 MUTATED           1          0          2          0        1
  CCDC141 WILD-TYPE        17          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC141 MUTATED           1         0
  CCDC141 WILD-TYPE        11         1
D774V3, multiclass
            clus
vv           CCDC141 MUTATED CCDC141 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                4               104
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                1                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
  CCDC141 MUTATED     0   6  11   4
  CCDC141 WILD-TYPE   9  61 238  37
D774V4, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  T1               0                 9
  T2               6                61
  T3              11               238
  T4               4                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
  CCDC141 MUTATED    16   3   2
  CCDC141 WILD-TYPE 204  78  64
D774V5, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  N0              16               204
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V6, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    17   2
  CCDC141 WILD-TYPE 268  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     17    2
  CCDC141 WILD-TYPE  268   46
   clus
vv  CCDC141 MUTATED CCDC141 WILD-TYPE
  0              17               268
  1               2                46
[1] 2 2
[1] FALSE
D774V7, binary
                   cls
clus                  0   1
  CCDC141 MUTATED     9  12
  CCDC141 WILD-TYPE 161 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED      9   12
  CCDC141 WILD-TYPE  161  185
        clus
vv       CCDC141 MUTATED CCDC141 WILD-TYPE
  FEMALE               9               161
  MALE                12               185
[1] 2 2
[1] FALSE
D774V8, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    18   1
  CCDC141 WILD-TYPE 282   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     18    1
  CCDC141 WILD-TYPE  282    7
     clus
vv    CCDC141 MUTATED CCDC141 WILD-TYPE
  NO               18               282
  YES               1                 7
[1] 2 2
[1] FALSE
D774V9, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    18   3
  CCDC141 WILD-TYPE 296  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     18    3
  CCDC141 WILD-TYPE  296   45
                               clus
vv                              CCDC141 MUTATED CCDC141 WILD-TYPE
  COLON ADENOCARCINOMA                       18               296
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC141 MUTATED    18   0   0   2
  CCDC141 WILD-TYPE 241   3  22  19
D774V10, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               0                22
  RX               2                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"
D774V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC141 MUTATED                                  0     1
  CCDC141 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC141 MUTATED                           0    12
  CCDC141 WILD-TYPE                        19   164
D774V12, multiclass
                                  clus
vv                                 CCDC141 MUTATED CCDC141 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         12               164
[1] 4 2
[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 = OAS1 MUTATION ANALYSIS
D775V1, survival
                sevent
clus2              0   1
  OAS1 MUTATED     5   2
  OAS1 WILD-TYPE 272  76
  OAS1 MUTATED OAS1 WILD-TYPE 
             7            348 
  OAS1 MUTATED OAS1 WILD-TYPE 
             2             76 
$`OAS1 MUTATED`
TCGA-AA-3950 TCGA-DM-A285 TCGA-AA-3660 TCGA-AA-3845 TCGA-AZ-4315 TCGA-D5-6534 
       24.00         5.88        78.08         0.00        58.39        43.27 
TCGA-G4-6307 
       55.04 

$`OAS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  OAS1 MUTATED OAS1 WILD-TYPE 
             0              0 
  OAS1 MUTATED OAS1 WILD-TYPE 
         78.08         148.01 
  OAS1 MUTATED OAS1 WILD-TYPE 
         43.27          22.01 
[1] "0.0 - 78.1 (43.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D775V2, continuous
                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      64        1       25       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OAS1 MUTATED           0          0          1          0        1         0
  OAS1 WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  OAS1 MUTATED           0
  OAS1 WILD-TYPE         1
D775V3, multiclass
            clus
vv           OAS1 MUTATED OAS1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  OAS1 MUTATED     0   0   8   0
  OAS1 WILD-TYPE   9  67 241  41
D775V4, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            8            241
  T4            0             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
  OAS1 MUTATED     6   1   1
  OAS1 WILD-TYPE 214  80  65
D775V5, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V6, binary
                cls
clus               0   1
  OAS1 MUTATED     7   1
  OAS1 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      7    1
  OAS1 WILD-TYPE  278   47
   clus
vv  OAS1 MUTATED OAS1 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D775V7, binary
                cls
clus               0   1
  OAS1 MUTATED     7   1
  OAS1 WILD-TYPE 163 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      7    1
  OAS1 WILD-TYPE  163  196
        clus
vv       OAS1 MUTATED OAS1 WILD-TYPE
  FEMALE            7            163
  MALE              1            196
[1] 2 2
[1] FALSE
D775V8, binary
                cls
clus               0   1
  OAS1 MUTATED     5   0
  OAS1 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      5    0
  OAS1 WILD-TYPE  295    8
     clus
vv    OAS1 MUTATED OAS1 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D775V9, binary
                cls
clus               0   1
  OAS1 MUTATED     5   3
  OAS1 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      5    3
  OAS1 WILD-TYPE  309   45
                               clus
vv                              OAS1 MUTATED OAS1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OAS1 MUTATED     7   0   0   0
  OAS1 WILD-TYPE 252   3  22  21
D775V10, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            0             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"
D775V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OAS1 MUTATED                                  0     0
  OAS1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OAS1 MUTATED                           0     4
  OAS1 WILD-TYPE                        19   172
D775V12, multiclass
                                  clus
vv                                 OAS1 MUTATED OAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = KIAA0406 MUTATION ANALYSIS
D776V1, survival
                    sevent
clus2                  0   1
  KIAA0406 MUTATED    10   4
  KIAA0406 WILD-TYPE 267  74
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                14                341 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 4                 74 
$`KIAA0406 MUTATED`
TCGA-AA-3950 TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3955 
       24.00        33.53        20.28         6.97         0.00        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 
       23.05         6.18 

$`KIAA0406 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.59        12.20        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 0                  0 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             49.41             148.01 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             17.29              22.09 
[1] "0.0 - 49.4 (17.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D776V2, continuous
                    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      64        1       23       100         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0406 MUTATED           0          0          1          1        0
  KIAA0406 WILD-TYPE        18          6         43         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0406 MUTATED           0         0
  KIAA0406 WILD-TYPE        12         1
D776V3, multiclass
            clus
vv           KIAA0406 MUTATED KIAA0406 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                 8                100
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA0406 MUTATED     0   1  12   1
  KIAA0406 WILD-TYPE   9  66 237  40
D776V4, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3               12                237
  T4                1                 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
  KIAA0406 MUTATED    12   0   2
  KIAA0406 WILD-TYPE 208  81  64
D776V5, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  N0               12                208
  N1                0                 81
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V6, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    12   0
  KIAA0406 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     12    0
  KIAA0406 WILD-TYPE  273   48
   clus
vv  KIAA0406 MUTATED KIAA0406 WILD-TYPE
  0               12                273
  1                0                 48
[1] 2 2
[1] FALSE
D776V7, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     6   8
  KIAA0406 WILD-TYPE 164 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      6    8
  KIAA0406 WILD-TYPE  164  189
        clus
vv       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  FEMALE                6                164
  MALE                  8                189
[1] 2 2
[1] FALSE
D776V8, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    12   0
  KIAA0406 WILD-TYPE 288   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     12    0
  KIAA0406 WILD-TYPE  288    8
     clus
vv    KIAA0406 MUTATED KIAA0406 WILD-TYPE
  NO                12                288
  YES                0                  8
[1] 2 2
[1] FALSE
D776V9, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    12   2
  KIAA0406 WILD-TYPE 302  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     12    2
  KIAA0406 WILD-TYPE  302   46
                               clus
vv                              KIAA0406 MUTATED KIAA0406 WILD-TYPE
  COLON ADENOCARCINOMA                        12                302
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0406 MUTATED     9   0   0   3
  KIAA0406 WILD-TYPE 250   3  22  18
D776V10, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D776V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0406 MUTATED                                  0     3
  KIAA0406 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0406 MUTATED                           1     4
  KIAA0406 WILD-TYPE                        18   172
D776V12, multiclass
                                  clus
vv                                 KIAA0406 MUTATED KIAA0406 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                172
[1] 4 2
[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 = DNASE1L3 MUTATION ANALYSIS
D777V1, survival
                    sevent
clus2                  0   1
  DNASE1L3 MUTATED     5   3
  DNASE1L3 WILD-TYPE 272  75
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                347 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 3                 75 
$`DNASE1L3 MUTATED`
TCGA-AZ-6601 TCGA-A6-2671 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A02W TCGA-AZ-5403 
      100.01        43.76        63.98        31.00        41.00        62.79 
TCGA-CA-6717 TCGA-CK-4952 
       12.76        15.62 

$`DNASE1L3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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              21.99 
[1] "12.8 - 100.0 (42.4)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1"  
D777V2, continuous
                    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      62        1       23       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNASE1L3 MUTATED           0          0          0          1        1
  DNASE1L3 WILD-TYPE        18          6         44         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  DNASE1L3 MUTATED           0         0
  DNASE1L3 WILD-TYPE        12         1
D777V3, multiclass
            clus
vv           DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                 1                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  DNASE1L3 MUTATED     1   1   5   1
  DNASE1L3 WILD-TYPE   8  66 244  40
D777V4, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  T1                1                  8
  T2                1                 66
  T3                5                244
  T4                1                 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
  DNASE1L3 MUTATED     6   0   2
  DNASE1L3 WILD-TYPE 214  81  64
D777V5, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  N0                6                214
  N1                0                 81
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V6, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     6   1
  DNASE1L3 WILD-TYPE 279  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      6    1
  DNASE1L3 WILD-TYPE  279   47
   clus
vv  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  0                6                279
  1                1                 47
[1] 2 2
[1] FALSE
D777V7, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     3   5
  DNASE1L3 WILD-TYPE 167 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      3    5
  DNASE1L3 WILD-TYPE  167  192
        clus
vv       DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  FEMALE                3                167
  MALE                  5                192
[1] 2 2
[1] FALSE
D777V8, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     7   0
  DNASE1L3 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      7    0
  DNASE1L3 WILD-TYPE  293    8
     clus
vv    DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D777V9, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     5   3
  DNASE1L3 WILD-TYPE 309  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      5    3
  DNASE1L3 WILD-TYPE  309   45
                               clus
vv                              DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  DNASE1L3 MUTATED     4   0   0   2
  DNASE1L3 WILD-TYPE 255   3  22  19
D777V10, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  R0                4                255
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D777V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNASE1L3 MUTATED                                  0     1
  DNASE1L3 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  DNASE1L3 MUTATED                           0     4
  DNASE1L3 WILD-TYPE                        19   172
D777V12, multiclass
                                  clus
vv                                 DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = OR8A1 MUTATION ANALYSIS
D778V1, survival
                 sevent
clus2               0   1
  OR8A1 MUTATED     4   0
  OR8A1 WILD-TYPE 273  78
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              4             351 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              0              78 
$`OR8A1 MUTATED`
TCGA-D5-6534 TCGA-D5-6539 TCGA-DM-A1HB TCGA-G4-6315 
       43.27        12.49       135.65        61.91 

$`OR8A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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-D5-6540 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  OR8A1 MUTATED OR8A1 WILD-TYPE 
          12.49            0.00 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
         135.65          148.01 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
          52.59           22.03 
[1] "12.5 - 135.7 (52.6)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "9400000"
D778V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8A1 MUTATED         0        0        0         1         0         0
  OR8A1 WILD-TYPE      64        1       26       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8A1 MUTATED           0          0          1          0        1         0
  OR8A1 WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  OR8A1 MUTATED           0
  OR8A1 WILD-TYPE         1
D778V3, multiclass
            clus
vv           OR8A1 MUTATED OR8A1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  OR8A1 MUTATED     0   0   4   0
  OR8A1 WILD-TYPE   9  67 245  41
D778V4, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             0              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
  OR8A1 MUTATED     2   2   0
  OR8A1 WILD-TYPE 218  79  66
D778V5, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  N0             2             218
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V6, binary
                 cls
clus                0   1
  OR8A1 MUTATED     3   1
  OR8A1 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      3    1
  OR8A1 WILD-TYPE  282   47
   clus
vv  OR8A1 MUTATED OR8A1 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D778V7, binary
                 cls
clus                0   1
  OR8A1 MUTATED     2   2
  OR8A1 WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      2    2
  OR8A1 WILD-TYPE  168  195
        clus
vv       OR8A1 MUTATED OR8A1 WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D778V8, binary
                 cls
clus                0   1
  OR8A1 MUTATED     3   0
  OR8A1 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      3    0
  OR8A1 WILD-TYPE  297    8
     clus
vv    OR8A1 MUTATED OR8A1 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D778V9, binary
                 cls
clus                0   1
  OR8A1 MUTATED     2   1
  OR8A1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      2    1
  OR8A1 WILD-TYPE  312   47
                               clus
vv                              OR8A1 MUTATED OR8A1 WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR8A1 MUTATED     3   0   0   0
  OR8A1 WILD-TYPE 256   3  22  21
D778V10, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D778V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8A1 MUTATED                                  0     0
  OR8A1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR8A1 MUTATED                           0     4
  OR8A1 WILD-TYPE                        19   172
D778V12, multiclass
                                  clus
vv                                 OR8A1 MUTATED OR8A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = RANBP1 MUTATION ANALYSIS
D779V1, survival
                  sevent
clus2                0   1
  RANBP1 MUTATED     5   1
  RANBP1 WILD-TYPE 272  77
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              349 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               1               77 
$`RANBP1 MUTATED`
TCGA-G4-6588 TCGA-A6-5665 TCGA-AZ-4315 TCGA-CM-5860 TCGA-F4-6460 TCGA-F4-6856 
       26.17        22.06        58.39        32.02        31.96        35.31 

$`RANBP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            21.99 
[1] "22.1 - 58.4 (32.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D779V2, continuous
                  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      63        1       26       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP1 MUTATED           0          0          1          0        0
  RANBP1 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  RANBP1 MUTATED           0         0
  RANBP1 WILD-TYPE        12         1
D779V3, multiclass
            clus
vv           RANBP1 MUTATED RANBP1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  RANBP1 MUTATED     0   1   5   0
  RANBP1 WILD-TYPE   9  66 244  41
D779V4, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              0               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
  RANBP1 MUTATED     5   1   0
  RANBP1 WILD-TYPE 215  80  66
D779V5, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V6, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      6    0
  RANBP1 WILD-TYPE  279   48
   clus
vv  RANBP1 MUTATED RANBP1 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D779V7, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     3   3
  RANBP1 WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      3    3
  RANBP1 WILD-TYPE  167  194
        clus
vv       RANBP1 MUTATED RANBP1 WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D779V8, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      6    0
  RANBP1 WILD-TYPE  294    8
     clus
vv    RANBP1 MUTATED RANBP1 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D779V9, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     5   1
  RANBP1 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      5    1
  RANBP1 WILD-TYPE  309   47
                               clus
vv                              RANBP1 MUTATED RANBP1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RANBP1 MUTATED     6   0   0   0
  RANBP1 WILD-TYPE 253   3  22  21
D779V10, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D779V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RANBP1 MUTATED                                  0     0
  RANBP1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RANBP1 MUTATED                           0     6
  RANBP1 WILD-TYPE                        19   170
D779V12, multiclass
                                  clus
vv                                 RANBP1 MUTATED RANBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = RBMX2 MUTATION ANALYSIS
D780V1, survival
                 sevent
clus2               0   1
  RBMX2 MUTATED    10   1
  RBMX2 WILD-TYPE 267  77
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             11             344 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
              1              77 
$`RBMX2 MUTATED`
TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6625 TCGA-AA-3492 TCGA-AA-3710 TCGA-AY-6197 
       63.62        26.17        91.79         3.02        26.99        21.44 
TCGA-AZ-4315 TCGA-CM-6171 TCGA-D5-6930 TCGA-F4-6806 TCGA-G4-6299 
       58.39        14.04        13.35        41.42        74.56 

$`RBMX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        43.04        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RBMX2 MUTATED RBMX2 WILD-TYPE 
           3.02            0.00 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
          91.79          148.01 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
          26.99           22.01 
[1] "3.0 - 91.8 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3.5"
D780V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBMX2 MUTATED         2        0        1         6         0         0
  RBMX2 WILD-TYPE      62        1       25       102         8         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  RBMX2 MUTATED           0
  RBMX2 WILD-TYPE         1
D780V3, multiclass
            clus
vv           RBMX2 MUTATED RBMX2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RBMX2 MUTATED     0   2   9   0
  RBMX2 WILD-TYPE   9  65 240  41
D780V4, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             0              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
  RBMX2 MUTATED     9   1   1
  RBMX2 WILD-TYPE 211  80  65
D780V5, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V6, binary
                 cls
clus                0   1
  RBMX2 MUTATED    10   0
  RBMX2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     10    0
  RBMX2 WILD-TYPE  275   48
   clus
vv  RBMX2 MUTATED RBMX2 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D780V7, binary
                 cls
clus                0   1
  RBMX2 MUTATED     6   5
  RBMX2 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED      6    5
  RBMX2 WILD-TYPE  164  192
        clus
vv       RBMX2 MUTATED RBMX2 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D780V8, binary
                 cls
clus                0   1
  RBMX2 MUTATED    10   1
  RBMX2 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     10    1
  RBMX2 WILD-TYPE  290    7
     clus
vv    RBMX2 MUTATED RBMX2 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D780V9, binary
                 cls
clus                0   1
  RBMX2 MUTATED    10   1
  RBMX2 WILD-TYPE 304  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     10    1
  RBMX2 WILD-TYPE  304   47
                               clus
vv                              RBMX2 MUTATED RBMX2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBMX2 MUTATED    11   0   0   0
  RBMX2 WILD-TYPE 248   3  22  21
D780V10, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D780V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBMX2 MUTATED                                  0     0
  RBMX2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBMX2 MUTATED                           0     9
  RBMX2 WILD-TYPE                        19   167
D780V12, multiclass
                                  clus
vv                                 RBMX2 MUTATED RBMX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(781) Variable = SLC35A5 MUTATION ANALYSIS
D781V1, survival
                   sevent
clus2                 0   1
  SLC35A5 MUTATED     5   2
  SLC35A5 WILD-TYPE 272  76
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                7               348 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                2                76 
$`SLC35A5 MUTATED`
TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3663 TCGA-AZ-4682 TCGA-CM-6163 TCGA-CM-6164 
       79.69        63.98         6.97        22.36        14.04        29.03 
TCGA-G4-6303 
       65.85 

$`SLC35A5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 
       21.44        17.82        58.39         1.41         5.13        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
             6.97              0.00 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
            79.69            148.01 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
            29.03             22.01 
[1] "7.0 - 79.7 (29.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D781V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC35A5 MUTATED         2        0        2         1         0         0
  SLC35A5 WILD-TYPE      62        1       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC35A5 MUTATED           0          0          0          0        1
  SLC35A5 WILD-TYPE        18          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC35A5 MUTATED           1         0
  SLC35A5 WILD-TYPE        11         1
D781V3, multiclass
            clus
vv           SLC35A5 MUTATED SLC35A5 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                1                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
  SLC35A5 MUTATED     1   1   5   0
  SLC35A5 WILD-TYPE   8  66 244  41
D781V4, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               5               244
  T4               0                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
  SLC35A5 MUTATED     6   1   0
  SLC35A5 WILD-TYPE 214  80  66
D781V5, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  N0               6               214
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V6, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     5   2
  SLC35A5 WILD-TYPE 280  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      5    2
  SLC35A5 WILD-TYPE  280   46
   clus
vv  SLC35A5 MUTATED SLC35A5 WILD-TYPE
  0               5               280
  1               2                46
[1] 2 2
[1] FALSE
D781V7, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     2   5
  SLC35A5 WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      2    5
  SLC35A5 WILD-TYPE  168  192
        clus
vv       SLC35A5 MUTATED SLC35A5 WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D781V8, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     7   0
  SLC35A5 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      7    0
  SLC35A5 WILD-TYPE  293    8
     clus
vv    SLC35A5 MUTATED SLC35A5 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D781V9, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     7   0
  SLC35A5 WILD-TYPE 307  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      7    0
  SLC35A5 WILD-TYPE  307   48
                               clus
vv                              SLC35A5 MUTATED SLC35A5 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC35A5 MUTATED     7   0   0   0
  SLC35A5 WILD-TYPE 252   3  22  21
D781V10, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D781V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC35A5 MUTATED                                  0     0
  SLC35A5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC35A5 MUTATED                           0     5
  SLC35A5 WILD-TYPE                        19   171
D781V12, multiclass
                                  clus
vv                                 SLC35A5 MUTATED SLC35A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = RAD51AP2 MUTATION ANALYSIS
D782V1, survival
                    sevent
clus2                  0   1
  RAD51AP2 MUTATED    13   2
  RAD51AP2 WILD-TYPE 264  76
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                15                340 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 2                 76 
$`RAD51AP2 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-3809 
       19.04        25.08        35.80        26.17        79.69        32.75 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 
       20.12        19.66        33.04         4.01        34.98        21.44 
TCGA-AZ-4315 TCGA-D5-5537 TCGA-F4-6856 
       58.39        45.40        35.31 

$`RAD51AP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-3810 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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
              4.01               0.00 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             79.69             148.01 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             32.75              21.99 
[1] "4.0 - 79.7 (32.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D782V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAD51AP2 MUTATED         2        0        0         8         3         0
  RAD51AP2 WILD-TYPE      62        1       26       100         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD51AP2 MUTATED           0          0          1          1        1
  RAD51AP2 WILD-TYPE        18          6         43         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  RAD51AP2 MUTATED           0         0
  RAD51AP2 WILD-TYPE        12         1
D782V3, multiclass
            clus
vv           RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 8                100
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  RAD51AP2 MUTATED     0   2  10   4
  RAD51AP2 WILD-TYPE   9  65 239  37
D782V4, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3               10                239
  T4                4                 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
  RAD51AP2 MUTATED    13   2   1
  RAD51AP2 WILD-TYPE 207  79  65
D782V5, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  N0               13                207
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V6, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    11   1
  RAD51AP2 WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     11    1
  RAD51AP2 WILD-TYPE  274   47
   clus
vv  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  0               11                274
  1                1                 47
[1] 2 2
[1] FALSE
D782V7, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED     6  10
  RAD51AP2 WILD-TYPE 164 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED      6   10
  RAD51AP2 WILD-TYPE  164  187
        clus
vv       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  FEMALE                6                164
  MALE                 10                187
[1] 2 2
[1] FALSE
D782V8, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    13   1
  RAD51AP2 WILD-TYPE 287   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     13    1
  RAD51AP2 WILD-TYPE  287    7
     clus
vv    RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  NO                13                287
  YES                1                  7
[1] 2 2
[1] FALSE
D782V9, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    11   5
  RAD51AP2 WILD-TYPE 303  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     11    5
  RAD51AP2 WILD-TYPE  303   43
                               clus
vv                              RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  RAD51AP2 MUTATED    13   0   1   1
  RAD51AP2 WILD-TYPE 246   3  21  20
D782V10, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  R0               13                246
  R1                0                  3
  R2                1                 21
  RX                1                 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"
D782V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAD51AP2 MUTATED                                  0     0
  RAD51AP2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  RAD51AP2 MUTATED                           0    11
  RAD51AP2 WILD-TYPE                        19   165
D782V12, multiclass
                                  clus
vv                                 RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          11                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(783) Variable = INADL MUTATION ANALYSIS
D783V1, survival
                 sevent
clus2               0   1
  INADL MUTATED    10   3
  INADL WILD-TYPE 267  75
  INADL MUTATED INADL WILD-TYPE 
             13             342 
  INADL MUTATED INADL WILD-TYPE 
              3              75 
$`INADL MUTATED`
TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3977 
      100.01        22.09        35.80         6.97         0.00        25.02 
TCGA-AA-A01R TCGA-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 TCGA-DM-A1D8 
       35.01         0.20        58.39        12.76        15.02        12.59 
TCGA-G4-6323 
       13.78 

$`INADL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6588 
      106.75         1.94        49.08         5.88        63.62        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-4682 
       33.01        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  INADL MUTATED INADL WILD-TYPE 
              0               0 
  INADL MUTATED INADL WILD-TYPE 
         100.01          148.01 
  INADL MUTATED INADL WILD-TYPE 
         15.020          22.075 
[1] "0.0 - 100.0 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D783V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INADL MUTATED         0        1        2         5         0         0
  INADL WILD-TYPE      64        0       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INADL MUTATED           2          0          0          1        0         0
  INADL WILD-TYPE        16          6         44         32       35        12
                 vv
clus              STAGE IVB
  INADL MUTATED           0
  INADL WILD-TYPE         1
D783V3, multiclass
            clus
vv           INADL MUTATED INADL WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  INADL MUTATED     0   2  10   0
  INADL WILD-TYPE   9  65 239  41
D783V4, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             0              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
  INADL MUTATED     9   2   2
  INADL WILD-TYPE 211  79  64
D783V5, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  N0             9             211
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V6, binary
                 cls
clus                0   1
  INADL MUTATED     8   0
  INADL WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED      8    0
  INADL WILD-TYPE  277   48
   clus
vv  INADL MUTATED INADL WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D783V7, binary
                 cls
clus                0   1
  INADL MUTATED     5   8
  INADL WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED      5    8
  INADL WILD-TYPE  165  189
        clus
vv       INADL MUTATED INADL WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D783V8, binary
                 cls
clus                0   1
  INADL MUTATED     9   1
  INADL WILD-TYPE 291   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED      9    1
  INADL WILD-TYPE  291    7
     clus
vv    INADL MUTATED INADL WILD-TYPE
  NO              9             291
  YES             1               7
[1] 2 2
[1] FALSE
D783V9, binary
                 cls
clus                0   1
  INADL MUTATED    10   3
  INADL WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED     10    3
  INADL WILD-TYPE  304   45
                               clus
vv                              INADL MUTATED INADL WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INADL MUTATED     9   0   0   1
  INADL WILD-TYPE 250   3  22  20
D783V10, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D783V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INADL MUTATED                                  0     1
  INADL WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INADL MUTATED                           1     7
  INADL WILD-TYPE                        18   169
D783V12, multiclass
                                  clus
vv                                 INADL MUTATED INADL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = LEF1 MUTATION ANALYSIS
D784V1, survival
                sevent
clus2              0   1
  LEF1 MUTATED     7   1
  LEF1 WILD-TYPE 270  77
  LEF1 MUTATED LEF1 WILD-TYPE 
             8            347 
  LEF1 MUTATED LEF1 WILD-TYPE 
             1             77 
$`LEF1 MUTATED`
TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-3553 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3994 
       35.80        63.98        24.00        10.06        33.04        27.02 
TCGA-AD-5900 TCGA-CA-6717 
       12.16        12.76 

$`LEF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LEF1 MUTATED LEF1 WILD-TYPE 
         10.06           0.00 
  LEF1 MUTATED LEF1 WILD-TYPE 
         63.98         148.01 
  LEF1 MUTATED LEF1 WILD-TYPE 
         25.51          22.03 
[1] "10.1 - 64.0 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D784V2, continuous
                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      62        1       25       104         8         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        17          6         43         33       35        12
                vv
clus             STAGE IVB
  LEF1 MUTATED           0
  LEF1 WILD-TYPE         1
D784V3, multiclass
            clus
vv           LEF1 MUTATED LEF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  LEF1 MUTATED     0   2   7   0
  LEF1 WILD-TYPE   9  65 242  41
D784V4, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            7            242
  T4            0             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
  LEF1 MUTATED     7   1   1
  LEF1 WILD-TYPE 213  80  65
D784V5, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V6, binary
                cls
clus               0   1
  LEF1 MUTATED     8   0
  LEF1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      8    0
  LEF1 WILD-TYPE  277   48
   clus
vv  LEF1 MUTATED LEF1 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D784V7, binary
                cls
clus               0   1
  LEF1 MUTATED     5   4
  LEF1 WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      5    4
  LEF1 WILD-TYPE  165  193
        clus
vv       LEF1 MUTATED LEF1 WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D784V8, binary
                cls
clus               0   1
  LEF1 MUTATED     8   0
  LEF1 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      8    0
  LEF1 WILD-TYPE  292    8
     clus
vv    LEF1 MUTATED LEF1 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D784V9, binary
                cls
clus               0   1
  LEF1 MUTATED     6   3
  LEF1 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      6    3
  LEF1 WILD-TYPE  308   45
                               clus
vv                              LEF1 MUTATED LEF1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LEF1 MUTATED     8   0   0   1
  LEF1 WILD-TYPE 251   3  22  20
D784V10, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D784V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEF1 MUTATED                                  0     1
  LEF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LEF1 MUTATED                           0     2
  LEF1 WILD-TYPE                        19   174
D784V12, multiclass
                                  clus
vv                                 LEF1 MUTATED LEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(785) Variable = SLC2A3 MUTATION ANALYSIS
D785V1, survival
                  sevent
clus2                0   1
  SLC2A3 MUTATED    10   1
  SLC2A3 WILD-TYPE 267  77
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              344 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
               1               77 
$`SLC2A3 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-A01D 
       26.17        79.69        22.06         8.38        19.66        10.98 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-CK-4950 TCGA-CM-6676 TCGA-DM-A1HA 
       33.01        58.39        85.45        11.08       131.51 

$`SLC2A3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
            8.38             0.00 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
          131.51           148.01 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
           26.17            22.01 
[1] "8.4 - 131.5 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.7"
D785V2, continuous
                  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      62        1       26       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC2A3 MUTATED           0          0          1          3        0
  SLC2A3 WILD-TYPE        18          6         43         30       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC2A3 MUTATED           1         0
  SLC2A3 WILD-TYPE        11         1
D785V3, multiclass
            clus
vv           SLC2A3 MUTATED SLC2A3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              3               30
  STAGE IV                0               35
  STAGE IVA               1               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
  SLC2A3 MUTATED     0   2   8   1
  SLC2A3 WILD-TYPE   9  65 241  40
D785V4, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              8              241
  T4              1               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
  SLC2A3 MUTATED     6   3   2
  SLC2A3 WILD-TYPE 214  78  64
D785V5, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  N0              6              214
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V6, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     9   1
  SLC2A3 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      9    1
  SLC2A3 WILD-TYPE  276   47
   clus
vv  SLC2A3 MUTATED SLC2A3 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D785V7, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     5   6
  SLC2A3 WILD-TYPE 165 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      5    6
  SLC2A3 WILD-TYPE  165  191
        clus
vv       SLC2A3 MUTATED SLC2A3 WILD-TYPE
  FEMALE              5              165
  MALE                6              191
[1] 2 2
[1] FALSE
D785V8, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED    10   0
  SLC2A3 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED     10    0
  SLC2A3 WILD-TYPE  290    8
     clus
vv    SLC2A3 MUTATED SLC2A3 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D785V9, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     8   3
  SLC2A3 WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      8    3
  SLC2A3 WILD-TYPE  306   45
                               clus
vv                              SLC2A3 MUTATED SLC2A3 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC2A3 MUTATED     8   1   0   0
  SLC2A3 WILD-TYPE 251   2  22  21
D785V10, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  R0              8              251
  R1              1                2
  R2              0               22
  RX              0               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"
D785V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC2A3 MUTATED                                  0     0
  SLC2A3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC2A3 MUTATED                           3     7
  SLC2A3 WILD-TYPE                        16   169
D785V12, multiclass
                                  clus
vv                                 SLC2A3 MUTATED SLC2A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         7              169
[1] 4 2
[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 = MLL4 MUTATION ANALYSIS
D786V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    25   7
  MLL4 WILD-TYPE 252  71
  MLL4 MUTATED MLL4 WILD-TYPE 
            32            323 
  MLL4 MUTATED MLL4 WILD-TYPE 
             7             71 
$`MLL4 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5661 
       19.04        19.04        24.00        26.17        79.69        33.53 
TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3831 
       24.39         3.02         6.97        37.05        10.06        17.98 
TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-5407 TCGA-AZ-6598 
       15.95        53.00        34.98        17.82        88.21        49.41 
TCGA-CA-5255 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 
       12.36        10.06        15.62        51.32        21.14        23.05 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6540 TCGA-DM-A1D9 
       15.02         5.03        14.04        12.95        16.14       140.38 
TCGA-G4-6299 TCGA-G4-6304 
       74.56        53.62 

$`MLL4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6651 
       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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
        1.02        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6747 
       14.30        17.56       148.01        85.45        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MLL4 MUTATED MLL4 WILD-TYPE 
          3.02           0.00 
  MLL4 MUTATED MLL4 WILD-TYPE 
        140.38         148.01 
  MLL4 MUTATED MLL4 WILD-TYPE 
         20.09          22.09 
[1] "3.0 - 140.4 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D786V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL4 MUTATED         6        0        6        13         2         0
  MLL4 WILD-TYPE      58        1       20        95         6         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        17          6         43         31       34        11
                vv
clus             STAGE IVB
  MLL4 MUTATED           0
  MLL4 WILD-TYPE         1
D786V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA            13             95
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             1             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
  MLL4 MUTATED     2   4  24   3
  MLL4 WILD-TYPE   7  63 225  38
D786V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1            2              7
  T2            4             63
  T3           24            225
  T4            3             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
  MLL4 MUTATED    28   2   3
  MLL4 WILD-TYPE 192  79  63
D786V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           28            192
  N1            2             79
  N2            3             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"
D786V6, binary
                cls
clus               0   1
  MLL4 MUTATED    29   2
  MLL4 WILD-TYPE 256  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     29    2
  MLL4 WILD-TYPE  256   46
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           29            256
  1            2             46
[1] 2 2
[1] FALSE
D786V7, binary
                cls
clus               0   1
  MLL4 MUTATED    18  15
  MLL4 WILD-TYPE 152 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     18   15
  MLL4 WILD-TYPE  152  182
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE           18            152
  MALE             15            182
[1] 2 2
[1] FALSE
D786V8, binary
                cls
clus               0   1
  MLL4 MUTATED    28   2
  MLL4 WILD-TYPE 272   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     28    2
  MLL4 WILD-TYPE  272    6
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            28            272
  YES            2              6
[1] 2 2
[1] FALSE
D786V9, binary
                cls
clus               0   1
  MLL4 MUTATED    30   3
  MLL4 WILD-TYPE 284  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     30    3
  MLL4 WILD-TYPE  284   45
                               clus
vv                              MLL4 MUTATED MLL4 WILD-TYPE
  COLON ADENOCARCINOMA                    30            284
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    23   0   1   5
  MLL4 WILD-TYPE 236   3  21  16
D786V10, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           23            236
  R1            0              3
  R2            1             21
  RX            5             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"
D786V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL4 MUTATED                                  0     2
  MLL4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED                           2    17
  MLL4 WILD-TYPE                        17   159
D786V12, multiclass
                                  clus
vv                                 MLL4 MUTATED MLL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      17            159
[1] 4 2
[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 = MTA2 MUTATION ANALYSIS
D787V1, survival
                sevent
clus2              0   1
  MTA2 MUTATED     7   5
  MTA2 WILD-TYPE 270  73
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            343 
  MTA2 MUTATED MTA2 WILD-TYPE 
             5             73 
$`MTA2 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-2672 TCGA-AA-3492 
       19.04        24.00       100.01        26.17        46.65         3.02 
TCGA-AA-3977 TCGA-AA-A01D TCGA-AY-4071 TCGA-CM-5344 TCGA-F4-6809 TCGA-G4-6299 
       25.02        10.98         0.95        22.03        13.25        74.56 

$`MTA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        43.76        42.90        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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09        16.31        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.060 
[1] "0.9 - 100.0 (23.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D787V2, continuous
                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      63        1       24       106         8         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        18          6         42         31       34        11
                vv
clus             STAGE IVB
  MTA2 MUTATED           0
  MTA2 WILD-TYPE         1
D787V3, multiclass
            clus
vv           MTA2 MUTATED MTA2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             1             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
  MTA2 MUTATED     1   1  10   0
  MTA2 WILD-TYPE   8  66 239  41
D787V4, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  T1            1              8
  T2            1             66
  T3           10            239
  T4            0             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
  MTA2 MUTATED     7   3   2
  MTA2 WILD-TYPE 213  78  64
D787V5, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  N0            7            213
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V6, binary
                cls
clus               0   1
  MTA2 MUTATED     8   2
  MTA2 WILD-TYPE 277  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      8    2
  MTA2 WILD-TYPE  277   46
   clus
vv  MTA2 MUTATED MTA2 WILD-TYPE
  0            8            277
  1            2             46
[1] 2 2
[1] FALSE
D787V7, binary
                cls
clus               0   1
  MTA2 MUTATED     8   4
  MTA2 WILD-TYPE 162 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      8    4
  MTA2 WILD-TYPE  162  193
        clus
vv       MTA2 MUTATED MTA2 WILD-TYPE
  FEMALE            8            162
  MALE              4            193
[1] 2 2
[1] FALSE
D787V8, binary
                cls
clus               0   1
  MTA2 MUTATED    11   1
  MTA2 WILD-TYPE 289   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED     11    1
  MTA2 WILD-TYPE  289    7
     clus
vv    MTA2 MUTATED MTA2 WILD-TYPE
  NO            11            289
  YES            1              7
[1] 2 2
[1] FALSE
D787V9, binary
                cls
clus               0   1
  MTA2 MUTATED     9   2
  MTA2 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      9    2
  MTA2 WILD-TYPE  305   46
                               clus
vv                              MTA2 MUTATED MTA2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTA2 MUTATED     9   0   1   0
  MTA2 WILD-TYPE 250   3  21  21
D787V10, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            1             21
  RX            0             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"
D787V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTA2 MUTATED                                  0     0
  MTA2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTA2 MUTATED                           0     7
  MTA2 WILD-TYPE                        19   169
D787V12, multiclass
                                  clus
vv                                 MTA2 MUTATED MTA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = MDN1 MUTATION ANALYSIS
D788V1, survival
                sevent
clus2              0   1
  MDN1 MUTATED    36  15
  MDN1 WILD-TYPE 241  63
  MDN1 MUTATED MDN1 WILD-TYPE 
            51            304 
  MDN1 MUTATED MDN1 WILD-TYPE 
            15             63 
$`MDN1 MUTATED`
TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AD-6888 
       14.53        13.02         0.92        85.05        19.04        15.52 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 
       26.17        79.69        42.90        22.06        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3685 TCGA-AA-3815 
        3.02        63.98        29.95        61.02        37.05        33.04 
TCGA-AA-3821 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3855 TCGA-AA-3877 TCGA-AA-3947 
        1.02        37.02         0.00        32.05        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       26.01        25.02        13.94        18.05         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6963 TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 
       83.24        27.42        16.31        58.39        49.41        12.10 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-6162 
       12.76        10.06        85.45        21.14        30.08        12.00 
TCGA-CM-6168 TCGA-CM-6680 TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6856 TCGA-G4-6293 
       12.99        12.03       135.65        81.37        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6317 
       74.56        53.62        36.00 

$`MDN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.69        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-3696 
       50.04        47.01        15.02        11.01         5.98         5.03 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       15.95        38.99        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 
       17.03        27.02        18.05         2.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21         6.77        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F TCGA-DM-A28G 
       44.32       131.51       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       13.25         0.53        47.41        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  MDN1 MUTATED MDN1 WILD-TYPE 
             0              0 
  MDN1 MUTATED MDN1 WILD-TYPE 
        135.65         148.01 
  MDN1 MUTATED MDN1 WILD-TYPE 
        27.420         21.875 
[1] "0.0 - 135.7 (27.4)" "0.0 - 148.0 (21.9)"
[1] "hr=" "1.1"
D788V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MDN1 MUTATED         7        0        8        16         5         0
  MDN1 WILD-TYPE      57        1       18        92         3         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MDN1 MUTATED           3          1          7          3        1         0
  MDN1 WILD-TYPE        15          5         37         30       34        12
                vv
clus             STAGE IVB
  MDN1 MUTATED           0
  MDN1 WILD-TYPE         1
D788V3, multiclass
            clus
vv           MDN1 MUTATED MDN1 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              8             18
  STAGE IIA            16             92
  STAGE IIB             5              3
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            1              5
  STAGE IIIB            7             37
  STAGE IIIC            3             30
  STAGE IV              1             34
  STAGE IVA             0             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
  MDN1 MUTATED     2   7  36   8
  MDN1 WILD-TYPE   7  60 213  33
D788V4, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  T1            2              7
  T2            7             60
  T3           36            213
  T4            8             33
[1] 4 2
[1] TRUE
[1] "dimension 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    38  10   5
  MDN1 WILD-TYPE 182  71  61
D788V5, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  N0           38            182
  N1           10             71
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V6, binary
                cls
clus               0   1
  MDN1 MUTATED    47   1
  MDN1 WILD-TYPE 238  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     47    1
  MDN1 WILD-TYPE  238   47
   clus
vv  MDN1 MUTATED MDN1 WILD-TYPE
  0           47            238
  1            1             47
[1] 2 2
[1] FALSE
D788V7, binary
                cls
clus               0   1
  MDN1 MUTATED    27  26
  MDN1 WILD-TYPE 143 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     27   26
  MDN1 WILD-TYPE  143  171
        clus
vv       MDN1 MUTATED MDN1 WILD-TYPE
  FEMALE           27            143
  MALE             26            171
[1] 2 2
[1] FALSE
D788V8, binary
                cls
clus               0   1
  MDN1 MUTATED    47   0
  MDN1 WILD-TYPE 253   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     47    0
  MDN1 WILD-TYPE  253    8
     clus
vv    MDN1 MUTATED MDN1 WILD-TYPE
  NO            47            253
  YES            0              8
[1] 2 2
[1] FALSE
D788V9, binary
                cls
clus               0   1
  MDN1 MUTATED    39  13
  MDN1 WILD-TYPE 275  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     39   13
  MDN1 WILD-TYPE  275   35
                               clus
vv                              MDN1 MUTATED MDN1 WILD-TYPE
  COLON ADENOCARCINOMA                    39            275
  COLON MUCINOUS ADENOCARCINOMA           13             35
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MDN1 MUTATED    38   2   0   3
  MDN1 WILD-TYPE 221   1  22  18
D788V10, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  R0           38            221
  R1            2              1
  R2            0             22
  RX            3             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"
D788V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MDN1 MUTATED                                  0     3
  MDN1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MDN1 MUTATED                           4    22
  MDN1 WILD-TYPE                        15   154
D788V12, multiclass
                                  clus
vv                                 MDN1 MUTATED MDN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      22            154
[1] 4 2
[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 = OR10G4 MUTATION ANALYSIS
D789V1, survival
                  sevent
clus2                0   1
  OR10G4 MUTATED     2   3
  OR10G4 WILD-TYPE 275  75
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               5              350 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               3               75 
$`OR10G4 MUTATED`
TCGA-AA-3715 TCGA-A6-6653 TCGA-AA-A00N TCGA-AZ-6599 TCGA-CM-5348 
       19.04        24.39         4.01         6.77        22.98 

$`OR10G4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OR10G4 MUTATED OR10G4 WILD-TYPE 
            4.01             0.00 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
           24.39           148.01 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
          19.040           22.075 
[1] "4.0 - 24.4 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "4.8"
D789V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR10G4 MUTATED         2        0        1         0         1         0
  OR10G4 WILD-TYPE      62        1       25       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR10G4 MUTATED           0          0          1          0        0
  OR10G4 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR10G4 MUTATED           0         0
  OR10G4 WILD-TYPE        12         1
D789V3, multiclass
            clus
vv           OR10G4 MUTATED OR10G4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               0              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  OR10G4 MUTATED     0   2   2   1
  OR10G4 WILD-TYPE   9  65 247  40
D789V4, multiclass
    clus
vv   OR10G4 MUTATED OR10G4 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              2              247
  T4              1               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
  OR10G4 MUTATED     4   1   0
  OR10G4 WILD-TYPE 216  80  66
D789V5, multiclass
    clus
vv   OR10G4 MUTATED OR10G4 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V6, binary
                  cls
clus                 0   1
  OR10G4 MUTATED     4   0
  OR10G4 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G4 MUTATED      4    0
  OR10G4 WILD-TYPE  281   48
   clus
vv  OR10G4 MUTATED OR10G4 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D789V7, binary
                  cls
clus                 0   1
  OR10G4 MUTATED     0   5
  OR10G4 WILD-TYPE 170 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G4 MUTATED      0    5
  OR10G4 WILD-TYPE  170  192
        clus
vv       OR10G4 MUTATED OR10G4 WILD-TYPE
  FEMALE              0              170
  MALE                5              192
[1] 2 2
[1] FALSE
D789V8, binary
                  cls
clus                 0   1
  OR10G4 MUTATED     4   0
  OR10G4 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G4 MUTATED      4    0
  OR10G4 WILD-TYPE  296    8
     clus
vv    OR10G4 MUTATED OR10G4 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D789V9, binary
                  cls
clus                 0   1
  OR10G4 MUTATED     4   1
  OR10G4 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G4 MUTATED      4    1
  OR10G4 WILD-TYPE  310   47
                               clus
vv                              OR10G4 MUTATED OR10G4 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR10G4 MUTATED     3   0   0   0
  OR10G4 WILD-TYPE 256   3  22  21
D789V10, multiclass
    clus
vv   OR10G4 MUTATED OR10G4 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D789V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR10G4 MUTATED                                  0     0
  OR10G4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR10G4 MUTATED                           0     3
  OR10G4 WILD-TYPE                        19   173
D789V12, multiclass
                                  clus
vv                                 OR10G4 MUTATED OR10G4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = NEB MUTATION ANALYSIS
D790V1, survival
               sevent
clus2             0   1
  NEB MUTATED    34  21
  NEB WILD-TYPE 243  57
  NEB MUTATED NEB WILD-TYPE 
           55           300 
  NEB MUTATED NEB WILD-TYPE 
           21            57 
$`NEB MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3952 TCGA-AD-6964 
        1.02         0.92        19.04        19.04         2.01        10.88 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-3810 
      100.01        49.08        22.09        26.17        79.69        36.53 
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3655 
       33.53         8.38        24.39        23.87        63.98        61.02 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3947 TCGA-AA-3949 
       26.99        10.06         0.00        10.06        33.01        26.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6197 
        2.01        25.02         4.01        34.98        35.01        21.44 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
       58.39        62.79        49.41         6.77        12.10        11.74 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-6747 TCGA-CK-6751 
        3.19        12.76        10.06       148.01        82.95       124.27 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6162 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 
       22.98        32.02        12.00        20.19        18.25         4.80 
TCGA-D5-6538 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A28F TCGA-G4-6293 
       17.13        49.91        13.32         7.50        35.97       133.18 
TCGA-G4-6309 
       85.48 

$`NEB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 
      106.75         1.94         5.88        63.62        35.80        91.79 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        32.75        32.91        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 
       22.52        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3812 
       15.02        11.01         5.98        37.05         5.03        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       38.99        37.02        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 
        5.13        22.36        88.21        29.56         5.23        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       55.92        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
      130.65        92.75        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  NEB MUTATED NEB WILD-TYPE 
            0             0 
  NEB MUTATED NEB WILD-TYPE 
       148.01        140.38 
  NEB MUTATED NEB WILD-TYPE 
        22.98         22.01 
[1] "0.0 - 148.0 (23.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.7"
D790V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEB MUTATED         5        0        7        18         3         0
  NEB WILD-TYPE      59        1       19        90         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEB MUTATED           7          0          8          3        4         0
  NEB WILD-TYPE        11          6         36         30       31        12
               vv
clus            STAGE IVB
  NEB MUTATED           0
  NEB WILD-TYPE         1
D790V3, multiclass
            clus
vv           NEB MUTATED NEB WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             7            19
  STAGE IIA           18            90
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            7            11
  STAGE IIIA           0             6
  STAGE IIIB           8            36
  STAGE IIIC           3            30
  STAGE IV             4            31
  STAGE IVA            0            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
  NEB MUTATED     0   7  43   7
  NEB WILD-TYPE   9  60 206  34
D790V4, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  T1           0             9
  T2           7            60
  T3          43           206
  T4           7            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
  NEB MUTATED    35  12  10
  NEB WILD-TYPE 185  69  56
D790V5, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  N0          35           185
  N1          12            69
  N2          10            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V6, binary
               cls
clus              0   1
  NEB MUTATED    42   4
  NEB WILD-TYPE 243  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     42    4
  NEB WILD-TYPE  243   44
   clus
vv  NEB MUTATED NEB WILD-TYPE
  0          42           243
  1           4            44
[1] 2 2
[1] FALSE
D790V7, binary
               cls
clus              0   1
  NEB MUTATED    24  33
  NEB WILD-TYPE 146 164
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     24   33
  NEB WILD-TYPE  146  164
        clus
vv       NEB MUTATED NEB WILD-TYPE
  FEMALE          24           146
  MALE            33           164
[1] 2 2
[1] FALSE
D790V8, binary
               cls
clus              0   1
  NEB MUTATED    44   2
  NEB WILD-TYPE 256   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     44    2
  NEB WILD-TYPE  256    6
     clus
vv    NEB MUTATED NEB WILD-TYPE
  NO           44           256
  YES           2             6
[1] 2 2
[1] FALSE
D790V9, binary
               cls
clus              0   1
  NEB MUTATED    47   9
  NEB WILD-TYPE 267  39
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     47    9
  NEB WILD-TYPE  267   39
                               clus
vv                              NEB MUTATED NEB WILD-TYPE
  COLON ADENOCARCINOMA                   47           267
  COLON MUCINOUS ADENOCARCINOMA           9            39
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NEB MUTATED    34   0   1   5
  NEB WILD-TYPE 225   3  21  16
D790V10, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  R0          34           225
  R1           0             3
  R2           1            21
  RX           5            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"
D790V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEB MUTATED                                  0     2
  NEB WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NEB MUTATED                           4    31
  NEB WILD-TYPE                        15   145
D790V12, multiclass
                                  clus
vv                                 NEB MUTATED NEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  4            15
  WHITE                                     31           145
[1] 4 2
[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 = PAXIP1 MUTATION ANALYSIS
D791V1, survival
                  sevent
clus2                0   1
  PAXIP1 MUTATED     9   7
  PAXIP1 WILD-TYPE 268  71
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              339 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               7               71 
$`PAXIP1 MUTATED`
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 
       15.52        10.88       100.01         8.38        20.12        19.66 
TCGA-AA-3811 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-6607 TCGA-CK-4952 
       10.06        31.00        25.02         4.01         3.19        15.62 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6533 TCGA-DM-A1D4 
       12.95        19.59        25.48        92.75 

$`PAXIP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       21.99        39.06        21.37        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-A6-6782 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
            3.19             0.00 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          100.01           148.01 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          17.605           22.360 
[1] "3.2 - 100.0 (17.6)" "0.0 - 148.0 (22.4)"
[1] "hr=" "2.2"
D791V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAXIP1 MUTATED         1        0        1         4         1         0
  PAXIP1 WILD-TYPE      63        1       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAXIP1 MUTATED           1          1          1          2        1
  PAXIP1 WILD-TYPE        17          5         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PAXIP1 MUTATED           0         0
  PAXIP1 WILD-TYPE        12         1
D791V3, multiclass
            clus
vv           PAXIP1 MUTATED PAXIP1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  PAXIP1 MUTATED     1   1   8   6
  PAXIP1 WILD-TYPE   8  66 241  35
D791V4, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              8              241
  T4              6               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
  PAXIP1 MUTATED     9   3   4
  PAXIP1 WILD-TYPE 211  78  62
D791V5, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V6, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    11   1
  PAXIP1 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     11    1
  PAXIP1 WILD-TYPE  274   47
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D791V7, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     4  12
  PAXIP1 WILD-TYPE 166 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      4   12
  PAXIP1 WILD-TYPE  166  185
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  FEMALE              4              166
  MALE               12              185
[1] 2 2
[1] FALSE
D791V8, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    13   0
  PAXIP1 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     13    0
  PAXIP1 WILD-TYPE  287    8
     clus
vv    PAXIP1 MUTATED PAXIP1 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D791V9, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    10   6
  PAXIP1 WILD-TYPE 304  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     10    6
  PAXIP1 WILD-TYPE  304   42
                               clus
vv                              PAXIP1 MUTATED PAXIP1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PAXIP1 MUTATED     8   0   0   1
  PAXIP1 WILD-TYPE 251   3  22  20
D791V10, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              1               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"
D791V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAXIP1 MUTATED                                  0     0
  PAXIP1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PAXIP1 MUTATED                           1    11
  PAXIP1 WILD-TYPE                        18   165
D791V12, multiclass
                                  clus
vv                                 PAXIP1 MUTATED PAXIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(792) Variable = OSTM1 MUTATION ANALYSIS
D792V1, survival
                 sevent
clus2               0   1
  OSTM1 MUTATED     3   2
  OSTM1 WILD-TYPE 274  76
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             350 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              2              76 
$`OSTM1 MUTATED`
TCGA-AA-3496 TCGA-AA-3511 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CM-6171 
        1.02         6.97        83.24        49.41        14.04 

$`OSTM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OSTM1 MUTATED OSTM1 WILD-TYPE 
           1.02            0.00 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
          83.24          148.01 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
         14.040          22.075 
[1] "1.0 - 83.2 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D792V2, continuous
                 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      63        1       23       107         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  OSTM1 MUTATED           0
  OSTM1 WILD-TYPE         1
D792V3, multiclass
            clus
vv           OSTM1 MUTATED OSTM1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OSTM1 MUTATED     0   1   3   1
  OSTM1 WILD-TYPE   9  66 246  40
D792V4, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             1              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
  OSTM1 MUTATED     5   0   0
  OSTM1 WILD-TYPE 215  81  66
D792V5, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V6, binary
                 cls
clus                0   1
  OSTM1 MUTATED     4   0
  OSTM1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      4    0
  OSTM1 WILD-TYPE  281   48
   clus
vv  OSTM1 MUTATED OSTM1 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D792V7, binary
                 cls
clus                0   1
  OSTM1 MUTATED     3   2
  OSTM1 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      3    2
  OSTM1 WILD-TYPE  167  195
        clus
vv       OSTM1 MUTATED OSTM1 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D792V8, binary
                 cls
clus                0   1
  OSTM1 MUTATED     4   0
  OSTM1 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      4    0
  OSTM1 WILD-TYPE  296    8
     clus
vv    OSTM1 MUTATED OSTM1 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D792V9, binary
                 cls
clus                0   1
  OSTM1 MUTATED     5   0
  OSTM1 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      5    0
  OSTM1 WILD-TYPE  309   48
                               clus
vv                              OSTM1 MUTATED OSTM1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OSTM1 MUTATED     4   0   0   0
  OSTM1 WILD-TYPE 255   3  22  21
D792V10, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D792V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSTM1 MUTATED                                  0     1
  OSTM1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OSTM1 MUTATED                           0     2
  OSTM1 WILD-TYPE                        19   174
D792V12, multiclass
                                  clus
vv                                 OSTM1 MUTATED OSTM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        2             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(793) Variable = UGT1A7 MUTATION ANALYSIS
D793V1, survival
                  sevent
clus2                0   1
  UGT1A7 MUTATED     6   2
  UGT1A7 WILD-TYPE 271  76
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              347 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               2               76 
$`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        12.59        16.14 
TCGA-D5-6930 TCGA-DM-A1D8 
       13.35        12.59 

$`UGT1A7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
            4.01             0.00 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
           88.21           148.01 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
          14.745           22.090 
[1] "4.0 - 88.2 (14.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D793V2, continuous
                  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      62        1       26       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A7 MUTATED           0          0          1          0        0
  UGT1A7 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT1A7 MUTATED           0         0
  UGT1A7 WILD-TYPE        12         1
D793V3, multiclass
            clus
vv           UGT1A7 MUTATED UGT1A7 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  UGT1A7 MUTATED     1   1   4   2
  UGT1A7 WILD-TYPE   8  66 245  39
D793V4, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              4              245
  T4              2               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
  UGT1A7 MUTATED     6   2   0
  UGT1A7 WILD-TYPE 214  79  66
D793V5, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  N0              6              214
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D793V6, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     7   0
  UGT1A7 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      7    0
  UGT1A7 WILD-TYPE  278   48
   clus
vv  UGT1A7 MUTATED UGT1A7 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D793V7, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     3   5
  UGT1A7 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      3    5
  UGT1A7 WILD-TYPE  167  192
        clus
vv       UGT1A7 MUTATED UGT1A7 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D793V8, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     6   0
  UGT1A7 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      6    0
  UGT1A7 WILD-TYPE  294    8
     clus
vv    UGT1A7 MUTATED UGT1A7 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D793V9, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     5   3
  UGT1A7 WILD-TYPE 309  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      5    3
  UGT1A7 WILD-TYPE  309   45
                               clus
vv                              UGT1A7 MUTATED UGT1A7 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UGT1A7 MUTATED     5   0   0   1
  UGT1A7 WILD-TYPE 254   3  22  20
D793V10, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D793V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT1A7 MUTATED                                  0     1
  UGT1A7 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT1A7 MUTATED                           0     5
  UGT1A7 WILD-TYPE                        19   171
D793V12, multiclass
                                  clus
vv                                 UGT1A7 MUTATED UGT1A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = ZNF658 MUTATION ANALYSIS
D794V1, survival
                  sevent
clus2                0   1
  ZNF658 MUTATED     4   5
  ZNF658 WILD-TYPE 273  73
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               9              346 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               5               73 
$`ZNF658 MUTATED`
TCGA-A6-2677 TCGA-AA-3662 TCGA-AA-3715 TCGA-CK-5912 TCGA-AA-3977 TCGA-AA-A00N 
       24.33         6.05        19.04        49.08        25.02         4.01 
TCGA-AZ-6598 TCGA-CM-5860 TCGA-D5-6928 
       49.41        32.02        11.64 

$`ZNF658 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF658 MUTATED ZNF658 WILD-TYPE 
            4.01             0.00 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
           49.41           148.01 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
          24.330           22.045 
[1] "4.0 - 49.4 (24.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.9"
D794V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF658 MUTATED         1        0        2         3         1         0
  ZNF658 WILD-TYPE      63        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF658 MUTATED           0          0          0          1        1
  ZNF658 WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF658 MUTATED           0         0
  ZNF658 WILD-TYPE        12         1
D794V3, multiclass
            clus
vv           ZNF658 MUTATED ZNF658 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF658 MUTATED     0   2   6   2
  ZNF658 WILD-TYPE   9  65 243  39
D794V4, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              6              243
  T4              2               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
  ZNF658 MUTATED     8   0   2
  ZNF658 WILD-TYPE 212  81  64
D794V5, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V6, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     6   1
  ZNF658 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      6    1
  ZNF658 WILD-TYPE  279   47
   clus
vv  ZNF658 MUTATED ZNF658 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D794V7, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     4   6
  ZNF658 WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      4    6
  ZNF658 WILD-TYPE  166  191
        clus
vv       ZNF658 MUTATED ZNF658 WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D794V8, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     8   0
  ZNF658 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      8    0
  ZNF658 WILD-TYPE  292    8
     clus
vv    ZNF658 MUTATED ZNF658 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D794V9, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     8   2
  ZNF658 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      8    2
  ZNF658 WILD-TYPE  306   46
                               clus
vv                              ZNF658 MUTATED ZNF658 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF658 MUTATED     6   0   1   1
  ZNF658 WILD-TYPE 253   3  21  20
D794V10, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              1               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"
D794V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF658 MUTATED                                  0     0
  ZNF658 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF658 MUTATED                           0     5
  ZNF658 WILD-TYPE                        19   171
D794V12, multiclass
                                  clus
vv                                 ZNF658 MUTATED ZNF658 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = ESCO2 MUTATION ANALYSIS
D795V1, survival
                 sevent
clus2               0   1
  ESCO2 MUTATED     7   3
  ESCO2 WILD-TYPE 270  75
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             10             345 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              3              75 
$`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 
       12.76        10.06        23.05        30.08 

$`ESCO2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4744 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ESCO2 MUTATED ESCO2 WILD-TYPE 
           4.01            0.00 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          58.39          148.01 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          17.10           22.09 
[1] "4.0 - 58.4 (17.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D795V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESCO2 MUTATED         0        0        1         6         2         0
  ESCO2 WILD-TYPE      64        1       25       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESCO2 MUTATED           1          0          0          0        0         0
  ESCO2 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  ESCO2 MUTATED           0
  ESCO2 WILD-TYPE         1
D795V3, multiclass
            clus
vv           ESCO2 MUTATED ESCO2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ESCO2 MUTATED     0   0   8   2
  ESCO2 WILD-TYPE   9  67 241  39
D795V4, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             8             241
  T4             2              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
  ESCO2 MUTATED     9   0   1
  ESCO2 WILD-TYPE 211  81  65
D795V5, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V6, binary
                 cls
clus                0   1
  ESCO2 MUTATED     9   0
  ESCO2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      9    0
  ESCO2 WILD-TYPE  276   48
   clus
vv  ESCO2 MUTATED ESCO2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D795V7, binary
                 cls
clus                0   1
  ESCO2 MUTATED     3   7
  ESCO2 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      3    7
  ESCO2 WILD-TYPE  167  190
        clus
vv       ESCO2 MUTATED ESCO2 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D795V8, binary
                 cls
clus                0   1
  ESCO2 MUTATED     9   0
  ESCO2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      9    0
  ESCO2 WILD-TYPE  291    8
     clus
vv    ESCO2 MUTATED ESCO2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D795V9, binary
                 cls
clus                0   1
  ESCO2 MUTATED     8   2
  ESCO2 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      8    2
  ESCO2 WILD-TYPE  306   46
                               clus
vv                              ESCO2 MUTATED ESCO2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESCO2 MUTATED     8   0   0   2
  ESCO2 WILD-TYPE 251   3  22  19
D795V10, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D795V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESCO2 MUTATED                                  0     2
  ESCO2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESCO2 MUTATED                           0     4
  ESCO2 WILD-TYPE                        19   172
D795V12, multiclass
                                  clus
vv                                 ESCO2 MUTATED ESCO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SV2A MUTATION ANALYSIS
D796V1, survival
                sevent
clus2              0   1
  SV2A MUTATED    18   3
  SV2A WILD-TYPE 259  75
  SV2A MUTATED SV2A WILD-TYPE 
            21            334 
  SV2A MUTATED SV2A WILD-TYPE 
             3             75 
$`SV2A MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-G4-6321 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 
        0.92        24.00        22.09        19.66         3.02        63.98 
TCGA-AA-3864 TCGA-AA-3956 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6600 
       53.00        34.03        34.98        27.09        49.41        12.10 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-6928 
       12.76        15.62        30.08        15.02        14.04        11.64 
TCGA-D5-6930 TCGA-DM-A28E TCGA-G4-6304 
       13.35       119.93        53.62 

$`SV2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.12        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21         6.77        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SV2A MUTATED SV2A WILD-TYPE 
          0.92           0.00 
  SV2A MUTATED SV2A WILD-TYPE 
        119.93         148.01 
  SV2A MUTATED SV2A WILD-TYPE 
        22.090         22.045 
[1] "0.9 - 119.9 (22.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D796V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SV2A MUTATED         3        0        4         7         2         0
  SV2A WILD-TYPE      61        1       22       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SV2A MUTATED           2          0          0          2        1         0
  SV2A WILD-TYPE        16          6         44         31       34        12
                vv
clus             STAGE IVB
  SV2A MUTATED           0
  SV2A WILD-TYPE         1
D796V3, multiclass
            clus
vv           SV2A MUTATED SV2A WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             0             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
  SV2A MUTATED     1   3  12   5
  SV2A WILD-TYPE   8  64 237  36
D796V4, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  T1            1              8
  T2            3             64
  T3           12            237
  T4            5             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
  SV2A MUTATED    16   4   1
  SV2A WILD-TYPE 204  77  65
D796V5, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  N0           16            204
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V6, binary
                cls
clus               0   1
  SV2A MUTATED    17   1
  SV2A WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     17    1
  SV2A WILD-TYPE  268   47
   clus
vv  SV2A MUTATED SV2A WILD-TYPE
  0           17            268
  1            1             47
[1] 2 2
[1] FALSE
D796V7, binary
                cls
clus               0   1
  SV2A MUTATED    12   9
  SV2A WILD-TYPE 158 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     12    9
  SV2A WILD-TYPE  158  188
        clus
vv       SV2A MUTATED SV2A WILD-TYPE
  FEMALE           12            158
  MALE              9            188
[1] 2 2
[1] FALSE
D796V8, binary
                cls
clus               0   1
  SV2A MUTATED    18   0
  SV2A WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     18    0
  SV2A WILD-TYPE  282    8
     clus
vv    SV2A MUTATED SV2A WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D796V9, binary
                cls
clus               0   1
  SV2A MUTATED    15   6
  SV2A WILD-TYPE 299  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     15    6
  SV2A WILD-TYPE  299   42
                               clus
vv                              SV2A MUTATED SV2A WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SV2A MUTATED    16   0   0   2
  SV2A WILD-TYPE 243   3  22  19
D796V10, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            2             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"
D796V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SV2A MUTATED                                  0     1
  SV2A WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SV2A MUTATED                           1    12
  SV2A WILD-TYPE                        18   164
D796V12, multiclass
                                  clus
vv                                 SV2A MUTATED SV2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      12            164
[1] 4 2
[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 = PSMB8 MUTATION ANALYSIS
D797V1, survival
                 sevent
clus2               0   1
  PSMB8 MUTATED     3   1
  PSMB8 WILD-TYPE 274  77
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              4             351 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              1              77 
$`PSMB8 MUTATED`
TCGA-A6-5661 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-5861 
       33.53        58.39        49.41        15.02 

$`PSMB8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PSMB8 MUTATED PSMB8 WILD-TYPE 
          15.02            0.00 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
          58.39          148.01 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
          41.47           22.03 
[1] "15.0 - 58.4 (41.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D797V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMB8 MUTATED         0        0        1         3         0         0
  PSMB8 WILD-TYPE      64        1       25       105         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  PSMB8 MUTATED           0
  PSMB8 WILD-TYPE         1
D797V3, multiclass
            clus
vv           PSMB8 MUTATED PSMB8 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PSMB8 MUTATED     0   0   4   0
  PSMB8 WILD-TYPE   9  67 245  41
D797V4, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             0              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
  PSMB8 MUTATED     4   0   0
  PSMB8 WILD-TYPE 216  81  66
D797V5, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V6, binary
                 cls
clus                0   1
  PSMB8 MUTATED     3   0
  PSMB8 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      3    0
  PSMB8 WILD-TYPE  282   48
   clus
vv  PSMB8 MUTATED PSMB8 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D797V7, binary
                 cls
clus                0   1
  PSMB8 MUTATED     3   1
  PSMB8 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      3    1
  PSMB8 WILD-TYPE  167  196
        clus
vv       PSMB8 MUTATED PSMB8 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D797V8, binary
                 cls
clus                0   1
  PSMB8 MUTATED     4   0
  PSMB8 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      4    0
  PSMB8 WILD-TYPE  296    8
     clus
vv    PSMB8 MUTATED PSMB8 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D797V9, binary
                 cls
clus                0   1
  PSMB8 MUTATED     4   0
  PSMB8 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      4    0
  PSMB8 WILD-TYPE  310   48
                               clus
vv                              PSMB8 MUTATED PSMB8 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMB8 MUTATED     3   0   0   0
  PSMB8 WILD-TYPE 256   3  22  21
D797V10, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D797V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMB8 MUTATED                                  0     0
  PSMB8 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSMB8 MUTATED                           1     3
  PSMB8 WILD-TYPE                        18   173
D797V12, multiclass
                                  clus
vv                                 PSMB8 MUTATED PSMB8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = CAMSAP1L1 MUTATION ANALYSIS
D798V1, survival
                     sevent
clus2                   0   1
  CAMSAP1L1 MUTATED    18   3
  CAMSAP1L1 WILD-TYPE 259  75
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 21                 334 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                  3                  75 
$`CAMSAP1L1 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-5661 
        1.02        19.04        35.80        32.75        30.44        33.53 
TCGA-A6-5664 TCGA-AA-3815 TCGA-AA-3877 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 
       22.09        33.04        31.00        27.09         0.20        58.39 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6927 TCGA-D5-6930 TCGA-F4-6570 
        6.77        12.76        12.00         9.44        13.35         6.18 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 
       53.62        85.48        61.91 

$`CAMSAP1L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        22.36        62.79        88.21        49.41 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        36.00        13.78        46.75 

  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                0.2                 0.0 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
              85.48              148.01 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
              27.09               22.01 
[1] "0.2 - 85.5 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D798V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAMSAP1L1 MUTATED         4        0        2         8         2         0
  CAMSAP1L1 WILD-TYPE      60        1       24       100         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAMSAP1L1 MUTATED           0          0          2          2        1
  CAMSAP1L1 WILD-TYPE        18          6         42         31       34
                     vv
clus                  STAGE IVA STAGE IVB
  CAMSAP1L1 MUTATED           0         0
  CAMSAP1L1 WILD-TYPE        12         1
D798V3, multiclass
            clus
vv           CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  STAGE I                    4                  60
  STAGE IA                   0                   1
  STAGE II                   2                  24
  STAGE IIA                  8                 100
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 2                  42
  STAGE IIIC                 2                  31
  STAGE IV                   1                  34
  STAGE IVA                  0                  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
  CAMSAP1L1 MUTATED     1   3  14   3
  CAMSAP1L1 WILD-TYPE   8  64 235  38
D798V4, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  T1                 1                   8
  T2                 3                  64
  T3                14                 235
  T4                 3                  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
  CAMSAP1L1 MUTATED    16   3   2
  CAMSAP1L1 WILD-TYPE 204  78  64
D798V5, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  N0                16                 204
  N1                 3                  78
  N2                 2                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V6, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    17   1
  CAMSAP1L1 WILD-TYPE 268  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     17    1
  CAMSAP1L1 WILD-TYPE  268   47
   clus
vv  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  0                17                 268
  1                 1                  47
[1] 2 2
[1] FALSE
D798V7, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    11  10
  CAMSAP1L1 WILD-TYPE 159 187
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     11   10
  CAMSAP1L1 WILD-TYPE  159  187
        clus
vv       CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  FEMALE                11                 159
  MALE                  10                 187
[1] 2 2
[1] FALSE
D798V8, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    18   0
  CAMSAP1L1 WILD-TYPE 282   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     18    0
  CAMSAP1L1 WILD-TYPE  282    8
     clus
vv    CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  NO                 18                 282
  YES                 0                   8
[1] 2 2
[1] FALSE
D798V9, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    15   6
  CAMSAP1L1 WILD-TYPE 299  42
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     15    6
  CAMSAP1L1 WILD-TYPE  299   42
                               clus
vv                              CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                         15                 299
  COLON MUCINOUS ADENOCARCINOMA                 6                  42
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  CAMSAP1L1 MUTATED    18   0   0   1
  CAMSAP1L1 WILD-TYPE 241   3  22  20
D798V10, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  R0                18                 241
  R1                 0                   3
  R2                 0                  22
  RX                 1                  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"
D798V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAMSAP1L1 MUTATED                                  0     1
  CAMSAP1L1 WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  CAMSAP1L1 MUTATED                           3    13
  CAMSAP1L1 WILD-TYPE                        16   163
D798V12, multiclass
                                  clus
vv                                 CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                   9
  BLACK OR AFRICAN AMERICAN                        3                  16
  WHITE                                           13                 163
[1] 4 2
[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 = MRPS18B MUTATION ANALYSIS
D799V1, survival
                   sevent
clus2                 0   1
  MRPS18B MUTATED     4   0
  MRPS18B WILD-TYPE 273  78
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                4               351 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                0                78 
$`MRPS18B MUTATED`
TCGA-AA-3662 TCGA-A6-2672 TCGA-DM-A28K TCGA-G4-6315 
        6.05        46.65        98.24        61.91 

$`MRPS18B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MRPS18B MUTATED MRPS18B WILD-TYPE 
             6.05              0.00 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
            98.24            148.01 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
            54.28             22.03 
[1] "6.0 - 98.2 (54.3)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9400000"
D799V2, continuous
                   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      64        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS18B MUTATED           0          0          1          0        2
  MRPS18B WILD-TYPE        18          6         43         33       33
                   vv
clus                STAGE IVA STAGE IVB
  MRPS18B MUTATED           0         0
  MRPS18B WILD-TYPE        12         1
D799V3, multiclass
            clus
vv           MRPS18B MUTATED MRPS18B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  MRPS18B MUTATED     0   0   3   1
  MRPS18B WILD-TYPE   9  67 246  40
D799V4, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               3               246
  T4               1                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
  MRPS18B MUTATED     1   2   1
  MRPS18B WILD-TYPE 219  79  65
D799V5, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  N0               1               219
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D799V6, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     2   2
  MRPS18B WILD-TYPE 283  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      2    2
  MRPS18B WILD-TYPE  283   46
   clus
vv  MRPS18B MUTATED MRPS18B WILD-TYPE
  0               2               283
  1               2                46
[1] 2 2
[1] FALSE
D799V7, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     2   2
  MRPS18B WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      2    2
  MRPS18B WILD-TYPE  168  195
        clus
vv       MRPS18B MUTATED MRPS18B WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D799V8, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     3   0
  MRPS18B WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      3    0
  MRPS18B WILD-TYPE  297    8
     clus
vv    MRPS18B MUTATED MRPS18B WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D799V9, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     3   1
  MRPS18B WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      3    1
  MRPS18B WILD-TYPE  311   47
                               clus
vv                              MRPS18B MUTATED MRPS18B WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  MRPS18B MUTATED     2   0   1   0
  MRPS18B WILD-TYPE 257   3  21  21
D799V10, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  R0               2               257
  R1               0                 3
  R2               1                21
  RX               0                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"
D799V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS18B MUTATED                                  0     0
  MRPS18B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MRPS18B MUTATED                           0     3
  MRPS18B WILD-TYPE                        19   173
D799V12, multiclass
                                  clus
vv                                 MRPS18B MUTATED MRPS18B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = INSRR MUTATION ANALYSIS
D800V1, survival
                 sevent
clus2               0   1
  INSRR MUTATED    19   6
  INSRR WILD-TYPE 258  72
  INSRR MUTATED INSRR WILD-TYPE 
             25             330 
  INSRR MUTATED INSRR WILD-TYPE 
              6              72 
$`INSRR MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6588 TCGA-G4-6628 
       24.00        25.08       100.01         5.88        26.17        79.69 
TCGA-A6-2676 TCGA-A6-6648 TCGA-AA-3518 TCGA-AA-3666 TCGA-AA-3941 TCGA-AA-3977 
       42.90        25.18         1.02         2.01        24.00        25.02 
TCGA-AU-3779 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4746 
       14.50        12.76        10.06       148.01        23.05        37.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6929 TCGA-F4-6570 
       17.03        12.00        25.48        17.13        13.41         6.18 
TCGA-G4-6304 
       53.62 

$`INSRR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 
       49.08        63.62        22.09        35.80        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         2.01       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-6163 TCGA-CM-6164 
        5.03        15.02        15.02        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  INSRR MUTATED INSRR WILD-TYPE 
           1.02            0.00 
  INSRR MUTATED INSRR WILD-TYPE 
         148.01          140.38 
  INSRR MUTATED INSRR WILD-TYPE 
          24.00           22.01 
[1] "1.0 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D800V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INSRR MUTATED         2        0        2         8         2         0
  INSRR WILD-TYPE      62        1       24       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSRR MUTATED           2          0          3          0        2         3
  INSRR WILD-TYPE        16          6         41         33       33         9
                 vv
clus              STAGE IVB
  INSRR MUTATED           0
  INSRR WILD-TYPE         1
D800V3, multiclass
            clus
vv           INSRR MUTATED INSRR WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              3               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
  INSRR MUTATED     0   3  17   6
  INSRR WILD-TYPE   9  64 232  35
D800V4, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  T1             0               9
  T2             3              64
  T3            17             232
  T4             6              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
  INSRR MUTATED    17   7   2
  INSRR WILD-TYPE 203  74  64
D800V5, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  N0            17             203
  N1             7              74
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V6, binary
                 cls
clus                0   1
  INSRR MUTATED    20   5
  INSRR WILD-TYPE 265  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     20    5
  INSRR WILD-TYPE  265   43
   clus
vv  INSRR MUTATED INSRR WILD-TYPE
  0            20             265
  1             5              43
[1] 2 2
[1] FALSE
D800V7, binary
                 cls
clus                0   1
  INSRR MUTATED    16  10
  INSRR WILD-TYPE 154 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     16   10
  INSRR WILD-TYPE  154  187
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  FEMALE            16             154
  MALE              10             187
[1] 2 2
[1] FALSE
D800V8, binary
                 cls
clus                0   1
  INSRR MUTATED    22   0
  INSRR WILD-TYPE 278   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     22    0
  INSRR WILD-TYPE  278    8
     clus
vv    INSRR MUTATED INSRR WILD-TYPE
  NO             22             278
  YES             0               8
[1] 2 2
[1] FALSE
D800V9, binary
                 cls
clus                0   1
  INSRR MUTATED    22   4
  INSRR WILD-TYPE 292  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     22    4
  INSRR WILD-TYPE  292   44
                               clus
vv                              INSRR MUTATED INSRR WILD-TYPE
  COLON ADENOCARCINOMA                     22             292
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INSRR MUTATED    20   0   0   2
  INSRR WILD-TYPE 239   3  22  19
D800V10, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  R0            20             239
  R1             0               3
  R2             0              22
  RX             2              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"
D800V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INSRR MUTATED                                  0     2
  INSRR WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INSRR MUTATED                           1    17
  INSRR WILD-TYPE                        18   159
D800V12, multiclass
                                  clus
vv                                 INSRR MUTATED INSRR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       17             159
[1] 4 2
[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 = PAAF1 MUTATION ANALYSIS
D801V1, survival
                 sevent
clus2               0   1
  PAAF1 MUTATED     4   1
  PAAF1 WILD-TYPE 273  77
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              5             350 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              1              77 
$`PAAF1 MUTATED`
TCGA-A6-5661 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-DM-A282 TCGA-G4-6315 
       33.53        58.39        29.56       139.17        61.91 

$`PAAF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PAAF1 MUTATED PAAF1 WILD-TYPE 
          29.56            0.00 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
         139.17          148.01 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
          58.39           21.99 
[1] "29.6 - 139.2 (58.4)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.2"
D801V2, continuous
                 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      64        1       26       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAAF1 MUTATED           0          0          0          0        1         0
  PAAF1 WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  PAAF1 MUTATED           0
  PAAF1 WILD-TYPE         1
D801V3, multiclass
            clus
vv           PAAF1 MUTATED PAAF1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  PAAF1 MUTATED     0   1   4   0
  PAAF1 WILD-TYPE   9  66 245  41
D801V4, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             0              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
  PAAF1 MUTATED     3   2   0
  PAAF1 WILD-TYPE 217  79  66
D801V5, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  N0             3             217
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V6, binary
                 cls
clus                0   1
  PAAF1 MUTATED     3   1
  PAAF1 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      3    1
  PAAF1 WILD-TYPE  282   47
   clus
vv  PAAF1 MUTATED PAAF1 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D801V7, binary
                 cls
clus                0   1
  PAAF1 MUTATED     3   2
  PAAF1 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      3    2
  PAAF1 WILD-TYPE  167  195
        clus
vv       PAAF1 MUTATED PAAF1 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D801V8, binary
                 cls
clus                0   1
  PAAF1 MUTATED     4   0
  PAAF1 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      4    0
  PAAF1 WILD-TYPE  296    8
     clus
vv    PAAF1 MUTATED PAAF1 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D801V9, binary
                 cls
clus                0   1
  PAAF1 MUTATED     5   0
  PAAF1 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      5    0
  PAAF1 WILD-TYPE  309   48
                               clus
vv                              PAAF1 MUTATED PAAF1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PAAF1 MUTATED     3   0   0   0
  PAAF1 WILD-TYPE 256   3  22  21
D801V10, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D801V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAAF1 MUTATED                                  0     0
  PAAF1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PAAF1 MUTATED                           1     4
  PAAF1 WILD-TYPE                        18   172
D801V12, multiclass
                                  clus
vv                                 PAAF1 MUTATED PAAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = JAK3 MUTATION ANALYSIS
D802V1, survival
                sevent
clus2              0   1
  JAK3 MUTATED    19   3
  JAK3 WILD-TYPE 258  75
  JAK3 MUTATED JAK3 WILD-TYPE 
            22            333 
  JAK3 MUTATED JAK3 WILD-TYPE 
             3             75 
$`JAK3 MUTATED`
TCGA-AA-3662 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5662 TCGA-A6-6648 
        6.05        63.62        35.80        26.17        23.61        25.18 
TCGA-A6-6651 TCGA-AA-3555 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00E TCGA-AU-6004 
       21.76        29.95        31.00        25.02        30.02        27.09 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 
       62.79        88.21        49.41        12.76        15.62        51.32 
TCGA-CM-4752 TCGA-D5-6537 TCGA-DM-A28H TCGA-G4-6307 
       13.02         4.80       117.07        55.04 

$`JAK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6625 
      100.01         1.94        49.08         5.88        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5664 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-A6-6652 
       32.71        27.09        22.52         8.38        25.08        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        1.41         5.13        22.36         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  JAK3 MUTATED JAK3 WILD-TYPE 
           4.8            0.0 
  JAK3 MUTATED JAK3 WILD-TYPE 
        117.07         148.01 
  JAK3 MUTATED JAK3 WILD-TYPE 
         28.52          21.99 
[1] "4.8 - 117.1 (28.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D802V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JAK3 MUTATED         4        0        3         7         0         0
  JAK3 WILD-TYPE      60        1       23       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK3 MUTATED           0          0          4          2        1         2
  JAK3 WILD-TYPE        18          6         40         31       34        10
                vv
clus             STAGE IVB
  JAK3 MUTATED           0
  JAK3 WILD-TYPE         1
D802V3, multiclass
            clus
vv           JAK3 MUTATED JAK3 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             2             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
  JAK3 MUTATED     2   3  16   3
  JAK3 WILD-TYPE   7  64 233  38
D802V4, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  T1            2              7
  T2            3             64
  T3           16            233
  T4            3             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
  JAK3 MUTATED    16   4   4
  JAK3 WILD-TYPE 204  77  62
D802V5, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  N0           16            204
  N1            4             77
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V6, binary
                cls
clus               0   1
  JAK3 MUTATED    14   3
  JAK3 WILD-TYPE 271  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     14    3
  JAK3 WILD-TYPE  271   45
   clus
vv  JAK3 MUTATED JAK3 WILD-TYPE
  0           14            271
  1            3             45
[1] 2 2
[1] FALSE
D802V7, binary
                cls
clus               0   1
  JAK3 MUTATED    13  11
  JAK3 WILD-TYPE 157 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     13   11
  JAK3 WILD-TYPE  157  186
        clus
vv       JAK3 MUTATED JAK3 WILD-TYPE
  FEMALE           13            157
  MALE             11            186
[1] 2 2
[1] FALSE
D802V8, binary
                cls
clus               0   1
  JAK3 MUTATED    18   1
  JAK3 WILD-TYPE 282   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     18    1
  JAK3 WILD-TYPE  282    7
     clus
vv    JAK3 MUTATED JAK3 WILD-TYPE
  NO            18            282
  YES            1              7
[1] 2 2
[1] FALSE
D802V9, binary
                cls
clus               0   1
  JAK3 MUTATED    20   4
  JAK3 WILD-TYPE 294  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     20    4
  JAK3 WILD-TYPE  294   44
                               clus
vv                              JAK3 MUTATED JAK3 WILD-TYPE
  COLON ADENOCARCINOMA                    20            294
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  JAK3 MUTATED    11   0   1   4
  JAK3 WILD-TYPE 248   3  21  17
D802V10, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            1             21
  RX            4             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"
D802V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK3 MUTATED                                  0     1
  JAK3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK3 MUTATED                           1    16
  JAK3 WILD-TYPE                        18   160
D802V12, multiclass
                                  clus
vv                                 JAK3 MUTATED JAK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      16            160
[1] 4 2
[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 = TMEM45A MUTATION ANALYSIS
D803V1, survival
                   sevent
clus2                 0   1
  TMEM45A MUTATED     3   1
  TMEM45A WILD-TYPE 274  77
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               351 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                1                77 
$`TMEM45A MUTATED`
TCGA-G4-6628 TCGA-A6-6138 TCGA-AZ-6598 TCGA-G4-6323 
       79.69        22.52        49.41        13.78 

$`TMEM45A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        46.75 

  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            22.030 
[1] "13.8 - 79.7 (36.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D803V2, continuous
                   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      62        0       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM45A MUTATED           0          0          0          0        0
  TMEM45A WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  TMEM45A MUTATED           0         0
  TMEM45A WILD-TYPE        12         1
D803V3, multiclass
            clus
vv           TMEM45A MUTATED TMEM45A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 1                 0
  STAGE II                 1                25
  STAGE IIA                0               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  TMEM45A MUTATED     0   2   1   0
  TMEM45A WILD-TYPE   9  65 248  41
D803V4, multiclass
    clus
vv   TMEM45A MUTATED TMEM45A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               1               248
  T4               0                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
  TMEM45A MUTATED     4   0   0
  TMEM45A WILD-TYPE 216  81  66
D803V5, multiclass
    clus
vv   TMEM45A MUTATED TMEM45A WILD-TYPE
  N0               4               216
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V6, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     2   0
  TMEM45A WILD-TYPE 283  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      2    0
  TMEM45A WILD-TYPE  283   48
   clus
vv  TMEM45A MUTATED TMEM45A WILD-TYPE
  0               2               283
  1               0                48
[1] 2 2
[1] FALSE
D803V7, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     1   3
  TMEM45A WILD-TYPE 169 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      1    3
  TMEM45A WILD-TYPE  169  194
        clus
vv       TMEM45A MUTATED TMEM45A WILD-TYPE
  FEMALE               1               169
  MALE                 3               194
[1] 2 2
[1] FALSE
D803V8, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     4   0
  TMEM45A WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      4    0
  TMEM45A WILD-TYPE  296    8
     clus
vv    TMEM45A MUTATED TMEM45A WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D803V9, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     4   0
  TMEM45A WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      4    0
  TMEM45A WILD-TYPE  310   48
                               clus
vv                              TMEM45A MUTATED TMEM45A WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM45A MUTATED     2   0   0   0
  TMEM45A WILD-TYPE 257   3  22  21
D803V10, multiclass
[1] "Remove cluster labels:" "TMEM45A MUTATED"       
clus
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        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-3527 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3662        TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AD-6895        TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       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-A6-2678        TCGA-A6-2683        TCGA-A6-3807        TCGA-A6-3808 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657        TCGA-A6-5659 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781        TCGA-AA-3489 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3492        TCGA-AA-3502        TCGA-AA-3510        TCGA-AA-3511 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532        TCGA-AA-3534 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544        TCGA-AA-3548 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555        TCGA-AA-3558 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3561        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3663 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3673 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693        TCGA-AA-3695 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3811 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3812        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-3845        TCGA-AA-3846        TCGA-AA-3848 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3861 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869        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-3941 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3955        TCGA-AA-3956 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3973        TCGA-AA-3975 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00J        TCGA-AA-A00K        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-A010        TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6889 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4682        TCGA-CA-5254 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952 
"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-G4-6315        TCGA-G4-6317        TCGA-G4-6626 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
D803V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM45A MUTATED                                  0     0
  TMEM45A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM45A MUTATED                           1     3
  TMEM45A WILD-TYPE                        18   173
D803V12, multiclass
                                  clus
vv                                 TMEM45A MUTATED TMEM45A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = UAP1L1 MUTATION ANALYSIS
D804V1, survival
                  sevent
clus2                0   1
  UAP1L1 MUTATED     5   2
  UAP1L1 WILD-TYPE 272  76
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               7              348 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               2               76 
$`UAP1L1 MUTATED`
TCGA-AA-3662 TCGA-AD-6895 TCGA-AA-3930 TCGA-AA-3977 TCGA-AD-5900 TCGA-DM-A28F 
        6.05        25.08         2.01        25.02        12.16        35.97 
TCGA-G4-6299 
       74.56 

$`UAP1L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
            2.01             0.00 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
           74.56           148.01 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
          25.020           22.045 
[1] "2.0 - 74.6 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D804V2, continuous
                  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      63        1       26       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UAP1L1 MUTATED           0          0          2          1        2
  UAP1L1 WILD-TYPE        18          6         42         32       33
                  vv
clus               STAGE IVA STAGE IVB
  UAP1L1 MUTATED           0         0
  UAP1L1 WILD-TYPE        12         1
D804V3, multiclass
            clus
vv           UAP1L1 MUTATED UAP1L1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               0               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
  UAP1L1 MUTATED     0   2   4   1
  UAP1L1 WILD-TYPE   9  65 245  40
D804V4, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              1               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
  UAP1L1 MUTATED     2   2   3
  UAP1L1 WILD-TYPE 218  79  63
D804V5, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  N0              2              218
  N1              2               79
  N2              3               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"
D804V6, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     3   2
  UAP1L1 WILD-TYPE 282  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      3    2
  UAP1L1 WILD-TYPE  282   46
   clus
vv  UAP1L1 MUTATED UAP1L1 WILD-TYPE
  0              3              282
  1              2               46
[1] 2 2
[1] FALSE
D804V7, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     1   6
  UAP1L1 WILD-TYPE 169 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      1    6
  UAP1L1 WILD-TYPE  169  191
        clus
vv       UAP1L1 MUTATED UAP1L1 WILD-TYPE
  FEMALE              1              169
  MALE                6              191
[1] 2 2
[1] FALSE
D804V8, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     6   0
  UAP1L1 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      6    0
  UAP1L1 WILD-TYPE  294    8
     clus
vv    UAP1L1 MUTATED UAP1L1 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D804V9, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     6   1
  UAP1L1 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      6    1
  UAP1L1 WILD-TYPE  308   47
                               clus
vv                              UAP1L1 MUTATED UAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UAP1L1 MUTATED     3   0   2   0
  UAP1L1 WILD-TYPE 256   3  20  21
D804V10, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              2               20
  RX              0               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"
D804V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UAP1L1 MUTATED                                  0     0
  UAP1L1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UAP1L1 MUTATED                           0     4
  UAP1L1 WILD-TYPE                        19   172
D804V12, multiclass
                                  clus
vv                                 UAP1L1 MUTATED UAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = OR6A2 MUTATION ANALYSIS
D805V1, survival
                 sevent
clus2               0   1
  OR6A2 MUTATED     6   2
  OR6A2 WILD-TYPE 271  76
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             347 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        13.78        46.75 

  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           22.09 
[1] "4.0 - 148.0 (14.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D805V2, continuous
                 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      64        1       26       105         7         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        16          6         43         32       35        12
                 vv
clus              STAGE IVB
  OR6A2 MUTATED           0
  OR6A2 WILD-TYPE         1
D805V3, multiclass
            clus
vv           OR6A2 MUTATED OR6A2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OR6A2 MUTATED     0   0   7   1
  OR6A2 WILD-TYPE   9  67 242  40
D805V4, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  OR6A2 MUTATED     4   2   2
  OR6A2 WILD-TYPE 216  79  64
D805V5, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V6, binary
                 cls
clus                0   1
  OR6A2 MUTATED     7   0
  OR6A2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      7    0
  OR6A2 WILD-TYPE  278   48
   clus
vv  OR6A2 MUTATED OR6A2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D805V7, binary
                 cls
clus                0   1
  OR6A2 MUTATED     4   4
  OR6A2 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      4    4
  OR6A2 WILD-TYPE  166  193
        clus
vv       OR6A2 MUTATED OR6A2 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D805V8, binary
                 cls
clus                0   1
  OR6A2 MUTATED     7   0
  OR6A2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      7    0
  OR6A2 WILD-TYPE  293    8
     clus
vv    OR6A2 MUTATED OR6A2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D805V9, binary
                 cls
clus                0   1
  OR6A2 MUTATED     5   3
  OR6A2 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      5    3
  OR6A2 WILD-TYPE  309   45
                               clus
vv                              OR6A2 MUTATED OR6A2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR6A2 MUTATED     6   0   0   1
  OR6A2 WILD-TYPE 253   3  22  20
D805V10, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D805V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6A2 MUTATED                                  0     1
  OR6A2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6A2 MUTATED                           1     4
  OR6A2 WILD-TYPE                        18   172
D805V12, multiclass
                                  clus
vv                                 OR6A2 MUTATED OR6A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = PTPN12 MUTATION ANALYSIS
D806V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED    11   3
  PTPN12 WILD-TYPE 266  75
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              14              341 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               3               75 
$`PTPN12 MUTATED`
TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6964 TCGA-G4-6586 TCGA-A6-6781 
        8.05         0.92        24.00        10.88        35.80        19.66 
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 
       63.98         6.97        26.99        20.98         4.01        34.98 
TCGA-AZ-6598 TCGA-CA-6717 
       49.41        12.76 

$`PTPN12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        26.17        91.79        79.69 
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-A6-5656 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-A6-6648 
       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-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        26.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
            0.92             0.00 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           63.98           148.01 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           20.32            22.09 
[1] "0.9 - 64.0 (20.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D806V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN12 MUTATED         0        0        4         5         3         0
  PTPN12 WILD-TYPE      64        1       22       103         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN12 MUTATED           1          0          2          1        0
  PTPN12 WILD-TYPE        17          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  PTPN12 MUTATED           0         0
  PTPN12 WILD-TYPE        12         1
D806V3, multiclass
            clus
vv           PTPN12 MUTATED PTPN12 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               5              103
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  PTPN12 MUTATED     0   1  10   6
  PTPN12 WILD-TYPE   9  66 239  35
D806V4, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             10              239
  T4              6               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
  PTPN12 MUTATED    12   3   2
  PTPN12 WILD-TYPE 208  78  64
D806V5, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  N0             12              208
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V6, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    13   0
  PTPN12 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     13    0
  PTPN12 WILD-TYPE  272   48
   clus
vv  PTPN12 MUTATED PTPN12 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D806V7, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     9   8
  PTPN12 WILD-TYPE 161 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      9    8
  PTPN12 WILD-TYPE  161  189
        clus
vv       PTPN12 MUTATED PTPN12 WILD-TYPE
  FEMALE              9              161
  MALE                8              189
[1] 2 2
[1] FALSE
D806V8, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    13   0
  PTPN12 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     13    0
  PTPN12 WILD-TYPE  287    8
     clus
vv    PTPN12 MUTATED PTPN12 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D806V9, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    13   4
  PTPN12 WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     13    4
  PTPN12 WILD-TYPE  301   44
                               clus
vv                              PTPN12 MUTATED PTPN12 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPN12 MUTATED    13   0   0   2
  PTPN12 WILD-TYPE 246   3  22  19
D806V10, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              2               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"
D806V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN12 MUTATED                                  0     1
  PTPN12 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN12 MUTATED                           0     5
  PTPN12 WILD-TYPE                        19   171
D806V12, multiclass
                                  clus
vv                                 PTPN12 MUTATED PTPN12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = OR2Y1 MUTATION ANALYSIS
D807V1, survival
                 sevent
clus2               0   1
  OR2Y1 MUTATED     6   1
  OR2Y1 WILD-TYPE 271  77
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              7             348 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              1              77 
$`OR2Y1 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6653 TCGA-AA-A00N TCGA-CA-5254 TCGA-CM-6166 
       35.80        26.17        24.39         4.01        12.69        21.99 
TCGA-D5-6540 
       16.14 

$`OR2Y1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.075 
[1] "4.0 - 35.8 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D807V2, continuous
                 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      61        1       26       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2Y1 MUTATED           0          0          0          0        0         0
  OR2Y1 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  OR2Y1 MUTATED           0
  OR2Y1 WILD-TYPE         1
D807V3, multiclass
            clus
vv           OR2Y1 MUTATED OR2Y1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR2Y1 MUTATED     0   3   3   1
  OR2Y1 WILD-TYPE   9  64 246  40
D807V4, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             3             246
  T4             1              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
  OR2Y1 MUTATED     7   0   0
  OR2Y1 WILD-TYPE 213  81  66
D807V5, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V6, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     7   0
  OR2Y1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      7    0
  OR2Y1 WILD-TYPE  278   48
   clus
vv  OR2Y1 MUTATED OR2Y1 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D807V7, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     4   3
  OR2Y1 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      4    3
  OR2Y1 WILD-TYPE  166  194
        clus
vv       OR2Y1 MUTATED OR2Y1 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D807V8, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     6   0
  OR2Y1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      6    0
  OR2Y1 WILD-TYPE  294    8
     clus
vv    OR2Y1 MUTATED OR2Y1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D807V9, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     5   2
  OR2Y1 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      5    2
  OR2Y1 WILD-TYPE  309   46
                               clus
vv                              OR2Y1 MUTATED OR2Y1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2Y1 MUTATED     5   0   0   1
  OR2Y1 WILD-TYPE 254   3  22  20
D807V10, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D807V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2Y1 MUTATED                                  0     1
  OR2Y1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2Y1 MUTATED                           0     5
  OR2Y1 WILD-TYPE                        19   171
D807V12, multiclass
                                  clus
vv                                 OR2Y1 MUTATED OR2Y1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = THOC6 MUTATION ANALYSIS
D808V1, survival
                 sevent
clus2               0   1
  THOC6 MUTATED     5   2
  THOC6 WILD-TYPE 272  76
  THOC6 MUTATED THOC6 WILD-TYPE 
              7             348 
  THOC6 MUTATED THOC6 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.045 
[1] "12.1 - 133.2 (30.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.1"
D808V2, continuous
                 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      64        1       26       107         7         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        15          6         44         32       33        12
                 vv
clus              STAGE IVB
  THOC6 MUTATED           0
  THOC6 WILD-TYPE         1
D808V3, multiclass
            clus
vv           THOC6 MUTATED THOC6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  THOC6 MUTATED     0   0   6   2
  THOC6 WILD-TYPE   9  67 243  39
D808V4, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             2              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
  THOC6 MUTATED     3   2   3
  THOC6 WILD-TYPE 217  79  63
D808V5, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  N0             3             217
  N1             2              79
  N2             3              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"
D808V6, binary
                 cls
clus                0   1
  THOC6 MUTATED     6   2
  THOC6 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      6    2
  THOC6 WILD-TYPE  279   46
   clus
vv  THOC6 MUTATED THOC6 WILD-TYPE
  0             6             279
  1             2              46
[1] 2 2
[1] FALSE
D808V7, binary
                 cls
clus                0   1
  THOC6 MUTATED     4   4
  THOC6 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      4    4
  THOC6 WILD-TYPE  166  193
        clus
vv       THOC6 MUTATED THOC6 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D808V8, binary
                 cls
clus                0   1
  THOC6 MUTATED     6   1
  THOC6 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      6    1
  THOC6 WILD-TYPE  294    7
     clus
vv    THOC6 MUTATED THOC6 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D808V9, binary
                 cls
clus                0   1
  THOC6 MUTATED     7   1
  THOC6 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      7    1
  THOC6 WILD-TYPE  307   47
                               clus
vv                              THOC6 MUTATED THOC6 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  THOC6 MUTATED     5   0   1   0
  THOC6 WILD-TYPE 254   3  21  21
D808V10, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             0              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"
D808V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THOC6 MUTATED                                  0     0
  THOC6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THOC6 MUTATED                           1     3
  THOC6 WILD-TYPE                        18   173
D808V12, multiclass
                                  clus
vv                                 THOC6 MUTATED THOC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = VASH1 MUTATION ANALYSIS
D809V1, survival
                 sevent
clus2               0   1
  VASH1 MUTATED     4   0
  VASH1 WILD-TYPE 273  78
  VASH1 MUTATED VASH1 WILD-TYPE 
              4             351 
  VASH1 MUTATED VASH1 WILD-TYPE 
              0              78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.09 
[1] "15.0 - 135.7 (19.1)" "0.0 - 148.0 (22.1)" 
[1] "hr="     "9200000"
D809V2, continuous
                 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      63        1       26       106         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  VASH1 MUTATED           0
  VASH1 WILD-TYPE         1
D809V3, multiclass
            clus
vv           VASH1 MUTATED VASH1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  VASH1 MUTATED     0   1   3   1
  VASH1 WILD-TYPE   9  66 246  40
D809V4, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             1              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
  VASH1 MUTATED     4   1   0
  VASH1 WILD-TYPE 216  80  66
D809V5, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D809V6, binary
                 cls
clus                0   1
  VASH1 MUTATED     4   0
  VASH1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      4    0
  VASH1 WILD-TYPE  281   48
   clus
vv  VASH1 MUTATED VASH1 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D809V7, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   2
  VASH1 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    2
  VASH1 WILD-TYPE  167  195
        clus
vv       VASH1 MUTATED VASH1 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D809V8, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   0
  VASH1 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    0
  VASH1 WILD-TYPE  297    8
     clus
vv    VASH1 MUTATED VASH1 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D809V9, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   1
  VASH1 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    1
  VASH1 WILD-TYPE  311   47
                               clus
vv                              VASH1 MUTATED VASH1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VASH1 MUTATED     3   0   0   1
  VASH1 WILD-TYPE 256   3  22  20
D809V10, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D809V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VASH1 MUTATED                                  0     0
  VASH1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VASH1 MUTATED                           0     5
  VASH1 WILD-TYPE                        19   171
D809V12, multiclass
                                  clus
vv                                 VASH1 MUTATED VASH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = MAP7D3 MUTATION ANALYSIS
D810V1, survival
                  sevent
clus2                0   1
  MAP7D3 MUTATED    13   3
  MAP7D3 WILD-TYPE 264  75
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              16              339 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               3               75 
$`MAP7D3 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 
       35.80        26.17        91.79        22.06         3.02        63.98 
TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3941 TCGA-AA-A03J TCGA-AZ-4315 TCGA-AZ-4616 
       78.08        26.99        24.00        40.96        58.39         5.13 
TCGA-CA-6717 TCGA-D5-6930 TCGA-DM-A28E TCGA-F4-6570 
       12.76        13.35       119.93         6.18 

$`MAP7D3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       22.09        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-AD-5900 TCGA-AD-6889 
        0.92        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       17.82         1.41        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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28F 
       44.32       131.51       135.65       139.17        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-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
            3.02             0.00 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
          119.93           148.01 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           26.58            21.99 
[1] "3.0 - 119.9 (26.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D810V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP7D3 MUTATED         1        0        3        11         0         0
  MAP7D3 WILD-TYPE      63        1       23        97         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D3 MUTATED           0          0          0          0        1
  MAP7D3 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  MAP7D3 MUTATED           1         0
  MAP7D3 WILD-TYPE        11         1
D810V3, multiclass
            clus
vv           MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              11               97
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  MAP7D3 MUTATED     0   1  15   1
  MAP7D3 WILD-TYPE   9  66 234  40
D810V4, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             15              234
  T4              1               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
  MAP7D3 MUTATED    15   1   1
  MAP7D3 WILD-TYPE 205  80  65
D810V5, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  N0             15              205
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V6, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   2
  MAP7D3 WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    2
  MAP7D3 WILD-TYPE  270   46
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0             15              270
  1              2               46
[1] 2 2
[1] FALSE
D810V7, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    13   4
  MAP7D3 WILD-TYPE 157 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     13    4
  MAP7D3 WILD-TYPE  157  193
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  FEMALE             13              157
  MALE                4              193
[1] 2 2
[1] FALSE
D810V8, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   0
  MAP7D3 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    0
  MAP7D3 WILD-TYPE  285    8
     clus
vv    MAP7D3 MUTATED MAP7D3 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D810V9, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   2
  MAP7D3 WILD-TYPE 299  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    2
  MAP7D3 WILD-TYPE  299   46
                               clus
vv                              MAP7D3 MUTATED MAP7D3 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP7D3 MUTATED    14   0   0   1
  MAP7D3 WILD-TYPE 245   3  22  20
D810V10, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              0               22
  RX              1               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"
D810V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP7D3 MUTATED                                  0     1
  MAP7D3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP7D3 MUTATED                           0     9
  MAP7D3 WILD-TYPE                        19   167
D810V12, multiclass
                                  clus
vv                                 MAP7D3 MUTATED MAP7D3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         9              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(811) Variable = SGK3 MUTATION ANALYSIS
D811V1, survival
                sevent
clus2              0   1
  SGK3 MUTATED     4   4
  SGK3 WILD-TYPE 273  74
  SGK3 MUTATED SGK3 WILD-TYPE 
             8            347 
  SGK3 MUTATED SGK3 WILD-TYPE 
             4             74 
$`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 
       13.35        60.79 

$`SGK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 
       40.96        12.16        83.24        24.53        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SGK3 MUTATED SGK3 WILD-TYPE 
          3.19           0.00 
  SGK3 MUTATED SGK3 WILD-TYPE 
         63.98         148.01 
  SGK3 MUTATED SGK3 WILD-TYPE 
        20.335         22.060 
[1] "3.2 - 64.0 (20.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D811V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGK3 MUTATED         0        0        1         4         0         0
  SGK3 WILD-TYPE      64        1       25       104         8         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        18          6         44         32       34        12
                vv
clus             STAGE IVB
  SGK3 MUTATED           0
  SGK3 WILD-TYPE         1
D811V3, multiclass
            clus
vv           SGK3 MUTATED SGK3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  SGK3 MUTATED     0   0   6   2
  SGK3 WILD-TYPE   9  67 243  39
D811V4, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            2             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
  SGK3 MUTATED     6   0   2
  SGK3 WILD-TYPE 214  81  64
D811V5, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V6, binary
                cls
clus               0   1
  SGK3 MUTATED     5   1
  SGK3 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      5    1
  SGK3 WILD-TYPE  280   47
   clus
vv  SGK3 MUTATED SGK3 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D811V7, binary
                cls
clus               0   1
  SGK3 MUTATED     0   8
  SGK3 WILD-TYPE 170 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      0    8
  SGK3 WILD-TYPE  170  189
        clus
vv       SGK3 MUTATED SGK3 WILD-TYPE
  FEMALE            0            170
  MALE              8            189
[1] 2 2
[1] FALSE
D811V8, binary
                cls
clus               0   1
  SGK3 MUTATED     7   0
  SGK3 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      7    0
  SGK3 WILD-TYPE  293    8
     clus
vv    SGK3 MUTATED SGK3 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D811V9, binary
                cls
clus               0   1
  SGK3 MUTATED     6   2
  SGK3 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      6    2
  SGK3 WILD-TYPE  308   46
                               clus
vv                              SGK3 MUTATED SGK3 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SGK3 MUTATED     4   0   0   0
  SGK3 WILD-TYPE 255   3  22  21
D811V10, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D811V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGK3 MUTATED                                  0     0
  SGK3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SGK3 MUTATED                           0     7
  SGK3 WILD-TYPE                        19   169
D811V12, multiclass
                                  clus
vv                                 SGK3 MUTATED SGK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = ARHGAP32 MUTATION ANALYSIS
D812V1, survival
                    sevent
clus2                  0   1
  ARHGAP32 MUTATED    20   3
  ARHGAP32 WILD-TYPE 257  75
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                23                332 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                 3                 75 
$`ARHGAP32 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 
       85.05        19.04        26.17        32.75        33.53        22.06 
TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
        3.02        29.95        33.04         4.01        34.98         1.02 
TCGA-AZ-4682 TCGA-CK-6751 TCGA-CM-5341 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6532 
       22.36       124.27        29.06        12.95        19.59        18.25 
TCGA-D5-6541 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-G4-6317 TCGA-G4-6323 
       15.58        12.43       119.70        36.00        13.78 

$`ARHGAP32 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        62.79        88.21        49.41         6.77 
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 
       12.36        12.39        12.59        12.59        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-CM-4743 
       51.32        21.99        21.14        82.95         2.01        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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-D5-6924 
       12.49        16.14         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        46.75 

  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
              1.02               0.00 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
            124.27             148.01 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
             22.36              22.01 
[1] "1.0 - 124.3 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D812V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP32 MUTATED         2        1        4         9         3         0
  ARHGAP32 WILD-TYPE      62        0       22        99         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP32 MUTATED           0          2          0          1        1
  ARHGAP32 WILD-TYPE        18          4         44         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP32 MUTATED           1         0
  ARHGAP32 WILD-TYPE        11         1
D812V3, multiclass
            clus
vv           ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  1                  0
  STAGE II                  4                 22
  STAGE IIA                 9                 99
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                2                  4
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 1                 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
  ARHGAP32 MUTATED     0   3  16   4
  ARHGAP32 WILD-TYPE   9  64 233  37
D812V4, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3               16                233
  T4                4                 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
  ARHGAP32 MUTATED    21   2   1
  ARHGAP32 WILD-TYPE 199  79  65
D812V5, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  N0               21                199
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V6, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    19   2
  ARHGAP32 WILD-TYPE 266  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     19    2
  ARHGAP32 WILD-TYPE  266   46
   clus
vv  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  0               19                266
  1                2                 46
[1] 2 2
[1] FALSE
D812V7, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    14  10
  ARHGAP32 WILD-TYPE 156 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     14   10
  ARHGAP32 WILD-TYPE  156  187
        clus
vv       ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  FEMALE               14                156
  MALE                 10                187
[1] 2 2
[1] FALSE
D812V8, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    19   1
  ARHGAP32 WILD-TYPE 281   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     19    1
  ARHGAP32 WILD-TYPE  281    7
     clus
vv    ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  NO                19                281
  YES                1                  7
[1] 2 2
[1] FALSE
D812V9, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    19   5
  ARHGAP32 WILD-TYPE 295  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     19    5
  ARHGAP32 WILD-TYPE  295   43
                               clus
vv                              ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  COLON ADENOCARCINOMA                        19                295
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP32 MUTATED    21   0   1   1
  ARHGAP32 WILD-TYPE 238   3  21  20
D812V10, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  R0               21                238
  R1                0                  3
  R2                1                 21
  RX                1                 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"
D812V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP32 MUTATED                                  0     0
  ARHGAP32 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP32 MUTATED                           2    13
  ARHGAP32 WILD-TYPE                        17   163
D812V12, multiclass
                                  clus
vv                                 ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          13                163
[1] 4 2
[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 = BRD8 MUTATION ANALYSIS
D813V1, survival
                sevent
clus2              0   1
  BRD8 MUTATED    12   3
  BRD8 WILD-TYPE 265  75
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            340 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3             75 
$`BRD8 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3994 
       19.04        19.04        22.06        24.39        29.95        27.02 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5860 
        4.01        12.16        58.39        49.41        51.32        32.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-DM-A28K 
       14.04        12.95        98.24 

$`BRD8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  BRD8 MUTATED BRD8 WILD-TYPE 
          4.01           0.00 
  BRD8 MUTATED BRD8 WILD-TYPE 
         98.24         148.01 
  BRD8 MUTATED BRD8 WILD-TYPE 
         24.39          22.01 
[1] "4.0 - 98.2 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D813V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRD8 MUTATED         3        0        2         7         1         0
  BRD8 WILD-TYPE      61        1       24       101         7         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  BRD8 MUTATED           0
  BRD8 WILD-TYPE         1
D813V3, multiclass
            clus
vv           BRD8 MUTATED BRD8 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  BRD8 MUTATED     0   3  11   1
  BRD8 WILD-TYPE   9  64 238  40
D813V4, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           11            238
  T4            1             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
  BRD8 MUTATED    14   1   0
  BRD8 WILD-TYPE 206  80  66
D813V5, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  N0           14            206
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V6, binary
                cls
clus               0   1
  BRD8 MUTATED    11   1
  BRD8 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     11    1
  BRD8 WILD-TYPE  274   47
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D813V7, binary
                cls
clus               0   1
  BRD8 MUTATED     5  10
  BRD8 WILD-TYPE 165 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      5   10
  BRD8 WILD-TYPE  165  187
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  FEMALE            5            165
  MALE             10            187
[1] 2 2
[1] FALSE
D813V8, binary
                cls
clus               0   1
  BRD8 MUTATED    12   1
  BRD8 WILD-TYPE 288   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     12    1
  BRD8 WILD-TYPE  288    7
     clus
vv    BRD8 MUTATED BRD8 WILD-TYPE
  NO            12            288
  YES            1              7
[1] 2 2
[1] FALSE
D813V9, binary
                cls
clus               0   1
  BRD8 MUTATED    10   5
  BRD8 WILD-TYPE 304  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     10    5
  BRD8 WILD-TYPE  304   43
                               clus
vv                              BRD8 MUTATED BRD8 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRD8 MUTATED    10   0   1   1
  BRD8 WILD-TYPE 249   3  21  20
D813V10, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            1             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"
D813V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD8 MUTATED                                  0     0
  BRD8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD8 MUTATED                           0    10
  BRD8 WILD-TYPE                        19   166
D813V12, multiclass
                                  clus
vv                                 BRD8 MUTATED BRD8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(814) Variable = SLC41A2 MUTATION ANALYSIS
D814V1, survival
                   sevent
clus2                 0   1
  SLC41A2 MUTATED     7   0
  SLC41A2 WILD-TYPE 270  78
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                7               348 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                0                78 
$`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 
       61.91 

$`SLC41A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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-D5-5541 
       10.06        12.03        45.40        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
            11.64              0.00 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
           135.65            148.01 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
           29.030            22.045 
[1] "11.6 - 135.7 (29.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D814V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC41A2 MUTATED         0        0        0         6         0         0
  SLC41A2 WILD-TYPE      64        1       26       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC41A2 MUTATED           0          0          1          0        1
  SLC41A2 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC41A2 MUTATED           0         0
  SLC41A2 WILD-TYPE        12         1
D814V3, multiclass
            clus
vv           SLC41A2 MUTATED SLC41A2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                6               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC41A2 MUTATED     0   0   8   0
  SLC41A2 WILD-TYPE   9  67 241  41
D814V4, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               8               241
  T4               0                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
  SLC41A2 MUTATED     6   2   0
  SLC41A2 WILD-TYPE 214  79  66
D814V5, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  N0               6               214
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V6, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     7   1
  SLC41A2 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      7    1
  SLC41A2 WILD-TYPE  278   47
   clus
vv  SLC41A2 MUTATED SLC41A2 WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D814V7, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     3   5
  SLC41A2 WILD-TYPE 167 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      3    5
  SLC41A2 WILD-TYPE  167  192
        clus
vv       SLC41A2 MUTATED SLC41A2 WILD-TYPE
  FEMALE               3               167
  MALE                 5               192
[1] 2 2
[1] FALSE
D814V8, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     6   0
  SLC41A2 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      6    0
  SLC41A2 WILD-TYPE  294    8
     clus
vv    SLC41A2 MUTATED SLC41A2 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D814V9, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     5   2
  SLC41A2 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      5    2
  SLC41A2 WILD-TYPE  309   46
                               clus
vv                              SLC41A2 MUTATED SLC41A2 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC41A2 MUTATED     6   0   0   1
  SLC41A2 WILD-TYPE 253   3  22  20
D814V10, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D814V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC41A2 MUTATED                                  0     1
  SLC41A2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC41A2 MUTATED                           1     5
  SLC41A2 WILD-TYPE                        18   171
D814V12, multiclass
                                  clus
vv                                 SLC41A2 MUTATED SLC41A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = EAPP MUTATION ANALYSIS
D815V1, survival
                sevent
clus2              0   1
  EAPP MUTATED     1   2
  EAPP WILD-TYPE 276  76
  EAPP MUTATED EAPP WILD-TYPE 
             3            352 
  EAPP MUTATED EAPP WILD-TYPE 
             2             76 
$`EAPP MUTATED`
TCGA-A6-4105 TCGA-AA-A03F TCGA-D5-6535 
       14.53        18.05        15.12 

$`EAPP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-A03J 
        5.03        14.01         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  EAPP MUTATED EAPP WILD-TYPE 
         14.53           0.00 
  EAPP MUTATED EAPP WILD-TYPE 
         18.05         148.01 
  EAPP MUTATED EAPP WILD-TYPE 
         15.12          22.09 
[1] "14.5 - 18.1 (15.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "4.6"
D815V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EAPP MUTATED         0        0        0         1         0         0
  EAPP WILD-TYPE      64        1       26       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EAPP MUTATED           2          0          1          0        0         0
  EAPP WILD-TYPE        16          6         43         33       35        12
                vv
clus             STAGE IVB
  EAPP MUTATED           0
  EAPP WILD-TYPE         1
D815V3, multiclass
            clus
vv           EAPP MUTATED EAPP WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  EAPP MUTATED     0   0   4   0
  EAPP WILD-TYPE   9  67 245  41
D815V4, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  T1            0              9
  T2            0             67
  T3            4            245
  T4            0             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
  EAPP MUTATED     1   1   2
  EAPP WILD-TYPE 219  80  64
D815V5, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  N0            1            219
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V6, binary
                cls
clus               0   1
  EAPP MUTATED     3   0
  EAPP WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      3    0
  EAPP WILD-TYPE  282   48
   clus
vv  EAPP MUTATED EAPP WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D815V7, binary
                cls
clus               0   1
  EAPP MUTATED     2   2
  EAPP WILD-TYPE 168 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      2    2
  EAPP WILD-TYPE  168  195
        clus
vv       EAPP MUTATED EAPP WILD-TYPE
  FEMALE            2            168
  MALE              2            195
[1] 2 2
[1] FALSE
D815V8, binary
                cls
clus               0   1
  EAPP MUTATED     3   0
  EAPP WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      3    0
  EAPP WILD-TYPE  297    8
     clus
vv    EAPP MUTATED EAPP WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D815V9, binary
                cls
clus               0   1
  EAPP MUTATED     3   1
  EAPP WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      3    1
  EAPP WILD-TYPE  311   47
                               clus
vv                              EAPP MUTATED EAPP WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EAPP MUTATED     2   0   0   1
  EAPP WILD-TYPE 257   3  22  20
D815V10, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  R0            2            257
  R1            0              3
  R2            0             22
  RX            1             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"
D815V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EAPP MUTATED                                  0     0
  EAPP WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EAPP MUTATED                           0     2
  EAPP WILD-TYPE                        19   174
D815V12, multiclass
[1] "Remove cluster labels:" "EAPP MUTATED"          
clus
  EAPP MUTATED EAPP WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-6649     TCGA-AD-6548     TCGA-AD-6888 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681     TCGA-AZ-6601 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285     TCGA-G4-6310 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-2676     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-A6-6651     TCGA-A6-6652     TCGA-A6-6653 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781     TCGA-A6-6782 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6899 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"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-5913     TCGA-CK-5914     TCGA-CK-5915 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 

Clustering(816) Variable = DNAJC7 MUTATION ANALYSIS
D816V1, survival
                  sevent
clus2                0   1
  DNAJC7 MUTATED     6   0
  DNAJC7 WILD-TYPE 271  78
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               6              349 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               0               78 
$`DNAJC7 MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-AA-A010 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5913 
       24.00        79.69        34.98        21.44        12.76        51.32 

$`DNAJC7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           12.76             0.00 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           79.69           148.01 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           29.49            22.03 
[1] "12.8 - 79.7 (29.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D816V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC7 MUTATED         1        0        0         4         2         0
  DNAJC7 WILD-TYPE      63        1       26       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC7 MUTATED           0          0          0          0        0
  DNAJC7 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  DNAJC7 MUTATED           0         0
  DNAJC7 WILD-TYPE        12         1
D816V3, multiclass
            clus
vv           DNAJC7 MUTATED DNAJC7 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  DNAJC7 MUTATED     0   1   4   2
  DNAJC7 WILD-TYPE   9  66 245  39
D816V4, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              2               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
  DNAJC7 MUTATED     7   0   0
  DNAJC7 WILD-TYPE 213  81  66
D816V5, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V6, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     4   0
  DNAJC7 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      4    0
  DNAJC7 WILD-TYPE  281   48
   clus
vv  DNAJC7 MUTATED DNAJC7 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D816V7, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     4   3
  DNAJC7 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      4    3
  DNAJC7 WILD-TYPE  166  194
        clus
vv       DNAJC7 MUTATED DNAJC7 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D816V8, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     6   0
  DNAJC7 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      6    0
  DNAJC7 WILD-TYPE  294    8
     clus
vv    DNAJC7 MUTATED DNAJC7 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D816V9, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     5   2
  DNAJC7 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      5    2
  DNAJC7 WILD-TYPE  309   46
                               clus
vv                              DNAJC7 MUTATED DNAJC7 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAJC7 MUTATED     4   0   0   3
  DNAJC7 WILD-TYPE 255   3  22  18
D816V10, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              3               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"
D816V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC7 MUTATED                                  0     1
  DNAJC7 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAJC7 MUTATED                           0     4
  DNAJC7 WILD-TYPE                        19   172
D816V12, multiclass
                                  clus
vv                                 DNAJC7 MUTATED DNAJC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = LBP MUTATION ANALYSIS
D817V1, survival
               sevent
clus2             0   1
  LBP MUTATED     6   0
  LBP WILD-TYPE 271  78
  LBP MUTATED LBP WILD-TYPE 
            6           349 
  LBP MUTATED LBP WILD-TYPE 
            0            78 
$`LBP MUTATED`
TCGA-AA-3660 TCGA-AD-5900 TCGA-CK-5913 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6307 
       78.08        12.16        51.32        35.31        44.68        55.04 

$`LBP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       65.85        53.62        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  LBP MUTATED LBP WILD-TYPE 
        12.16          0.00 
  LBP MUTATED LBP WILD-TYPE 
        78.08        148.01 
  LBP MUTATED LBP WILD-TYPE 
        48.00         21.99 
[1] "12.2 - 78.1 (48.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D817V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LBP MUTATED         2        0        1         1         0         0
  LBP WILD-TYPE      62        1       25       107         8         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        18          6         43         33       34        12
               vv
clus            STAGE IVB
  LBP MUTATED           0
  LBP WILD-TYPE         1
D817V3, multiclass
            clus
vv           LBP MUTATED LBP WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            1           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  LBP MUTATED     0   3   3   1
  LBP WILD-TYPE   9  64 246  40
D817V4, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  T1           0             9
  T2           3            64
  T3           3           246
  T4           1            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
  LBP MUTATED     5   1   1
  LBP WILD-TYPE 215  80  65
D817V5, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  N0           5           215
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V6, binary
               cls
clus              0   1
  LBP MUTATED     4   1
  LBP WILD-TYPE 281  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      4    1
  LBP WILD-TYPE  281   47
   clus
vv  LBP MUTATED LBP WILD-TYPE
  0           4           281
  1           1            47
[1] 2 2
[1] FALSE
D817V7, binary
               cls
clus              0   1
  LBP MUTATED     3   4
  LBP WILD-TYPE 167 193
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      3    4
  LBP WILD-TYPE  167  193
        clus
vv       LBP MUTATED LBP WILD-TYPE
  FEMALE           3           167
  MALE             4           193
[1] 2 2
[1] FALSE
D817V8, binary
               cls
clus              0   1
  LBP MUTATED     6   0
  LBP WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      6    0
  LBP WILD-TYPE  294    8
     clus
vv    LBP MUTATED LBP WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D817V9, binary
               cls
clus              0   1
  LBP MUTATED     5   2
  LBP WILD-TYPE 309  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      5    2
  LBP WILD-TYPE  309   46
                               clus
vv                              LBP MUTATED LBP WILD-TYPE
  COLON ADENOCARCINOMA                    5           309
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  LBP MUTATED     5   0   1   1
  LBP WILD-TYPE 254   3  21  20
D817V10, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  R0           5           254
  R1           0             3
  R2           1            21
  RX           1            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"
D817V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LBP MUTATED                                  0     0
  LBP WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LBP MUTATED                           0     5
  LBP WILD-TYPE                        19   171
D817V12, multiclass
                                  clus
vv                                 LBP MUTATED LBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      5           171
[1] 4 2
[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 = ZNF180 MUTATION ANALYSIS
D818V1, survival
                  sevent
clus2                0   1
  ZNF180 MUTATED    10   3
  ZNF180 WILD-TYPE 267  75
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              13              342 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
               3               75 
$`ZNF180 MUTATED`
TCGA-AA-3713 TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-3866 
       19.04        32.75        63.98        78.08        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 
        4.80 

$`ZNF180 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        30.05        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF180 MUTATED ZNF180 WILD-TYPE 
            4.01             0.00 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
           78.08           148.01 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
          21.440           22.075 
[1] "4.0 - 78.1 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D818V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF180 MUTATED         1        0        3         3         2         0
  ZNF180 WILD-TYPE      63        1       23       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF180 MUTATED           0          0          2          0        2
  ZNF180 WILD-TYPE        18          6         42         33       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF180 MUTATED           0         0
  ZNF180 WILD-TYPE        12         1
D818V3, multiclass
            clus
vv           ZNF180 MUTATED ZNF180 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  ZNF180 MUTATED     0   2   9   3
  ZNF180 WILD-TYPE   9  65 240  38
D818V4, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              9              240
  T4              3               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
  ZNF180 MUTATED    11   3   0
  ZNF180 WILD-TYPE 209  78  66
D818V5, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  N0             11              209
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V6, binary
                  cls
clus                 0   1
  ZNF180 MUTATED     9   2
  ZNF180 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED      9    2
  ZNF180 WILD-TYPE  276   46
   clus
vv  ZNF180 MUTATED ZNF180 WILD-TYPE
  0              9              276
  1              2               46
[1] 2 2
[1] FALSE
D818V7, binary
                  cls
clus                 0   1
  ZNF180 MUTATED     4  10
  ZNF180 WILD-TYPE 166 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED      4   10
  ZNF180 WILD-TYPE  166  187
        clus
vv       ZNF180 MUTATED ZNF180 WILD-TYPE
  FEMALE              4              166
  MALE               10              187
[1] 2 2
[1] FALSE
D818V8, binary
                  cls
clus                 0   1
  ZNF180 MUTATED    11   1
  ZNF180 WILD-TYPE 289   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED     11    1
  ZNF180 WILD-TYPE  289    7
     clus
vv    ZNF180 MUTATED ZNF180 WILD-TYPE
  NO              11              289
  YES              1                7
[1] 2 2
[1] FALSE
D818V9, binary
                  cls
clus                 0   1
  ZNF180 MUTATED    11   3
  ZNF180 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED     11    3
  ZNF180 WILD-TYPE  303   45
                               clus
vv                              ZNF180 MUTATED ZNF180 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF180 MUTATED    10   0   1   1
  ZNF180 WILD-TYPE 249   3  21  20
D818V10, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              1               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"
D818V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF180 MUTATED                                  0     1
  ZNF180 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF180 MUTATED                           1     4
  ZNF180 WILD-TYPE                        18   172
D818V12, multiclass
                                  clus
vv                                 ZNF180 MUTATED ZNF180 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = PCDH19 MUTATION ANALYSIS
D819V1, survival
                  sevent
clus2                0   1
  PCDH19 MUTATED     9   4
  PCDH19 WILD-TYPE 268  74
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              13              342 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               4               74 
$`PCDH19 MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AA-3492 TCGA-AA-3845 
        0.92        35.80        26.17        91.79         3.02         0.00 
TCGA-AA-3854 TCGA-AA-3947 TCGA-AA-A004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-DM-A1HB 
       36.03        33.01        13.94        58.39        62.79       135.65 
TCGA-F4-6570 
        6.18 

$`PCDH19 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PCDH19 MUTATED PCDH19 WILD-TYPE 
               0                0 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
          135.65           148.01 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
           33.01            22.01 
[1] "0.0 - 135.7 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D819V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH19 MUTATED         1        0        2         8         1         0
  PCDH19 WILD-TYPE      63        1       24       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH19 MUTATED           1          0          1          0        0
  PCDH19 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  PCDH19 MUTATED           0         0
  PCDH19 WILD-TYPE        12         1
D819V3, multiclass
            clus
vv           PCDH19 MUTATED PCDH19 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  PCDH19 MUTATED     0   1  12   1
  PCDH19 WILD-TYPE   9  66 237  40
D819V4, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             12              237
  T4              1               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
  PCDH19 MUTATED    12   2   0
  PCDH19 WILD-TYPE 208  79  66
D819V5, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  N0             12              208
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V6, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    13   0
  PCDH19 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     13    0
  PCDH19 WILD-TYPE  272   48
   clus
vv  PCDH19 MUTATED PCDH19 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D819V7, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    10   4
  PCDH19 WILD-TYPE 160 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     10    4
  PCDH19 WILD-TYPE  160  193
        clus
vv       PCDH19 MUTATED PCDH19 WILD-TYPE
  FEMALE             10              160
  MALE                4              193
[1] 2 2
[1] FALSE
D819V8, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    11   0
  PCDH19 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     11    0
  PCDH19 WILD-TYPE  289    8
     clus
vv    PCDH19 MUTATED PCDH19 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D819V9, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    11   2
  PCDH19 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     11    2
  PCDH19 WILD-TYPE  303   46
                               clus
vv                              PCDH19 MUTATED PCDH19 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PCDH19 MUTATED    12   0   0   0
  PCDH19 WILD-TYPE 247   3  22  21
D819V10, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              0               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"
D819V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH19 MUTATED                                  0     0
  PCDH19 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PCDH19 MUTATED                           0     7
  PCDH19 WILD-TYPE                        19   169
D819V12, multiclass
                                  clus
vv                                 PCDH19 MUTATED PCDH19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = MACF1 MUTATION ANALYSIS
D820V1, survival
                 sevent
clus2               0   1
  MACF1 MUTATED    43  13
  MACF1 WILD-TYPE 234  65
  MACF1 MUTATED MACF1 WILD-TYPE 
             56             299 
  MACF1 MUTATED MACF1 WILD-TYPE 
             13              65 
$`MACF1 MUTATED`
TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3713 TCGA-AD-6895 TCGA-AZ-6601 
       13.02        17.95         6.05        19.04        25.08       100.01 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
       35.80        26.17        79.69        46.65        42.90        42.28 
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3811 
       22.06        24.39        20.12         3.02        63.98        10.06 
TCGA-AA-3815 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       33.04         0.00        53.00        26.01         2.01        25.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 
       38.04        30.02        18.05         4.01         0.99        34.98 
TCGA-AA-A01R TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 
       35.01         5.79        21.44        58.39        62.79        49.41 
TCGA-AZ-6600 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5861 
       12.10        12.39        12.76        15.62       124.27        15.02 
TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6535 
        5.03        12.00        16.04        14.04        12.95        15.12 
TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 
       17.85         9.04         9.44        11.64        13.35         6.18 
TCGA-F4-6703 TCGA-G4-6315 
       47.87        61.91 

$`MACF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       10.88       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2683 TCGA-A6-3807 
       22.09        91.79        43.76        43.76        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       23.87        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        33.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       13.94        19.00        34.03        18.05        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
        0.20        17.82         1.41         5.13        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        25.48        43.27         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  MACF1 MUTATED MACF1 WILD-TYPE 
              0               0 
  MACF1 MUTATED MACF1 WILD-TYPE 
         124.27          148.01 
  MACF1 MUTATED MACF1 WILD-TYPE 
         18.545          22.420 
[1] "0.0 - 124.3 (18.5)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D820V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MACF1 MUTATED         6        0        6        23         3         0
  MACF1 WILD-TYPE      58        1       20        85         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MACF1 MUTATED           4          0          8          2        4         1
  MACF1 WILD-TYPE        14          6         36         31       31        11
                 vv
clus              STAGE IVB
  MACF1 MUTATED           0
  MACF1 WILD-TYPE         1
D820V3, multiclass
            clus
vv           MACF1 MUTATED MACF1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA             23              85
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              4              14
  STAGE IIIA             0               6
  STAGE IIIB             8              36
  STAGE IIIC             2              31
  STAGE IV               4              31
  STAGE IVA              1              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
  MACF1 MUTATED     0   7  42   9
  MACF1 WILD-TYPE   9  60 207  32
D820V4, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  T1             0               9
  T2             7              60
  T3            42             207
  T4             9              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
  MACF1 MUTATED    40  11   7
  MACF1 WILD-TYPE 180  70  59
D820V5, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  N0            40             180
  N1            11              70
  N2             7              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V6, binary
                 cls
clus                0   1
  MACF1 MUTATED    45   5
  MACF1 WILD-TYPE 240  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     45    5
  MACF1 WILD-TYPE  240   43
   clus
vv  MACF1 MUTATED MACF1 WILD-TYPE
  0            45             240
  1             5              43
[1] 2 2
[1] FALSE
D820V7, binary
                 cls
clus                0   1
  MACF1 MUTATED    26  32
  MACF1 WILD-TYPE 144 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     26   32
  MACF1 WILD-TYPE  144  165
        clus
vv       MACF1 MUTATED MACF1 WILD-TYPE
  FEMALE            26             144
  MALE              32             165
[1] 2 2
[1] FALSE
D820V8, binary
                 cls
clus                0   1
  MACF1 MUTATED    48   3
  MACF1 WILD-TYPE 252   5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     48    3
  MACF1 WILD-TYPE  252    5
     clus
vv    MACF1 MUTATED MACF1 WILD-TYPE
  NO             48             252
  YES             3               5
[1] 2 2
[1] FALSE
D820V9, binary
                 cls
clus                0   1
  MACF1 MUTATED    43  15
  MACF1 WILD-TYPE 271  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     43   15
  MACF1 WILD-TYPE  271   33
                               clus
vv                              MACF1 MUTATED MACF1 WILD-TYPE
  COLON ADENOCARCINOMA                     43             271
  COLON MUCINOUS ADENOCARCINOMA            15              33
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MACF1 MUTATED    42   0   2   4
  MACF1 WILD-TYPE 217   3  20  17
D820V10, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  R0            42             217
  R1             0               3
  R2             2              20
  RX             4              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"
D820V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MACF1 MUTATED                                  0     2
  MACF1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MACF1 MUTATED                           1    33
  MACF1 WILD-TYPE                        18   143
D820V12, multiclass
                                  clus
vv                                 MACF1 MUTATED MACF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       33             143
[1] 4 2
[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 = MYH15 MUTATION ANALYSIS
D821V1, survival
                 sevent
clus2               0   1
  MYH15 MUTATED    20   4
  MYH15 WILD-TYPE 257  74
  MYH15 MUTATED MYH15 WILD-TYPE 
             24             331 
  MYH15 MUTATED MYH15 WILD-TYPE 
              4              74 
$`MYH15 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-6138 
        6.05        19.04        24.00        10.88        79.69        22.52 
TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3864 
       24.39        23.87        63.98         6.97        26.99        53.00 
TCGA-AA-A010 TCGA-AD-6890 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6674 
       34.98        24.53        58.39        12.76        15.02        12.95 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D4 
       55.92        18.25        43.27        13.35        38.20        92.75 

$`MYH15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5656 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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       54.61        19.59        56.09        20.19        25.48        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 
        7.53        12.39        10.13        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        13.41        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-A1DA TCGA-DM-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYH15 MUTATED MYH15 WILD-TYPE 
           6.05            0.00 
  MYH15 MUTATED MYH15 WILD-TYPE 
          92.75          148.01 
  MYH15 MUTATED MYH15 WILD-TYPE 
         24.195          21.990 
[1] "6.0 - 92.8 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D821V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH15 MUTATED         3        0        4        11         1         0
  MYH15 WILD-TYPE      61        1       22        97         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH15 MUTATED           0          0          2          1        1         0
  MYH15 WILD-TYPE        18          6         42         32       34        12
                 vv
clus              STAGE IVB
  MYH15 MUTATED           0
  MYH15 WILD-TYPE         1
D821V3, multiclass
            clus
vv           MYH15 MUTATED MYH15 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             11              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  MYH15 MUTATED     1   3  18   3
  MYH15 WILD-TYPE   8  64 231  38
D821V4, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            18             231
  T4             3              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
  MYH15 MUTATED    20   2   3
  MYH15 WILD-TYPE 200  79  63
D821V5, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  N0            20             200
  N1             2              79
  N2             3              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"
D821V6, binary
                 cls
clus                0   1
  MYH15 MUTATED    22   1
  MYH15 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     22    1
  MYH15 WILD-TYPE  263   47
   clus
vv  MYH15 MUTATED MYH15 WILD-TYPE
  0            22             263
  1             1              47
[1] 2 2
[1] FALSE
D821V7, binary
                 cls
clus                0   1
  MYH15 MUTATED     9  16
  MYH15 WILD-TYPE 161 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED      9   16
  MYH15 WILD-TYPE  161  181
        clus
vv       MYH15 MUTATED MYH15 WILD-TYPE
  FEMALE             9             161
  MALE              16             181
[1] 2 2
[1] FALSE
D821V8, binary
                 cls
clus                0   1
  MYH15 MUTATED    22   0
  MYH15 WILD-TYPE 278   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     22    0
  MYH15 WILD-TYPE  278    8
     clus
vv    MYH15 MUTATED MYH15 WILD-TYPE
  NO             22             278
  YES             0               8
[1] 2 2
[1] FALSE
D821V9, binary
                 cls
clus                0   1
  MYH15 MUTATED    20   4
  MYH15 WILD-TYPE 294  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     20    4
  MYH15 WILD-TYPE  294   44
                               clus
vv                              MYH15 MUTATED MYH15 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYH15 MUTATED    16   0   1   1
  MYH15 WILD-TYPE 243   3  21  20
D821V10, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             1              21
  RX             1              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"
D821V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH15 MUTATED                                  0     1
  MYH15 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYH15 MUTATED                           0    15
  MYH15 WILD-TYPE                        19   161
D821V12, multiclass
                                  clus
vv                                 MYH15 MUTATED MYH15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       15             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(822) Variable = PLK2 MUTATION ANALYSIS
D822V1, survival
                sevent
clus2              0   1
  PLK2 MUTATED     3   2
  PLK2 WILD-TYPE 274  76
  PLK2 MUTATED PLK2 WILD-TYPE 
             5            350 
  PLK2 MUTATED PLK2 WILD-TYPE 
             2             76 
$`PLK2 MUTATED`
TCGA-AA-3516 TCGA-G4-6588 TCGA-D5-6541 TCGA-DM-A1HB TCGA-DM-A28C 
       13.02        26.17        15.58       135.65        81.37 

$`PLK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      131.51       139.17       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PLK2 MUTATED PLK2 WILD-TYPE 
         13.02           0.00 
  PLK2 MUTATED PLK2 WILD-TYPE 
        135.65         148.01 
  PLK2 MUTATED PLK2 WILD-TYPE 
        26.170         22.045 
[1] "13.0 - 135.7 (26.2)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.1"
D822V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLK2 MUTATED         0        0        0         4         0         0
  PLK2 WILD-TYPE      64        1       26       104         8         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        17          6         43         33       35        12
                vv
clus             STAGE IVB
  PLK2 MUTATED           0
  PLK2 WILD-TYPE         1
D822V3, multiclass
            clus
vv           PLK2 MUTATED PLK2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PLK2 MUTATED     0   0   6   0
  PLK2 WILD-TYPE   9  67 243  41
D822V4, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            0             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
  PLK2 MUTATED     4   1   1
  PLK2 WILD-TYPE 216  80  65
D822V5, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V6, binary
                cls
clus               0   1
  PLK2 MUTATED     6   0
  PLK2 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      6    0
  PLK2 WILD-TYPE  279   48
   clus
vv  PLK2 MUTATED PLK2 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D822V7, binary
                cls
clus               0   1
  PLK2 MUTATED     3   3
  PLK2 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      3    3
  PLK2 WILD-TYPE  167  194
        clus
vv       PLK2 MUTATED PLK2 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D822V8, binary
                cls
clus               0   1
  PLK2 MUTATED     3   0
  PLK2 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      3    0
  PLK2 WILD-TYPE  297    8
     clus
vv    PLK2 MUTATED PLK2 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D822V9, binary
                cls
clus               0   1
  PLK2 MUTATED     4   1
  PLK2 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      4    1
  PLK2 WILD-TYPE  310   47
                               clus
vv                              PLK2 MUTATED PLK2 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PLK2 MUTATED     3   0   0   0
  PLK2 WILD-TYPE 256   3  22  21
D822V10, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D822V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLK2 MUTATED                                  0     0
  PLK2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PLK2 MUTATED                           0     4
  PLK2 WILD-TYPE                        19   172
D822V12, multiclass
                                  clus
vv                                 PLK2 MUTATED PLK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = ZNF619 MUTATION ANALYSIS
D823V1, survival
                  sevent
clus2                0   1
  ZNF619 MUTATED     8   2
  ZNF619 WILD-TYPE 269  76
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              10              345 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
               2               76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF619 MUTATED ZNF619 WILD-TYPE 
               0                0 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
           63.98           148.01 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
           25.33            22.06 
[1] "0.0 - 64.0 (25.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D823V2, continuous
                  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      63        1       24       105         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF619 MUTATED           1          0          0          1        0
  ZNF619 WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF619 MUTATED           0         0
  ZNF619 WILD-TYPE        12         1
D823V3, multiclass
            clus
vv           ZNF619 MUTATED ZNF619 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF619 MUTATED     1   0   6   4
  ZNF619 WILD-TYPE   8  67 243  37
D823V4, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              6              243
  T4              4               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
  ZNF619 MUTATED     9   1   1
  ZNF619 WILD-TYPE 211  80  65
D823V5, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  N0              9              211
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V6, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     9   0
  ZNF619 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      9    0
  ZNF619 WILD-TYPE  276   48
   clus
vv  ZNF619 MUTATED ZNF619 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D823V7, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     4   7
  ZNF619 WILD-TYPE 166 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      4    7
  ZNF619 WILD-TYPE  166  190
        clus
vv       ZNF619 MUTATED ZNF619 WILD-TYPE
  FEMALE              4              166
  MALE                7              190
[1] 2 2
[1] FALSE
D823V8, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     7   1
  ZNF619 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      7    1
  ZNF619 WILD-TYPE  293    7
     clus
vv    ZNF619 MUTATED ZNF619 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D823V9, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     6   5
  ZNF619 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      6    5
  ZNF619 WILD-TYPE  308   43
                               clus
vv                              ZNF619 MUTATED ZNF619 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF619 MUTATED    10   0   0   1
  ZNF619 WILD-TYPE 249   3  22  20
D823V10, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              1               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"
D823V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF619 MUTATED                                  0     0
  ZNF619 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF619 MUTATED                           0     4
  ZNF619 WILD-TYPE                        19   172
D823V12, multiclass
                                  clus
vv                                 ZNF619 MUTATED ZNF619 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = WNK1 MUTATION ANALYSIS
D824V1, survival
                sevent
clus2              0   1
  WNK1 MUTATED    15   3
  WNK1 WILD-TYPE 262  75
  WNK1 MUTATED WNK1 WILD-TYPE 
            18            337 
  WNK1 MUTATED WNK1 WILD-TYPE 
             3             75 
$`WNK1 MUTATED`
TCGA-AD-6895 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-6648 TCGA-AA-3655 TCGA-AA-3815 
       25.08         1.94        26.17        25.18        61.02        33.04 
TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 
        0.00        25.02         4.01        34.98        35.01        58.39 
TCGA-CA-5254 TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-6535 TCGA-DM-A28K TCGA-F4-6806 
       12.69        15.02        12.99        15.12        98.24        41.42 

$`WNK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  WNK1 MUTATED WNK1 WILD-TYPE 
             0              0 
  WNK1 MUTATED WNK1 WILD-TYPE 
         98.24         148.01 
  WNK1 MUTATED WNK1 WILD-TYPE 
         25.13          21.99 
[1] "0.0 - 98.2 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D824V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNK1 MUTATED         2        0        1         8         2         0
  WNK1 WILD-TYPE      62        1       25       100         6         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        17          5         42         33       35        11
                vv
clus             STAGE IVB
  WNK1 MUTATED           0
  WNK1 WILD-TYPE         1
D824V3, multiclass
            clus
vv           WNK1 MUTATED WNK1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  WNK1 MUTATED     0   4  13   2
  WNK1 WILD-TYPE   9  63 236  39
D824V4, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           13            236
  T4            2             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
  WNK1 MUTATED    15   3   1
  WNK1 WILD-TYPE 205  78  65
D824V5, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  N0           15            205
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V6, binary
                cls
clus               0   1
  WNK1 MUTATED    15   1
  WNK1 WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     15    1
  WNK1 WILD-TYPE  270   47
   clus
vv  WNK1 MUTATED WNK1 WILD-TYPE
  0           15            270
  1            1             47
[1] 2 2
[1] FALSE
D824V7, binary
                cls
clus               0   1
  WNK1 MUTATED    10   9
  WNK1 WILD-TYPE 160 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     10    9
  WNK1 WILD-TYPE  160  188
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  FEMALE           10            160
  MALE              9            188
[1] 2 2
[1] FALSE
D824V8, binary
                cls
clus               0   1
  WNK1 MUTATED    14   1
  WNK1 WILD-TYPE 286   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     14    1
  WNK1 WILD-TYPE  286    7
     clus
vv    WNK1 MUTATED WNK1 WILD-TYPE
  NO            14            286
  YES            1              7
[1] 2 2
[1] FALSE
D824V9, binary
                cls
clus               0   1
  WNK1 MUTATED    16   3
  WNK1 WILD-TYPE 298  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     16    3
  WNK1 WILD-TYPE  298   45
                               clus
vv                              WNK1 MUTATED WNK1 WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNK1 MUTATED    12   0   0   3
  WNK1 WILD-TYPE 247   3  22  18
D824V10, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            3             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"
D824V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK1 MUTATED                                  0     1
  WNK1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK1 MUTATED                           1    10
  WNK1 WILD-TYPE                        18   166
D824V12, multiclass
                                  clus
vv                                 WNK1 MUTATED WNK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(825) Variable = TRIM54 MUTATION ANALYSIS
D825V1, survival
                  sevent
clus2                0   1
  TRIM54 MUTATED     5   3
  TRIM54 WILD-TYPE 272  75
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               8              347 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               3               75 
$`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        14.04        25.48 
TCGA-DM-A1D4 TCGA-F4-6460 
       92.75        31.96 

$`TRIM54 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TRIM54 MUTATED TRIM54 WILD-TYPE 
            12.2              0.0 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
           92.75           148.01 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
           30.99            21.99 
[1] "12.2 - 92.8 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D825V2, continuous
                  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      63        1       25       104         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM54 MUTATED           0          0          1          0        0
  TRIM54 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM54 MUTATED           0         0
  TRIM54 WILD-TYPE        12         1
D825V3, multiclass
            clus
vv           TRIM54 MUTATED TRIM54 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TRIM54 MUTATED     1   0   6   2
  TRIM54 WILD-TYPE   8  67 243  39
D825V4, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              6              243
  T4              2               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
  TRIM54 MUTATED     8   1   0
  TRIM54 WILD-TYPE 212  80  66
D825V5, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V6, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     8   0
  TRIM54 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      8    0
  TRIM54 WILD-TYPE  277   48
   clus
vv  TRIM54 MUTATED TRIM54 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D825V7, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     4   5
  TRIM54 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      4    5
  TRIM54 WILD-TYPE  166  192
        clus
vv       TRIM54 MUTATED TRIM54 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D825V8, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     7   0
  TRIM54 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      7    0
  TRIM54 WILD-TYPE  293    8
     clus
vv    TRIM54 MUTATED TRIM54 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D825V9, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     9   0
  TRIM54 WILD-TYPE 305  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      9    0
  TRIM54 WILD-TYPE  305   48
                               clus
vv                              TRIM54 MUTATED TRIM54 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM54 MUTATED     5   0   0   1
  TRIM54 WILD-TYPE 254   3  22  20
D825V10, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D825V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM54 MUTATED                                  0     1
  TRIM54 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM54 MUTATED                           0     6
  TRIM54 WILD-TYPE                        19   170
D825V12, multiclass
                                  clus
vv                                 TRIM54 MUTATED TRIM54 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = GTF3C3 MUTATION ANALYSIS
D826V1, survival
                  sevent
clus2                0   1
  GTF3C3 MUTATED    11   4
  GTF3C3 WILD-TYPE 266  74
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              15              340 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               4               74 
$`GTF3C3 MUTATED`
TCGA-AA-3496 TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-3977 TCGA-AA-A010 
        1.02        10.88        79.69        33.53        25.02        34.98 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6163 TCGA-CM-6674 
       58.39        49.41        12.59        12.76        14.04        12.95 
TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-F4-6807 
       24.43        49.91        43.04 

$`GTF3C3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        12.00        11.38        10.26       119.70        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-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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
            1.02             0.00 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           79.69           148.01 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           25.02            22.01 
[1] "1.0 - 79.7 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D826V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTF3C3 MUTATED         2        0        2         6         1         0
  GTF3C3 WILD-TYPE      62        1       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C3 MUTATED           0          0          1          1        0
  GTF3C3 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  GTF3C3 MUTATED           0         0
  GTF3C3 WILD-TYPE        12         1
D826V3, multiclass
            clus
vv           GTF3C3 MUTATED GTF3C3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  GTF3C3 MUTATED     1   2  10   2
  GTF3C3 WILD-TYPE   8  65 239  39
D826V4, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             10              239
  T4              2               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
  GTF3C3 MUTATED    12   1   2
  GTF3C3 WILD-TYPE 208  80  64
D826V5, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  N0             12              208
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V6, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    12   0
  GTF3C3 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     12    0
  GTF3C3 WILD-TYPE  273   48
   clus
vv  GTF3C3 MUTATED GTF3C3 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D826V7, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED     5  10
  GTF3C3 WILD-TYPE 165 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      5   10
  GTF3C3 WILD-TYPE  165  187
        clus
vv       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  FEMALE              5              165
  MALE               10              187
[1] 2 2
[1] FALSE
D826V8, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    12   0
  GTF3C3 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     12    0
  GTF3C3 WILD-TYPE  288    8
     clus
vv    GTF3C3 MUTATED GTF3C3 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D826V9, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    13   2
  GTF3C3 WILD-TYPE 301  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     13    2
  GTF3C3 WILD-TYPE  301   46
                               clus
vv                              GTF3C3 MUTATED GTF3C3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GTF3C3 MUTATED     8   0   0   2
  GTF3C3 WILD-TYPE 251   3  22  19
D826V10, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              2               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"
D826V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF3C3 MUTATED                                  0     2
  GTF3C3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GTF3C3 MUTATED                           1     9
  GTF3C3 WILD-TYPE                        18   167
D826V12, multiclass
                                  clus
vv                                 GTF3C3 MUTATED GTF3C3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(827) Variable = OR51A4 MUTATION ANALYSIS
D827V1, survival
                  sevent
clus2                0   1
  OR51A4 MUTATED     5   1
  OR51A4 WILD-TYPE 272  77
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               6              349 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               1               77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.09 
[1] "1.0 - 53.0 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D827V2, continuous
                  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      62        1       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51A4 MUTATED           0          0          1          2        0
  OR51A4 WILD-TYPE        18          6         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51A4 MUTATED           0         0
  OR51A4 WILD-TYPE        12         1
D827V3, multiclass
            clus
vv           OR51A4 MUTATED OR51A4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  OR51A4 MUTATED     0   2   3   3
  OR51A4 WILD-TYPE   9  65 246  38
D827V4, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              3              246
  T4              3               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
  OR51A4 MUTATED     5   2   1
  OR51A4 WILD-TYPE 215  79  65
D827V5, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  N0              5              215
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V6, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   0
  OR51A4 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    0
  OR51A4 WILD-TYPE  281   48
   clus
vv  OR51A4 MUTATED OR51A4 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D827V7, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   4
  OR51A4 WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    4
  OR51A4 WILD-TYPE  166  193
        clus
vv       OR51A4 MUTATED OR51A4 WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D827V8, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     6   0
  OR51A4 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      6    0
  OR51A4 WILD-TYPE  294    8
     clus
vv    OR51A4 MUTATED OR51A4 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D827V9, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   4
  OR51A4 WILD-TYPE 310  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    4
  OR51A4 WILD-TYPE  310   44
                               clus
vv                              OR51A4 MUTATED OR51A4 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51A4 MUTATED     5   0   0   2
  OR51A4 WILD-TYPE 254   3  22  19
D827V10, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D827V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51A4 MUTATED                                  0     0
  OR51A4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51A4 MUTATED                           0     5
  OR51A4 WILD-TYPE                        19   171
D827V12, multiclass
                                  clus
vv                                 OR51A4 MUTATED OR51A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = SLC25A17 MUTATION ANALYSIS
D828V1, survival
                    sevent
clus2                  0   1
  SLC25A17 MUTATED     4   3
  SLC25A17 WILD-TYPE 273  75
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 7                348 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                 75 
$`SLC25A17 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-6601 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00N 
       19.04        24.00       100.01        22.06        63.98         4.01 
TCGA-AD-5900 
       12.16 

$`SLC25A17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              4.01               0.00 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
            100.01             148.01 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
             22.06              22.06 
[1] "4.0 - 100.0 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D828V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC25A17 MUTATED         1        0        3         2         1         0
  SLC25A17 WILD-TYPE      63        1       23       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A17 MUTATED           0          0          0          0        0
  SLC25A17 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A17 MUTATED           0         0
  SLC25A17 WILD-TYPE        12         1
D828V3, multiclass
            clus
vv           SLC25A17 MUTATED SLC25A17 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                 2                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SLC25A17 MUTATED     0   1   5   1
  SLC25A17 WILD-TYPE   9  66 244  40
D828V4, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                5                244
  T4                1                 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
  SLC25A17 MUTATED     7   0   0
  SLC25A17 WILD-TYPE 213  81  66
D828V5, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  N0                7                213
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V6, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     6   0
  SLC25A17 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      6    0
  SLC25A17 WILD-TYPE  279   48
   clus
vv  SLC25A17 MUTATED SLC25A17 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D828V7, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     2   5
  SLC25A17 WILD-TYPE 168 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      2    5
  SLC25A17 WILD-TYPE  168  192
        clus
vv       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  FEMALE                2                168
  MALE                  5                192
[1] 2 2
[1] FALSE
D828V8, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     6   0
  SLC25A17 WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      6    0
  SLC25A17 WILD-TYPE  294    8
     clus
vv    SLC25A17 MUTATED SLC25A17 WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D828V9, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     4   3
  SLC25A17 WILD-TYPE 310  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      4    3
  SLC25A17 WILD-TYPE  310   45
                               clus
vv                              SLC25A17 MUTATED SLC25A17 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC25A17 MUTATED     6   0   0   0
  SLC25A17 WILD-TYPE 253   3  22  21
D828V10, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D828V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A17 MUTATED                                  0     0
  SLC25A17 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A17 MUTATED                           0     3
  SLC25A17 WILD-TYPE                        19   173
D828V12, multiclass
                                  clus
vv                                 SLC25A17 MUTATED SLC25A17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[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 = GNA14 MUTATION ANALYSIS
D829V1, survival
                 sevent
clus2               0   1
  GNA14 MUTATED     7   3
  GNA14 WILD-TYPE 270  75
  GNA14 MUTATED GNA14 WILD-TYPE 
             10             345 
  GNA14 MUTATED GNA14 WILD-TYPE 
              3              75 
$`GNA14 MUTATED`
TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3966 
       13.02         0.99        63.98         1.02        31.00         2.01 
TCGA-AY-6197 TCGA-D5-5538 TCGA-DM-A1HB TCGA-DM-A28G 
       21.44        54.61       135.65        60.79 

$`GNA14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GNA14 MUTATED GNA14 WILD-TYPE 
           0.99            0.00 
  GNA14 MUTATED GNA14 WILD-TYPE 
         135.65          148.01 
  GNA14 MUTATED GNA14 WILD-TYPE 
          26.22           22.06 
[1] "1.0 - 135.7 (26.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D829V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNA14 MUTATED         3        0        1         3         0         0
  GNA14 WILD-TYPE      61        1       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNA14 MUTATED           1          0          2          0        0         0
  GNA14 WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  GNA14 MUTATED           0
  GNA14 WILD-TYPE         1
D829V3, multiclass
            clus
vv           GNA14 MUTATED GNA14 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GNA14 MUTATED     1   2   7   0
  GNA14 WILD-TYPE   8  65 242  41
D829V4, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             0              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
  GNA14 MUTATED     7   2   1
  GNA14 WILD-TYPE 213  79  65
D829V5, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V6, binary
                 cls
clus                0   1
  GNA14 MUTATED     9   0
  GNA14 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      9    0
  GNA14 WILD-TYPE  276   48
   clus
vv  GNA14 MUTATED GNA14 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D829V7, binary
                 cls
clus                0   1
  GNA14 MUTATED     5   5
  GNA14 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      5    5
  GNA14 WILD-TYPE  165  192
        clus
vv       GNA14 MUTATED GNA14 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D829V8, binary
                 cls
clus                0   1
  GNA14 MUTATED     7   0
  GNA14 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      7    0
  GNA14 WILD-TYPE  293    8
     clus
vv    GNA14 MUTATED GNA14 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D829V9, binary
                 cls
clus                0   1
  GNA14 MUTATED     4   5
  GNA14 WILD-TYPE 310  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      4    5
  GNA14 WILD-TYPE  310   43
                               clus
vv                              GNA14 MUTATED GNA14 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GNA14 MUTATED     6   0   0   0
  GNA14 WILD-TYPE 253   3  22  21
D829V10, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D829V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNA14 MUTATED                                  0     0
  GNA14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNA14 MUTATED                           0     4
  GNA14 WILD-TYPE                        19   172
D829V12, multiclass
                                  clus
vv                                 GNA14 MUTATED GNA14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = PREX2 MUTATION ANALYSIS
D830V1, survival
                 sevent
clus2               0   1
  PREX2 MUTATED    24   5
  PREX2 WILD-TYPE 253  73
  PREX2 MUTATED PREX2 WILD-TYPE 
             29             326 
  PREX2 MUTATED PREX2 WILD-TYPE 
              5              73 
$`PREX2 MUTATED`
TCGA-AA-3672 TCGA-AD-6548 TCGA-DM-A285 TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6142 
        0.92        21.37         5.88        42.90        30.44        25.08 
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3544 TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-3941 
       24.39        63.98        14.01        78.08        33.04        24.00 
TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 
       33.01         4.01        35.01        58.39        12.20        12.76 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6676 
       85.45        51.32        21.99        12.99        15.02        11.08 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-F4-6570 TCGA-G4-6323 
        4.80        17.13        16.14         6.18        13.78 

$`PREX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52         8.38        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3949 TCGA-AA-3955 
       27.02        18.05        31.00         2.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.59        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        13.02        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 
       54.61        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-D5-6541 
       25.48        43.27        15.12        17.85        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6626 
       36.00        46.75 

  PREX2 MUTATED PREX2 WILD-TYPE 
           0.92            0.00 
  PREX2 MUTATED PREX2 WILD-TYPE 
          85.45          148.01 
  PREX2 MUTATED PREX2 WILD-TYPE 
          21.37           22.09 
[1] "0.9 - 85.5 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D830V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PREX2 MUTATED         7        1        2         7         3         0
  PREX2 WILD-TYPE      57        0       24       101         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PREX2 MUTATED           2          0          4          0        3         2
  PREX2 WILD-TYPE        16          6         40         33       32        10
                 vv
clus              STAGE IVB
  PREX2 MUTATED           0
  PREX2 WILD-TYPE         1
D830V3, multiclass
            clus
vv           PREX2 MUTATED PREX2 WILD-TYPE
  STAGE I                7              57
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              2              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
  PREX2 MUTATED     0   7  18   5
  PREX2 WILD-TYPE   9  60 231  36
D830V4, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  T1             0               9
  T2             7              60
  T3            18             231
  T4             5              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
  PREX2 MUTATED    20   7   4
  PREX2 WILD-TYPE 200  74  62
D830V5, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  N0            20             200
  N1             7              74
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V6, binary
                 cls
clus                0   1
  PREX2 MUTATED    22   5
  PREX2 WILD-TYPE 263  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     22    5
  PREX2 WILD-TYPE  263   43
   clus
vv  PREX2 MUTATED PREX2 WILD-TYPE
  0            22             263
  1             5              43
[1] 2 2
[1] FALSE
D830V7, binary
                 cls
clus                0   1
  PREX2 MUTATED    17  14
  PREX2 WILD-TYPE 153 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     17   14
  PREX2 WILD-TYPE  153  183
        clus
vv       PREX2 MUTATED PREX2 WILD-TYPE
  FEMALE            17             153
  MALE              14             183
[1] 2 2
[1] FALSE
D830V8, binary
                 cls
clus                0   1
  PREX2 MUTATED    25   1
  PREX2 WILD-TYPE 275   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     25    1
  PREX2 WILD-TYPE  275    7
     clus
vv    PREX2 MUTATED PREX2 WILD-TYPE
  NO             25             275
  YES             1               7
[1] 2 2
[1] FALSE
D830V9, binary
                 cls
clus                0   1
  PREX2 MUTATED    24   7
  PREX2 WILD-TYPE 290  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     24    7
  PREX2 WILD-TYPE  290   41
                               clus
vv                              PREX2 MUTATED PREX2 WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PREX2 MUTATED    21   1   2   4
  PREX2 WILD-TYPE 238   2  20  17
D830V10, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  R0            21             238
  R1             1               2
  R2             2              20
  RX             4              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"
D830V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PREX2 MUTATED                                  0     2
  PREX2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PREX2 MUTATED                           3    15
  PREX2 WILD-TYPE                        16   161
D830V12, multiclass
                                  clus
vv                                 PREX2 MUTATED PREX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       15             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(831) Variable = MAOA MUTATION ANALYSIS
D831V1, survival
                sevent
clus2              0   1
  MAOA MUTATED     4   1
  MAOA WILD-TYPE 273  77
  MAOA MUTATED MAOA WILD-TYPE 
             5            350 
  MAOA MUTATED MAOA WILD-TYPE 
             1             77 
$`MAOA MUTATED`
TCGA-AA-3525 TCGA-AZ-6601 TCGA-AA-A00R TCGA-D5-6922 TCGA-G4-6317 
        8.05       100.01         0.99        10.13        36.00 

$`MAOA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MAOA MUTATED MAOA WILD-TYPE 
          0.99           0.00 
  MAOA MUTATED MAOA WILD-TYPE 
        100.01         148.01 
  MAOA MUTATED MAOA WILD-TYPE 
        10.130         22.075 
[1] "1.0 - 100.0 (10.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D831V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAOA MUTATED         1        0        1         0         0         0
  MAOA WILD-TYPE      63        1       25       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAOA MUTATED           0          1          1          1        0         0
  MAOA WILD-TYPE        18          5         43         32       35        12
                vv
clus             STAGE IVB
  MAOA MUTATED           0
  MAOA WILD-TYPE         1
D831V3, multiclass
            clus
vv           MAOA MUTATED MAOA WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  MAOA MUTATED     0   1   4   0
  MAOA WILD-TYPE   9  66 245  41
D831V4, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            0             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
  MAOA MUTATED     2   2   1
  MAOA WILD-TYPE 218  79  65
D831V5, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  N0            2            218
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D831V6, binary
                cls
clus               0   1
  MAOA MUTATED     4   0
  MAOA WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      4    0
  MAOA WILD-TYPE  281   48
   clus
vv  MAOA MUTATED MAOA WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D831V7, binary
                cls
clus               0   1
  MAOA MUTATED     2   3
  MAOA WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      2    3
  MAOA WILD-TYPE  168  194
        clus
vv       MAOA MUTATED MAOA WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D831V8, binary
                cls
clus               0   1
  MAOA MUTATED     4   0
  MAOA WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      4    0
  MAOA WILD-TYPE  296    8
     clus
vv    MAOA MUTATED MAOA WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D831V9, binary
                cls
clus               0   1
  MAOA MUTATED     5   0
  MAOA WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      5    0
  MAOA WILD-TYPE  309   48
                               clus
vv                              MAOA MUTATED MAOA WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAOA MUTATED     4   0   0   0
  MAOA WILD-TYPE 255   3  22  21
D831V10, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D831V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAOA MUTATED                                  0     0
  MAOA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAOA MUTATED                           0     3
  MAOA WILD-TYPE                        19   173
D831V12, multiclass
                                  clus
vv                                 MAOA MUTATED MAOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = CD55 MUTATION ANALYSIS
D832V1, survival
                sevent
clus2              0   1
  CD55 MUTATED     7   0
  CD55 WILD-TYPE 270  78
  CD55 MUTATED CD55 WILD-TYPE 
             7            348 
  CD55 MUTATED CD55 WILD-TYPE 
             0             78 
$`CD55 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3518 TCGA-AA-3877 TCGA-AZ-5407 TCGA-CA-5255 
        0.92        19.04         1.02        31.00        88.21        12.36 
TCGA-CM-6674 
       12.95 

$`CD55 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CD55 MUTATED CD55 WILD-TYPE 
          0.92           0.00 
  CD55 MUTATED CD55 WILD-TYPE 
         88.21         148.01 
  CD55 MUTATED CD55 WILD-TYPE 
         12.95          22.09 
[1] "0.9 - 88.2 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D832V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD55 MUTATED         2        0        0         3         0         0
  CD55 WILD-TYPE      62        1       26       105         8         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        17          6         44         33       34        12
                vv
clus             STAGE IVB
  CD55 MUTATED           0
  CD55 WILD-TYPE         1
D832V3, multiclass
            clus
vv           CD55 MUTATED CD55 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  CD55 MUTATED     2   0   5   0
  CD55 WILD-TYPE   7  67 244  41
D832V4, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  T1            2              7
  T2            0             67
  T3            5            244
  T4            0             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
  CD55 MUTATED     6   1   0
  CD55 WILD-TYPE 214  80  66
D832V5, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V6, binary
                cls
clus               0   1
  CD55 MUTATED     6   1
  CD55 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      6    1
  CD55 WILD-TYPE  279   47
   clus
vv  CD55 MUTATED CD55 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D832V7, binary
                cls
clus               0   1
  CD55 MUTATED     4   3
  CD55 WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      4    3
  CD55 WILD-TYPE  166  194
        clus
vv       CD55 MUTATED CD55 WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D832V8, binary
                cls
clus               0   1
  CD55 MUTATED     4   2
  CD55 WILD-TYPE 296   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      4    2
  CD55 WILD-TYPE  296    6
     clus
vv    CD55 MUTATED CD55 WILD-TYPE
  NO             4            296
  YES            2              6
[1] 2 2
[1] FALSE
D832V9, binary
                cls
clus               0   1
  CD55 MUTATED     6   1
  CD55 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      6    1
  CD55 WILD-TYPE  308   47
                               clus
vv                              CD55 MUTATED CD55 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD55 MUTATED     4   0   1   1
  CD55 WILD-TYPE 255   3  21  20
D832V10, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            1             21
  RX            1             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"
D832V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD55 MUTATED                                  0     1
  CD55 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD55 MUTATED                           0     2
  CD55 WILD-TYPE                        19   174
D832V12, multiclass
                                  clus
vv                                 CD55 MUTATED CD55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(833) Variable = MATN3 MUTATION ANALYSIS
D833V1, survival
                 sevent
clus2               0   1
  MATN3 MUTATED     4   2
  MATN3 WILD-TYPE 273  76
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             349 
  MATN3 MUTATED MATN3 WILD-TYPE 
              2              76 
$`MATN3 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3950 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-A00N 
        0.92        19.04        24.00        22.06        19.66         4.01 

$`MATN3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.09 
[1] "0.9 - 24.0 (19.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D833V2, continuous
                 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      64        1       25       106         7         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        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  MATN3 MUTATED           0
  MATN3 WILD-TYPE         1
D833V3, multiclass
            clus
vv           MATN3 MUTATED MATN3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  MATN3 MUTATED     0   0   4   2
  MATN3 WILD-TYPE   9  67 245  39
D833V4, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             2              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
  MATN3 MUTATED     4   2   0
  MATN3 WILD-TYPE 216  79  66
D833V5, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V6, binary
                 cls
clus                0   1
  MATN3 MUTATED     5   0
  MATN3 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      5    0
  MATN3 WILD-TYPE  280   48
   clus
vv  MATN3 MUTATED MATN3 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D833V7, binary
                 cls
clus                0   1
  MATN3 MUTATED     3   3
  MATN3 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      3    3
  MATN3 WILD-TYPE  167  194
        clus
vv       MATN3 MUTATED MATN3 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D833V8, binary
                 cls
clus                0   1
  MATN3 MUTATED     5   0
  MATN3 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      5    0
  MATN3 WILD-TYPE  295    8
     clus
vv    MATN3 MUTATED MATN3 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D833V9, binary
                 cls
clus                0   1
  MATN3 MUTATED     3   3
  MATN3 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      3    3
  MATN3 WILD-TYPE  311   45
                               clus
vv                              MATN3 MUTATED MATN3 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MATN3 MUTATED     6   0   0   0
  MATN3 WILD-TYPE 253   3  22  21
D833V10, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D833V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MATN3 MUTATED                                  0     0
  MATN3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MATN3 MUTATED                           0     2
  MATN3 WILD-TYPE                        19   174
D833V12, multiclass
[1] "Remove cluster labels:" "MATN3 MUTATED"         
clus
  MATN3 MUTATED MATN3 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6782      TCGA-AD-5900 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899      TCGA-AD-6901 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6603 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      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-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 

Clustering(834) Variable = OR6C75 MUTATION ANALYSIS
D834V1, survival
                  sevent
clus2                0   1
  OR6C75 MUTATED     6   1
  OR6C75 WILD-TYPE 271  77
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               7              348 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               1               77 
$`OR6C75 MUTATED`
TCGA-AZ-6601 TCGA-AA-3710 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-5255 TCGA-CM-6170 
      100.01        26.99        25.02        58.39        12.36        15.02 
TCGA-D5-6932 
       11.38 

$`OR6C75 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.69        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  OR6C75 MUTATED OR6C75 WILD-TYPE 
           11.38             0.00 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
          100.01           148.01 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
          25.020           22.045 
[1] "11.4 - 100.0 (25.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.1"
D834V2, continuous
                  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      63        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR6C75 MUTATED           0          0          0          0        0
  OR6C75 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR6C75 MUTATED           0         0
  OR6C75 WILD-TYPE        12         1
D834V3, multiclass
            clus
vv           OR6C75 MUTATED OR6C75 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  OR6C75 MUTATED     0   2   5   0
  OR6C75 WILD-TYPE   9  65 244  41
D834V4, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              0               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
  OR6C75 MUTATED     7   0   0
  OR6C75 WILD-TYPE 213  81  66
D834V5, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V6, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     6   0
  OR6C75 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      6    0
  OR6C75 WILD-TYPE  279   48
   clus
vv  OR6C75 MUTATED OR6C75 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D834V7, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     2   5
  OR6C75 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      2    5
  OR6C75 WILD-TYPE  168  192
        clus
vv       OR6C75 MUTATED OR6C75 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D834V8, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     6   1
  OR6C75 WILD-TYPE 294   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      6    1
  OR6C75 WILD-TYPE  294    7
     clus
vv    OR6C75 MUTATED OR6C75 WILD-TYPE
  NO               6              294
  YES              1                7
[1] 2 2
[1] FALSE
D834V9, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     7   0
  OR6C75 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      7    0
  OR6C75 WILD-TYPE  307   48
                               clus
vv                              OR6C75 MUTATED OR6C75 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR6C75 MUTATED     4   0   0   1
  OR6C75 WILD-TYPE 255   3  22  20
D834V10, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D834V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6C75 MUTATED                                  0     1
  OR6C75 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR6C75 MUTATED                           0     4
  OR6C75 WILD-TYPE                        19   172
D834V12, multiclass
                                  clus
vv                                 OR6C75 MUTATED OR6C75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = NAP1L1 MUTATION ANALYSIS
D835V1, survival
                  sevent
clus2                0   1
  NAP1L1 MUTATED     6   1
  NAP1L1 WILD-TYPE 271  77
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               7              348 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               1               77 
$`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        24.53        58.39        12.76 
TCGA-DM-A1HB 
      135.65 

$`NAP1L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
           12.76             0.00 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
          135.65           148.01 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
           25.02            22.01 
[1] "12.8 - 135.7 (25.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.2"
D835V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAP1L1 MUTATED         0        0        0         3         0         1
  NAP1L1 WILD-TYPE      64        1       26       105         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAP1L1 MUTATED           0          0          1          0        0
  NAP1L1 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  NAP1L1 MUTATED           0         0
  NAP1L1 WILD-TYPE        12         1
D835V3, multiclass
            clus
vv           NAP1L1 MUTATED NAP1L1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  NAP1L1 MUTATED     1   1   4   1
  NAP1L1 WILD-TYPE   8  66 245  40
D835V4, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              4              245
  T4              1               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
  NAP1L1 MUTATED     6   1   0
  NAP1L1 WILD-TYPE 214  80  66
D835V5, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V6, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     5   0
  NAP1L1 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      5    0
  NAP1L1 WILD-TYPE  280   48
   clus
vv  NAP1L1 MUTATED NAP1L1 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D835V7, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     0   7
  NAP1L1 WILD-TYPE 170 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      0    7
  NAP1L1 WILD-TYPE  170  190
        clus
vv       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  FEMALE              0              170
  MALE                7              190
[1] 2 2
[1] FALSE
D835V8, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     6   0
  NAP1L1 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      6    0
  NAP1L1 WILD-TYPE  294    8
     clus
vv    NAP1L1 MUTATED NAP1L1 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D835V9, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     5   1
  NAP1L1 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      5    1
  NAP1L1 WILD-TYPE  309   47
                               clus
vv                              NAP1L1 MUTATED NAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NAP1L1 MUTATED     1   0   0   1
  NAP1L1 WILD-TYPE 258   3  22  20
D835V10, multiclass
[1] "Remove cluster labels:" "NAP1L1 MUTATED"        
clus
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               2              303 
      TCGA-A6-2677       TCGA-AA-3496       TCGA-AA-3520       TCGA-AA-3521 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4682       TCGA-CA-5254 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5913 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
D835V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L1 MUTATED                                  0     1
  NAP1L1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L1 MUTATED                           0     5
  NAP1L1 WILD-TYPE                        19   171
D835V12, multiclass
                                  clus
vv                                 NAP1L1 MUTATED NAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = SLC22A3 MUTATION ANALYSIS
D836V1, survival
                   sevent
clus2                 0   1
  SLC22A3 MUTATED     9   3
  SLC22A3 WILD-TYPE 268  75
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               12               343 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
                3                75 
$`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        83.24        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 

$`SLC22A3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        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-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 
       12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
             6.18              0.00 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
           148.01            140.38 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
            32.99             21.99 
[1] "6.2 - 148.0 (33.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.3"
D836V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A3 MUTATED         3        0        1         4         1         0
  SLC22A3 WILD-TYPE      61        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A3 MUTATED           1          0          1          1        0
  SLC22A3 WILD-TYPE        17          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A3 MUTATED           0         0
  SLC22A3 WILD-TYPE        12         1
D836V3, multiclass
            clus
vv           SLC22A3 MUTATED SLC22A3 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC22A3 MUTATED     1   2   7   2
  SLC22A3 WILD-TYPE   8  65 242  39
D836V4, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               7               242
  T4               2                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
  SLC22A3 MUTATED     9   3   0
  SLC22A3 WILD-TYPE 211  78  66
D836V5, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  N0               9               211
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V6, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    11   0
  SLC22A3 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     11    0
  SLC22A3 WILD-TYPE  274   48
   clus
vv  SLC22A3 MUTATED SLC22A3 WILD-TYPE
  0              11               274
  1               0                48
[1] 2 2
[1] FALSE
D836V7, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED     8   4
  SLC22A3 WILD-TYPE 162 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED      8    4
  SLC22A3 WILD-TYPE  162  193
        clus
vv       SLC22A3 MUTATED SLC22A3 WILD-TYPE
  FEMALE               8               162
  MALE                 4               193
[1] 2 2
[1] FALSE
D836V8, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    11   0
  SLC22A3 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     11    0
  SLC22A3 WILD-TYPE  289    8
     clus
vv    SLC22A3 MUTATED SLC22A3 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D836V9, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    10   2
  SLC22A3 WILD-TYPE 304  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     10    2
  SLC22A3 WILD-TYPE  304   46
                               clus
vv                              SLC22A3 MUTATED SLC22A3 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC22A3 MUTATED    12   0   0   0
  SLC22A3 WILD-TYPE 247   3  22  21
D836V10, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               0                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"
D836V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A3 MUTATED                                  0     1
  SLC22A3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC22A3 MUTATED                           2     6
  SLC22A3 WILD-TYPE                        17   170
D836V12, multiclass
                                  clus
vv                                 SLC22A3 MUTATED SLC22A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = HRSP12 MUTATION ANALYSIS
D837V1, survival
                  sevent
clus2                0   1
  HRSP12 MUTATED     5   1
  HRSP12 WILD-TYPE 272  77
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               6              349 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               1               77 
$`HRSP12 MUTATED`
TCGA-AA-3662 TCGA-AA-3510 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
        6.05        63.98        33.01        34.98        58.39        49.41 

$`HRSP12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  HRSP12 MUTATED HRSP12 WILD-TYPE 
            6.05             0.00 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
           63.98           148.01 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
          42.195           21.990 
[1] "6.0 - 64.0 (42.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D837V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HRSP12 MUTATED         0        0        2         1         2         0
  HRSP12 WILD-TYPE      64        1       24       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HRSP12 MUTATED           0          0          0          0        1
  HRSP12 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  HRSP12 MUTATED           0         0
  HRSP12 WILD-TYPE        12         1
D837V3, multiclass
            clus
vv           HRSP12 MUTATED HRSP12 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               1              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  HRSP12 MUTATED     0   0   3   3
  HRSP12 WILD-TYPE   9  67 246  38
D837V4, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              3              246
  T4              3               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
  HRSP12 MUTATED     5   0   1
  HRSP12 WILD-TYPE 215  81  65
D837V5, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V6, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     4   1
  HRSP12 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      4    1
  HRSP12 WILD-TYPE  281   47
   clus
vv  HRSP12 MUTATED HRSP12 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D837V7, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     4   2
  HRSP12 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      4    2
  HRSP12 WILD-TYPE  166  195
        clus
vv       HRSP12 MUTATED HRSP12 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D837V8, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     6   0
  HRSP12 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      6    0
  HRSP12 WILD-TYPE  294    8
     clus
vv    HRSP12 MUTATED HRSP12 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D837V9, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     5   1
  HRSP12 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      5    1
  HRSP12 WILD-TYPE  309   47
                               clus
vv                              HRSP12 MUTATED HRSP12 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HRSP12 MUTATED     4   0   1   0
  HRSP12 WILD-TYPE 255   3  21  21
D837V10, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              1               21
  RX              0               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"
D837V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRSP12 MUTATED                                  0     0
  HRSP12 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HRSP12 MUTATED                           0     2
  HRSP12 WILD-TYPE                        19   174
D837V12, multiclass
[1] "Remove cluster labels:" "HRSP12 MUTATED"        
clus
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6603 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       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-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 

Clustering(838) Variable = RYR2 MUTATION ANALYSIS
D838V1, survival
                sevent
clus2              0   1
  RYR2 MUTATED    58  23
  RYR2 WILD-TYPE 219  55
  RYR2 MUTATED RYR2 WILD-TYPE 
            81            274 
  RYR2 MUTATED RYR2 WILD-TYPE 
            23             55 
$`RYR2 MUTATED`
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 
        6.05         0.92        19.04        19.04        29.98        24.00 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-3807 
        1.94         5.88        22.09        26.17        79.69        34.65 
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       32.75        33.53        22.06        24.39        20.12         3.02 
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3815 
       63.98         6.97         2.01         5.03        26.99        33.04 
TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-3982 
       53.00        26.01         2.01        21.99        25.02        27.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A029 
        4.01        34.98        31.00        35.01        37.02        51.98 
TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6901 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6386 
       39.98        12.16        22.42        27.09        16.31        17.82 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       58.39        22.36        62.79        49.41         6.77        12.10 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-5860 
       12.76        10.06        85.45        21.14        37.02        32.02 
TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-6534 
       15.02        15.02        14.04        11.01        11.08        43.27 
TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XD 
       16.14        14.30        11.64        13.35        11.38        24.43 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 
       13.32        12.59       139.17        35.97        31.96         6.18 
TCGA-F4-6805 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       34.42        33.67       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 
       44.68        55.04        36.00 

$`RYR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       13.02        17.95        23.01        19.99        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       36.00        85.05        14.93        31.07        24.03        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 
      106.75       100.01        49.08        63.62        35.80        91.79 
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-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.08        25.18        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        78.08        54.02 
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-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       37.05        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        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-A02F 
        1.02         1.02        33.04         1.02        26.01        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       40.96        83.24        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       14.50         0.95        33.01         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        5.13        88.21        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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-5862 
       13.02        29.06        22.03        22.98        30.08         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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-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        54.61        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04         9.44        13.41        12.00        10.26       119.70 
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-A1HA TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
       44.32       131.51       135.65        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-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  RYR2 MUTATED RYR2 WILD-TYPE 
          0.92           0.00 
  RYR2 MUTATED RYR2 WILD-TYPE 
        139.17         148.01 
  RYR2 MUTATED RYR2 WILD-TYPE 
         24.39          21.60 
[1] "0.9 - 139.2 (24.4)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1.4"
D838V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RYR2 MUTATED        15        0       10        24         4         0
  RYR2 WILD-TYPE      49        1       16        84         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RYR2 MUTATED           5          1          8          5        7         1
  RYR2 WILD-TYPE        13          5         36         28       28        11
                vv
clus             STAGE IVB
  RYR2 MUTATED           0
  RYR2 WILD-TYPE         1
D838V3, multiclass
            clus
vv           RYR2 MUTATED RYR2 WILD-TYPE
  STAGE I              15             49
  STAGE IA              0              1
  STAGE II             10             16
  STAGE IIA            24             84
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             5             13
  STAGE IIIA            1              5
  STAGE IIIB            8             36
  STAGE IIIC            5             28
  STAGE IV              7             28
  STAGE IVA             1             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
  RYR2 MUTATED     2  17  58   7
  RYR2 WILD-TYPE   7  50 191  34
D838V4, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  T1            2              7
  T2           17             50
  T3           58            191
  T4            7             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
  RYR2 MUTATED    58  17   9
  RYR2 WILD-TYPE 162  64  57
D838V5, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  N0           58            162
  N1           17             64
  N2            9             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V6, binary
                cls
clus               0   1
  RYR2 MUTATED    65   8
  RYR2 WILD-TYPE 220  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     65    8
  RYR2 WILD-TYPE  220   40
   clus
vv  RYR2 MUTATED RYR2 WILD-TYPE
  0           65            220
  1            8             40
[1] 2 2
[1] FALSE
D838V7, binary
                cls
clus               0   1
  RYR2 MUTATED    45  39
  RYR2 WILD-TYPE 125 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     45   39
  RYR2 WILD-TYPE  125  158
        clus
vv       RYR2 MUTATED RYR2 WILD-TYPE
  FEMALE           45            125
  MALE             39            158
[1] 2 2
[1] FALSE
D838V8, binary
                cls
clus               0   1
  RYR2 MUTATED    68   2
  RYR2 WILD-TYPE 232   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     68    2
  RYR2 WILD-TYPE  232    6
     clus
vv    RYR2 MUTATED RYR2 WILD-TYPE
  NO            68            232
  YES            2              6
[1] 2 2
[1] FALSE
D838V9, binary
                cls
clus               0   1
  RYR2 MUTATED    68  15
  RYR2 WILD-TYPE 246  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     68   15
  RYR2 WILD-TYPE  246   33
                               clus
vv                              RYR2 MUTATED RYR2 WILD-TYPE
  COLON ADENOCARCINOMA                    68            246
  COLON MUCINOUS ADENOCARCINOMA           15             33
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RYR2 MUTATED    58   2   3   4
  RYR2 WILD-TYPE 201   1  19  17
D838V10, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  R0           58            201
  R1            2              1
  R2            3             19
  RX            4             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"
D838V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RYR2 MUTATED                                  0     2
  RYR2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RYR2 MUTATED                           6    48
  RYR2 WILD-TYPE                        13   128
D838V12, multiclass
                                  clus
vv                                 RYR2 MUTATED RYR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   6             13
  WHITE                                      48            128
[1] 4 2
[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 = ZNF605 MUTATION ANALYSIS
D839V1, survival
                  sevent
clus2                0   1
  ZNF605 MUTATED     5   3
  ZNF605 WILD-TYPE 272  75
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              347 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               3               75 
$`ZNF605 MUTATED`
TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-6141 TCGA-AZ-4315 TCGA-CA-6718 
        1.94        26.17        46.65         8.38        58.39        10.06 
TCGA-D5-6539 TCGA-DM-A0XD 
       12.49        24.43 

$`ZNF605 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF605 MUTATED ZNF605 WILD-TYPE 
            1.94             0.00 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
           58.39           148.01 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
           18.46            22.06 
[1] "1.9 - 58.4 (18.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D839V2, continuous
                  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      64        1       26       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF605 MUTATED           0          1          1          0        0
  ZNF605 WILD-TYPE        18          5         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF605 MUTATED           0         0
  ZNF605 WILD-TYPE        12         1
D839V3, multiclass
            clus
vv           ZNF605 MUTATED ZNF605 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF605 MUTATED     0   1   7   0
  ZNF605 WILD-TYPE   9  66 242  41
D839V4, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              0               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
  ZNF605 MUTATED     6   2   0
  ZNF605 WILD-TYPE 214  79  66
D839V5, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  N0              6              214
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V6, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     8   0
  ZNF605 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      8    0
  ZNF605 WILD-TYPE  277   48
   clus
vv  ZNF605 MUTATED ZNF605 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D839V7, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     4   4
  ZNF605 WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      4    4
  ZNF605 WILD-TYPE  166  193
        clus
vv       ZNF605 MUTATED ZNF605 WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D839V8, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     7   0
  ZNF605 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      7    0
  ZNF605 WILD-TYPE  293    8
     clus
vv    ZNF605 MUTATED ZNF605 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D839V9, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     8   0
  ZNF605 WILD-TYPE 306  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      8    0
  ZNF605 WILD-TYPE  306   48
                               clus
vv                              ZNF605 MUTATED ZNF605 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF605 MUTATED     4   0   0   1
  ZNF605 WILD-TYPE 255   3  22  20
D839V10, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D839V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF605 MUTATED                                  0     1
  ZNF605 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF605 MUTATED                           1     6
  ZNF605 WILD-TYPE                        18   170
D839V12, multiclass
                                  clus
vv                                 ZNF605 MUTATED ZNF605 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = C1ORF168 MUTATION ANALYSIS
D840V1, survival
                    sevent
clus2                  0   1
  C1ORF168 MUTATED    10   4
  C1ORF168 WILD-TYPE 267  74
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                14                341 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                 4                 74 
$`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 
        6.18        53.62 

$`C1ORF168 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
              4.01               0.00 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
            117.07             148.01 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
            26.005             22.030 
[1] "4.0 - 117.1 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D840V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF168 MUTATED         4        0        0         4         3         0
  C1ORF168 WILD-TYPE      60        1       26       104         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF168 MUTATED           0          0          1          1        0
  C1ORF168 WILD-TYPE        18          6         43         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C1ORF168 MUTATED           0         0
  C1ORF168 WILD-TYPE        12         1
D840V3, multiclass
            clus
vv           C1ORF168 MUTATED C1ORF168 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 4                104
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C1ORF168 MUTATED     2   3   6   3
  C1ORF168 WILD-TYPE   7  64 243  38
D840V4, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  T1                2                  7
  T2                3                 64
  T3                6                243
  T4                3                 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
  C1ORF168 MUTATED    12   1   1
  C1ORF168 WILD-TYPE 208  80  65
D840V5, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  N0               12                208
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V6, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    13   0
  C1ORF168 WILD-TYPE 272  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     13    0
  C1ORF168 WILD-TYPE  272   48
   clus
vv  C1ORF168 MUTATED C1ORF168 WILD-TYPE
  0               13                272
  1                0                 48
[1] 2 2
[1] FALSE
D840V7, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED     6   8
  C1ORF168 WILD-TYPE 164 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED      6    8
  C1ORF168 WILD-TYPE  164  189
        clus
vv       C1ORF168 MUTATED C1ORF168 WILD-TYPE
  FEMALE                6                164
  MALE                  8                189
[1] 2 2
[1] FALSE
D840V8, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    12   0
  C1ORF168 WILD-TYPE 288   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     12    0
  C1ORF168 WILD-TYPE  288    8
     clus
vv    C1ORF168 MUTATED C1ORF168 WILD-TYPE
  NO                12                288
  YES                0                  8
[1] 2 2
[1] FALSE
D840V9, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    12   2
  C1ORF168 WILD-TYPE 302  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     12    2
  C1ORF168 WILD-TYPE  302   46
                               clus
vv                              C1ORF168 MUTATED C1ORF168 WILD-TYPE
  COLON ADENOCARCINOMA                        12                302
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C1ORF168 MUTATED     7   0   0   3
  C1ORF168 WILD-TYPE 252   3  22  18
D840V10, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D840V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF168 MUTATED                                  0     2
  C1ORF168 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF168 MUTATED                           1     7
  C1ORF168 WILD-TYPE                        18   169
D840V12, multiclass
                                  clus
vv                                 C1ORF168 MUTATED C1ORF168 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           7                169
[1] 4 2
[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 = PGAP3 MUTATION ANALYSIS
D841V1, survival
                 sevent
clus2               0   1
  PGAP3 MUTATED     4   3
  PGAP3 WILD-TYPE 273  75
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              7             348 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              3              75 
$`PGAP3 MUTATED`
TCGA-AA-3525 TCGA-AA-3972 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AA-3710 TCGA-AZ-6598 
        8.05        50.99        25.08       100.01        26.99        49.41 
TCGA-F4-6459 
        8.61 

$`PGAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PGAP3 MUTATED PGAP3 WILD-TYPE 
           8.05            0.00 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
         100.01          148.01 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
          26.99           22.01 
[1] "8.1 - 100.0 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D841V2, continuous
                 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      64        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGAP3 MUTATED           0          0          3          0        1         0
  PGAP3 WILD-TYPE        18          6         41         33       34        12
                 vv
clus              STAGE IVB
  PGAP3 MUTATED           0
  PGAP3 WILD-TYPE         1
D841V3, multiclass
            clus
vv           PGAP3 MUTATED PGAP3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  PGAP3 MUTATED     0   0   7   0
  PGAP3 WILD-TYPE   9  67 242  41
D841V4, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             0              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
  PGAP3 MUTATED     3   3   1
  PGAP3 WILD-TYPE 217  78  65
D841V5, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  N0             3             217
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V6, binary
                 cls
clus                0   1
  PGAP3 MUTATED     5   1
  PGAP3 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      5    1
  PGAP3 WILD-TYPE  280   47
   clus
vv  PGAP3 MUTATED PGAP3 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D841V7, binary
                 cls
clus                0   1
  PGAP3 MUTATED     3   4
  PGAP3 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      3    4
  PGAP3 WILD-TYPE  167  193
        clus
vv       PGAP3 MUTATED PGAP3 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D841V8, binary
                 cls
clus                0   1
  PGAP3 MUTATED     7   0
  PGAP3 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      7    0
  PGAP3 WILD-TYPE  293    8
     clus
vv    PGAP3 MUTATED PGAP3 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D841V9, binary
                 cls
clus                0   1
  PGAP3 MUTATED     7   0
  PGAP3 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      7    0
  PGAP3 WILD-TYPE  307   48
                               clus
vv                              PGAP3 MUTATED PGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PGAP3 MUTATED     4   0   1   0
  PGAP3 WILD-TYPE 255   3  21  21
D841V10, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D841V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PGAP3 MUTATED                                  0     0
  PGAP3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PGAP3 MUTATED                           0     4
  PGAP3 WILD-TYPE                        19   172
D841V12, multiclass
                                  clus
vv                                 PGAP3 MUTATED PGAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = AGTR2 MUTATION ANALYSIS
D842V1, survival
                 sevent
clus2               0   1
  AGTR2 MUTATED     9   6
  AGTR2 WILD-TYPE 268  72
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             15             340 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
              6              72 
$`AGTR2 MUTATED`
TCGA-AD-6895 TCGA-AZ-6601 TCGA-DM-A285 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3821 
       25.08       100.01         5.88        32.75        32.71         1.02 
TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A017 TCGA-AD-6889 TCGA-AD-6899 TCGA-CA-6717 
        7.96         4.01        15.02        83.24         5.79        12.76 
TCGA-CM-6171 TCGA-D5-6539 TCGA-G4-6323 
       14.04        12.49        13.78 

$`AGTR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6626 
       85.48        61.91        36.00        46.75 

  AGTR2 MUTATED AGTR2 WILD-TYPE 
           1.02            0.00 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
         100.01          148.01 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
         13.780          22.225 
[1] "1.0 - 100.0 (13.8)" "0.0 - 148.0 (22.2)"
[1] "hr=" "2.1"
D842V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGTR2 MUTATED         2        1        1         3         2         1
  AGTR2 WILD-TYPE      62        0       25       105         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGTR2 MUTATED           0          0          1          1        2         0
  AGTR2 WILD-TYPE        18          6         43         32       33        12
                 vv
clus              STAGE IVB
  AGTR2 MUTATED           0
  AGTR2 WILD-TYPE         1
D842V3, multiclass
            clus
vv           AGTR2 MUTATED AGTR2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  AGTR2 MUTATED     0   2   8   4
  AGTR2 WILD-TYPE   9  65 241  37
D842V4, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             4              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
  AGTR2 MUTATED    11   1   3
  AGTR2 WILD-TYPE 209  80  63
D842V5, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  N0            11             209
  N1             1              80
  N2             3              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"
D842V6, binary
                 cls
clus                0   1
  AGTR2 MUTATED    11   2
  AGTR2 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED     11    2
  AGTR2 WILD-TYPE  274   46
   clus
vv  AGTR2 MUTATED AGTR2 WILD-TYPE
  0            11             274
  1             2              46
[1] 2 2
[1] FALSE
D842V7, binary
                 cls
clus                0   1
  AGTR2 MUTATED     6   9
  AGTR2 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED      6    9
  AGTR2 WILD-TYPE  164  188
        clus
vv       AGTR2 MUTATED AGTR2 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D842V8, binary
                 cls
clus                0   1
  AGTR2 MUTATED    13   0
  AGTR2 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED     13    0
  AGTR2 WILD-TYPE  287    8
     clus
vv    AGTR2 MUTATED AGTR2 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D842V9, binary
                 cls
clus                0   1
  AGTR2 MUTATED     9   6
  AGTR2 WILD-TYPE 305  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED      9    6
  AGTR2 WILD-TYPE  305   42
                               clus
vv                              AGTR2 MUTATED AGTR2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGTR2 MUTATED     9   0   1   1
  AGTR2 WILD-TYPE 250   3  21  20
D842V10, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             1              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"
D842V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGTR2 MUTATED                                  0     2
  AGTR2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGTR2 MUTATED                           1     8
  AGTR2 WILD-TYPE                        18   168
D842V12, multiclass
                                  clus
vv                                 AGTR2 MUTATED AGTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = RAE1 MUTATION ANALYSIS
D843V1, survival
                sevent
clus2              0   1
  RAE1 MUTATED     4   1
  RAE1 WILD-TYPE 273  77
  RAE1 MUTATED RAE1 WILD-TYPE 
             5            350 
  RAE1 MUTATED RAE1 WILD-TYPE 
             1             77 
$`RAE1 MUTATED`
TCGA-A6-3809 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-A00A TCGA-DM-A1DA 
       32.75        24.69        20.12        38.04         7.50 

$`RAE1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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         22.045 
[1] "7.5 - 38.0 (24.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D843V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAE1 MUTATED         0        0        0         2         2         0
  RAE1 WILD-TYPE      64        1       26       106         6         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        18          6         44         32       35        11
                vv
clus             STAGE IVB
  RAE1 MUTATED           0
  RAE1 WILD-TYPE         1
D843V3, multiclass
            clus
vv           RAE1 MUTATED RAE1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  RAE1 MUTATED     0   0   4   2
  RAE1 WILD-TYPE   9  67 245  39
D843V4, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            4            245
  T4            2             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
  RAE1 MUTATED     5   0   1
  RAE1 WILD-TYPE 215  81  65
D843V5, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D843V6, binary
                cls
clus               0   1
  RAE1 MUTATED     3   1
  RAE1 WILD-TYPE 282  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      3    1
  RAE1 WILD-TYPE  282   47
   clus
vv  RAE1 MUTATED RAE1 WILD-TYPE
  0            3            282
  1            1             47
[1] 2 2
[1] FALSE
D843V7, binary
                cls
clus               0   1
  RAE1 MUTATED     3   3
  RAE1 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      3    3
  RAE1 WILD-TYPE  167  194
        clus
vv       RAE1 MUTATED RAE1 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D843V8, binary
                cls
clus               0   1
  RAE1 MUTATED     4   0
  RAE1 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      4    0
  RAE1 WILD-TYPE  296    8
     clus
vv    RAE1 MUTATED RAE1 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D843V9, binary
                cls
clus               0   1
  RAE1 MUTATED     4   2
  RAE1 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      4    2
  RAE1 WILD-TYPE  310   46
                               clus
vv                              RAE1 MUTATED RAE1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RAE1 MUTATED     2   0   0   1
  RAE1 WILD-TYPE 257   3  22  20
D843V10, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            0             22
  RX            1             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"
D843V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAE1 MUTATED                                  0     0
  RAE1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAE1 MUTATED                           1     4
  RAE1 WILD-TYPE                        18   172
D843V12, multiclass
                                  clus
vv                                 RAE1 MUTATED RAE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = PAGE2 MUTATION ANALYSIS
D844V1, survival
                 sevent
clus2               0   1
  PAGE2 MUTATED     6   0
  PAGE2 WILD-TYPE 271  78
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              6             349 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              0              78 
$`PAGE2 MUTATED`
TCGA-G4-6625 TCGA-AA-3861 TCGA-CM-6162 TCGA-D5-5539 TCGA-DM-A282 TCGA-G4-6299 
       91.79        30.05        12.00        19.59       139.17        74.56 

$`PAGE2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65        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        43.04        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-G4-6626 
       46.75 

  PAGE2 MUTATED PAGE2 WILD-TYPE 
             12               0 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
         139.17          148.01 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
         52.305          22.030 
[1] "12.0 - 139.2 (52.3)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D844V2, continuous
                 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      64        1       26       104         8         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        18          5         43         32       34        12
                 vv
clus              STAGE IVB
  PAGE2 MUTATED           0
  PAGE2 WILD-TYPE         1
D844V3, multiclass
            clus
vv           PAGE2 MUTATED PAGE2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  PAGE2 MUTATED     0   0   7   1
  PAGE2 WILD-TYPE   9  67 242  40
D844V4, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  PAGE2 MUTATED     4   2   2
  PAGE2 WILD-TYPE 216  79  64
D844V5, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V6, binary
                 cls
clus                0   1
  PAGE2 MUTATED     7   1
  PAGE2 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      7    1
  PAGE2 WILD-TYPE  278   47
   clus
vv  PAGE2 MUTATED PAGE2 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D844V7, binary
                 cls
clus                0   1
  PAGE2 MUTATED     5   3
  PAGE2 WILD-TYPE 165 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      5    3
  PAGE2 WILD-TYPE  165  194
        clus
vv       PAGE2 MUTATED PAGE2 WILD-TYPE
  FEMALE             5             165
  MALE               3             194
[1] 2 2
[1] FALSE
D844V8, binary
                 cls
clus                0   1
  PAGE2 MUTATED     5   0
  PAGE2 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      5    0
  PAGE2 WILD-TYPE  295    8
     clus
vv    PAGE2 MUTATED PAGE2 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D844V9, binary
                 cls
clus                0   1
  PAGE2 MUTATED     5   3
  PAGE2 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      5    3
  PAGE2 WILD-TYPE  309   45
                               clus
vv                              PAGE2 MUTATED PAGE2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PAGE2 MUTATED     6   0   1   0
  PAGE2 WILD-TYPE 253   3  21  21
D844V10, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             0              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"
D844V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAGE2 MUTATED                                  0     0
  PAGE2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PAGE2 MUTATED                           0     5
  PAGE2 WILD-TYPE                        19   171
D844V12, multiclass
                                  clus
vv                                 PAGE2 MUTATED PAGE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = HNMT MUTATION ANALYSIS
D845V1, survival
                sevent
clus2              0   1
  HNMT MUTATED     5   2
  HNMT WILD-TYPE 272  76
  HNMT MUTATED HNMT WILD-TYPE 
             7            348 
  HNMT MUTATED HNMT WILD-TYPE 
             2             76 
$`HNMT MUTATED`
TCGA-AD-6964 TCGA-A6-6653 TCGA-AA-A010 TCGA-CK-4948 TCGA-D5-5538 TCGA-D5-6536 
       10.88        24.39        34.98       148.01        54.61        17.85 
TCGA-DM-A1HB 
      135.65 

$`HNMT WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HNMT MUTATED HNMT WILD-TYPE 
         10.88           0.00 
  HNMT MUTATED HNMT WILD-TYPE 
        148.01         140.38 
  HNMT MUTATED HNMT WILD-TYPE 
         34.98          22.01 
[1] "10.9 - 148.0 (35.0)" "0.0 - 140.4 (22.0)" 
[1] "hr=" "1.4"
D845V2, continuous
                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      63        1       26       106         7         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        17          6         42         33       35        12
                vv
clus             STAGE IVB
  HNMT MUTATED           0
  HNMT WILD-TYPE         1
D845V3, multiclass
            clus
vv           HNMT MUTATED HNMT WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  HNMT MUTATED     0   1   5   2
  HNMT WILD-TYPE   9  66 244  39
D845V4, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            2             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
  HNMT MUTATED     4   3   1
  HNMT WILD-TYPE 216  78  65
D845V5, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  N0            4            216
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V6, binary
                cls
clus               0   1
  HNMT MUTATED     7   0
  HNMT WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      7    0
  HNMT WILD-TYPE  278   48
   clus
vv  HNMT MUTATED HNMT WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D845V7, binary
                cls
clus               0   1
  HNMT MUTATED     4   4
  HNMT WILD-TYPE 166 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      4    4
  HNMT WILD-TYPE  166  193
        clus
vv       HNMT MUTATED HNMT WILD-TYPE
  FEMALE            4            166
  MALE              4            193
[1] 2 2
[1] FALSE
D845V8, binary
                cls
clus               0   1
  HNMT MUTATED     6   0
  HNMT WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      6    0
  HNMT WILD-TYPE  294    8
     clus
vv    HNMT MUTATED HNMT WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D845V9, binary
                cls
clus               0   1
  HNMT MUTATED     7   0
  HNMT WILD-TYPE 307  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      7    0
  HNMT WILD-TYPE  307   48
                               clus
vv                              HNMT MUTATED HNMT WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HNMT MUTATED     5   0   0   0
  HNMT WILD-TYPE 254   3  22  21
D845V10, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D845V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNMT MUTATED                                  0     0
  HNMT WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HNMT MUTATED                           0     6
  HNMT WILD-TYPE                        19   170
D845V12, multiclass
                                  clus
vv                                 HNMT MUTATED HNMT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = AHCTF1 MUTATION ANALYSIS
D846V1, survival
                  sevent
clus2                0   1
  AHCTF1 MUTATED    16   5
  AHCTF1 WILD-TYPE 261  73
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              21              334 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               5               73 
$`AHCTF1 MUTATED`
TCGA-AA-3496 TCGA-G4-6628 TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3947 
        1.02        79.69        22.52        24.39         1.02        33.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01I TCGA-AZ-4315 
       34.03         2.01        25.02        34.98        31.00        58.39 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-6715 TCGA-CA-6717 
       88.21        49.41         6.77        12.10        12.59        12.76 
TCGA-CK-6751 TCGA-DM-A0XF TCGA-F4-6570 
      124.27        38.20         6.18 

$`AHCTF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6141 
       23.61        22.09        22.06        32.71        27.09         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       20.98        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        1.41         5.13        22.36        62.79        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        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
            1.02             0.00 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          124.27           148.01 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
           25.02            21.99 
[1] "1.0 - 124.3 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D846V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AHCTF1 MUTATED         7        0        2         6         2         0
  AHCTF1 WILD-TYPE      57        1       24       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AHCTF1 MUTATED           0          0          1          1        1
  AHCTF1 WILD-TYPE        18          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  AHCTF1 MUTATED           0         0
  AHCTF1 WILD-TYPE        12         1
D846V3, multiclass
            clus
vv           AHCTF1 MUTATED AHCTF1 WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  AHCTF1 MUTATED     1   7  10   3
  AHCTF1 WILD-TYPE   8  60 239  38
D846V4, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  T1              1                8
  T2              7               60
  T3             10              239
  T4              3               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
  AHCTF1 MUTATED    18   2   1
  AHCTF1 WILD-TYPE 202  79  65
D846V5, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  N0             18              202
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V6, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    16   1
  AHCTF1 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     16    1
  AHCTF1 WILD-TYPE  269   47
   clus
vv  AHCTF1 MUTATED AHCTF1 WILD-TYPE
  0             16              269
  1              1               47
[1] 2 2
[1] FALSE
D846V7, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    10  11
  AHCTF1 WILD-TYPE 160 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     10   11
  AHCTF1 WILD-TYPE  160  186
        clus
vv       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  FEMALE             10              160
  MALE               11              186
[1] 2 2
[1] FALSE
D846V8, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    17   0
  AHCTF1 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     17    0
  AHCTF1 WILD-TYPE  283    8
     clus
vv    AHCTF1 MUTATED AHCTF1 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D846V9, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    16   4
  AHCTF1 WILD-TYPE 298  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     16    4
  AHCTF1 WILD-TYPE  298   44
                               clus
vv                              AHCTF1 MUTATED AHCTF1 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AHCTF1 MUTATED     9   0   0   3
  AHCTF1 WILD-TYPE 250   3  22  18
D846V10, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              3               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"
D846V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHCTF1 MUTATED                                  0     2
  AHCTF1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHCTF1 MUTATED                           1    10
  AHCTF1 WILD-TYPE                        18   166
D846V12, multiclass
                                  clus
vv                                 AHCTF1 MUTATED AHCTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(847) Variable = PRPH2 MUTATION ANALYSIS
D847V1, survival
                 sevent
clus2               0   1
  PRPH2 MUTATED     6   3
  PRPH2 WILD-TYPE 271  75
  PRPH2 MUTATED PRPH2 WILD-TYPE 
              9             346 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
              3              75 
$`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 
       44.32        44.68        55.04 

$`PRPH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       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        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       35.31       133.18        74.56        65.85        53.62        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PRPH2 MUTATED PRPH2 WILD-TYPE 
           0.92            0.00 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
          55.04          148.01 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
         25.020          22.045 
[1] "0.9 - 55.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D847V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPH2 MUTATED         0        0        1         2         1         0
  PRPH2 WILD-TYPE      64        1       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRPH2 MUTATED           2          0          2          0        0         0
  PRPH2 WILD-TYPE        16          6         42         33       35        12
                 vv
clus              STAGE IVB
  PRPH2 MUTATED           0
  PRPH2 WILD-TYPE         1
D847V3, multiclass
            clus
vv           PRPH2 MUTATED PRPH2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PRPH2 MUTATED     0   2   6   2
  PRPH2 WILD-TYPE   9  65 243  39
D847V4, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  PRPH2 MUTATED     6   2   2
  PRPH2 WILD-TYPE 214  79  64
D847V5, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V6, binary
                 cls
clus                0   1
  PRPH2 MUTATED     9   0
  PRPH2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      9    0
  PRPH2 WILD-TYPE  276   48
   clus
vv  PRPH2 MUTATED PRPH2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D847V7, binary
                 cls
clus                0   1
  PRPH2 MUTATED     3   7
  PRPH2 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      3    7
  PRPH2 WILD-TYPE  167  190
        clus
vv       PRPH2 MUTATED PRPH2 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D847V8, binary
                 cls
clus                0   1
  PRPH2 MUTATED     6   1
  PRPH2 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      6    1
  PRPH2 WILD-TYPE  294    7
     clus
vv    PRPH2 MUTATED PRPH2 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D847V9, binary
                 cls
clus                0   1
  PRPH2 MUTATED     8   2
  PRPH2 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      8    2
  PRPH2 WILD-TYPE  306   46
                               clus
vv                              PRPH2 MUTATED PRPH2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRPH2 MUTATED     6   0   0   1
  PRPH2 WILD-TYPE 253   3  22  20
D847V10, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D847V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRPH2 MUTATED                                  0     1
  PRPH2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRPH2 MUTATED                           0     4
  PRPH2 WILD-TYPE                        19   172
D847V12, multiclass
                                  clus
vv                                 PRPH2 MUTATED PRPH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = NOD2 MUTATION ANALYSIS
D848V1, survival
                sevent
clus2              0   1
  NOD2 MUTATED    14   2
  NOD2 WILD-TYPE 263  76
  NOD2 MUTATED NOD2 WILD-TYPE 
            16            339 
  NOD2 MUTATED NOD2 WILD-TYPE 
             2             76 
$`NOD2 MUTATED`
TCGA-AD-6964 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3977 
       10.88        22.09        35.80        26.17        22.06        25.02 
TCGA-AA-A01R TCGA-AD-6901 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6162 
       35.01        22.42        23.05        20.02        15.02        12.00 
TCGA-CM-6165 TCGA-D5-6538 TCGA-F4-6855 TCGA-F4-6856 
       16.04        17.13        47.41        35.31 

$`NOD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 
      100.01         1.94        49.08         5.88        63.62        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-4746 
       21.99        21.14        82.95         2.01       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-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-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-G4-6293 TCGA-G4-6299 
       43.04        33.67        13.25         0.53       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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NOD2 MUTATED NOD2 WILD-TYPE 
         10.88           0.00 
  NOD2 MUTATED NOD2 WILD-TYPE 
         47.41         148.01 
  NOD2 MUTATED NOD2 WILD-TYPE 
        22.255         21.990 
[1] "10.9 - 47.4 (22.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D848V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOD2 MUTATED         2        0        0         7         0         0
  NOD2 WILD-TYPE      62        1       26       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOD2 MUTATED           2          0          2          0        0         0
  NOD2 WILD-TYPE        16          6         42         33       35        12
                vv
clus             STAGE IVB
  NOD2 MUTATED           0
  NOD2 WILD-TYPE         1
D848V3, multiclass
            clus
vv           NOD2 MUTATED NOD2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  NOD2 MUTATED     0   4  11   1
  NOD2 WILD-TYPE   9  63 238  40
D848V4, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           11            238
  T4            1             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
  NOD2 MUTATED    11   2   3
  NOD2 WILD-TYPE 209  79  63
D848V5, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  N0           11            209
  N1            2             79
  N2            3             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"
D848V6, binary
                cls
clus               0   1
  NOD2 MUTATED    12   0
  NOD2 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     12    0
  NOD2 WILD-TYPE  273   48
   clus
vv  NOD2 MUTATED NOD2 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D848V7, binary
                cls
clus               0   1
  NOD2 MUTATED     8   8
  NOD2 WILD-TYPE 162 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED      8    8
  NOD2 WILD-TYPE  162  189
        clus
vv       NOD2 MUTATED NOD2 WILD-TYPE
  FEMALE            8            162
  MALE              8            189
[1] 2 2
[1] FALSE
D848V8, binary
                cls
clus               0   1
  NOD2 MUTATED    15   1
  NOD2 WILD-TYPE 285   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     15    1
  NOD2 WILD-TYPE  285    7
     clus
vv    NOD2 MUTATED NOD2 WILD-TYPE
  NO            15            285
  YES            1              7
[1] 2 2
[1] FALSE
D848V9, binary
                cls
clus               0   1
  NOD2 MUTATED    13   3
  NOD2 WILD-TYPE 301  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     13    3
  NOD2 WILD-TYPE  301   45
                               clus
vv                              NOD2 MUTATED NOD2 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOD2 MUTATED    13   0   0   0
  NOD2 WILD-TYPE 246   3  22  21
D848V10, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            0             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"
D848V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOD2 MUTATED                                  0     0
  NOD2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOD2 MUTATED                           0    14
  NOD2 WILD-TYPE                        19   162
D848V12, multiclass
                                  clus
vv                                 NOD2 MUTATED NOD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      14            162
[1] 4 2
[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 = PTCH2 MUTATION ANALYSIS
D849V1, survival
                 sevent
clus2               0   1
  PTCH2 MUTATED    13   4
  PTCH2 WILD-TYPE 264  74
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             17             338 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
              4              74 
$`PTCH2 MUTATED`
TCGA-AZ-6601 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3821 
      100.01        24.39        63.98        78.08        10.06         1.02 
TCGA-AA-3947 TCGA-AA-A00E TCGA-AD-6889 TCGA-AU-6004 TCGA-CM-4743 TCGA-CM-5348 
       33.01        30.02        83.24        27.09        23.05        22.98 
TCGA-CM-5861 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6928 TCGA-DM-A1D7 
       15.02        17.13        12.49        11.64        13.32 

$`PTCH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85         4.80        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PTCH2 MUTATED PTCH2 WILD-TYPE 
           1.02            0.00 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
         100.01          148.01 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
          23.05           22.01 
[1] "1.0 - 100.0 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D849V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTCH2 MUTATED         3        0        3         6         1         0
  PTCH2 WILD-TYPE      61        1       23       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH2 MUTATED           1          0          2          0        0         0
  PTCH2 WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  PTCH2 MUTATED           0
  PTCH2 WILD-TYPE         1
D849V3, multiclass
            clus
vv           PTCH2 MUTATED PTCH2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PTCH2 MUTATED     0   3  13   1
  PTCH2 WILD-TYPE   9  64 236  40
D849V4, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            13             236
  T4             1              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
  PTCH2 MUTATED    14   1   2
  PTCH2 WILD-TYPE 206  80  64
D849V5, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  N0            14             206
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V6, binary
                 cls
clus                0   1
  PTCH2 MUTATED    17   0
  PTCH2 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     17    0
  PTCH2 WILD-TYPE  268   48
   clus
vv  PTCH2 MUTATED PTCH2 WILD-TYPE
  0            17             268
  1             0              48
[1] 2 2
[1] FALSE
D849V7, binary
                 cls
clus                0   1
  PTCH2 MUTATED     8   9
  PTCH2 WILD-TYPE 162 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED      8    9
  PTCH2 WILD-TYPE  162  188
        clus
vv       PTCH2 MUTATED PTCH2 WILD-TYPE
  FEMALE             8             162
  MALE               9             188
[1] 2 2
[1] FALSE
D849V8, binary
                 cls
clus                0   1
  PTCH2 MUTATED    15   0
  PTCH2 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     15    0
  PTCH2 WILD-TYPE  285    8
     clus
vv    PTCH2 MUTATED PTCH2 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D849V9, binary
                 cls
clus                0   1
  PTCH2 MUTATED    13   3
  PTCH2 WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     13    3
  PTCH2 WILD-TYPE  301   45
                               clus
vv                              PTCH2 MUTATED PTCH2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTCH2 MUTATED    14   0   0   0
  PTCH2 WILD-TYPE 245   3  22  21
D849V10, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             0              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"
D849V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTCH2 MUTATED                                  0     1
  PTCH2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTCH2 MUTATED                           0    10
  PTCH2 WILD-TYPE                        19   166
D849V12, multiclass
                                  clus
vv                                 PTCH2 MUTATED PTCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(850) Variable = GPR126 MUTATION ANALYSIS
D850V1, survival
                  sevent
clus2                0   1
  GPR126 MUTATED    12   2
  GPR126 WILD-TYPE 265  76
  GPR126 MUTATED GPR126 WILD-TYPE 
              14              341 
  GPR126 MUTATED GPR126 WILD-TYPE 
               2               76 
$`GPR126 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3864 
        0.92        19.04        22.06         8.38         3.02        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 
       13.41        35.31 

$`GPR126 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPR126 MUTATED GPR126 WILD-TYPE 
            0.92             0.00 
  GPR126 MUTATED GPR126 WILD-TYPE 
           88.21           148.01 
  GPR126 MUTATED GPR126 WILD-TYPE 
           20.55            22.09 
[1] "0.9 - 88.2 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D850V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR126 MUTATED         2        0        4         5         2         0
  GPR126 WILD-TYPE      62        1       22       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR126 MUTATED           1          0          0          0        1
  GPR126 WILD-TYPE        17          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  GPR126 MUTATED           0         0
  GPR126 WILD-TYPE        12         1
D850V3, multiclass
            clus
vv           GPR126 MUTATED GPR126 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               5              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  GPR126 MUTATED     1   1  11   3
  GPR126 WILD-TYPE   8  66 238  38
D850V4, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  T1              1                8
  T2              1               66
  T3             11              238
  T4              3               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
  GPR126 MUTATED    14   2   0
  GPR126 WILD-TYPE 206  79  66
D850V5, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  N0             14              206
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V6, binary
                  cls
clus                 0   1
  GPR126 MUTATED    15   1
  GPR126 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     15    1
  GPR126 WILD-TYPE  270   47
   clus
vv  GPR126 MUTATED GPR126 WILD-TYPE
  0             15              270
  1              1               47
[1] 2 2
[1] FALSE
D850V7, binary
                  cls
clus                 0   1
  GPR126 MUTATED    10   6
  GPR126 WILD-TYPE 160 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     10    6
  GPR126 WILD-TYPE  160  191
        clus
vv       GPR126 MUTATED GPR126 WILD-TYPE
  FEMALE             10              160
  MALE                6              191
[1] 2 2
[1] FALSE
D850V8, binary
                  cls
clus                 0   1
  GPR126 MUTATED    14   0
  GPR126 WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     14    0
  GPR126 WILD-TYPE  286    8
     clus
vv    GPR126 MUTATED GPR126 WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D850V9, binary
                  cls
clus                 0   1
  GPR126 MUTATED    13   3
  GPR126 WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     13    3
  GPR126 WILD-TYPE  301   45
                               clus
vv                              GPR126 MUTATED GPR126 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR126 MUTATED    13   0   0   1
  GPR126 WILD-TYPE 246   3  22  20
D850V10, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              1               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"
D850V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR126 MUTATED                                  0     1
  GPR126 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR126 MUTATED                           1     6
  GPR126 WILD-TYPE                        18   170
D850V12, multiclass
                                  clus
vv                                 GPR126 MUTATED GPR126 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = DDX17 MUTATION ANALYSIS
D851V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     3   5
  DDX17 WILD-TYPE 274  73
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             347 
  DDX17 MUTATED DDX17 WILD-TYPE 
              5              73 
$`DDX17 MUTATED`
TCGA-G4-6628 TCGA-A6-2676 TCGA-AA-3852 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-6598 
       79.69        42.90         0.00         4.01        83.24        49.41 
TCGA-CM-4746 TCGA-CM-6674 
       37.02        12.95 

$`DDX17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DDX17 MUTATED DDX17 WILD-TYPE 
              0               0 
  DDX17 MUTATED DDX17 WILD-TYPE 
          83.24          148.01 
  DDX17 MUTATED DDX17 WILD-TYPE 
          39.96           22.03 
[1] "0.0 - 83.2 (40.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D851V2, continuous
                 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      62        1       25       105         6         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  DDX17 MUTATED           0
  DDX17 WILD-TYPE         1
D851V3, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DDX17 MUTATED     0   2   4   2
  DDX17 WILD-TYPE   9  65 245  39
D851V4, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             2              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
  DDX17 MUTATED     8   0   0
  DDX17 WILD-TYPE 212  81  66
D851V5, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V6, binary
                 cls
clus                0   1
  DDX17 MUTATED     7   0
  DDX17 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      7    0
  DDX17 WILD-TYPE  278   48
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D851V7, binary
                 cls
clus                0   1
  DDX17 MUTATED     2   6
  DDX17 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      2    6
  DDX17 WILD-TYPE  168  191
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D851V8, binary
                 cls
clus                0   1
  DDX17 MUTATED     6   0
  DDX17 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      6    0
  DDX17 WILD-TYPE  294    8
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D851V9, binary
                 cls
clus                0   1
  DDX17 MUTATED     6   2
  DDX17 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      6    2
  DDX17 WILD-TYPE  308   46
                               clus
vv                              DDX17 MUTATED DDX17 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX17 MUTATED     7   0   0   0
  DDX17 WILD-TYPE 252   3  22  21
D851V10, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D851V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX17 MUTATED                                  0     1
  DDX17 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED                           1     4
  DDX17 WILD-TYPE                        18   172
D851V12, multiclass
                                  clus
vv                                 DDX17 MUTATED DDX17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = TOP2A MUTATION ANALYSIS
D852V1, survival
                 sevent
clus2               0   1
  TOP2A MUTATED    14   2
  TOP2A WILD-TYPE 263  76
  TOP2A MUTATED TOP2A WILD-TYPE 
             16             339 
  TOP2A MUTATED TOP2A WILD-TYPE 
              2              76 
$`TOP2A MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3697 TCGA-AD-6895 TCGA-A6-5665 TCGA-AA-3510 
        1.02         0.92        85.05        25.08        22.06        63.98 
TCGA-AA-3663 TCGA-AD-6890 TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-6718 TCGA-CK-5913 
        6.97        24.53        27.09        17.82        10.06        51.32 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6539 TCGA-F4-6570 
       14.04        13.05        12.49         6.18 

$`TOP2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TOP2A MUTATED TOP2A WILD-TYPE 
           0.92            0.00 
  TOP2A MUTATED TOP2A WILD-TYPE 
          85.05          148.01 
  TOP2A MUTATED TOP2A WILD-TYPE 
          15.93           22.09 
[1] "0.9 - 85.0 (15.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D852V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOP2A MUTATED         2        0        4         5         0         0
  TOP2A WILD-TYPE      62        1       22       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOP2A MUTATED           1          0          2          0        0         0
  TOP2A WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  TOP2A MUTATED           1
  TOP2A WILD-TYPE         0
D852V3, multiclass
            clus
vv           TOP2A MUTATED TOP2A WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              12
  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     1   2  14   0
  TOP2A WILD-TYPE   8  65 235  41
D852V4, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  T1             1               8
  T2             2              65
  T3            14             235
  T4             0              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
  TOP2A MUTATED    13   3   1
  TOP2A WILD-TYPE 207  78  65
D852V5, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  N0            13             207
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V6, binary
                 cls
clus                0   1
  TOP2A MUTATED    14   1
  TOP2A WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     14    1
  TOP2A WILD-TYPE  271   47
   clus
vv  TOP2A MUTATED TOP2A WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D852V7, binary
                 cls
clus                0   1
  TOP2A MUTATED    10   7
  TOP2A WILD-TYPE 160 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     10    7
  TOP2A WILD-TYPE  160  190
        clus
vv       TOP2A MUTATED TOP2A WILD-TYPE
  FEMALE            10             160
  MALE               7             190
[1] 2 2
[1] FALSE
D852V8, binary
                 cls
clus                0   1
  TOP2A MUTATED    14   0
  TOP2A WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     14    0
  TOP2A WILD-TYPE  286    8
     clus
vv    TOP2A MUTATED TOP2A WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D852V9, binary
                 cls
clus                0   1
  TOP2A MUTATED    17   0
  TOP2A WILD-TYPE 297  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     17    0
  TOP2A WILD-TYPE  297   48
                               clus
vv                              TOP2A MUTATED TOP2A WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TOP2A MUTATED    14   0   0   2
  TOP2A WILD-TYPE 245   3  22  19
D852V10, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D852V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOP2A MUTATED                                  0     1
  TOP2A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TOP2A MUTATED                           2     8
  TOP2A WILD-TYPE                        17   168
D852V12, multiclass
                                  clus
vv                                 TOP2A MUTATED TOP2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = CACNG3 MUTATION ANALYSIS
D853V1, survival
                  sevent
clus2                0   1
  CACNG3 MUTATED     6   2
  CACNG3 WILD-TYPE 271  76
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              347 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               2               76 
$`CACNG3 MUTATED`
TCGA-AA-3672 TCGA-A6-3808 TCGA-AA-3492 TCGA-AA-3833 TCGA-AA-A010 TCGA-AA-A01D 
        0.92        33.34         3.02        15.95        34.98        10.98 
TCGA-CA-6717 TCGA-CM-4746 
       12.76        37.02 

$`CACNG3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        34.65        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01F TCGA-AA-A01G 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CACNG3 MUTATED CACNG3 WILD-TYPE 
            0.92             0.00 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
           37.02           148.01 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
          14.355           22.090 
[1] "0.9 - 37.0 (14.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D853V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CACNG3 MUTATED         1        0        1         3         1         0
  CACNG3 WILD-TYPE      63        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNG3 MUTATED           1          0          0          1        0
  CACNG3 WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  CACNG3 MUTATED           0         0
  CACNG3 WILD-TYPE        12         1
D853V3, multiclass
            clus
vv           CACNG3 MUTATED CACNG3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  CACNG3 MUTATED     0   1   6   1
  CACNG3 WILD-TYPE   9  66 243  40
D853V4, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              6              243
  T4              1               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
  CACNG3 MUTATED     6   1   1
  CACNG3 WILD-TYPE 214  80  65
D853V5, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D853V6, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     8   0
  CACNG3 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      8    0
  CACNG3 WILD-TYPE  277   48
   clus
vv  CACNG3 MUTATED CACNG3 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D853V7, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     5   3
  CACNG3 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      5    3
  CACNG3 WILD-TYPE  165  194
        clus
vv       CACNG3 MUTATED CACNG3 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D853V8, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     8   0
  CACNG3 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      8    0
  CACNG3 WILD-TYPE  292    8
     clus
vv    CACNG3 MUTATED CACNG3 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D853V9, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     6   2
  CACNG3 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      6    2
  CACNG3 WILD-TYPE  308   46
                               clus
vv                              CACNG3 MUTATED CACNG3 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CACNG3 MUTATED     7   0   0   1
  CACNG3 WILD-TYPE 252   3  22  20
D853V10, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D853V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNG3 MUTATED                                  0     1
  CACNG3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CACNG3 MUTATED                           1     1
  CACNG3 WILD-TYPE                        18   175
D853V12, multiclass
                                  clus
vv                                 CACNG3 MUTATED CACNG3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         1              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(854) Variable = CBX3 MUTATION ANALYSIS
D854V1, survival
                sevent
clus2              0   1
  CBX3 MUTATED     5   1
  CBX3 WILD-TYPE 272  77
  CBX3 MUTATED CBX3 WILD-TYPE 
             6            349 
  CBX3 MUTATED CBX3 WILD-TYPE 
             1             77 
$`CBX3 MUTATED`
TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3977 TCGA-AD-6889 
       24.00        35.80        33.53        20.12        25.02        83.24 

$`CBX3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CBX3 MUTATED CBX3 WILD-TYPE 
         20.12           0.00 
  CBX3 MUTATED CBX3 WILD-TYPE 
         83.24         148.01 
  CBX3 MUTATED CBX3 WILD-TYPE 
        29.275         21.990 
[1] "20.1 - 83.2 (29.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D854V2, continuous
                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      64        1       26       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBX3 MUTATED           0          0          0          0        0         0
  CBX3 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  CBX3 MUTATED           0
  CBX3 WILD-TYPE         1
D854V3, multiclass
            clus
vv           CBX3 MUTATED CBX3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CBX3 MUTATED     0   1   5   0
  CBX3 WILD-TYPE   9  66 244  41
D854V4, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            0             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
  CBX3 MUTATED     6   0   0
  CBX3 WILD-TYPE 214  81  66
D854V5, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V6, binary
                cls
clus               0   1
  CBX3 MUTATED     4   0
  CBX3 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      4    0
  CBX3 WILD-TYPE  281   48
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D854V7, binary
                cls
clus               0   1
  CBX3 MUTATED     3   3
  CBX3 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      3    3
  CBX3 WILD-TYPE  167  194
        clus
vv       CBX3 MUTATED CBX3 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D854V8, binary
                cls
clus               0   1
  CBX3 MUTATED     6   0
  CBX3 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      6    0
  CBX3 WILD-TYPE  294    8
     clus
vv    CBX3 MUTATED CBX3 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D854V9, binary
                cls
clus               0   1
  CBX3 MUTATED     4   2
  CBX3 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      4    2
  CBX3 WILD-TYPE  310   46
                               clus
vv                              CBX3 MUTATED CBX3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CBX3 MUTATED     4   0   0   0
  CBX3 WILD-TYPE 255   3  22  21
D854V10, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D854V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBX3 MUTATED                                  0     1
  CBX3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CBX3 MUTATED                           1     2
  CBX3 WILD-TYPE                        18   174
D854V12, multiclass
                                  clus
vv                                 CBX3 MUTATED CBX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(855) Variable = DLL3 MUTATION ANALYSIS
D855V1, survival
                sevent
clus2              0   1
  DLL3 MUTATED     5   1
  DLL3 WILD-TYPE 272  77
  DLL3 MUTATED DLL3 WILD-TYPE 
             6            349 
  DLL3 MUTATED DLL3 WILD-TYPE 
             1             77 
$`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 

$`DLL3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DLL3 MUTATED DLL3 WILD-TYPE 
          9.44           0.00 
  DLL3 MUTATED DLL3 WILD-TYPE 
         49.41         148.01 
  DLL3 MUTATED DLL3 WILD-TYPE 
         28.70          22.03 
[1] "9.4 - 49.4 (28.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D855V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLL3 MUTATED         1        0        1         1         2         0
  DLL3 WILD-TYPE      63        1       25       107         6         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  DLL3 MUTATED           0
  DLL3 WILD-TYPE         1
D855V3, multiclass
            clus
vv           DLL3 MUTATED DLL3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  DLL3 MUTATED     0   1   3   2
  DLL3 WILD-TYPE   9  66 246  39
D855V4, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            2             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
  DLL3 MUTATED     5   1   0
  DLL3 WILD-TYPE 215  80  66
D855V5, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V6, binary
                cls
clus               0   1
  DLL3 MUTATED     5   0
  DLL3 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      5    0
  DLL3 WILD-TYPE  280   48
   clus
vv  DLL3 MUTATED DLL3 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D855V7, binary
                cls
clus               0   1
  DLL3 MUTATED     4   2
  DLL3 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      4    2
  DLL3 WILD-TYPE  166  195
        clus
vv       DLL3 MUTATED DLL3 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D855V8, binary
                cls
clus               0   1
  DLL3 MUTATED     6   0
  DLL3 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      6    0
  DLL3 WILD-TYPE  294    8
     clus
vv    DLL3 MUTATED DLL3 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D855V9, binary
                cls
clus               0   1
  DLL3 MUTATED     4   2
  DLL3 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      4    2
  DLL3 WILD-TYPE  310   46
                               clus
vv                              DLL3 MUTATED DLL3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DLL3 MUTATED     4   0   0   0
  DLL3 WILD-TYPE 255   3  22  21
D855V10, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D855V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLL3 MUTATED                                  0     0
  DLL3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLL3 MUTATED                           0     4
  DLL3 WILD-TYPE                        19   172
D855V12, multiclass
                                  clus
vv                                 DLL3 MUTATED DLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = KIFAP3 MUTATION ANALYSIS
D856V1, survival
                  sevent
clus2                0   1
  KIFAP3 MUTATED     8   0
  KIFAP3 WILD-TYPE 269  78
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               8              347 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               0               78 
$`KIFAP3 MUTATED`
TCGA-AA-3713 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A00A TCGA-AU-6004 TCGA-CA-6717 
       19.04         6.97        33.04        38.04        27.09        12.76 
TCGA-CM-4746 TCGA-D5-6540 
       37.02        16.14 

$`KIFAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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           22.060 
[1] "7.0 - 38.0 (23.1)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D856V2, continuous
                  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      61        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIFAP3 MUTATED           0          0          0          0        1
  KIFAP3 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  KIFAP3 MUTATED           0         0
  KIFAP3 WILD-TYPE        12         1
D856V3, multiclass
            clus
vv           KIFAP3 MUTATED KIFAP3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  KIFAP3 MUTATED     0   3   5   1
  KIFAP3 WILD-TYPE   9  64 244  40
D856V4, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              1               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
  KIFAP3 MUTATED     9   0   0
  KIFAP3 WILD-TYPE 211  81  66
D856V5, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V6, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     8   1
  KIFAP3 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      8    1
  KIFAP3 WILD-TYPE  277   47
   clus
vv  KIFAP3 MUTATED KIFAP3 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D856V7, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     3   6
  KIFAP3 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      3    6
  KIFAP3 WILD-TYPE  167  191
        clus
vv       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D856V8, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     6   1
  KIFAP3 WILD-TYPE 294   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      6    1
  KIFAP3 WILD-TYPE  294    7
     clus
vv    KIFAP3 MUTATED KIFAP3 WILD-TYPE
  NO               6              294
  YES              1                7
[1] 2 2
[1] FALSE
D856V9, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     7   2
  KIFAP3 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      7    2
  KIFAP3 WILD-TYPE  307   46
                               clus
vv                              KIFAP3 MUTATED KIFAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIFAP3 MUTATED     7   0   1   1
  KIFAP3 WILD-TYPE 252   3  21  20
D856V10, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              1               21
  RX              1               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"
D856V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIFAP3 MUTATED                                  0     1
  KIFAP3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIFAP3 MUTATED                           1     2
  KIFAP3 WILD-TYPE                        18   174
D856V12, multiclass
                                  clus
vv                                 KIFAP3 MUTATED KIFAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(857) Variable = CRYGA MUTATION ANALYSIS
D857V1, survival
                 sevent
clus2               0   1
  CRYGA MUTATED     4   1
  CRYGA WILD-TYPE 273  77
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             350 
  CRYGA MUTATED CRYGA WILD-TYPE 
              1              77 
$`CRYGA MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6653 TCGA-A6-6780 TCGA-AZ-6598 
       35.80        26.17        24.39        20.12        49.41 

$`CRYGA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CRYGA MUTATED CRYGA WILD-TYPE 
          20.12            0.00 
  CRYGA MUTATED CRYGA WILD-TYPE 
          49.41          148.01 
  CRYGA MUTATED CRYGA WILD-TYPE 
          26.17           22.01 
[1] "20.1 - 49.4 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D857V2, continuous
                 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      63        1       25       105         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  CRYGA MUTATED           0
  CRYGA WILD-TYPE         1
D857V3, multiclass
            clus
vv           CRYGA MUTATED CRYGA WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CRYGA MUTATED     0   1   4   0
  CRYGA WILD-TYPE   9  66 245  41
D857V4, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             0              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
  CRYGA MUTATED     5   0   0
  CRYGA WILD-TYPE 215  81  66
D857V5, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V6, binary
                 cls
clus                0   1
  CRYGA MUTATED     3   0
  CRYGA WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      3    0
  CRYGA WILD-TYPE  282   48
   clus
vv  CRYGA MUTATED CRYGA WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D857V7, binary
                 cls
clus                0   1
  CRYGA MUTATED     3   2
  CRYGA WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      3    2
  CRYGA WILD-TYPE  167  195
        clus
vv       CRYGA MUTATED CRYGA WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D857V8, binary
                 cls
clus                0   1
  CRYGA MUTATED     5   0
  CRYGA WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      5    0
  CRYGA WILD-TYPE  295    8
     clus
vv    CRYGA MUTATED CRYGA WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D857V9, binary
                 cls
clus                0   1
  CRYGA MUTATED     4   1
  CRYGA WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      4    1
  CRYGA WILD-TYPE  310   47
                               clus
vv                              CRYGA MUTATED CRYGA WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CRYGA MUTATED     2   0   0   0
  CRYGA WILD-TYPE 257   3  22  21
D857V10, multiclass
[1] "Remove cluster labels:" "CRYGA MUTATED"         
clus
  CRYGA MUTATED CRYGA WILD-TYPE 
              2             303 
     TCGA-A6-2677      TCGA-AA-3496      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-3527 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AD-6895      TCGA-AZ-4681      TCGA-CK-5912      TCGA-G4-6310 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-3810      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5661 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-5665      TCGA-A6-6781      TCGA-AA-3489      TCGA-AA-3492 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3526 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3542      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3561 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3663      TCGA-AA-3664 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3673      TCGA-AA-3678 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3811      TCGA-AA-3812 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861      TCGA-AA-3864 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872      TCGA-AA-3875 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3941      TCGA-AA-3947 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3949      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-3973      TCGA-AA-3975      TCGA-AA-3984 
"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-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A010 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A029 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6965 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AZ-4315      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-5913 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6315 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
D857V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRYGA MUTATED                                  0     0
  CRYGA WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CRYGA MUTATED                           0     5
  CRYGA WILD-TYPE                        19   171
D857V12, multiclass
                                  clus
vv                                 CRYGA MUTATED CRYGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = MCF2 MUTATION ANALYSIS
D858V1, survival
                sevent
clus2              0   1
  MCF2 MUTATED    25   3
  MCF2 WILD-TYPE 252  75
  MCF2 MUTATED MCF2 WILD-TYPE 
            28            327 
  MCF2 MUTATED MCF2 WILD-TYPE 
             3             75 
$`MCF2 MUTATED`
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-G4-6586 TCGA-G4-6588 
        6.05         0.92        85.05        19.04        35.80        26.17 
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3663 
       22.06        24.39        63.98        26.01        29.95         6.97 
TCGA-AA-3930 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
        2.01        21.99        25.02        18.05         4.01        34.98 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6534 
       58.39        88.21        12.69        12.76        10.06        43.27 
TCGA-D5-6541 TCGA-D5-7000 TCGA-DM-A28E TCGA-G4-6304 
       15.58        10.26       119.93        53.62 

$`MCF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       13.02        17.95        23.01        19.99        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        63.62        22.09        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03         2.01        16.08        13.05        34.06        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-A28C TCGA-DM-A28F 
       44.32       131.51       135.65       139.17        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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MCF2 MUTATED MCF2 WILD-TYPE 
          0.92           0.00 
  MCF2 MUTATED MCF2 WILD-TYPE 
        119.93         148.01 
  MCF2 MUTATED MCF2 WILD-TYPE 
        23.225         22.030 
[1] "0.9 - 119.9 (23.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D858V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCF2 MUTATED         5        0        3        11         3         0
  MCF2 WILD-TYPE      59        1       23        97         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCF2 MUTATED           1          0          1          0        3         0
  MCF2 WILD-TYPE        17          6         43         33       32        12
                vv
clus             STAGE IVB
  MCF2 MUTATED           0
  MCF2 WILD-TYPE         1
D858V3, multiclass
            clus
vv           MCF2 MUTATED MCF2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            11             97
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              3             32
  STAGE IVA             0             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
  MCF2 MUTATED     1   5  17   5
  MCF2 WILD-TYPE   8  62 232  36
D858V4, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  T1            1              8
  T2            5             62
  T3           17            232
  T4            5             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
  MCF2 MUTATED    24   2   2
  MCF2 WILD-TYPE 196  79  64
D858V5, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  N0           24            196
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V6, binary
                cls
clus               0   1
  MCF2 MUTATED    24   3
  MCF2 WILD-TYPE 261  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     24    3
  MCF2 WILD-TYPE  261   45
   clus
vv  MCF2 MUTATED MCF2 WILD-TYPE
  0           24            261
  1            3             45
[1] 2 2
[1] FALSE
D858V7, binary
                cls
clus               0   1
  MCF2 MUTATED    15  13
  MCF2 WILD-TYPE 155 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     15   13
  MCF2 WILD-TYPE  155  184
        clus
vv       MCF2 MUTATED MCF2 WILD-TYPE
  FEMALE           15            155
  MALE             13            184
[1] 2 2
[1] FALSE
D858V8, binary
                cls
clus               0   1
  MCF2 MUTATED    25   1
  MCF2 WILD-TYPE 275   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     25    1
  MCF2 WILD-TYPE  275    7
     clus
vv    MCF2 MUTATED MCF2 WILD-TYPE
  NO            25            275
  YES            1              7
[1] 2 2
[1] FALSE
D858V9, binary
                cls
clus               0   1
  MCF2 MUTATED    22   6
  MCF2 WILD-TYPE 292  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     22    6
  MCF2 WILD-TYPE  292   42
                               clus
vv                              MCF2 MUTATED MCF2 WILD-TYPE
  COLON ADENOCARCINOMA                    22            292
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MCF2 MUTATED    18   0   3   3
  MCF2 WILD-TYPE 241   3  19  18
D858V10, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  R0           18            241
  R1            0              3
  R2            3             19
  RX            3             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"
D858V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCF2 MUTATED                                  0     3
  MCF2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCF2 MUTATED                           0    11
  MCF2 WILD-TYPE                        19   165
D858V12, multiclass
                                  clus
vv                                 MCF2 MUTATED MCF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      11            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(859) Variable = USP16 MUTATION ANALYSIS
D859V1, survival
                 sevent
clus2               0   1
  USP16 MUTATED     5   2
  USP16 WILD-TYPE 272  76
  USP16 MUTATED USP16 WILD-TYPE 
              7             348 
  USP16 MUTATED USP16 WILD-TYPE 
              2              76 
$`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 
       54.61 

$`USP16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  USP16 MUTATED USP16 WILD-TYPE 
           4.01            0.00 
  USP16 MUTATED USP16 WILD-TYPE 
          54.61          148.01 
  USP16 MUTATED USP16 WILD-TYPE 
          31.00           21.99 
[1] "4.0 - 54.6 (31.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D859V2, continuous
                 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      62        1       25       106         7         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        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  USP16 MUTATED           0
  USP16 WILD-TYPE         1
D859V3, multiclass
            clus
vv           USP16 MUTATED USP16 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  USP16 MUTATED     1   1   5   1
  USP16 WILD-TYPE   8  66 244  40
D859V4, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             5             244
  T4             1              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
  USP16 MUTATED     6   2   0
  USP16 WILD-TYPE 214  79  66
D859V5, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V6, binary
                 cls
clus                0   1
  USP16 MUTATED     6   1
  USP16 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      6    1
  USP16 WILD-TYPE  279   47
   clus
vv  USP16 MUTATED USP16 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D859V7, binary
                 cls
clus                0   1
  USP16 MUTATED     7   1
  USP16 WILD-TYPE 163 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      7    1
  USP16 WILD-TYPE  163  196
        clus
vv       USP16 MUTATED USP16 WILD-TYPE
  FEMALE             7             163
  MALE               1             196
[1] 2 2
[1] FALSE
D859V8, binary
                 cls
clus                0   1
  USP16 MUTATED     5   0
  USP16 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      5    0
  USP16 WILD-TYPE  295    8
     clus
vv    USP16 MUTATED USP16 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D859V9, binary
                 cls
clus                0   1
  USP16 MUTATED     6   2
  USP16 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      6    2
  USP16 WILD-TYPE  308   46
                               clus
vv                              USP16 MUTATED USP16 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP16 MUTATED     7   0   0   1
  USP16 WILD-TYPE 252   3  22  20
D859V10, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D859V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP16 MUTATED                                  0     0
  USP16 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP16 MUTATED                           1     3
  USP16 WILD-TYPE                        18   173
D859V12, multiclass
                                  clus
vv                                 USP16 MUTATED USP16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = ASPM MUTATION ANALYSIS
D860V1, survival
                sevent
clus2              0   1
  ASPM MUTATED    33   8
  ASPM WILD-TYPE 244  70
  ASPM MUTATED ASPM WILD-TYPE 
            41            314 
  ASPM MUTATED ASPM WILD-TYPE 
             8             70 
$`ASPM MUTATED`
TCGA-AA-3543 TCGA-AA-A00Z TCGA-AD-6895 TCGA-DM-A285 TCGA-G4-6588 TCGA-G4-6628 
        0.99        21.99        25.08         5.88        26.17        79.69 
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3555 
       22.06        24.39        20.12        19.66        63.98        29.95 
TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00J 
       10.06        53.00        33.01        25.02        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6901 TCGA-AZ-4315 
        4.01        42.02        34.98        83.24        22.42        58.39 
TCGA-AZ-4323 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-5916 TCGA-CK-6748 
        1.41        12.59        12.20        12.76        21.14         2.01 
TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6540 TCGA-D5-6926 TCGA-D5-6928 
       15.02        14.04        11.01        16.14         9.04        11.64 
TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6703 TCGA-F4-6856 
       13.41       135.65        81.37        47.87        35.31 

$`ASPM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       50.99        26.01        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 
       49.08        63.62        22.09        35.80        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        27.02        27.02 
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-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       18.05        27.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.36        12.39        12.59        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.99        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-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       12.39        10.13        12.43        14.30         9.44        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F 
        7.50        44.32       131.51       139.17       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ASPM MUTATED ASPM WILD-TYPE 
          0.99           0.00 
  ASPM MUTATED ASPM WILD-TYPE 
        135.65         148.01 
  ASPM MUTATED ASPM WILD-TYPE 
         21.99          22.09 
[1] "1.0 - 135.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D860V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASPM MUTATED         8        0        2        14         3         0
  ASPM WILD-TYPE      56        1       24        94         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASPM MUTATED           1          0          6          1        4         1
  ASPM WILD-TYPE        17          6         38         32       31        11
                vv
clus             STAGE IVB
  ASPM MUTATED           0
  ASPM WILD-TYPE         1
D860V3, multiclass
            clus
vv           ASPM MUTATED ASPM WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            14             94
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            6             38
  STAGE IIIC            1             32
  STAGE IV              4             31
  STAGE IVA             1             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
  ASPM MUTATED     1   8  24   9
  ASPM WILD-TYPE   8  59 225  32
D860V4, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  T1            1              8
  T2            8             59
  T3           24            225
  T4            9             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
  ASPM MUTATED    29  10   3
  ASPM WILD-TYPE 191  71  63
D860V5, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  N0           29            191
  N1           10             71
  N2            3             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"
D860V6, binary
                cls
clus               0   1
  ASPM MUTATED    33   5
  ASPM WILD-TYPE 252  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     33    5
  ASPM WILD-TYPE  252   43
   clus
vv  ASPM MUTATED ASPM WILD-TYPE
  0           33            252
  1            5             43
[1] 2 2
[1] FALSE
D860V7, binary
                cls
clus               0   1
  ASPM MUTATED    15  27
  ASPM WILD-TYPE 155 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     15   27
  ASPM WILD-TYPE  155  170
        clus
vv       ASPM MUTATED ASPM WILD-TYPE
  FEMALE           15            155
  MALE             27            170
[1] 2 2
[1] FALSE
D860V8, binary
                cls
clus               0   1
  ASPM MUTATED    36   1
  ASPM WILD-TYPE 264   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     36    1
  ASPM WILD-TYPE  264    7
     clus
vv    ASPM MUTATED ASPM WILD-TYPE
  NO            36            264
  YES            1              7
[1] 2 2
[1] FALSE
D860V9, binary
                cls
clus               0   1
  ASPM MUTATED    28  13
  ASPM WILD-TYPE 286  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     28   13
  ASPM WILD-TYPE  286   35
                               clus
vv                              ASPM MUTATED ASPM WILD-TYPE
  COLON ADENOCARCINOMA                    28            286
  COLON MUCINOUS ADENOCARCINOMA           13             35
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ASPM MUTATED    29   0   0   5
  ASPM WILD-TYPE 230   3  22  16
D860V10, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  R0           29            230
  R1            0              3
  R2            0             22
  RX            5             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"
D860V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASPM MUTATED                                  0     4
  ASPM WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ASPM MUTATED                           0    24
  ASPM WILD-TYPE                        19   152
D860V12, multiclass
                                  clus
vv                                 ASPM MUTATED ASPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      24            152
[1] 4 2
[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 = MACC1 MUTATION ANALYSIS
D861V1, survival
                 sevent
clus2               0   1
  MACC1 MUTATED    12   5
  MACC1 WILD-TYPE 265  73
  MACC1 MUTATED MACC1 WILD-TYPE 
             17             338 
  MACC1 MUTATED MACC1 WILD-TYPE 
              5              73 
$`MACC1 MUTATED`
TCGA-AA-3516 TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3977 
       13.02         3.02         1.02        38.99         0.00        25.02 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-6196 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CK-5914 
       34.98         1.02         0.20        49.41        51.32        21.99 
TCGA-CM-6167 TCGA-CM-6675 TCGA-D5-6535 TCGA-D5-6928 TCGA-DM-A0XF 
       14.99        13.05        15.12        11.64        38.20 

$`MACC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3842 
       33.04         0.99        25.02        17.98        15.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MACC1 MUTATED MACC1 WILD-TYPE 
              0               0 
  MACC1 MUTATED MACC1 WILD-TYPE 
          51.32          148.01 
  MACC1 MUTATED MACC1 WILD-TYPE 
         14.990          22.225 
[1] "0.0 - 51.3 (15.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.9"
D861V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MACC1 MUTATED         1        0        4         4         1         0
  MACC1 WILD-TYPE      63        1       22       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MACC1 MUTATED           1          0          2          3        0         0
  MACC1 WILD-TYPE        17          6         42         30       35        12
                 vv
clus              STAGE IVB
  MACC1 MUTATED           1
  MACC1 WILD-TYPE         0
D861V3, multiclass
            clus
vv           MACC1 MUTATED MACC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              12
  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
  MACC1 MUTATED     0   2  14   2
  MACC1 WILD-TYPE   9  65 235  39
D861V4, multiclass
    clus
vv   MACC1 MUTATED MACC1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            14             235
  T4             2              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
  MACC1 MUTATED    11   2   5
  MACC1 WILD-TYPE 209  79  61
D861V5, multiclass
    clus
vv   MACC1 MUTATED MACC1 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D861V6, binary
                 cls
clus                0   1
  MACC1 MUTATED    11   1
  MACC1 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACC1 MUTATED     11    1
  MACC1 WILD-TYPE  274   47
   clus
vv  MACC1 MUTATED MACC1 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D861V7, binary
                 cls
clus                0   1
  MACC1 MUTATED    12   6
  MACC1 WILD-TYPE 158 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACC1 MUTATED     12    6
  MACC1 WILD-TYPE  158  191
        clus
vv       MACC1 MUTATED MACC1 WILD-TYPE
  FEMALE            12             158
  MALE               6             191
[1] 2 2
[1] FALSE
D861V8, binary
                 cls
clus                0   1
  MACC1 MUTATED    12   0
  MACC1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACC1 MUTATED     12    0
  MACC1 WILD-TYPE  288    8
     clus
vv    MACC1 MUTATED MACC1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D861V9, binary
                 cls
clus                0   1
  MACC1 MUTATED    12   5
  MACC1 WILD-TYPE 302  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACC1 MUTATED     12    5
  MACC1 WILD-TYPE  302   43
                               clus
vv                              MACC1 MUTATED MACC1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MACC1 MUTATED    11   0   0   3
  MACC1 WILD-TYPE 248   3  22  18
D861V10, multiclass
    clus
vv   MACC1 MUTATED MACC1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             3              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"
D861V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MACC1 MUTATED                                  0     0
  MACC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MACC1 MUTATED                           2     7
  MACC1 WILD-TYPE                        17   169
D861V12, multiclass
                                  clus
vv                                 MACC1 MUTATED MACC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        7             169
[1] 4 2
[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 = YLPM1 MUTATION ANALYSIS
D862V1, survival
                 sevent
clus2               0   1
  YLPM1 MUTATED    17   4
  YLPM1 WILD-TYPE 260  74
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             21             334 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              4              74 
$`YLPM1 MUTATED`
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3972 TCGA-G4-6586 TCGA-A6-6781 TCGA-AA-3510 
       36.00        19.04        50.99        35.80        19.66        63.98 
TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-A010 TCGA-AA-A01P 
        6.97        33.04         0.99         1.02        34.98        38.07 
TCGA-AY-6386 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 
       17.82        12.76        51.32        21.14        23.05        15.02 
TCGA-CM-6171 TCGA-D5-6540 TCGA-G4-6309 
       14.04        16.14        85.48 

$`YLPM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 
       24.03        29.98        12.99        24.00         2.01        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       35.05        25.02        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-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        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-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-6718 
       12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  YLPM1 MUTATED YLPM1 WILD-TYPE 
           0.99            0.00 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
          85.48          148.01 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
         21.140          22.075 
[1] "1.0 - 85.5 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D862V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YLPM1 MUTATED         4        0        2         8         1         0
  YLPM1 WILD-TYPE      60        1       24       100         7         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        17          6         42         32       32        12
                 vv
clus              STAGE IVB
  YLPM1 MUTATED           0
  YLPM1 WILD-TYPE         1
D862V3, multiclass
            clus
vv           YLPM1 MUTATED YLPM1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              0              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
  YLPM1 MUTATED     1   3  16   2
  YLPM1 WILD-TYPE   8  64 233  39
D862V4, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            16             233
  T4             2              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
  YLPM1 MUTATED    16   5   1
  YLPM1 WILD-TYPE 204  76  65
D862V5, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  N0            16             204
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V6, binary
                 cls
clus                0   1
  YLPM1 MUTATED    17   3
  YLPM1 WILD-TYPE 268  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     17    3
  YLPM1 WILD-TYPE  268   45
   clus
vv  YLPM1 MUTATED YLPM1 WILD-TYPE
  0            17             268
  1             3              45
[1] 2 2
[1] FALSE
D862V7, binary
                 cls
clus                0   1
  YLPM1 MUTATED    14   8
  YLPM1 WILD-TYPE 156 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     14    8
  YLPM1 WILD-TYPE  156  189
        clus
vv       YLPM1 MUTATED YLPM1 WILD-TYPE
  FEMALE            14             156
  MALE               8             189
[1] 2 2
[1] FALSE
D862V8, binary
                 cls
clus                0   1
  YLPM1 MUTATED    18   2
  YLPM1 WILD-TYPE 282   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     18    2
  YLPM1 WILD-TYPE  282    6
     clus
vv    YLPM1 MUTATED YLPM1 WILD-TYPE
  NO             18             282
  YES             2               6
[1] 2 2
[1] FALSE
D862V9, binary
                 cls
clus                0   1
  YLPM1 MUTATED    17   5
  YLPM1 WILD-TYPE 297  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     17    5
  YLPM1 WILD-TYPE  297   43
                               clus
vv                              YLPM1 MUTATED YLPM1 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  YLPM1 MUTATED    16   0   3   3
  YLPM1 WILD-TYPE 243   3  19  18
D862V10, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             3              19
  RX             3              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"
D862V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YLPM1 MUTATED                                  0     1
  YLPM1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YLPM1 MUTATED                           2     8
  YLPM1 WILD-TYPE                        17   168
D862V12, multiclass
                                  clus
vv                                 YLPM1 MUTATED YLPM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = MIA3 MUTATION ANALYSIS
D863V1, survival
                sevent
clus2              0   1
  MIA3 MUTATED    13   4
  MIA3 WILD-TYPE 264  74
  MIA3 MUTATED MIA3 WILD-TYPE 
            17            338 
  MIA3 MUTATED MIA3 WILD-TYPE 
             4             74 
$`MIA3 MUTATED`
TCGA-G4-6586 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-3968 
       35.80        24.39        63.98        32.05         2.01        21.99 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       25.02         4.01        34.98        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5861 TCGA-DM-A0X9 TCGA-G4-6309 
       10.06        21.14        15.02       119.70        85.48 

$`MIA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MIA3 MUTATED MIA3 WILD-TYPE 
          2.01           0.00 
  MIA3 MUTATED MIA3 WILD-TYPE 
        119.70         148.01 
  MIA3 MUTATED MIA3 WILD-TYPE 
         25.02          22.01 
[1] "2.0 - 119.7 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D863V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIA3 MUTATED         5        0        2         8         2         0
  MIA3 WILD-TYPE      59        1       24       100         6         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  MIA3 MUTATED           0
  MIA3 WILD-TYPE         1
D863V3, multiclass
            clus
vv           MIA3 MUTATED MIA3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MIA3 MUTATED     1   5  11   2
  MIA3 WILD-TYPE   8  62 238  39
D863V4, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  T1            1              8
  T2            5             62
  T3           11            238
  T4            2             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
  MIA3 MUTATED    18   1   0
  MIA3 WILD-TYPE 202  80  66
D863V5, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  N0           18            202
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V6, binary
                cls
clus               0   1
  MIA3 MUTATED    16   0
  MIA3 WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     16    0
  MIA3 WILD-TYPE  269   48
   clus
vv  MIA3 MUTATED MIA3 WILD-TYPE
  0           16            269
  1            0             48
[1] 2 2
[1] FALSE
D863V7, binary
                cls
clus               0   1
  MIA3 MUTATED    10   9
  MIA3 WILD-TYPE 160 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     10    9
  MIA3 WILD-TYPE  160  188
        clus
vv       MIA3 MUTATED MIA3 WILD-TYPE
  FEMALE           10            160
  MALE              9            188
[1] 2 2
[1] FALSE
D863V8, binary
                cls
clus               0   1
  MIA3 MUTATED    14   0
  MIA3 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     14    0
  MIA3 WILD-TYPE  286    8
     clus
vv    MIA3 MUTATED MIA3 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D863V9, binary
                cls
clus               0   1
  MIA3 MUTATED    16   3
  MIA3 WILD-TYPE 298  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     16    3
  MIA3 WILD-TYPE  298   45
                               clus
vv                              MIA3 MUTATED MIA3 WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MIA3 MUTATED    10   0   0   4
  MIA3 WILD-TYPE 249   3  22  17
D863V10, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            4             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"
D863V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIA3 MUTATED                                  0     2
  MIA3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MIA3 MUTATED                           1     8
  MIA3 WILD-TYPE                        18   168
D863V12, multiclass
                                  clus
vv                                 MIA3 MUTATED MIA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = SLC7A6 MUTATION ANALYSIS
D864V1, survival
                  sevent
clus2                0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 271  78
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               6              349 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               0               78 
$`SLC7A6 MUTATED`
TCGA-AA-3660 TCGA-AZ-5407 TCGA-CA-5797 TCGA-CM-6680 TCGA-DM-A1HB TCGA-F4-6855 
       78.08        88.21        12.59        12.03       135.65        47.41 

$`SLC7A6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
           12.03             0.00 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
          135.65           148.01 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
          62.745           22.030 
[1] "12.0 - 135.7 (62.7)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D864V2, continuous
                  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      63        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A6 MUTATED           0          0          2          0        0
  SLC7A6 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC7A6 MUTATED           0         0
  SLC7A6 WILD-TYPE        12         1
D864V3, multiclass
            clus
vv           SLC7A6 MUTATED SLC7A6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SLC7A6 MUTATED     1   0   5   0
  SLC7A6 WILD-TYPE   8  67 244  41
D864V4, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              5              244
  T4              0               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
  SLC7A6 MUTATED     4   1   1
  SLC7A6 WILD-TYPE 216  80  65
D864V5, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V6, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      6    0
  SLC7A6 WILD-TYPE  279   48
   clus
vv  SLC7A6 MUTATED SLC7A6 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D864V7, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     4   2
  SLC7A6 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      4    2
  SLC7A6 WILD-TYPE  166  195
        clus
vv       SLC7A6 MUTATED SLC7A6 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D864V8, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     5   0
  SLC7A6 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      5    0
  SLC7A6 WILD-TYPE  295    8
     clus
vv    SLC7A6 MUTATED SLC7A6 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D864V9, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     5   0
  SLC7A6 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      5    0
  SLC7A6 WILD-TYPE  309   48
                               clus
vv                              SLC7A6 MUTATED SLC7A6 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC7A6 MUTATED     4   0   0   0
  SLC7A6 WILD-TYPE 255   3  22  21
D864V10, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D864V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC7A6 MUTATED                                  0     1
  SLC7A6 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC7A6 MUTATED                           0     4
  SLC7A6 WILD-TYPE                        19   172
D864V12, multiclass
                                  clus
vv                                 SLC7A6 MUTATED SLC7A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = TGFBR2 MUTATION ANALYSIS
D865V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    16   5
  TGFBR2 WILD-TYPE 261  73
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              21              334 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               5               73 
$`TGFBR2 MUTATED`
TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-3808 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3514 
       10.88        26.17        33.34         8.38         3.02         1.02 
TCGA-AA-3968 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A03F 
       21.99        34.98         1.02        35.01        51.98        18.05 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-5540 TCGA-D5-6931 
       15.62        23.05        15.02        12.95        56.09        12.00 
TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6303 
      135.65        31.96        65.85 

$`TGFBR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       38.07         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.075 
[1] "1.0 - 135.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D865V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGFBR2 MUTATED         3        0        3         6         1         0
  TGFBR2 WILD-TYPE      61        1       23       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR2 MUTATED           2          0          2          2        1
  TGFBR2 WILD-TYPE        16          6         42         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TGFBR2 MUTATED           0         0
  TGFBR2 WILD-TYPE        12         1
D865V3, multiclass
            clus
vv           TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  TGFBR2 MUTATED     0   3  14   4
  TGFBR2 WILD-TYPE   9  64 235  37
D865V4, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             14              235
  T4              4               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
  TGFBR2 MUTATED    13   3   5
  TGFBR2 WILD-TYPE 207  78  61
D865V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0             13              207
  N1              3               78
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    19   1
  TGFBR2 WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     19    1
  TGFBR2 WILD-TYPE  266   47
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D865V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    11  10
  TGFBR2 WILD-TYPE 159 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     11   10
  TGFBR2 WILD-TYPE  159  187
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE             11              159
  MALE               10              187
[1] 2 2
[1] FALSE
D865V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    17   1
  TGFBR2 WILD-TYPE 283   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     17    1
  TGFBR2 WILD-TYPE  283    7
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO              17              283
  YES              1                7
[1] 2 2
[1] FALSE
D865V9, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    17   3
  TGFBR2 WILD-TYPE 297  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     17    3
  TGFBR2 WILD-TYPE  297   45
                               clus
vv                              TGFBR2 MUTATED TGFBR2 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TGFBR2 MUTATED    17   0   0   1
  TGFBR2 WILD-TYPE 242   3  22  20
D865V10, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              0               22
  RX              1               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"
D865V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR2 MUTATED                                  0     0
  TGFBR2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED                           1    12
  TGFBR2 WILD-TYPE                        18   164
D865V12, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = RAB42 MUTATION ANALYSIS
D866V1, survival
                 sevent
clus2               0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 274  78
  RAB42 MUTATED RAB42 WILD-TYPE 
              3             352 
  RAB42 MUTATED RAB42 WILD-TYPE 
              0              78 
$`RAB42 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-G4-6304 
       19.66         6.97        53.62 

$`RAB42 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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          22.075 
[1] "7.0 - 53.6 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D866V2, continuous
                 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      64        1       24       108         7         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  RAB42 MUTATED           0
  RAB42 WILD-TYPE         1
D866V3, multiclass
            clus
vv           RAB42 MUTATED RAB42 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              0             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RAB42 MUTATED     0   0   1   3
  RAB42 WILD-TYPE   9  67 248  38
D866V4, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             1             248
  T4             3              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
  RAB42 MUTATED     3   1   0
  RAB42 WILD-TYPE 217  80  66
D866V5, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V6, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    0
  RAB42 WILD-TYPE  282   48
   clus
vv  RAB42 MUTATED RAB42 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D866V7, binary
                 cls
clus                0   1
  RAB42 MUTATED     2   2
  RAB42 WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      2    2
  RAB42 WILD-TYPE  168  195
        clus
vv       RAB42 MUTATED RAB42 WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D866V8, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    0
  RAB42 WILD-TYPE  297    8
     clus
vv    RAB42 MUTATED RAB42 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D866V9, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   1
  RAB42 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    1
  RAB42 WILD-TYPE  311   47
                               clus
vv                              RAB42 MUTATED RAB42 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RAB42 MUTATED     4   0   0   0
  RAB42 WILD-TYPE 255   3  22  21
D866V10, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D866V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB42 MUTATED                                  0     0
  RAB42 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB42 MUTATED                           0     2
  RAB42 WILD-TYPE                        19   174
D866V12, multiclass
[1] "Remove cluster labels:" "RAB42 MUTATED"         
clus
  RAB42 MUTATED RAB42 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6782 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"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-5913      TCGA-CK-5914      TCGA-CK-5915 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 

Clustering(867) Variable = PIK3C3 MUTATION ANALYSIS
D867V1, survival
                  sevent
clus2                0   1
  PIK3C3 MUTATED    17   5
  PIK3C3 WILD-TYPE 260  73
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              22              333 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
               5               73 
$`PIK3C3 MUTATED`
TCGA-AA-3554 TCGA-AD-6888 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3492 
       17.95        15.52       100.01        35.80        22.06         3.02 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A00J TCGA-AD-6889 TCGA-AU-6004 
       29.95        78.08        53.00        18.05        83.24        27.09 
TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-6748 TCGA-CM-4752 TCGA-CM-6168 TCGA-D5-6533 
       21.44        12.76         2.01        13.02        12.99        25.48 
TCGA-D5-6536 TCGA-D5-6540 TCGA-F4-6703 TCGA-G4-6626 
       17.85        16.14        47.87        46.75 

$`PIK3C3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       24.00        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       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        14.04        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        54.61        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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
            2.01             0.00 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
          100.01           148.01 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
           21.75            22.09 
[1] "2.0 - 100.0 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D867V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C3 MUTATED         2        0        5        12         0         0
  PIK3C3 WILD-TYPE      62        1       21        96         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C3 MUTATED           0          0          2          0        1
  PIK3C3 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PIK3C3 MUTATED           0         0
  PIK3C3 WILD-TYPE        12         1
D867V3, multiclass
            clus
vv           PIK3C3 MUTATED PIK3C3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA              12               96
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  PIK3C3 MUTATED     0   2  18   3
  PIK3C3 WILD-TYPE   9  65 231  38
D867V4, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             18              231
  T4              3               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
  PIK3C3 MUTATED    20   3   0
  PIK3C3 WILD-TYPE 200  78  66
D867V5, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  N0             20              200
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V6, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    21   1
  PIK3C3 WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     21    1
  PIK3C3 WILD-TYPE  264   47
   clus
vv  PIK3C3 MUTATED PIK3C3 WILD-TYPE
  0             21              264
  1              1               47
[1] 2 2
[1] FALSE
D867V7, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    11  12
  PIK3C3 WILD-TYPE 159 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     11   12
  PIK3C3 WILD-TYPE  159  185
        clus
vv       PIK3C3 MUTATED PIK3C3 WILD-TYPE
  FEMALE             11              159
  MALE               12              185
[1] 2 2
[1] FALSE
D867V8, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    21   0
  PIK3C3 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     21    0
  PIK3C3 WILD-TYPE  279    8
     clus
vv    PIK3C3 MUTATED PIK3C3 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D867V9, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    18   5
  PIK3C3 WILD-TYPE 296  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     18    5
  PIK3C3 WILD-TYPE  296   43
                               clus
vv                              PIK3C3 MUTATED PIK3C3 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3C3 MUTATED    20   0   0   2
  PIK3C3 WILD-TYPE 239   3  22  19
D867V10, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  R0             20              239
  R1              0                3
  R2              0               22
  RX              2               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"
D867V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C3 MUTATED                                  0     2
  PIK3C3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3C3 MUTATED                           2    12
  PIK3C3 WILD-TYPE                        17   164
D867V12, multiclass
                                  clus
vv                                 PIK3C3 MUTATED PIK3C3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        12              164
[1] 4 2
[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 = FAM189B MUTATION ANALYSIS
D868V1, survival
                   sevent
clus2                 0   1
  FAM189B MUTATED    10   1
  FAM189B WILD-TYPE 267  77
  FAM189B MUTATED FAM189B WILD-TYPE 
               11               344 
  FAM189B MUTATED FAM189B WILD-TYPE 
                1                77 
$`FAM189B MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-A6-5657 TCGA-AA-3663 TCGA-AA-A00E TCGA-AA-A00J 
        0.92        25.08        31.63         6.97        30.02        18.05 
TCGA-AY-6196 TCGA-AZ-6598 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB 
        0.20        49.41        16.14        13.35       135.65 

$`FAM189B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        88.21         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FAM189B MUTATED FAM189B WILD-TYPE 
              0.2               0.0 
  FAM189B MUTATED FAM189B WILD-TYPE 
           135.65            148.01 
  FAM189B MUTATED FAM189B WILD-TYPE 
           18.050            22.075 
[1] "0.2 - 135.7 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D868V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM189B MUTATED         1        0        2         2         0         0
  FAM189B WILD-TYPE      63        1       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM189B MUTATED           1          0          4          1        0
  FAM189B WILD-TYPE        17          6         40         32       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM189B MUTATED           0         0
  FAM189B WILD-TYPE        12         1
D868V3, multiclass
            clus
vv           FAM189B MUTATED FAM189B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM189B MUTATED     0   1   9   1
  FAM189B WILD-TYPE   9  66 240  40
D868V4, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               9               240
  T4               1                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
  FAM189B MUTATED     5   5   1
  FAM189B WILD-TYPE 215  76  65
D868V5, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  N0               5               215
  N1               5                76
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V6, binary
                   cls
clus                  0   1
  FAM189B MUTATED     9   0
  FAM189B WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      9    0
  FAM189B WILD-TYPE  276   48
   clus
vv  FAM189B MUTATED FAM189B WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D868V7, binary
                   cls
clus                  0   1
  FAM189B MUTATED     2   9
  FAM189B WILD-TYPE 168 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      2    9
  FAM189B WILD-TYPE  168  188
        clus
vv       FAM189B MUTATED FAM189B WILD-TYPE
  FEMALE               2               168
  MALE                 9               188
[1] 2 2
[1] FALSE
D868V8, binary
                   cls
clus                  0   1
  FAM189B MUTATED     9   0
  FAM189B WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      9    0
  FAM189B WILD-TYPE  291    8
     clus
vv    FAM189B MUTATED FAM189B WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D868V9, binary
                   cls
clus                  0   1
  FAM189B MUTATED     6   4
  FAM189B WILD-TYPE 308  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      6    4
  FAM189B WILD-TYPE  308   44
                               clus
vv                              FAM189B MUTATED FAM189B WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM189B MUTATED     9   0   0   0
  FAM189B WILD-TYPE 250   3  22  21
D868V10, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               0                22
  RX               0                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"
D868V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM189B MUTATED                                  0     0
  FAM189B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM189B MUTATED                           1     6
  FAM189B WILD-TYPE                        18   170
D868V12, multiclass
                                  clus
vv                                 FAM189B MUTATED FAM189B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[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 = SLC24A2 MUTATION ANALYSIS
D869V1, survival
                   sevent
clus2                 0   1
  SLC24A2 MUTATED    11   6
  SLC24A2 WILD-TYPE 266  72
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               17               338 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
                6                72 
$`SLC24A2 MUTATED`
TCGA-AA-3713 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00A 
       19.04        20.12         3.02        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 
       16.14        13.35        13.32       140.38        44.32 

$`SLC24A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        19.66        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        12.59         7.50       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
             3.02              0.00 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
           140.38            148.01 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
           20.120            22.075 
[1] "3.0 - 140.4 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D869V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC24A2 MUTATED         1        0        1         9         2         0
  SLC24A2 WILD-TYPE      63        1       25        99         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC24A2 MUTATED           0          0          0          1        1
  SLC24A2 WILD-TYPE        18          6         44         32       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC24A2 MUTATED           0         0
  SLC24A2 WILD-TYPE        12         1
D869V3, multiclass
            clus
vv           SLC24A2 MUTATED SLC24A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                9                99
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC24A2 MUTATED     0   3  12   2
  SLC24A2 WILD-TYPE   9  64 237  39
D869V4, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              12               237
  T4               2                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
  SLC24A2 MUTATED    15   1   1
  SLC24A2 WILD-TYPE 205  80  65
D869V5, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  N0              15               205
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V6, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    13   1
  SLC24A2 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     13    1
  SLC24A2 WILD-TYPE  272   47
   clus
vv  SLC24A2 MUTATED SLC24A2 WILD-TYPE
  0              13               272
  1               1                47
[1] 2 2
[1] FALSE
D869V7, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED     6  11
  SLC24A2 WILD-TYPE 164 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED      6   11
  SLC24A2 WILD-TYPE  164  186
        clus
vv       SLC24A2 MUTATED SLC24A2 WILD-TYPE
  FEMALE               6               164
  MALE                11               186
[1] 2 2
[1] FALSE
D869V8, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    13   1
  SLC24A2 WILD-TYPE 287   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     13    1
  SLC24A2 WILD-TYPE  287    7
     clus
vv    SLC24A2 MUTATED SLC24A2 WILD-TYPE
  NO               13               287
  YES               1                 7
[1] 2 2
[1] FALSE
D869V9, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    11   5
  SLC24A2 WILD-TYPE 303  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     11    5
  SLC24A2 WILD-TYPE  303   43
                               clus
vv                              SLC24A2 MUTATED SLC24A2 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC24A2 MUTATED     7   1   1   2
  SLC24A2 WILD-TYPE 252   2  21  19
D869V10, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  R0               7               252
  R1               1                 2
  R2               1                21
  RX               2                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"
D869V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC24A2 MUTATED                                  0     2
  SLC24A2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC24A2 MUTATED                           1     8
  SLC24A2 WILD-TYPE                        18   168
D869V12, multiclass
                                  clus
vv                                 SLC24A2 MUTATED SLC24A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          8               168
[1] 4 2
[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 = YES1 MUTATION ANALYSIS
D870V1, survival
                sevent
clus2              0   1
  YES1 MUTATED     5   4
  YES1 WILD-TYPE 272  74
  YES1 MUTATED YES1 WILD-TYPE 
             9            346 
  YES1 MUTATED YES1 WILD-TYPE 
             4             74 
$`YES1 MUTATED`
TCGA-AZ-6601 TCGA-AA-3663 TCGA-AA-3819 TCGA-AU-3779 TCGA-AZ-6599 TCGA-CA-6718 
      100.01         6.97        25.02        14.50         6.77        10.06 
TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6809 
       11.64       135.65        13.25 

$`YES1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  YES1 MUTATED YES1 WILD-TYPE 
          6.77           0.00 
  YES1 MUTATED YES1 WILD-TYPE 
        135.65         148.01 
  YES1 MUTATED YES1 WILD-TYPE 
         13.25          22.09 
[1] "6.8 - 135.7 (13.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D870V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YES1 MUTATED         1        0        2         4         0         0
  YES1 WILD-TYPE      63        1       24       104         8         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        18          6         43         33       35        11
                vv
clus             STAGE IVB
  YES1 MUTATED           0
  YES1 WILD-TYPE         1
D870V3, multiclass
            clus
vv           YES1 MUTATED YES1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  YES1 MUTATED     0   1   8   0
  YES1 WILD-TYPE   9  66 241  41
D870V4, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            0             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
  YES1 MUTATED     7   2   0
  YES1 WILD-TYPE 213  79  66
D870V5, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  N0            7            213
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V6, binary
                cls
clus               0   1
  YES1 MUTATED     7   1
  YES1 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      7    1
  YES1 WILD-TYPE  278   47
   clus
vv  YES1 MUTATED YES1 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D870V7, binary
                cls
clus               0   1
  YES1 MUTATED     3   6
  YES1 WILD-TYPE 167 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      3    6
  YES1 WILD-TYPE  167  191
        clus
vv       YES1 MUTATED YES1 WILD-TYPE
  FEMALE            3            167
  MALE              6            191
[1] 2 2
[1] FALSE
D870V8, binary
                cls
clus               0   1
  YES1 MUTATED     8   0
  YES1 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      8    0
  YES1 WILD-TYPE  292    8
     clus
vv    YES1 MUTATED YES1 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D870V9, binary
                cls
clus               0   1
  YES1 MUTATED     7   1
  YES1 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      7    1
  YES1 WILD-TYPE  307   47
                               clus
vv                              YES1 MUTATED YES1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  YES1 MUTATED     5   0   0   1
  YES1 WILD-TYPE 254   3  22  20
D870V10, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D870V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YES1 MUTATED                                  0     1
  YES1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  YES1 MUTATED                           0     6
  YES1 WILD-TYPE                        19   170
D870V12, multiclass
                                  clus
vv                                 YES1 MUTATED YES1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = KIAA0649 MUTATION ANALYSIS
D871V1, survival
                    sevent
clus2                  0   1
  KIAA0649 MUTATED     7   3
  KIAA0649 WILD-TYPE 270  75
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                345 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                 3                 75 
$`KIAA0649 MUTATED`
TCGA-AA-3672 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3818 
        0.92        26.17        22.06         3.02         6.97         0.99 
TCGA-AD-5900 TCGA-CK-5913 TCGA-CM-5348 TCGA-F4-6570 
       12.16        51.32        22.98         6.18 

$`KIAA0649 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05        33.04        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
              0.92               0.00 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             51.32             148.01 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             9.565             22.090 
[1] "0.9 - 51.3 (9.6)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D871V2, continuous
                    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      63        1       24       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0649 MUTATED           1          0          1          0        0
  KIAA0649 WILD-TYPE        17          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0649 MUTATED           0         0
  KIAA0649 WILD-TYPE        12         1
D871V3, multiclass
            clus
vv           KIAA0649 MUTATED KIAA0649 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 5                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA0649 MUTATED     0   1   9   0
  KIAA0649 WILD-TYPE   9  66 240  41
D871V4, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                9                240
  T4                0                 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
  KIAA0649 MUTATED     8   2   0
  KIAA0649 WILD-TYPE 212  79  66
D871V5, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  N0                8                212
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V6, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     8   0
  KIAA0649 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      8    0
  KIAA0649 WILD-TYPE  277   48
   clus
vv  KIAA0649 MUTATED KIAA0649 WILD-TYPE
  0                8                277
  1                0                 48
[1] 2 2
[1] FALSE
D871V7, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     7   3
  KIAA0649 WILD-TYPE 163 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      7    3
  KIAA0649 WILD-TYPE  163  194
        clus
vv       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  FEMALE                7                163
  MALE                  3                194
[1] 2 2
[1] FALSE
D871V8, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     9   0
  KIAA0649 WILD-TYPE 291   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      9    0
  KIAA0649 WILD-TYPE  291    8
     clus
vv    KIAA0649 MUTATED KIAA0649 WILD-TYPE
  NO                 9                291
  YES                0                  8
[1] 2 2
[1] FALSE
D871V9, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     9   1
  KIAA0649 WILD-TYPE 305  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      9    1
  KIAA0649 WILD-TYPE  305   47
                               clus
vv                              KIAA0649 MUTATED KIAA0649 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0649 MUTATED     9   0   0   1
  KIAA0649 WILD-TYPE 250   3  22  20
D871V10, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D871V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0649 MUTATED                                  0     0
  KIAA0649 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0649 MUTATED                           0     6
  KIAA0649 WILD-TYPE                        19   170
D871V12, multiclass
                                  clus
vv                                 KIAA0649 MUTATED KIAA0649 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = TCEAL5 MUTATION ANALYSIS
D872V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED     3   2
  TCEAL5 WILD-TYPE 274  76
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              350 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               2               76 
$`TCEAL5 MUTATED`
TCGA-A6-6138 TCGA-AA-A01P TCGA-AD-6889 TCGA-CM-6162 TCGA-G4-6306 
       22.52        38.07        83.24        12.00        44.68 

$`TCEAL5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              12                0 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           83.24           148.01 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           38.07            22.01 
[1] "12.0 - 83.2 (38.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D872V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCEAL5 MUTATED         1        0        0         1         0         0
  TCEAL5 WILD-TYPE      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCEAL5 MUTATED           1          0          1          0        0
  TCEAL5 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TCEAL5 MUTATED           0         0
  TCEAL5 WILD-TYPE        12         1
D872V3, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TCEAL5 MUTATED     0   2   3   0
  TCEAL5 WILD-TYPE   9  65 246  41
D872V4, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              3              246
  T4              0               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
  TCEAL5 MUTATED     3   2   0
  TCEAL5 WILD-TYPE 217  79  66
D872V5, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0              3              217
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V6, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     5   0
  TCEAL5 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      5    0
  TCEAL5 WILD-TYPE  280   48
   clus
vv  TCEAL5 MUTATED TCEAL5 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D872V7, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     2   3
  TCEAL5 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      2    3
  TCEAL5 WILD-TYPE  168  194
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D872V8, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     5   0
  TCEAL5 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      5    0
  TCEAL5 WILD-TYPE  295    8
     clus
vv    TCEAL5 MUTATED TCEAL5 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D872V9, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     4   1
  TCEAL5 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      4    1
  TCEAL5 WILD-TYPE  310   47
                               clus
vv                              TCEAL5 MUTATED TCEAL5 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     4   0   0   0
  TCEAL5 WILD-TYPE 255   3  22  21
D872V10, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D872V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEAL5 MUTATED                                  0     1
  TCEAL5 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL5 MUTATED                           0     3
  TCEAL5 WILD-TYPE                        19   173
D872V12, multiclass
                                  clus
vv                                 TCEAL5 MUTATED TCEAL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = PIK3R4 MUTATION ANALYSIS
D873V1, survival
                  sevent
clus2                0   1
  PIK3R4 MUTATED    11   4
  PIK3R4 WILD-TYPE 266  74
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              15              340 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
               4               74 
$`PIK3R4 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5660 TCGA-AA-3555 TCGA-AA-3851 
       19.04        26.17        42.90        29.19        29.95        33.07 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6965 TCGA-AZ-6598 
       38.04         4.01        34.98         1.02        26.47        49.41 
TCGA-CA-5255 TCGA-CM-5861 TCGA-F4-6459 
       12.36        15.02         8.61 

$`PIK3R4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
            1.02             0.00 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
           49.41           148.01 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
           26.47            22.01 
[1] "1.0 - 49.4 (26.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D873V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3R4 MUTATED         0        0        2         7         3         0
  PIK3R4 WILD-TYPE      64        1       24       101         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R4 MUTATED           0          0          1          2        1
  PIK3R4 WILD-TYPE        18          6         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PIK3R4 MUTATED           0         0
  PIK3R4 WILD-TYPE        12         1
D873V3, multiclass
            clus
vv           PIK3R4 MUTATED PIK3R4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  PIK3R4 MUTATED     0   0  12   4
  PIK3R4 WILD-TYPE   9  67 237  37
D873V4, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             12              237
  T4              4               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
  PIK3R4 MUTATED    13   0   3
  PIK3R4 WILD-TYPE 207  81  63
D873V5, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  N0             13              207
  N1              0               81
  N2              3               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"
D873V6, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    14   1
  PIK3R4 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     14    1
  PIK3R4 WILD-TYPE  271   47
   clus
vv  PIK3R4 MUTATED PIK3R4 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D873V7, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED     9   7
  PIK3R4 WILD-TYPE 161 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED      9    7
  PIK3R4 WILD-TYPE  161  190
        clus
vv       PIK3R4 MUTATED PIK3R4 WILD-TYPE
  FEMALE              9              161
  MALE                7              190
[1] 2 2
[1] FALSE
D873V8, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    11   2
  PIK3R4 WILD-TYPE 289   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     11    2
  PIK3R4 WILD-TYPE  289    6
     clus
vv    PIK3R4 MUTATED PIK3R4 WILD-TYPE
  NO              11              289
  YES              2                6
[1] 2 2
[1] FALSE
D873V9, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    14   2
  PIK3R4 WILD-TYPE 300  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     14    2
  PIK3R4 WILD-TYPE  300   46
                               clus
vv                              PIK3R4 MUTATED PIK3R4 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R4 MUTATED    11   1   1   1
  PIK3R4 WILD-TYPE 248   2  21  20
D873V10, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  R0             11              248
  R1              1                2
  R2              1               21
  RX              1               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"
D873V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R4 MUTATED                                  0     1
  PIK3R4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R4 MUTATED                           1     6
  PIK3R4 WILD-TYPE                        18   170
D873V12, multiclass
                                  clus
vv                                 PIK3R4 MUTATED PIK3R4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = MTF1 MUTATION ANALYSIS
D874V1, survival
                sevent
clus2              0   1
  MTF1 MUTATED     8   0
  MTF1 WILD-TYPE 269  78
  MTF1 MUTATED MTF1 WILD-TYPE 
             8            347 
  MTF1 MUTATED MTF1 WILD-TYPE 
             0             78 
$`MTF1 MUTATED`
TCGA-AD-6895 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-A00J TCGA-CA-6717 TCGA-CM-5861 
       25.08        24.00        33.01        18.05        12.76        15.02 
TCGA-D5-6536 TCGA-D5-6541 
       17.85        15.58 

$`MTF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00         2.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MTF1 MUTATED MTF1 WILD-TYPE 
         12.76           0.00 
  MTF1 MUTATED MTF1 WILD-TYPE 
         33.01         148.01 
  MTF1 MUTATED MTF1 WILD-TYPE 
         17.95          22.09 
[1] "12.8 - 33.0 (18.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D874V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTF1 MUTATED         0        0        0         5         1         0
  MTF1 WILD-TYPE      64        1       26       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTF1 MUTATED           0          0          2          0        0         1
  MTF1 WILD-TYPE        18          6         42         33       35        11
                vv
clus             STAGE IVB
  MTF1 MUTATED           0
  MTF1 WILD-TYPE         1
D874V3, multiclass
            clus
vv           MTF1 MUTATED MTF1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  MTF1 MUTATED     0   0   6   3
  MTF1 WILD-TYPE   9  67 243  38
D874V4, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            3             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
  MTF1 MUTATED     6   3   0
  MTF1 WILD-TYPE 214  78  66
D874V5, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  N0            6            214
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V6, binary
                cls
clus               0   1
  MTF1 MUTATED     8   1
  MTF1 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      8    1
  MTF1 WILD-TYPE  277   47
   clus
vv  MTF1 MUTATED MTF1 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D874V7, binary
                cls
clus               0   1
  MTF1 MUTATED     4   5
  MTF1 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      4    5
  MTF1 WILD-TYPE  166  192
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D874V8, binary
                cls
clus               0   1
  MTF1 MUTATED     8   0
  MTF1 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      8    0
  MTF1 WILD-TYPE  292    8
     clus
vv    MTF1 MUTATED MTF1 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D874V9, binary
                cls
clus               0   1
  MTF1 MUTATED     6   3
  MTF1 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      6    3
  MTF1 WILD-TYPE  308   45
                               clus
vv                              MTF1 MUTATED MTF1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTF1 MUTATED     8   0   0   1
  MTF1 WILD-TYPE 251   3  22  20
D874V10, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D874V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTF1 MUTATED                                  0     1
  MTF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTF1 MUTATED                           0     4
  MTF1 WILD-TYPE                        19   172
D874V12, multiclass
                                  clus
vv                                 MTF1 MUTATED MTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = GAPVD1 MUTATION ANALYSIS
D875V1, survival
                  sevent
clus2                0   1
  GAPVD1 MUTATED    16   6
  GAPVD1 WILD-TYPE 261  72
  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
              22              333 
  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
               6               72 
$`GAPVD1 MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AZ-6601 TCGA-G4-6310 TCGA-G4-6588 TCGA-A6-5664 
        1.02        13.02       100.01        63.62        26.17        22.09 
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-3956 
        8.38        20.12         3.02        78.08        33.04        34.03 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-5403 TCGA-CM-6168 
       34.98        83.24         0.20        21.44        62.79        12.99 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-G4-6626 
        9.44        11.64        13.35        46.75 

$`GAPVD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        22.09        35.80        91.79        79.69 
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-A6-5656 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-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        19.66        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
             0.2              0.0 
  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
          100.01           148.01 
  GAPVD1 MUTATED GAPVD1 WILD-TYPE 
          21.765           22.060 
[1] "0.2 - 100.0 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D875V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAPVD1 MUTATED         0        0        5        12         1         0
  GAPVD1 WILD-TYPE      64        1       21        96         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GAPVD1 MUTATED           1          0          1          2        0
  GAPVD1 WILD-TYPE        17          6         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GAPVD1 MUTATED           0         0
  GAPVD1 WILD-TYPE        12         1
D875V3, multiclass
            clus
vv           GAPVD1 MUTATED GAPVD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA              12               96
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  GAPVD1 MUTATED     0   0  20   2
  GAPVD1 WILD-TYPE   9  67 229  39
D875V4, multiclass
    clus
vv   GAPVD1 MUTATED GAPVD1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             20              229
  T4              2               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
  GAPVD1 MUTATED    18   1   3
  GAPVD1 WILD-TYPE 202  80  63
D875V5, multiclass
    clus
vv   GAPVD1 MUTATED GAPVD1 WILD-TYPE
  N0             18              202
  N1              1               80
  N2              3               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"
D875V6, binary
                  cls
clus                 0   1
  GAPVD1 MUTATED    17   0
  GAPVD1 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPVD1 MUTATED     17    0
  GAPVD1 WILD-TYPE  268   48
   clus
vv  GAPVD1 MUTATED GAPVD1 WILD-TYPE
  0             17              268
  1              0               48
[1] 2 2
[1] FALSE
D875V7, binary
                  cls
clus                 0   1
  GAPVD1 MUTATED     8  14
  GAPVD1 WILD-TYPE 162 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPVD1 MUTATED      8   14
  GAPVD1 WILD-TYPE  162  183
        clus
vv       GAPVD1 MUTATED GAPVD1 WILD-TYPE
  FEMALE              8              162
  MALE               14              183
[1] 2 2
[1] FALSE
D875V8, binary
                  cls
clus                 0   1
  GAPVD1 MUTATED    19   1
  GAPVD1 WILD-TYPE 281   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPVD1 MUTATED     19    1
  GAPVD1 WILD-TYPE  281    7
     clus
vv    GAPVD1 MUTATED GAPVD1 WILD-TYPE
  NO              19              281
  YES              1                7
[1] 2 2
[1] FALSE
D875V9, binary
                  cls
clus                 0   1
  GAPVD1 MUTATED    17   5
  GAPVD1 WILD-TYPE 297  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPVD1 MUTATED     17    5
  GAPVD1 WILD-TYPE  297   43
                               clus
vv                              GAPVD1 MUTATED GAPVD1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GAPVD1 MUTATED    16   0   0   0
  GAPVD1 WILD-TYPE 243   3  22  21
D875V10, multiclass
    clus
vv   GAPVD1 MUTATED GAPVD1 WILD-TYPE
  R0             16              243
  R1              0                3
  R2              0               22
  RX              0               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"
D875V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAPVD1 MUTATED                                  0     1
  GAPVD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAPVD1 MUTATED                           3    11
  GAPVD1 WILD-TYPE                        16   165
D875V12, multiclass
                                  clus
vv                                 GAPVD1 MUTATED GAPVD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        11              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(876) Variable = CCDC3 MUTATION ANALYSIS
D876V1, survival
                 sevent
clus2               0   1
  CCDC3 MUTATED     2   2
  CCDC3 WILD-TYPE 275  76
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              4             351 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              2              76 
$`CCDC3 MUTATED`
TCGA-AA-3713 TCGA-CM-5862 TCGA-CM-6678 TCGA-D5-6537 
       19.04         5.03        11.01         4.80 

$`CCDC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CCDC3 MUTATED CCDC3 WILD-TYPE 
            4.8             0.0 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
          19.04          148.01 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
           8.02           22.09 
[1] "4.8 - 19.0 (8.0)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "5.5"
D876V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC3 MUTATED         0        0        0         0         0         0
  CCDC3 WILD-TYPE      64        1       26       108         8         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        18          6         43         33       34        10
                 vv
clus              STAGE IVB
  CCDC3 MUTATED           0
  CCDC3 WILD-TYPE         1
D876V3, multiclass
            clus
vv           CCDC3 MUTATED CCDC3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              2              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
  CCDC3 MUTATED     0   0   3   1
  CCDC3 WILD-TYPE   9  67 246  40
D876V4, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             1              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
  CCDC3 MUTATED     1   3   0
  CCDC3 WILD-TYPE 219  78  66
D876V5, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  N0             1             219
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V6, binary
                 cls
clus                0   1
  CCDC3 MUTATED     0   3
  CCDC3 WILD-TYPE 285  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      0    3
  CCDC3 WILD-TYPE  285   45
   clus
vv  CCDC3 MUTATED CCDC3 WILD-TYPE
  0             0             285
  1             3              45
[1] 2 2
[1] FALSE
D876V7, binary
                 cls
clus                0   1
  CCDC3 MUTATED     1   3
  CCDC3 WILD-TYPE 169 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      1    3
  CCDC3 WILD-TYPE  169  194
        clus
vv       CCDC3 MUTATED CCDC3 WILD-TYPE
  FEMALE             1             169
  MALE               3             194
[1] 2 2
[1] FALSE
D876V8, binary
                 cls
clus                0   1
  CCDC3 MUTATED     3   1
  CCDC3 WILD-TYPE 297   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      3    1
  CCDC3 WILD-TYPE  297    7
     clus
vv    CCDC3 MUTATED CCDC3 WILD-TYPE
  NO              3             297
  YES             1               7
[1] 2 2
[1] FALSE
D876V9, binary
                 cls
clus                0   1
  CCDC3 MUTATED     4   0
  CCDC3 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      4    0
  CCDC3 WILD-TYPE  310   48
                               clus
vv                              CCDC3 MUTATED CCDC3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCDC3 MUTATED     3   0   1   0
  CCDC3 WILD-TYPE 256   3  21  21
D876V10, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             1              21
  RX             0              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"
D876V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC3 MUTATED                                  0     0
  CCDC3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCDC3 MUTATED                           0     3
  CCDC3 WILD-TYPE                        19   173
D876V12, multiclass
                                  clus
vv                                 CCDC3 MUTATED CCDC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = SERPINA9 MUTATION ANALYSIS
D877V1, survival
                    sevent
clus2                  0   1
  SERPINA9 MUTATED     6   3
  SERPINA9 WILD-TYPE 271  75
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                 9                346 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                 3                 75 
$`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 
       22.98        13.05        12.43 

$`SERPINA9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
             10.06               0.00 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
             49.41             148.01 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
            22.420             22.025 
[1] "10.1 - 49.4 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D877V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SERPINA9 MUTATED         1        0        1         2         0         0
  SERPINA9 WILD-TYPE      63        1       25       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINA9 MUTATED           1          0          3          0        0
  SERPINA9 WILD-TYPE        17          6         41         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINA9 MUTATED           0         1
  SERPINA9 WILD-TYPE        12         0
D877V3, multiclass
            clus
vv           SERPINA9 MUTATED SERPINA9 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 12
  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   1   9   0
  SERPINA9 WILD-TYPE   9  66 240  41
D877V4, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                9                240
  T4                0                 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
  SERPINA9 MUTATED     5   3   2
  SERPINA9 WILD-TYPE 215  78  64
D877V5, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  N0                5                215
  N1                3                 78
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V6, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED     7   1
  SERPINA9 WILD-TYPE 278  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED      7    1
  SERPINA9 WILD-TYPE  278   47
   clus
vv  SERPINA9 MUTATED SERPINA9 WILD-TYPE
  0                7                278
  1                1                 47
[1] 2 2
[1] FALSE
D877V7, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED     2   8
  SERPINA9 WILD-TYPE 168 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED      2    8
  SERPINA9 WILD-TYPE  168  189
        clus
vv       SERPINA9 MUTATED SERPINA9 WILD-TYPE
  FEMALE                2                168
  MALE                  8                189
[1] 2 2
[1] FALSE
D877V8, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED     9   0
  SERPINA9 WILD-TYPE 291   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED      9    0
  SERPINA9 WILD-TYPE  291    8
     clus
vv    SERPINA9 MUTATED SERPINA9 WILD-TYPE
  NO                 9                291
  YES                0                  8
[1] 2 2
[1] FALSE
D877V9, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED    10   0
  SERPINA9 WILD-TYPE 304  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED     10    0
  SERPINA9 WILD-TYPE  304   48
                               clus
vv                              SERPINA9 MUTATED SERPINA9 WILD-TYPE
  COLON ADENOCARCINOMA                        10                304
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SERPINA9 MUTATED     7   0   0   1
  SERPINA9 WILD-TYPE 252   3  22  20
D877V10, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D877V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINA9 MUTATED                                  0     1
  SERPINA9 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SERPINA9 MUTATED                           2     6
  SERPINA9 WILD-TYPE                        17   170
D877V12, multiclass
                                  clus
vv                                 SERPINA9 MUTATED SERPINA9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                           6                170
[1] 4 2
[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 = ZC3H12C MUTATION ANALYSIS
D878V1, survival
                   sevent
clus2                 0   1
  ZC3H12C MUTATED     9   2
  ZC3H12C WILD-TYPE 268  76
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               11               344 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
                2                76 
$`ZC3H12C MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 
        0.92        35.80        15.02        10.06         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-F4-6856 
        4.01        34.98        58.39        12.76        35.31 

$`ZC3H12C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
             0.92              0.00 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
            58.39            148.01 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
           15.020            22.075 
[1] "0.9 - 58.4 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D878V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZC3H12C MUTATED         1        0        0         5         2         0
  ZC3H12C WILD-TYPE      63        1       26       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H12C MUTATED           2          0          0          0        1
  ZC3H12C WILD-TYPE        16          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  ZC3H12C MUTATED           0         0
  ZC3H12C WILD-TYPE        12         1
D878V3, multiclass
            clus
vv           ZC3H12C MUTATED ZC3H12C WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  ZC3H12C MUTATED     0   2   8   2
  ZC3H12C WILD-TYPE   9  65 241  39
D878V4, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               8               241
  T4               2                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
  ZC3H12C MUTATED     9   1   2
  ZC3H12C WILD-TYPE 211  80  64
D878V5, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  N0               9               211
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V6, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED    10   1
  ZC3H12C WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED     10    1
  ZC3H12C WILD-TYPE  275   47
   clus
vv  ZC3H12C MUTATED ZC3H12C WILD-TYPE
  0              10               275
  1               1                47
[1] 2 2
[1] FALSE
D878V7, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED     6   6
  ZC3H12C WILD-TYPE 164 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED      6    6
  ZC3H12C WILD-TYPE  164  191
        clus
vv       ZC3H12C MUTATED ZC3H12C WILD-TYPE
  FEMALE               6               164
  MALE                 6               191
[1] 2 2
[1] FALSE
D878V8, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED     9   0
  ZC3H12C WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED      9    0
  ZC3H12C WILD-TYPE  291    8
     clus
vv    ZC3H12C MUTATED ZC3H12C WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D878V9, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED     8   4
  ZC3H12C WILD-TYPE 306  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED      8    4
  ZC3H12C WILD-TYPE  306   44
                               clus
vv                              ZC3H12C MUTATED ZC3H12C WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZC3H12C MUTATED     8   0   1   1
  ZC3H12C WILD-TYPE 251   3  21  20
D878V10, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               1                21
  RX               1                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"
D878V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H12C MUTATED                                  0     1
  ZC3H12C WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZC3H12C MUTATED                           0     3
  ZC3H12C WILD-TYPE                        19   173
D878V12, multiclass
                                  clus
vv                                 ZC3H12C MUTATED ZC3H12C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = PRRT2 MUTATION ANALYSIS
D879V1, survival
                 sevent
clus2               0   1
  PRRT2 MUTATED     6   0
  PRRT2 WILD-TYPE 271  78
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             349 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              0              78 
$`PRRT2 MUTATED`
TCGA-G4-6588 TCGA-AA-3663 TCGA-AD-5900 TCGA-AY-6197 TCGA-CK-4948 TCGA-G4-6306 
       26.17         6.97        12.16        21.44       148.01        44.68 

$`PRRT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PRRT2 MUTATED PRRT2 WILD-TYPE 
           6.97            0.00 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
         148.01          140.38 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
         23.805          22.060 
[1] "7.0 - 148.0 (23.8)" "0.0 - 140.4 (22.1)"
[1] "hr="     "9300000"
D879V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRRT2 MUTATED         1        0        1         2         0         0
  PRRT2 WILD-TYPE      63        1       25       106         8         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  PRRT2 MUTATED           0
  PRRT2 WILD-TYPE         1
D879V3, multiclass
            clus
vv           PRRT2 MUTATED PRRT2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PRRT2 MUTATED     0   2   4   0
  PRRT2 WILD-TYPE   9  65 245  41
D879V4, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             0              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
  PRRT2 MUTATED     5   1   0
  PRRT2 WILD-TYPE 215  80  66
D879V5, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V6, binary
                 cls
clus                0   1
  PRRT2 MUTATED     4   0
  PRRT2 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      4    0
  PRRT2 WILD-TYPE  281   48
   clus
vv  PRRT2 MUTATED PRRT2 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D879V7, binary
                 cls
clus                0   1
  PRRT2 MUTATED     2   4
  PRRT2 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      2    4
  PRRT2 WILD-TYPE  168  193
        clus
vv       PRRT2 MUTATED PRRT2 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D879V8, binary
                 cls
clus                0   1
  PRRT2 MUTATED     6   0
  PRRT2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      6    0
  PRRT2 WILD-TYPE  294    8
     clus
vv    PRRT2 MUTATED PRRT2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D879V9, binary
                 cls
clus                0   1
  PRRT2 MUTATED     5   1
  PRRT2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      5    1
  PRRT2 WILD-TYPE  309   47
                               clus
vv                              PRRT2 MUTATED PRRT2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRRT2 MUTATED     6   0   0   0
  PRRT2 WILD-TYPE 253   3  22  21
D879V10, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D879V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRRT2 MUTATED                                  0     0
  PRRT2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRRT2 MUTATED                           0     5
  PRRT2 WILD-TYPE                        19   171
D879V12, multiclass
                                  clus
vv                                 PRRT2 MUTATED PRRT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = H2AFJ MUTATION ANALYSIS
D880V1, survival
                 sevent
clus2               0   1
  H2AFJ MUTATED     3   0
  H2AFJ WILD-TYPE 274  78
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             352 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              0              78 
$`H2AFJ MUTATED`
TCGA-AA-3713 TCGA-AA-3663 TCGA-CM-5348 
       19.04         6.97        22.98 

$`H2AFJ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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          22.075 
[1] "7.0 - 23.0 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D880V2, continuous
                 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      64        1       25       108         8         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  H2AFJ MUTATED           0
  H2AFJ WILD-TYPE         1
D880V3, multiclass
            clus
vv           H2AFJ MUTATED H2AFJ WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  H2AFJ MUTATED     0   0   3   0
  H2AFJ WILD-TYPE   9  67 246  41
D880V4, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             0              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
  H2AFJ MUTATED     2   1   0
  H2AFJ WILD-TYPE 218  80  66
D880V5, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  N0             2             218
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V6, binary
                 cls
clus                0   1
  H2AFJ MUTATED     2   1
  H2AFJ WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      2    1
  H2AFJ WILD-TYPE  283   47
   clus
vv  H2AFJ MUTATED H2AFJ WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D880V7, binary
                 cls
clus                0   1
  H2AFJ MUTATED     0   3
  H2AFJ WILD-TYPE 170 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      0    3
  H2AFJ WILD-TYPE  170  194
        clus
vv       H2AFJ MUTATED H2AFJ WILD-TYPE
  FEMALE             0             170
  MALE               3             194
[1] 2 2
[1] FALSE
D880V8, binary
                 cls
clus                0   1
  H2AFJ MUTATED     2   1
  H2AFJ WILD-TYPE 298   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      2    1
  H2AFJ WILD-TYPE  298    7
     clus
vv    H2AFJ MUTATED H2AFJ WILD-TYPE
  NO              2             298
  YES             1               7
[1] 2 2
[1] FALSE
D880V9, binary
                 cls
clus                0   1
  H2AFJ MUTATED     3   0
  H2AFJ WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      3    0
  H2AFJ WILD-TYPE  311   48
                               clus
vv                              H2AFJ MUTATED H2AFJ WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  H2AFJ MUTATED     2   0   1   0
  H2AFJ WILD-TYPE 257   3  21  21
D880V10, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  R0             2             257
  R1             0               3
  R2             1              21
  RX             0              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"
D880V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  H2AFJ MUTATED                                  0     0
  H2AFJ WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  H2AFJ MUTATED                           0     1
  H2AFJ WILD-TYPE                        19   175
D880V12, multiclass
[1] "Remove cluster labels:" "H2AFJ MUTATED"         
clus
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              1             205 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6607      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-5913      TCGA-CK-5914 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6626 
"H2AFJ WILD-TYPE" 

Clustering(881) Variable = SLC25A44 MUTATION ANALYSIS
D881V1, survival
                    sevent
clus2                  0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 272  78
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                350 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 0                 78 
$`SLC25A44 MUTATED`
TCGA-AA-3966 TCGA-AA-A01Q TCGA-CA-6715 TCGA-CM-6162 TCGA-D5-5541 
        2.01         1.02        12.59        12.00        55.92 

$`SLC25A44 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        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        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
              1.02               0.00 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
             55.92             148.01 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
             12.00              22.09 
[1] "1.0 - 55.9 (12.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D881V2, continuous
                    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      64        1       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A44 MUTATED           0          0          3          0        0
  SLC25A44 WILD-TYPE        18          6         41         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A44 MUTATED           0         0
  SLC25A44 WILD-TYPE        12         1
D881V3, multiclass
            clus
vv           SLC25A44 MUTATED SLC25A44 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 1                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SLC25A44 MUTATED     0   0   5   0
  SLC25A44 WILD-TYPE   9  67 244  41
D881V4, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                5                244
  T4                0                 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
  SLC25A44 MUTATED     2   3   0
  SLC25A44 WILD-TYPE 218  78  66
D881V5, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  N0                2                218
  N1                3                 78
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V6, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      5    0
  SLC25A44 WILD-TYPE  280   48
   clus
vv  SLC25A44 MUTATED SLC25A44 WILD-TYPE
  0                5                280
  1                0                 48
[1] 2 2
[1] FALSE
D881V7, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     3   2
  SLC25A44 WILD-TYPE 167 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      3    2
  SLC25A44 WILD-TYPE  167  195
        clus
vv       SLC25A44 MUTATED SLC25A44 WILD-TYPE
  FEMALE                3                167
  MALE                  2                195
[1] 2 2
[1] FALSE
D881V8, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     3   0
  SLC25A44 WILD-TYPE 297   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      3    0
  SLC25A44 WILD-TYPE  297    8
     clus
vv    SLC25A44 MUTATED SLC25A44 WILD-TYPE
  NO                 3                297
  YES                0                  8
[1] 2 2
[1] FALSE
D881V9, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     3   2
  SLC25A44 WILD-TYPE 311  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      3    2
  SLC25A44 WILD-TYPE  311   46
                               clus
vv                              SLC25A44 MUTATED SLC25A44 WILD-TYPE
  COLON ADENOCARCINOMA                         3                311
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC25A44 MUTATED     3   0   0   1
  SLC25A44 WILD-TYPE 256   3  22  20
D881V10, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D881V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A44 MUTATED                                  0     1
  SLC25A44 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A44 MUTATED                           0     2
  SLC25A44 WILD-TYPE                        19   174
D881V12, multiclass
                                  clus
vv                                 SLC25A44 MUTATED SLC25A44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           2                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(882) Variable = CHD1 MUTATION ANALYSIS
D882V1, survival
                sevent
clus2              0   1
  CHD1 MUTATED    19   4
  CHD1 WILD-TYPE 258  74
  CHD1 MUTATED CHD1 WILD-TYPE 
            23            332 
  CHD1 MUTATED CHD1 WILD-TYPE 
             4             74 
$`CHD1 MUTATED`
TCGA-A6-6649 TCGA-AA-3672 TCGA-AA-3713 TCGA-A6-5659 TCGA-A6-6138 TCGA-AA-3526 
       24.16         0.92        19.04        30.44        22.52        19.07 
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        12.16        58.39        11.74        12.76        10.06 
TCGA-CK-5916 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A0XF TCGA-F4-6856 
       21.14        12.00        13.35        38.20        35.31 

$`CHD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         1.02         9.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        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        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        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-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CHD1 MUTATED CHD1 WILD-TYPE 
          0.92           0.00 
  CHD1 MUTATED CHD1 WILD-TYPE 
         58.39         148.01 
  CHD1 MUTATED CHD1 WILD-TYPE 
        22.520         22.045 
[1] "0.9 - 58.4 (22.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D882V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD1 MUTATED         7        0        1         6         1         0
  CHD1 WILD-TYPE      57        1       25       102         7         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        17          6         41         32       33        12
                vv
clus             STAGE IVB
  CHD1 MUTATED           0
  CHD1 WILD-TYPE         1
D882V3, multiclass
            clus
vv           CHD1 MUTATED CHD1 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  CHD1 MUTATED     1   7  13   2
  CHD1 WILD-TYPE   8  60 236  39
D882V4, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  T1            1              8
  T2            7             60
  T3           13            236
  T4            2             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
  CHD1 MUTATED    17   4   2
  CHD1 WILD-TYPE 203  77  64
D882V5, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  N0           17            203
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V6, binary
                cls
clus               0   1
  CHD1 MUTATED    19   2
  CHD1 WILD-TYPE 266  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     19    2
  CHD1 WILD-TYPE  266   46
   clus
vv  CHD1 MUTATED CHD1 WILD-TYPE
  0           19            266
  1            2             46
[1] 2 2
[1] FALSE
D882V7, binary
                cls
clus               0   1
  CHD1 MUTATED     7  16
  CHD1 WILD-TYPE 163 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED      7   16
  CHD1 WILD-TYPE  163  181
        clus
vv       CHD1 MUTATED CHD1 WILD-TYPE
  FEMALE            7            163
  MALE             16            181
[1] 2 2
[1] FALSE
D882V8, binary
                cls
clus               0   1
  CHD1 MUTATED    21   1
  CHD1 WILD-TYPE 279   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     21    1
  CHD1 WILD-TYPE  279    7
     clus
vv    CHD1 MUTATED CHD1 WILD-TYPE
  NO            21            279
  YES            1              7
[1] 2 2
[1] FALSE
D882V9, binary
                cls
clus               0   1
  CHD1 MUTATED    15   7
  CHD1 WILD-TYPE 299  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     15    7
  CHD1 WILD-TYPE  299   41
                               clus
vv                              CHD1 MUTATED CHD1 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD1 MUTATED    13   0   1   3
  CHD1 WILD-TYPE 246   3  21  18
D882V10, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            1             21
  RX            3             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"
D882V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD1 MUTATED                                  0     2
  CHD1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD1 MUTATED                           0    11
  CHD1 WILD-TYPE                        19   165
D882V12, multiclass
                                  clus
vv                                 CHD1 MUTATED CHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      11            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(883) Variable = ZBTB33 MUTATION ANALYSIS
D883V1, survival
                  sevent
clus2                0   1
  ZBTB33 MUTATED     9   7
  ZBTB33 WILD-TYPE 268  71
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              339 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
               7               71 
$`ZBTB33 MUTATED`
TCGA-AA-3552 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-6780 TCGA-AA-3510 
       13.02        19.04       100.01        35.80        20.12        63.98 
TCGA-AA-3660 TCGA-AA-3947 TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-6599 
       78.08        33.01        38.07        35.01        83.24         6.77 
TCGA-CK-5916 TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6541 
       21.14        15.02        14.04        15.58 

$`ZBTB33 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.060 
[1] "6.8 - 100.0 (27.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D883V2, continuous
                  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      60        1       22       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB33 MUTATED           2          0          0          1        0
  ZBTB33 WILD-TYPE        16          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB33 MUTATED           0         0
  ZBTB33 WILD-TYPE        12         1
D883V3, multiclass
            clus
vv           ZBTB33 MUTATED ZBTB33 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZBTB33 MUTATED     1   3  11   1
  ZBTB33 WILD-TYPE   8  64 238  40
D883V4, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             11              238
  T4              1               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
  ZBTB33 MUTATED    13   1   2
  ZBTB33 WILD-TYPE 207  80  64
D883V5, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  N0             13              207
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V6, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    14   0
  ZBTB33 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     14    0
  ZBTB33 WILD-TYPE  271   48
   clus
vv  ZBTB33 MUTATED ZBTB33 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D883V7, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED     7   9
  ZBTB33 WILD-TYPE 163 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED      7    9
  ZBTB33 WILD-TYPE  163  188
        clus
vv       ZBTB33 MUTATED ZBTB33 WILD-TYPE
  FEMALE              7              163
  MALE                9              188
[1] 2 2
[1] FALSE
D883V8, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    15   1
  ZBTB33 WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     15    1
  ZBTB33 WILD-TYPE  285    7
     clus
vv    ZBTB33 MUTATED ZBTB33 WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D883V9, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    13   3
  ZBTB33 WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     13    3
  ZBTB33 WILD-TYPE  301   45
                               clus
vv                              ZBTB33 MUTATED ZBTB33 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB33 MUTATED    12   0   0   1
  ZBTB33 WILD-TYPE 247   3  22  20
D883V10, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              1               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"
D883V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB33 MUTATED                                  0     1
  ZBTB33 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB33 MUTATED                           0     8
  ZBTB33 WILD-TYPE                        19   168
D883V12, multiclass
                                  clus
vv                                 ZBTB33 MUTATED ZBTB33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = ZNF691 MUTATION ANALYSIS
D884V1, survival
                  sevent
clus2                0   1
  ZNF691 MUTATED     5   2
  ZNF691 WILD-TYPE 272  76
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               7              348 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               2               76 
$`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 
       61.91 

$`ZNF691 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  ZNF691 MUTATED ZNF691 WILD-TYPE 
           13.02             0.00 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
          139.17           148.01 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
          23.050           22.045 
[1] "13.0 - 139.2 (23.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.2"
D884V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF691 MUTATED         0        0        1         3         0         0
  ZNF691 WILD-TYPE      64        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF691 MUTATED           1          0          0          1        1
  ZNF691 WILD-TYPE        17          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF691 MUTATED           0         0
  ZNF691 WILD-TYPE        12         1
D884V3, multiclass
            clus
vv           ZNF691 MUTATED ZNF691 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF691 MUTATED     0   0   6   1
  ZNF691 WILD-TYPE   9  67 243  40
D884V4, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              1               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
  ZNF691 MUTATED     4   1   2
  ZNF691 WILD-TYPE 216  80  64
D884V5, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V6, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     5   1
  ZNF691 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      5    1
  ZNF691 WILD-TYPE  280   47
   clus
vv  ZNF691 MUTATED ZNF691 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D884V7, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     4   3
  ZNF691 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      4    3
  ZNF691 WILD-TYPE  166  194
        clus
vv       ZNF691 MUTATED ZNF691 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D884V8, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     5   0
  ZNF691 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      5    0
  ZNF691 WILD-TYPE  295    8
     clus
vv    ZNF691 MUTATED ZNF691 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D884V9, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     5   2
  ZNF691 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      5    2
  ZNF691 WILD-TYPE  309   46
                               clus
vv                              ZNF691 MUTATED ZNF691 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF691 MUTATED     3   0   0   1
  ZNF691 WILD-TYPE 256   3  22  20
D884V10, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              1               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"
D884V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF691 MUTATED                                  0     0
  ZNF691 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF691 MUTATED                           0     6
  ZNF691 WILD-TYPE                        19   170
D884V12, multiclass
                                  clus
vv                                 ZNF691 MUTATED ZNF691 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = EFTUD2 MUTATION ANALYSIS
D885V1, survival
                  sevent
clus2                0   1
  EFTUD2 MUTATED     9   5
  EFTUD2 WILD-TYPE 268  73
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              14              341 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
               5               73 
$`EFTUD2 MUTATED`
TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3662 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-3809 
       13.02         0.99         6.05        10.88       100.01        32.75 
TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-A01R TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       63.98        38.99        35.01        14.04        12.95        11.08 
TCGA-DM-A0XD TCGA-DM-A0XF 
       24.43        38.20 

$`EFTUD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52        25.08       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-3810 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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3518 
        7.04         3.02        35.01         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
       13.35        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
            0.99             0.00 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
          100.01           148.01 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
          19.235           22.060 
[1] "1.0 - 100.0 (19.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D885V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFTUD2 MUTATED         3        0        2         3         1         0
  EFTUD2 WILD-TYPE      61        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFTUD2 MUTATED           2          0          0          1        1
  EFTUD2 WILD-TYPE        16          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  EFTUD2 MUTATED           0         0
  EFTUD2 WILD-TYPE        12         1
D885V3, multiclass
            clus
vv           EFTUD2 MUTATED EFTUD2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  EFTUD2 MUTATED     0   3   8   3
  EFTUD2 WILD-TYPE   9  64 241  38
D885V4, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              8              241
  T4              3               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
  EFTUD2 MUTATED     9   0   5
  EFTUD2 WILD-TYPE 211  81  61
D885V5, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V6, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED    12   1
  EFTUD2 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED     12    1
  EFTUD2 WILD-TYPE  273   47
   clus
vv  EFTUD2 MUTATED EFTUD2 WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D885V7, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED     5   9
  EFTUD2 WILD-TYPE 165 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED      5    9
  EFTUD2 WILD-TYPE  165  188
        clus
vv       EFTUD2 MUTATED EFTUD2 WILD-TYPE
  FEMALE              5              165
  MALE                9              188
[1] 2 2
[1] FALSE
D885V8, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED    11   1
  EFTUD2 WILD-TYPE 289   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED     11    1
  EFTUD2 WILD-TYPE  289    7
     clus
vv    EFTUD2 MUTATED EFTUD2 WILD-TYPE
  NO              11              289
  YES              1                7
[1] 2 2
[1] FALSE
D885V9, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED     9   4
  EFTUD2 WILD-TYPE 305  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED      9    4
  EFTUD2 WILD-TYPE  305   44
                               clus
vv                              EFTUD2 MUTATED EFTUD2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EFTUD2 MUTATED     8   0   1   0
  EFTUD2 WILD-TYPE 251   3  21  21
D885V10, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              1               21
  RX              0               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"
D885V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFTUD2 MUTATED                                  0     0
  EFTUD2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EFTUD2 MUTATED                           0     8
  EFTUD2 WILD-TYPE                        19   168
D885V12, multiclass
                                  clus
vv                                 EFTUD2 MUTATED EFTUD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = METTL9 MUTATION ANALYSIS
D886V1, survival
                  sevent
clus2                0   1
  METTL9 MUTATED     4   0
  METTL9 WILD-TYPE 273  78
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              351 
  METTL9 MUTATED METTL9 WILD-TYPE 
               0               78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.060 
[1] "12.8 - 27.4 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D886V2, continuous
                  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      63        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL9 MUTATED           0          0          0          0        0
  METTL9 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  METTL9 MUTATED           0         0
  METTL9 WILD-TYPE        12         1
D886V3, multiclass
            clus
vv           METTL9 MUTATED METTL9 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  METTL9 MUTATED     0   1   3   0
  METTL9 WILD-TYPE   9  66 246  41
D886V4, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              3              246
  T4              0               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
  METTL9 MUTATED     4   0   0
  METTL9 WILD-TYPE 216  81  66
D886V5, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  N0              4              216
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V6, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   0
  METTL9 WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    0
  METTL9 WILD-TYPE  282   48
   clus
vv  METTL9 MUTATED METTL9 WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D886V7, binary
                  cls
clus                 0   1
  METTL9 MUTATED     2   2
  METTL9 WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      2    2
  METTL9 WILD-TYPE  168  195
        clus
vv       METTL9 MUTATED METTL9 WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D886V8, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   0
  METTL9 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    0
  METTL9 WILD-TYPE  297    8
     clus
vv    METTL9 MUTATED METTL9 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D886V9, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   1
  METTL9 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    1
  METTL9 WILD-TYPE  311   47
                               clus
vv                              METTL9 MUTATED METTL9 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  METTL9 MUTATED     2   0   0   1
  METTL9 WILD-TYPE 257   3  22  20
D886V10, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              1               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"
D886V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METTL9 MUTATED                                  0     1
  METTL9 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  METTL9 MUTATED                           0     3
  METTL9 WILD-TYPE                        19   173
D886V12, multiclass
                                  clus
vv                                 METTL9 MUTATED METTL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = CEL MUTATION ANALYSIS
D887V1, survival
               sevent
clus2             0   1
  CEL MUTATED     7   2
  CEL WILD-TYPE 270  76
  CEL MUTATED CEL WILD-TYPE 
            9           346 
  CEL MUTATED CEL WILD-TYPE 
            2            76 
$`CEL MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3980 TCGA-AZ-6598 
       19.04        26.17        79.69        19.66        27.02        49.41 
TCGA-CM-6171 TCGA-F4-6570 TCGA-G4-6309 
       14.04         6.18        85.48 

$`CEL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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        22.045 
[1] "6.2 - 85.5 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D887V2, continuous
               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      61        1       25       106         8         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        18          6         43         32       34        12
               vv
clus            STAGE IVB
  CEL MUTATED           0
  CEL WILD-TYPE         1
D887V3, multiclass
            clus
vv           CEL MUTATED CEL WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            2           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             1            34
  STAGE IVA            0            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
  CEL MUTATED     0   3   5   1
  CEL WILD-TYPE   9  64 244  40
D887V4, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  T1           0             9
  T2           3            64
  T3           5           244
  T4           1            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
  CEL MUTATED     7   2   0
  CEL WILD-TYPE 213  79  66
D887V5, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  N0           7           213
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V6, binary
               cls
clus              0   1
  CEL MUTATED     6   1
  CEL WILD-TYPE 279  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      6    1
  CEL WILD-TYPE  279   47
   clus
vv  CEL MUTATED CEL WILD-TYPE
  0           6           279
  1           1            47
[1] 2 2
[1] FALSE
D887V7, binary
               cls
clus              0   1
  CEL MUTATED     6   3
  CEL WILD-TYPE 164 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      6    3
  CEL WILD-TYPE  164  194
        clus
vv       CEL MUTATED CEL WILD-TYPE
  FEMALE           6           164
  MALE             3           194
[1] 2 2
[1] FALSE
D887V8, binary
               cls
clus              0   1
  CEL MUTATED     8   1
  CEL WILD-TYPE 292   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      8    1
  CEL WILD-TYPE  292    7
     clus
vv    CEL MUTATED CEL WILD-TYPE
  NO            8           292
  YES           1             7
[1] 2 2
[1] FALSE
D887V9, binary
               cls
clus              0   1
  CEL MUTATED     8   1
  CEL WILD-TYPE 306  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      8    1
  CEL WILD-TYPE  306   47
                               clus
vv                              CEL MUTATED CEL WILD-TYPE
  COLON ADENOCARCINOMA                    8           306
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CEL MUTATED     6   0   1   0
  CEL WILD-TYPE 253   3  21  21
D887V10, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  R0           6           253
  R1           0             3
  R2           1            21
  RX           0            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"
D887V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEL MUTATED                                  0     0
  CEL WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CEL MUTATED                           1     6
  CEL WILD-TYPE                        18   170
D887V12, multiclass
                                  clus
vv                                 CEL MUTATED CEL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      6           170
[1] 4 2
[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 = OR10J1 MUTATION ANALYSIS
D888V1, survival
                  sevent
clus2                0   1
  OR10J1 MUTATED     8   4
  OR10J1 WILD-TYPE 269  74
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              12              343 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
               4               74 
$`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        25.48        35.74         6.18        44.68 

$`OR10J1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       18.05         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        12.76        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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        54.61        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 
       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  OR10J1 MUTATED OR10J1 WILD-TYPE 
            4.01             0.00 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           44.68           148.01 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           16.29            22.09 
[1] "4.0 - 44.7 (16.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D888V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR10J1 MUTATED         2        0        0         4         1         0
  OR10J1 WILD-TYPE      62        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR10J1 MUTATED           0          0          2          0        1
  OR10J1 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  OR10J1 MUTATED           1         0
  OR10J1 WILD-TYPE        11         1
D888V3, multiclass
            clus
vv           OR10J1 MUTATED OR10J1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  OR10J1 MUTATED     1   2   5   5
  OR10J1 WILD-TYPE   8  65 244  36
D888V4, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              5              244
  T4              5               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
  OR10J1 MUTATED     9   3   1
  OR10J1 WILD-TYPE 211  78  65
D888V5, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V6, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    11   2
  OR10J1 WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    2
  OR10J1 WILD-TYPE  274   46
   clus
vv  OR10J1 MUTATED OR10J1 WILD-TYPE
  0             11              274
  1              2               46
[1] 2 2
[1] FALSE
D888V7, binary
                  cls
clus                 0   1
  OR10J1 MUTATED     8   5
  OR10J1 WILD-TYPE 162 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED      8    5
  OR10J1 WILD-TYPE  162  192
        clus
vv       OR10J1 MUTATED OR10J1 WILD-TYPE
  FEMALE              8              162
  MALE                5              192
[1] 2 2
[1] FALSE
D888V8, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    11   0
  OR10J1 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    0
  OR10J1 WILD-TYPE  289    8
     clus
vv    OR10J1 MUTATED OR10J1 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D888V9, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    11   2
  OR10J1 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    2
  OR10J1 WILD-TYPE  303   46
                               clus
vv                              OR10J1 MUTATED OR10J1 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR10J1 MUTATED    10   0   0   2
  OR10J1 WILD-TYPE 249   3  22  19
D888V10, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D888V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR10J1 MUTATED                                  0     1
  OR10J1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR10J1 MUTATED                           0     8
  OR10J1 WILD-TYPE                        19   168
D888V12, multiclass
                                  clus
vv                                 OR10J1 MUTATED OR10J1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = PRKCD MUTATION ANALYSIS
D889V1, survival
                 sevent
clus2               0   1
  PRKCD MUTATED    12   0
  PRKCD WILD-TYPE 265  78
  PRKCD MUTATED PRKCD WILD-TYPE 
             12             343 
  PRKCD MUTATED PRKCD WILD-TYPE 
              0              78 
$`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 
       12.16        17.56        12.00        15.58        13.35        12.00 

$`PRKCD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PRKCD MUTATED PRKCD WILD-TYPE 
             12               0 
  PRKCD MUTATED PRKCD WILD-TYPE 
          35.01          148.01 
  PRKCD MUTATED PRKCD WILD-TYPE 
          18.61           22.09 
[1] "12.0 - 35.0 (18.6)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9400000"
D889V2, continuous
                 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      63        1       26       101         8         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        17          6         42         31       35        12
                 vv
clus              STAGE IVB
  PRKCD MUTATED           0
  PRKCD WILD-TYPE         1
D889V3, multiclass
            clus
vv           PRKCD MUTATED PRKCD WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  PRKCD MUTATED     0   1   9   3
  PRKCD WILD-TYPE   9  66 240  38
D889V4, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             3              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
  PRKCD MUTATED     8   3   2
  PRKCD WILD-TYPE 212  78  64
D889V5, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  N0             8             212
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D889V6, binary
                 cls
clus                0   1
  PRKCD MUTATED    11   0
  PRKCD WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED     11    0
  PRKCD WILD-TYPE  274   48
   clus
vv  PRKCD MUTATED PRKCD WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D889V7, binary
                 cls
clus                0   1
  PRKCD MUTATED     7   6
  PRKCD WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      7    6
  PRKCD WILD-TYPE  163  191
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D889V8, binary
                 cls
clus                0   1
  PRKCD MUTATED    11   1
  PRKCD WILD-TYPE 289   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED     11    1
  PRKCD WILD-TYPE  289    7
     clus
vv    PRKCD MUTATED PRKCD WILD-TYPE
  NO             11             289
  YES             1               7
[1] 2 2
[1] FALSE
D889V9, binary
                 cls
clus                0   1
  PRKCD MUTATED     8   5
  PRKCD WILD-TYPE 306  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      8    5
  PRKCD WILD-TYPE  306   43
                               clus
vv                              PRKCD MUTATED PRKCD WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKCD MUTATED    12   0   0   1
  PRKCD WILD-TYPE 247   3  22  20
D889V10, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D889V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCD MUTATED                                  0     0
  PRKCD WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCD MUTATED                           1     8
  PRKCD WILD-TYPE                        18   168
D889V12, multiclass
                                  clus
vv                                 PRKCD MUTATED PRKCD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = SMC1B MUTATION ANALYSIS
D890V1, survival
                 sevent
clus2               0   1
  SMC1B MUTATED    13   5
  SMC1B WILD-TYPE 264  73
  SMC1B MUTATED SMC1B WILD-TYPE 
             18             337 
  SMC1B MUTATED SMC1B WILD-TYPE 
              5              73 
$`SMC1B MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-6653 
       19.04        24.00       100.01        35.80        32.75        24.39 
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-A010 TCGA-AZ-4315 
       23.87         3.02        63.98         6.97        34.98        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6680 TCGA-D5-6931 TCGA-F4-6809 TCGA-G4-6309 
       12.76        10.06        12.03        12.00        13.25        85.48 

$`SMC1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5665 
       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-A6-6651 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-3502 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SMC1B MUTATED SMC1B WILD-TYPE 
           3.02            0.00 
  SMC1B MUTATED SMC1B WILD-TYPE 
         100.01          148.01 
  SMC1B MUTATED SMC1B WILD-TYPE 
         23.935          22.030 
[1] "3.0 - 100.0 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D890V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC1B MUTATED         1        0        5         6         2         0
  SMC1B WILD-TYPE      63        1       21       102         6         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        18          6         41         32       35        11
                 vv
clus              STAGE IVB
  SMC1B MUTATED           0
  SMC1B WILD-TYPE         1
D890V3, multiclass
            clus
vv           SMC1B MUTATED SMC1B WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  SMC1B MUTATED     0   1  14   4
  SMC1B WILD-TYPE   9  66 235  37
D890V4, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  T1             0               9
  T2             1              66
  T3            14             235
  T4             4              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
  SMC1B MUTATED    14   3   2
  SMC1B WILD-TYPE 206  78  64
D890V5, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  N0            14             206
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V6, binary
                 cls
clus                0   1
  SMC1B MUTATED    18   1
  SMC1B WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     18    1
  SMC1B WILD-TYPE  267   47
   clus
vv  SMC1B MUTATED SMC1B WILD-TYPE
  0            18             267
  1             1              47
[1] 2 2
[1] FALSE
D890V7, binary
                 cls
clus                0   1
  SMC1B MUTATED    10   9
  SMC1B WILD-TYPE 160 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     10    9
  SMC1B WILD-TYPE  160  188
        clus
vv       SMC1B MUTATED SMC1B WILD-TYPE
  FEMALE            10             160
  MALE               9             188
[1] 2 2
[1] FALSE
D890V8, binary
                 cls
clus                0   1
  SMC1B MUTATED    18   0
  SMC1B WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     18    0
  SMC1B WILD-TYPE  282    8
     clus
vv    SMC1B MUTATED SMC1B WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D890V9, binary
                 cls
clus                0   1
  SMC1B MUTATED    16   3
  SMC1B WILD-TYPE 298  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     16    3
  SMC1B WILD-TYPE  298   45
                               clus
vv                              SMC1B MUTATED SMC1B WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMC1B MUTATED    14   0   0   2
  SMC1B WILD-TYPE 245   3  22  19
D890V10, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D890V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC1B MUTATED                                  0     2
  SMC1B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMC1B MUTATED                           1     9
  SMC1B WILD-TYPE                        18   167
D890V12, multiclass
                                  clus
vv                                 SMC1B MUTATED SMC1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(891) Variable = AP1M1 MUTATION ANALYSIS
D891V1, survival
                 sevent
clus2               0   1
  AP1M1 MUTATED     8   1
  AP1M1 WILD-TYPE 269  77
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             346 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              1              77 
$`AP1M1 MUTATED`
TCGA-AZ-6601 TCGA-A6-5665 TCGA-AA-3819 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-5407 
      100.01        22.06        25.02        35.01        21.44        88.21 
TCGA-CK-5913 TCGA-D5-6533 TCGA-D5-6536 
       51.32        25.48        17.85 

$`AP1M1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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-D5-6537 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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  AP1M1 MUTATED AP1M1 WILD-TYPE 
          17.85            0.00 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
         100.01          148.01 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
          25.48           21.99 
[1] "17.9 - 100.0 (25.5)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.1"
D891V2, continuous
                 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      63        1       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP1M1 MUTATED           1          0          0          0        0         0
  AP1M1 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  AP1M1 MUTATED           0
  AP1M1 WILD-TYPE         1
D891V3, multiclass
            clus
vv           AP1M1 MUTATED AP1M1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  AP1M1 MUTATED     1   0   7   1
  AP1M1 WILD-TYPE   8  67 242  40
D891V4, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             7             242
  T4             1              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
  AP1M1 MUTATED     8   0   1
  AP1M1 WILD-TYPE 212  81  65
D891V5, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V6, binary
                 cls
clus                0   1
  AP1M1 MUTATED     7   0
  AP1M1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      7    0
  AP1M1 WILD-TYPE  278   48
   clus
vv  AP1M1 MUTATED AP1M1 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D891V7, binary
                 cls
clus                0   1
  AP1M1 MUTATED     5   4
  AP1M1 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      5    4
  AP1M1 WILD-TYPE  165  193
        clus
vv       AP1M1 MUTATED AP1M1 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D891V8, binary
                 cls
clus                0   1
  AP1M1 MUTATED     8   1
  AP1M1 WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      8    1
  AP1M1 WILD-TYPE  292    7
     clus
vv    AP1M1 MUTATED AP1M1 WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D891V9, binary
                 cls
clus                0   1
  AP1M1 MUTATED     8   1
  AP1M1 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      8    1
  AP1M1 WILD-TYPE  306   47
                               clus
vv                              AP1M1 MUTATED AP1M1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AP1M1 MUTATED     6   0   0   1
  AP1M1 WILD-TYPE 253   3  22  20
D891V10, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D891V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP1M1 MUTATED                                  0     0
  AP1M1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP1M1 MUTATED                           0     7
  AP1M1 WILD-TYPE                        19   169
D891V12, multiclass
                                  clus
vv                                 AP1M1 MUTATED AP1M1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = CCDC55 MUTATION ANALYSIS
D892V1, survival
                  sevent
clus2                0   1
  CCDC55 MUTATED    10   1
  CCDC55 WILD-TYPE 267  77
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              11              344 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               1               77 
$`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-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCDC55 MUTATED CCDC55 WILD-TYPE 
            2.01             0.00 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
           98.24           148.01 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
           27.42            21.99 
[1] "2.0 - 98.2 (27.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3.3"
D892V2, continuous
                  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      63        1       26       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC55 MUTATED           0          0          2          0        0
  CCDC55 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CCDC55 MUTATED           0         0
  CCDC55 WILD-TYPE        12         1
D892V3, multiclass
            clus
vv           CCDC55 MUTATED CCDC55 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CCDC55 MUTATED     0   1  11   1
  CCDC55 WILD-TYPE   9  66 238  40
D892V4, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             11              238
  T4              1               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
  CCDC55 MUTATED    11   2   0
  CCDC55 WILD-TYPE 209  79  66
D892V5, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  N0             11              209
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V6, binary
                  cls
clus                 0   1
  CCDC55 MUTATED    10   0
  CCDC55 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED     10    0
  CCDC55 WILD-TYPE  275   48
   clus
vv  CCDC55 MUTATED CCDC55 WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D892V7, binary
                  cls
clus                 0   1
  CCDC55 MUTATED     4   9
  CCDC55 WILD-TYPE 166 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      4    9
  CCDC55 WILD-TYPE  166  188
        clus
vv       CCDC55 MUTATED CCDC55 WILD-TYPE
  FEMALE              4              166
  MALE                9              188
[1] 2 2
[1] FALSE
D892V8, binary
                  cls
clus                 0   1
  CCDC55 MUTATED     9   0
  CCDC55 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      9    0
  CCDC55 WILD-TYPE  291    8
     clus
vv    CCDC55 MUTATED CCDC55 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D892V9, binary
                  cls
clus                 0   1
  CCDC55 MUTATED    10   3
  CCDC55 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED     10    3
  CCDC55 WILD-TYPE  304   45
                               clus
vv                              CCDC55 MUTATED CCDC55 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC55 MUTATED     6   0   0   3
  CCDC55 WILD-TYPE 253   3  22  18
D892V10, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              3               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"
D892V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC55 MUTATED                                  0     1
  CCDC55 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC55 MUTATED                           2     8
  CCDC55 WILD-TYPE                        17   168
D892V12, multiclass
                                  clus
vv                                 CCDC55 MUTATED CCDC55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         8              168
[1] 4 2
[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 = MOV10 MUTATION ANALYSIS
D893V1, survival
                 sevent
clus2               0   1
  MOV10 MUTATED    13   0
  MOV10 WILD-TYPE 264  78
  MOV10 MUTATED MOV10 WILD-TYPE 
             13             342 
  MOV10 MUTATED MOV10 WILD-TYPE 
              0              78 
$`MOV10 MUTATED`
TCGA-G4-6586 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3812 TCGA-AA-3966 TCGA-AA-A00E 
       35.80        19.66        61.02        35.05         2.01        30.02 
TCGA-AU-3779 TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-5344 TCGA-CM-5349 TCGA-DM-A1HA 
       14.50        17.56        21.99        22.03        30.08       131.51 
TCGA-G4-6293 
      133.18 

$`MOV10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       148.01        85.45        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MOV10 MUTATED MOV10 WILD-TYPE 
           2.01            0.00 
  MOV10 MUTATED MOV10 WILD-TYPE 
         133.18          148.01 
  MOV10 MUTATED MOV10 WILD-TYPE 
         30.020          22.025 
[1] "2.0 - 133.2 (30.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.7e+07"
D893V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOV10 MUTATED         0        0        1         6         0         0
  MOV10 WILD-TYPE      64        1       25       102         8         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        17          6         41         31       35        12
                 vv
clus              STAGE IVB
  MOV10 MUTATED           0
  MOV10 WILD-TYPE         1
D893V3, multiclass
            clus
vv           MOV10 MUTATED MOV10 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  MOV10 MUTATED     0   0  11   2
  MOV10 WILD-TYPE   9  67 238  39
D893V4, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            11             238
  T4             2              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
  MOV10 MUTATED     7   5   1
  MOV10 WILD-TYPE 213  76  65
D893V5, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  N0             7             213
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V6, binary
                 cls
clus                0   1
  MOV10 MUTATED    11   0
  MOV10 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     11    0
  MOV10 WILD-TYPE  274   48
   clus
vv  MOV10 MUTATED MOV10 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D893V7, binary
                 cls
clus                0   1
  MOV10 MUTATED     8   5
  MOV10 WILD-TYPE 162 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED      8    5
  MOV10 WILD-TYPE  162  192
        clus
vv       MOV10 MUTATED MOV10 WILD-TYPE
  FEMALE             8             162
  MALE               5             192
[1] 2 2
[1] FALSE
D893V8, binary
                 cls
clus                0   1
  MOV10 MUTATED    10   0
  MOV10 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     10    0
  MOV10 WILD-TYPE  290    8
     clus
vv    MOV10 MUTATED MOV10 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D893V9, binary
                 cls
clus                0   1
  MOV10 MUTATED    11   2
  MOV10 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     11    2
  MOV10 WILD-TYPE  303   46
                               clus
vv                              MOV10 MUTATED MOV10 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MOV10 MUTATED     9   0   0   2
  MOV10 WILD-TYPE 250   3  22  19
D893V10, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D893V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOV10 MUTATED                                  0     0
  MOV10 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MOV10 MUTATED                           0     9
  MOV10 WILD-TYPE                        19   167
D893V12, multiclass
                                  clus
vv                                 MOV10 MUTATED MOV10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(894) Variable = GRINA MUTATION ANALYSIS
D894V1, survival
                 sevent
clus2               0   1
  GRINA MUTATED     3   1
  GRINA WILD-TYPE 274  77
  GRINA MUTATED GRINA WILD-TYPE 
              4             351 
  GRINA MUTATED GRINA WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 
       61.91        36.00        13.78 

  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          21.990 
[1] "22.1 - 85.5 (37.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D894V2, continuous
                 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      64        1       26       106         8         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        18          5         43         33       35        12
                 vv
clus              STAGE IVB
  GRINA MUTATED           0
  GRINA WILD-TYPE         1
D894V3, multiclass
            clus
vv           GRINA MUTATED GRINA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GRINA MUTATED     0   1   3   0
  GRINA WILD-TYPE   9  66 246  41
D894V4, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             0              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
  GRINA MUTATED     2   2   0
  GRINA WILD-TYPE 218  79  66
D894V5, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  N0             2             218
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V6, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  281   48
   clus
vv  GRINA MUTATED GRINA WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D894V7, binary
                 cls
clus                0   1
  GRINA MUTATED     3   1
  GRINA WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      3    1
  GRINA WILD-TYPE  167  196
        clus
vv       GRINA MUTATED GRINA WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D894V8, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  296    8
     clus
vv    GRINA MUTATED GRINA WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D894V9, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  310   48
                               clus
vv                              GRINA MUTATED GRINA WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GRINA MUTATED     4   0   0   0
  GRINA WILD-TYPE 255   3  22  21
D894V10, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D894V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRINA MUTATED                                  0     0
  GRINA WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRINA MUTATED                           1     3
  GRINA WILD-TYPE                        18   173
D894V12, multiclass
                                  clus
vv                                 GRINA MUTATED GRINA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = CAPRIN1 MUTATION ANALYSIS
D895V1, survival
                   sevent
clus2                 0   1
  CAPRIN1 MUTATED     8   3
  CAPRIN1 WILD-TYPE 269  75
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               11               344 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
                3                75 
$`CAPRIN1 MUTATED`
TCGA-AA-3496 TCGA-A6-2672 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3548 TCGA-AA-A01R 
        1.02        46.65        32.75         3.02        33.99        35.01 
TCGA-AD-6901 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6540 TCGA-G4-6626 
       22.42        37.02        14.04        16.14        46.75 

$`CAPRIN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 
       36.00        13.78 

  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
             1.02              0.00 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
            46.75            148.01 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
            32.75             22.01 
[1] "1.0 - 46.8 (32.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D895V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAPRIN1 MUTATED         3        0        2         1         1         0
  CAPRIN1 WILD-TYPE      61        1       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAPRIN1 MUTATED           1          0          1          1        0
  CAPRIN1 WILD-TYPE        17          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  CAPRIN1 MUTATED           0         0
  CAPRIN1 WILD-TYPE        12         1
D895V3, multiclass
            clus
vv           CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                1               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  CAPRIN1 MUTATED     0   3   7   1
  CAPRIN1 WILD-TYPE   9  64 242  40
D895V4, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               7               242
  T4               1                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
  CAPRIN1 MUTATED     8   1   2
  CAPRIN1 WILD-TYPE 212  80  64
D895V5, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  N0               8               212
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V6, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED    10   0
  CAPRIN1 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED     10    0
  CAPRIN1 WILD-TYPE  275   48
   clus
vv  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  0              10               275
  1               0                48
[1] 2 2
[1] FALSE
D895V7, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED     6   5
  CAPRIN1 WILD-TYPE 164 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED      6    5
  CAPRIN1 WILD-TYPE  164  192
        clus
vv       CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  FEMALE               6               164
  MALE                 5               192
[1] 2 2
[1] FALSE
D895V8, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED     9   1
  CAPRIN1 WILD-TYPE 291   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED      9    1
  CAPRIN1 WILD-TYPE  291    7
     clus
vv    CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  NO                9               291
  YES               1                 7
[1] 2 2
[1] FALSE
D895V9, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED     8   3
  CAPRIN1 WILD-TYPE 306  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED      8    3
  CAPRIN1 WILD-TYPE  306   45
                               clus
vv                              CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CAPRIN1 MUTATED    10   0   0   0
  CAPRIN1 WILD-TYPE 249   3  22  21
D895V10, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               0                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"
D895V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPRIN1 MUTATED                                  0     0
  CAPRIN1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CAPRIN1 MUTATED                           1     6
  CAPRIN1 WILD-TYPE                        18   170
D895V12, multiclass
                                  clus
vv                                 CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[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 = OR7C1 MUTATION ANALYSIS
D896V1, survival
                 sevent
clus2               0   1
  OR7C1 MUTATED     5   4
  OR7C1 WILD-TYPE 272  74
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              9             346 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              4              74 
$`OR7C1 MUTATED`
TCGA-AA-3516 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3982 
       13.02         3.02         1.02         1.02        53.00        27.02 
TCGA-AD-5900 TCGA-AY-4071 TCGA-AZ-6603 
       12.16         0.95        29.56 

$`OR7C1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       27.42        26.47        14.50        27.09        16.31        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  OR7C1 MUTATED OR7C1 WILD-TYPE 
           0.95            0.00 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          53.00          148.01 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          12.16           22.09 
[1] "0.9 - 53.0 (12.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.5"
D896V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR7C1 MUTATED         3        0        2         1         0         0
  OR7C1 WILD-TYPE      61        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR7C1 MUTATED           1          0          1          0        0         0
  OR7C1 WILD-TYPE        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  OR7C1 MUTATED           0
  OR7C1 WILD-TYPE         1
D896V3, multiclass
            clus
vv           OR7C1 MUTATED OR7C1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR7C1 MUTATED     1   3   5   0
  OR7C1 WILD-TYPE   8  64 244  41
D896V4, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  T1             1               8
  T2             3              64
  T3             5             244
  T4             0              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
  OR7C1 MUTATED     6   2   1
  OR7C1 WILD-TYPE 214  79  65
D896V5, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V6, binary
                 cls
clus                0   1
  OR7C1 MUTATED     6   0
  OR7C1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      6    0
  OR7C1 WILD-TYPE  279   48
   clus
vv  OR7C1 MUTATED OR7C1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D896V7, binary
                 cls
clus                0   1
  OR7C1 MUTATED     6   3
  OR7C1 WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      6    3
  OR7C1 WILD-TYPE  164  194
        clus
vv       OR7C1 MUTATED OR7C1 WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D896V8, binary
                 cls
clus                0   1
  OR7C1 MUTATED     8   0
  OR7C1 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      8    0
  OR7C1 WILD-TYPE  292    8
     clus
vv    OR7C1 MUTATED OR7C1 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D896V9, binary
                 cls
clus                0   1
  OR7C1 MUTATED     5   3
  OR7C1 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      5    3
  OR7C1 WILD-TYPE  309   45
                               clus
vv                              OR7C1 MUTATED OR7C1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR7C1 MUTATED     6   0   0   0
  OR7C1 WILD-TYPE 253   3  22  21
D896V10, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D896V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR7C1 MUTATED                                  0     0
  OR7C1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR7C1 MUTATED                           0     3
  OR7C1 WILD-TYPE                        19   173
D896V12, multiclass
                                  clus
vv                                 OR7C1 MUTATED OR7C1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(897) Variable = CBLL1 MUTATION ANALYSIS
D897V1, survival
                 sevent
clus2               0   1
  CBLL1 MUTATED     4   1
  CBLL1 WILD-TYPE 273  77
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              5             350 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              1              77 
$`CBLL1 MUTATED`
TCGA-A6-5657 TCGA-AA-3663 TCGA-AY-6197 TCGA-AZ-5407 TCGA-F4-6570 
       31.63         6.97        21.44        88.21         6.18 

$`CBLL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CBLL1 MUTATED CBLL1 WILD-TYPE 
           6.18            0.00 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          88.21          148.01 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
         21.440          22.075 
[1] "6.2 - 88.2 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D897V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBLL1 MUTATED         1        0        1         2         0         0
  CBLL1 WILD-TYPE      63        1       25       106         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  CBLL1 MUTATED           0
  CBLL1 WILD-TYPE         1
D897V3, multiclass
            clus
vv           CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CBLL1 MUTATED     1   0   4   0
  CBLL1 WILD-TYPE   8  67 245  41
D897V4, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             4             245
  T4             0              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
  CBLL1 MUTATED     4   1   0
  CBLL1 WILD-TYPE 216  80  66
D897V5, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V6, binary
                 cls
clus                0   1
  CBLL1 MUTATED     4   0
  CBLL1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      4    0
  CBLL1 WILD-TYPE  281   48
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D897V7, binary
                 cls
clus                0   1
  CBLL1 MUTATED     2   3
  CBLL1 WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      2    3
  CBLL1 WILD-TYPE  168  194
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D897V8, binary
                 cls
clus                0   1
  CBLL1 MUTATED     5   0
  CBLL1 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      5    0
  CBLL1 WILD-TYPE  295    8
     clus
vv    CBLL1 MUTATED CBLL1 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D897V9, binary
                 cls
clus                0   1
  CBLL1 MUTATED     5   0
  CBLL1 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      5    0
  CBLL1 WILD-TYPE  309   48
                               clus
vv                              CBLL1 MUTATED CBLL1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CBLL1 MUTATED     4   0   0   0
  CBLL1 WILD-TYPE 255   3  22  21
D897V10, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D897V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBLL1 MUTATED                                  0     0
  CBLL1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CBLL1 MUTATED                           1     3
  CBLL1 WILD-TYPE                        18   173
D897V12, multiclass
                                  clus
vv                                 CBLL1 MUTATED CBLL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = SNAPC1 MUTATION ANALYSIS
D898V1, survival
                  sevent
clus2                0   1
  SNAPC1 MUTATED     3   4
  SNAPC1 WILD-TYPE 274  74
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              348 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               4               74 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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           22.045 
[1] "4.0 - 53.0 (36.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D898V2, continuous
                  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      63        1       24       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC1 MUTATED           0          0          0          0        0
  SNAPC1 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SNAPC1 MUTATED           0         0
  SNAPC1 WILD-TYPE        12         1
D898V3, multiclass
            clus
vv           SNAPC1 MUTATED SNAPC1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SNAPC1 MUTATED     0   1   4   2
  SNAPC1 WILD-TYPE   9  66 245  39
D898V4, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              2               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
  SNAPC1 MUTATED     7   0   0
  SNAPC1 WILD-TYPE 213  81  66
D898V5, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V6, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     6   0
  SNAPC1 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      6    0
  SNAPC1 WILD-TYPE  279   48
   clus
vv  SNAPC1 MUTATED SNAPC1 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D898V7, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     4   3
  SNAPC1 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      4    3
  SNAPC1 WILD-TYPE  166  194
        clus
vv       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D898V8, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     6   0
  SNAPC1 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      6    0
  SNAPC1 WILD-TYPE  294    8
     clus
vv    SNAPC1 MUTATED SNAPC1 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D898V9, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     4   3
  SNAPC1 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      4    3
  SNAPC1 WILD-TYPE  310   45
                               clus
vv                              SNAPC1 MUTATED SNAPC1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SNAPC1 MUTATED     5   0   0   1
  SNAPC1 WILD-TYPE 254   3  22  20
D898V10, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D898V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNAPC1 MUTATED                                  0     1
  SNAPC1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SNAPC1 MUTATED                           0     3
  SNAPC1 WILD-TYPE                        19   173
D898V12, multiclass
                                  clus
vv                                 SNAPC1 MUTATED SNAPC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = CETN3 MUTATION ANALYSIS
D899V1, survival
                 sevent
clus2               0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 271  78
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             349 
  CETN3 MUTATED CETN3 WILD-TYPE 
              0              78 
$`CETN3 MUTATED`
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-6781 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6171 
       35.80        79.69        19.66        12.76        12.00        14.04 

$`CETN3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CETN3 MUTATED CETN3 WILD-TYPE 
             12               0 
  CETN3 MUTATED CETN3 WILD-TYPE 
          79.69          148.01 
  CETN3 MUTATED CETN3 WILD-TYPE 
          16.85           22.09 
[1] "12.0 - 79.7 (16.9)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D899V2, continuous
                 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      62        1       26       106         8         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  CETN3 MUTATED           0
  CETN3 WILD-TYPE         1
D899V3, multiclass
            clus
vv           CETN3 MUTATED CETN3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CETN3 MUTATED     0   2   3   1
  CETN3 WILD-TYPE   9  65 246  40
D899V4, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             1              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
  CETN3 MUTATED     4   2   0
  CETN3 WILD-TYPE 216  79  66
D899V5, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V6, binary
                 cls
clus                0   1
  CETN3 MUTATED     5   0
  CETN3 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      5    0
  CETN3 WILD-TYPE  280   48
   clus
vv  CETN3 MUTATED CETN3 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D899V7, binary
                 cls
clus                0   1
  CETN3 MUTATED     3   3
  CETN3 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      3    3
  CETN3 WILD-TYPE  167  194
        clus
vv       CETN3 MUTATED CETN3 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D899V8, binary
                 cls
clus                0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      6    0
  CETN3 WILD-TYPE  294    8
     clus
vv    CETN3 MUTATED CETN3 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D899V9, binary
                 cls
clus                0   1
  CETN3 MUTATED     3   3
  CETN3 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      3    3
  CETN3 WILD-TYPE  311   45
                               clus
vv                              CETN3 MUTATED CETN3 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CETN3 MUTATED     5   0   0   1
  CETN3 WILD-TYPE 254   3  22  20
D899V10, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D899V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CETN3 MUTATED                                  0     1
  CETN3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CETN3 MUTATED                           0     5
  CETN3 WILD-TYPE                        19   171
D899V12, multiclass
                                  clus
vv                                 CETN3 MUTATED CETN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = CXXC5 MUTATION ANALYSIS
D900V1, survival
                 sevent
clus2               0   1
  CXXC5 MUTATED     4   1
  CXXC5 WILD-TYPE 273  77
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              5             350 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CXXC5 MUTATED CXXC5 WILD-TYPE 
           5.79            0.00 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
          50.04          148.01 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
          15.02           22.09 
[1] "5.8 - 50.0 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D900V2, continuous
                 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      64        1       25       105         7         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  CXXC5 MUTATED           0
  CXXC5 WILD-TYPE         1
D900V3, multiclass
            clus
vv           CXXC5 MUTATED CXXC5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CXXC5 MUTATED     0   0   4   2
  CXXC5 WILD-TYPE   9  67 245  39
D900V4, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             2              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
  CXXC5 MUTATED     5   0   1
  CXXC5 WILD-TYPE 215  81  65
D900V5, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D900V6, binary
                 cls
clus                0   1
  CXXC5 MUTATED     3   0
  CXXC5 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      3    0
  CXXC5 WILD-TYPE  282   48
   clus
vv  CXXC5 MUTATED CXXC5 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D900V7, binary
                 cls
clus                0   1
  CXXC5 MUTATED     3   3
  CXXC5 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      3    3
  CXXC5 WILD-TYPE  167  194
        clus
vv       CXXC5 MUTATED CXXC5 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D900V8, binary
                 cls
clus                0   1
  CXXC5 MUTATED     5   0
  CXXC5 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      5    0
  CXXC5 WILD-TYPE  295    8
     clus
vv    CXXC5 MUTATED CXXC5 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D900V9, binary
                 cls
clus                0   1
  CXXC5 MUTATED     4   2
  CXXC5 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      4    2
  CXXC5 WILD-TYPE  310   46
                               clus
vv                              CXXC5 MUTATED CXXC5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CXXC5 MUTATED     3   0   0   1
  CXXC5 WILD-TYPE 256   3  22  20
D900V10, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D900V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXXC5 MUTATED                                  0     0
  CXXC5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXXC5 MUTATED                           0     5
  CXXC5 WILD-TYPE                        19   171
D900V12, multiclass
                                  clus
vv                                 CXXC5 MUTATED CXXC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = GMNN MUTATION ANALYSIS
D901V1, survival
                sevent
clus2              0   1
  GMNN MUTATED     2   1
  GMNN WILD-TYPE 275  77
  GMNN MUTATED GMNN WILD-TYPE 
             3            352 
  GMNN MUTATED GMNN WILD-TYPE 
             1             77 
$`GMNN MUTATED`
TCGA-AA-A010 TCGA-D5-5538 TCGA-D5-6538 
       34.98        54.61        17.13 

$`GMNN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  GMNN MUTATED GMNN WILD-TYPE 
         17.13           0.00 
  GMNN MUTATED GMNN WILD-TYPE 
         54.61         148.01 
  GMNN MUTATED GMNN WILD-TYPE 
        34.980         22.045 
[1] "17.1 - 54.6 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D901V2, continuous
                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      64        1       26       108         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GMNN MUTATED           0          0          2          0        0         0
  GMNN WILD-TYPE        18          6         42         33       35        12
                vv
clus             STAGE IVB
  GMNN MUTATED           0
  GMNN WILD-TYPE         1
D901V3, multiclass
            clus
vv           GMNN MUTATED GMNN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             0            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GMNN MUTATED     0   0   2   1
  GMNN WILD-TYPE   9  67 247  40
D901V4, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  T1            0              9
  T2            0             67
  T3            2            247
  T4            1             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
  GMNN MUTATED     1   1   1
  GMNN WILD-TYPE 219  80  65
D901V5, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  N0            1            219
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V6, binary
                cls
clus               0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    0
  GMNN WILD-TYPE  282   48
   clus
vv  GMNN MUTATED GMNN WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D901V7, binary
                cls
clus               0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 167 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    0
  GMNN WILD-TYPE  167  197
        clus
vv       GMNN MUTATED GMNN WILD-TYPE
  FEMALE            3            167
  MALE              0            197
[1] 2 2
[1] FALSE
D901V8, binary
                cls
clus               0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    0
  GMNN WILD-TYPE  297    8
     clus
vv    GMNN MUTATED GMNN WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D901V9, binary
                cls
clus               0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    0
  GMNN WILD-TYPE  311   48
                               clus
vv                              GMNN MUTATED GMNN WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GMNN MUTATED     3   0   0   0
  GMNN WILD-TYPE 256   3  22  21
D901V10, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D901V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GMNN MUTATED                                  0     0
  GMNN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GMNN MUTATED                           0     2
  GMNN WILD-TYPE                        19   174
D901V12, multiclass
[1] "Remove cluster labels:" "GMNN MUTATED"          
clus
  GMNN MUTATED GMNN WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6651     TCGA-A6-6652 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-6600     TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-6607     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6539 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 

Clustering(902) Variable = POLD3 MUTATION ANALYSIS
D902V1, survival
                 sevent
clus2               0   1
  POLD3 MUTATED    10   1
  POLD3 WILD-TYPE 267  77
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             344 
  POLD3 MUTATED POLD3 WILD-TYPE 
              1              77 
$`POLD3 MUTATED`
TCGA-AA-3672 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3518 
        0.92        26.17        79.69         8.38        19.66         1.02 
TCGA-AZ-4315 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-F4-6856 
       58.39        16.14        12.00        92.75        35.31 

$`POLD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-A6-6782 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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          22.075 
[1] "0.9 - 92.8 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D902V2, continuous
                 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      61        1       26       103         8         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        17          6         44         31       35        12
                 vv
clus              STAGE IVB
  POLD3 MUTATED           0
  POLD3 WILD-TYPE         1
D902V3, multiclass
            clus
vv           POLD3 MUTATED POLD3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  POLD3 MUTATED     0   3   6   2
  POLD3 WILD-TYPE   9  64 243  39
D902V4, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             6             243
  T4             2              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
  POLD3 MUTATED     8   2   1
  POLD3 WILD-TYPE 212  79  65
D902V5, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V6, binary
                 cls
clus                0   1
  POLD3 MUTATED    10   0
  POLD3 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED     10    0
  POLD3 WILD-TYPE  275   48
   clus
vv  POLD3 MUTATED POLD3 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D902V7, binary
                 cls
clus                0   1
  POLD3 MUTATED     3   8
  POLD3 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED      3    8
  POLD3 WILD-TYPE  167  189
        clus
vv       POLD3 MUTATED POLD3 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D902V8, binary
                 cls
clus                0   1
  POLD3 MUTATED     9   0
  POLD3 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED      9    0
  POLD3 WILD-TYPE  291    8
     clus
vv    POLD3 MUTATED POLD3 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D902V9, binary
                 cls
clus                0   1
  POLD3 MUTATED     8   3
  POLD3 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED      8    3
  POLD3 WILD-TYPE  306   45
                               clus
vv                              POLD3 MUTATED POLD3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  POLD3 MUTATED     9   0   0   0
  POLD3 WILD-TYPE 250   3  22  21
D902V10, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D902V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLD3 MUTATED                                  0     0
  POLD3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  POLD3 MUTATED                           1     8
  POLD3 WILD-TYPE                        18   168
D902V12, multiclass
                                  clus
vv                                 POLD3 MUTATED POLD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = FAM155B MUTATION ANALYSIS
D903V1, survival
                   sevent
clus2                 0   1
  FAM155B MUTATED     6   2
  FAM155B WILD-TYPE 271  76
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               347 
  FAM155B MUTATED FAM155B WILD-TYPE 
                2                76 
$`FAM155B MUTATED`
TCGA-AA-3815 TCGA-AA-3819 TCGA-AD-6889 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5403 
       33.04        25.02        83.24        33.01        58.39        62.79 
TCGA-CK-5913 TCGA-CM-5348 
       51.32        22.98 

$`FAM155B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  FAM155B MUTATED FAM155B WILD-TYPE 
            22.98              0.00 
  FAM155B MUTATED FAM155B WILD-TYPE 
            83.24            148.01 
  FAM155B MUTATED FAM155B WILD-TYPE 
            42.18             21.99 
[1] "23.0 - 83.2 (42.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D903V2, continuous
                   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      64        1       25       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM155B MUTATED           0          0          1          0        0
  FAM155B WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM155B MUTATED           1         0
  FAM155B WILD-TYPE        11         1
D903V3, multiclass
            clus
vv           FAM155B MUTATED FAM155B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  FAM155B MUTATED     0   0   8   0
  FAM155B WILD-TYPE   9  67 241  41
D903V4, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               8               241
  T4               0                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
  FAM155B MUTATED     6   2   0
  FAM155B WILD-TYPE 214  79  66
D903V5, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  N0               6               214
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V6, binary
                   cls
clus                  0   1
  FAM155B MUTATED     5   1
  FAM155B WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      5    1
  FAM155B WILD-TYPE  280   47
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0               5               280
  1               1                47
[1] 2 2
[1] FALSE
D903V7, binary
                   cls
clus                  0   1
  FAM155B MUTATED     4   4
  FAM155B WILD-TYPE 166 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      4    4
  FAM155B WILD-TYPE  166  193
        clus
vv       FAM155B MUTATED FAM155B WILD-TYPE
  FEMALE               4               166
  MALE                 4               193
[1] 2 2
[1] FALSE
D903V8, binary
                   cls
clus                  0   1
  FAM155B MUTATED     8   0
  FAM155B WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      8    0
  FAM155B WILD-TYPE  292    8
     clus
vv    FAM155B MUTATED FAM155B WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D903V9, binary
                   cls
clus                  0   1
  FAM155B MUTATED     8   0
  FAM155B WILD-TYPE 306  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      8    0
  FAM155B WILD-TYPE  306   48
                               clus
vv                              FAM155B MUTATED FAM155B WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM155B MUTATED     6   0   0   1
  FAM155B WILD-TYPE 253   3  22  20
D903V10, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D903V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM155B MUTATED                                  0     1
  FAM155B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM155B MUTATED                           1     4
  FAM155B WILD-TYPE                        18   172
D903V12, multiclass
                                  clus
vv                                 FAM155B MUTATED FAM155B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = CTTN MUTATION ANALYSIS
D904V1, survival
                sevent
clus2              0   1
  CTTN MUTATED     4   0
  CTTN WILD-TYPE 273  78
  CTTN MUTATED CTTN WILD-TYPE 
             4            351 
  CTTN MUTATED CTTN WILD-TYPE 
             0             78 
$`CTTN MUTATED`
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-4950 TCGA-CK-4952 
       27.09        58.39        85.45        15.62 

$`CTTN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56       148.01        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CTTN MUTATED CTTN WILD-TYPE 
         15.62           0.00 
  CTTN MUTATED CTTN WILD-TYPE 
         85.45         148.01 
  CTTN MUTATED CTTN WILD-TYPE 
         42.74          22.03 
[1] "15.6 - 85.5 (42.7)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D904V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTTN MUTATED         1        0        0         1         0         0
  CTTN WILD-TYPE      63        1       26       107         8         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  CTTN MUTATED           0
  CTTN WILD-TYPE         1
D904V3, multiclass
            clus
vv           CTTN MUTATED CTTN WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  CTTN MUTATED     0   1   2   1
  CTTN WILD-TYPE   9  66 247  40
D904V4, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            1             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
  CTTN MUTATED     2   1   1
  CTTN WILD-TYPE 218  80  65
D904V5, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  N0            2            218
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V6, binary
                cls
clus               0   1
  CTTN MUTATED     4   0
  CTTN WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      4    0
  CTTN WILD-TYPE  281   48
   clus
vv  CTTN MUTATED CTTN WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D904V7, binary
                cls
clus               0   1
  CTTN MUTATED     3   1
  CTTN WILD-TYPE 167 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      3    1
  CTTN WILD-TYPE  167  196
        clus
vv       CTTN MUTATED CTTN WILD-TYPE
  FEMALE            3            167
  MALE              1            196
[1] 2 2
[1] FALSE
D904V8, binary
                cls
clus               0   1
  CTTN MUTATED     2   0
  CTTN WILD-TYPE 298   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      2    0
  CTTN WILD-TYPE  298    8
     clus
vv    CTTN MUTATED CTTN WILD-TYPE
  NO             2            298
  YES            0              8
[1] 2 2
[1] FALSE
D904V9, binary
                cls
clus               0   1
  CTTN MUTATED     2   2
  CTTN WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      2    2
  CTTN WILD-TYPE  312   46
                               clus
vv                              CTTN MUTATED CTTN WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTTN MUTATED     2   1   0   1
  CTTN WILD-TYPE 257   2  22  20
D904V10, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  R0            2            257
  R1            1              2
  R2            0             22
  RX            1             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"
D904V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTTN MUTATED                                  0     0
  CTTN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTTN MUTATED                           1     3
  CTTN WILD-TYPE                        18   173
D904V12, multiclass
                                  clus
vv                                 CTTN MUTATED CTTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = PIGC MUTATION ANALYSIS
D905V1, survival
                sevent
clus2              0   1
  PIGC MUTATED     2   2
  PIGC WILD-TYPE 275  76
  PIGC MUTATED PIGC WILD-TYPE 
             4            351 
  PIGC MUTATED PIGC WILD-TYPE 
             2             76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79        88.21        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.06 
[1] "6.8 - 49.4 (22.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D905V2, continuous
                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      62        1       25       107         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  PIGC MUTATED           0
  PIGC WILD-TYPE         1
D905V3, multiclass
            clus
vv           PIGC MUTATED PIGC WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PIGC MUTATED     0   2   2   0
  PIGC WILD-TYPE   9  65 247  41
D905V4, multiclass
    clus
vv   PIGC MUTATED PIGC WILD-TYPE
  T1            0              9
  T2            2             65
  T3            2            247
  T4            0             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
  PIGC MUTATED     4   0   0
  PIGC WILD-TYPE 216  81  66
D905V5, multiclass
    clus
vv   PIGC MUTATED PIGC WILD-TYPE
  N0            4            216
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V6, binary
                cls
clus               0   1
  PIGC MUTATED     2   0
  PIGC WILD-TYPE 283  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      2    0
  PIGC WILD-TYPE  283   48
   clus
vv  PIGC MUTATED PIGC WILD-TYPE
  0            2            283
  1            0             48
[1] 2 2
[1] FALSE
D905V7, binary
                cls
clus               0   1
  PIGC MUTATED     3   1
  PIGC WILD-TYPE 167 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      3    1
  PIGC WILD-TYPE  167  196
        clus
vv       PIGC MUTATED PIGC WILD-TYPE
  FEMALE            3            167
  MALE              1            196
[1] 2 2
[1] FALSE
D905V8, binary
                cls
clus               0   1
  PIGC MUTATED     4   0
  PIGC WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      4    0
  PIGC WILD-TYPE  296    8
     clus
vv    PIGC MUTATED PIGC WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D905V9, binary
                cls
clus               0   1
  PIGC MUTATED     4   0
  PIGC WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      4    0
  PIGC WILD-TYPE  310   48
                               clus
vv                              PIGC MUTATED PIGC WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PIGC MUTATED     2   0   0   0
  PIGC WILD-TYPE 257   3  22  21
D905V10, multiclass
[1] "Remove cluster labels:" "PIGC MUTATED"          
clus
  PIGC MUTATED PIGC WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     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-3527 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-2676     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-3502     TCGA-AA-3510 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660 
"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-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     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-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3975     TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00W     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-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4682 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6162 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
D905V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGC MUTATED                                  0     0
  PIGC WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGC MUTATED                           0     4
  PIGC WILD-TYPE                        19   172
D905V12, multiclass
                                  clus
vv                                 PIGC MUTATED PIGC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = CSGALNACT1 MUTATION ANALYSIS
D906V1, survival
                      sevent
clus2                    0   1
  CSGALNACT1 MUTATED     6   2
  CSGALNACT1 WILD-TYPE 271  76
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  347 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   2                   76 
$`CSGALNACT1 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6781 TCGA-AA-3489 TCGA-AD-6899 TCGA-AU-3779 
       35.80        26.17        19.66         7.04         5.79        14.50 
TCGA-CA-6716 TCGA-CA-6717 
       12.20        12.76 

$`CSGALNACT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        20.28         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       24.53        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.69        12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                5.79                 0.00 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
               35.80               148.01 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
               13.63                22.09 
[1] "5.8 - 35.8 (13.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D906V2, continuous
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSGALNACT1 MUTATED         0        0        1         5         0         0
  CSGALNACT1 WILD-TYPE      64        1       25       103         8         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSGALNACT1 MUTATED           0          0          0          2        0
  CSGALNACT1 WILD-TYPE        18          6         44         31       35
                      vv
clus                   STAGE IVA STAGE IVB
  CSGALNACT1 MUTATED           0         0
  CSGALNACT1 WILD-TYPE        12         1
D906V3, multiclass
            clus
vv           CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  STAGE I                     0                   64
  STAGE IA                    0                    1
  STAGE II                    1                   25
  STAGE IIA                   5                  103
  STAGE IIB                   0                    8
  STAGE IIC                   0                    1
  STAGE III                   0                   18
  STAGE IIIA                  0                    6
  STAGE IIIB                  0                   44
  STAGE IIIC                  2                   31
  STAGE IV                    0                   35
  STAGE IVA                   0                   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
  CSGALNACT1 MUTATED     0   0   6   2
  CSGALNACT1 WILD-TYPE   9  67 243  39
D906V4, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  T1                  0                    9
  T2                  0                   67
  T3                  6                  243
  T4                  2                   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
  CSGALNACT1 MUTATED     6   1   1
  CSGALNACT1 WILD-TYPE 214  80  65
D906V5, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  N0                  6                  214
  N1                  1                   80
  N2                  1                   65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V6, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     6   0
  CSGALNACT1 WILD-TYPE 279  48
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      6    0
  CSGALNACT1 WILD-TYPE  279   48
   clus
vv  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  0                  6                  279
  1                  0                   48
[1] 2 2
[1] FALSE
D906V7, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     3   5
  CSGALNACT1 WILD-TYPE 167 192
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      3    5
  CSGALNACT1 WILD-TYPE  167  192
        clus
vv       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  FEMALE                  3                  167
  MALE                    5                  192
[1] 2 2
[1] FALSE
D906V8, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     8   0
  CSGALNACT1 WILD-TYPE 292   8
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      8    0
  CSGALNACT1 WILD-TYPE  292    8
     clus
vv    CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  NO                   8                  292
  YES                  0                    8
[1] 2 2
[1] FALSE
D906V9, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     5   3
  CSGALNACT1 WILD-TYPE 309  45
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      5    3
  CSGALNACT1 WILD-TYPE  309   45
                               clus
vv                              CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  COLON ADENOCARCINOMA                           5                  309
  COLON MUCINOUS ADENOCARCINOMA                  3                   45
[1] 2 2
[1] FALSE
                      vv
clus                    R0  R1  R2  RX
  CSGALNACT1 MUTATED     5   0   0   2
  CSGALNACT1 WILD-TYPE 254   3  22  19
D906V10, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  R0                  5                  254
  R1                  0                    3
  R2                  0                   22
  RX                  2                   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"
D906V11, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSGALNACT1 MUTATED                                  0     2
  CSGALNACT1 WILD-TYPE                                1     8
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT1 MUTATED                           0     5
  CSGALNACT1 WILD-TYPE                        19   171
D906V12, multiclass
                                  clus
vv                                 CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             2                    8
  BLACK OR AFRICAN AMERICAN                         0                   19
  WHITE                                             5                  171
[1] 4 2
[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 = CACHD1 MUTATION ANALYSIS
D907V1, survival
                  sevent
clus2                0   1
  CACHD1 MUTATED    16   4
  CACHD1 WILD-TYPE 261  74
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              20              335 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
               4               74 
$`CACHD1 MUTATED`
TCGA-AA-3516 TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6141 
       13.02        24.00        35.80        46.65        22.06         8.38 
TCGA-A6-6648 TCGA-A6-6781 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       25.18        19.66         2.01        25.02         4.01        34.98 
TCGA-AA-A01I TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5862 
       31.00        14.50        58.39        10.06        30.08         5.03 
TCGA-CM-6162 TCGA-D5-6538 
       12.00        17.13 

$`CACHD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        79.69        43.76        43.76        42.90        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-A6-6142 TCGA-A6-6651 TCGA-A6-6652 
       32.71        27.09        22.52        25.08        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       15.02        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CACHD1 MUTATED CACHD1 WILD-TYPE 
            2.01             0.00 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
           58.39           148.01 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
           20.86            22.09 
[1] "2.0 - 58.4 (20.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D907V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CACHD1 MUTATED         1        0        0        10         2         0
  CACHD1 WILD-TYPE      63        1       26        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACHD1 MUTATED           1          0          3          1        0
  CACHD1 WILD-TYPE        17          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  CACHD1 MUTATED           2         0
  CACHD1 WILD-TYPE        10         1
D907V3, multiclass
            clus
vv           CACHD1 MUTATED CACHD1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA              10               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               2               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
  CACHD1 MUTATED     0   2  16   3
  CACHD1 WILD-TYPE   9  65 233  38
D907V4, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             16              233
  T4              3               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
  CACHD1 MUTATED    15   4   2
  CACHD1 WILD-TYPE 205  77  64
D907V5, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  N0             15              205
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V6, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    17   2
  CACHD1 WILD-TYPE 268  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     17    2
  CACHD1 WILD-TYPE  268   46
   clus
vv  CACHD1 MUTATED CACHD1 WILD-TYPE
  0             17              268
  1              2               46
[1] 2 2
[1] FALSE
D907V7, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    12   9
  CACHD1 WILD-TYPE 158 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     12    9
  CACHD1 WILD-TYPE  158  188
        clus
vv       CACHD1 MUTATED CACHD1 WILD-TYPE
  FEMALE             12              158
  MALE                9              188
[1] 2 2
[1] FALSE
D907V8, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    18   0
  CACHD1 WILD-TYPE 282   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     18    0
  CACHD1 WILD-TYPE  282    8
     clus
vv    CACHD1 MUTATED CACHD1 WILD-TYPE
  NO              18              282
  YES              0                8
[1] 2 2
[1] FALSE
D907V9, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    15   6
  CACHD1 WILD-TYPE 299  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     15    6
  CACHD1 WILD-TYPE  299   42
                               clus
vv                              CACHD1 MUTATED CACHD1 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CACHD1 MUTATED    15   0   0   1
  CACHD1 WILD-TYPE 244   3  22  20
D907V10, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              1               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"
D907V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACHD1 MUTATED                                  0     1
  CACHD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CACHD1 MUTATED                           1    11
  CACHD1 WILD-TYPE                        18   165
D907V12, multiclass
                                  clus
vv                                 CACHD1 MUTATED CACHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(908) Variable = DBN1 MUTATION ANALYSIS
D908V1, survival
                sevent
clus2              0   1
  DBN1 MUTATED     7   2
  DBN1 WILD-TYPE 270  76
  DBN1 MUTATED DBN1 WILD-TYPE 
             9            346 
  DBN1 MUTATED DBN1 WILD-TYPE 
             2             76 
$`DBN1 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-A6-5662 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-D5-6533 
       19.04        24.00        23.61        49.41        12.10        25.48 
TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-7000 
       16.14        14.30        10.26 

$`DBN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21         6.77        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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  DBN1 MUTATED DBN1 WILD-TYPE 
         10.26           0.00 
  DBN1 MUTATED DBN1 WILD-TYPE 
         49.41         148.01 
  DBN1 MUTATED DBN1 WILD-TYPE 
        19.040         22.075 
[1] "10.3 - 49.4 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D908V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DBN1 MUTATED         2        0        1         2         0         0
  DBN1 WILD-TYPE      62        1       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DBN1 MUTATED           0          0          0          0        2         1
  DBN1 WILD-TYPE        18          6         44         33       33        11
                vv
clus             STAGE IVB
  DBN1 MUTATED           0
  DBN1 WILD-TYPE         1
D908V3, multiclass
            clus
vv           DBN1 MUTATED DBN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             1             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
  DBN1 MUTATED     0   2   5   2
  DBN1 WILD-TYPE   9  65 244  39
D908V4, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            2             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
  DBN1 MUTATED     7   1   1
  DBN1 WILD-TYPE 213  80  65
D908V5, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V6, binary
                cls
clus               0   1
  DBN1 MUTATED     5   3
  DBN1 WILD-TYPE 280  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      5    3
  DBN1 WILD-TYPE  280   45
   clus
vv  DBN1 MUTATED DBN1 WILD-TYPE
  0            5            280
  1            3             45
[1] 2 2
[1] FALSE
D908V7, binary
                cls
clus               0   1
  DBN1 MUTATED     4   5
  DBN1 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      4    5
  DBN1 WILD-TYPE  166  192
        clus
vv       DBN1 MUTATED DBN1 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D908V8, binary
                cls
clus               0   1
  DBN1 MUTATED     8   1
  DBN1 WILD-TYPE 292   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      8    1
  DBN1 WILD-TYPE  292    7
     clus
vv    DBN1 MUTATED DBN1 WILD-TYPE
  NO             8            292
  YES            1              7
[1] 2 2
[1] FALSE
D908V9, binary
                cls
clus               0   1
  DBN1 MUTATED     6   3
  DBN1 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      6    3
  DBN1 WILD-TYPE  308   45
                               clus
vv                              DBN1 MUTATED DBN1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DBN1 MUTATED     5   0   1   0
  DBN1 WILD-TYPE 254   3  21  21
D908V10, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            1             21
  RX            0             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"
D908V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DBN1 MUTATED                                  0     0
  DBN1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DBN1 MUTATED                           1     6
  DBN1 WILD-TYPE                        18   170
D908V12, multiclass
                                  clus
vv                                 DBN1 MUTATED DBN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = CRTC1 MUTATION ANALYSIS
D909V1, survival
                 sevent
clus2               0   1
  CRTC1 MUTATED    11   2
  CRTC1 WILD-TYPE 266  76
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             342 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              2              76 
$`CRTC1 MUTATED`
TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6653 
       10.88        35.80        26.17        79.69        22.06        24.39 
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3667 TCGA-AY-6197 TCGA-CM-6162 TCGA-D5-6930 
       20.12         3.02        14.01        21.44        12.00        13.35 
TCGA-G4-6315 
       61.91 

$`CRTC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  CRTC1 MUTATED CRTC1 WILD-TYPE 
           3.02            0.00 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
          79.69          148.01 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
          21.44           22.09 
[1] "3.0 - 79.7 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D909V2, continuous
                 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      61        1       25       102         8         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  CRTC1 MUTATED           0
  CRTC1 WILD-TYPE         1
D909V3, multiclass
            clus
vv           CRTC1 MUTATED CRTC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  CRTC1 MUTATED     0   3   9   1
  CRTC1 WILD-TYPE   9  64 240  40
D909V4, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             1              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
  CRTC1 MUTATED    10   2   1
  CRTC1 WILD-TYPE 210  79  65
D909V5, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V6, binary
                 cls
clus                0   1
  CRTC1 MUTATED     9   1
  CRTC1 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      9    1
  CRTC1 WILD-TYPE  276   47
   clus
vv  CRTC1 MUTATED CRTC1 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D909V7, binary
                 cls
clus                0   1
  CRTC1 MUTATED     6   7
  CRTC1 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      6    7
  CRTC1 WILD-TYPE  164  190
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D909V8, binary
                 cls
clus                0   1
  CRTC1 MUTATED    13   0
  CRTC1 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED     13    0
  CRTC1 WILD-TYPE  287    8
     clus
vv    CRTC1 MUTATED CRTC1 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D909V9, binary
                 cls
clus                0   1
  CRTC1 MUTATED    10   3
  CRTC1 WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED     10    3
  CRTC1 WILD-TYPE  304   45
                               clus
vv                              CRTC1 MUTATED CRTC1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CRTC1 MUTATED    10   0   0   0
  CRTC1 WILD-TYPE 249   3  22  21
D909V10, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D909V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRTC1 MUTATED                                  0     0
  CRTC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CRTC1 MUTATED                           0    11
  CRTC1 WILD-TYPE                        19   165
D909V12, multiclass
                                  clus
vv                                 CRTC1 MUTATED CRTC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(910) Variable = RRAGD MUTATION ANALYSIS
D910V1, survival
                 sevent
clus2               0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 270  78
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             348 
  RRAGD MUTATED RRAGD WILD-TYPE 
              0              78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.075 
[1] "14.5 - 88.2 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D910V2, continuous
                 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      62        1       26       106         8         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        18          6         42         33       35        11
                 vv
clus              STAGE IVB
  RRAGD MUTATED           0
  RRAGD WILD-TYPE         1
D910V3, multiclass
            clus
vv           RRAGD MUTATED RRAGD WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  RRAGD MUTATED     1   1   5   0
  RRAGD WILD-TYPE   8  66 244  41
D910V4, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  T1             1               8
  T2             1              66
  T3             5             244
  T4             0              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
  RRAGD MUTATED     4   1   2
  RRAGD WILD-TYPE 216  80  64
D910V5, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  N0             4             216
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V6, binary
                 cls
clus                0   1
  RRAGD MUTATED     5   1
  RRAGD WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      5    1
  RRAGD WILD-TYPE  280   47
   clus
vv  RRAGD MUTATED RRAGD WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D910V7, binary
                 cls
clus                0   1
  RRAGD MUTATED     4   3
  RRAGD WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      4    3
  RRAGD WILD-TYPE  166  194
        clus
vv       RRAGD MUTATED RRAGD WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D910V8, binary
                 cls
clus                0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      7    0
  RRAGD WILD-TYPE  293    8
     clus
vv    RRAGD MUTATED RRAGD WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D910V9, binary
                 cls
clus                0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      7    0
  RRAGD WILD-TYPE  307   48
                               clus
vv                              RRAGD MUTATED RRAGD WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RRAGD MUTATED     3   0   1   1
  RRAGD WILD-TYPE 256   3  21  20
D910V10, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  R0             3             256
  R1             0               3
  R2             1              21
  RX             1              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"
D910V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRAGD MUTATED                                  0     0
  RRAGD WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RRAGD MUTATED                           0     6
  RRAGD WILD-TYPE                        19   170
D910V12, multiclass
                                  clus
vv                                 RRAGD MUTATED RRAGD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = CTNNA3 MUTATION ANALYSIS
D911V1, survival
                  sevent
clus2                0   1
  CTNNA3 MUTATED    20   6
  CTNNA3 WILD-TYPE 257  72
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              329 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
               6               72 
$`CTNNA3 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 
        1.02        19.04        10.88       100.01        35.80        26.17 
TCGA-A6-2678 TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3966 
       42.28        24.39         6.97         0.00        53.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y TCGA-AY-6197 TCGA-AY-6386 
       25.02         4.01        34.98        39.98        21.44        17.82 
TCGA-AZ-5407 TCGA-CM-6171 TCGA-D5-6540 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 
       88.21        14.04        16.14        13.41        13.35        10.26 
TCGA-F4-6570 TCGA-F4-6855 
        6.18        47.41 

$`CTNNA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        63.62        22.09        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.90        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        17.03        10.06        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
        0.92        41.00        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01         0.20        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        49.41         6.77 
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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
               0                0 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
          100.01           148.01 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
           18.43            22.09 
[1] "0.0 - 100.0 (18.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D911V2, continuous
                  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      57        1       21       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNA3 MUTATED           0          0          2          0        1
  CTNNA3 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CTNNA3 MUTATED           0         0
  CTNNA3 WILD-TYPE        12         1
D911V3, multiclass
            clus
vv           CTNNA3 MUTATED CTNNA3 WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CTNNA3 MUTATED     1   7  14   4
  CTNNA3 WILD-TYPE   8  60 235  37
D911V4, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  T1              1                8
  T2              7               60
  T3             14              235
  T4              4               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
  CTNNA3 MUTATED    22   3   1
  CTNNA3 WILD-TYPE 198  78  65
D911V5, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  N0             22              198
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V6, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    22   1
  CTNNA3 WILD-TYPE 263  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     22    1
  CTNNA3 WILD-TYPE  263   47
   clus
vv  CTNNA3 MUTATED CTNNA3 WILD-TYPE
  0             22              263
  1              1               47
[1] 2 2
[1] FALSE
D911V7, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    13  13
  CTNNA3 WILD-TYPE 157 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     13   13
  CTNNA3 WILD-TYPE  157  184
        clus
vv       CTNNA3 MUTATED CTNNA3 WILD-TYPE
  FEMALE             13              157
  MALE               13              184
[1] 2 2
[1] FALSE
D911V8, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    22   0
  CTNNA3 WILD-TYPE 278   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     22    0
  CTNNA3 WILD-TYPE  278    8
     clus
vv    CTNNA3 MUTATED CTNNA3 WILD-TYPE
  NO              22              278
  YES              0                8
[1] 2 2
[1] FALSE
D911V9, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    21   5
  CTNNA3 WILD-TYPE 293  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     21    5
  CTNNA3 WILD-TYPE  293   43
                               clus
vv                              CTNNA3 MUTATED CTNNA3 WILD-TYPE
  COLON ADENOCARCINOMA                      21              293
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNA3 MUTATED    20   0   0   0
  CTNNA3 WILD-TYPE 239   3  22  21
D911V10, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  R0             20              239
  R1              0                3
  R2              0               22
  RX              0               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"
D911V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNA3 MUTATED                                  0     0
  CTNNA3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNA3 MUTATED                           1    15
  CTNNA3 WILD-TYPE                        18   161
D911V12, multiclass
                                  clus
vv                                 CTNNA3 MUTATED CTNNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        15              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(912) Variable = EML4 MUTATION ANALYSIS
D912V1, survival
                sevent
clus2              0   1
  EML4 MUTATED     8   1
  EML4 WILD-TYPE 269  77
  EML4 MUTATED EML4 WILD-TYPE 
             9            346 
  EML4 MUTATED EML4 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-F4-6460 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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         22.045 
[1] "8.6 - 119.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.9"
D912V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EML4 MUTATED         1        0        1         6         0         0
  EML4 WILD-TYPE      63        1       25       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EML4 MUTATED           0          0          1          0        0         0
  EML4 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  EML4 MUTATED           0
  EML4 WILD-TYPE         1
D912V3, multiclass
            clus
vv           EML4 MUTATED EML4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  EML4 MUTATED     0   2   8   0
  EML4 WILD-TYPE   9  65 241  41
D912V4, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            0             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
  EML4 MUTATED     9   0   1
  EML4 WILD-TYPE 211  81  65
D912V5, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  N0            9            211
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V6, binary
                cls
clus               0   1
  EML4 MUTATED     9   0
  EML4 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      9    0
  EML4 WILD-TYPE  276   48
   clus
vv  EML4 MUTATED EML4 WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D912V7, binary
                cls
clus               0   1
  EML4 MUTATED     5   5
  EML4 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      5    5
  EML4 WILD-TYPE  165  192
        clus
vv       EML4 MUTATED EML4 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D912V8, binary
                cls
clus               0   1
  EML4 MUTATED     8   0
  EML4 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      8    0
  EML4 WILD-TYPE  292    8
     clus
vv    EML4 MUTATED EML4 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D912V9, binary
                cls
clus               0   1
  EML4 MUTATED     7   3
  EML4 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      7    3
  EML4 WILD-TYPE  307   45
                               clus
vv                              EML4 MUTATED EML4 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EML4 MUTATED     7   0   0   1
  EML4 WILD-TYPE 252   3  22  20
D912V10, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D912V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EML4 MUTATED                                  0     1
  EML4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EML4 MUTATED                           0     5
  EML4 WILD-TYPE                        19   171
D912V12, multiclass
                                  clus
vv                                 EML4 MUTATED EML4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = PLA2G15 MUTATION ANALYSIS
D913V1, survival
                   sevent
clus2                 0   1
  PLA2G15 MUTATED     2   3
  PLA2G15 WILD-TYPE 275  75
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                5               350 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                3                75 
$`PLA2G15 MUTATED`
TCGA-AZ-6601 TCGA-AA-3811 TCGA-CM-4743 TCGA-D5-6534 TCGA-DM-A1D7 
      100.01        10.06        23.05        43.27        13.32 

$`PLA2G15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            10.06              0.00 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           100.01            148.01 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           23.050            22.045 
[1] "10.1 - 100.0 (23.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2"  
D913V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLA2G15 MUTATED         0        0        1         3         0         0
  PLA2G15 WILD-TYPE      64        1       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G15 MUTATED           1          0          0          0        0
  PLA2G15 WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  PLA2G15 MUTATED           0         0
  PLA2G15 WILD-TYPE        12         1
D913V3, multiclass
            clus
vv           PLA2G15 MUTATED PLA2G15 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  PLA2G15 MUTATED     0   0   5   0
  PLA2G15 WILD-TYPE   9  67 244  41
D913V4, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  PLA2G15 MUTATED     4   0   1
  PLA2G15 WILD-TYPE 216  81  65
D913V5, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  N0               4               216
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V6, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     5   0
  PLA2G15 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      5    0
  PLA2G15 WILD-TYPE  280   48
   clus
vv  PLA2G15 MUTATED PLA2G15 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D913V7, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     2   3
  PLA2G15 WILD-TYPE 168 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      2    3
  PLA2G15 WILD-TYPE  168  194
        clus
vv       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  FEMALE               2               168
  MALE                 3               194
[1] 2 2
[1] FALSE
D913V8, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     4   0
  PLA2G15 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      4    0
  PLA2G15 WILD-TYPE  296    8
     clus
vv    PLA2G15 MUTATED PLA2G15 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D913V9, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     3   1
  PLA2G15 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      3    1
  PLA2G15 WILD-TYPE  311   47
                               clus
vv                              PLA2G15 MUTATED PLA2G15 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLA2G15 MUTATED     3   0   0   0
  PLA2G15 WILD-TYPE 256   3  22  21
D913V10, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D913V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLA2G15 MUTATED                                  0     0
  PLA2G15 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLA2G15 MUTATED                           0     4
  PLA2G15 WILD-TYPE                        19   172
D913V12, multiclass
                                  clus
vv                                 PLA2G15 MUTATED PLA2G15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = USP29 MUTATION ANALYSIS
D914V1, survival
                 sevent
clus2               0   1
  USP29 MUTATED    12   4
  USP29 WILD-TYPE 265  74
  USP29 MUTATED USP29 WILD-TYPE 
             16             339 
  USP29 MUTATED USP29 WILD-TYPE 
              4              74 
$`USP29 MUTATED`
TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3950 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-A00N 
        0.99         0.92        24.00         3.02        26.99         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-6535 
       34.98        12.16        58.39        10.06        85.45        15.12 
TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A28H TCGA-F4-6570 
       11.64        12.00       117.07         6.18 

$`USP29 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  USP29 MUTATED USP29 WILD-TYPE 
           0.92            0.00 
  USP29 MUTATED USP29 WILD-TYPE 
         117.07          148.01 
  USP29 MUTATED USP29 WILD-TYPE 
          12.08           22.09 
[1] "0.9 - 117.1 (12.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D914V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP29 MUTATED         3        0        1         7         2         0
  USP29 WILD-TYPE      61        1       25       101         6         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        17          6         42         31       35        12
                 vv
clus              STAGE IVB
  USP29 MUTATED           0
  USP29 WILD-TYPE         1
D914V3, multiclass
            clus
vv           USP29 MUTATED USP29 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  USP29 MUTATED     0   3  12   3
  USP29 WILD-TYPE   9  64 237  38
D914V4, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             3              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
  USP29 MUTATED    13   3   2
  USP29 WILD-TYPE 207  78  64
D914V5, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  N0            13             207
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V6, binary
                 cls
clus                0   1
  USP29 MUTATED    15   0
  USP29 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     15    0
  USP29 WILD-TYPE  270   48
   clus
vv  USP29 MUTATED USP29 WILD-TYPE
  0            15             270
  1             0              48
[1] 2 2
[1] FALSE
D914V7, binary
                 cls
clus                0   1
  USP29 MUTATED     9   9
  USP29 WILD-TYPE 161 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED      9    9
  USP29 WILD-TYPE  161  188
        clus
vv       USP29 MUTATED USP29 WILD-TYPE
  FEMALE             9             161
  MALE               9             188
[1] 2 2
[1] FALSE
D914V8, binary
                 cls
clus                0   1
  USP29 MUTATED    14   0
  USP29 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     14    0
  USP29 WILD-TYPE  286    8
     clus
vv    USP29 MUTATED USP29 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D914V9, binary
                 cls
clus                0   1
  USP29 MUTATED    12   6
  USP29 WILD-TYPE 302  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     12    6
  USP29 WILD-TYPE  302   42
                               clus
vv                              USP29 MUTATED USP29 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP29 MUTATED    13   1   0   3
  USP29 WILD-TYPE 246   2  22  18
D914V10, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  R0            13             246
  R1             1               2
  R2             0              22
  RX             3              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"
D914V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP29 MUTATED                                  0     1
  USP29 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP29 MUTATED                           1     8
  USP29 WILD-TYPE                        18   168
D914V12, multiclass
                                  clus
vv                                 USP29 MUTATED USP29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = BAIAP2L1 MUTATION ANALYSIS
D915V1, survival
                    sevent
clus2                  0   1
  BAIAP2L1 MUTATED     9   3
  BAIAP2L1 WILD-TYPE 268  75
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                12                343 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                 3                 75 
$`BAIAP2L1 MUTATED`
TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6588 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 
       10.88        35.80        26.17         6.97         2.01        25.02 
TCGA-AA-A01R TCGA-AD-5900 TCGA-AZ-4315 TCGA-D5-6927 TCGA-DM-A1DA TCGA-F4-6570 
       35.01        12.16        58.39         9.44         7.50         6.18 

$`BAIAP2L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
              2.01               0.00 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
             58.39             148.01 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
             11.52              22.09 
[1] "2.0 - 58.4 (11.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D915V2, continuous
                    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      63        1       25       102         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAIAP2L1 MUTATED           1          0          0          1        0
  BAIAP2L1 WILD-TYPE        17          6         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  BAIAP2L1 MUTATED           0         0
  BAIAP2L1 WILD-TYPE        12         1
D915V3, multiclass
            clus
vv           BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 6                102
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  BAIAP2L1 MUTATED     0   2   9   1
  BAIAP2L1 WILD-TYPE   9  65 240  40
D915V4, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                9                240
  T4                1                 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
  BAIAP2L1 MUTATED     9   0   3
  BAIAP2L1 WILD-TYPE 211  81  63
D915V5, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  N0                9                211
  N1                0                 81
  N2                3                 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"
D915V6, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   0
  BAIAP2L1 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    0
  BAIAP2L1 WILD-TYPE  276   48
   clus
vv  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D915V7, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     5   7
  BAIAP2L1 WILD-TYPE 165 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      5    7
  BAIAP2L1 WILD-TYPE  165  190
        clus
vv       BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  FEMALE                5                165
  MALE                  7                190
[1] 2 2
[1] FALSE
D915V8, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   1
  BAIAP2L1 WILD-TYPE 291   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    1
  BAIAP2L1 WILD-TYPE  291    7
     clus
vv    BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  NO                 9                291
  YES                1                  7
[1] 2 2
[1] FALSE
D915V9, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   3
  BAIAP2L1 WILD-TYPE 305  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    3
  BAIAP2L1 WILD-TYPE  305   45
                               clus
vv                              BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  BAIAP2L1 MUTATED     8   0   0   0
  BAIAP2L1 WILD-TYPE 251   3  22  21
D915V10, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  R0                8                251
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D915V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAIAP2L1 MUTATED                                  0     0
  BAIAP2L1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  BAIAP2L1 MUTATED                           0     8
  BAIAP2L1 WILD-TYPE                        19   168
D915V12, multiclass
                                  clus
vv                                 BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           8                168
[1] 4 2
[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 = ZNF799 MUTATION ANALYSIS
D916V1, survival
                  sevent
clus2                0   1
  ZNF799 MUTATED     5   1
  ZNF799 WILD-TYPE 272  77
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               6              349 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               1               77 
$`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 

$`ZNF799 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZNF799 MUTATED ZNF799 WILD-TYPE 
            6.05             0.00 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
           88.21           148.01 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
           39.65            22.03 
[1] "6.0 - 88.2 (39.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D916V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF799 MUTATED         1        0        0         3         1         0
  ZNF799 WILD-TYPE      63        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF799 MUTATED           0          0          0          0        1
  ZNF799 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF799 MUTATED           0         0
  ZNF799 WILD-TYPE        12         1
D916V3, multiclass
            clus
vv           ZNF799 MUTATED ZNF799 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF799 MUTATED     1   0   3   2
  ZNF799 WILD-TYPE   8  67 246  39
D916V4, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              3              246
  T4              2               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
  ZNF799 MUTATED     5   0   1
  ZNF799 WILD-TYPE 215  81  65
D916V5, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V6, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     5   1
  ZNF799 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      5    1
  ZNF799 WILD-TYPE  280   47
   clus
vv  ZNF799 MUTATED ZNF799 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D916V7, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     3   3
  ZNF799 WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      3    3
  ZNF799 WILD-TYPE  167  194
        clus
vv       ZNF799 MUTATED ZNF799 WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D916V8, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     5   0
  ZNF799 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      5    0
  ZNF799 WILD-TYPE  295    8
     clus
vv    ZNF799 MUTATED ZNF799 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D916V9, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     6   0
  ZNF799 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      6    0
  ZNF799 WILD-TYPE  308   48
                               clus
vv                              ZNF799 MUTATED ZNF799 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF799 MUTATED     3   0   1   0
  ZNF799 WILD-TYPE 256   3  21  21
D916V10, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              1               21
  RX              0               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"
D916V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF799 MUTATED                                  0     0
  ZNF799 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF799 MUTATED                           0     4
  ZNF799 WILD-TYPE                        19   172
D916V12, multiclass
                                  clus
vv                                 ZNF799 MUTATED ZNF799 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = ATIC MUTATION ANALYSIS
D917V1, survival
                sevent
clus2              0   1
  ATIC MUTATED     8   5
  ATIC WILD-TYPE 269  73
  ATIC MUTATED ATIC WILD-TYPE 
            13            342 
  ATIC MUTATED ATIC WILD-TYPE 
             5             73 
$`ATIC MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-G4-6310 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3663 
       13.02         0.92        63.62        32.71        19.66         6.97 
TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-6599 TCGA-CA-5796 TCGA-CK-4950 TCGA-CK-5916 
        4.01        35.01         6.77        12.39        85.45        21.14 
TCGA-DM-A1D4 
       92.75 

$`ATIC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.36        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      148.01        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ATIC MUTATED ATIC WILD-TYPE 
          0.92           0.00 
  ATIC MUTATED ATIC WILD-TYPE 
         92.75         148.01 
  ATIC MUTATED ATIC WILD-TYPE 
         19.66          22.09 
[1] "0.9 - 92.8 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D917V2, continuous
                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      62        1       25       106         7         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        15          6         42         32       35        12
                vv
clus             STAGE IVB
  ATIC MUTATED           0
  ATIC WILD-TYPE         1
D917V3, multiclass
            clus
vv           ATIC MUTATED ATIC WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  ATIC MUTATED     1   1   8   3
  ATIC WILD-TYPE   8  66 241  38
D917V4, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  T1            1              8
  T2            1             66
  T3            8            241
  T4            3             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
  ATIC MUTATED     7   4   2
  ATIC WILD-TYPE 213  77  64
D917V5, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  N0            7            213
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V6, binary
                cls
clus               0   1
  ATIC MUTATED    11   0
  ATIC WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED     11    0
  ATIC WILD-TYPE  274   48
   clus
vv  ATIC MUTATED ATIC WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D917V7, binary
                cls
clus               0   1
  ATIC MUTATED     5   8
  ATIC WILD-TYPE 165 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED      5    8
  ATIC WILD-TYPE  165  189
        clus
vv       ATIC MUTATED ATIC WILD-TYPE
  FEMALE            5            165
  MALE              8            189
[1] 2 2
[1] FALSE
D917V8, binary
                cls
clus               0   1
  ATIC MUTATED     9   2
  ATIC WILD-TYPE 291   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED      9    2
  ATIC WILD-TYPE  291    6
     clus
vv    ATIC MUTATED ATIC WILD-TYPE
  NO             9            291
  YES            2              6
[1] 2 2
[1] FALSE
D917V9, binary
                cls
clus               0   1
  ATIC MUTATED     7   6
  ATIC WILD-TYPE 307  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED      7    6
  ATIC WILD-TYPE  307   42
                               clus
vv                              ATIC MUTATED ATIC WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ATIC MUTATED     7   1   0   1
  ATIC WILD-TYPE 252   2  22  20
D917V10, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  R0            7            252
  R1            1              2
  R2            0             22
  RX            1             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"
D917V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATIC MUTATED                                  0     1
  ATIC WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATIC MUTATED                           1     6
  ATIC WILD-TYPE                        18   170
D917V12, multiclass
                                  clus
vv                                 ATIC MUTATED ATIC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = CPZ MUTATION ANALYSIS
D918V1, survival
               sevent
clus2             0   1
  CPZ MUTATED    10   4
  CPZ WILD-TYPE 267  74
  CPZ MUTATED CPZ WILD-TYPE 
           14           341 
  CPZ MUTATED CPZ WILD-TYPE 
            4            74 
$`CPZ MUTATED`
TCGA-G4-6586 TCGA-A6-2676 TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-A010 
       35.80        42.90        31.63        22.06        20.12        34.98 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6162 
       58.39        49.41        11.74        21.14        23.05        12.00 
TCGA-D5-6928 TCGA-F4-6856 
       11.64        35.31 

$`CPZ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CPZ MUTATED CPZ WILD-TYPE 
        11.64          0.00 
  CPZ MUTATED CPZ WILD-TYPE 
        58.39        148.01 
  CPZ MUTATED CPZ WILD-TYPE 
        27.34         21.99 
[1] "11.6 - 58.4 (27.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D918V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPZ MUTATED         2        0        1         7         2         0
  CPZ WILD-TYPE      62        1       25       101         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPZ MUTATED           0          0          2          0        1         0
  CPZ WILD-TYPE        18          6         42         33       34        12
               vv
clus            STAGE IVB
  CPZ MUTATED           0
  CPZ WILD-TYPE         1
D918V3, multiclass
            clus
vv           CPZ MUTATED CPZ WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            7           101
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  CPZ MUTATED     1   1  10   3
  CPZ WILD-TYPE   8  66 239  38
D918V4, multiclass
    clus
vv   CPZ MUTATED CPZ WILD-TYPE
  T1           1             8
  T2           1            66
  T3          10           239
  T4           3            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
  CPZ MUTATED    12   2   1
  CPZ WILD-TYPE 208  79  65
D918V5, multiclass
    clus
vv   CPZ MUTATED CPZ WILD-TYPE
  N0          12           208
  N1           2            79
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V6, binary
               cls
clus              0   1
  CPZ MUTATED    12   1
  CPZ WILD-TYPE 273  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPZ MUTATED     12    1
  CPZ WILD-TYPE  273   47
   clus
vv  CPZ MUTATED CPZ WILD-TYPE
  0          12           273
  1           1            47
[1] 2 2
[1] FALSE
D918V7, binary
               cls
clus              0   1
  CPZ MUTATED     8   7
  CPZ WILD-TYPE 162 190
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPZ MUTATED      8    7
  CPZ WILD-TYPE  162  190
        clus
vv       CPZ MUTATED CPZ WILD-TYPE
  FEMALE           8           162
  MALE             7           190
[1] 2 2
[1] FALSE
D918V8, binary
               cls
clus              0   1
  CPZ MUTATED    14   0
  CPZ WILD-TYPE 286   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPZ MUTATED     14    0
  CPZ WILD-TYPE  286    8
     clus
vv    CPZ MUTATED CPZ WILD-TYPE
  NO           14           286
  YES           0             8
[1] 2 2
[1] FALSE
D918V9, binary
               cls
clus              0   1
  CPZ MUTATED    11   4
  CPZ WILD-TYPE 303  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPZ MUTATED     11    4
  CPZ WILD-TYPE  303   44
                               clus
vv                              CPZ MUTATED CPZ WILD-TYPE
  COLON ADENOCARCINOMA                   11           303
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CPZ MUTATED    11   0   0   1
  CPZ WILD-TYPE 248   3  22  20
D918V10, multiclass
    clus
vv   CPZ MUTATED CPZ WILD-TYPE
  R0          11           248
  R1           0             3
  R2           0            22
  RX           1            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"
D918V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPZ MUTATED                                  0     0
  CPZ WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CPZ MUTATED                           1    12
  CPZ WILD-TYPE                        18   164
D918V12, multiclass
                                  clus
vv                                 CPZ MUTATED CPZ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                     12           164
[1] 4 2
[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 = GRIA4 MUTATION ANALYSIS
D919V1, survival
                 sevent
clus2               0   1
  GRIA4 MUTATED    27   3
  GRIA4 WILD-TYPE 250  75
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             30             325 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
              3              75 
$`GRIA4 MUTATED`
TCGA-AA-3554 TCGA-AA-3867 TCGA-G4-6310 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6782 
       17.95        24.03        63.62        42.90        33.53        20.28 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3678 TCGA-AA-3851 TCGA-AA-3877 TCGA-AA-A010 
       63.98         6.97        47.01        33.07        31.00        34.98 
TCGA-AA-A01Z TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5348 
       37.02        58.39        12.59        12.76        20.02        22.98 
TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-6924 TCGA-DM-A1HB TCGA-DM-A28C 
       30.08        17.03        13.05        14.30       135.65        81.37 
TCGA-F4-6460 TCGA-F4-6805 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6307 TCGA-G4-6317 
       31.96        34.42        33.67        35.31        55.04        36.00 

$`GRIA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04         3.02        35.01         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        50.04        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       37.02         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        23.05        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17       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 
       43.04        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-G4-6323 
       65.85        53.62        44.68        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  GRIA4 MUTATED GRIA4 WILD-TYPE 
           6.97            0.00 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
         135.65          148.01 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
          33.30           21.76 
[1] "7.0 - 135.7 (33.3)" "0.0 - 148.0 (21.8)"
[1] "hr=" "2.9"
D919V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRIA4 MUTATED         4        0        3         9         3         0
  GRIA4 WILD-TYPE      60        1       23        99         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRIA4 MUTATED           1          0          6          1        1         1
  GRIA4 WILD-TYPE        17          6         38         32       34        11
                 vv
clus              STAGE IVB
  GRIA4 MUTATED           1
  GRIA4 WILD-TYPE         0
D919V3, multiclass
            clus
vv           GRIA4 MUTATED GRIA4 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              9              99
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              11
  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   3  20   5
  GRIA4 WILD-TYPE   7  64 229  36
D919V4, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  T1             2               7
  T2             3              64
  T3            20             229
  T4             5              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
  GRIA4 MUTATED    19   8   3
  GRIA4 WILD-TYPE 201  73  63
D919V5, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  N0            19             201
  N1             8              73
  N2             3              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"
D919V6, binary
                 cls
clus                0   1
  GRIA4 MUTATED    25   3
  GRIA4 WILD-TYPE 260  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     25    3
  GRIA4 WILD-TYPE  260   45
   clus
vv  GRIA4 MUTATED GRIA4 WILD-TYPE
  0            25             260
  1             3              45
[1] 2 2
[1] FALSE
D919V7, binary
                 cls
clus                0   1
  GRIA4 MUTATED    13  17
  GRIA4 WILD-TYPE 157 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     13   17
  GRIA4 WILD-TYPE  157  180
        clus
vv       GRIA4 MUTATED GRIA4 WILD-TYPE
  FEMALE            13             157
  MALE              17             180
[1] 2 2
[1] FALSE
D919V8, binary
                 cls
clus                0   1
  GRIA4 MUTATED    27   1
  GRIA4 WILD-TYPE 273   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     27    1
  GRIA4 WILD-TYPE  273    7
     clus
vv    GRIA4 MUTATED GRIA4 WILD-TYPE
  NO             27             273
  YES             1               7
[1] 2 2
[1] FALSE
D919V9, binary
                 cls
clus                0   1
  GRIA4 MUTATED    26   3
  GRIA4 WILD-TYPE 288  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     26    3
  GRIA4 WILD-TYPE  288   45
                               clus
vv                              GRIA4 MUTATED GRIA4 WILD-TYPE
  COLON ADENOCARCINOMA                     26             288
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GRIA4 MUTATED    24   0   1   2
  GRIA4 WILD-TYPE 235   3  21  19
D919V10, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  R0            24             235
  R1             0               3
  R2             1              21
  RX             2              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"
D919V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRIA4 MUTATED                                  0     2
  GRIA4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRIA4 MUTATED                           2    17
  GRIA4 WILD-TYPE                        17   159
D919V12, multiclass
                                  clus
vv                                 GRIA4 MUTATED GRIA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       17             159
[1] 4 2
[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 = NDUFAF1 MUTATION ANALYSIS
D920V1, survival
                   sevent
clus2                 0   1
  NDUFAF1 MUTATED     6   1
  NDUFAF1 WILD-TYPE 271  77
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               348 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                1                77 
$`NDUFAF1 MUTATED`
TCGA-AA-3713 TCGA-G4-6310 TCGA-G4-6588 TCGA-A6-6781 TCGA-AY-6386 TCGA-D5-6537 
       19.04        63.62        26.17        19.66        17.82         4.80 
TCGA-DM-A28H 
      117.07 

$`NDUFAF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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            22.075 
[1] "4.8 - 117.1 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D920V2, continuous
                   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      64        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDUFAF1 MUTATED           0          0          3          2        1
  NDUFAF1 WILD-TYPE        18          6         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  NDUFAF1 MUTATED           0         0
  NDUFAF1 WILD-TYPE        12         1
D920V3, multiclass
            clus
vv           NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  NDUFAF1 MUTATED     0   0   6   1
  NDUFAF1 WILD-TYPE   9  67 243  40
D920V4, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               6               243
  T4               1                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
  NDUFAF1 MUTATED     2   4   1
  NDUFAF1 WILD-TYPE 218  77  65
D920V5, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  N0               2               218
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V6, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     4   1
  NDUFAF1 WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      4    1
  NDUFAF1 WILD-TYPE  281   47
   clus
vv  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D920V7, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     2   5
  NDUFAF1 WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      2    5
  NDUFAF1 WILD-TYPE  168  192
        clus
vv       NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D920V8, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     4   2
  NDUFAF1 WILD-TYPE 296   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      4    2
  NDUFAF1 WILD-TYPE  296    6
     clus
vv    NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  NO                4               296
  YES               2                 6
[1] 2 2
[1] FALSE
D920V9, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     6   1
  NDUFAF1 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      6    1
  NDUFAF1 WILD-TYPE  308   47
                               clus
vv                              NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  NDUFAF1 MUTATED     5   0   1   0
  NDUFAF1 WILD-TYPE 254   3  21  21
D920V10, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               1                21
  RX               0                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"
D920V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDUFAF1 MUTATED                                  0     0
  NDUFAF1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NDUFAF1 MUTATED                           1     5
  NDUFAF1 WILD-TYPE                        18   171
D920V12, multiclass
                                  clus
vv                                 NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = SKIL MUTATION ANALYSIS
D921V1, survival
                sevent
clus2              0   1
  SKIL MUTATED     4   3
  SKIL WILD-TYPE 273  75
  SKIL MUTATED SKIL WILD-TYPE 
             7            348 
  SKIL MUTATED SKIL WILD-TYPE 
             3             75 
$`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 
       65.85 

$`SKIL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SKIL MUTATED SKIL WILD-TYPE 
          6.97           0.00 
  SKIL MUTATED SKIL WILD-TYPE 
         65.85         148.01 
  SKIL MUTATED SKIL WILD-TYPE 
         35.31          22.01 
[1] "7.0 - 65.8 (35.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D921V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKIL MUTATED         1        0        1         2         0         0
  SKIL WILD-TYPE      63        1       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SKIL MUTATED           0          0          1          0        1         0
  SKIL WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  SKIL MUTATED           1
  SKIL WILD-TYPE         0
D921V3, multiclass
            clus
vv           SKIL MUTATED SKIL WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             12
  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   1   6   0
  SKIL WILD-TYPE   9  66 243  41
D921V4, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            0             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
  SKIL MUTATED     4   2   1
  SKIL WILD-TYPE 216  79  65
D921V5, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  N0            4            216
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V6, binary
                cls
clus               0   1
  SKIL MUTATED     5   2
  SKIL WILD-TYPE 280  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      5    2
  SKIL WILD-TYPE  280   46
   clus
vv  SKIL MUTATED SKIL WILD-TYPE
  0            5            280
  1            2             46
[1] 2 2
[1] FALSE
D921V7, binary
                cls
clus               0   1
  SKIL MUTATED     2   5
  SKIL WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      2    5
  SKIL WILD-TYPE  168  192
        clus
vv       SKIL MUTATED SKIL WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D921V8, binary
                cls
clus               0   1
  SKIL MUTATED     5   0
  SKIL WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      5    0
  SKIL WILD-TYPE  295    8
     clus
vv    SKIL MUTATED SKIL WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D921V9, binary
                cls
clus               0   1
  SKIL MUTATED     5   2
  SKIL WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      5    2
  SKIL WILD-TYPE  309   46
                               clus
vv                              SKIL MUTATED SKIL WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SKIL MUTATED     5   0   0   0
  SKIL WILD-TYPE 254   3  22  21
D921V10, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D921V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKIL MUTATED                                  0     0
  SKIL WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SKIL MUTATED                           1     5
  SKIL WILD-TYPE                        18   171
D921V12, multiclass
                                  clus
vv                                 SKIL MUTATED SKIL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = ATP10B MUTATION ANALYSIS
D922V1, survival
                  sevent
clus2                0   1
  ATP10B MUTATED     9   6
  ATP10B WILD-TYPE 268  72
  ATP10B MUTATED ATP10B WILD-TYPE 
              15              340 
  ATP10B MUTATED ATP10B WILD-TYPE 
               6               72 
$`ATP10B MUTATED`
TCGA-AA-3715 TCGA-DM-A285 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3845 
       19.04         5.88        22.06        19.66        61.02         0.00 
TCGA-AD-6889 TCGA-AY-5543 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       83.24        33.01         6.77        12.76        10.06        23.05 
TCGA-CM-4747 TCGA-D5-6926 TCGA-F4-6854 
       25.02         9.04         0.53 

$`ATP10B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 
        2.01       124.27        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ATP10B MUTATED ATP10B WILD-TYPE 
               0                0 
  ATP10B MUTATED ATP10B WILD-TYPE 
           83.24           148.01 
  ATP10B MUTATED ATP10B WILD-TYPE 
          19.040           22.225 
[1] "0.0 - 83.2 (19.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.3"
D922V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP10B MUTATED         1        0        2         7         0         0
  ATP10B WILD-TYPE      63        1       24       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP10B MUTATED           0          0          1          1        1
  ATP10B WILD-TYPE        18          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ATP10B MUTATED           2         0
  ATP10B WILD-TYPE        10         1
D922V3, multiclass
            clus
vv           ATP10B MUTATED ATP10B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               2               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
  ATP10B MUTATED     0   1  11   3
  ATP10B WILD-TYPE   9  66 238  38
D922V4, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  T1              0                9
  T2              1               66
  T3             11              238
  T4              3               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
  ATP10B MUTATED    10   4   1
  ATP10B WILD-TYPE 210  77  65
D922V5, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  N0             10              210
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V6, binary
                  cls
clus                 0   1
  ATP10B MUTATED    10   3
  ATP10B WILD-TYPE 275  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     10    3
  ATP10B WILD-TYPE  275   45
   clus
vv  ATP10B MUTATED ATP10B WILD-TYPE
  0             10              275
  1              3               45
[1] 2 2
[1] FALSE
D922V7, binary
                  cls
clus                 0   1
  ATP10B MUTATED     5  10
  ATP10B WILD-TYPE 165 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED      5   10
  ATP10B WILD-TYPE  165  187
        clus
vv       ATP10B MUTATED ATP10B WILD-TYPE
  FEMALE              5              165
  MALE               10              187
[1] 2 2
[1] FALSE
D922V8, binary
                  cls
clus                 0   1
  ATP10B MUTATED    12   1
  ATP10B WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     12    1
  ATP10B WILD-TYPE  288    7
     clus
vv    ATP10B MUTATED ATP10B WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D922V9, binary
                  cls
clus                 0   1
  ATP10B MUTATED    12   3
  ATP10B WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     12    3
  ATP10B WILD-TYPE  302   45
                               clus
vv                              ATP10B MUTATED ATP10B WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP10B MUTATED    11   0   0   2
  ATP10B WILD-TYPE 248   3  22  19
D922V10, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              2               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"
D922V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP10B MUTATED                                  0     3
  ATP10B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP10B MUTATED                           1     8
  ATP10B WILD-TYPE                        18   168
D922V12, multiclass
                                  clus
vv                                 ATP10B MUTATED ATP10B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = NUP205 MUTATION ANALYSIS
D923V1, survival
                  sevent
clus2                0   1
  NUP205 MUTATED    18   4
  NUP205 WILD-TYPE 259  74
  NUP205 MUTATED NUP205 WILD-TYPE 
              22              333 
  NUP205 MUTATED NUP205 WILD-TYPE 
               4               74 
$`NUP205 MUTATED`
TCGA-AA-3870 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3821 
       29.98         8.38        63.98         6.97        14.01         1.02 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 
       33.01        34.98        38.07        12.16        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 
       10.06        16.14         9.44        53.62 

$`NUP205 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 
       13.94        61.02        78.08        54.02         2.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        88.21        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NUP205 MUTATED NUP205 WILD-TYPE 
            1.02             0.00 
  NUP205 MUTATED NUP205 WILD-TYPE 
           82.95           148.01 
  NUP205 MUTATED NUP205 WILD-TYPE 
           18.79            22.09 
[1] "1.0 - 83.0 (18.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D923V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP205 MUTATED         4        0        3        10         3         0
  NUP205 WILD-TYPE      60        1       23        98         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP205 MUTATED           1          0          1          0        1
  NUP205 WILD-TYPE        17          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  NUP205 MUTATED           1         0
  NUP205 WILD-TYPE        11         1
D923V3, multiclass
            clus
vv           NUP205 MUTATED NUP205 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              10               98
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  NUP205 MUTATED     0   4  17   3
  NUP205 WILD-TYPE   9  63 232  38
D923V4, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             17              232
  T4              3               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
  NUP205 MUTATED    21   2   1
  NUP205 WILD-TYPE 199  79  65
D923V5, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  N0             21              199
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V6, binary
                  cls
clus                 0   1
  NUP205 MUTATED    18   2
  NUP205 WILD-TYPE 267  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     18    2
  NUP205 WILD-TYPE  267   46
   clus
vv  NUP205 MUTATED NUP205 WILD-TYPE
  0             18              267
  1              2               46
[1] 2 2
[1] FALSE
D923V7, binary
                  cls
clus                 0   1
  NUP205 MUTATED    11  13
  NUP205 WILD-TYPE 159 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     11   13
  NUP205 WILD-TYPE  159  184
        clus
vv       NUP205 MUTATED NUP205 WILD-TYPE
  FEMALE             11              159
  MALE               13              184
[1] 2 2
[1] FALSE
D923V8, binary
                  cls
clus                 0   1
  NUP205 MUTATED    21   0
  NUP205 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     21    0
  NUP205 WILD-TYPE  279    8
     clus
vv    NUP205 MUTATED NUP205 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D923V9, binary
                  cls
clus                 0   1
  NUP205 MUTATED    18   6
  NUP205 WILD-TYPE 296  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     18    6
  NUP205 WILD-TYPE  296   42
                               clus
vv                              NUP205 MUTATED NUP205 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUP205 MUTATED    19   0   0   3
  NUP205 WILD-TYPE 240   3  22  18
D923V10, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  R0             19              240
  R1              0                3
  R2              0               22
  RX              3               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"
D923V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP205 MUTATED                                  0     2
  NUP205 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP205 MUTATED                           1    11
  NUP205 WILD-TYPE                        18   165
D923V12, multiclass
                                  clus
vv                                 NUP205 MUTATED NUP205 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(924) Variable = ALK MUTATION ANALYSIS
D924V1, survival
               sevent
clus2             0   1
  ALK MUTATED    24  10
  ALK WILD-TYPE 253  68
  ALK MUTATED ALK WILD-TYPE 
           34           321 
  ALK MUTATED ALK WILD-TYPE 
           10            68 
$`ALK MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3562 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
       14.53         1.02        19.99        19.04        19.04        24.00 
TCGA-AA-3976 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-A6-2676 TCGA-A6-5666 TCGA-AA-3510 
       26.01       100.01         1.94        42.90        32.71        63.98 
TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3845 TCGA-AA-3977 
        1.02         6.97        26.99         0.99         0.00        25.02 
TCGA-AA-A00N TCGA-AA-A01R TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6162 TCGA-CM-6163 
        4.01        35.01        12.76        13.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-DM-A1D8 
       16.04        15.02        16.14        13.35        13.32        12.59 
TCGA-DM-A1HA TCGA-F4-6703 TCGA-G4-6304 TCGA-G4-6307 
      131.51        47.87        53.62        55.04 

$`ALK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       85.05        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        29.03        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
      140.38         7.50        44.32       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-F4-6704 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 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
      133.18        74.56        65.85        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ALK MUTATED ALK WILD-TYPE 
            0             0 
  ALK MUTATED ALK WILD-TYPE 
       131.51        148.01 
  ALK MUTATED ALK WILD-TYPE 
        16.09         22.42 
[1] "0.0 - 131.5 (16.1)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.5"
D924V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALK MUTATED         3        0        5        12         3         1
  ALK WILD-TYPE      61        1       21        96         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALK MUTATED           2          2          2          2        1         0
  ALK WILD-TYPE        16          4         42         31       34        12
               vv
clus            STAGE IVB
  ALK MUTATED           0
  ALK WILD-TYPE         1
D924V3, multiclass
            clus
vv           ALK MUTATED ALK WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             5            21
  STAGE IIA           12            96
  STAGE IIB            3             5
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           2             4
  STAGE IIIB           2            42
  STAGE IIIC           2            31
  STAGE IV             1            34
  STAGE IVA            0            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
  ALK MUTATED     1   5  25   4
  ALK WILD-TYPE   8  62 224  37
D924V4, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  T1           1             8
  T2           5            62
  T3          25           224
  T4           4            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
  ALK MUTATED    26   5   4
  ALK WILD-TYPE 194  76  62
D924V5, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  N0          26           194
  N1           5            76
  N2           4            62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V6, binary
               cls
clus              0   1
  ALK MUTATED    32   1
  ALK WILD-TYPE 253  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     32    1
  ALK WILD-TYPE  253   47
   clus
vv  ALK MUTATED ALK WILD-TYPE
  0          32           253
  1           1            47
[1] 2 2
[1] FALSE
D924V7, binary
               cls
clus              0   1
  ALK MUTATED    13  22
  ALK WILD-TYPE 157 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     13   22
  ALK WILD-TYPE  157  175
        clus
vv       ALK MUTATED ALK WILD-TYPE
  FEMALE          13           157
  MALE            22           175
[1] 2 2
[1] FALSE
D924V8, binary
               cls
clus              0   1
  ALK MUTATED    24   2
  ALK WILD-TYPE 276   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     24    2
  ALK WILD-TYPE  276    6
     clus
vv    ALK MUTATED ALK WILD-TYPE
  NO           24           276
  YES           2             6
[1] 2 2
[1] FALSE
D924V9, binary
               cls
clus              0   1
  ALK MUTATED    27   7
  ALK WILD-TYPE 287  41
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     27    7
  ALK WILD-TYPE  287   41
                               clus
vv                              ALK MUTATED ALK WILD-TYPE
  COLON ADENOCARCINOMA                   27           287
  COLON MUCINOUS ADENOCARCINOMA           7            41
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ALK MUTATED    25   0   1   1
  ALK WILD-TYPE 234   3  21  20
D924V10, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  R0          25           234
  R1           0             3
  R2           1            21
  RX           1            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"
D924V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALK MUTATED                                  0     1
  ALK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ALK MUTATED                           1    17
  ALK WILD-TYPE                        18   159
D924V12, multiclass
                                  clus
vv                                 ALK MUTATED ALK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                     17           159
[1] 4 2
[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 = GRB14 MUTATION ANALYSIS
D925V1, survival
                 sevent
clus2               0   1
  GRB14 MUTATED     5   3
  GRB14 WILD-TYPE 272  75
  GRB14 MUTATED GRB14 WILD-TYPE 
              8             347 
  GRB14 MUTATED GRB14 WILD-TYPE 
              3              75 
$`GRB14 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3710 TCGA-AA-3949 TCGA-AZ-6599 TCGA-CM-6163 
       13.02        19.04        26.99        26.01         6.77        14.04 
TCGA-D5-6536 TCGA-DM-A1D6 
       17.85        49.91 

$`GRB14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GRB14 MUTATED GRB14 WILD-TYPE 
           6.77            0.00 
  GRB14 MUTATED GRB14 WILD-TYPE 
          49.91          148.01 
  GRB14 MUTATED GRB14 WILD-TYPE 
         18.445          22.090 
[1] "6.8 - 49.9 (18.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D925V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRB14 MUTATED         2        0        0         4         0         0
  GRB14 WILD-TYPE      62        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRB14 MUTATED           1          0          1          0        1         0
  GRB14 WILD-TYPE        17          6         43         33       34        12
                 vv
clus              STAGE IVB
  GRB14 MUTATED           0
  GRB14 WILD-TYPE         1
D925V3, multiclass
            clus
vv           GRB14 MUTATED GRB14 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GRB14 MUTATED     1   1   7   0
  GRB14 WILD-TYPE   8  66 242  41
D925V4, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             7             242
  T4             0              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
  GRB14 MUTATED     7   1   1
  GRB14 WILD-TYPE 213  80  65
D925V5, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V6, binary
                 cls
clus                0   1
  GRB14 MUTATED     7   1
  GRB14 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      7    1
  GRB14 WILD-TYPE  278   47
   clus
vv  GRB14 MUTATED GRB14 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D925V7, binary
                 cls
clus                0   1
  GRB14 MUTATED     4   5
  GRB14 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      4    5
  GRB14 WILD-TYPE  166  192
        clus
vv       GRB14 MUTATED GRB14 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D925V8, binary
                 cls
clus                0   1
  GRB14 MUTATED     6   1
  GRB14 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      6    1
  GRB14 WILD-TYPE  294    7
     clus
vv    GRB14 MUTATED GRB14 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D925V9, binary
                 cls
clus                0   1
  GRB14 MUTATED     6   3
  GRB14 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      6    3
  GRB14 WILD-TYPE  308   45
                               clus
vv                              GRB14 MUTATED GRB14 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GRB14 MUTATED     5   0   1   0
  GRB14 WILD-TYPE 254   3  21  21
D925V10, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             0              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"
D925V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRB14 MUTATED                                  0     0
  GRB14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRB14 MUTATED                           0     4
  GRB14 WILD-TYPE                        19   172
D925V12, multiclass
                                  clus
vv                                 GRB14 MUTATED GRB14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = NSUN6 MUTATION ANALYSIS
D926V1, survival
                 sevent
clus2               0   1
  NSUN6 MUTATED     6   2
  NSUN6 WILD-TYPE 271  76
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              8             347 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              2              76 
$`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        12.16         3.19 
TCGA-CM-5861 TCGA-D5-6540 
       15.02        16.14 

$`NSUN6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NSUN6 MUTATED NSUN6 WILD-TYPE 
           3.02            0.00 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
          63.98          148.01 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
          15.58           22.09 
[1] "3.0 - 64.0 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D926V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NSUN6 MUTATED         2        0        2         1         1         0
  NSUN6 WILD-TYPE      62        1       24       107         7         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        18          6         44         32       34        12
                 vv
clus              STAGE IVB
  NSUN6 MUTATED           0
  NSUN6 WILD-TYPE         1
D926V3, multiclass
            clus
vv           NSUN6 MUTATED NSUN6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  NSUN6 MUTATED     0   2   3   3
  NSUN6 WILD-TYPE   9  65 246  38
D926V4, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             3              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
  NSUN6 MUTATED     6   1   1
  NSUN6 WILD-TYPE 214  80  65
D926V5, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V6, binary
                 cls
clus                0   1
  NSUN6 MUTATED     5   1
  NSUN6 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      5    1
  NSUN6 WILD-TYPE  280   47
   clus
vv  NSUN6 MUTATED NSUN6 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D926V7, binary
                 cls
clus                0   1
  NSUN6 MUTATED     3   5
  NSUN6 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      3    5
  NSUN6 WILD-TYPE  167  192
        clus
vv       NSUN6 MUTATED NSUN6 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D926V8, binary
                 cls
clus                0   1
  NSUN6 MUTATED     8   0
  NSUN6 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      8    0
  NSUN6 WILD-TYPE  292    8
     clus
vv    NSUN6 MUTATED NSUN6 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D926V9, binary
                 cls
clus                0   1
  NSUN6 MUTATED     5   3
  NSUN6 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      5    3
  NSUN6 WILD-TYPE  309   45
                               clus
vv                              NSUN6 MUTATED NSUN6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NSUN6 MUTATED     7   0   0   0
  NSUN6 WILD-TYPE 252   3  22  21
D926V10, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D926V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSUN6 MUTATED                                  0     0
  NSUN6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NSUN6 MUTATED                           0     5
  NSUN6 WILD-TYPE                        19   171
D926V12, multiclass
                                  clus
vv                                 NSUN6 MUTATED NSUN6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(927) Variable = SAMD9L MUTATION ANALYSIS
D927V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED    14   6
  SAMD9L WILD-TYPE 263  72
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              20              335 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               6               72 
$`SAMD9L MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-4681 TCGA-G4-6586 TCGA-G4-6588 
        1.02        19.04        25.08       106.75        35.80        26.17 
TCGA-A6-3809 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       32.75         5.03        10.06        25.02         4.01        34.98 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6170 TCGA-CM-6676 TCGA-DM-A0XD 
       58.39        49.41        12.76        15.02        11.08        24.43 
TCGA-DM-A282 TCGA-G4-6309 
      139.17        85.48 

$`SAMD9L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        63.62        22.09        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3710 TCGA-AA-3812 TCGA-AA-3815 
       11.01         5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C 
      140.38         7.50        44.32       131.51       135.65        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            1.02             0.00 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          139.17           148.01 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
           25.05            21.99 
[1] "1.0 - 139.2 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D927V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAMD9L MUTATED         2        0        3         8         3         0
  SAMD9L WILD-TYPE      62        1       23       100         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD9L MUTATED           2          0          2          0        1
  SAMD9L WILD-TYPE        16          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  SAMD9L MUTATED           0         0
  SAMD9L WILD-TYPE        12         1
D927V3, multiclass
            clus
vv           SAMD9L MUTATED SAMD9L WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               8              100
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  SAMD9L MUTATED     0   3  16   3
  SAMD9L WILD-TYPE   9  64 233  38
D927V4, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  T1              0                9
  T2              3               64
  T3             16              233
  T4              3               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
  SAMD9L MUTATED    17   3   2
  SAMD9L WILD-TYPE 203  78  64
D927V5, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  N0             17              203
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V6, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    19   1
  SAMD9L WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     19    1
  SAMD9L WILD-TYPE  266   47
   clus
vv  SAMD9L MUTATED SAMD9L WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D927V7, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    13   9
  SAMD9L WILD-TYPE 157 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     13    9
  SAMD9L WILD-TYPE  157  188
        clus
vv       SAMD9L MUTATED SAMD9L WILD-TYPE
  FEMALE             13              157
  MALE                9              188
[1] 2 2
[1] FALSE
D927V8, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    16   0
  SAMD9L WILD-TYPE 284   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     16    0
  SAMD9L WILD-TYPE  284    8
     clus
vv    SAMD9L MUTATED SAMD9L WILD-TYPE
  NO              16              284
  YES              0                8
[1] 2 2
[1] FALSE
D927V9, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    19   3
  SAMD9L WILD-TYPE 295  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     19    3
  SAMD9L WILD-TYPE  295   45
                               clus
vv                              SAMD9L MUTATED SAMD9L WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SAMD9L MUTATED    16   0   1   1
  SAMD9L WILD-TYPE 243   3  21  20
D927V10, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  R0             16              243
  R1              0                3
  R2              1               21
  RX              1               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"
D927V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD9L MUTATED                                  0     1
  SAMD9L WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SAMD9L MUTATED                           1    11
  SAMD9L WILD-TYPE                        18   165
D927V12, multiclass
                                  clus
vv                                 SAMD9L MUTATED SAMD9L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(928) Variable = PPP2R5E MUTATION ANALYSIS
D928V1, survival
                   sevent
clus2                 0   1
  PPP2R5E MUTATED     8   0
  PPP2R5E WILD-TYPE 269  78
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               347 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                0                78 
$`PPP2R5E MUTATED`
TCGA-AD-6895 TCGA-A6-5661 TCGA-AA-A00J TCGA-AA-A01Q TCGA-CA-6717 TCGA-CM-4746 
       25.08        33.53        18.05         1.02        12.76        37.02 
TCGA-D5-6541 TCGA-DM-A1HB 
       15.58       135.65 

$`PPP2R5E WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
             1.02              0.00 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
           135.65            148.01 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
           21.565            22.060 
[1] "1.0 - 135.7 (21.6)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D928V2, continuous
                   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      63        1       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R5E MUTATED           0          0          3          0        0
  PPP2R5E WILD-TYPE        18          6         41         33       35
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R5E MUTATED           0         0
  PPP2R5E WILD-TYPE        12         1
D928V3, multiclass
            clus
vv           PPP2R5E MUTATED PPP2R5E WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  PPP2R5E MUTATED     0   1   6   1
  PPP2R5E WILD-TYPE   9  66 243  40
D928V4, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               1                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
  PPP2R5E MUTATED     5   3   0
  PPP2R5E WILD-TYPE 215  78  66
D928V5, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  N0               5               215
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V6, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     8   0
  PPP2R5E WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      8    0
  PPP2R5E WILD-TYPE  277   48
   clus
vv  PPP2R5E MUTATED PPP2R5E WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D928V7, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     2   6
  PPP2R5E WILD-TYPE 168 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      2    6
  PPP2R5E WILD-TYPE  168  191
        clus
vv       PPP2R5E MUTATED PPP2R5E WILD-TYPE
  FEMALE               2               168
  MALE                 6               191
[1] 2 2
[1] FALSE
D928V8, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     6   0
  PPP2R5E WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      6    0
  PPP2R5E WILD-TYPE  294    8
     clus
vv    PPP2R5E MUTATED PPP2R5E WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D928V9, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     5   2
  PPP2R5E WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      5    2
  PPP2R5E WILD-TYPE  309   46
                               clus
vv                              PPP2R5E MUTATED PPP2R5E WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PPP2R5E MUTATED     6   0   0   1
  PPP2R5E WILD-TYPE 253   3  22  20
D928V10, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D928V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R5E MUTATED                                  0     1
  PPP2R5E WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R5E MUTATED                           2     3
  PPP2R5E WILD-TYPE                        17   173
D928V12, multiclass
                                  clus
vv                                 PPP2R5E MUTATED PPP2R5E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          3               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(929) Variable = LUM MUTATION ANALYSIS
D929V1, survival
               sevent
clus2             0   1
  LUM MUTATED     8   3
  LUM WILD-TYPE 269  75
  LUM MUTATED LUM WILD-TYPE 
           11           344 
  LUM MUTATED LUM WILD-TYPE 
            3            75 
$`LUM MUTATED`
TCGA-DM-A285 TCGA-AA-3510 TCGA-AA-3548 TCGA-AA-3845 TCGA-AA-A010 TCGA-AA-A01R 
        5.88        63.98        33.99         0.00        34.98        35.01 
TCGA-AZ-6600 TCGA-CM-6161 TCGA-D5-6536 TCGA-D5-6538 TCGA-DM-A1HB 
       12.10        15.02        17.85        17.13       135.65 

$`LUM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LUM MUTATED LUM WILD-TYPE 
            0             0 
  LUM MUTATED LUM WILD-TYPE 
       135.65        148.01 
  LUM MUTATED LUM WILD-TYPE 
       17.850        22.075 
[1] "0.0 - 135.7 (17.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D929V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LUM MUTATED         1        0        2         2         1         0
  LUM WILD-TYPE      63        1       24       106         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LUM MUTATED           1          0          2          1        2         0
  LUM WILD-TYPE        17          6         42         32       33        12
               vv
clus            STAGE IVB
  LUM MUTATED           0
  LUM WILD-TYPE         1
D929V3, multiclass
            clus
vv           LUM MUTATED LUM WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            2           106
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           1            32
  STAGE IV             2            33
  STAGE IVA            0            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
  LUM MUTATED     0   1   8   3
  LUM WILD-TYPE   9  66 241  38
D929V4, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  T1           0             9
  T2           1            66
  T3           8           241
  T4           3            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
  LUM MUTATED     6   2   4
  LUM WILD-TYPE 214  79  62
D929V5, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  N0           6           214
  N1           2            79
  N2           4            62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V6, binary
               cls
clus              0   1
  LUM MUTATED    10   2
  LUM WILD-TYPE 275  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED     10    2
  LUM WILD-TYPE  275   46
   clus
vv  LUM MUTATED LUM WILD-TYPE
  0          10           275
  1           2            46
[1] 2 2
[1] FALSE
D929V7, binary
               cls
clus              0   1
  LUM MUTATED     7   5
  LUM WILD-TYPE 163 192
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      7    5
  LUM WILD-TYPE  163  192
        clus
vv       LUM MUTATED LUM WILD-TYPE
  FEMALE           7           163
  MALE             5           192
[1] 2 2
[1] FALSE
D929V8, binary
               cls
clus              0   1
  LUM MUTATED     7   1
  LUM WILD-TYPE 293   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      7    1
  LUM WILD-TYPE  293    7
     clus
vv    LUM MUTATED LUM WILD-TYPE
  NO            7           293
  YES           1             7
[1] 2 2
[1] FALSE
D929V9, binary
               cls
clus              0   1
  LUM MUTATED     9   2
  LUM WILD-TYPE 305  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      9    2
  LUM WILD-TYPE  305   46
                               clus
vv                              LUM MUTATED LUM WILD-TYPE
  COLON ADENOCARCINOMA                    9           305
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  LUM MUTATED     9   0   0   0
  LUM WILD-TYPE 250   3  22  21
D929V10, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  R0           9           250
  R1           0             3
  R2           0            22
  RX           0            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"
D929V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LUM MUTATED                                  0     0
  LUM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LUM MUTATED                           1     5
  LUM WILD-TYPE                        18   171
D929V12, multiclass
                                  clus
vv                                 LUM MUTATED LUM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      5           171
[1] 4 2
[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 = MTTP MUTATION ANALYSIS
D930V1, survival
                sevent
clus2              0   1
  MTTP MUTATED    13   9
  MTTP WILD-TYPE 264  69
  MTTP MUTATED MTTP WILD-TYPE 
            22            333 
  MTTP MUTATED MTTP WILD-TYPE 
             9             69 
$`MTTP MUTATED`
TCGA-AD-6888 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 
       15.52        35.80        26.17        42.90        33.53        22.06 
TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       24.39         3.02        10.06         2.01        25.02         4.01 
TCGA-AA-A02K TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-6165 
       14.01        12.10        12.76        21.14        13.02        16.04 
TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-6534 TCGA-F4-6459 
       14.99        12.95        43.27         8.61 

$`MTTP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 
       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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MTTP MUTATED MTTP WILD-TYPE 
          2.01           0.00 
  MTTP MUTATED MTTP WILD-TYPE 
         43.27         148.01 
  MTTP MUTATED MTTP WILD-TYPE 
        15.255         22.420 
[1] "2.0 - 43.3 (15.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "3"  
D930V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTTP MUTATED         2        0        1        11         2         0
  MTTP WILD-TYPE      62        1       25        97         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTTP MUTATED           1          0          2          1        2         0
  MTTP WILD-TYPE        17          6         42         32       33        12
                vv
clus             STAGE IVB
  MTTP MUTATED           0
  MTTP WILD-TYPE         1
D930V3, multiclass
            clus
vv           MTTP MUTATED MTTP WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA            11             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  MTTP MUTATED     1   2  16   4
  MTTP WILD-TYPE   8  65 233  37
D930V4, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  T1            1              8
  T2            2             65
  T3           16            233
  T4            4             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
  MTTP MUTATED    17   2   4
  MTTP WILD-TYPE 203  79  62
D930V5, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  N0           17            203
  N1            2             79
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V6, binary
                cls
clus               0   1
  MTTP MUTATED    20   2
  MTTP WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     20    2
  MTTP WILD-TYPE  265   46
   clus
vv  MTTP MUTATED MTTP WILD-TYPE
  0           20            265
  1            2             46
[1] 2 2
[1] FALSE
D930V7, binary
                cls
clus               0   1
  MTTP MUTATED    13  10
  MTTP WILD-TYPE 157 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     13   10
  MTTP WILD-TYPE  157  187
        clus
vv       MTTP MUTATED MTTP WILD-TYPE
  FEMALE           13            157
  MALE             10            187
[1] 2 2
[1] FALSE
D930V8, binary
                cls
clus               0   1
  MTTP MUTATED    20   0
  MTTP WILD-TYPE 280   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     20    0
  MTTP WILD-TYPE  280    8
     clus
vv    MTTP MUTATED MTTP WILD-TYPE
  NO            20            280
  YES            0              8
[1] 2 2
[1] FALSE
D930V9, binary
                cls
clus               0   1
  MTTP MUTATED    19   4
  MTTP WILD-TYPE 295  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     19    4
  MTTP WILD-TYPE  295   44
                               clus
vv                              MTTP MUTATED MTTP WILD-TYPE
  COLON ADENOCARCINOMA                    19            295
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTTP MUTATED    16   0   1   2
  MTTP WILD-TYPE 243   3  21  19
D930V10, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  R0           16            243
  R1            0              3
  R2            1             21
  RX            2             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"
D930V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTTP MUTATED                                  0     1
  MTTP WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTTP MUTATED                           4    11
  MTTP WILD-TYPE                        15   165
D930V12, multiclass
                                  clus
vv                                 MTTP MUTATED MTTP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      11            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(931) Variable = GAD2 MUTATION ANALYSIS
D931V1, survival
                sevent
clus2              0   1
  GAD2 MUTATED    11   5
  GAD2 WILD-TYPE 266  73
  GAD2 MUTATED GAD2 WILD-TYPE 
            16            339 
  GAD2 MUTATED GAD2 WILD-TYPE 
             5             73 
$`GAD2 MUTATED`
TCGA-AA-3950 TCGA-A6-2676 TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3966 TCGA-AA-3989 
       24.00        42.90         8.38        23.87         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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 
       13.05        34.06        25.02        27.02        27.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-CM-4744 
       51.32        21.99        21.14        82.95         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-6166 TCGA-CM-6167 
       15.02        12.00        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       13.35        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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         22.060 
[1] "2.0 - 135.7 (19.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D931V2, continuous
                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      62        1       26       102         7         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        18          6         40         32       34        11
                vv
clus             STAGE IVB
  GAD2 MUTATED           0
  GAD2 WILD-TYPE         1
D931V3, multiclass
            clus
vv           GAD2 MUTATED GAD2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  GAD2 MUTATED     0   2  12   2
  GAD2 WILD-TYPE   9  65 237  39
D931V4, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           12            237
  T4            2             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
  GAD2 MUTATED     9   5   2
  GAD2 WILD-TYPE 211  76  64
D931V5, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  N0            9            211
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V6, binary
                cls
clus               0   1
  GAD2 MUTATED    12   2
  GAD2 WILD-TYPE 273  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     12    2
  GAD2 WILD-TYPE  273   46
   clus
vv  GAD2 MUTATED GAD2 WILD-TYPE
  0           12            273
  1            2             46
[1] 2 2
[1] FALSE
D931V7, binary
                cls
clus               0   1
  GAD2 MUTATED     7   9
  GAD2 WILD-TYPE 163 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED      7    9
  GAD2 WILD-TYPE  163  188
        clus
vv       GAD2 MUTATED GAD2 WILD-TYPE
  FEMALE            7            163
  MALE              9            188
[1] 2 2
[1] FALSE
D931V8, binary
                cls
clus               0   1
  GAD2 MUTATED    14   0
  GAD2 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     14    0
  GAD2 WILD-TYPE  286    8
     clus
vv    GAD2 MUTATED GAD2 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D931V9, binary
                cls
clus               0   1
  GAD2 MUTATED    11   4
  GAD2 WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     11    4
  GAD2 WILD-TYPE  303   44
                               clus
vv                              GAD2 MUTATED GAD2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAD2 MUTATED    10   0   1   1
  GAD2 WILD-TYPE 249   3  21  20
D931V10, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            1             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"
D931V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAD2 MUTATED                                  0     0
  GAD2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAD2 MUTATED                           1    11
  GAD2 WILD-TYPE                        18   165
D931V12, multiclass
                                  clus
vv                                 GAD2 MUTATED GAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(932) Variable = UBR2 MUTATION ANALYSIS
D932V1, survival
                sevent
clus2              0   1
  UBR2 MUTATED    11   3
  UBR2 WILD-TYPE 266  75
  UBR2 MUTATED UBR2 WILD-TYPE 
            14            341 
  UBR2 MUTATED UBR2 WILD-TYPE 
             3             75 
$`UBR2 MUTATED`
TCGA-DM-A285 TCGA-A6-5666 TCGA-AA-3558 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-A010 
        5.88        32.71        20.98        53.00         2.01        34.98 
TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-D5-6922 TCGA-D5-6930 
        1.02        58.39        12.59        12.76        10.13        13.35 
TCGA-DM-A1DA TCGA-DM-A28F 
        7.50        35.97 

$`UBR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        44.32       131.51       135.65       139.17        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  UBR2 MUTATED UBR2 WILD-TYPE 
          1.02           0.00 
  UBR2 MUTATED UBR2 WILD-TYPE 
         58.39         148.01 
  UBR2 MUTATED UBR2 WILD-TYPE 
        13.055         22.090 
[1] "1.0 - 58.4 (13.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D932V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBR2 MUTATED         1        0        2         5         1         1
  UBR2 WILD-TYPE      63        1       24       103         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR2 MUTATED           0          1          2          1        1         0
  UBR2 WILD-TYPE        18          5         42         32       34        12
                vv
clus             STAGE IVB
  UBR2 MUTATED           0
  UBR2 WILD-TYPE         1
D932V3, multiclass
            clus
vv           UBR2 MUTATED UBR2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  UBR2 MUTATED     0   1  12   2
  UBR2 WILD-TYPE   9  66 237  39
D932V4, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           12            237
  T4            2             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
  UBR2 MUTATED    10   3   2
  UBR2 WILD-TYPE 210  78  64
D932V5, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  N0           10            210
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V6, binary
                cls
clus               0   1
  UBR2 MUTATED    14   1
  UBR2 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED     14    1
  UBR2 WILD-TYPE  271   47
   clus
vv  UBR2 MUTATED UBR2 WILD-TYPE
  0           14            271
  1            1             47
[1] 2 2
[1] FALSE
D932V7, binary
                cls
clus               0   1
  UBR2 MUTATED     6   9
  UBR2 WILD-TYPE 164 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED      6    9
  UBR2 WILD-TYPE  164  188
        clus
vv       UBR2 MUTATED UBR2 WILD-TYPE
  FEMALE            6            164
  MALE              9            188
[1] 2 2
[1] FALSE
D932V8, binary
                cls
clus               0   1
  UBR2 MUTATED     9   0
  UBR2 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED      9    0
  UBR2 WILD-TYPE  291    8
     clus
vv    UBR2 MUTATED UBR2 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D932V9, binary
                cls
clus               0   1
  UBR2 MUTATED    11   4
  UBR2 WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED     11    4
  UBR2 WILD-TYPE  303   44
                               clus
vv                              UBR2 MUTATED UBR2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UBR2 MUTATED     7   0   1   2
  UBR2 WILD-TYPE 252   3  21  19
D932V10, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            2             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"
D932V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBR2 MUTATED                                  0     2
  UBR2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBR2 MUTATED                           0     7
  UBR2 WILD-TYPE                        19   169
D932V12, multiclass
                                  clus
vv                                 UBR2 MUTATED UBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = SMC2 MUTATION ANALYSIS
D933V1, survival
                sevent
clus2              0   1
  SMC2 MUTATED    14  10
  SMC2 WILD-TYPE 263  68
  SMC2 MUTATED SMC2 WILD-TYPE 
            24            331 
  SMC2 MUTATED SMC2 WILD-TYPE 
            10             68 
$`SMC2 MUTATED`
TCGA-AA-3979 TCGA-AA-3492 TCGA-AA-3819 TCGA-AA-A01Z TCGA-AD-6889 TCGA-AD-6890 
       24.00         3.02        25.02        37.02        83.24        24.53 
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        25.48         4.80        16.14 
TCGA-D5-6920 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6626 
       12.39        49.91        35.97         6.18       133.18        46.75 

$`SMC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        12.16         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 
        0.95         0.20        21.44        58.39         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        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        54.61        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-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6323 
       13.78 

  SMC2 MUTATED SMC2 WILD-TYPE 
          1.41           0.00 
  SMC2 MUTATED SMC2 WILD-TYPE 
        133.18         148.01 
  SMC2 MUTATED SMC2 WILD-TYPE 
        23.525         22.030 
[1] "1.4 - 133.2 (23.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D933V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC2 MUTATED         1        0        3        11         1         0
  SMC2 WILD-TYPE      63        1       23        97         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC2 MUTATED           1          0          3          0        1         2
  SMC2 WILD-TYPE        17          6         41         33       34        10
                vv
clus             STAGE IVB
  SMC2 MUTATED           0
  SMC2 WILD-TYPE         1
D933V3, multiclass
            clus
vv           SMC2 MUTATED SMC2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            11             97
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             2             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
  SMC2 MUTATED     1   1  20   3
  SMC2 WILD-TYPE   8  66 229  38
D933V4, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  T1            1              8
  T2            1             66
  T3           20            229
  T4            3             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
  SMC2 MUTATED    18   6   1
  SMC2 WILD-TYPE 202  75  65
D933V5, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  N0           18            202
  N1            6             75
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V6, binary
                cls
clus               0   1
  SMC2 MUTATED    18   3
  SMC2 WILD-TYPE 267  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     18    3
  SMC2 WILD-TYPE  267   45
   clus
vv  SMC2 MUTATED SMC2 WILD-TYPE
  0           18            267
  1            3             45
[1] 2 2
[1] FALSE
D933V7, binary
                cls
clus               0   1
  SMC2 MUTATED    11  14
  SMC2 WILD-TYPE 159 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     11   14
  SMC2 WILD-TYPE  159  183
        clus
vv       SMC2 MUTATED SMC2 WILD-TYPE
  FEMALE           11            159
  MALE             14            183
[1] 2 2
[1] FALSE
D933V8, binary
                cls
clus               0   1
  SMC2 MUTATED    22   0
  SMC2 WILD-TYPE 278   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     22    0
  SMC2 WILD-TYPE  278    8
     clus
vv    SMC2 MUTATED SMC2 WILD-TYPE
  NO            22            278
  YES            0              8
[1] 2 2
[1] FALSE
D933V9, binary
                cls
clus               0   1
  SMC2 MUTATED    22   3
  SMC2 WILD-TYPE 292  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     22    3
  SMC2 WILD-TYPE  292   45
                               clus
vv                              SMC2 MUTATED SMC2 WILD-TYPE
  COLON ADENOCARCINOMA                    22            292
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMC2 MUTATED    17   0   0   3
  SMC2 WILD-TYPE 242   3  22  18
D933V10, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  R0           17            242
  R1            0              3
  R2            0             22
  RX            3             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"
D933V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC2 MUTATED                                  0     3
  SMC2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMC2 MUTATED                           3    15
  SMC2 WILD-TYPE                        16   161
D933V12, multiclass
                                  clus
vv                                 SMC2 MUTATED SMC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      15            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(934) Variable = PSD3 MUTATION ANALYSIS
D934V1, survival
                sevent
clus2              0   1
  PSD3 MUTATED     8   2
  PSD3 WILD-TYPE 269  76
  PSD3 MUTATED PSD3 WILD-TYPE 
            10            345 
  PSD3 MUTATED PSD3 WILD-TYPE 
             2             76 
$`PSD3 MUTATED`
TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AD-6899 
       26.17        33.53        63.98         6.97        33.04         5.79 
TCGA-AZ-6599 TCGA-CM-4743 TCGA-CM-4747 TCGA-D5-6529 
        6.77        23.05        25.02        20.19 

$`PSD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PSD3 MUTATED PSD3 WILD-TYPE 
          5.79           0.00 
  PSD3 MUTATED PSD3 WILD-TYPE 
         63.98         148.01 
  PSD3 MUTATED PSD3 WILD-TYPE 
        24.035         22.030 
[1] "5.8 - 64.0 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D934V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSD3 MUTATED         1        0        2         5         0         0
  PSD3 WILD-TYPE      63        1       24       103         8         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        18          6         44         32       35        11
                vv
clus             STAGE IVB
  PSD3 MUTATED           0
  PSD3 WILD-TYPE         1
D934V3, multiclass
            clus
vv           PSD3 MUTATED PSD3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  PSD3 MUTATED     0   1   7   2
  PSD3 WILD-TYPE   9  66 242  39
D934V4, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            2             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
  PSD3 MUTATED     8   1   1
  PSD3 WILD-TYPE 212  80  65
D934V5, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D934V6, binary
                cls
clus               0   1
  PSD3 MUTATED     7   1
  PSD3 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      7    1
  PSD3 WILD-TYPE  278   47
   clus
vv  PSD3 MUTATED PSD3 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D934V7, binary
                cls
clus               0   1
  PSD3 MUTATED     3   7
  PSD3 WILD-TYPE 167 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      3    7
  PSD3 WILD-TYPE  167  190
        clus
vv       PSD3 MUTATED PSD3 WILD-TYPE
  FEMALE            3            167
  MALE              7            190
[1] 2 2
[1] FALSE
D934V8, binary
                cls
clus               0   1
  PSD3 MUTATED    10   0
  PSD3 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED     10    0
  PSD3 WILD-TYPE  290    8
     clus
vv    PSD3 MUTATED PSD3 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D934V9, binary
                cls
clus               0   1
  PSD3 MUTATED     9   1
  PSD3 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      9    1
  PSD3 WILD-TYPE  305   47
                               clus
vv                              PSD3 MUTATED PSD3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PSD3 MUTATED     8   0   0   0
  PSD3 WILD-TYPE 251   3  22  21
D934V10, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D934V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSD3 MUTATED                                  0     0
  PSD3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PSD3 MUTATED                           1     6
  PSD3 WILD-TYPE                        18   170
D934V12, multiclass
                                  clus
vv                                 PSD3 MUTATED PSD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = PANK1 MUTATION ANALYSIS
D935V1, survival
                 sevent
clus2               0   1
  PANK1 MUTATED     6   1
  PANK1 WILD-TYPE 271  77
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             348 
  PANK1 MUTATED PANK1 WILD-TYPE 
              1              77 
$`PANK1 MUTATED`
TCGA-AA-3713 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 
       19.04        32.75        33.53        24.39         4.01        34.98 
TCGA-AZ-4315 
       58.39 

$`PANK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PANK1 MUTATED PANK1 WILD-TYPE 
           4.01            0.00 
  PANK1 MUTATED PANK1 WILD-TYPE 
          58.39          148.01 
  PANK1 MUTATED PANK1 WILD-TYPE 
          32.75           22.01 
[1] "4.0 - 58.4 (32.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D935V2, continuous
                 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      63        1       26       106         5         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  PANK1 MUTATED           0
  PANK1 WILD-TYPE         1
D935V3, multiclass
            clus
vv           PANK1 MUTATED PANK1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  PANK1 MUTATED     0   1   3   3
  PANK1 WILD-TYPE   9  66 246  38
D935V4, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             3              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
  PANK1 MUTATED     7   0   0
  PANK1 WILD-TYPE 213  81  66
D935V5, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V6, binary
                 cls
clus                0   1
  PANK1 MUTATED     6   1
  PANK1 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      6    1
  PANK1 WILD-TYPE  279   47
   clus
vv  PANK1 MUTATED PANK1 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D935V7, binary
                 cls
clus                0   1
  PANK1 MUTATED     3   4
  PANK1 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      3    4
  PANK1 WILD-TYPE  167  193
        clus
vv       PANK1 MUTATED PANK1 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D935V8, binary
                 cls
clus                0   1
  PANK1 MUTATED     5   1
  PANK1 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      5    1
  PANK1 WILD-TYPE  295    7
     clus
vv    PANK1 MUTATED PANK1 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D935V9, binary
                 cls
clus                0   1
  PANK1 MUTATED     5   2
  PANK1 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      5    2
  PANK1 WILD-TYPE  309   46
                               clus
vv                              PANK1 MUTATED PANK1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PANK1 MUTATED     5   0   1   0
  PANK1 WILD-TYPE 254   3  21  21
D935V10, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             0              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"
D935V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PANK1 MUTATED                                  0     0
  PANK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PANK1 MUTATED                           1     3
  PANK1 WILD-TYPE                        18   173
D935V12, multiclass
                                  clus
vv                                 PANK1 MUTATED PANK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = C4ORF49 MUTATION ANALYSIS
D936V1, survival
                   sevent
clus2                 0   1
  C4ORF49 MUTATED     5   0
  C4ORF49 WILD-TYPE 272  78
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               350 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                0                78 
$`C4ORF49 MUTATED`
TCGA-AA-3510 TCGA-CK-5914 TCGA-D5-5539 TCGA-DM-A1HB TCGA-G4-6293 
       63.98        21.99        19.59       135.65       133.18 

$`C4ORF49 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
            19.59              0.00 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
           135.65            148.01 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
           63.980            22.045 
[1] "19.6 - 135.7 (64.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.7e+07"
D936V2, continuous
                   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      64        1       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF49 MUTATED           1          1          2          0        0
  C4ORF49 WILD-TYPE        17          5         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C4ORF49 MUTATED           0         0
  C4ORF49 WILD-TYPE        12         1
D936V3, multiclass
            clus
vv           C4ORF49 MUTATED C4ORF49 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                0               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C4ORF49 MUTATED     0   0   5   0
  C4ORF49 WILD-TYPE   9  67 244  41
D936V4, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  C4ORF49 MUTATED     1   4   0
  C4ORF49 WILD-TYPE 219  77  66
D936V5, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  N0               1               219
  N1               4                77
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V6, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     4   0
  C4ORF49 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      4    0
  C4ORF49 WILD-TYPE  281   48
   clus
vv  C4ORF49 MUTATED C4ORF49 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D936V7, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     1   4
  C4ORF49 WILD-TYPE 169 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      1    4
  C4ORF49 WILD-TYPE  169  193
        clus
vv       C4ORF49 MUTATED C4ORF49 WILD-TYPE
  FEMALE               1               169
  MALE                 4               193
[1] 2 2
[1] FALSE
D936V8, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     3   0
  C4ORF49 WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      3    0
  C4ORF49 WILD-TYPE  297    8
     clus
vv    C4ORF49 MUTATED C4ORF49 WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D936V9, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     3   1
  C4ORF49 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      3    1
  C4ORF49 WILD-TYPE  311   47
                               clus
vv                              C4ORF49 MUTATED C4ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C4ORF49 MUTATED     3   0   0   1
  C4ORF49 WILD-TYPE 256   3  22  20
D936V10, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               1                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"
D936V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C4ORF49 MUTATED                                  0     0
  C4ORF49 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C4ORF49 MUTATED                           0     4
  C4ORF49 WILD-TYPE                        19   172
D936V12, multiclass
                                  clus
vv                                 C4ORF49 MUTATED C4ORF49 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = ADM MUTATION ANALYSIS
D937V1, survival
               sevent
clus2             0   1
  ADM MUTATED     5   1
  ADM WILD-TYPE 272  77
  ADM MUTATED ADM WILD-TYPE 
            6           349 
  ADM MUTATED ADM WILD-TYPE 
            1            77 
$`ADM MUTATED`
TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A01D TCGA-CM-4743 
       26.17        33.53        63.98        25.02        10.98        23.05 

$`ADM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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        21.990 
[1] "11.0 - 64.0 (25.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D937V2, continuous
               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      64        1       25       105         8         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        18          6         44         32       35        12
               vv
clus            STAGE IVB
  ADM MUTATED           0
  ADM WILD-TYPE         1
D937V3, multiclass
            clus
vv           ADM MUTATED ADM WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            3           105
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  ADM MUTATED     0   1   5   0
  ADM WILD-TYPE   9  66 244  41
D937V4, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  T1           0             9
  T2           1            66
  T3           5           244
  T4           0            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
  ADM MUTATED     5   0   1
  ADM WILD-TYPE 215  81  65
D937V5, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  N0           5           215
  N1           0            81
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V6, binary
               cls
clus              0   1
  ADM MUTATED     5   0
  ADM WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      5    0
  ADM WILD-TYPE  280   48
   clus
vv  ADM MUTATED ADM WILD-TYPE
  0           5           280
  1           0            48
[1] 2 2
[1] FALSE
D937V7, binary
               cls
clus              0   1
  ADM MUTATED     3   3
  ADM WILD-TYPE 167 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      3    3
  ADM WILD-TYPE  167  194
        clus
vv       ADM MUTATED ADM WILD-TYPE
  FEMALE           3           167
  MALE             3           194
[1] 2 2
[1] FALSE
D937V8, binary
               cls
clus              0   1
  ADM MUTATED     6   0
  ADM WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      6    0
  ADM WILD-TYPE  294    8
     clus
vv    ADM MUTATED ADM WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D937V9, binary
               cls
clus              0   1
  ADM MUTATED     5   1
  ADM WILD-TYPE 309  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      5    1
  ADM WILD-TYPE  309   47
                               clus
vv                              ADM MUTATED ADM WILD-TYPE
  COLON ADENOCARCINOMA                    5           309
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ADM MUTATED     5   0   0   0
  ADM WILD-TYPE 254   3  22  21
D937V10, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  R0           5           254
  R1           0             3
  R2           0            22
  RX           0            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"
D937V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADM MUTATED                                  0     0
  ADM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ADM MUTATED                           1     2
  ADM WILD-TYPE                        18   174
D937V12, multiclass
                                  clus
vv                                 ADM MUTATED ADM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      2           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(938) Variable = DCAF12L2 MUTATION ANALYSIS
D938V1, survival
                    sevent
clus2                  0   1
  DCAF12L2 MUTATED    12   4
  DCAF12L2 WILD-TYPE 265  74
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                16                339 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                 4                 74 
$`DCAF12L2 MUTATED`
TCGA-AA-3713 TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3660 TCGA-AA-3821 TCGA-AA-3977 
       19.04        22.06        23.87        78.08         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 
       14.04        31.96         6.18        55.04 

$`DCAF12L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6569 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
              1.02               0.00 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
             78.08             148.01 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
            23.145             21.990 
[1] "1.0 - 78.1 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D938V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCAF12L2 MUTATED         4        0        1         3         2         0
  DCAF12L2 WILD-TYPE      60        1       25       105         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCAF12L2 MUTATED           0          0          3          0        1
  DCAF12L2 WILD-TYPE        18          6         41         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  DCAF12L2 MUTATED           1         0
  DCAF12L2 WILD-TYPE        11         1
D938V3, multiclass
            clus
vv           DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 3                105
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 1                 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
  DCAF12L2 MUTATED     1   4   9   3
  DCAF12L2 WILD-TYPE   8  63 240  38
D938V4, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  T1                1                  8
  T2                4                 63
  T3                9                240
  T4                3                 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
  DCAF12L2 MUTATED    13   4   0
  DCAF12L2 WILD-TYPE 207  77  66
D938V5, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  N0               13                207
  N1                4                 77
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V6, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    12   2
  DCAF12L2 WILD-TYPE 273  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     12    2
  DCAF12L2 WILD-TYPE  273   46
   clus
vv  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  0               12                273
  1                2                 46
[1] 2 2
[1] FALSE
D938V7, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    13   4
  DCAF12L2 WILD-TYPE 157 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     13    4
  DCAF12L2 WILD-TYPE  157  193
        clus
vv       DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  FEMALE               13                157
  MALE                  4                193
[1] 2 2
[1] FALSE
D938V8, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    14   1
  DCAF12L2 WILD-TYPE 286   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     14    1
  DCAF12L2 WILD-TYPE  286    7
     clus
vv    DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  NO                14                286
  YES                1                  7
[1] 2 2
[1] FALSE
D938V9, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    16   1
  DCAF12L2 WILD-TYPE 298  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     16    1
  DCAF12L2 WILD-TYPE  298   47
                               clus
vv                              DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  COLON ADENOCARCINOMA                        16                298
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  DCAF12L2 MUTATED    11   0   1   2
  DCAF12L2 WILD-TYPE 248   3  21  19
D938V10, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  R0               11                248
  R1                0                  3
  R2                1                 21
  RX                2                 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"
D938V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCAF12L2 MUTATED                                  0     0
  DCAF12L2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  DCAF12L2 MUTATED                           0    12
  DCAF12L2 WILD-TYPE                        19   164
D938V12, multiclass
                                  clus
vv                                 DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          12                164
[1] 4 2
[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 = DIAPH2 MUTATION ANALYSIS
D939V1, survival
                  sevent
clus2                0   1
  DIAPH2 MUTATED    13   6
  DIAPH2 WILD-TYPE 264  72
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              19              336 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
               6               72 
$`DIAPH2 MUTATED`
TCGA-AA-3552 TCGA-AA-3692 TCGA-AD-6548 TCGA-A6-6782 TCGA-AA-3555 TCGA-AA-3815 
       13.02        36.00        21.37        20.28        29.95        33.04 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6899 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       25.02         4.01         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 
       13.78 

$`DIAPH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66         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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       53.62        55.04        85.48        61.91        36.00        46.75 

  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
            4.01             0.00 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
          117.07           148.01 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
           20.28            22.09 
[1] "4.0 - 117.1 (20.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D939V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIAPH2 MUTATED         1        1        1         8         2         0
  DIAPH2 WILD-TYPE      63        0       25       100         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIAPH2 MUTATED           0          0          1          3        1
  DIAPH2 WILD-TYPE        18          6         43         30       34
                  vv
clus               STAGE IVA STAGE IVB
  DIAPH2 MUTATED           0         1
  DIAPH2 WILD-TYPE        12         0
D939V3, multiclass
            clus
vv           DIAPH2 MUTATED DIAPH2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                1                0
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              3               30
  STAGE IV                1               34
  STAGE IVA               0               12
  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     0   3  13   4
  DIAPH2 WILD-TYPE   9  64 236  37
D939V4, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             13              236
  T4              4               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
  DIAPH2 MUTATED    15   1   5
  DIAPH2 WILD-TYPE 205  80  61
D939V5, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  N0             15              205
  N1              1               80
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D939V6, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    15   2
  DIAPH2 WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     15    2
  DIAPH2 WILD-TYPE  270   46
   clus
vv  DIAPH2 MUTATED DIAPH2 WILD-TYPE
  0             15              270
  1              2               46
[1] 2 2
[1] FALSE
D939V7, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED     7  14
  DIAPH2 WILD-TYPE 163 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED      7   14
  DIAPH2 WILD-TYPE  163  183
        clus
vv       DIAPH2 MUTATED DIAPH2 WILD-TYPE
  FEMALE              7              163
  MALE               14              183
[1] 2 2
[1] FALSE
D939V8, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    16   1
  DIAPH2 WILD-TYPE 284   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     16    1
  DIAPH2 WILD-TYPE  284    7
     clus
vv    DIAPH2 MUTATED DIAPH2 WILD-TYPE
  NO              16              284
  YES              1                7
[1] 2 2
[1] FALSE
D939V9, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    16   5
  DIAPH2 WILD-TYPE 298  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     16    5
  DIAPH2 WILD-TYPE  298   43
                               clus
vv                              DIAPH2 MUTATED DIAPH2 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DIAPH2 MUTATED    12   0   1   4
  DIAPH2 WILD-TYPE 247   3  21  17
D939V10, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              1               21
  RX              4               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"
D939V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIAPH2 MUTATED                                  0     4
  DIAPH2 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DIAPH2 MUTATED                           2     7
  DIAPH2 WILD-TYPE                        17   169
D939V12, multiclass
                                  clus
vv                                 DIAPH2 MUTATED DIAPH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         7              169
[1] 4 2
[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 = FBXO34 MUTATION ANALYSIS
D940V1, survival
                  sevent
clus2                0   1
  FBXO34 MUTATED     5   4
  FBXO34 WILD-TYPE 272  74
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              346 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               4               74 
$`FBXO34 MUTATED`
TCGA-AA-3672 TCGA-AA-3663 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-6747 
        0.92         6.97        58.39        49.41        10.06        82.95 
TCGA-CM-6171 TCGA-D5-6537 TCGA-DM-A1D4 
       14.04         4.80        92.75 

$`FBXO34 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FBXO34 MUTATED FBXO34 WILD-TYPE 
            0.92             0.00 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
           92.75           148.01 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
          14.040           22.075 
[1] "0.9 - 92.8 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D940V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO34 MUTATED         1        0        2         4         0         0
  FBXO34 WILD-TYPE      63        1       24       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO34 MUTATED           1          0          1          0        0
  FBXO34 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXO34 MUTATED           0         0
  FBXO34 WILD-TYPE        12         1
D940V3, multiclass
            clus
vv           FBXO34 MUTATED FBXO34 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  FBXO34 MUTATED     0   1   8   0
  FBXO34 WILD-TYPE   9  66 241  41
D940V4, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              8              241
  T4              0               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
  FBXO34 MUTATED     7   2   0
  FBXO34 WILD-TYPE 213  79  66
D940V5, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V6, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     6   0
  FBXO34 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      6    0
  FBXO34 WILD-TYPE  279   48
   clus
vv  FBXO34 MUTATED FBXO34 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D940V7, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     4   5
  FBXO34 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      4    5
  FBXO34 WILD-TYPE  166  192
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D940V8, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     8   0
  FBXO34 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      8    0
  FBXO34 WILD-TYPE  292    8
     clus
vv    FBXO34 MUTATED FBXO34 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D940V9, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     9   0
  FBXO34 WILD-TYPE 305  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      9    0
  FBXO34 WILD-TYPE  305   48
                               clus
vv                              FBXO34 MUTATED FBXO34 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXO34 MUTATED     5   0   0   2
  FBXO34 WILD-TYPE 254   3  22  19
D940V10, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D940V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO34 MUTATED                                  0     1
  FBXO34 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO34 MUTATED                           0     6
  FBXO34 WILD-TYPE                        19   170
D940V12, multiclass
                                  clus
vv                                 FBXO34 MUTATED FBXO34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = SCN4A MUTATION ANALYSIS
D941V1, survival
                 sevent
clus2               0   1
  SCN4A MUTATED    15   6
  SCN4A WILD-TYPE 262  72
  SCN4A MUTATED SCN4A WILD-TYPE 
             21             334 
  SCN4A MUTATED SCN4A WILD-TYPE 
              6              72 
$`SCN4A MUTATED`
TCGA-AA-3715 TCGA-AA-3979 TCGA-AD-6895 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3869 
       19.04        24.00        25.08        32.75         3.02        27.02 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
       33.01        25.02        12.16        83.24        27.09        58.39 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 TCGA-CM-5344 TCGA-D5-6533 
       12.69        12.76        10.06        20.02        22.03        25.48 
TCGA-D5-6928 TCGA-DM-A1DB TCGA-F4-6856 
       11.64        44.32        35.31 

$`SCN4A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        23.05        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        14.04        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        54.61        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50       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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SCN4A MUTATED SCN4A WILD-TYPE 
           3.02            0.00 
  SCN4A MUTATED SCN4A WILD-TYPE 
          83.24          148.01 
  SCN4A MUTATED SCN4A WILD-TYPE 
          25.02           21.99 
[1] "3.0 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D941V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN4A MUTATED         5        0        3         8         2         0
  SCN4A WILD-TYPE      59        1       23       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN4A MUTATED           0          0          2          0        1         0
  SCN4A WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  SCN4A MUTATED           0
  SCN4A WILD-TYPE         1
D941V3, multiclass
            clus
vv           SCN4A MUTATED SCN4A WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  SCN4A MUTATED     0   6  12   5
  SCN4A WILD-TYPE   9  61 237  36
D941V4, multiclass
    clus
vv   SCN4A MUTATED SCN4A WILD-TYPE
  T1             0               9
  T2             6              61
  T3            12             237
  T4             5              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
  SCN4A MUTATED    20   2   1
  SCN4A WILD-TYPE 200  79  65
D941V5, multiclass
    clus
vv   SCN4A MUTATED SCN4A WILD-TYPE
  N0            20             200
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V6, binary
                 cls
clus                0   1
  SCN4A MUTATED    19   1
  SCN4A WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED     19    1
  SCN4A WILD-TYPE  266   47
   clus
vv  SCN4A MUTATED SCN4A WILD-TYPE
  0            19             266
  1             1              47
[1] 2 2
[1] FALSE
D941V7, binary
                 cls
clus                0   1
  SCN4A MUTATED     8  15
  SCN4A WILD-TYPE 162 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED      8   15
  SCN4A WILD-TYPE  162  182
        clus
vv       SCN4A MUTATED SCN4A WILD-TYPE
  FEMALE             8             162
  MALE              15             182
[1] 2 2
[1] FALSE
D941V8, binary
                 cls
clus                0   1
  SCN4A MUTATED    19   0
  SCN4A WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED     19    0
  SCN4A WILD-TYPE  281    8
     clus
vv    SCN4A MUTATED SCN4A WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D941V9, binary
                 cls
clus                0   1
  SCN4A MUTATED    17   6
  SCN4A WILD-TYPE 297  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED     17    6
  SCN4A WILD-TYPE  297   42
                               clus
vv                              SCN4A MUTATED SCN4A WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCN4A MUTATED    16   0   1   4
  SCN4A WILD-TYPE 243   3  21  17
D941V10, multiclass
    clus
vv   SCN4A MUTATED SCN4A WILD-TYPE
  R0            16             243
  R1             0               3
  R2             1              21
  RX             4              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"
D941V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCN4A MUTATED                                  0     4
  SCN4A WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCN4A MUTATED                           0    12
  SCN4A WILD-TYPE                        19   164
D941V12, multiclass
                                  clus
vv                                 SCN4A MUTATED SCN4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               6
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = SATB1 MUTATION ANALYSIS
D942V1, survival
                 sevent
clus2               0   1
  SATB1 MUTATED    10   4
  SATB1 WILD-TYPE 267  74
  SATB1 MUTATED SATB1 WILD-TYPE 
             14             341 
  SATB1 MUTATED SATB1 WILD-TYPE 
              4              74 
$`SATB1 MUTATED`
TCGA-G4-6628 TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-6598 
       79.69        25.18        20.12        33.04        83.24        49.41 
TCGA-CA-6718 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 
       10.06        18.25        16.14        11.64       135.65        35.31 
TCGA-G4-6315 TCGA-G4-6626 
       61.91        46.75 

$`SATB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        36.00        13.78 

  SATB1 MUTATED SATB1 WILD-TYPE 
          10.06            0.00 
  SATB1 MUTATED SATB1 WILD-TYPE 
         135.65          148.01 
  SATB1 MUTATED SATB1 WILD-TYPE 
         34.175          21.990 
[1] "10.1 - 135.7 (34.2)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.2"
D942V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SATB1 MUTATED         3        0        1         7         0         0
  SATB1 WILD-TYPE      61        1       25       101         8         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        17          6         43         33       33        11
                 vv
clus              STAGE IVB
  SATB1 MUTATED           0
  SATB1 WILD-TYPE         1
D942V3, multiclass
            clus
vv           SATB1 MUTATED SATB1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              1              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
  SATB1 MUTATED     0   3  12   1
  SATB1 WILD-TYPE   9  64 237  40
D942V4, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            12             237
  T4             1              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
  SATB1 MUTATED    12   3   1
  SATB1 WILD-TYPE 208  78  65
D942V5, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  N0            12             208
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V6, binary
                 cls
clus                0   1
  SATB1 MUTATED    11   3
  SATB1 WILD-TYPE 274  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     11    3
  SATB1 WILD-TYPE  274   45
   clus
vv  SATB1 MUTATED SATB1 WILD-TYPE
  0            11             274
  1             3              45
[1] 2 2
[1] FALSE
D942V7, binary
                 cls
clus                0   1
  SATB1 MUTATED     3  13
  SATB1 WILD-TYPE 167 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED      3   13
  SATB1 WILD-TYPE  167  184
        clus
vv       SATB1 MUTATED SATB1 WILD-TYPE
  FEMALE             3             167
  MALE              13             184
[1] 2 2
[1] FALSE
D942V8, binary
                 cls
clus                0   1
  SATB1 MUTATED    13   0
  SATB1 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     13    0
  SATB1 WILD-TYPE  287    8
     clus
vv    SATB1 MUTATED SATB1 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D942V9, binary
                 cls
clus                0   1
  SATB1 MUTATED    11   4
  SATB1 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     11    4
  SATB1 WILD-TYPE  303   44
                               clus
vv                              SATB1 MUTATED SATB1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SATB1 MUTATED    10   0   1   1
  SATB1 WILD-TYPE 249   3  21  20
D942V10, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             1              21
  RX             1              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"
D942V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SATB1 MUTATED                                  0     2
  SATB1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SATB1 MUTATED                           0    11
  SATB1 WILD-TYPE                        19   165
D942V12, multiclass
                                  clus
vv                                 SATB1 MUTATED SATB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(943) Variable = ZNF334 MUTATION ANALYSIS
D943V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED    17   2
  ZNF334 WILD-TYPE 260  76
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              19              336 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               2               76 
$`ZNF334 MUTATED`
TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3544 TCGA-AA-3678 TCGA-AA-3821 
       79.69        63.98         1.02        14.01        47.01         1.02 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 
       33.01        25.02        34.98        58.39         5.23        12.76 
TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-6166 TCGA-D5-6536 TCGA-D5-6931 TCGA-DM-A1D7 
       37.02        30.08        21.99        17.85        12.00        13.32 
TCGA-F4-6569 
       35.74 

$`ZNF334 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        3.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            1.02             0.00 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           79.69           148.01 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
          25.020           22.045 
[1] "1.0 - 79.7 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D943V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF334 MUTATED         6        0        1         6         2         0
  ZNF334 WILD-TYPE      58        1       25       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF334 MUTATED           1          0          1          1        0
  ZNF334 WILD-TYPE        17          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF334 MUTATED           0         0
  ZNF334 WILD-TYPE        12         1
D943V3, multiclass
            clus
vv           ZNF334 MUTATED ZNF334 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF334 MUTATED     0   8   7   4
  ZNF334 WILD-TYPE   9  59 242  37
D943V4, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  T1              0                9
  T2              8               59
  T3              7              242
  T4              4               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
  ZNF334 MUTATED    16   2   1
  ZNF334 WILD-TYPE 204  79  65
D943V5, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  N0             16              204
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V6, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    18   0
  ZNF334 WILD-TYPE 267  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     18    0
  ZNF334 WILD-TYPE  267   48
   clus
vv  ZNF334 MUTATED ZNF334 WILD-TYPE
  0             18              267
  1              0               48
[1] 2 2
[1] FALSE
D943V7, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     7  12
  ZNF334 WILD-TYPE 163 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      7   12
  ZNF334 WILD-TYPE  163  185
        clus
vv       ZNF334 MUTATED ZNF334 WILD-TYPE
  FEMALE              7              163
  MALE               12              185
[1] 2 2
[1] FALSE
D943V8, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    17   0
  ZNF334 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     17    0
  ZNF334 WILD-TYPE  283    8
     clus
vv    ZNF334 MUTATED ZNF334 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D943V9, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    15   3
  ZNF334 WILD-TYPE 299  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     15    3
  ZNF334 WILD-TYPE  299   45
                               clus
vv                              ZNF334 MUTATED ZNF334 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF334 MUTATED    15   0   0   1
  ZNF334 WILD-TYPE 244   3  22  20
D943V10, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              1               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"
D943V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF334 MUTATED                                  0     1
  ZNF334 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF334 MUTATED                           1     9
  ZNF334 WILD-TYPE                        18   167
D943V12, multiclass
                                  clus
vv                                 ZNF334 MUTATED ZNF334 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(944) Variable = NCAPD3 MUTATION ANALYSIS
D944V1, survival
                  sevent
clus2                0   1
  NCAPD3 MUTATED    21   4
  NCAPD3 WILD-TYPE 256  74
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              25              330 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
               4               74 
$`NCAPD3 MUTATED`
TCGA-AA-3713 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3514 
       19.04        35.80        32.75        22.06        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3869 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 
        1.02        61.02        27.02        34.98        83.24        27.42 
TCGA-AD-6965 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5861 
       26.47        58.39        12.76        10.06        23.05        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-5541 TCGA-DM-A1D9 
       12.00        21.99        15.02        14.04        55.92       140.38 
TCGA-F4-6570 
        6.18 

$`NCAPD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        53.00        17.03        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       29.03        16.04        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-D5-6529 
       12.03        45.40        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
            1.02             0.00 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
          140.38           148.01 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
           23.05            22.01 
[1] "1.0 - 140.4 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D944V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCAPD3 MUTATED         4        0        2        11         2         0
  NCAPD3 WILD-TYPE      60        1       24        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD3 MUTATED           0          0          2          1        2
  NCAPD3 WILD-TYPE        18          6         42         32       33
                  vv
clus               STAGE IVA STAGE IVB
  NCAPD3 MUTATED           0         0
  NCAPD3 WILD-TYPE        12         1
D944V3, multiclass
            clus
vv           NCAPD3 MUTATED NCAPD3 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              11               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               0               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
  NCAPD3 MUTATED     0   4  17   4
  NCAPD3 WILD-TYPE   9  63 232  37
D944V4, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             17              232
  T4              4               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
  NCAPD3 MUTATED    21   2   2
  NCAPD3 WILD-TYPE 199  79  64
D944V5, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  N0             21              199
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V6, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    22   2
  NCAPD3 WILD-TYPE 263  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     22    2
  NCAPD3 WILD-TYPE  263   46
   clus
vv  NCAPD3 MUTATED NCAPD3 WILD-TYPE
  0             22              263
  1              2               46
[1] 2 2
[1] FALSE
D944V7, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    13  12
  NCAPD3 WILD-TYPE 157 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     13   12
  NCAPD3 WILD-TYPE  157  185
        clus
vv       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  FEMALE             13              157
  MALE               12              185
[1] 2 2
[1] FALSE
D944V8, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    22   1
  NCAPD3 WILD-TYPE 278   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     22    1
  NCAPD3 WILD-TYPE  278    7
     clus
vv    NCAPD3 MUTATED NCAPD3 WILD-TYPE
  NO              22              278
  YES              1                7
[1] 2 2
[1] FALSE
D944V9, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    22   3
  NCAPD3 WILD-TYPE 292  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     22    3
  NCAPD3 WILD-TYPE  292   45
                               clus
vv                              NCAPD3 MUTATED NCAPD3 WILD-TYPE
  COLON ADENOCARCINOMA                      22              292
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NCAPD3 MUTATED    18   1   2   2
  NCAPD3 WILD-TYPE 241   2  20  19
D944V10, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  R0             18              241
  R1              1                2
  R2              2               20
  RX              2               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"
D944V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCAPD3 MUTATED                                  0     3
  NCAPD3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NCAPD3 MUTATED                           0    15
  NCAPD3 WILD-TYPE                        19   161
D944V12, multiclass
                                  clus
vv                                 NCAPD3 MUTATED NCAPD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        15              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(945) Variable = KLF5 MUTATION ANALYSIS
D945V1, survival
                sevent
clus2              0   1
  KLF5 MUTATED     8   3
  KLF5 WILD-TYPE 269  75
  KLF5 MUTATED KLF5 WILD-TYPE 
            11            344 
  KLF5 MUTATED KLF5 WILD-TYPE 
             3             75 
$`KLF5 MUTATED`
TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-5666 TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-6599 
        1.94        26.17        32.71         1.02        27.09         6.77 
TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-5539 TCGA-F4-6569 TCGA-G4-6626 
       15.02        14.04        19.59        35.74        46.75 

$`KLF5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6164 
        5.03        15.02        15.02        17.03        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-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 
       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 
       36.00        13.78 

  KLF5 MUTATED KLF5 WILD-TYPE 
          1.02           0.00 
  KLF5 MUTATED KLF5 WILD-TYPE 
         46.75         148.01 
  KLF5 MUTATED KLF5 WILD-TYPE 
        19.590         22.075 
[1] "1.0 - 46.8 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D945V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF5 MUTATED         5        0        1         2         0         1
  KLF5 WILD-TYPE      59        1       25       106         8         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        18          4         44         33       35        12
                vv
clus             STAGE IVB
  KLF5 MUTATED           0
  KLF5 WILD-TYPE         1
D945V3, multiclass
            clus
vv           KLF5 MUTATED KLF5 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            2              4
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  KLF5 MUTATED     1   5   4   1
  KLF5 WILD-TYPE   8  62 245  40
D945V4, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  T1            1              8
  T2            5             62
  T3            4            245
  T4            1             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
  KLF5 MUTATED     9   2   0
  KLF5 WILD-TYPE 211  79  66
D945V5, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  N0            9            211
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V6, binary
                cls
clus               0   1
  KLF5 MUTATED    10   0
  KLF5 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     10    0
  KLF5 WILD-TYPE  275   48
   clus
vv  KLF5 MUTATED KLF5 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D945V7, binary
                cls
clus               0   1
  KLF5 MUTATED     5   6
  KLF5 WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      5    6
  KLF5 WILD-TYPE  165  191
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D945V8, binary
                cls
clus               0   1
  KLF5 MUTATED     9   0
  KLF5 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      9    0
  KLF5 WILD-TYPE  291    8
     clus
vv    KLF5 MUTATED KLF5 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D945V9, binary
                cls
clus               0   1
  KLF5 MUTATED    10   1
  KLF5 WILD-TYPE 304  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     10    1
  KLF5 WILD-TYPE  304   47
                               clus
vv                              KLF5 MUTATED KLF5 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLF5 MUTATED     8   0   0   0
  KLF5 WILD-TYPE 251   3  22  21
D945V10, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D945V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF5 MUTATED                                  0     0
  KLF5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLF5 MUTATED                           0    10
  KLF5 WILD-TYPE                        19   166
D945V12, multiclass
                                  clus
vv                                 KLF5 MUTATED KLF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(946) Variable = DSC2 MUTATION ANALYSIS
D946V1, survival
                sevent
clus2              0   1
  DSC2 MUTATED    10   4
  DSC2 WILD-TYPE 267  74
  DSC2 MUTATED DSC2 WILD-TYPE 
            14            341 
  DSC2 MUTATED DSC2 WILD-TYPE 
             4             74 
$`DSC2 MUTATED`
TCGA-AA-3662 TCGA-AZ-6601 TCGA-A6-2672 TCGA-A6-5666 TCGA-A6-6142 TCGA-AA-A00N 
        6.05       100.01        46.65        32.71        25.08         4.01 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-6161 
       58.39        49.41        12.76        10.06        37.02        15.02 
TCGA-D5-6540 TCGA-DM-A0X9 
       16.14       119.70 

$`DSC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-A6-6648 
       22.09        22.06        27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DSC2 MUTATED DSC2 WILD-TYPE 
          4.01           0.00 
  DSC2 MUTATED DSC2 WILD-TYPE 
        119.70         148.01 
  DSC2 MUTATED DSC2 WILD-TYPE 
        28.895         22.030 
[1] "4.0 - 119.7 (28.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D946V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSC2 MUTATED         3        0        2         4         1         1
  DSC2 WILD-TYPE      61        1       24       104         7         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        18          6         43         33       34        11
                vv
clus             STAGE IVB
  DSC2 MUTATED           0
  DSC2 WILD-TYPE         1
D946V3, multiclass
            clus
vv           DSC2 MUTATED DSC2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  DSC2 MUTATED     0   3   8   3
  DSC2 WILD-TYPE   9  64 241  38
D946V4, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            8            241
  T4            3             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
  DSC2 MUTATED    11   2   1
  DSC2 WILD-TYPE 209  79  65
D946V5, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  N0           11            209
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D946V6, binary
                cls
clus               0   1
  DSC2 MUTATED    11   2
  DSC2 WILD-TYPE 274  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     11    2
  DSC2 WILD-TYPE  274   46
   clus
vv  DSC2 MUTATED DSC2 WILD-TYPE
  0           11            274
  1            2             46
[1] 2 2
[1] FALSE
D946V7, binary
                cls
clus               0   1
  DSC2 MUTATED     6   8
  DSC2 WILD-TYPE 164 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      6    8
  DSC2 WILD-TYPE  164  189
        clus
vv       DSC2 MUTATED DSC2 WILD-TYPE
  FEMALE            6            164
  MALE              8            189
[1] 2 2
[1] FALSE
D946V8, binary
                cls
clus               0   1
  DSC2 MUTATED    12   0
  DSC2 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     12    0
  DSC2 WILD-TYPE  288    8
     clus
vv    DSC2 MUTATED DSC2 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D946V9, binary
                cls
clus               0   1
  DSC2 MUTATED    11   3
  DSC2 WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     11    3
  DSC2 WILD-TYPE  303   45
                               clus
vv                              DSC2 MUTATED DSC2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DSC2 MUTATED     6   0   1   2
  DSC2 WILD-TYPE 253   3  21  19
D946V10, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            1             21
  RX            2             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"
D946V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSC2 MUTATED                                  0     2
  DSC2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSC2 MUTATED                           1     9
  DSC2 WILD-TYPE                        18   167
D946V12, multiclass
                                  clus
vv                                 DSC2 MUTATED DSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       9            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(947) Variable = NUPL2 MUTATION ANALYSIS
D947V1, survival
                 sevent
clus2               0   1
  NUPL2 MUTATED     7   4
  NUPL2 WILD-TYPE 270  74
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             344 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              4              74 
$`NUPL2 MUTATED`
TCGA-AD-6895 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A010 
       25.08        63.98        33.04        30.02        18.05        34.98 
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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        6.77         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NUPL2 MUTATED NUPL2 WILD-TYPE 
           12.1             0.0 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          63.98          148.01 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          29.56           21.99 
[1] "12.1 - 64.0 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D947V2, continuous
                 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      63        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUPL2 MUTATED           0          0          1          1        1         0
  NUPL2 WILD-TYPE        18          6         43         32       34        12
                 vv
clus              STAGE IVB
  NUPL2 MUTATED           0
  NUPL2 WILD-TYPE         1
D947V3, multiclass
            clus
vv           NUPL2 MUTATED NUPL2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  NUPL2 MUTATED     1   1   7   2
  NUPL2 WILD-TYPE   8  66 242  39
D947V4, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             7             242
  T4             2              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
  NUPL2 MUTATED     7   3   1
  NUPL2 WILD-TYPE 213  78  65
D947V5, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V6, binary
                 cls
clus                0   1
  NUPL2 MUTATED     9   1
  NUPL2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      9    1
  NUPL2 WILD-TYPE  276   47
   clus
vv  NUPL2 MUTATED NUPL2 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D947V7, binary
                 cls
clus                0   1
  NUPL2 MUTATED     5   6
  NUPL2 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      5    6
  NUPL2 WILD-TYPE  165  191
        clus
vv       NUPL2 MUTATED NUPL2 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D947V8, binary
                 cls
clus                0   1
  NUPL2 MUTATED     9   0
  NUPL2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      9    0
  NUPL2 WILD-TYPE  291    8
     clus
vv    NUPL2 MUTATED NUPL2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D947V9, binary
                 cls
clus                0   1
  NUPL2 MUTATED    10   0
  NUPL2 WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED     10    0
  NUPL2 WILD-TYPE  304   48
                               clus
vv                              NUPL2 MUTATED NUPL2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NUPL2 MUTATED     7   0   0   1
  NUPL2 WILD-TYPE 252   3  22  20
D947V10, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D947V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUPL2 MUTATED                                  0     0
  NUPL2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NUPL2 MUTATED                           1     5
  NUPL2 WILD-TYPE                        18   171
D947V12, multiclass
                                  clus
vv                                 NUPL2 MUTATED NUPL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = ZSWIM3 MUTATION ANALYSIS
D948V1, survival
                  sevent
clus2                0   1
  ZSWIM3 MUTATED    10   2
  ZSWIM3 WILD-TYPE 267  76
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              12              343 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
               2               76 
$`ZSWIM3 MUTATED`
TCGA-AA-3554 TCGA-G4-6310 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3542 TCGA-AA-A00A 
       17.95        63.62         3.02         1.02        12.99        38.04 
TCGA-AA-A010 TCGA-CK-4950 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1D4 TCGA-DM-A1HB 
       34.98        85.45        16.14        15.58        92.75       135.65 

$`ZSWIM3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
            1.02             0.00 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
          135.65           148.01 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
          26.465           22.060 
[1] "1.0 - 135.7 (26.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D948V2, continuous
                  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      63        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZSWIM3 MUTATED           0          0          3          1        0
  ZSWIM3 WILD-TYPE        18          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZSWIM3 MUTATED           0         0
  ZSWIM3 WILD-TYPE        12         1
D948V3, multiclass
            clus
vv           ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZSWIM3 MUTATED     0   1  10   1
  ZSWIM3 WILD-TYPE   9  66 239  40
D948V4, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             10              239
  T4              1               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
  ZSWIM3 MUTATED     8   3   1
  ZSWIM3 WILD-TYPE 212  78  65
D948V5, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  N0              8              212
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V6, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED    12   0
  ZSWIM3 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED     12    0
  ZSWIM3 WILD-TYPE  273   48
   clus
vv  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D948V7, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED     5   7
  ZSWIM3 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED      5    7
  ZSWIM3 WILD-TYPE  165  190
        clus
vv       ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D948V8, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED     8   1
  ZSWIM3 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED      8    1
  ZSWIM3 WILD-TYPE  292    7
     clus
vv    ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D948V9, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED     9   2
  ZSWIM3 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED      9    2
  ZSWIM3 WILD-TYPE  305   46
                               clus
vv                              ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZSWIM3 MUTATED     9   1   0   0
  ZSWIM3 WILD-TYPE 250   2  22  21
D948V10, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  R0              9              250
  R1              1                2
  R2              0               22
  RX              0               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"
D948V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZSWIM3 MUTATED                                  0     0
  ZSWIM3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZSWIM3 MUTATED                           1     5
  ZSWIM3 WILD-TYPE                        18   171
D948V12, multiclass
                                  clus
vv                                 ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = C5ORF34 MUTATION ANALYSIS
D949V1, survival
                   sevent
clus2                 0   1
  C5ORF34 MUTATED     8   2
  C5ORF34 WILD-TYPE 269  76
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               10               345 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
                2                76 
$`C5ORF34 MUTATED`
TCGA-G4-6588 TCGA-A6-6137 TCGA-AA-3815 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 
       26.17        27.09        33.04         4.01        27.09        12.76 
TCGA-D5-5539 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1DA 
       19.59        16.14        13.35         7.50 

$`C5ORF34 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
             4.01              0.00 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
            33.04            148.01 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
           17.865            22.090 
[1] "4.0 - 33.0 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D949V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF34 MUTATED         2        0        0         4         1         0
  C5ORF34 WILD-TYPE      62        1       26       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF34 MUTATED           0          1          1          1        0
  C5ORF34 WILD-TYPE        18          5         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF34 MUTATED           0         0
  C5ORF34 WILD-TYPE        12         1
D949V3, multiclass
            clus
vv           C5ORF34 MUTATED C5ORF34 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  C5ORF34 MUTATED     0   2   7   1
  C5ORF34 WILD-TYPE   9  65 242  40
D949V4, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               7               242
  T4               1                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
  C5ORF34 MUTATED     7   2   1
  C5ORF34 WILD-TYPE 213  79  65
D949V5, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  N0               7               213
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V6, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED    10   0
  C5ORF34 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED     10    0
  C5ORF34 WILD-TYPE  275   48
   clus
vv  C5ORF34 MUTATED C5ORF34 WILD-TYPE
  0              10               275
  1               0                48
[1] 2 2
[1] FALSE
D949V7, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED     4   6
  C5ORF34 WILD-TYPE 166 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED      4    6
  C5ORF34 WILD-TYPE  166  191
        clus
vv       C5ORF34 MUTATED C5ORF34 WILD-TYPE
  FEMALE               4               166
  MALE                 6               191
[1] 2 2
[1] FALSE
D949V8, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED     7   0
  C5ORF34 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED      7    0
  C5ORF34 WILD-TYPE  293    8
     clus
vv    C5ORF34 MUTATED C5ORF34 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D949V9, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED     5   5
  C5ORF34 WILD-TYPE 309  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED      5    5
  C5ORF34 WILD-TYPE  309   43
                               clus
vv                              C5ORF34 MUTATED C5ORF34 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C5ORF34 MUTATED     7   0   0   1
  C5ORF34 WILD-TYPE 252   3  22  20
D949V10, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               1                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"
D949V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF34 MUTATED                                  0     1
  C5ORF34 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF34 MUTATED                           0     7
  C5ORF34 WILD-TYPE                        19   169
D949V12, multiclass
                                  clus
vv                                 C5ORF34 MUTATED C5ORF34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = YSK4 MUTATION ANALYSIS
D950V1, survival
                sevent
clus2              0   1
  YSK4 MUTATED    20   6
  YSK4 WILD-TYPE 257  72
  YSK4 MUTATED YSK4 WILD-TYPE 
            26            329 
  YSK4 MUTATED YSK4 WILD-TYPE 
             6             72 
$`YSK4 MUTATED`
TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6895 TCGA-G4-6628 
       13.02        85.05        19.04        19.04        25.08        79.69 
TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N 
       22.52        24.39        29.95        15.95        25.02         4.01 
TCGA-AA-A010 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       34.98        33.01        21.44        58.39        12.76        10.06 
TCGA-CM-4752 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6540 TCGA-DM-A1D9 
       13.02        20.19        18.25         4.80        16.14       140.38 
TCGA-DM-A28E TCGA-G4-6626 
      119.93        46.75 

$`YSK4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.00        36.00        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 
       63.62        22.09        35.80        26.17        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        56.09        55.92        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67        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 
       55.04        85.48        61.91        36.00        13.78 

  YSK4 MUTATED YSK4 WILD-TYPE 
          4.01           0.00 
  YSK4 MUTATED YSK4 WILD-TYPE 
        140.38         148.01 
  YSK4 MUTATED YSK4 WILD-TYPE 
         21.98          22.06 
[1] "4.0 - 140.4 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D950V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YSK4 MUTATED         4        0        2        12         2         0
  YSK4 WILD-TYPE      60        1       24        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YSK4 MUTATED           1          0          2          0        1         1
  YSK4 WILD-TYPE        17          6         42         33       34        11
                vv
clus             STAGE IVB
  YSK4 MUTATED           0
  YSK4 WILD-TYPE         1
D950V3, multiclass
            clus
vv           YSK4 MUTATED YSK4 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA            12             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  YSK4 MUTATED     0   5  19   2
  YSK4 WILD-TYPE   9  62 230  39
D950V4, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           19            230
  T4            2             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
  YSK4 MUTATED    22   3   1
  YSK4 WILD-TYPE 198  78  65
D950V5, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  N0           22            198
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V6, binary
                cls
clus               0   1
  YSK4 MUTATED    21   2
  YSK4 WILD-TYPE 264  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     21    2
  YSK4 WILD-TYPE  264   46
   clus
vv  YSK4 MUTATED YSK4 WILD-TYPE
  0           21            264
  1            2             46
[1] 2 2
[1] FALSE
D950V7, binary
                cls
clus               0   1
  YSK4 MUTATED     7  19
  YSK4 WILD-TYPE 163 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED      7   19
  YSK4 WILD-TYPE  163  178
        clus
vv       YSK4 MUTATED YSK4 WILD-TYPE
  FEMALE            7            163
  MALE             19            178
[1] 2 2
[1] FALSE
D950V8, binary
                cls
clus               0   1
  YSK4 MUTATED    22   1
  YSK4 WILD-TYPE 278   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     22    1
  YSK4 WILD-TYPE  278    7
     clus
vv    YSK4 MUTATED YSK4 WILD-TYPE
  NO            22            278
  YES            1              7
[1] 2 2
[1] FALSE
D950V9, binary
                cls
clus               0   1
  YSK4 MUTATED    21   5
  YSK4 WILD-TYPE 293  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     21    5
  YSK4 WILD-TYPE  293   43
                               clus
vv                              YSK4 MUTATED YSK4 WILD-TYPE
  COLON ADENOCARCINOMA                    21            293
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  YSK4 MUTATED    17   0   1   2
  YSK4 WILD-TYPE 242   3  21  19
D950V10, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  R0           17            242
  R1            0              3
  R2            1             21
  RX            2             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"
D950V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YSK4 MUTATED                                  0     2
  YSK4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  YSK4 MUTATED                           2    13
  YSK4 WILD-TYPE                        17   163
D950V12, multiclass
                                  clus
vv                                 YSK4 MUTATED YSK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      13            163
[1] 4 2
[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 = CBLN3 MUTATION ANALYSIS
D951V1, survival
                 sevent
clus2               0   1
  CBLN3 MUTATED     6   0
  CBLN3 WILD-TYPE 271  78
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             349 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              0              78 
$`CBLN3 MUTATED`
TCGA-AA-3713 TCGA-G4-6321 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6536 TCGA-F4-6856 
       19.04        22.09        12.76        14.04        17.85        35.31 

$`CBLN3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.090 
[1] "12.8 - 35.3 (18.4)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D951V2, continuous
                 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      62        1       26       106         8         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        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  CBLN3 MUTATED           0
  CBLN3 WILD-TYPE         1
D951V3, multiclass
            clus
vv           CBLN3 MUTATED CBLN3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  CBLN3 MUTATED     0   3   3   0
  CBLN3 WILD-TYPE   9  64 246  41
D951V4, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             3             246
  T4             0              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
  CBLN3 MUTATED     5   1   0
  CBLN3 WILD-TYPE 215  80  66
D951V5, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V6, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   1
  CBLN3 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    1
  CBLN3 WILD-TYPE  281   47
   clus
vv  CBLN3 MUTATED CBLN3 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D951V7, binary
                 cls
clus                0   1
  CBLN3 MUTATED     2   4
  CBLN3 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      2    4
  CBLN3 WILD-TYPE  168  193
        clus
vv       CBLN3 MUTATED CBLN3 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D951V8, binary
                 cls
clus                0   1
  CBLN3 MUTATED     5   1
  CBLN3 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      5    1
  CBLN3 WILD-TYPE  295    7
     clus
vv    CBLN3 MUTATED CBLN3 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D951V9, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   2
  CBLN3 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    2
  CBLN3 WILD-TYPE  310   46
                               clus
vv                              CBLN3 MUTATED CBLN3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CBLN3 MUTATED     4   0   1   1
  CBLN3 WILD-TYPE 255   3  21  20
D951V10, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             1              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"
D951V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBLN3 MUTATED                                  0     1
  CBLN3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CBLN3 MUTATED                           0     4
  CBLN3 WILD-TYPE                        19   172
D951V12, multiclass
                                  clus
vv                                 CBLN3 MUTATED CBLN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = GGA2 MUTATION ANALYSIS
D952V1, survival
                sevent
clus2              0   1
  GGA2 MUTATED     8   3
  GGA2 WILD-TYPE 269  75
  GGA2 MUTATED GGA2 WILD-TYPE 
            11            344 
  GGA2 MUTATED GGA2 WILD-TYPE 
             3             75 
$`GGA2 MUTATED`
TCGA-AA-3516 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3877 
       13.02        22.06        63.98        26.99        10.06        31.00 
TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-DM-A1HB 
       20.98         4.01        34.98        58.39       135.65 

$`GGA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GGA2 MUTATED GGA2 WILD-TYPE 
          4.01           0.00 
  GGA2 MUTATED GGA2 WILD-TYPE 
        135.65         148.01 
  GGA2 MUTATED GGA2 WILD-TYPE 
         26.99          22.01 
[1] "4.0 - 135.7 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D952V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGA2 MUTATED         1        0        1         4         2         0
  GGA2 WILD-TYPE      63        1       25       104         6         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        16          6         42         33       35        12
                vv
clus             STAGE IVB
  GGA2 MUTATED           0
  GGA2 WILD-TYPE         1
D952V3, multiclass
            clus
vv           GGA2 MUTATED GGA2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GGA2 MUTATED     1   1   8   2
  GGA2 WILD-TYPE   8  66 241  39
D952V4, multiclass
    clus
vv   GGA2 MUTATED GGA2 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            8            241
  T4            2             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
  GGA2 MUTATED     8   1   3
  GGA2 WILD-TYPE 212  80  63
D952V5, multiclass
    clus
vv   GGA2 MUTATED GGA2 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            3             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"
D952V6, binary
                cls
clus               0   1
  GGA2 MUTATED    12   0
  GGA2 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED     12    0
  GGA2 WILD-TYPE  273   48
   clus
vv  GGA2 MUTATED GGA2 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D952V7, binary
                cls
clus               0   1
  GGA2 MUTATED     7   5
  GGA2 WILD-TYPE 163 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED      7    5
  GGA2 WILD-TYPE  163  192
        clus
vv       GGA2 MUTATED GGA2 WILD-TYPE
  FEMALE            7            163
  MALE              5            192
[1] 2 2
[1] FALSE
D952V8, binary
                cls
clus               0   1
  GGA2 MUTATED     9   0
  GGA2 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED      9    0
  GGA2 WILD-TYPE  291    8
     clus
vv    GGA2 MUTATED GGA2 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D952V9, binary
                cls
clus               0   1
  GGA2 MUTATED     8   3
  GGA2 WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED      8    3
  GGA2 WILD-TYPE  306   45
                               clus
vv                              GGA2 MUTATED GGA2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GGA2 MUTATED    10   0   0   0
  GGA2 WILD-TYPE 249   3  22  21
D952V10, multiclass
    clus
vv   GGA2 MUTATED GGA2 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            0             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"
D952V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGA2 MUTATED                                  0     0
  GGA2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GGA2 MUTATED                           0     3
  GGA2 WILD-TYPE                        19   173
D952V12, multiclass
                                  clus
vv                                 GGA2 MUTATED GGA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = ING1 MUTATION ANALYSIS
D953V1, survival
                sevent
clus2              0   1
  ING1 MUTATED     8   2
  ING1 WILD-TYPE 269  76
  ING1 MUTATED ING1 WILD-TYPE 
            10            345 
  ING1 MUTATED ING1 WILD-TYPE 
             2             76 
$`ING1 MUTATED`
TCGA-G4-6586 TCGA-A6-2672 TCGA-AA-3502 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01F 
       35.80        46.65        35.01        26.01        34.98        32.02 
TCGA-AA-A03F TCGA-CK-4950 TCGA-DM-A28K TCGA-F4-6570 
       18.05        85.45        98.24         6.18 

$`ING1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       22.09        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         21.990 
[1] "6.2 - 98.2 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D953V2, continuous
                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      63        1       26       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ING1 MUTATED           1          0          4          0        0         0
  ING1 WILD-TYPE        17          6         40         33       35        12
                vv
clus             STAGE IVB
  ING1 MUTATED           0
  ING1 WILD-TYPE         1
D953V3, multiclass
            clus
vv           ING1 MUTATED ING1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ING1 MUTATED     0   1   8   1
  ING1 WILD-TYPE   9  66 241  40
D953V4, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            1             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
  ING1 MUTATED     5   4   1
  ING1 WILD-TYPE 215  77  65
D953V5, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  N0            5            215
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V6, binary
                cls
clus               0   1
  ING1 MUTATED    10   0
  ING1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED     10    0
  ING1 WILD-TYPE  275   48
   clus
vv  ING1 MUTATED ING1 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D953V7, binary
                cls
clus               0   1
  ING1 MUTATED     7   3
  ING1 WILD-TYPE 163 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      7    3
  ING1 WILD-TYPE  163  194
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  FEMALE            7            163
  MALE              3            194
[1] 2 2
[1] FALSE
D953V8, binary
                cls
clus               0   1
  ING1 MUTATED     9   0
  ING1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      9    0
  ING1 WILD-TYPE  291    8
     clus
vv    ING1 MUTATED ING1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D953V9, binary
                cls
clus               0   1
  ING1 MUTATED     6   4
  ING1 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      6    4
  ING1 WILD-TYPE  308   44
                               clus
vv                              ING1 MUTATED ING1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ING1 MUTATED     8   1   0   0
  ING1 WILD-TYPE 251   2  22  21
D953V10, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  R0            8            251
  R1            1              2
  R2            0             22
  RX            0             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"
D953V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ING1 MUTATED                                  0     0
  ING1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ING1 MUTATED                           1     4
  ING1 WILD-TYPE                        18   172
D953V12, multiclass
                                  clus
vv                                 ING1 MUTATED ING1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(954) Variable = LYG1 MUTATION ANALYSIS
D954V1, survival
                sevent
clus2              0   1
  LYG1 MUTATED     5   1
  LYG1 WILD-TYPE 272  77
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            349 
  LYG1 MUTATED LYG1 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07         0.00        36.03         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.030 
[1] "7.0 - 64.0 (28.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D954V2, continuous
                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      63        1       24       107         8         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        17          6         44         33       35        12
                vv
clus             STAGE IVB
  LYG1 MUTATED           0
  LYG1 WILD-TYPE         1
D954V3, multiclass
            clus
vv           LYG1 MUTATED LYG1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  LYG1 MUTATED     0   2   4   0
  LYG1 WILD-TYPE   9  65 245  41
D954V4, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            4            245
  T4            0             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
  LYG1 MUTATED     5   0   1
  LYG1 WILD-TYPE 215  81  65
D954V5, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V6, binary
                cls
clus               0   1
  LYG1 MUTATED     5   0
  LYG1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    0
  LYG1 WILD-TYPE  280   48
   clus
vv  LYG1 MUTATED LYG1 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D954V7, binary
                cls
clus               0   1
  LYG1 MUTATED     0   6
  LYG1 WILD-TYPE 170 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      0    6
  LYG1 WILD-TYPE  170  191
        clus
vv       LYG1 MUTATED LYG1 WILD-TYPE
  FEMALE            0            170
  MALE              6            191
[1] 2 2
[1] FALSE
D954V8, binary
                cls
clus               0   1
  LYG1 MUTATED     5   1
  LYG1 WILD-TYPE 295   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    1
  LYG1 WILD-TYPE  295    7
     clus
vv    LYG1 MUTATED LYG1 WILD-TYPE
  NO             5            295
  YES            1              7
[1] 2 2
[1] FALSE
D954V9, binary
                cls
clus               0   1
  LYG1 MUTATED     5   1
  LYG1 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    1
  LYG1 WILD-TYPE  309   47
                               clus
vv                              LYG1 MUTATED LYG1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LYG1 MUTATED     4   0   0   1
  LYG1 WILD-TYPE 255   3  22  20
D954V10, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            1             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"
D954V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LYG1 MUTATED                                  0     1
  LYG1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LYG1 MUTATED                           0     0
  LYG1 WILD-TYPE                        19   176
D954V12, multiclass
[1] "Remove cluster labels:" "LYG1 MUTATED"          
clus
  LYG1 MUTATED LYG1 WILD-TYPE 
             1            205 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6600     TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6607     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-5913     TCGA-CK-5914     TCGA-CK-5915 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6309     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6626 
"LYG1 WILD-TYPE" 

Clustering(955) Variable = PRPF4B MUTATION ANALYSIS
D955V1, survival
                  sevent
clus2                0   1
  PRPF4B MUTATED    14   1
  PRPF4B WILD-TYPE 263  77
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              15              340 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               1               77 
$`PRPF4B MUTATED`
TCGA-AA-3697 TCGA-AD-6895 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3955 TCGA-AA-A00A 
       85.05        25.08        19.66         6.97        20.98        38.04 
TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4746 
       34.98        12.76       148.01        51.32        21.14        37.02 
TCGA-CM-6166 TCGA-CM-6674 TCGA-D5-6533 
       21.99        12.95        25.48 

$`PRPF4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 
       14.30        17.56        85.45        15.62        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        29.03        16.04        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        54.61        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PRPF4B MUTATED PRPF4B WILD-TYPE 
            6.97             0.00 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
          148.01           140.38 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
          25.080           22.045 
[1] "7.0 - 148.0 (25.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "4.2"
D955V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPF4B MUTATED         3        0        2         4         1         0
  PRPF4B WILD-TYPE      61        1       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF4B MUTATED           1          0          2          1        0
  PRPF4B WILD-TYPE        17          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  PRPF4B MUTATED           0         0
  PRPF4B WILD-TYPE        12         1
D955V3, multiclass
            clus
vv           PRPF4B MUTATED PRPF4B WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  PRPF4B MUTATED     1   3   8   3
  PRPF4B WILD-TYPE   8  64 241  38
D955V4, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  T1              1                8
  T2              3               64
  T3              8              241
  T4              3               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
  PRPF4B MUTATED    11   3   1
  PRPF4B WILD-TYPE 209  78  65
D955V5, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  N0             11              209
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V6, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    13   0
  PRPF4B WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     13    0
  PRPF4B WILD-TYPE  272   48
   clus
vv  PRPF4B MUTATED PRPF4B WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D955V7, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     6   9
  PRPF4B WILD-TYPE 164 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      6    9
  PRPF4B WILD-TYPE  164  188
        clus
vv       PRPF4B MUTATED PRPF4B WILD-TYPE
  FEMALE              6              164
  MALE                9              188
[1] 2 2
[1] FALSE
D955V8, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    15   0
  PRPF4B WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     15    0
  PRPF4B WILD-TYPE  285    8
     clus
vv    PRPF4B MUTATED PRPF4B WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D955V9, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    13   2
  PRPF4B WILD-TYPE 301  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     13    2
  PRPF4B WILD-TYPE  301   46
                               clus
vv                              PRPF4B MUTATED PRPF4B WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRPF4B MUTATED    12   0   0   3
  PRPF4B WILD-TYPE 247   3  22  18
D955V10, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              3               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"
D955V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRPF4B MUTATED                                  0     1
  PRPF4B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRPF4B MUTATED                           1     8
  PRPF4B WILD-TYPE                        18   168
D955V12, multiclass
                                  clus
vv                                 PRPF4B MUTATED PRPF4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = TDRD7 MUTATION ANALYSIS
D956V1, survival
                 sevent
clus2               0   1
  TDRD7 MUTATED    12   3
  TDRD7 WILD-TYPE 265  75
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             15             340 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
              3              75 
$`TDRD7 MUTATED`
TCGA-AZ-6601 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3681 
      100.01        30.44        22.06         8.38         3.02         5.98 
TCGA-AA-3710 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5864 
       26.99         4.01        34.98        58.39        12.76        15.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6532 
       15.02        14.04        18.25 

$`TDRD7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3811 
       47.01        15.02        11.01        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TDRD7 MUTATED TDRD7 WILD-TYPE 
           3.02            0.00 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
         100.01          148.01 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
         15.020          22.225 
[1] "3.0 - 100.0 (15.0)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1"  
D956V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TDRD7 MUTATED         4        0        2         6         2         0
  TDRD7 WILD-TYPE      60        1       24       102         6         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  TDRD7 MUTATED           0
  TDRD7 WILD-TYPE         1
D956V3, multiclass
            clus
vv           TDRD7 MUTATED TDRD7 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  TDRD7 MUTATED     0   4   9   2
  TDRD7 WILD-TYPE   9  63 240  39
D956V4, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             9             240
  T4             2              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
  TDRD7 MUTATED    14   1   0
  TDRD7 WILD-TYPE 206  80  66
D956V5, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  N0            14             206
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V6, binary
                 cls
clus                0   1
  TDRD7 MUTATED    15   0
  TDRD7 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     15    0
  TDRD7 WILD-TYPE  270   48
   clus
vv  TDRD7 MUTATED TDRD7 WILD-TYPE
  0            15             270
  1             0              48
[1] 2 2
[1] FALSE
D956V7, binary
                 cls
clus                0   1
  TDRD7 MUTATED     7   8
  TDRD7 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED      7    8
  TDRD7 WILD-TYPE  163  189
        clus
vv       TDRD7 MUTATED TDRD7 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D956V8, binary
                 cls
clus                0   1
  TDRD7 MUTATED    14   0
  TDRD7 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     14    0
  TDRD7 WILD-TYPE  286    8
     clus
vv    TDRD7 MUTATED TDRD7 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D956V9, binary
                 cls
clus                0   1
  TDRD7 MUTATED    13   2
  TDRD7 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     13    2
  TDRD7 WILD-TYPE  301   46
                               clus
vv                              TDRD7 MUTATED TDRD7 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TDRD7 MUTATED    12   0   0   1
  TDRD7 WILD-TYPE 247   3  22  20
D956V10, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D956V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDRD7 MUTATED                                  0     1
  TDRD7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TDRD7 MUTATED                           1     8
  TDRD7 WILD-TYPE                        18   168
D956V12, multiclass
                                  clus
vv                                 TDRD7 MUTATED TDRD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = ADAMTS19 MUTATION ANALYSIS
D957V1, survival
                    sevent
clus2                  0   1
  ADAMTS19 MUTATED    13   6
  ADAMTS19 WILD-TYPE 264  72
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                19                336 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                 6                 72 
$`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 
      133.18 

$`ADAMTS19 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        27.42        26.47        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41        12.10        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
              4.01               0.00 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
            135.65             148.01 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
             27.09              22.01 
[1] "4.0 - 135.7 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D957V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTS19 MUTATED         2        0        0         7         3         0
  ADAMTS19 WILD-TYPE      62        1       26       101         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS19 MUTATED           2          0          4          0        0
  ADAMTS19 WILD-TYPE        16          6         40         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTS19 MUTATED           1         0
  ADAMTS19 WILD-TYPE        11         1
D957V3, multiclass
            clus
vv           ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 7                101
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                0                  6
  STAGE IIIB                4                 40
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  ADAMTS19 MUTATED     0   2  11   6
  ADAMTS19 WILD-TYPE   9  65 238  35
D957V4, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3               11                238
  T4                6                 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
  ADAMTS19 MUTATED    12   7   0
  ADAMTS19 WILD-TYPE 208  74  66
D957V5, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  N0               12                208
  N1                7                 74
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V6, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    15   1
  ADAMTS19 WILD-TYPE 270  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     15    1
  ADAMTS19 WILD-TYPE  270   47
   clus
vv  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  0               15                270
  1                1                 47
[1] 2 2
[1] FALSE
D957V7, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED     9  10
  ADAMTS19 WILD-TYPE 161 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED      9   10
  ADAMTS19 WILD-TYPE  161  187
        clus
vv       ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  FEMALE                9                161
  MALE                 10                187
[1] 2 2
[1] FALSE
D957V8, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    15   0
  ADAMTS19 WILD-TYPE 285   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     15    0
  ADAMTS19 WILD-TYPE  285    8
     clus
vv    ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  NO                15                285
  YES                0                  8
[1] 2 2
[1] FALSE
D957V9, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    14   4
  ADAMTS19 WILD-TYPE 300  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     14    4
  ADAMTS19 WILD-TYPE  300   44
                               clus
vv                              ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  COLON ADENOCARCINOMA                        14                300
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ADAMTS19 MUTATED    14   0   0   0
  ADAMTS19 WILD-TYPE 245   3  22  21
D957V10, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  R0               14                245
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D957V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS19 MUTATED                                  0     0
  ADAMTS19 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS19 MUTATED                           0    15
  ADAMTS19 WILD-TYPE                        19   161
D957V12, multiclass
                                  clus
vv                                 ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          15                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(958) Variable = MALT1 MUTATION ANALYSIS
D958V1, survival
                 sevent
clus2               0   1
  MALT1 MUTATED     8   3
  MALT1 WILD-TYPE 269  75
  MALT1 MUTATED MALT1 WILD-TYPE 
             11             344 
  MALT1 MUTATED MALT1 WILD-TYPE 
              3              75 
$`MALT1 MUTATED`
TCGA-AA-3516 TCGA-AA-3662 TCGA-G4-6625 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 
       13.02         6.05        91.79        22.06         3.02        33.04 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6901 
       53.00        31.00        25.02        34.98        22.42 

$`MALT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MALT1 MUTATED MALT1 WILD-TYPE 
           3.02            0.00 
  MALT1 MUTATED MALT1 WILD-TYPE 
          91.79          148.01 
  MALT1 MUTATED MALT1 WILD-TYPE 
          25.02           21.99 
[1] "3.0 - 91.8 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D958V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MALT1 MUTATED         1        0        2         3         1         0
  MALT1 WILD-TYPE      63        1       24       105         7         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        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  MALT1 MUTATED           0
  MALT1 WILD-TYPE         1
D958V3, multiclass
            clus
vv           MALT1 MUTATED MALT1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  MALT1 MUTATED     1   1   7   2
  MALT1 WILD-TYPE   8  66 242  39
D958V4, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             7             242
  T4             2              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
  MALT1 MUTATED     9   0   2
  MALT1 WILD-TYPE 211  81  64
D958V5, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V6, binary
                 cls
clus                0   1
  MALT1 MUTATED     8   1
  MALT1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      8    1
  MALT1 WILD-TYPE  277   47
   clus
vv  MALT1 MUTATED MALT1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D958V7, binary
                 cls
clus                0   1
  MALT1 MUTATED     8   3
  MALT1 WILD-TYPE 162 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      8    3
  MALT1 WILD-TYPE  162  194
        clus
vv       MALT1 MUTATED MALT1 WILD-TYPE
  FEMALE             8             162
  MALE               3             194
[1] 2 2
[1] FALSE
D958V8, binary
                 cls
clus                0   1
  MALT1 MUTATED    11   0
  MALT1 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED     11    0
  MALT1 WILD-TYPE  289    8
     clus
vv    MALT1 MUTATED MALT1 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D958V9, binary
                 cls
clus                0   1
  MALT1 MUTATED     9   2
  MALT1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      9    2
  MALT1 WILD-TYPE  305   46
                               clus
vv                              MALT1 MUTATED MALT1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MALT1 MUTATED     7   0   1   0
  MALT1 WILD-TYPE 252   3  21  21
D958V10, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             0              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"
D958V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MALT1 MUTATED                                  0     0
  MALT1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MALT1 MUTATED                           0     3
  MALT1 WILD-TYPE                        19   173
D958V12, multiclass
                                  clus
vv                                 MALT1 MUTATED MALT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = JMJD6 MUTATION ANALYSIS
D959V1, survival
                 sevent
clus2               0   1
  JMJD6 MUTATED     8   0
  JMJD6 WILD-TYPE 269  78
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              8             347 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              0              78 
$`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        12.16        22.98 
TCGA-D5-6540 TCGA-G4-6293 
       16.14       133.18 

$`JMJD6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  JMJD6 MUTATED JMJD6 WILD-TYPE 
           6.97            0.00 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
         133.18          148.01 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
          24.03           22.03 
[1] "7.0 - 133.2 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D959V2, continuous
                 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      62        1       25       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JMJD6 MUTATED           2          0          1          0        0         1
  JMJD6 WILD-TYPE        16          6         43         33       35        11
                 vv
clus              STAGE IVB
  JMJD6 MUTATED           0
  JMJD6 WILD-TYPE         1
D959V3, multiclass
            clus
vv           JMJD6 MUTATED JMJD6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  JMJD6 MUTATED     0   2   5   1
  JMJD6 WILD-TYPE   9  65 244  40
D959V4, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             1              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
  JMJD6 MUTATED     4   3   1
  JMJD6 WILD-TYPE 216  78  65
D959V5, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  N0             4             216
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V6, binary
                 cls
clus                0   1
  JMJD6 MUTATED     6   1
  JMJD6 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      6    1
  JMJD6 WILD-TYPE  279   47
   clus
vv  JMJD6 MUTATED JMJD6 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D959V7, binary
                 cls
clus                0   1
  JMJD6 MUTATED     3   5
  JMJD6 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      3    5
  JMJD6 WILD-TYPE  167  192
        clus
vv       JMJD6 MUTATED JMJD6 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D959V8, binary
                 cls
clus                0   1
  JMJD6 MUTATED     7   1
  JMJD6 WILD-TYPE 293   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      7    1
  JMJD6 WILD-TYPE  293    7
     clus
vv    JMJD6 MUTATED JMJD6 WILD-TYPE
  NO              7             293
  YES             1               7
[1] 2 2
[1] FALSE
D959V9, binary
                 cls
clus                0   1
  JMJD6 MUTATED     5   3
  JMJD6 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      5    3
  JMJD6 WILD-TYPE  309   45
                               clus
vv                              JMJD6 MUTATED JMJD6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  JMJD6 MUTATED     7   0   0   0
  JMJD6 WILD-TYPE 252   3  22  21
D959V10, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D959V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JMJD6 MUTATED                                  0     0
  JMJD6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  JMJD6 MUTATED                           0     5
  JMJD6 WILD-TYPE                        19   171
D959V12, multiclass
                                  clus
vv                                 JMJD6 MUTATED JMJD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = THUMPD3 MUTATION ANALYSIS
D960V1, survival
                   sevent
clus2                 0   1
  THUMPD3 MUTATED     8   2
  THUMPD3 WILD-TYPE 269  76
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               10               345 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
                2                76 
$`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 
       12.49        35.74        65.85        53.62 

$`THUMPD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6570 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 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
      133.18        74.56        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
             12.1               0.0 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
            65.85            148.01 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
            32.50             22.03 
[1] "12.1 - 65.8 (32.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D960V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THUMPD3 MUTATED         1        0        0         4         3         0
  THUMPD3 WILD-TYPE      63        1       26       104         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THUMPD3 MUTATED           0          0          0          0        2
  THUMPD3 WILD-TYPE        18          6         44         33       33
                   vv
clus                STAGE IVA STAGE IVB
  THUMPD3 MUTATED           0         0
  THUMPD3 WILD-TYPE        12         1
D960V3, multiclass
            clus
vv           THUMPD3 MUTATED THUMPD3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  THUMPD3 MUTATED     0   1   6   4
  THUMPD3 WILD-TYPE   9  66 243  37
D960V4, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               4                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
  THUMPD3 MUTATED     9   2   0
  THUMPD3 WILD-TYPE 211  79  66
D960V5, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  N0               9               211
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V6, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED     8   2
  THUMPD3 WILD-TYPE 277  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED      8    2
  THUMPD3 WILD-TYPE  277   46
   clus
vv  THUMPD3 MUTATED THUMPD3 WILD-TYPE
  0               8               277
  1               2                46
[1] 2 2
[1] FALSE
D960V7, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED     5   6
  THUMPD3 WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED      5    6
  THUMPD3 WILD-TYPE  165  191
        clus
vv       THUMPD3 MUTATED THUMPD3 WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D960V8, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED    10   0
  THUMPD3 WILD-TYPE 290   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED     10    0
  THUMPD3 WILD-TYPE  290    8
     clus
vv    THUMPD3 MUTATED THUMPD3 WILD-TYPE
  NO               10               290
  YES               0                 8
[1] 2 2
[1] FALSE
D960V9, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED    10   1
  THUMPD3 WILD-TYPE 304  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED     10    1
  THUMPD3 WILD-TYPE  304   47
                               clus
vv                              THUMPD3 MUTATED THUMPD3 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  THUMPD3 MUTATED     8   0   0   2
  THUMPD3 WILD-TYPE 251   3  22  19
D960V10, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               2                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"
D960V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THUMPD3 MUTATED                                  0     1
  THUMPD3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  THUMPD3 MUTATED                           2     6
  THUMPD3 WILD-TYPE                        17   170
D960V12, multiclass
                                  clus
vv                                 THUMPD3 MUTATED THUMPD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = STAU2 MUTATION ANALYSIS
D961V1, survival
                 sevent
clus2               0   1
  STAU2 MUTATED     7   2
  STAU2 WILD-TYPE 270  76
  STAU2 MUTATED STAU2 WILD-TYPE 
              9             346 
  STAU2 MUTATED STAU2 WILD-TYPE 
              2              76 
$`STAU2 MUTATED`
TCGA-G4-6586 TCGA-AA-3821 TCGA-AA-A00A TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 
       35.80         1.02        38.04        12.16        58.39        12.76 
TCGA-CK-5913 TCGA-CK-5916 TCGA-F4-6460 
       51.32        21.14        31.96 

$`STAU2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       15.62        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6569 
       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  STAU2 MUTATED STAU2 WILD-TYPE 
           1.02            0.00 
  STAU2 MUTATED STAU2 WILD-TYPE 
          58.39          148.01 
  STAU2 MUTATED STAU2 WILD-TYPE 
         31.960          22.045 
[1] "1.0 - 58.4 (32.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D961V2, continuous
                 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      61        1       26       102         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  STAU2 MUTATED           0
  STAU2 WILD-TYPE         1
D961V3, multiclass
            clus
vv           STAU2 MUTATED STAU2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  STAU2 MUTATED     1   2   7   0
  STAU2 WILD-TYPE   8  65 242  41
D961V4, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             0              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
  STAU2 MUTATED     9   1   0
  STAU2 WILD-TYPE 211  80  66
D961V5, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V6, binary
                 cls
clus                0   1
  STAU2 MUTATED     8   0
  STAU2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      8    0
  STAU2 WILD-TYPE  277   48
   clus
vv  STAU2 MUTATED STAU2 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D961V7, binary
                 cls
clus                0   1
  STAU2 MUTATED     6   4
  STAU2 WILD-TYPE 164 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      6    4
  STAU2 WILD-TYPE  164  193
        clus
vv       STAU2 MUTATED STAU2 WILD-TYPE
  FEMALE             6             164
  MALE               4             193
[1] 2 2
[1] FALSE
D961V8, binary
                 cls
clus                0   1
  STAU2 MUTATED     9   0
  STAU2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      9    0
  STAU2 WILD-TYPE  291    8
     clus
vv    STAU2 MUTATED STAU2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D961V9, binary
                 cls
clus                0   1
  STAU2 MUTATED     7   3
  STAU2 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      7    3
  STAU2 WILD-TYPE  307   45
                               clus
vv                              STAU2 MUTATED STAU2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAU2 MUTATED     7   0   0   3
  STAU2 WILD-TYPE 252   3  22  18
D961V10, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             3              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"
D961V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAU2 MUTATED                                  0     1
  STAU2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAU2 MUTATED                           0     6
  STAU2 WILD-TYPE                        19   170
D961V12, multiclass
                                  clus
vv                                 STAU2 MUTATED STAU2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = KIAA1797 MUTATION ANALYSIS
D962V1, survival
                    sevent
clus2                  0   1
  KIAA1797 MUTATED    16   4
  KIAA1797 WILD-TYPE 261  74
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                20                335 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                 4                 74 
$`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        12.16        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 
      133.18        46.75 

$`KIAA1797 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        13.78 

  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
              1.02               0.00 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            133.18             148.01 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            17.195             22.360 
[1] "1.0 - 133.2 (17.2)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D962V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1797 MUTATED         2        0        4         9         1         0
  KIAA1797 WILD-TYPE      62        1       22        99         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1797 MUTATED           1          0          2          1        0
  KIAA1797 WILD-TYPE        17          6         42         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1797 MUTATED           0         0
  KIAA1797 WILD-TYPE        12         1
D962V3, multiclass
            clus
vv           KIAA1797 MUTATED KIAA1797 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                 9                 99
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA1797 MUTATED     0   2  17   1
  KIAA1797 WILD-TYPE   9  65 232  40
D962V4, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3               17                232
  T4                1                 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
  KIAA1797 MUTATED    16   3   1
  KIAA1797 WILD-TYPE 204  78  65
D962V5, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  N0               16                204
  N1                3                 78
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V6, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    16   0
  KIAA1797 WILD-TYPE 269  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     16    0
  KIAA1797 WILD-TYPE  269   48
   clus
vv  KIAA1797 MUTATED KIAA1797 WILD-TYPE
  0               16                269
  1                0                 48
[1] 2 2
[1] FALSE
D962V7, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED     8  12
  KIAA1797 WILD-TYPE 162 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED      8   12
  KIAA1797 WILD-TYPE  162  185
        clus
vv       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  FEMALE                8                162
  MALE                 12                185
[1] 2 2
[1] FALSE
D962V8, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    18   0
  KIAA1797 WILD-TYPE 282   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     18    0
  KIAA1797 WILD-TYPE  282    8
     clus
vv    KIAA1797 MUTATED KIAA1797 WILD-TYPE
  NO                18                282
  YES                0                  8
[1] 2 2
[1] FALSE
D962V9, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    16   4
  KIAA1797 WILD-TYPE 298  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     16    4
  KIAA1797 WILD-TYPE  298   44
                               clus
vv                              KIAA1797 MUTATED KIAA1797 WILD-TYPE
  COLON ADENOCARCINOMA                        16                298
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1797 MUTATED    16   0   0   2
  KIAA1797 WILD-TYPE 243   3  22  19
D962V10, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  R0               16                243
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D962V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1797 MUTATED                                  0     1
  KIAA1797 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1797 MUTATED                           2    12
  KIAA1797 WILD-TYPE                        17   164
D962V12, multiclass
                                  clus
vv                                 KIAA1797 MUTATED KIAA1797 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          12                164
[1] 4 2
[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 = MKI67 MUTATION ANALYSIS
D963V1, survival
                 sevent
clus2               0   1
  MKI67 MUTATED    27   8
  MKI67 WILD-TYPE 250  70
  MKI67 MUTATED MKI67 WILD-TYPE 
             35             320 
  MKI67 MUTATED MKI67 WILD-TYPE 
              8              70 
$`MKI67 MUTATED`
TCGA-AA-3525 TCGA-AA-3697 TCGA-AA-3715 TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-3809 
        8.05        85.05        19.04        79.69        42.90        32.75 
TCGA-A6-5660 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3815 
       29.19        24.39        23.87        20.12        63.98        33.04 
TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A 
        0.00        33.01        26.01         2.01        25.02        38.04 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AU-6004 
       30.02         4.01        34.98         1.02        14.50        27.09 
TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-6162 TCGA-D5-6924 
       49.41        10.06        15.62        30.08        12.00        14.30 
TCGA-DM-A1DB TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 
       44.32        98.24         6.18        47.87        61.91 

$`MKI67 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        43.76        46.65        43.76        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-A6-5661 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-A6-6138 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-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       31.00         2.01        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        27.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        19.00        34.03        18.05        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       24.53         5.79        22.42        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MKI67 MUTATED MKI67 WILD-TYPE 
              0               0 
  MKI67 MUTATED MKI67 WILD-TYPE 
          98.24          148.01 
  MKI67 MUTATED MKI67 WILD-TYPE 
          27.09           21.99 
[1] "0.0 - 98.2 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D963V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MKI67 MUTATED         3        0        5        15         5         0
  MKI67 WILD-TYPE      61        1       21        93         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKI67 MUTATED           0          0          4          2        1         0
  MKI67 WILD-TYPE        18          6         40         31       34        12
                 vv
clus              STAGE IVB
  MKI67 MUTATED           0
  MKI67 WILD-TYPE         1
D963V3, multiclass
            clus
vv           MKI67 MUTATED MKI67 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             15              93
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  MKI67 MUTATED     0   4  26   6
  MKI67 WILD-TYPE   9  63 223  35
D963V4, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            26             223
  T4             6              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
  MKI67 MUTATED    29   5   2
  MKI67 WILD-TYPE 191  76  64
D963V5, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  N0            29             191
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V6, binary
                 cls
clus                0   1
  MKI67 MUTATED    32   1
  MKI67 WILD-TYPE 253  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     32    1
  MKI67 WILD-TYPE  253   47
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0            32             253
  1             1              47
[1] 2 2
[1] FALSE
D963V7, binary
                 cls
clus                0   1
  MKI67 MUTATED    18  18
  MKI67 WILD-TYPE 152 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     18   18
  MKI67 WILD-TYPE  152  179
        clus
vv       MKI67 MUTATED MKI67 WILD-TYPE
  FEMALE            18             152
  MALE              18             179
[1] 2 2
[1] FALSE
D963V8, binary
                 cls
clus                0   1
  MKI67 MUTATED    27   0
  MKI67 WILD-TYPE 273   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     27    0
  MKI67 WILD-TYPE  273    8
     clus
vv    MKI67 MUTATED MKI67 WILD-TYPE
  NO             27             273
  YES             0               8
[1] 2 2
[1] FALSE
D963V9, binary
                 cls
clus                0   1
  MKI67 MUTATED    27   9
  MKI67 WILD-TYPE 287  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     27    9
  MKI67 WILD-TYPE  287   39
                               clus
vv                              MKI67 MUTATED MKI67 WILD-TYPE
  COLON ADENOCARCINOMA                     27             287
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MKI67 MUTATED    25   0   0   2
  MKI67 WILD-TYPE 234   3  22  19
D963V10, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0            25             234
  R1             0               3
  R2             0              22
  RX             2              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"
D963V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKI67 MUTATED                                  0     1
  MKI67 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MKI67 MUTATED                           1    18
  MKI67 WILD-TYPE                        18   158
D963V12, multiclass
                                  clus
vv                                 MKI67 MUTATED MKI67 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       18             158
[1] 4 2
[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 = HAUS6 MUTATION ANALYSIS
D964V1, survival
                 sevent
clus2               0   1
  HAUS6 MUTATED     6   3
  HAUS6 WILD-TYPE 271  75
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              9             346 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              3              75 
$`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 
       38.20        92.75       135.65 

$`HAUS6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
          18.25            0.00 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
         135.65          148.01 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          38.20           21.99 
[1] "18.2 - 135.7 (38.2)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.2"
D964V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAUS6 MUTATED         1        0        1         4         1         0
  HAUS6 WILD-TYPE      63        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS6 MUTATED           0          1          1          1        1         0
  HAUS6 WILD-TYPE        18          5         43         32       34        12
                 vv
clus              STAGE IVB
  HAUS6 MUTATED           0
  HAUS6 WILD-TYPE         1
D964V3, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  HAUS6 MUTATED     1   2   7   2
  HAUS6 WILD-TYPE   8  65 242  39
D964V4, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             2              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
  HAUS6 MUTATED     8   2   2
  HAUS6 WILD-TYPE 212  79  64
D964V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V6, binary
                 cls
clus                0   1
  HAUS6 MUTATED     9   1
  HAUS6 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      9    1
  HAUS6 WILD-TYPE  276   47
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D964V7, binary
                 cls
clus                0   1
  HAUS6 MUTATED     6   6
  HAUS6 WILD-TYPE 164 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      6    6
  HAUS6 WILD-TYPE  164  191
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  FEMALE             6             164
  MALE               6             191
[1] 2 2
[1] FALSE
D964V8, binary
                 cls
clus                0   1
  HAUS6 MUTATED     6   0
  HAUS6 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      6    0
  HAUS6 WILD-TYPE  294    8
     clus
vv    HAUS6 MUTATED HAUS6 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D964V9, binary
                 cls
clus                0   1
  HAUS6 MUTATED     9   1
  HAUS6 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      9    1
  HAUS6 WILD-TYPE  305   47
                               clus
vv                              HAUS6 MUTATED HAUS6 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HAUS6 MUTATED     5   0   1   2
  HAUS6 WILD-TYPE 254   3  21  19
D964V10, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             2              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"
D964V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAUS6 MUTATED                                  0     0
  HAUS6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HAUS6 MUTATED                           0     8
  HAUS6 WILD-TYPE                        19   168
D964V12, multiclass
                                  clus
vv                                 HAUS6 MUTATED HAUS6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = DNAH6 MUTATION ANALYSIS
D965V1, survival
                 sevent
clus2               0   1
  DNAH6 MUTATED    16   4
  DNAH6 WILD-TYPE 261  74
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             20             335 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
              4              74 
$`DNAH6 MUTATED`
TCGA-G4-6588 TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 
       26.17        30.44         8.38        19.66         3.02        63.98 
TCGA-AA-3663 TCGA-AA-3977 TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 
        6.97        25.02        12.16        83.24        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4747 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 
       12.76        10.06        25.02        12.00        14.04        12.95 
TCGA-D5-6928 TCGA-F4-6703 
       11.64        47.87 

$`DNAH6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6142 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.12        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6704 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DNAH6 MUTATED DNAH6 WILD-TYPE 
           3.02            0.00 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          83.24          148.01 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          16.85           22.09 
[1] "3.0 - 83.2 (16.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D965V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH6 MUTATED         3        0        4         9         0         0
  DNAH6 WILD-TYPE      61        1       22        99         8         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        18          6         43         32       35        11
                 vv
clus              STAGE IVB
  DNAH6 MUTATED           0
  DNAH6 WILD-TYPE         1
D965V3, multiclass
            clus
vv           DNAH6 MUTATED DNAH6 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              9              99
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  DNAH6 MUTATED     0   4  14   2
  DNAH6 WILD-TYPE   9  63 235  39
D965V4, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            14             235
  T4             2              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
  DNAH6 MUTATED    17   3   0
  DNAH6 WILD-TYPE 203  78  66
D965V5, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  N0            17             203
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V6, binary
                 cls
clus                0   1
  DNAH6 MUTATED    15   1
  DNAH6 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     15    1
  DNAH6 WILD-TYPE  270   47
   clus
vv  DNAH6 MUTATED DNAH6 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D965V7, binary
                 cls
clus                0   1
  DNAH6 MUTATED     5  15
  DNAH6 WILD-TYPE 165 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      5   15
  DNAH6 WILD-TYPE  165  182
        clus
vv       DNAH6 MUTATED DNAH6 WILD-TYPE
  FEMALE             5             165
  MALE              15             182
[1] 2 2
[1] FALSE
D965V8, binary
                 cls
clus                0   1
  DNAH6 MUTATED    20   0
  DNAH6 WILD-TYPE 280   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     20    0
  DNAH6 WILD-TYPE  280    8
     clus
vv    DNAH6 MUTATED DNAH6 WILD-TYPE
  NO             20             280
  YES             0               8
[1] 2 2
[1] FALSE
D965V9, binary
                 cls
clus                0   1
  DNAH6 MUTATED    15   5
  DNAH6 WILD-TYPE 299  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     15    5
  DNAH6 WILD-TYPE  299   43
                               clus
vv                              DNAH6 MUTATED DNAH6 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNAH6 MUTATED    15   0   0   2
  DNAH6 WILD-TYPE 244   3  22  19
D965V10, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             2              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"
D965V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH6 MUTATED                                  0     3
  DNAH6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNAH6 MUTATED                           1    12
  DNAH6 WILD-TYPE                        18   164
D965V12, multiclass
                                  clus
vv                                 DNAH6 MUTATED DNAH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = TRYX3 MUTATION ANALYSIS
D966V1, survival
                 sevent
clus2               0   1
  TRYX3 MUTATED     3   3
  TRYX3 WILD-TYPE 274  75
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              6             349 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              3              75 
$`TRYX3 MUTATED`
TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3660 TCGA-AA-3852 TCGA-CA-6718 TCGA-D5-6926 
       10.88        22.06        78.08         0.00        10.06         9.04 

$`TRYX3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TRYX3 MUTATED TRYX3 WILD-TYPE 
              0               0 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
          78.08          148.01 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
          10.47           22.09 
[1] "0.0 - 78.1 (10.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3"  
D966V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRYX3 MUTATED         0        0        1         3         0         0
  TRYX3 WILD-TYPE      64        1       25       105         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  TRYX3 MUTATED           0
  TRYX3 WILD-TYPE         1
D966V3, multiclass
            clus
vv           TRYX3 MUTATED TRYX3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  TRYX3 MUTATED     0   0   4   2
  TRYX3 WILD-TYPE   9  67 245  39
D966V4, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             2              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
  TRYX3 MUTATED     4   1   1
  TRYX3 WILD-TYPE 216  80  65
D966V5, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V6, binary
                 cls
clus                0   1
  TRYX3 MUTATED     5   0
  TRYX3 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      5    0
  TRYX3 WILD-TYPE  280   48
   clus
vv  TRYX3 MUTATED TRYX3 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D966V7, binary
                 cls
clus                0   1
  TRYX3 MUTATED     2   4
  TRYX3 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      2    4
  TRYX3 WILD-TYPE  168  193
        clus
vv       TRYX3 MUTATED TRYX3 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D966V8, binary
                 cls
clus                0   1
  TRYX3 MUTATED     4   1
  TRYX3 WILD-TYPE 296   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      4    1
  TRYX3 WILD-TYPE  296    7
     clus
vv    TRYX3 MUTATED TRYX3 WILD-TYPE
  NO              4             296
  YES             1               7
[1] 2 2
[1] FALSE
D966V9, binary
                 cls
clus                0   1
  TRYX3 MUTATED     5   1
  TRYX3 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      5    1
  TRYX3 WILD-TYPE  309   47
                               clus
vv                              TRYX3 MUTATED TRYX3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRYX3 MUTATED     4   0   0   1
  TRYX3 WILD-TYPE 255   3  22  20
D966V10, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D966V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRYX3 MUTATED                                  0     1
  TRYX3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRYX3 MUTATED                           0     3
  TRYX3 WILD-TYPE                        19   173
D966V12, multiclass
                                  clus
vv                                 TRYX3 MUTATED TRYX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = PER3 MUTATION ANALYSIS
D967V1, survival
                sevent
clus2              0   1
  PER3 MUTATED    11   5
  PER3 WILD-TYPE 266  73
  PER3 MUTATED PER3 WILD-TYPE 
            16            339 
  PER3 MUTATED PER3 WILD-TYPE 
             5             73 
$`PER3 MUTATED`
TCGA-AZ-6601 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3680 
      100.01        22.06        32.71         6.97        50.04        11.01 
TCGA-AA-3818 TCGA-AA-3949 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 
        0.99        26.01        30.02         4.01        83.24        58.39 
TCGA-CK-4947 TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-6162 
       17.56        37.02        32.02        12.00 

$`PER3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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-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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PER3 MUTATED PER3 WILD-TYPE 
          0.99           0.00 
  PER3 MUTATED PER3 WILD-TYPE 
        100.01         148.01 
  PER3 MUTATED PER3 WILD-TYPE 
        28.015         21.990 
[1] "1.0 - 100.0 (28.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D967V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PER3 MUTATED         1        0        3         7         1         1
  PER3 WILD-TYPE      63        1       23       101         7         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        18          6         41         33       34        12
                vv
clus             STAGE IVB
  PER3 MUTATED           0
  PER3 WILD-TYPE         1
D967V3, multiclass
            clus
vv           PER3 MUTATED PER3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  PER3 MUTATED     0   1  12   4
  PER3 WILD-TYPE   9  66 237  37
D967V4, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           12            237
  T4            4             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
  PER3 MUTATED    13   3   1
  PER3 WILD-TYPE 207  78  65
D967V5, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  N0           13            207
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V6, binary
                cls
clus               0   1
  PER3 MUTATED    16   1
  PER3 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     16    1
  PER3 WILD-TYPE  269   47
   clus
vv  PER3 MUTATED PER3 WILD-TYPE
  0           16            269
  1            1             47
[1] 2 2
[1] FALSE
D967V7, binary
                cls
clus               0   1
  PER3 MUTATED     8   9
  PER3 WILD-TYPE 162 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      8    9
  PER3 WILD-TYPE  162  188
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  FEMALE            8            162
  MALE              9            188
[1] 2 2
[1] FALSE
D967V8, binary
                cls
clus               0   1
  PER3 MUTATED    14   0
  PER3 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     14    0
  PER3 WILD-TYPE  286    8
     clus
vv    PER3 MUTATED PER3 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D967V9, binary
                cls
clus               0   1
  PER3 MUTATED    14   3
  PER3 WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     14    3
  PER3 WILD-TYPE  300   45
                               clus
vv                              PER3 MUTATED PER3 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PER3 MUTATED    13   0   1   1
  PER3 WILD-TYPE 246   3  21  20
D967V10, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            1             21
  RX            1             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"
D967V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PER3 MUTATED                                  0     1
  PER3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PER3 MUTATED                           1     7
  PER3 WILD-TYPE                        18   169
D967V12, multiclass
                                  clus
vv                                 PER3 MUTATED PER3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = ZNF443 MUTATION ANALYSIS
D968V1, survival
                  sevent
clus2                0   1
  ZNF443 MUTATED     6   2
  ZNF443 WILD-TYPE 271  76
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               8              347 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               2               76 
$`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 
       12.95        13.05 

$`ZNF443 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF443 MUTATED ZNF443 WILD-TYPE 
            4.01             0.00 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
           38.99           148.01 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
           13.00            22.09 
[1] "4.0 - 39.0 (13.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D968V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF443 MUTATED         1        0        0         3         2         0
  ZNF443 WILD-TYPE      63        1       26       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF443 MUTATED           0          0          0          0        1
  ZNF443 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF443 MUTATED           0         1
  ZNF443 WILD-TYPE        12         0
D968V3, multiclass
            clus
vv           ZNF443 MUTATED ZNF443 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               12
  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   0   5   2
  ZNF443 WILD-TYPE   8  67 244  39
D968V4, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              5              244
  T4              2               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
  ZNF443 MUTATED     6   0   2
  ZNF443 WILD-TYPE 214  81  64
D968V5, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V6, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     6   2
  ZNF443 WILD-TYPE 279  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      6    2
  ZNF443 WILD-TYPE  279   46
   clus
vv  ZNF443 MUTATED ZNF443 WILD-TYPE
  0              6              279
  1              2               46
[1] 2 2
[1] FALSE
D968V7, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     2   6
  ZNF443 WILD-TYPE 168 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      2    6
  ZNF443 WILD-TYPE  168  191
        clus
vv       ZNF443 MUTATED ZNF443 WILD-TYPE
  FEMALE              2              168
  MALE                6              191
[1] 2 2
[1] FALSE
D968V8, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     7   0
  ZNF443 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      7    0
  ZNF443 WILD-TYPE  293    8
     clus
vv    ZNF443 MUTATED ZNF443 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D968V9, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     4   4
  ZNF443 WILD-TYPE 310  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      4    4
  ZNF443 WILD-TYPE  310   44
                               clus
vv                              ZNF443 MUTATED ZNF443 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF443 MUTATED     6   0   1   1
  ZNF443 WILD-TYPE 253   3  21  20
D968V10, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              1               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"
D968V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF443 MUTATED                                  0     1
  ZNF443 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF443 MUTATED                           1     1
  ZNF443 WILD-TYPE                        18   175
D968V12, multiclass
                                  clus
vv                                 ZNF443 MUTATED ZNF443 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         1              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(969) Variable = ACAT2 MUTATION ANALYSIS
D969V1, survival
                 sevent
clus2               0   1
  ACAT2 MUTATED     3   5
  ACAT2 WILD-TYPE 274  73
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              8             347 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              5              73 
$`ACAT2 MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-AD-6889 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-6747 
       19.04        34.98        83.24        10.06       148.01        82.95 
TCGA-CM-5862 TCGA-D5-6537 
        5.03         4.80 

$`ACAT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ACAT2 MUTATED ACAT2 WILD-TYPE 
            4.8             0.0 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
         148.01          140.38 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
          27.01           22.06 
[1] "4.8 - 148.0 (27.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "2"  
D969V2, continuous
                 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      64        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAT2 MUTATED           1          0          1          0        0         1
  ACAT2 WILD-TYPE        17          6         43         33       35        11
                 vv
clus              STAGE IVB
  ACAT2 MUTATED           0
  ACAT2 WILD-TYPE         1
D969V3, multiclass
            clus
vv           ACAT2 MUTATED ACAT2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  ACAT2 MUTATED     0   0   7   1
  ACAT2 WILD-TYPE   9  67 242  40
D969V4, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  ACAT2 MUTATED     5   3   0
  ACAT2 WILD-TYPE 215  78  66
D969V5, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  N0             5             215
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V6, binary
                 cls
clus                0   1
  ACAT2 MUTATED     5   1
  ACAT2 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      5    1
  ACAT2 WILD-TYPE  280   47
   clus
vv  ACAT2 MUTATED ACAT2 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D969V7, binary
                 cls
clus                0   1
  ACAT2 MUTATED     3   5
  ACAT2 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      3    5
  ACAT2 WILD-TYPE  167  192
        clus
vv       ACAT2 MUTATED ACAT2 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D969V8, binary
                 cls
clus                0   1
  ACAT2 MUTATED     8   0
  ACAT2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      8    0
  ACAT2 WILD-TYPE  292    8
     clus
vv    ACAT2 MUTATED ACAT2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D969V9, binary
                 cls
clus                0   1
  ACAT2 MUTATED     8   0
  ACAT2 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      8    0
  ACAT2 WILD-TYPE  306   48
                               clus
vv                              ACAT2 MUTATED ACAT2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACAT2 MUTATED     6   0   0   2
  ACAT2 WILD-TYPE 253   3  22  19
D969V10, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D969V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACAT2 MUTATED                                  0     2
  ACAT2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACAT2 MUTATED                           0     4
  ACAT2 WILD-TYPE                        19   172
D969V12, multiclass
                                  clus
vv                                 ACAT2 MUTATED ACAT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = TRIM46 MUTATION ANALYSIS
D970V1, survival
                  sevent
clus2                0   1
  TRIM46 MUTATED     8   6
  TRIM46 WILD-TYPE 269  72
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              14              341 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
               6               72 
$`TRIM46 MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AA-3845 TCGA-AD-6889 TCGA-AY-6197 
       19.04        10.88       100.01         0.00        83.24        21.44 
TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5861 TCGA-D5-6539 
       58.39        10.06        37.02        22.03        15.02        12.49 
TCGA-DM-A0X9 TCGA-DM-A1HB 
      119.70       135.65 

$`TRIM46 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TRIM46 MUTATED TRIM46 WILD-TYPE 
               0                0 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
          135.65           148.01 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
          21.735           22.090 
[1] "0.0 - 135.7 (21.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D970V2, continuous
                  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      63        1       23       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM46 MUTATED           0          0          2          0        0
  TRIM46 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM46 MUTATED           0         0
  TRIM46 WILD-TYPE        12         1
D970V3, multiclass
            clus
vv           TRIM46 MUTATED TRIM46 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TRIM46 MUTATED     0   1  12   2
  TRIM46 WILD-TYPE   9  66 237  39
D970V4, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             12              237
  T4              2               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
  TRIM46 MUTATED    12   2   1
  TRIM46 WILD-TYPE 208  79  65
D970V5, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  N0             12              208
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V6, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    13   0
  TRIM46 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     13    0
  TRIM46 WILD-TYPE  272   48
   clus
vv  TRIM46 MUTATED TRIM46 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D970V7, binary
                  cls
clus                 0   1
  TRIM46 MUTATED     6   9
  TRIM46 WILD-TYPE 164 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED      6    9
  TRIM46 WILD-TYPE  164  188
        clus
vv       TRIM46 MUTATED TRIM46 WILD-TYPE
  FEMALE              6              164
  MALE                9              188
[1] 2 2
[1] FALSE
D970V8, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    11   0
  TRIM46 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     11    0
  TRIM46 WILD-TYPE  289    8
     clus
vv    TRIM46 MUTATED TRIM46 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D970V9, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    14   0
  TRIM46 WILD-TYPE 300  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     14    0
  TRIM46 WILD-TYPE  300   48
                               clus
vv                              TRIM46 MUTATED TRIM46 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM46 MUTATED    10   0   0   1
  TRIM46 WILD-TYPE 249   3  22  20
D970V10, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              1               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"
D970V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM46 MUTATED                                  0     2
  TRIM46 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM46 MUTATED                           1     9
  TRIM46 WILD-TYPE                        18   167
D970V12, multiclass
                                  clus
vv                                 TRIM46 MUTATED TRIM46 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(971) Variable = C16ORF45 MUTATION ANALYSIS
D971V1, survival
                    sevent
clus2                  0   1
  C16ORF45 MUTATED     5   0
  C16ORF45 WILD-TYPE 272  78
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 5                350 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 0                 78 
$`C16ORF45 MUTATED`
TCGA-A6-6141 TCGA-AA-3941 TCGA-AA-3982 TCGA-F4-6703 TCGA-G4-6306 
        8.38        24.00        27.02        47.87        44.68 

$`C16ORF45 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
              8.38               0.00 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
             47.87             148.01 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
             27.02              22.01 
[1] "8.4 - 47.9 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D971V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C16ORF45 MUTATED         0        0        0         2         0         0
  C16ORF45 WILD-TYPE      64        1       26       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF45 MUTATED           0          0          1          0        0
  C16ORF45 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C16ORF45 MUTATED           1         0
  C16ORF45 WILD-TYPE        11         1
D971V3, multiclass
            clus
vv           C16ORF45 MUTATED C16ORF45 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  C16ORF45 MUTATED     0   1   3   1
  C16ORF45 WILD-TYPE   9  66 246  40
D971V4, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                3                246
  T4                1                 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
  C16ORF45 MUTATED     3   2   0
  C16ORF45 WILD-TYPE 217  79  66
D971V5, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  N0                3                217
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V6, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     4   1
  C16ORF45 WILD-TYPE 281  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      4    1
  C16ORF45 WILD-TYPE  281   47
   clus
vv  C16ORF45 MUTATED C16ORF45 WILD-TYPE
  0                4                281
  1                1                 47
[1] 2 2
[1] FALSE
D971V7, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     1   4
  C16ORF45 WILD-TYPE 169 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      1    4
  C16ORF45 WILD-TYPE  169  193
        clus
vv       C16ORF45 MUTATED C16ORF45 WILD-TYPE
  FEMALE                1                169
  MALE                  4                193
[1] 2 2
[1] FALSE
D971V8, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     5   0
  C16ORF45 WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      5    0
  C16ORF45 WILD-TYPE  295    8
     clus
vv    C16ORF45 MUTATED C16ORF45 WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D971V9, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     5   0
  C16ORF45 WILD-TYPE 309  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      5    0
  C16ORF45 WILD-TYPE  309   48
                               clus
vv                              C16ORF45 MUTATED C16ORF45 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C16ORF45 MUTATED     3   0   0   0
  C16ORF45 WILD-TYPE 256   3  22  21
D971V10, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D971V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C16ORF45 MUTATED                                  0     0
  C16ORF45 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C16ORF45 MUTATED                           1     2
  C16ORF45 WILD-TYPE                        18   174
D971V12, multiclass
                                  clus
vv                                 C16ORF45 MUTATED C16ORF45 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           2                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(972) Variable = APBB1IP MUTATION ANALYSIS
D972V1, survival
                   sevent
clus2                 0   1
  APBB1IP MUTATED    12   5
  APBB1IP WILD-TYPE 265  73
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               17               338 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                5                73 
$`APBB1IP MUTATED`
TCGA-A6-4105 TCGA-AA-3697 TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6628 TCGA-AA-3510 
       14.53        85.05        25.08        10.88        79.69        63.98 
TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00N TCGA-AD-6965 TCGA-AZ-5407 TCGA-AZ-6599 
       31.00        27.02         4.01        26.47        88.21         6.77 
TCGA-CM-5344 TCGA-D5-6534 TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6807 
       22.03        43.27       119.93         6.18        43.04 

$`APBB1IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 
       83.24        24.53         5.79        22.42        27.42        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28F 
       44.32       131.51       135.65       139.17        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  APBB1IP MUTATED APBB1IP WILD-TYPE 
             4.01              0.00 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
           119.93            148.01 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
            27.02             21.99 
[1] "4.0 - 119.9 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D972V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APBB1IP MUTATED         4        0        2         5         1         0
  APBB1IP WILD-TYPE      60        1       24       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APBB1IP MUTATED           0          0          3          2        0
  APBB1IP WILD-TYPE        18          6         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  APBB1IP MUTATED           0         0
  APBB1IP WILD-TYPE        12         1
D972V3, multiclass
            clus
vv           APBB1IP MUTATED APBB1IP WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  APBB1IP MUTATED     2   2  11   3
  APBB1IP WILD-TYPE   7  65 238  38
D972V4, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  T1               2                 7
  T2               2                65
  T3              11               238
  T4               3                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
  APBB1IP MUTATED    12   3   3
  APBB1IP WILD-TYPE 208  78  63
D972V5, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  N0              12               208
  N1               3                78
  N2               3                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"
D972V6, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    16   0
  APBB1IP WILD-TYPE 269  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     16    0
  APBB1IP WILD-TYPE  269   48
   clus
vv  APBB1IP MUTATED APBB1IP WILD-TYPE
  0              16               269
  1               0                48
[1] 2 2
[1] FALSE
D972V7, binary
                   cls
clus                  0   1
  APBB1IP MUTATED     8  10
  APBB1IP WILD-TYPE 162 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED      8   10
  APBB1IP WILD-TYPE  162  187
        clus
vv       APBB1IP MUTATED APBB1IP WILD-TYPE
  FEMALE               8               162
  MALE                10               187
[1] 2 2
[1] FALSE
D972V8, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    15   0
  APBB1IP WILD-TYPE 285   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     15    0
  APBB1IP WILD-TYPE  285    8
     clus
vv    APBB1IP MUTATED APBB1IP WILD-TYPE
  NO               15               285
  YES               0                 8
[1] 2 2
[1] FALSE
D972V9, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    14   4
  APBB1IP WILD-TYPE 300  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     14    4
  APBB1IP WILD-TYPE  300   44
                               clus
vv                              APBB1IP MUTATED APBB1IP WILD-TYPE
  COLON ADENOCARCINOMA                       14               300
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  APBB1IP MUTATED    12   1   0   0
  APBB1IP WILD-TYPE 247   2  22  21
D972V10, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  R0              12               247
  R1               1                 2
  R2               0                22
  RX               0                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"
D972V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APBB1IP MUTATED                                  0     0
  APBB1IP WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  APBB1IP MUTATED                           0    12
  APBB1IP WILD-TYPE                        19   164
D972V12, multiclass
                                  clus
vv                                 APBB1IP MUTATED APBB1IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         12               164
[1] 4 2
[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 = HSD17B11 MUTATION ANALYSIS
D973V1, survival
                    sevent
clus2                  0   1
  HSD17B11 MUTATED     4   0
  HSD17B11 WILD-TYPE 273  78
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                351 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 0                 78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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              22.09 
[1] "15.6 - 33.7 (18.6)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D973V2, continuous
                    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      63        1       26       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSD17B11 MUTATED           0          0          0          1        0
  HSD17B11 WILD-TYPE        18          6         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  HSD17B11 MUTATED           1         0
  HSD17B11 WILD-TYPE        11         1
D973V3, multiclass
            clus
vv           HSD17B11 MUTATED HSD17B11 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 1                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  HSD17B11 MUTATED     1   0   1   2
  HSD17B11 WILD-TYPE   8  67 248  39
D973V4, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  T1                1                  8
  T2                0                 67
  T3                1                248
  T4                2                 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
  HSD17B11 MUTATED     2   1   1
  HSD17B11 WILD-TYPE 218  80  65
D973V5, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  N0                2                218
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V6, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   1
  HSD17B11 WILD-TYPE 282  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    1
  HSD17B11 WILD-TYPE  282   47
   clus
vv  HSD17B11 MUTATED HSD17B11 WILD-TYPE
  0                3                282
  1                1                 47
[1] 2 2
[1] FALSE
D973V7, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   1
  HSD17B11 WILD-TYPE 167 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    1
  HSD17B11 WILD-TYPE  167  196
        clus
vv       HSD17B11 MUTATED HSD17B11 WILD-TYPE
  FEMALE                3                167
  MALE                  1                196
[1] 2 2
[1] FALSE
D973V8, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   0
  HSD17B11 WILD-TYPE 297   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    0
  HSD17B11 WILD-TYPE  297    8
     clus
vv    HSD17B11 MUTATED HSD17B11 WILD-TYPE
  NO                 3                297
  YES                0                  8
[1] 2 2
[1] FALSE
D973V9, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   1
  HSD17B11 WILD-TYPE 311  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    1
  HSD17B11 WILD-TYPE  311   47
                               clus
vv                              HSD17B11 MUTATED HSD17B11 WILD-TYPE
  COLON ADENOCARCINOMA                         3                311
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HSD17B11 MUTATED     3   0   0   1
  HSD17B11 WILD-TYPE 256   3  22  20
D973V10, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D973V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSD17B11 MUTATED                                  0     0
  HSD17B11 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HSD17B11 MUTATED                           0     4
  HSD17B11 WILD-TYPE                        19   172
D973V12, multiclass
                                  clus
vv                                 HSD17B11 MUTATED HSD17B11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = DPCR1 MUTATION ANALYSIS
D974V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED    11   1
  DPCR1 WILD-TYPE 266  77
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             12             343 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              77 
$`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 

$`DPCR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.39        23.87        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       56.09        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           6.18            0.00 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          63.98          148.01 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          23.77           22.06 
[1] "6.2 - 64.0 (23.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D974V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPCR1 MUTATED         1        0        1         5         1         0
  DPCR1 WILD-TYPE      63        1       25       103         7         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        18          6         43         32       35        11
                 vv
clus              STAGE IVB
  DPCR1 MUTATED           0
  DPCR1 WILD-TYPE         1
D974V3, multiclass
            clus
vv           DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  DPCR1 MUTATED     0   1   8   3
  DPCR1 WILD-TYPE   9  66 241  38
D974V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             3              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
  DPCR1 MUTATED     9   3   0
  DPCR1 WILD-TYPE 211  78  66
D974V5, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  N0             9             211
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     8   1
  DPCR1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      8    1
  DPCR1 WILD-TYPE  277   47
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D974V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED     5   7
  DPCR1 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      5    7
  DPCR1 WILD-TYPE  165  190
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D974V8, binary
                 cls
clus                0   1
  DPCR1 MUTATED    12   0
  DPCR1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED     12    0
  DPCR1 WILD-TYPE  288    8
     clus
vv    DPCR1 MUTATED DPCR1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D974V9, binary
                 cls
clus                0   1
  DPCR1 MUTATED     8   4
  DPCR1 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      8    4
  DPCR1 WILD-TYPE  306   44
                               clus
vv                              DPCR1 MUTATED DPCR1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DPCR1 MUTATED     9   0   0   0
  DPCR1 WILD-TYPE 250   3  22  21
D974V10, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D974V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPCR1 MUTATED                                  0     0
  DPCR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED                           1     9
  DPCR1 WILD-TYPE                        18   167
D974V12, multiclass
                                  clus
vv                                 DPCR1 MUTATED DPCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(975) Variable = DCLRE1A MUTATION ANALYSIS
D975V1, survival
                   sevent
clus2                 0   1
  DCLRE1A MUTATED     5   4
  DCLRE1A WILD-TYPE 272  74
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                9               346 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                4                74 
$`DCLRE1A MUTATED`
TCGA-AZ-6608 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01P TCGA-AD-6889 
        1.94        26.99        25.02         4.01        38.07        83.24 
TCGA-AU-6004 TCGA-CM-6676 TCGA-CM-6680 
       27.09        11.08        12.03 

$`DCLRE1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
             1.94              0.00 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
            83.24            148.01 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
           25.020            22.045 
[1] "1.9 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D975V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLRE1A MUTATED         2        0        1         2         1         0
  DCLRE1A WILD-TYPE      62        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1A MUTATED           1          1          1          0        0
  DCLRE1A WILD-TYPE        17          5         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  DCLRE1A MUTATED           0         0
  DCLRE1A WILD-TYPE        12         1
D975V3, multiclass
            clus
vv           DCLRE1A MUTATED DCLRE1A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  DCLRE1A MUTATED     0   4   4   2
  DCLRE1A WILD-TYPE   9  63 245  39
D975V4, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               4               245
  T4               2                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
  DCLRE1A MUTATED     7   2   1
  DCLRE1A WILD-TYPE 213  79  65
D975V5, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  N0               7               213
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V6, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     9   0
  DCLRE1A WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      9    0
  DCLRE1A WILD-TYPE  276   48
   clus
vv  DCLRE1A MUTATED DCLRE1A WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D975V7, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     6   4
  DCLRE1A WILD-TYPE 164 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      6    4
  DCLRE1A WILD-TYPE  164  193
        clus
vv       DCLRE1A MUTATED DCLRE1A WILD-TYPE
  FEMALE               6               164
  MALE                 4               193
[1] 2 2
[1] FALSE
D975V8, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     7   0
  DCLRE1A WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      7    0
  DCLRE1A WILD-TYPE  293    8
     clus
vv    DCLRE1A MUTATED DCLRE1A WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D975V9, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     9   1
  DCLRE1A WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      9    1
  DCLRE1A WILD-TYPE  305   47
                               clus
vv                              DCLRE1A MUTATED DCLRE1A WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DCLRE1A MUTATED     8   0   0   0
  DCLRE1A WILD-TYPE 251   3  22  21
D975V10, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               0                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"
D975V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCLRE1A MUTATED                                  0     1
  DCLRE1A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DCLRE1A MUTATED                           0     4
  DCLRE1A WILD-TYPE                        19   172
D975V12, multiclass
                                  clus
vv                                 DCLRE1A MUTATED DCLRE1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = C7ORF50 MUTATION ANALYSIS
D976V1, survival
                   sevent
clus2                 0   1
  C7ORF50 MUTATED     4   1
  C7ORF50 WILD-TYPE 273  77
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               350 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            14.01              0.00 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
           135.65            148.01 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            22.06             22.06 
[1] "14.0 - 135.7 (22.1)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.7"
D976V2, continuous
                   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      62        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF50 MUTATED           0          0          1          0        0
  C7ORF50 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF50 MUTATED           0         0
  C7ORF50 WILD-TYPE        12         1
D976V3, multiclass
            clus
vv           C7ORF50 MUTATED C7ORF50 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C7ORF50 MUTATED     0   2   3   0
  C7ORF50 WILD-TYPE   9  65 246  41
D976V4, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               3               246
  T4               0                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
  C7ORF50 MUTATED     4   1   0
  C7ORF50 WILD-TYPE 216  80  66
D976V5, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V6, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   0
  C7ORF50 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    0
  C7ORF50 WILD-TYPE  281   48
   clus
vv  C7ORF50 MUTATED C7ORF50 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D976V7, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   1
  C7ORF50 WILD-TYPE 166 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    1
  C7ORF50 WILD-TYPE  166  196
        clus
vv       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  FEMALE               4               166
  MALE                 1               196
[1] 2 2
[1] FALSE
D976V8, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   0
  C7ORF50 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    0
  C7ORF50 WILD-TYPE  296    8
     clus
vv    C7ORF50 MUTATED C7ORF50 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D976V9, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   0
  C7ORF50 WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    0
  C7ORF50 WILD-TYPE  310   48
                               clus
vv                              C7ORF50 MUTATED C7ORF50 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF50 MUTATED     3   0   0   0
  C7ORF50 WILD-TYPE 256   3  22  21
D976V10, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D976V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF50 MUTATED                                  0     0
  C7ORF50 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF50 MUTATED                           0     4
  C7ORF50 WILD-TYPE                        19   172
D976V12, multiclass
                                  clus
vv                                 C7ORF50 MUTATED C7ORF50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = WDR5 MUTATION ANALYSIS
D977V1, survival
                sevent
clus2              0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 272  77
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            349 
  WDR5 MUTATED WDR5 WILD-TYPE 
             1             77 
$`WDR5 MUTATED`
TCGA-G4-6586 TCGA-AA-3864 TCGA-AU-6004 TCGA-D5-6538 TCGA-F4-6809 TCGA-G4-6309 
       35.80        53.00        27.09        17.13        13.25        85.48 

$`WDR5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.030 
[1] "13.2 - 85.5 (31.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D977V2, continuous
                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      63        1       25       107         8         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        18          6         42         33       35        11
                vv
clus             STAGE IVB
  WDR5 MUTATED           0
  WDR5 WILD-TYPE         1
D977V3, multiclass
            clus
vv           WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  WDR5 MUTATED     0   1   5   0
  WDR5 WILD-TYPE   9  66 244  41
D977V4, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            0             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
  WDR5 MUTATED     3   2   1
  WDR5 WILD-TYPE 217  79  65
D977V5, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  N0            3            217
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V6, binary
                cls
clus               0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    1
  WDR5 WILD-TYPE  280   47
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D977V7, binary
                cls
clus               0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 165 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    1
  WDR5 WILD-TYPE  165  196
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  FEMALE            5            165
  MALE              1            196
[1] 2 2
[1] FALSE
D977V8, binary
                cls
clus               0   1
  WDR5 MUTATED     5   0
  WDR5 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    0
  WDR5 WILD-TYPE  295    8
     clus
vv    WDR5 MUTATED WDR5 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D977V9, binary
                cls
clus               0   1
  WDR5 MUTATED     6   0
  WDR5 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      6    0
  WDR5 WILD-TYPE  308   48
                               clus
vv                              WDR5 MUTATED WDR5 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WDR5 MUTATED     6   0   0   0
  WDR5 WILD-TYPE 253   3  22  21
D977V10, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D977V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR5 MUTATED                                  0     0
  WDR5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WDR5 MUTATED                           1     4
  WDR5 WILD-TYPE                        18   172
D977V12, multiclass
                                  clus
vv                                 WDR5 MUTATED WDR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = MAGI1 MUTATION ANALYSIS
D978V1, survival
                 sevent
clus2               0   1
  MAGI1 MUTATED    19   3
  MAGI1 WILD-TYPE 258  75
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             22             333 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
              3              75 
$`MAGI1 MUTATED`
TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3672 TCGA-A6-6652 TCGA-A6-6653 TCGA-AA-3492 
        0.99        19.99         0.92        24.69        24.39         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3831 TCGA-AA-3864 TCGA-AA-A01I 
       35.01        63.98         1.02        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 
       11.01         6.18        85.48        61.91 

$`MAGI1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.08        25.18        21.76        23.87        20.12        19.66 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82        58.39         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAGI1 MUTATED MAGI1 WILD-TYPE 
           0.92            0.00 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
          85.48          148.01 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
         18.985          22.090 
[1] "0.9 - 85.5 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D978V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGI1 MUTATED         5        0        3         7         0         0
  MAGI1 WILD-TYPE      59        1       23       101         8         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        16          6         42         32       33        11
                 vv
clus              STAGE IVB
  MAGI1 MUTATED           0
  MAGI1 WILD-TYPE         1
D978V3, multiclass
            clus
vv           MAGI1 MUTATED MAGI1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              1              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
  MAGI1 MUTATED     0   5  17   1
  MAGI1 WILD-TYPE   9  62 232  40
D978V4, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            17             232
  T4             1              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
  MAGI1 MUTATED    16   4   3
  MAGI1 WILD-TYPE 204  77  63
D978V5, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  N0            16             204
  N1             4              77
  N2             3              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"
D978V6, binary
                 cls
clus                0   1
  MAGI1 MUTATED    19   3
  MAGI1 WILD-TYPE 266  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     19    3
  MAGI1 WILD-TYPE  266   45
   clus
vv  MAGI1 MUTATED MAGI1 WILD-TYPE
  0            19             266
  1             3              45
[1] 2 2
[1] FALSE
D978V7, binary
                 cls
clus                0   1
  MAGI1 MUTATED    10  13
  MAGI1 WILD-TYPE 160 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     10   13
  MAGI1 WILD-TYPE  160  184
        clus
vv       MAGI1 MUTATED MAGI1 WILD-TYPE
  FEMALE            10             160
  MALE              13             184
[1] 2 2
[1] FALSE
D978V8, binary
                 cls
clus                0   1
  MAGI1 MUTATED    20   1
  MAGI1 WILD-TYPE 280   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     20    1
  MAGI1 WILD-TYPE  280    7
     clus
vv    MAGI1 MUTATED MAGI1 WILD-TYPE
  NO             20             280
  YES             1               7
[1] 2 2
[1] FALSE
D978V9, binary
                 cls
clus                0   1
  MAGI1 MUTATED    20   3
  MAGI1 WILD-TYPE 294  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     20    3
  MAGI1 WILD-TYPE  294   45
                               clus
vv                              MAGI1 MUTATED MAGI1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MAGI1 MUTATED    19   0   0   1
  MAGI1 WILD-TYPE 240   3  22  20
D978V10, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             0              22
  RX             1              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"
D978V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGI1 MUTATED                                  0     1
  MAGI1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAGI1 MUTATED                           2     8
  MAGI1 WILD-TYPE                        17   168
D978V12, multiclass
                                  clus
vv                                 MAGI1 MUTATED MAGI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = PARG MUTATION ANALYSIS
D979V1, survival
                sevent
clus2              0   1
  PARG MUTATED     9   2
  PARG WILD-TYPE 268  76
  PARG MUTATED PARG WILD-TYPE 
            11            344 
  PARG MUTATED PARG WILD-TYPE 
             2             76 
$`PARG MUTATED`
TCGA-AA-3662 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-CA-6717 
        6.05        26.17        22.06         3.02        63.98        12.76 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6928 TCGA-F4-6459 
       14.04        12.95        20.19        11.64         8.61 

$`PARG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PARG MUTATED PARG WILD-TYPE 
          3.02           0.00 
  PARG MUTATED PARG WILD-TYPE 
         63.98         148.01 
  PARG MUTATED PARG WILD-TYPE 
         12.95          22.39 
[1] "3.0 - 64.0 (12.9)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D979V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARG MUTATED         1        0        2         6         0         0
  PARG WILD-TYPE      63        1       24       102         8         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  PARG MUTATED           0
  PARG WILD-TYPE         1
D979V3, multiclass
            clus
vv           PARG MUTATED PARG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  PARG MUTATED     0   1   9   1
  PARG WILD-TYPE   9  66 240  40
D979V4, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  T1            0              9
  T2            1             66
  T3            9            240
  T4            1             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
  PARG MUTATED     9   0   2
  PARG WILD-TYPE 211  81  64
D979V5, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  N0            9            211
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D979V6, binary
                cls
clus               0   1
  PARG MUTATED    10   1
  PARG WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     10    1
  PARG WILD-TYPE  275   47
   clus
vv  PARG MUTATED PARG WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D979V7, binary
                cls
clus               0   1
  PARG MUTATED     6   5
  PARG WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      6    5
  PARG WILD-TYPE  164  192
        clus
vv       PARG MUTATED PARG WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D979V8, binary
                cls
clus               0   1
  PARG MUTATED    11   0
  PARG WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     11    0
  PARG WILD-TYPE  289    8
     clus
vv    PARG MUTATED PARG WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D979V9, binary
                cls
clus               0   1
  PARG MUTATED     9   2
  PARG WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      9    2
  PARG WILD-TYPE  305   46
                               clus
vv                              PARG MUTATED PARG WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PARG MUTATED     9   0   1   1
  PARG WILD-TYPE 250   3  21  20
D979V10, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  R0            9            250
  R1            0              3
  R2            1             21
  RX            1             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"
D979V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARG MUTATED                                  0     1
  PARG WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PARG MUTATED                           0     7
  PARG WILD-TYPE                        19   169
D979V12, multiclass
                                  clus
vv                                 PARG MUTATED PARG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = VPS52 MUTATION ANALYSIS
D980V1, survival
                 sevent
clus2               0   1
  VPS52 MUTATED     5   5
  VPS52 WILD-TYPE 272  73
  VPS52 MUTATED VPS52 WILD-TYPE 
             10             345 
  VPS52 MUTATED VPS52 WILD-TYPE 
              5              73 
$`VPS52 MUTATED`
TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3877 TCGA-AA-A00N TCGA-AA-A01D TCGA-AZ-6605 
        3.02        33.04        31.00         4.01        10.98         5.23 
TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 TCGA-G4-6626 
       12.76        23.05        15.02        46.75 

$`VPS52 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10        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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  VPS52 MUTATED VPS52 WILD-TYPE 
           3.02            0.00 
  VPS52 MUTATED VPS52 WILD-TYPE 
          46.75          148.01 
  VPS52 MUTATED VPS52 WILD-TYPE 
          13.89           22.09 
[1] "3.0 - 46.8 (13.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.5"
D980V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS52 MUTATED         1        0        1         6         1         0
  VPS52 WILD-TYPE      63        1       25       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VPS52 MUTATED           0          0          1          1        0         0
  VPS52 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  VPS52 MUTATED           0
  VPS52 WILD-TYPE         1
D980V3, multiclass
            clus
vv           VPS52 MUTATED VPS52 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  VPS52 MUTATED     1   0   8   2
  VPS52 WILD-TYPE   8  67 241  39
D980V4, multiclass
    clus
vv   VPS52 MUTATED VPS52 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             8             241
  T4             2              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
  VPS52 MUTATED     9   1   1
  VPS52 WILD-TYPE 211  80  65
D980V5, multiclass
    clus
vv   VPS52 MUTATED VPS52 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V6, binary
                 cls
clus                0   1
  VPS52 MUTATED    11   0
  VPS52 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS52 MUTATED     11    0
  VPS52 WILD-TYPE  274   48
   clus
vv  VPS52 MUTATED VPS52 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D980V7, binary
                 cls
clus                0   1
  VPS52 MUTATED     6   5
  VPS52 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS52 MUTATED      6    5
  VPS52 WILD-TYPE  164  192
        clus
vv       VPS52 MUTATED VPS52 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D980V8, binary
                 cls
clus                0   1
  VPS52 MUTATED     9   0
  VPS52 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS52 MUTATED      9    0
  VPS52 WILD-TYPE  291    8
     clus
vv    VPS52 MUTATED VPS52 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D980V9, binary
                 cls
clus                0   1
  VPS52 MUTATED     7   4
  VPS52 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS52 MUTATED      7    4
  VPS52 WILD-TYPE  307   44
                               clus
vv                              VPS52 MUTATED VPS52 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VPS52 MUTATED     9   0   0   1
  VPS52 WILD-TYPE 250   3  22  20
D980V10, multiclass
    clus
vv   VPS52 MUTATED VPS52 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D980V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS52 MUTATED                                  0     1
  VPS52 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VPS52 MUTATED                           0     4
  VPS52 WILD-TYPE                        19   172
D980V12, multiclass
                                  clus
vv                                 VPS52 MUTATED VPS52 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = RRM2B MUTATION ANALYSIS
D981V1, survival
                 sevent
clus2               0   1
  RRM2B MUTATED     2   3
  RRM2B WILD-TYPE 275  75
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             350 
  RRM2B MUTATED RRM2B WILD-TYPE 
              3              75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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          22.075 
[1] "4.8 - 64.0 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D981V2, continuous
                 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      64        1       25       105         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  RRM2B MUTATED           0
  RRM2B WILD-TYPE         1
D981V3, multiclass
            clus
vv           RRM2B MUTATED RRM2B WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RRM2B MUTATED     0   0   5   0
  RRM2B WILD-TYPE   9  67 244  41
D981V4, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             0              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
  RRM2B MUTATED     4   1   0
  RRM2B WILD-TYPE 216  80  66
D981V5, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V6, binary
                 cls
clus                0   1
  RRM2B MUTATED     3   0
  RRM2B WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      3    0
  RRM2B WILD-TYPE  282   48
   clus
vv  RRM2B MUTATED RRM2B WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D981V7, binary
                 cls
clus                0   1
  RRM2B MUTATED     0   5
  RRM2B WILD-TYPE 170 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      0    5
  RRM2B WILD-TYPE  170  192
        clus
vv       RRM2B MUTATED RRM2B WILD-TYPE
  FEMALE             0             170
  MALE               5             192
[1] 2 2
[1] FALSE
D981V8, binary
                 cls
clus                0   1
  RRM2B MUTATED     4   0
  RRM2B WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      4    0
  RRM2B WILD-TYPE  296    8
     clus
vv    RRM2B MUTATED RRM2B WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D981V9, binary
                 cls
clus                0   1
  RRM2B MUTATED     5   0
  RRM2B WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      5    0
  RRM2B WILD-TYPE  309   48
                               clus
vv                              RRM2B MUTATED RRM2B WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RRM2B MUTATED     3   0   0   1
  RRM2B WILD-TYPE 256   3  22  20
D981V10, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D981V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRM2B MUTATED                                  0     1
  RRM2B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RRM2B MUTATED                           0     3
  RRM2B WILD-TYPE                        19   173
D981V12, multiclass
                                  clus
vv                                 RRM2B MUTATED RRM2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = OR4C15 MUTATION ANALYSIS
D982V1, survival
                  sevent
clus2                0   1
  OR4C15 MUTATED     7   5
  OR4C15 WILD-TYPE 270  73
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              12              343 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
               5               73 
$`OR4C15 MUTATED`
TCGA-AA-3713 TCGA-AZ-6608 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00N TCGA-AZ-4315 
       19.04         1.94        22.06        63.98         4.01        58.39 
TCGA-AZ-6605 TCGA-CA-6718 TCGA-CM-6162 TCGA-D5-6920 TCGA-DM-A1D9 TCGA-DM-A28G 
        5.23        10.06        12.00        12.39       140.38        60.79 

$`OR4C15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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-6717 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  OR4C15 MUTATED OR4C15 WILD-TYPE 
            1.94             0.00 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
          140.38           148.01 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
          15.715           22.090 
[1] "1.9 - 140.4 (15.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D982V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4C15 MUTATED         0        0        2         6         1         0
  OR4C15 WILD-TYPE      64        1       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4C15 MUTATED           0          1          2          0        1
  OR4C15 WILD-TYPE        18          5         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  OR4C15 MUTATED           0         0
  OR4C15 WILD-TYPE        12         1
D982V3, multiclass
            clus
vv           OR4C15 MUTATED OR4C15 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  OR4C15 MUTATED     0   1   9   3
  OR4C15 WILD-TYPE   9  66 240  38
D982V4, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              9              240
  T4              3               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
  OR4C15 MUTATED    10   3   0
  OR4C15 WILD-TYPE 210  78  66
D982V5, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  N0             10              210
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V6, binary
                  cls
clus                 0   1
  OR4C15 MUTATED    12   1
  OR4C15 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED     12    1
  OR4C15 WILD-TYPE  273   47
   clus
vv  OR4C15 MUTATED OR4C15 WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D982V7, binary
                  cls
clus                 0   1
  OR4C15 MUTATED     6   7
  OR4C15 WILD-TYPE 164 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED      6    7
  OR4C15 WILD-TYPE  164  190
        clus
vv       OR4C15 MUTATED OR4C15 WILD-TYPE
  FEMALE              6              164
  MALE                7              190
[1] 2 2
[1] FALSE
D982V8, binary
                  cls
clus                 0   1
  OR4C15 MUTATED     8   1
  OR4C15 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED      8    1
  OR4C15 WILD-TYPE  292    7
     clus
vv    OR4C15 MUTATED OR4C15 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D982V9, binary
                  cls
clus                 0   1
  OR4C15 MUTATED    11   2
  OR4C15 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED     11    2
  OR4C15 WILD-TYPE  303   46
                               clus
vv                              OR4C15 MUTATED OR4C15 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR4C15 MUTATED     7   0   1   1
  OR4C15 WILD-TYPE 252   3  21  20
D982V10, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              1               21
  RX              1               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"
D982V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4C15 MUTATED                                  0     1
  OR4C15 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4C15 MUTATED                           0     8
  OR4C15 WILD-TYPE                        19   168
D982V12, multiclass
                                  clus
vv                                 OR4C15 MUTATED OR4C15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(983) Variable = MANBA MUTATION ANALYSIS
D983V1, survival
                 sevent
clus2               0   1
  MANBA MUTATED    10   2
  MANBA WILD-TYPE 267  76
  MANBA MUTATED MANBA WILD-TYPE 
             12             343 
  MANBA MUTATED MANBA WILD-TYPE 
              2              76 
$`MANBA MUTATED`
TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3672 TCGA-AD-6964 TCGA-AA-3555 TCGA-AA-A00N 
        8.05        17.95         0.92        10.88        29.95         4.01 
TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-6168 TCGA-D5-6533 
        1.02        58.39        17.56        21.99        12.99        25.48 

$`MANBA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       14.30       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MANBA MUTATED MANBA WILD-TYPE 
           0.92            0.00 
  MANBA MUTATED MANBA WILD-TYPE 
          58.39          148.01 
  MANBA MUTATED MANBA WILD-TYPE 
         15.275          22.360 
[1] "0.9 - 58.4 (15.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D983V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MANBA MUTATED         0        0        1         4         1         0
  MANBA WILD-TYPE      64        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MANBA MUTATED           1          0          3          0        0         0
  MANBA WILD-TYPE        17          6         41         33       35        12
                 vv
clus              STAGE IVB
  MANBA MUTATED           0
  MANBA WILD-TYPE         1
D983V3, multiclass
            clus
vv           MANBA MUTATED MANBA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MANBA MUTATED     0   0   8   4
  MANBA WILD-TYPE   9  67 241  37
D983V4, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  T1             0               9
  T2             0              67
  T3             8             241
  T4             4              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
  MANBA MUTATED     7   4   1
  MANBA WILD-TYPE 213  77  65
D983V5, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  N0             7             213
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V6, binary
                 cls
clus                0   1
  MANBA MUTATED    10   0
  MANBA WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED     10    0
  MANBA WILD-TYPE  275   48
   clus
vv  MANBA MUTATED MANBA WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D983V7, binary
                 cls
clus                0   1
  MANBA MUTATED     7   5
  MANBA WILD-TYPE 163 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED      7    5
  MANBA WILD-TYPE  163  192
        clus
vv       MANBA MUTATED MANBA WILD-TYPE
  FEMALE             7             163
  MALE               5             192
[1] 2 2
[1] FALSE
D983V8, binary
                 cls
clus                0   1
  MANBA MUTATED     9   0
  MANBA WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED      9    0
  MANBA WILD-TYPE  291    8
     clus
vv    MANBA MUTATED MANBA WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D983V9, binary
                 cls
clus                0   1
  MANBA MUTATED    10   2
  MANBA WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED     10    2
  MANBA WILD-TYPE  304   46
                               clus
vv                              MANBA MUTATED MANBA WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MANBA MUTATED     9   0   0   2
  MANBA WILD-TYPE 250   3  22  19
D983V10, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D983V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MANBA MUTATED                                  0     0
  MANBA WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MANBA MUTATED                           1     5
  MANBA WILD-TYPE                        18   171
D983V12, multiclass
                                  clus
vv                                 MANBA MUTATED MANBA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = IKBKB MUTATION ANALYSIS
D984V1, survival
                 sevent
clus2               0   1
  IKBKB MUTATED     6   1
  IKBKB WILD-TYPE 271  77
  IKBKB MUTATED IKBKB WILD-TYPE 
              7             348 
  IKBKB MUTATED IKBKB WILD-TYPE 
              1              77 
$`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 
       18.25 

$`IKBKB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IKBKB MUTATED IKBKB WILD-TYPE 
           6.77            0.00 
  IKBKB MUTATED IKBKB WILD-TYPE 
          34.98          148.01 
  IKBKB MUTATED IKBKB WILD-TYPE 
         18.250          22.075 
[1] "6.8 - 35.0 (18.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D984V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKBKB MUTATED         1        0        0         3         1         1
  IKBKB WILD-TYPE      63        1       26       105         7         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  IKBKB MUTATED           0
  IKBKB WILD-TYPE         1
D984V3, multiclass
            clus
vv           IKBKB MUTATED IKBKB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  IKBKB MUTATED     0   1   4   2
  IKBKB WILD-TYPE   9  66 245  39
D984V4, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             2              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
  IKBKB MUTATED     6   1   0
  IKBKB WILD-TYPE 214  80  66
D984V5, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V6, binary
                 cls
clus                0   1
  IKBKB MUTATED     6   0
  IKBKB WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      6    0
  IKBKB WILD-TYPE  279   48
   clus
vv  IKBKB MUTATED IKBKB WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D984V7, binary
                 cls
clus                0   1
  IKBKB MUTATED     2   5
  IKBKB WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      2    5
  IKBKB WILD-TYPE  168  192
        clus
vv       IKBKB MUTATED IKBKB WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D984V8, binary
                 cls
clus                0   1
  IKBKB MUTATED     7   0
  IKBKB WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      7    0
  IKBKB WILD-TYPE  293    8
     clus
vv    IKBKB MUTATED IKBKB WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D984V9, binary
                 cls
clus                0   1
  IKBKB MUTATED     6   1
  IKBKB WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      6    1
  IKBKB WILD-TYPE  308   47
                               clus
vv                              IKBKB MUTATED IKBKB WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IKBKB MUTATED     3   0   0   2
  IKBKB WILD-TYPE 256   3  22  19
D984V10, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             2              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"
D984V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IKBKB MUTATED                                  0     2
  IKBKB WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IKBKB MUTATED                           0     3
  IKBKB WILD-TYPE                        19   173
D984V12, multiclass
                                  clus
vv                                 IKBKB MUTATED IKBKB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = PIK3C2G MUTATION ANALYSIS
D985V1, survival
                   sevent
clus2                 0   1
  PIK3C2G MUTATED    17   2
  PIK3C2G WILD-TYPE 260  76
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               19               336 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
                2                76 
$`PIK3C2G MUTATED`
TCGA-AD-6895 TCGA-G4-6586 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 
       25.08        35.80        25.02         1.02        25.02        34.98 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-6534 
        6.77        12.76        30.08        15.02        12.95        43.27 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      135.65        81.37        35.31        53.62        44.68        85.48 
TCGA-G4-6317 
       36.00 

$`PIK3C2G WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       33.04         0.99        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-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        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 
       43.04        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       74.56        65.85        55.04        61.91        13.78        46.75 

  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
             1.02              0.00 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
           135.65            148.01 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
            34.98             21.99 
[1] "1.0 - 135.7 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.8"
D985V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C2G MUTATED         4        0        0         8         2         0
  PIK3C2G WILD-TYPE      60        1       26       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2G MUTATED           0          0          3          1        0
  PIK3C2G WILD-TYPE        18          6         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  PIK3C2G MUTATED           0         0
  PIK3C2G WILD-TYPE        12         1
D985V3, multiclass
            clus
vv           PIK3C2G MUTATED PIK3C2G WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                8               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  PIK3C2G MUTATED     0   6  12   2
  PIK3C2G WILD-TYPE   9  61 237  39
D985V4, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  T1               0                 9
  T2               6                61
  T3              12               237
  T4               2                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
  PIK3C2G MUTATED    16   3   1
  PIK3C2G WILD-TYPE 204  78  65
D985V5, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  N0              16               204
  N1               3                78
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V6, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    17   0
  PIK3C2G WILD-TYPE 268  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     17    0
  PIK3C2G WILD-TYPE  268   48
   clus
vv  PIK3C2G MUTATED PIK3C2G WILD-TYPE
  0              17               268
  1               0                48
[1] 2 2
[1] FALSE
D985V7, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    11   9
  PIK3C2G WILD-TYPE 159 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     11    9
  PIK3C2G WILD-TYPE  159  188
        clus
vv       PIK3C2G MUTATED PIK3C2G WILD-TYPE
  FEMALE              11               159
  MALE                 9               188
[1] 2 2
[1] FALSE
D985V8, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    17   0
  PIK3C2G WILD-TYPE 283   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     17    0
  PIK3C2G WILD-TYPE  283    8
     clus
vv    PIK3C2G MUTATED PIK3C2G WILD-TYPE
  NO               17               283
  YES               0                 8
[1] 2 2
[1] FALSE
D985V9, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    15   4
  PIK3C2G WILD-TYPE 299  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     15    4
  PIK3C2G WILD-TYPE  299   44
                               clus
vv                              PIK3C2G MUTATED PIK3C2G WILD-TYPE
  COLON ADENOCARCINOMA                       15               299
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PIK3C2G MUTATED    15   0   0   1
  PIK3C2G WILD-TYPE 244   3  22  20
D985V10, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  R0              15               244
  R1               0                 3
  R2               0                22
  RX               1                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"
D985V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C2G MUTATED                                  0     1
  PIK3C2G WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3C2G MUTATED                           1    13
  PIK3C2G WILD-TYPE                        18   163
D985V12, multiclass
                                  clus
vv                                 PIK3C2G MUTATED PIK3C2G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         13               163
[1] 4 2
[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 = RTN4 MUTATION ANALYSIS
D986V1, survival
                sevent
clus2              0   1
  RTN4 MUTATED    16   3
  RTN4 WILD-TYPE 261  75
  RTN4 MUTATED RTN4 WILD-TYPE 
            19            336 
  RTN4 MUTATED RTN4 WILD-TYPE 
             3             75 
$`RTN4 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-G4-6628 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3510 
       19.04        19.04        79.69        32.75         3.02        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-5900 
        1.02         1.02        29.95         0.99        34.98        12.16 
TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-6171 
       58.39        12.20        12.76        10.06        85.45        14.04 
TCGA-D5-6540 
       16.14 

$`RTN4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3517 
       19.66        20.28         7.04        35.01         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       42.02        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6719 TCGA-CK-4947 
       12.36        12.39        12.59        12.59        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RTN4 MUTATED RTN4 WILD-TYPE 
          0.99           0.00 
  RTN4 MUTATED RTN4 WILD-TYPE 
         85.45         148.01 
  RTN4 MUTATED RTN4 WILD-TYPE 
        16.140         22.225 
[1] "1.0 - 85.5 (16.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.4"
D986V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RTN4 MUTATED         6        0        3         6         2         0
  RTN4 WILD-TYPE      58        1       23       102         6         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  RTN4 MUTATED           0
  RTN4 WILD-TYPE         1
D986V3, multiclass
            clus
vv           RTN4 MUTATED RTN4 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  RTN4 MUTATED     0   6  11   2
  RTN4 WILD-TYPE   9  61 238  39
D986V4, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  T1            0              9
  T2            6             61
  T3           11            238
  T4            2             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
  RTN4 MUTATED    18   1   0
  RTN4 WILD-TYPE 202  80  66
D986V5, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  N0           18            202
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V6, binary
                cls
clus               0   1
  RTN4 MUTATED    17   1
  RTN4 WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     17    1
  RTN4 WILD-TYPE  268   47
   clus
vv  RTN4 MUTATED RTN4 WILD-TYPE
  0           17            268
  1            1             47
[1] 2 2
[1] FALSE
D986V7, binary
                cls
clus               0   1
  RTN4 MUTATED     9  10
  RTN4 WILD-TYPE 161 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED      9   10
  RTN4 WILD-TYPE  161  187
        clus
vv       RTN4 MUTATED RTN4 WILD-TYPE
  FEMALE            9            161
  MALE             10            187
[1] 2 2
[1] FALSE
D986V8, binary
                cls
clus               0   1
  RTN4 MUTATED    16   1
  RTN4 WILD-TYPE 284   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     16    1
  RTN4 WILD-TYPE  284    7
     clus
vv    RTN4 MUTATED RTN4 WILD-TYPE
  NO            16            284
  YES            1              7
[1] 2 2
[1] FALSE
D986V9, binary
                cls
clus               0   1
  RTN4 MUTATED    13   6
  RTN4 WILD-TYPE 301  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     13    6
  RTN4 WILD-TYPE  301   42
                               clus
vv                              RTN4 MUTATED RTN4 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RTN4 MUTATED    14   1   1   3
  RTN4 WILD-TYPE 245   2  21  18
D986V10, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  R0           14            245
  R1            1              2
  R2            1             21
  RX            3             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"
D986V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RTN4 MUTATED                                  0     3
  RTN4 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RTN4 MUTATED                           1     6
  RTN4 WILD-TYPE                        18   170
D986V12, multiclass
                                  clus
vv                                 RTN4 MUTATED RTN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = C7ORF58 MUTATION ANALYSIS
D987V1, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    16   4
  C7ORF58 WILD-TYPE 261  74
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               20               335 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
                4                74 
$`C7ORF58 MUTATED`
TCGA-A6-6649 TCGA-AA-3672 TCGA-AA-3697 TCGA-AZ-6601 TCGA-A6-2676 TCGA-A6-5662 
       24.16         0.92        85.05       100.01        42.90        23.61 
TCGA-A6-6780 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 
       20.12        26.01         4.01        34.98        27.09        58.39 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A28H 
       12.69        12.76        10.06        10.13        13.35       117.07 
TCGA-F4-6856 TCGA-G4-6309 
       35.31        85.48 

$`C7ORF58 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        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-A6-5664 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-A6-6651 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.92              0.00 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           117.07            148.01 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           25.085            21.990 
[1] "0.9 - 117.1 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D987V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF58 MUTATED         2        0        2         6         3         0
  C7ORF58 WILD-TYPE      62        1       24       102         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED           2          1          3          1        0
  C7ORF58 WILD-TYPE        16          5         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF58 MUTATED           1         0
  C7ORF58 WILD-TYPE        11         1
D987V3, multiclass
            clus
vv           C7ORF58 MUTATED C7ORF58 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                6               102
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               1                 5
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  C7ORF58 MUTATED     0   2  16   3
  C7ORF58 WILD-TYPE   9  65 233  38
D987V4, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              16               233
  T4               3                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
  C7ORF58 MUTATED    13   5   3
  C7ORF58 WILD-TYPE 207  76  63
D987V5, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0              13               207
  N1               5                76
  N2               3                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"
D987V6, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    19   1
  C7ORF58 WILD-TYPE 266  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     19    1
  C7ORF58 WILD-TYPE  266   47
   clus
vv  C7ORF58 MUTATED C7ORF58 WILD-TYPE
  0              19               266
  1               1                47
[1] 2 2
[1] FALSE
D987V7, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     7  14
  C7ORF58 WILD-TYPE 163 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      7   14
  C7ORF58 WILD-TYPE  163  183
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  FEMALE               7               163
  MALE                14               183
[1] 2 2
[1] FALSE
D987V8, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    17   0
  C7ORF58 WILD-TYPE 283   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     17    0
  C7ORF58 WILD-TYPE  283    8
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO               17               283
  YES               0                 8
[1] 2 2
[1] FALSE
D987V9, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    15   6
  C7ORF58 WILD-TYPE 299  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     15    6
  C7ORF58 WILD-TYPE  299   42
                               clus
vv                              C7ORF58 MUTATED C7ORF58 WILD-TYPE
  COLON ADENOCARCINOMA                       15               299
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF58 MUTATED    13   0   0   3
  C7ORF58 WILD-TYPE 246   3  22  18
D987V10, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               3                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"
D987V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF58 MUTATED                                  0     3
  C7ORF58 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF58 MUTATED                           1    11
  C7ORF58 WILD-TYPE                        18   165
D987V12, multiclass
                                  clus
vv                                 C7ORF58 MUTATED C7ORF58 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               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(988) Variable = WDR75 MUTATION ANALYSIS
D988V1, survival
                 sevent
clus2               0   1
  WDR75 MUTATED     4   3
  WDR75 WILD-TYPE 273  75
  WDR75 MUTATED WDR75 WILD-TYPE 
              7             348 
  WDR75 MUTATED WDR75 WILD-TYPE 
              3              75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 
        2.01       124.27        23.05        20.02        37.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.075 
[1] "1.0 - 30.0 (6.2)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "3.9"
D988V2, continuous
                 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      64        1       26       104         7         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        18          6         44         32       35        11
                 vv
clus              STAGE IVB
  WDR75 MUTATED           0
  WDR75 WILD-TYPE         1
D988V3, multiclass
            clus
vv           WDR75 MUTATED WDR75 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  WDR75 MUTATED     0   1   4   3
  WDR75 WILD-TYPE   9  66 245  38
D988V4, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             3              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
  WDR75 MUTATED     6   1   1
  WDR75 WILD-TYPE 214  80  65
D988V5, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V6, binary
                 cls
clus                0   1
  WDR75 MUTATED     5   1
  WDR75 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      5    1
  WDR75 WILD-TYPE  280   47
   clus
vv  WDR75 MUTATED WDR75 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D988V7, binary
                 cls
clus                0   1
  WDR75 MUTATED     2   6
  WDR75 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      2    6
  WDR75 WILD-TYPE  168  191
        clus
vv       WDR75 MUTATED WDR75 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D988V8, binary
                 cls
clus                0   1
  WDR75 MUTATED     5   0
  WDR75 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      5    0
  WDR75 WILD-TYPE  295    8
     clus
vv    WDR75 MUTATED WDR75 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D988V9, binary
                 cls
clus                0   1
  WDR75 MUTATED     6   2
  WDR75 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      6    2
  WDR75 WILD-TYPE  308   46
                               clus
vv                              WDR75 MUTATED WDR75 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR75 MUTATED     6   0   0   0
  WDR75 WILD-TYPE 253   3  22  21
D988V10, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D988V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR75 MUTATED                                  0     0
  WDR75 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR75 MUTATED                           0     3
  WDR75 WILD-TYPE                        19   173
D988V12, multiclass
                                  clus
vv                                 WDR75 MUTATED WDR75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = FAM20B MUTATION ANALYSIS
D989V1, survival
                  sevent
clus2                0   1
  FAM20B MUTATED     8   2
  FAM20B WILD-TYPE 269  76
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              345 
  FAM20B MUTATED FAM20B WILD-TYPE 
               2               76 
$`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        83.24 
TCGA-CM-5344 TCGA-D5-6536 TCGA-D5-6929 TCGA-G4-6309 
       22.03        17.85        13.41        85.48 

$`FAM20B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.090 
[1] "2.0 - 85.5 (20.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D989V2, continuous
                  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      64        1       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM20B MUTATED           0          0          2          1        1
  FAM20B WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  FAM20B MUTATED           0         0
  FAM20B WILD-TYPE        12         1
D989V3, multiclass
            clus
vv           FAM20B MUTATED FAM20B WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  FAM20B MUTATED     0   0   8   2
  FAM20B WILD-TYPE   9  67 241  39
D989V4, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  T1              0                9
  T2              0               67
  T3              8              241
  T4              2               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
  FAM20B MUTATED     6   4   0
  FAM20B WILD-TYPE 214  77  66
D989V5, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  N0              6              214
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V6, binary
                  cls
clus                 0   1
  FAM20B MUTATED     8   1
  FAM20B WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      8    1
  FAM20B WILD-TYPE  277   47
   clus
vv  FAM20B MUTATED FAM20B WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D989V7, binary
                  cls
clus                 0   1
  FAM20B MUTATED     5   5
  FAM20B WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      5    5
  FAM20B WILD-TYPE  165  192
        clus
vv       FAM20B MUTATED FAM20B WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D989V8, binary
                  cls
clus                 0   1
  FAM20B MUTATED     8   0
  FAM20B WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      8    0
  FAM20B WILD-TYPE  292    8
     clus
vv    FAM20B MUTATED FAM20B WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D989V9, binary
                  cls
clus                 0   1
  FAM20B MUTATED     7   3
  FAM20B WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      7    3
  FAM20B WILD-TYPE  307   45
                               clus
vv                              FAM20B MUTATED FAM20B WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM20B MUTATED     9   0   0   0
  FAM20B WILD-TYPE 250   3  22  21
D989V10, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D989V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM20B MUTATED                                  0     1
  FAM20B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM20B MUTATED                           1     5
  FAM20B WILD-TYPE                        18   171
D989V12, multiclass
                                  clus
vv                                 FAM20B MUTATED FAM20B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = CEP164 MUTATION ANALYSIS
D990V1, survival
                  sevent
clus2                0   1
  CEP164 MUTATED    19   3
  CEP164 WILD-TYPE 258  75
  CEP164 MUTATED CEP164 WILD-TYPE 
              22              333 
  CEP164 MUTATED CEP164 WILD-TYPE 
               3               75 
$`CEP164 MUTATED`
TCGA-A6-4105 TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6654 
       14.53        19.04        25.08        26.17        22.06        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3833 
       20.12        19.66         1.02        29.95        26.99        15.95 
TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AU-3779 
        2.01        27.02        34.98        35.01        83.24        14.50 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6535 
       27.09        49.41        12.76        15.12 

$`CEP164 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       21.76        24.69        24.39        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02         7.96        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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        27.42        26.47        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CEP164 MUTATED CEP164 WILD-TYPE 
            1.02             0.00 
  CEP164 MUTATED CEP164 WILD-TYPE 
           83.24           148.01 
  CEP164 MUTATED CEP164 WILD-TYPE 
          22.965           22.030 
[1] "1.0 - 83.2 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D990V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEP164 MUTATED         1        0        1        12         2         0
  CEP164 WILD-TYPE      63        1       25        96         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP164 MUTATED           1          0          4          1        1
  CEP164 WILD-TYPE        17          6         40         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CEP164 MUTATED           0         0
  CEP164 WILD-TYPE        12         1
D990V3, multiclass
            clus
vv           CEP164 MUTATED CEP164 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              12               96
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CEP164 MUTATED     0   1  19   3
  CEP164 WILD-TYPE   9  66 230  38
D990V4, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             19              230
  T4              3               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
  CEP164 MUTATED    17   5   1
  CEP164 WILD-TYPE 203  76  65
D990V5, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  N0             17              203
  N1              5               76
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V6, binary
                  cls
clus                 0   1
  CEP164 MUTATED    17   1
  CEP164 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     17    1
  CEP164 WILD-TYPE  268   47
   clus
vv  CEP164 MUTATED CEP164 WILD-TYPE
  0             17              268
  1              1               47
[1] 2 2
[1] FALSE
D990V7, binary
                  cls
clus                 0   1
  CEP164 MUTATED    14   9
  CEP164 WILD-TYPE 156 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     14    9
  CEP164 WILD-TYPE  156  188
        clus
vv       CEP164 MUTATED CEP164 WILD-TYPE
  FEMALE             14              156
  MALE                9              188
[1] 2 2
[1] FALSE
D990V8, binary
                  cls
clus                 0   1
  CEP164 MUTATED    17   2
  CEP164 WILD-TYPE 283   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     17    2
  CEP164 WILD-TYPE  283    6
     clus
vv    CEP164 MUTATED CEP164 WILD-TYPE
  NO              17              283
  YES              2                6
[1] 2 2
[1] FALSE
D990V9, binary
                  cls
clus                 0   1
  CEP164 MUTATED    16   7
  CEP164 WILD-TYPE 298  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     16    7
  CEP164 WILD-TYPE  298   41
                               clus
vv                              CEP164 MUTATED CEP164 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CEP164 MUTATED    14   0   1   3
  CEP164 WILD-TYPE 245   3  21  18
D990V10, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              1               21
  RX              3               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"
D990V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEP164 MUTATED                                  0     2
  CEP164 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CEP164 MUTATED                           0    12
  CEP164 WILD-TYPE                        19   164
D990V12, multiclass
                                  clus
vv                                 CEP164 MUTATED CEP164 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        12              164
[1] 4 2
[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 = SF1 MUTATION ANALYSIS
D991V1, survival
               sevent
clus2             0   1
  SF1 MUTATED    11   2
  SF1 WILD-TYPE 266  76
  SF1 MUTATED SF1 WILD-TYPE 
           13           342 
  SF1 MUTATED SF1 WILD-TYPE 
            2            76 
$`SF1 MUTATED`
TCGA-AD-6895 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6142 TCGA-AA-3821 TCGA-AA-3947 
       25.08        31.63        29.19        25.08         1.02        33.01 
TCGA-AA-3977 TCGA-AA-A02Y TCGA-AZ-6603 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5868 
       25.02        39.98        29.56        10.06        23.05        17.03 
TCGA-DM-A1HB 
      135.65 

$`SF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       32.75        36.53        32.91        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SF1 MUTATED SF1 WILD-TYPE 
         1.02          0.00 
  SF1 MUTATED SF1 WILD-TYPE 
       135.65        148.01 
  SF1 MUTATED SF1 WILD-TYPE 
        25.08         21.99 
[1] "1.0 - 135.7 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D991V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SF1 MUTATED         2        0        1         2         1         0
  SF1 WILD-TYPE      62        1       25       106         7         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        18          6         41         32       35        10
               vv
clus            STAGE IVB
  SF1 MUTATED           0
  SF1 WILD-TYPE         1
D991V3, multiclass
            clus
vv           SF1 MUTATED SF1 WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            2           106
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           3            41
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            2            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
  SF1 MUTATED     0   4   7   3
  SF1 WILD-TYPE   9  63 242  38
D991V4, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  T1           0             9
  T2           4            63
  T3           7           242
  T4           3            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
  SF1 MUTATED     7   6   1
  SF1 WILD-TYPE 213  75  65
D991V5, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  N0           7           213
  N1           6            75
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V6, binary
               cls
clus              0   1
  SF1 MUTATED    10   2
  SF1 WILD-TYPE 275  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     10    2
  SF1 WILD-TYPE  275   46
   clus
vv  SF1 MUTATED SF1 WILD-TYPE
  0          10           275
  1           2            46
[1] 2 2
[1] FALSE
D991V7, binary
               cls
clus              0   1
  SF1 MUTATED     6   8
  SF1 WILD-TYPE 164 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      6    8
  SF1 WILD-TYPE  164  189
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  FEMALE           6           164
  MALE             8           189
[1] 2 2
[1] FALSE
D991V8, binary
               cls
clus              0   1
  SF1 MUTATED    12   0
  SF1 WILD-TYPE 288   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     12    0
  SF1 WILD-TYPE  288    8
     clus
vv    SF1 MUTATED SF1 WILD-TYPE
  NO           12           288
  YES           0             8
[1] 2 2
[1] FALSE
D991V9, binary
               cls
clus              0   1
  SF1 MUTATED    11   2
  SF1 WILD-TYPE 303  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     11    2
  SF1 WILD-TYPE  303   46
                               clus
vv                              SF1 MUTATED SF1 WILD-TYPE
  COLON ADENOCARCINOMA                   11           303
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SF1 MUTATED     8   0   0   1
  SF1 WILD-TYPE 251   3  22  20
D991V10, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  R0           8           251
  R1           0             3
  R2           0            22
  RX           1            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"
D991V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SF1 MUTATED                                  0     1
  SF1 WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SF1 MUTATED                           2     6
  SF1 WILD-TYPE                        17   170
D991V12, multiclass
                                  clus
vv                                 SF1 MUTATED SF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                      6           170
[1] 4 2
[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 = KIF16B MUTATION ANALYSIS
D992V1, survival
                  sevent
clus2                0   1
  KIF16B MUTATED    21   3
  KIF16B WILD-TYPE 256  75
  KIF16B MUTATED KIF16B WILD-TYPE 
              24              331 
  KIF16B MUTATED KIF16B WILD-TYPE 
               3               75 
$`KIF16B MUTATED`
TCGA-AA-3950 TCGA-AD-6548 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 
       24.00        21.37        24.39         6.97        33.04        53.00 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AY-6196 
       26.01         2.01        25.02        30.02         4.01         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 
       17.82        58.39        12.59        12.76        51.32        21.99 
TCGA-CM-5861 TCGA-CM-5864 TCGA-D5-6537 TCGA-D5-6923 TCGA-D5-6930 TCGA-F4-6570 
       15.02        15.02         4.80        12.43        13.35         6.18 

$`KIF16B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        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-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        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KIF16B MUTATED KIF16B WILD-TYPE 
             0.2              0.0 
  KIF16B MUTATED KIF16B WILD-TYPE 
           58.39           148.01 
  KIF16B MUTATED KIF16B WILD-TYPE 
           16.42            22.36 
[1] "0.2 - 58.4 (16.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D992V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF16B MUTATED         5        0        3        11         1         0
  KIF16B WILD-TYPE      59        1       23        97         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF16B MUTATED           0          0          4          1        0
  KIF16B WILD-TYPE        18          6         40         32       35
                  vv
clus               STAGE IVA STAGE IVB
  KIF16B MUTATED           0         0
  KIF16B WILD-TYPE        12         1
D992V3, multiclass
            clus
vv           KIF16B MUTATED KIF16B WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              11               97
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  KIF16B MUTATED     0   6  18   2
  KIF16B WILD-TYPE   9  61 231  39
D992V4, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  T1              0                9
  T2              6               61
  T3             18              231
  T4              2               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
  KIF16B MUTATED    21   4   1
  KIF16B WILD-TYPE 199  77  65
D992V5, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  N0             21              199
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V6, binary
                  cls
clus                 0   1
  KIF16B MUTATED    20   0
  KIF16B WILD-TYPE 265  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     20    0
  KIF16B WILD-TYPE  265   48
   clus
vv  KIF16B MUTATED KIF16B WILD-TYPE
  0             20              265
  1              0               48
[1] 2 2
[1] FALSE
D992V7, binary
                  cls
clus                 0   1
  KIF16B MUTATED    10  16
  KIF16B WILD-TYPE 160 181
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     10   16
  KIF16B WILD-TYPE  160  181
        clus
vv       KIF16B MUTATED KIF16B WILD-TYPE
  FEMALE             10              160
  MALE               16              181
[1] 2 2
[1] FALSE
D992V8, binary
                  cls
clus                 0   1
  KIF16B MUTATED    20   0
  KIF16B WILD-TYPE 280   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     20    0
  KIF16B WILD-TYPE  280    8
     clus
vv    KIF16B MUTATED KIF16B WILD-TYPE
  NO              20              280
  YES              0                8
[1] 2 2
[1] FALSE
D992V9, binary
                  cls
clus                 0   1
  KIF16B MUTATED    19   7
  KIF16B WILD-TYPE 295  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     19    7
  KIF16B WILD-TYPE  295   41
                               clus
vv                              KIF16B MUTATED KIF16B WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIF16B MUTATED    19   0   0   4
  KIF16B WILD-TYPE 240   3  22  17
D992V10, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  R0             19              240
  R1              0                3
  R2              0               22
  RX              4               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"
D992V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF16B MUTATED                                  0     2
  KIF16B WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF16B MUTATED                           1    13
  KIF16B WILD-TYPE                        18   163
D992V12, multiclass
                                  clus
vv                                 KIF16B MUTATED KIF16B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        13              163
[1] 4 2
[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 = COL6A5 MUTATION ANALYSIS
D993V1, survival
                  sevent
clus2                0   1
  COL6A5 MUTATED    25   6
  COL6A5 WILD-TYPE 252  72
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              31              324 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
               6               72 
$`COL6A5 MUTATED`
TCGA-AZ-6608 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 
        1.94        26.17        79.69        33.53         8.38        24.39 
TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R 
       63.98        33.04        20.98        25.02         4.01        35.01 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       14.50        58.39        49.41        12.76        10.06        23.05 
TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6676 
       15.02        29.03        12.99        14.04        13.05        11.08 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-F4-6460 
       12.43        14.30        13.35       130.65        92.75        31.96 
TCGA-F4-6805 
       34.42 

$`COL6A5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64        13.41        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-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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  COL6A5 MUTATED COL6A5 WILD-TYPE 
            1.94             0.00 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
          130.65           148.01 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
          23.050           22.045 
[1] "1.9 - 130.7 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D993V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL6A5 MUTATED         6        0        2        17         2         0
  COL6A5 WILD-TYPE      58        1       24        91         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL6A5 MUTATED           1          1          2          0        0
  COL6A5 WILD-TYPE        17          5         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  COL6A5 MUTATED           0         1
  COL6A5 WILD-TYPE        12         0
D993V3, multiclass
            clus
vv           COL6A5 MUTATED COL6A5 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              17               91
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               12
  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   9  22   2
  COL6A5 WILD-TYPE   9  58 227  39
D993V4, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  T1              0                9
  T2              9               58
  T3             22              227
  T4              2               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
  COL6A5 MUTATED    28   2   3
  COL6A5 WILD-TYPE 192  79  63
D993V5, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  N0             28              192
  N1              2               79
  N2              3               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"
D993V6, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    29   1
  COL6A5 WILD-TYPE 256  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     29    1
  COL6A5 WILD-TYPE  256   47
   clus
vv  COL6A5 MUTATED COL6A5 WILD-TYPE
  0             29              256
  1              1               47
[1] 2 2
[1] FALSE
D993V7, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    14  19
  COL6A5 WILD-TYPE 156 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     14   19
  COL6A5 WILD-TYPE  156  178
        clus
vv       COL6A5 MUTATED COL6A5 WILD-TYPE
  FEMALE             14              156
  MALE               19              178
[1] 2 2
[1] FALSE
D993V8, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    27   1
  COL6A5 WILD-TYPE 273   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     27    1
  COL6A5 WILD-TYPE  273    7
     clus
vv    COL6A5 MUTATED COL6A5 WILD-TYPE
  NO              27              273
  YES              1                7
[1] 2 2
[1] FALSE
D993V9, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    29   4
  COL6A5 WILD-TYPE 285  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     29    4
  COL6A5 WILD-TYPE  285   44
                               clus
vv                              COL6A5 MUTATED COL6A5 WILD-TYPE
  COLON ADENOCARCINOMA                      29              285
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  COL6A5 MUTATED    23   0   0   3
  COL6A5 WILD-TYPE 236   3  22  18
D993V10, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  R0             23              236
  R1              0                3
  R2              0               22
  RX              3               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"
D993V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL6A5 MUTATED                                  0     2
  COL6A5 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL6A5 MUTATED                           4    20
  COL6A5 WILD-TYPE                        15   156
D993V12, multiclass
                                  clus
vv                                 COL6A5 MUTATED COL6A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                        20              156
[1] 4 2
[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 = CYP2C18 MUTATION ANALYSIS
D994V1, survival
                   sevent
clus2                 0   1
  CYP2C18 MUTATED     3   2
  CYP2C18 WILD-TYPE 274  76
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                5               350 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                2                76 
$`CYP2C18 MUTATED`
TCGA-G4-6310 TCGA-AD-6889 TCGA-AZ-5403 TCGA-CM-5860 TCGA-F4-6856 
       63.62        83.24        62.79        32.02        35.31 

$`CYP2C18 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            32.02              0.00 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            83.24            148.01 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            62.79             21.99 
[1] "32.0 - 83.2 (62.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D994V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP2C18 MUTATED         1        0        1         2         0         0
  CYP2C18 WILD-TYPE      63        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP2C18 MUTATED           0          0          1          0        0
  CYP2C18 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  CYP2C18 MUTATED           0         0
  CYP2C18 WILD-TYPE        12         1
D994V3, multiclass
            clus
vv           CYP2C18 MUTATED CYP2C18 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  CYP2C18 MUTATED     0   1   4   0
  CYP2C18 WILD-TYPE   9  66 245  41
D994V4, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               0                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
  CYP2C18 MUTATED     4   1   0
  CYP2C18 WILD-TYPE 216  80  66
D994V5, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V6, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     4   0
  CYP2C18 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      4    0
  CYP2C18 WILD-TYPE  281   48
   clus
vv  CYP2C18 MUTATED CYP2C18 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D994V7, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     0   5
  CYP2C18 WILD-TYPE 170 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      0    5
  CYP2C18 WILD-TYPE  170  192
        clus
vv       CYP2C18 MUTATED CYP2C18 WILD-TYPE
  FEMALE               0               170
  MALE                 5               192
[1] 2 2
[1] FALSE
D994V8, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     4   1
  CYP2C18 WILD-TYPE 296   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      4    1
  CYP2C18 WILD-TYPE  296    7
     clus
vv    CYP2C18 MUTATED CYP2C18 WILD-TYPE
  NO                4               296
  YES               1                 7
[1] 2 2
[1] FALSE
D994V9, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     4   1
  CYP2C18 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      4    1
  CYP2C18 WILD-TYPE  310   47
                               clus
vv                              CYP2C18 MUTATED CYP2C18 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP2C18 MUTATED     4   0   0   0
  CYP2C18 WILD-TYPE 255   3  22  21
D994V10, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D994V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP2C18 MUTATED                                  0     1
  CYP2C18 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP2C18 MUTATED                           0     4
  CYP2C18 WILD-TYPE                        19   172
D994V12, multiclass
                                  clus
vv                                 CYP2C18 MUTATED CYP2C18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = ITGA5 MUTATION ANALYSIS
D995V1, survival
                 sevent
clus2               0   1
  ITGA5 MUTATED    14   1
  ITGA5 WILD-TYPE 263  77
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             15             340 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
              1              77 
$`ITGA5 MUTATED`
TCGA-G4-6586 TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A010 
       35.80         6.97        31.00        30.02         0.99        34.98 
TCGA-AA-A02J TCGA-AZ-4315 TCGA-CA-6715 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5863 
        5.03        58.39        12.59        37.02        15.02        15.02 
TCGA-D5-6928 TCGA-D5-6930 TCGA-G4-6293 
       11.64        13.35       133.18 

$`ITGA5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ITGA5 MUTATED ITGA5 WILD-TYPE 
           0.99            0.00 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
         133.18          148.01 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
         15.020          22.075 
[1] "1.0 - 133.2 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3.3"
D995V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGA5 MUTATED         3        0        1         6         1         0
  ITGA5 WILD-TYPE      61        1       25       102         7         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        17          6         42         33       33        12
                 vv
clus              STAGE IVB
  ITGA5 MUTATED           0
  ITGA5 WILD-TYPE         1
D995V3, multiclass
            clus
vv           ITGA5 MUTATED ITGA5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  ITGA5 MUTATED     1   2  10   3
  ITGA5 WILD-TYPE   8  65 239  38
D995V4, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            10             239
  T4             3              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
  ITGA5 MUTATED    12   3   1
  ITGA5 WILD-TYPE 208  78  65
D995V5, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  N0            12             208
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V6, binary
                 cls
clus                0   1
  ITGA5 MUTATED    14   2
  ITGA5 WILD-TYPE 271  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     14    2
  ITGA5 WILD-TYPE  271   46
   clus
vv  ITGA5 MUTATED ITGA5 WILD-TYPE
  0            14             271
  1             2              46
[1] 2 2
[1] FALSE
D995V7, binary
                 cls
clus                0   1
  ITGA5 MUTATED     8   8
  ITGA5 WILD-TYPE 162 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED      8    8
  ITGA5 WILD-TYPE  162  189
        clus
vv       ITGA5 MUTATED ITGA5 WILD-TYPE
  FEMALE             8             162
  MALE               8             189
[1] 2 2
[1] FALSE
D995V8, binary
                 cls
clus                0   1
  ITGA5 MUTATED    13   0
  ITGA5 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     13    0
  ITGA5 WILD-TYPE  287    8
     clus
vv    ITGA5 MUTATED ITGA5 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D995V9, binary
                 cls
clus                0   1
  ITGA5 MUTATED    12   4
  ITGA5 WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     12    4
  ITGA5 WILD-TYPE  302   44
                               clus
vv                              ITGA5 MUTATED ITGA5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITGA5 MUTATED    13   0   2   1
  ITGA5 WILD-TYPE 246   3  20  20
D995V10, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             2              20
  RX             1              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"
D995V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGA5 MUTATED                                  0     1
  ITGA5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGA5 MUTATED                           1     7
  ITGA5 WILD-TYPE                        18   169
D995V12, multiclass
                                  clus
vv                                 ITGA5 MUTATED ITGA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = KRTAP5-3 MUTATION ANALYSIS
D996V1, survival
                    sevent
clus2                  0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 273  78
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                351 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 0                 78 
$`KRTAP5-3 MUTATED`
TCGA-G4-6310 TCGA-AA-3966 TCGA-CA-6717 TCGA-CM-6169 
       63.62         2.01        12.76        13.02 

$`KRTAP5-3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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              22.09 
[1] "2.0 - 63.6 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D996V2, continuous
                    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      64        1       26       105         8         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        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  KRTAP5-3 MUTATED           0         0
  KRTAP5-3 WILD-TYPE        12         1
D996V3, multiclass
            clus
vv           KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 3                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KRTAP5-3 MUTATED     0   0   4   0
  KRTAP5-3 WILD-TYPE   9  67 245  41
D996V4, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                4                245
  T4                0                 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
  KRTAP5-3 MUTATED     3   1   0
  KRTAP5-3 WILD-TYPE 217  80  66
D996V5, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  N0                3                217
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V6, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      4    0
  KRTAP5-3 WILD-TYPE  281   48
   clus
vv  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D996V7, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     1   3
  KRTAP5-3 WILD-TYPE 169 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      1    3
  KRTAP5-3 WILD-TYPE  169  194
        clus
vv       KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  FEMALE                1                169
  MALE                  3                194
[1] 2 2
[1] FALSE
D996V8, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     2   1
  KRTAP5-3 WILD-TYPE 298   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      2    1
  KRTAP5-3 WILD-TYPE  298    7
     clus
vv    KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  NO                 2                298
  YES                1                  7
[1] 2 2
[1] FALSE
D996V9, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     2   2
  KRTAP5-3 WILD-TYPE 312  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      2    2
  KRTAP5-3 WILD-TYPE  312   46
                               clus
vv                              KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  COLON ADENOCARCINOMA                         2                312
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KRTAP5-3 MUTATED     2   0   0   1
  KRTAP5-3 WILD-TYPE 257   3  22  20
D996V10, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  R0                2                257
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D996V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-3 MUTATED                                  0     1
  KRTAP5-3 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-3 MUTATED                           1     1
  KRTAP5-3 WILD-TYPE                        18   175
D996V12, multiclass
                                  clus
vv                                 KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           1                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(997) Variable = NOL9 MUTATION ANALYSIS
D997V1, survival
                sevent
clus2              0   1
  NOL9 MUTATED     7   0
  NOL9 WILD-TYPE 270  78
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            348 
  NOL9 MUTATED NOL9 WILD-TYPE 
             0             78 
$`NOL9 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3982 TCGA-AA-A02F TCGA-CA-6719 
       35.80        26.17        79.69        27.02        39.98        14.30 
TCGA-DM-A1HB 
      135.65 

$`NOL9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       22.09        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NOL9 MUTATED NOL9 WILD-TYPE 
          14.3            0.0 
  NOL9 MUTATED NOL9 WILD-TYPE 
        135.65         148.01 
  NOL9 MUTATED NOL9 WILD-TYPE 
         35.80          21.99 
[1] "14.3 - 135.7 (35.8)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D997V2, continuous
                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      63        1       26       105         8         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        18          6         42         33       34        12
                vv
clus             STAGE IVB
  NOL9 MUTATED           0
  NOL9 WILD-TYPE         1
D997V3, multiclass
            clus
vv           NOL9 MUTATED NOL9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  NOL9 MUTATED     0   1   6   0
  NOL9 WILD-TYPE   9  66 243  41
D997V4, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            0             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
  NOL9 MUTATED     4   3   0
  NOL9 WILD-TYPE 216  78  66
D997V5, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  N0            4            216
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V6, binary
                cls
clus               0   1
  NOL9 MUTATED     6   1
  NOL9 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      6    1
  NOL9 WILD-TYPE  279   47
   clus
vv  NOL9 MUTATED NOL9 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D997V7, binary
                cls
clus               0   1
  NOL9 MUTATED     3   4
  NOL9 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      3    4
  NOL9 WILD-TYPE  167  193
        clus
vv       NOL9 MUTATED NOL9 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D997V8, binary
                cls
clus               0   1
  NOL9 MUTATED     6   0
  NOL9 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      6    0
  NOL9 WILD-TYPE  294    8
     clus
vv    NOL9 MUTATED NOL9 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D997V9, binary
                cls
clus               0   1
  NOL9 MUTATED     6   0
  NOL9 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      6    0
  NOL9 WILD-TYPE  308   48
                               clus
vv                              NOL9 MUTATED NOL9 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOL9 MUTATED     3   0   1   1
  NOL9 WILD-TYPE 256   3  21  20
D997V10, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            1             21
  RX            1             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"
D997V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOL9 MUTATED                                  0     1
  NOL9 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOL9 MUTATED                           0     4
  NOL9 WILD-TYPE                        19   172
D997V12, multiclass
                                  clus
vv                                 NOL9 MUTATED NOL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = RAPGEF6 MUTATION ANALYSIS
D998V1, survival
                   sevent
clus2                 0   1
  RAPGEF6 MUTATED    13   4
  RAPGEF6 WILD-TYPE 264  74
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               17               338 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
                4                74 
$`RAPGEF6 MUTATED`
TCGA-AA-3516 TCGA-AA-3554 TCGA-AD-6895 TCGA-A6-5664 TCGA-A6-6781 TCGA-AA-3660 
       13.02        17.95        25.08        22.09        19.66        78.08 
TCGA-AA-3848 TCGA-AA-A010 TCGA-AA-A01F TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-5913 
       10.06        34.98        32.02        27.09        12.76        51.32 
TCGA-CM-5348 TCGA-D5-6928 TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6309 
       22.98        11.64         8.61         6.18        85.48 

$`RAPGEF6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
             6.18              0.00 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
            85.48            148.01 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
           22.090            22.045 
[1] "6.2 - 85.5 (22.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D998V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAPGEF6 MUTATED         1        0        1         5         1         0
  RAPGEF6 WILD-TYPE      63        1       25       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAPGEF6 MUTATED           1          0          5          3        0
  RAPGEF6 WILD-TYPE        17          6         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  RAPGEF6 MUTATED           0         0
  RAPGEF6 WILD-TYPE        12         1
D998V3, multiclass
            clus
vv           RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               5                39
  STAGE IIIC               3                30
  STAGE IV                 0                35
  STAGE IVA                0                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
  RAPGEF6 MUTATED     0   1  13   3
  RAPGEF6 WILD-TYPE   9  66 236  38
D998V4, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              13               236
  T4               3                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
  RAPGEF6 MUTATED     8   5   4
  RAPGEF6 WILD-TYPE 212  76  62
D998V5, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  N0               8               212
  N1               5                76
  N2               4                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V6, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    14   0
  RAPGEF6 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     14    0
  RAPGEF6 WILD-TYPE  271   48
   clus
vv  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  0              14               271
  1               0                48
[1] 2 2
[1] FALSE
D998V7, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    10   7
  RAPGEF6 WILD-TYPE 160 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     10    7
  RAPGEF6 WILD-TYPE  160  190
        clus
vv       RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  FEMALE              10               160
  MALE                 7               190
[1] 2 2
[1] FALSE
D998V8, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    16   0
  RAPGEF6 WILD-TYPE 284   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     16    0
  RAPGEF6 WILD-TYPE  284    8
     clus
vv    RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  NO               16               284
  YES               0                 8
[1] 2 2
[1] FALSE
D998V9, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    13   4
  RAPGEF6 WILD-TYPE 301  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     13    4
  RAPGEF6 WILD-TYPE  301   44
                               clus
vv                              RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RAPGEF6 MUTATED    13   0   0   2
  RAPGEF6 WILD-TYPE 246   3  22  19
D998V10, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               2                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"
D998V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAPGEF6 MUTATED                                  0     1
  RAPGEF6 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RAPGEF6 MUTATED                           2     8
  RAPGEF6 WILD-TYPE                        17   168
D998V12, multiclass
                                  clus
vv                                 RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          8               168
[1] 4 2
[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 = ERCC3 MUTATION ANALYSIS
D999V1, survival
                 sevent
clus2               0   1
  ERCC3 MUTATED    11   6
  ERCC3 WILD-TYPE 266  72
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             17             338 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              6              72 
$`ERCC3 MUTATED`
TCGA-AA-3516 TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3845 
       13.02        31.63        22.06         3.02        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 
       12.39        13.35       140.38         6.18        46.75 

$`ERCC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 
       36.00        13.78 

  ERCC3 MUTATED ERCC3 WILD-TYPE 
              0               0 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
         140.38          148.01 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
          22.06           22.06 
[1] "0.0 - 140.4 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D999V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC3 MUTATED         0        0        1        10         2         0
  ERCC3 WILD-TYPE      64        1       25        98         6         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        17          6         40         32       35        12
                 vv
clus              STAGE IVB
  ERCC3 MUTATED           0
  ERCC3 WILD-TYPE         1
D999V3, multiclass
            clus
vv           ERCC3 MUTATED ERCC3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ERCC3 MUTATED     0   0  16   3
  ERCC3 WILD-TYPE   9  67 233  38
D999V4, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            16             233
  T4             3              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
  ERCC3 MUTATED    13   4   2
  ERCC3 WILD-TYPE 207  77  64
D999V5, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  N0            13             207
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V6, binary
                 cls
clus                0   1
  ERCC3 MUTATED    18   0
  ERCC3 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     18    0
  ERCC3 WILD-TYPE  267   48
   clus
vv  ERCC3 MUTATED ERCC3 WILD-TYPE
  0            18             267
  1             0              48
[1] 2 2
[1] FALSE
D999V7, binary
                 cls
clus                0   1
  ERCC3 MUTATED    13   6
  ERCC3 WILD-TYPE 157 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     13    6
  ERCC3 WILD-TYPE  157  191
        clus
vv       ERCC3 MUTATED ERCC3 WILD-TYPE
  FEMALE            13             157
  MALE               6             191
[1] 2 2
[1] FALSE
D999V8, binary
                 cls
clus                0   1
  ERCC3 MUTATED    15   0
  ERCC3 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     15    0
  ERCC3 WILD-TYPE  285    8
     clus
vv    ERCC3 MUTATED ERCC3 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D999V9, binary
                 cls
clus                0   1
  ERCC3 MUTATED    15   4
  ERCC3 WILD-TYPE 299  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     15    4
  ERCC3 WILD-TYPE  299   44
                               clus
vv                              ERCC3 MUTATED ERCC3 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERCC3 MUTATED    13   1   0   2
  ERCC3 WILD-TYPE 246   2  22  19
D999V10, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  R0            13             246
  R1             1               2
  R2             0              22
  RX             2              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"
D999V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC3 MUTATED                                  0     1
  ERCC3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERCC3 MUTATED                           2     9
  ERCC3 WILD-TYPE                        17   167
D999V12, multiclass
                                  clus
vv                                 ERCC3 MUTATED ERCC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(1000) Variable = GABPA MUTATION ANALYSIS
D1000V1, survival
                 sevent
clus2               0   1
  GABPA MUTATED     8   3
  GABPA WILD-TYPE 269  75
  GABPA MUTATED GABPA WILD-TYPE 
             11             344 
  GABPA MUTATED GABPA WILD-TYPE 
              3              75 
$`GABPA MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-6142 TCGA-AA-A00N 
        0.92        24.00        25.08        26.17        25.08         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-6161 TCGA-D5-6533 TCGA-DM-A0XD 
       34.98        83.24        15.02        25.48        24.43 

$`GABPA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6648 
       22.06        32.71        27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GABPA MUTATED GABPA WILD-TYPE 
           0.92            0.00 
  GABPA MUTATED GABPA WILD-TYPE 
          83.24          148.01 
  GABPA MUTATED GABPA WILD-TYPE 
          25.08           21.99 
[1] "0.9 - 83.2 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1000V2, continuous
                 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      63        1       26       104         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GABPA MUTATED           1          0          1          0        0         1
  GABPA WILD-TYPE        17          6         43         33       35        11
                 vv
clus              STAGE IVB
  GABPA MUTATED           0
  GABPA WILD-TYPE         1
D1000V3, multiclass
            clus
vv           GABPA MUTATED GABPA WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  GABPA MUTATED     0   1   7   3
  GABPA WILD-TYPE   9  66 242  38
D1000V4, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             3              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
  GABPA MUTATED     8   3   0
  GABPA WILD-TYPE 212  78  66
D1000V5, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V6, binary
                 cls
clus                0   1
  GABPA MUTATED    10   1
  GABPA WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED     10    1
  GABPA WILD-TYPE  275   47
   clus
vv  GABPA MUTATED GABPA WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1000V7, binary
                 cls
clus                0   1
  GABPA MUTATED     7   4
  GABPA WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      7    4
  GABPA WILD-TYPE  163  193
        clus
vv       GABPA MUTATED GABPA WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D1000V8, binary
                 cls
clus                0   1
  GABPA MUTATED     9   0
  GABPA WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      9    0
  GABPA WILD-TYPE  291    8
     clus
vv    GABPA MUTATED GABPA WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1000V9, binary
                 cls
clus                0   1
  GABPA MUTATED     9   2
  GABPA WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      9    2
  GABPA WILD-TYPE  305   46
                               clus
vv                              GABPA MUTATED GABPA WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GABPA MUTATED     9   0   0   0
  GABPA WILD-TYPE 250   3  22  21
D1000V10, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1000V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABPA MUTATED                                  0     1
  GABPA WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GABPA MUTATED                           0     6
  GABPA WILD-TYPE                        19   170
D1000V12, multiclass
                                  clus
vv                                 GABPA MUTATED GABPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = NXF3 MUTATION ANALYSIS
D1001V1, survival
                sevent
clus2              0   1
  NXF3 MUTATED     6   4
  NXF3 WILD-TYPE 271  74
  NXF3 MUTATED NXF3 WILD-TYPE 
            10            345 
  NXF3 MUTATED NXF3 WILD-TYPE 
             4             74 
$`NXF3 MUTATED`
TCGA-AZ-6608 TCGA-CK-5912 TCGA-A6-6781 TCGA-AA-3821 TCGA-AU-3779 TCGA-CA-6717 
        1.94        49.08        19.66         1.02        14.50        12.76 
TCGA-CK-5913 TCGA-CM-5862 TCGA-DM-A1DB TCGA-G4-6317 
       51.32         5.03        44.32        36.00 

$`NXF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      106.75       100.01         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  NXF3 MUTATED NXF3 WILD-TYPE 
          1.02           0.00 
  NXF3 MUTATED NXF3 WILD-TYPE 
         51.32         148.01 
  NXF3 MUTATED NXF3 WILD-TYPE 
         17.08          22.09 
[1] "1.0 - 51.3 (17.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1001V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NXF3 MUTATED         2        0        0         4         0         0
  NXF3 WILD-TYPE      62        1       26       104         8         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        18          5         44         31       35        11
                vv
clus             STAGE IVB
  NXF3 MUTATED           0
  NXF3 WILD-TYPE         1
D1001V3, multiclass
            clus
vv           NXF3 MUTATED NXF3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             1             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
  NXF3 MUTATED     0   3   6   1
  NXF3 WILD-TYPE   9  64 243  40
D1001V4, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            6            243
  T4            1             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
  NXF3 MUTATED     6   3   1
  NXF3 WILD-TYPE 214  78  65
D1001V5, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  N0            6            214
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V6, binary
                cls
clus               0   1
  NXF3 MUTATED     5   1
  NXF3 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      5    1
  NXF3 WILD-TYPE  280   47
   clus
vv  NXF3 MUTATED NXF3 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D1001V7, binary
                cls
clus               0   1
  NXF3 MUTATED     5   5
  NXF3 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      5    5
  NXF3 WILD-TYPE  165  192
        clus
vv       NXF3 MUTATED NXF3 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D1001V8, binary
                cls
clus               0   1
  NXF3 MUTATED     9   0
  NXF3 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      9    0
  NXF3 WILD-TYPE  291    8
     clus
vv    NXF3 MUTATED NXF3 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1001V9, binary
                cls
clus               0   1
  NXF3 MUTATED     7   3
  NXF3 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      7    3
  NXF3 WILD-TYPE  307   45
                               clus
vv                              NXF3 MUTATED NXF3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NXF3 MUTATED     5   0   0   3
  NXF3 WILD-TYPE 254   3  22  18
D1001V10, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            3             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"
D1001V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NXF3 MUTATED                                  0     1
  NXF3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NXF3 MUTATED                           0     8
  NXF3 WILD-TYPE                        19   168
D1001V12, multiclass
                                  clus
vv                                 NXF3 MUTATED NXF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = LRIG2 MUTATION ANALYSIS
D1002V1, survival
                 sevent
clus2               0   1
  LRIG2 MUTATED     6   3
  LRIG2 WILD-TYPE 271  75
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             346 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              3              75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LRIG2 MUTATED LRIG2 WILD-TYPE 
              0               0 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
          63.98          148.01 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
         17.560          22.225 
[1] "0.0 - 64.0 (17.6)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2"  
D1002V2, continuous
                 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      63        1       25       103         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  LRIG2 MUTATED           0
  LRIG2 WILD-TYPE         1
D1002V3, multiclass
            clus
vv           LRIG2 MUTATED LRIG2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LRIG2 MUTATED     0   1   6   2
  LRIG2 WILD-TYPE   9  66 243  39
D1002V4, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             2              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
  LRIG2 MUTATED     8   1   0
  LRIG2 WILD-TYPE 212  80  66
D1002V5, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V6, binary
                 cls
clus                0   1
  LRIG2 MUTATED     7   0
  LRIG2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      7    0
  LRIG2 WILD-TYPE  278   48
   clus
vv  LRIG2 MUTATED LRIG2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1002V7, binary
                 cls
clus                0   1
  LRIG2 MUTATED     5   4
  LRIG2 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      5    4
  LRIG2 WILD-TYPE  165  193
        clus
vv       LRIG2 MUTATED LRIG2 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1002V8, binary
                 cls
clus                0   1
  LRIG2 MUTATED     8   0
  LRIG2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      8    0
  LRIG2 WILD-TYPE  292    8
     clus
vv    LRIG2 MUTATED LRIG2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1002V9, binary
                 cls
clus                0   1
  LRIG2 MUTATED     8   1
  LRIG2 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      8    1
  LRIG2 WILD-TYPE  306   47
                               clus
vv                              LRIG2 MUTATED LRIG2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LRIG2 MUTATED     7   0   0   1
  LRIG2 WILD-TYPE 252   3  22  20
D1002V10, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1002V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRIG2 MUTATED                                  0     0
  LRIG2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRIG2 MUTATED                           0     6
  LRIG2 WILD-TYPE                        19   170
D1002V12, multiclass
                                  clus
vv                                 LRIG2 MUTATED LRIG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = BRSK1 MUTATION ANALYSIS
D1003V1, survival
                 sevent
clus2               0   1
  BRSK1 MUTATED    10   7
  BRSK1 WILD-TYPE 267  71
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             17             338 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
              7              71 
$`BRSK1 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-G4-6588 TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3663 
        6.05        19.04        26.17        42.90         3.02         6.97 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3848 TCGA-AA-3977 TCGA-AA-A00J 
       26.99        10.06         1.02        10.06        25.02        18.05 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-6676 TCGA-D5-6536 TCGA-G4-6307 
       49.41         6.77        11.08        17.85        55.04 

$`BRSK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3812 
       15.02        11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79        88.21        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  BRSK1 MUTATED BRSK1 WILD-TYPE 
           1.02            0.00 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
          55.04          148.01 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
         17.850          22.225 
[1] "1.0 - 55.0 (17.9)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.6"
D1003V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRSK1 MUTATED         3        0        4         3         1         0
  BRSK1 WILD-TYPE      61        1       22       105         7         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        17          6         42         32       34        12
                 vv
clus              STAGE IVB
  BRSK1 MUTATED           0
  BRSK1 WILD-TYPE         1
D1003V3, multiclass
            clus
vv           BRSK1 MUTATED BRSK1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  BRSK1 MUTATED     0   4  10   3
  BRSK1 WILD-TYPE   9  63 239  38
D1003V4, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            10             239
  T4             3              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
  BRSK1 MUTATED    12   2   3
  BRSK1 WILD-TYPE 208  79  63
D1003V5, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             3              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"
D1003V6, binary
                 cls
clus                0   1
  BRSK1 MUTATED    13   1
  BRSK1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     13    1
  BRSK1 WILD-TYPE  272   47
   clus
vv  BRSK1 MUTATED BRSK1 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D1003V7, binary
                 cls
clus                0   1
  BRSK1 MUTATED    10   7
  BRSK1 WILD-TYPE 160 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     10    7
  BRSK1 WILD-TYPE  160  190
        clus
vv       BRSK1 MUTATED BRSK1 WILD-TYPE
  FEMALE            10             160
  MALE               7             190
[1] 2 2
[1] FALSE
D1003V8, binary
                 cls
clus                0   1
  BRSK1 MUTATED    17   0
  BRSK1 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     17    0
  BRSK1 WILD-TYPE  283    8
     clus
vv    BRSK1 MUTATED BRSK1 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D1003V9, binary
                 cls
clus                0   1
  BRSK1 MUTATED    15   2
  BRSK1 WILD-TYPE 299  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     15    2
  BRSK1 WILD-TYPE  299   46
                               clus
vv                              BRSK1 MUTATED BRSK1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRSK1 MUTATED    13   0   1   0
  BRSK1 WILD-TYPE 246   3  21  21
D1003V10, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             1              21
  RX             0              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"
D1003V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRSK1 MUTATED                                  0     0
  BRSK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRSK1 MUTATED                           0     7
  BRSK1 WILD-TYPE                        19   169
D1003V12, multiclass
                                  clus
vv                                 BRSK1 MUTATED BRSK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = E2F5 MUTATION ANALYSIS
D1004V1, survival
                sevent
clus2              0   1
  E2F5 MUTATED     6   0
  E2F5 WILD-TYPE 271  78
  E2F5 MUTATED E2F5 WILD-TYPE 
             6            349 
  E2F5 MUTATED E2F5 WILD-TYPE 
             0             78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.06 
[1] "12.2 - 58.4 (25.4)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D1004V2, continuous
                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      63        1       26       104         7         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        18          6         44         33       34        12
                vv
clus             STAGE IVB
  E2F5 MUTATED           0
  E2F5 WILD-TYPE         1
D1004V3, multiclass
            clus
vv           E2F5 MUTATED E2F5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  E2F5 MUTATED     0   1   4   2
  E2F5 WILD-TYPE   9  66 245  39
D1004V4, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            2             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
  E2F5 MUTATED     6   1   0
  E2F5 WILD-TYPE 214  80  66
D1004V5, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V6, binary
                cls
clus               0   1
  E2F5 MUTATED     6   1
  E2F5 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      6    1
  E2F5 WILD-TYPE  279   47
   clus
vv  E2F5 MUTATED E2F5 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D1004V7, binary
                cls
clus               0   1
  E2F5 MUTATED     2   5
  E2F5 WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      2    5
  E2F5 WILD-TYPE  168  192
        clus
vv       E2F5 MUTATED E2F5 WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D1004V8, binary
                cls
clus               0   1
  E2F5 MUTATED     6   0
  E2F5 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      6    0
  E2F5 WILD-TYPE  294    8
     clus
vv    E2F5 MUTATED E2F5 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1004V9, binary
                cls
clus               0   1
  E2F5 MUTATED     4   3
  E2F5 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      4    3
  E2F5 WILD-TYPE  310   45
                               clus
vv                              E2F5 MUTATED E2F5 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  E2F5 MUTATED     4   0   1   2
  E2F5 WILD-TYPE 255   3  21  19
D1004V10, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            1             21
  RX            2             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"
D1004V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  E2F5 MUTATED                                  0     2
  E2F5 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  E2F5 MUTATED                           0     3
  E2F5 WILD-TYPE                        19   173
D1004V12, multiclass
                                  clus
vv                                 E2F5 MUTATED E2F5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = SEC31A MUTATION ANALYSIS
D1005V1, survival
                  sevent
clus2                0   1
  SEC31A MUTATED    10   3
  SEC31A WILD-TYPE 267  75
  SEC31A MUTATED SEC31A WILD-TYPE 
              13              342 
  SEC31A MUTATED SEC31A WILD-TYPE 
               3               75 
$`SEC31A MUTATED`
TCGA-AA-3543 TCGA-AA-3662 TCGA-AD-6895 TCGA-A6-5665 TCGA-AA-3710 TCGA-AA-3819 
        0.99         6.05        25.08        22.06        26.99        25.02 
TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6167 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6309 
       83.24        12.76        14.99         6.18        35.31        85.48 
TCGA-G4-6626 
       46.75 

$`SEC31A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
        5.03        10.06        35.05        33.04         0.99         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 

  SEC31A MUTATED SEC31A WILD-TYPE 
            0.99             0.00 
  SEC31A MUTATED SEC31A WILD-TYPE 
           85.48           148.01 
  SEC31A MUTATED SEC31A WILD-TYPE 
           25.02            22.01 
[1] "1.0 - 85.5 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1005V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEC31A MUTATED         2        0        0         7         0         0
  SEC31A WILD-TYPE      62        1       26       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC31A MUTATED           0          0          2          1        1
  SEC31A WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  SEC31A MUTATED           0         0
  SEC31A WILD-TYPE        12         1
D1005V3, multiclass
            clus
vv           SEC31A MUTATED SEC31A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  SEC31A MUTATED     0   2  10   1
  SEC31A WILD-TYPE   9  65 239  40
D1005V4, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              1               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
  SEC31A MUTATED     9   2   2
  SEC31A WILD-TYPE 211  79  64
D1005V5, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  N0              9              211
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V6, binary
                  cls
clus                 0   1
  SEC31A MUTATED    12   1
  SEC31A WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     12    1
  SEC31A WILD-TYPE  273   47
   clus
vv  SEC31A MUTATED SEC31A WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D1005V7, binary
                  cls
clus                 0   1
  SEC31A MUTATED     7   6
  SEC31A WILD-TYPE 163 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      7    6
  SEC31A WILD-TYPE  163  191
        clus
vv       SEC31A MUTATED SEC31A WILD-TYPE
  FEMALE              7              163
  MALE                6              191
[1] 2 2
[1] FALSE
D1005V8, binary
                  cls
clus                 0   1
  SEC31A MUTATED    13   0
  SEC31A WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     13    0
  SEC31A WILD-TYPE  287    8
     clus
vv    SEC31A MUTATED SEC31A WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1005V9, binary
                  cls
clus                 0   1
  SEC31A MUTATED    10   3
  SEC31A WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     10    3
  SEC31A WILD-TYPE  304   45
                               clus
vv                              SEC31A MUTATED SEC31A WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SEC31A MUTATED    11   0   1   1
  SEC31A WILD-TYPE 248   3  21  20
D1005V10, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  R0             11              248
  R1              0                3
  R2              1               21
  RX              1               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"
D1005V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC31A MUTATED                                  0     2
  SEC31A WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SEC31A MUTATED                           2     5
  SEC31A WILD-TYPE                        17   171
D1005V12, multiclass
                                  clus
vv                                 SEC31A MUTATED SEC31A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         5              171
[1] 4 2
[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 = CTSZ MUTATION ANALYSIS
D1006V1, survival
                sevent
clus2              0   1
  CTSZ MUTATED     4   2
  CTSZ WILD-TYPE 273  76
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            349 
  CTSZ MUTATED CTSZ WILD-TYPE 
             2             76 
$`CTSZ MUTATED`
TCGA-AA-3715 TCGA-A6-6652 TCGA-AA-3968 TCGA-D5-6932 TCGA-F4-6856 TCGA-G4-6303 
       19.04        24.69        21.99        11.38        35.31        65.85 

$`CTSZ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
        2.01        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        47.41       133.18        74.56        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-G4-6626 
       46.75 

  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          22.06 
[1] "11.4 - 65.8 (23.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1006V2, continuous
                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      62        1       25       107         8         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        18          6         44         33       34        11
                vv
clus             STAGE IVB
  CTSZ MUTATED           0
  CTSZ WILD-TYPE         1
D1006V3, multiclass
            clus
vv           CTSZ MUTATED CTSZ WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  CTSZ MUTATED     0   2   4   0
  CTSZ WILD-TYPE   9  65 245  41
D1006V4, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  T1            0              9
  T2            2             65
  T3            4            245
  T4            0             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
  CTSZ MUTATED     5   1   0
  CTSZ WILD-TYPE 215  80  66
D1006V5, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  N0            5            215
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V6, binary
                cls
clus               0   1
  CTSZ MUTATED     4   2
  CTSZ WILD-TYPE 281  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      4    2
  CTSZ WILD-TYPE  281   46
   clus
vv  CTSZ MUTATED CTSZ WILD-TYPE
  0            4            281
  1            2             46
[1] 2 2
[1] FALSE
D1006V7, binary
                cls
clus               0   1
  CTSZ MUTATED     2   4
  CTSZ WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      2    4
  CTSZ WILD-TYPE  168  193
        clus
vv       CTSZ MUTATED CTSZ WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1006V8, binary
                cls
clus               0   1
  CTSZ MUTATED     6   0
  CTSZ WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      6    0
  CTSZ WILD-TYPE  294    8
     clus
vv    CTSZ MUTATED CTSZ WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1006V9, binary
                cls
clus               0   1
  CTSZ MUTATED     5   1
  CTSZ WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      5    1
  CTSZ WILD-TYPE  309   47
                               clus
vv                              CTSZ MUTATED CTSZ WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTSZ MUTATED     5   0   0   0
  CTSZ WILD-TYPE 254   3  22  21
D1006V10, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1006V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTSZ MUTATED                                  0     0
  CTSZ WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTSZ MUTATED                           1     3
  CTSZ WILD-TYPE                        18   173
D1006V12, multiclass
                                  clus
vv                                 CTSZ MUTATED CTSZ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = NUFIP1 MUTATION ANALYSIS
D1007V1, survival
                  sevent
clus2                0   1
  NUFIP1 MUTATED     7   0
  NUFIP1 WILD-TYPE 270  78
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               7              348 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               0               78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
            6.97             0.00 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
           63.98           148.01 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
          34.980           22.045 
[1] "7.0 - 64.0 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9400000"
D1007V2, continuous
                  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      64        1       23       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP1 MUTATED           0          0          0          0        0
  NUFIP1 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  NUFIP1 MUTATED           0         0
  NUFIP1 WILD-TYPE        12         1
D1007V3, multiclass
            clus
vv           NUFIP1 MUTATED NUFIP1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  NUFIP1 MUTATED     0   0   6   2
  NUFIP1 WILD-TYPE   9  67 243  39
D1007V4, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              2               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
  NUFIP1 MUTATED     8   0   0
  NUFIP1 WILD-TYPE 212  81  66
D1007V5, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V6, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     6   0
  NUFIP1 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      6    0
  NUFIP1 WILD-TYPE  279   48
   clus
vv  NUFIP1 MUTATED NUFIP1 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1007V7, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     3   5
  NUFIP1 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      3    5
  NUFIP1 WILD-TYPE  167  192
        clus
vv       NUFIP1 MUTATED NUFIP1 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D1007V8, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     7   0
  NUFIP1 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      7    0
  NUFIP1 WILD-TYPE  293    8
     clus
vv    NUFIP1 MUTATED NUFIP1 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1007V9, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     6   2
  NUFIP1 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      6    2
  NUFIP1 WILD-TYPE  308   46
                               clus
vv                              NUFIP1 MUTATED NUFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUFIP1 MUTATED     5   0   0   2
  NUFIP1 WILD-TYPE 254   3  22  19
D1007V10, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D1007V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUFIP1 MUTATED                                  0     1
  NUFIP1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUFIP1 MUTATED                           0     3
  NUFIP1 WILD-TYPE                        19   173
D1007V12, multiclass
                                  clus
vv                                 NUFIP1 MUTATED NUFIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = OR5H15 MUTATION ANALYSIS
D1008V1, survival
                  sevent
clus2                0   1
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 272  78
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               5              350 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               0               78 
$`OR5H15 MUTATED`
TCGA-A6-5659 TCGA-CM-4744 TCGA-CM-5349 TCGA-CM-5861 TCGA-F4-6569 
       30.44        20.02        30.08        15.02        35.74 

$`OR5H15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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           22.045 
[1] "15.0 - 35.7 (30.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1008V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5H15 MUTATED         3        0        0         2         0         0
  OR5H15 WILD-TYPE      61        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5H15 MUTATED           0          0          0          0        0
  OR5H15 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR5H15 MUTATED           0         0
  OR5H15 WILD-TYPE        12         1
D1008V3, multiclass
            clus
vv           OR5H15 MUTATED OR5H15 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  OR5H15 MUTATED     0   3   2   0
  OR5H15 WILD-TYPE   9  64 247  41
D1008V4, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              2              247
  T4              0               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
  OR5H15 MUTATED     5   0   0
  OR5H15 WILD-TYPE 215  81  66
D1008V5, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V6, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      5    0
  OR5H15 WILD-TYPE  280   48
   clus
vv  OR5H15 MUTATED OR5H15 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1008V7, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     2   3
  OR5H15 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      2    3
  OR5H15 WILD-TYPE  168  194
        clus
vv       OR5H15 MUTATED OR5H15 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D1008V8, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      5    0
  OR5H15 WILD-TYPE  295    8
     clus
vv    OR5H15 MUTATED OR5H15 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1008V9, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      5    0
  OR5H15 WILD-TYPE  309   48
                               clus
vv                              OR5H15 MUTATED OR5H15 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR5H15 MUTATED     5   0   0   0
  OR5H15 WILD-TYPE 254   3  22  21
D1008V10, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1008V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5H15 MUTATED                                  0     0
  OR5H15 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR5H15 MUTATED                           0     5
  OR5H15 WILD-TYPE                        19   171
D1008V12, multiclass
                                  clus
vv                                 OR5H15 MUTATED OR5H15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = TPR MUTATION ANALYSIS
D1009V1, survival
               sevent
clus2             0   1
  TPR MUTATED    20   3
  TPR WILD-TYPE 257  75
  TPR MUTATED TPR WILD-TYPE 
           23           332 
  TPR MUTATED TPR WILD-TYPE 
            3            75 
$`TPR MUTATED`
TCGA-AA-3496 TCGA-AZ-4681 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 
        1.02       106.75        32.71         8.38        19.66         3.02 
TCGA-AA-3679 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3966 
       15.02        26.99        10.06        53.00        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-5254 TCGA-CA-6717 
       25.02         4.01        34.98        35.01        12.69        12.76 
TCGA-CM-4746 TCGA-CM-5861 TCGA-DM-A28H TCGA-G4-6299 TCGA-G4-6309 
       37.02        15.02       117.07        74.56        85.48 

$`TPR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        22.06        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3815 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TPR MUTATED TPR WILD-TYPE 
         1.02          0.00 
  TPR MUTATED TPR WILD-TYPE 
       117.07        148.01 
  TPR MUTATED TPR WILD-TYPE 
       24.000        22.045 
[1] "1.0 - 117.1 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1009V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPR MUTATED         1        0        3         8         2         1
  TPR WILD-TYPE      63        1       23       100         6         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        16          6         43         30       34        11
               vv
clus            STAGE IVB
  TPR MUTATED           0
  TPR WILD-TYPE         1
D1009V3, multiclass
            clus
vv           TPR MUTATED TPR WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            8           100
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           3            30
  STAGE IV             1            34
  STAGE IVA            1            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
  TPR MUTATED     0   2  17   5
  TPR WILD-TYPE   9  65 232  36
D1009V4, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  T1           0             9
  T2           2            65
  T3          17           232
  T4           5            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
  TPR MUTATED    16   3   5
  TPR WILD-TYPE 204  78  61
D1009V5, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  N0          16           204
  N1           3            78
  N2           5            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V6, binary
               cls
clus              0   1
  TPR MUTATED    20   2
  TPR WILD-TYPE 265  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     20    2
  TPR WILD-TYPE  265   46
   clus
vv  TPR MUTATED TPR WILD-TYPE
  0          20           265
  1           2            46
[1] 2 2
[1] FALSE
D1009V7, binary
               cls
clus              0   1
  TPR MUTATED    12  12
  TPR WILD-TYPE 158 185
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     12   12
  TPR WILD-TYPE  158  185
        clus
vv       TPR MUTATED TPR WILD-TYPE
  FEMALE          12           158
  MALE            12           185
[1] 2 2
[1] FALSE
D1009V8, binary
               cls
clus              0   1
  TPR MUTATED    18   1
  TPR WILD-TYPE 282   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     18    1
  TPR WILD-TYPE  282    7
     clus
vv    TPR MUTATED TPR WILD-TYPE
  NO           18           282
  YES           1             7
[1] 2 2
[1] FALSE
D1009V9, binary
               cls
clus              0   1
  TPR MUTATED    19   5
  TPR WILD-TYPE 295  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     19    5
  TPR WILD-TYPE  295   43
                               clus
vv                              TPR MUTATED TPR WILD-TYPE
  COLON ADENOCARCINOMA                   19           295
  COLON MUCINOUS ADENOCARCINOMA           5            43
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TPR MUTATED    16   0   1   2
  TPR WILD-TYPE 243   3  21  19
D1009V10, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  R0          16           243
  R1           0             3
  R2           1            21
  RX           2            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"
D1009V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPR MUTATED                                  0     2
  TPR WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TPR MUTATED                           3     6
  TPR WILD-TYPE                        16   170
D1009V12, multiclass
                                  clus
vv                                 TPR MUTATED TPR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  3            16
  WHITE                                      6           170
[1] 4 2
[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 = BAZ2B MUTATION ANALYSIS
D1010V1, survival
                 sevent
clus2               0   1
  BAZ2B MUTATED    11   3
  BAZ2B WILD-TYPE 266  75
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             14             341 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
              3              75 
$`BAZ2B MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AA-3950 TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-5660 
        1.02        19.04        24.00        49.08        26.17        29.19 
TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-A010 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 
       63.98         2.01        34.98        12.36        12.76        10.06 
TCGA-D5-6922 TCGA-DM-A1HB 
       10.13       135.65 

$`BAZ2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  BAZ2B MUTATED BAZ2B WILD-TYPE 
           1.02            0.00 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
         135.65          148.01 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
          21.52           22.06 
[1] "1.0 - 135.7 (21.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1010V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAZ2B MUTATED         1        0        3         6         2         0
  BAZ2B WILD-TYPE      63        1       23       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAZ2B MUTATED           0          1          1          1        0         0
  BAZ2B WILD-TYPE        18          5         43         32       35        12
                 vv
clus              STAGE IVB
  BAZ2B MUTATED           0
  BAZ2B WILD-TYPE         1
D1010V3, multiclass
            clus
vv           BAZ2B MUTATED BAZ2B WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  BAZ2B MUTATED     0   1  12   2
  BAZ2B WILD-TYPE   9  66 237  39
D1010V4, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  T1             0               9
  T2             1              66
  T3            12             237
  T4             2              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
  BAZ2B MUTATED    12   2   1
  BAZ2B WILD-TYPE 208  79  65
D1010V5, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  N0            12             208
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V6, binary
                 cls
clus                0   1
  BAZ2B MUTATED    13   0
  BAZ2B WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     13    0
  BAZ2B WILD-TYPE  272   48
   clus
vv  BAZ2B MUTATED BAZ2B WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D1010V7, binary
                 cls
clus                0   1
  BAZ2B MUTATED     6   9
  BAZ2B WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED      6    9
  BAZ2B WILD-TYPE  164  188
        clus
vv       BAZ2B MUTATED BAZ2B WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D1010V8, binary
                 cls
clus                0   1
  BAZ2B MUTATED    10   1
  BAZ2B WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     10    1
  BAZ2B WILD-TYPE  290    7
     clus
vv    BAZ2B MUTATED BAZ2B WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1010V9, binary
                 cls
clus                0   1
  BAZ2B MUTATED    11   3
  BAZ2B WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     11    3
  BAZ2B WILD-TYPE  303   45
                               clus
vv                              BAZ2B MUTATED BAZ2B WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BAZ2B MUTATED     7   0   0   5
  BAZ2B WILD-TYPE 252   3  22  16
D1010V10, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             5              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"
D1010V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAZ2B MUTATED                                  0     3
  BAZ2B WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BAZ2B MUTATED                           1     5
  BAZ2B WILD-TYPE                        18   171
D1010V12, multiclass
                                  clus
vv                                 BAZ2B MUTATED BAZ2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = USP44 MUTATION ANALYSIS
D1011V1, survival
                 sevent
clus2               0   1
  USP44 MUTATED    11   3
  USP44 WILD-TYPE 266  75
  USP44 MUTATED USP44 WILD-TYPE 
             14             341 
  USP44 MUTATED USP44 WILD-TYPE 
              3              75 
$`USP44 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-G4-6588 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 
        0.92        19.04        26.17        53.00         2.01        25.02 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-5344 TCGA-DM-A1D0 
       38.04         4.01        34.98        83.24        22.03       130.65 
TCGA-DM-A1DA TCGA-F4-6807 
        7.50        43.04 

$`USP44 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C 
      140.38        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-F4-6808 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  USP44 MUTATED USP44 WILD-TYPE 
           0.92            0.00 
  USP44 MUTATED USP44 WILD-TYPE 
         130.65          148.01 
  USP44 MUTATED USP44 WILD-TYPE 
         25.595          21.990 
[1] "0.9 - 130.7 (25.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1011V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP44 MUTATED         0        0        2         6         2         0
  USP44 WILD-TYPE      64        1       24       102         6         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        17          6         43         31       34        12
                 vv
clus              STAGE IVB
  USP44 MUTATED           0
  USP44 WILD-TYPE         1
D1011V3, multiclass
            clus
vv           USP44 MUTATED USP44 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  USP44 MUTATED     0   1  12   3
  USP44 WILD-TYPE   9  66 237  38
D1011V4, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            12             237
  T4             3              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
  USP44 MUTATED    12   2   2
  USP44 WILD-TYPE 208  79  64
D1011V5, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V6, binary
                 cls
clus                0   1
  USP44 MUTATED    14   1
  USP44 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     14    1
  USP44 WILD-TYPE  271   47
   clus
vv  USP44 MUTATED USP44 WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D1011V7, binary
                 cls
clus                0   1
  USP44 MUTATED    10   6
  USP44 WILD-TYPE 160 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     10    6
  USP44 WILD-TYPE  160  191
        clus
vv       USP44 MUTATED USP44 WILD-TYPE
  FEMALE            10             160
  MALE               6             191
[1] 2 2
[1] FALSE
D1011V8, binary
                 cls
clus                0   1
  USP44 MUTATED     9   1
  USP44 WILD-TYPE 291   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED      9    1
  USP44 WILD-TYPE  291    7
     clus
vv    USP44 MUTATED USP44 WILD-TYPE
  NO              9             291
  YES             1               7
[1] 2 2
[1] FALSE
D1011V9, binary
                 cls
clus                0   1
  USP44 MUTATED    14   2
  USP44 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     14    2
  USP44 WILD-TYPE  300   46
                               clus
vv                              USP44 MUTATED USP44 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP44 MUTATED    11   0   1   0
  USP44 WILD-TYPE 248   3  21  21
D1011V10, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             0              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"
D1011V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP44 MUTATED                                  0     1
  USP44 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP44 MUTATED                           0     5
  USP44 WILD-TYPE                        19   171
D1011V12, multiclass
                                  clus
vv                                 USP44 MUTATED USP44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = EIF4G2 MUTATION ANALYSIS
D1012V1, survival
                  sevent
clus2                0   1
  EIF4G2 MUTATED     8   5
  EIF4G2 WILD-TYPE 269  73
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              13              342 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
               5               73 
$`EIF4G2 MUTATED`
TCGA-G4-6588 TCGA-A6-5657 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-A00N 
       26.17        31.63        10.06        33.01        26.01         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CK-5916 TCGA-CM-5862 TCGA-DM-A1D8 
       34.98        58.39        12.59        21.14         5.03        12.59 
TCGA-DM-A28K 
       98.24 

$`EIF4G2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
            4.01             0.00 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
           98.24           148.01 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
          26.010           22.045 
[1] "4.0 - 98.2 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1012V2, continuous
                  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      63        1       26       103         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G2 MUTATED           1          0          2          0        0
  EIF4G2 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  EIF4G2 MUTATED           1         0
  EIF4G2 WILD-TYPE        11         1
D1012V3, multiclass
            clus
vv           EIF4G2 MUTATED EIF4G2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  EIF4G2 MUTATED     1   0  10   4
  EIF4G2 WILD-TYPE   8  67 239  37
D1012V4, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  T1              1                8
  T2              0               67
  T3             10              239
  T4              4               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
  EIF4G2 MUTATED    10   4   1
  EIF4G2 WILD-TYPE 210  77  65
D1012V5, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  N0             10              210
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1012V6, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    12   1
  EIF4G2 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     12    1
  EIF4G2 WILD-TYPE  273   47
   clus
vv  EIF4G2 MUTATED EIF4G2 WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D1012V7, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED     9   6
  EIF4G2 WILD-TYPE 161 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED      9    6
  EIF4G2 WILD-TYPE  161  191
        clus
vv       EIF4G2 MUTATED EIF4G2 WILD-TYPE
  FEMALE              9              161
  MALE                6              191
[1] 2 2
[1] FALSE
D1012V8, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    10   0
  EIF4G2 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     10    0
  EIF4G2 WILD-TYPE  290    8
     clus
vv    EIF4G2 MUTATED EIF4G2 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D1012V9, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    11   4
  EIF4G2 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     11    4
  EIF4G2 WILD-TYPE  303   44
                               clus
vv                              EIF4G2 MUTATED EIF4G2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF4G2 MUTATED    11   0   0   2
  EIF4G2 WILD-TYPE 248   3  22  19
D1012V10, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              2               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"
D1012V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4G2 MUTATED                                  0     1
  EIF4G2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF4G2 MUTATED                           1     7
  EIF4G2 WILD-TYPE                        18   169
D1012V12, multiclass
                                  clus
vv                                 EIF4G2 MUTATED EIF4G2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = EYS MUTATION ANALYSIS
D1013V1, survival
               sevent
clus2             0   1
  EYS MUTATED    30   8
  EYS WILD-TYPE 247  70
  EYS MUTATED EYS WILD-TYPE 
           38           317 
  EYS MUTATED EYS WILD-TYPE 
            8            70 
$`EYS MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-6141 
        1.02        13.02        10.88        79.69        32.75         8.38 
TCGA-A6-6782 TCGA-AA-3511 TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3861 TCGA-AA-3930 
       20.28         6.97        33.04        17.98        30.05         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A01Q TCGA-AD-6899 
       25.02        27.02        18.05         4.01         1.02         5.79 
TCGA-AD-6963 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 
       27.42        21.44        58.39        12.76        10.06        51.32 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       23.05        22.98        15.02        13.05        11.08        11.01 
TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A1DA 
       25.48        16.14         9.44        11.64        12.00         7.50 
TCGA-DM-A28E TCGA-F4-6570 
      119.93         6.18 

$`EYS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5665 
       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-A6-6651 
       32.71        27.09        22.52        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        19.66         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        27.02        27.02         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        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        21.99        21.14        82.95         2.01 
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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        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 
       54.61        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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        13.41        13.35        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  EYS MUTATED EYS WILD-TYPE 
         1.02          0.00 
  EYS MUTATED EYS WILD-TYPE 
       119.93        148.01 
  EYS MUTATED EYS WILD-TYPE 
       14.035        23.010 
[1] "1.0 - 119.9 (14.0)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1.2"
D1013V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EYS MUTATED         3        0        3        15         3         0
  EYS WILD-TYPE      61        1       23        93         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EYS MUTATED           1          0          3          3        1         1
  EYS WILD-TYPE        17          6         41         30       34        11
               vv
clus            STAGE IVB
  EYS MUTATED           1
  EYS WILD-TYPE         0
D1013V3, multiclass
            clus
vv           EYS MUTATED EYS WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA           15            93
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           3            41
  STAGE IIIC           3            30
  STAGE IV             1            34
  STAGE IVA            1            11
  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   4  24  10
  EYS WILD-TYPE   9  63 225  31
D1013V4, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  T1           0             9
  T2           4            63
  T3          24           225
  T4          10            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
  EYS MUTATED    27   4   7
  EYS WILD-TYPE 193  77  59
D1013V5, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  N0          27           193
  N1           4            77
  N2           7            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V6, binary
               cls
clus              0   1
  EYS MUTATED    28   3
  EYS WILD-TYPE 257  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     28    3
  EYS WILD-TYPE  257   45
   clus
vv  EYS MUTATED EYS WILD-TYPE
  0          28           257
  1           3            45
[1] 2 2
[1] FALSE
D1013V7, binary
               cls
clus              0   1
  EYS MUTATED    12  26
  EYS WILD-TYPE 158 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     12   26
  EYS WILD-TYPE  158  171
        clus
vv       EYS MUTATED EYS WILD-TYPE
  FEMALE          12           158
  MALE            26           171
[1] 2 2
[1] FALSE
D1013V8, binary
               cls
clus              0   1
  EYS MUTATED    33   0
  EYS WILD-TYPE 267   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     33    0
  EYS WILD-TYPE  267    8
     clus
vv    EYS MUTATED EYS WILD-TYPE
  NO           33           267
  YES           0             8
[1] 2 2
[1] FALSE
D1013V9, binary
               cls
clus              0   1
  EYS MUTATED    29   9
  EYS WILD-TYPE 285  39
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     29    9
  EYS WILD-TYPE  285   39
                               clus
vv                              EYS MUTATED EYS WILD-TYPE
  COLON ADENOCARCINOMA                   29           285
  COLON MUCINOUS ADENOCARCINOMA           9            39
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  EYS MUTATED    25   0   1   3
  EYS WILD-TYPE 234   3  21  18
D1013V10, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  R0          25           234
  R1           0             3
  R2           1            21
  RX           3            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"
D1013V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EYS MUTATED                                  0     2
  EYS WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  EYS MUTATED                           2    22
  EYS WILD-TYPE                        17   154
D1013V12, multiclass
                                  clus
vv                                 EYS MUTATED EYS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                     22           154
[1] 4 2
[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 = ST8SIA6 MUTATION ANALYSIS
D1014V1, survival
                   sevent
clus2                 0   1
  ST8SIA6 MUTATED     7   2
  ST8SIA6 WILD-TYPE 270  76
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                9               346 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                2                76 
$`ST8SIA6 MUTATED`
TCGA-AD-6895 TCGA-AD-6964 TCGA-AA-3492 TCGA-AA-A00E TCGA-AA-A010 TCGA-AZ-4315 
       25.08        10.88         3.02        30.02        34.98        58.39 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 
       12.76        51.32       124.27 

$`ST8SIA6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        21.37        15.52       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95         2.01        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
             3.02              0.00 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
           124.27            148.01 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
            30.02             22.01 
[1] "3.0 - 124.3 (30.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1014V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST8SIA6 MUTATED         1        0        1         4         2         0
  ST8SIA6 WILD-TYPE      63        1       25       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST8SIA6 MUTATED           0          0          1          0        0
  ST8SIA6 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ST8SIA6 MUTATED           0         0
  ST8SIA6 WILD-TYPE        12         1
D1014V3, multiclass
            clus
vv           ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ST8SIA6 MUTATED     0   1   6   3
  ST8SIA6 WILD-TYPE   9  66 243  38
D1014V4, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               3                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
  ST8SIA6 MUTATED     8   1   1
  ST8SIA6 WILD-TYPE 212  80  65
D1014V5, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  N0               8               212
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V6, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     6   0
  ST8SIA6 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      6    0
  ST8SIA6 WILD-TYPE  279   48
   clus
vv  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1014V7, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     5   5
  ST8SIA6 WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      5    5
  ST8SIA6 WILD-TYPE  165  192
        clus
vv       ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D1014V8, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     9   0
  ST8SIA6 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      9    0
  ST8SIA6 WILD-TYPE  291    8
     clus
vv    ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D1014V9, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     8   2
  ST8SIA6 WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      8    2
  ST8SIA6 WILD-TYPE  306   46
                               clus
vv                              ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ST8SIA6 MUTATED     5   0   0   4
  ST8SIA6 WILD-TYPE 254   3  22  17
D1014V10, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               4                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"
D1014V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST8SIA6 MUTATED                                  0     1
  ST8SIA6 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ST8SIA6 MUTATED                           0     6
  ST8SIA6 WILD-TYPE                        19   170
D1014V12, multiclass
                                  clus
vv                                 ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = C6ORF222 MUTATION ANALYSIS
D1015V1, survival
                    sevent
clus2                  0   1
  C6ORF222 MUTATED     5   1
  C6ORF222 WILD-TYPE 272  77
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                349 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 1                 77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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             22.030 
[1] "4.0 - 35.0 (23.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1015V2, continuous
                    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      63        1       25       106         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF222 MUTATED           0          0          0          0        0
  C6ORF222 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF222 MUTATED           0         0
  C6ORF222 WILD-TYPE        12         1
D1015V3, multiclass
            clus
vv           C6ORF222 MUTATED C6ORF222 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 2                106
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C6ORF222 MUTATED     0   1   3   2
  C6ORF222 WILD-TYPE   9  66 246  39
D1015V4, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                3                246
  T4                2                 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
  C6ORF222 MUTATED     6   0   0
  C6ORF222 WILD-TYPE 214  81  66
D1015V5, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  N0                6                214
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V6, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     6   0
  C6ORF222 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      6    0
  C6ORF222 WILD-TYPE  279   48
   clus
vv  C6ORF222 MUTATED C6ORF222 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D1015V7, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     3   3
  C6ORF222 WILD-TYPE 167 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      3    3
  C6ORF222 WILD-TYPE  167  194
        clus
vv       C6ORF222 MUTATED C6ORF222 WILD-TYPE
  FEMALE                3                167
  MALE                  3                194
[1] 2 2
[1] FALSE
D1015V8, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     5   0
  C6ORF222 WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      5    0
  C6ORF222 WILD-TYPE  295    8
     clus
vv    C6ORF222 MUTATED C6ORF222 WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D1015V9, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     5   1
  C6ORF222 WILD-TYPE 309  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      5    1
  C6ORF222 WILD-TYPE  309   47
                               clus
vv                              C6ORF222 MUTATED C6ORF222 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C6ORF222 MUTATED     5   0   0   0
  C6ORF222 WILD-TYPE 254   3  22  21
D1015V10, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1015V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF222 MUTATED                                  0     0
  C6ORF222 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF222 MUTATED                           0     2
  C6ORF222 WILD-TYPE                        19   174
D1015V12, multiclass
[1] "Remove cluster labels:" "C6ORF222 MUTATED"      
clus
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5666 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         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-6889         TCGA-AD-6890         TCGA-AD-6899 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6901         TCGA-AD-6963         TCGA-AD-6965 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4682 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         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-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5913         TCGA-CK-5914 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 

Clustering(1016) Variable = TPK1 MUTATION ANALYSIS
D1016V1, survival
                sevent
clus2              0   1
  TPK1 MUTATED     3   2
  TPK1 WILD-TYPE 274  76
  TPK1 MUTATED TPK1 WILD-TYPE 
             5            350 
  TPK1 MUTATED TPK1 WILD-TYPE 
             2             76 
$`TPK1 MUTATED`
TCGA-A6-6138 TCGA-A6-6780 TCGA-AD-6901 TCGA-DM-A28K TCGA-G4-6626 
       22.52        20.12        22.42        98.24        46.75 

$`TPK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 
       36.00        13.78 

  TPK1 MUTATED TPK1 WILD-TYPE 
         20.12           0.00 
  TPK1 MUTATED TPK1 WILD-TYPE 
         98.24         148.01 
  TPK1 MUTATED TPK1 WILD-TYPE 
         22.52          22.01 
[1] "20.1 - 98.2 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1016V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPK1 MUTATED         1        0        0         3         0         0
  TPK1 WILD-TYPE      63        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPK1 MUTATED           0          0          0          0        0         0
  TPK1 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  TPK1 MUTATED           0
  TPK1 WILD-TYPE         1
D1016V3, multiclass
            clus
vv           TPK1 MUTATED TPK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TPK1 MUTATED     0   1   4   0
  TPK1 WILD-TYPE   9  66 245  41
D1016V4, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            0             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
  TPK1 MUTATED     5   0   0
  TPK1 WILD-TYPE 215  81  66
D1016V5, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V6, binary
                cls
clus               0   1
  TPK1 MUTATED     3   0
  TPK1 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      3    0
  TPK1 WILD-TYPE  282   48
   clus
vv  TPK1 MUTATED TPK1 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1016V7, binary
                cls
clus               0   1
  TPK1 MUTATED     0   5
  TPK1 WILD-TYPE 170 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      0    5
  TPK1 WILD-TYPE  170  192
        clus
vv       TPK1 MUTATED TPK1 WILD-TYPE
  FEMALE            0            170
  MALE              5            192
[1] 2 2
[1] FALSE
D1016V8, binary
                cls
clus               0   1
  TPK1 MUTATED     4   0
  TPK1 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      4    0
  TPK1 WILD-TYPE  296    8
     clus
vv    TPK1 MUTATED TPK1 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1016V9, binary
                cls
clus               0   1
  TPK1 MUTATED     3   2
  TPK1 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      3    2
  TPK1 WILD-TYPE  311   46
                               clus
vv                              TPK1 MUTATED TPK1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TPK1 MUTATED     1   0   0   0
  TPK1 WILD-TYPE 258   3  22  21
D1016V10, multiclass
[1] "Remove cluster labels:" "TPK1 MUTATED"          
clus
  TPK1 MUTATED TPK1 WILD-TYPE 
             1            304 
    TCGA-A6-2677     TCGA-AA-3496     TCGA-AA-3520     TCGA-AA-3521 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3527 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3502     TCGA-AA-3510 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3845     TCGA-AA-3846 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3975     TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4682 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6309     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
D1016V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPK1 MUTATED                                  0     0
  TPK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPK1 MUTATED                           0     5
  TPK1 WILD-TYPE                        19   171
D1016V12, multiclass
                                  clus
vv                                 TPK1 MUTATED TPK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = ZNF555 MUTATION ANALYSIS
D1017V1, survival
                  sevent
clus2                0   1
  ZNF555 MUTATED     7   1
  ZNF555 WILD-TYPE 270  77
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               8              347 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               1               77 
$`ZNF555 MUTATED`
TCGA-AA-3715 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3833 TCGA-CK-6747 
       19.04        63.98         1.02        29.95        15.95        82.95 
TCGA-D5-5539 TCGA-G4-6293 
       19.59       133.18 

$`ZNF555 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        3.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02         1.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF555 MUTATED ZNF555 WILD-TYPE 
            1.02             0.00 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
          133.18           148.01 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
           24.77            22.06 
[1] "1.0 - 133.2 (24.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D1017V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF555 MUTATED         0        0        2         4         0         0
  ZNF555 WILD-TYPE      64        1       24       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF555 MUTATED           1          1          0          0        0
  ZNF555 WILD-TYPE        17          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF555 MUTATED           0         0
  ZNF555 WILD-TYPE        12         1
D1017V3, multiclass
            clus
vv           ZNF555 MUTATED ZNF555 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF555 MUTATED     0   0   8   0
  ZNF555 WILD-TYPE   9  67 241  41
D1017V4, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              8              241
  T4              0               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
  ZNF555 MUTATED     6   2   0
  ZNF555 WILD-TYPE 214  79  66
D1017V5, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  N0              6              214
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V6, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     7   0
  ZNF555 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      7    0
  ZNF555 WILD-TYPE  278   48
   clus
vv  ZNF555 MUTATED ZNF555 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1017V7, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     5   3
  ZNF555 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      5    3
  ZNF555 WILD-TYPE  165  194
        clus
vv       ZNF555 MUTATED ZNF555 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1017V8, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     7   0
  ZNF555 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      7    0
  ZNF555 WILD-TYPE  293    8
     clus
vv    ZNF555 MUTATED ZNF555 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1017V9, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     6   2
  ZNF555 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      6    2
  ZNF555 WILD-TYPE  308   46
                               clus
vv                              ZNF555 MUTATED ZNF555 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF555 MUTATED     7   0   0   1
  ZNF555 WILD-TYPE 252   3  22  20
D1017V10, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1017V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF555 MUTATED                                  0     0
  ZNF555 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF555 MUTATED                           0     3
  ZNF555 WILD-TYPE                        19   173
D1017V12, multiclass
                                  clus
vv                                 ZNF555 MUTATED ZNF555 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = CASP1 MUTATION ANALYSIS
D1018V1, survival
                 sevent
clus2               0   1
  CASP1 MUTATED     4   1
  CASP1 WILD-TYPE 273  77
  CASP1 MUTATED CASP1 WILD-TYPE 
              5             350 
  CASP1 MUTATED CASP1 WILD-TYPE 
              1              77 
$`CASP1 MUTATED`
TCGA-G4-6628 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3977 TCGA-CK-4952 
       79.69         6.97        10.06        25.02        15.62 

$`CASP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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          22.075 
[1] "7.0 - 79.7 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1018V2, continuous
                 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      63        1       25       108         7         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        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  CASP1 MUTATED           0
  CASP1 WILD-TYPE         1
D1018V3, multiclass
            clus
vv           CASP1 MUTATED CASP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CASP1 MUTATED     0   2   2   2
  CASP1 WILD-TYPE   9  65 247  39
D1018V4, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             2             247
  T4             2              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
  CASP1 MUTATED     4   0   2
  CASP1 WILD-TYPE 216  81  64
D1018V5, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V6, binary
                 cls
clus                0   1
  CASP1 MUTATED     4   0
  CASP1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      4    0
  CASP1 WILD-TYPE  281   48
   clus
vv  CASP1 MUTATED CASP1 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1018V7, binary
                 cls
clus                0   1
  CASP1 MUTATED     3   3
  CASP1 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      3    3
  CASP1 WILD-TYPE  167  194
        clus
vv       CASP1 MUTATED CASP1 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1018V8, binary
                 cls
clus                0   1
  CASP1 MUTATED     4   0
  CASP1 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      4    0
  CASP1 WILD-TYPE  296    8
     clus
vv    CASP1 MUTATED CASP1 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1018V9, binary
                 cls
clus                0   1
  CASP1 MUTATED     5   1
  CASP1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      5    1
  CASP1 WILD-TYPE  309   47
                               clus
vv                              CASP1 MUTATED CASP1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP1 MUTATED     3   0   0   2
  CASP1 WILD-TYPE 256   3  22  19
D1018V10, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             2              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"
D1018V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP1 MUTATED                                  0     0
  CASP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP1 MUTATED                           0     3
  CASP1 WILD-TYPE                        19   173
D1018V12, multiclass
                                  clus
vv                                 CASP1 MUTATED CASP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = IFNA2 MUTATION ANALYSIS
D1019V1, survival
                 sevent
clus2               0   1
  IFNA2 MUTATED     7   2
  IFNA2 WILD-TYPE 270  76
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              9             346 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              2              76 
$`IFNA2 MUTATED`
TCGA-AA-3672 TCGA-A6-2676 TCGA-AA-A00N TCGA-AU-3779 TCGA-CM-6161 TCGA-CM-6171 
        0.92        42.90         4.01        14.50        15.02        14.04 
TCGA-D5-6930 TCGA-F4-6806 TCGA-F4-6856 
       13.35        41.42        35.31 

$`IFNA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  IFNA2 MUTATED IFNA2 WILD-TYPE 
           0.92            0.00 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
          42.90          148.01 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
          14.50           22.09 
[1] "0.9 - 42.9 (14.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1019V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFNA2 MUTATED         4        0        0         2         2         0
  IFNA2 WILD-TYPE      60        1       26       106         6         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  IFNA2 MUTATED           0
  IFNA2 WILD-TYPE         1
D1019V3, multiclass
            clus
vv           IFNA2 MUTATED IFNA2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  IFNA2 MUTATED     0   4   3   2
  IFNA2 WILD-TYPE   9  63 246  39
D1019V4, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             3             246
  T4             2              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
  IFNA2 MUTATED     8   1   0
  IFNA2 WILD-TYPE 212  80  66
D1019V5, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V6, binary
                 cls
clus                0   1
  IFNA2 MUTATED     9   0
  IFNA2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      9    0
  IFNA2 WILD-TYPE  276   48
   clus
vv  IFNA2 MUTATED IFNA2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1019V7, binary
                 cls
clus                0   1
  IFNA2 MUTATED     6   3
  IFNA2 WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      6    3
  IFNA2 WILD-TYPE  164  194
        clus
vv       IFNA2 MUTATED IFNA2 WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D1019V8, binary
                 cls
clus                0   1
  IFNA2 MUTATED     8   0
  IFNA2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      8    0
  IFNA2 WILD-TYPE  292    8
     clus
vv    IFNA2 MUTATED IFNA2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1019V9, binary
                 cls
clus                0   1
  IFNA2 MUTATED     6   3
  IFNA2 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      6    3
  IFNA2 WILD-TYPE  308   45
                               clus
vv                              IFNA2 MUTATED IFNA2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IFNA2 MUTATED     9   0   0   0
  IFNA2 WILD-TYPE 250   3  22  21
D1019V10, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1019V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNA2 MUTATED                                  0     0
  IFNA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFNA2 MUTATED                           0     7
  IFNA2 WILD-TYPE                        19   169
D1019V12, multiclass
                                  clus
vv                                 IFNA2 MUTATED IFNA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = IL1RL1 MUTATION ANALYSIS
D1020V1, survival
                  sevent
clus2                0   1
  IL1RL1 MUTATED    10   3
  IL1RL1 WILD-TYPE 267  75
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              13              342 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
               3               75 
$`IL1RL1 MUTATED`
TCGA-DM-A285 TCGA-A6-5666 TCGA-A6-6782 TCGA-AA-3811 TCGA-AY-6197 TCGA-CA-6717 
        5.88        32.71        20.28        10.06        21.44        12.76 
TCGA-CA-6718 TCGA-CM-6674 TCGA-CM-6677 TCGA-D5-6930 TCGA-F4-6569 TCGA-F4-6856 
       10.06        12.95        11.08        13.35        35.74        35.31 
TCGA-G4-6309 
       85.48 

$`IL1RL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-6678 
       15.02        14.04        11.01        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
            5.88             0.00 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
           85.48           148.01 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
          13.350           22.225 
[1] "5.9 - 85.5 (13.3)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D1020V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL1RL1 MUTATED         2        0        1         6         1         1
  IL1RL1 WILD-TYPE      62        1       25       102         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1RL1 MUTATED           1          0          1          0        1
  IL1RL1 WILD-TYPE        17          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  IL1RL1 MUTATED           0         0
  IL1RL1 WILD-TYPE        12         1
D1020V3, multiclass
            clus
vv           IL1RL1 MUTATED IL1RL1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  IL1RL1 MUTATED     0   2   9   3
  IL1RL1 WILD-TYPE   9  65 240  38
D1020V4, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              9              240
  T4              3               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
  IL1RL1 MUTATED    11   1   2
  IL1RL1 WILD-TYPE 209  80  64
D1020V5, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  N0             11              209
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V6, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    11   1
  IL1RL1 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     11    1
  IL1RL1 WILD-TYPE  274   47
   clus
vv  IL1RL1 MUTATED IL1RL1 WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D1020V7, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED     5   9
  IL1RL1 WILD-TYPE 165 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED      5    9
  IL1RL1 WILD-TYPE  165  188
        clus
vv       IL1RL1 MUTATED IL1RL1 WILD-TYPE
  FEMALE              5              165
  MALE                9              188
[1] 2 2
[1] FALSE
D1020V8, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    12   0
  IL1RL1 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     12    0
  IL1RL1 WILD-TYPE  288    8
     clus
vv    IL1RL1 MUTATED IL1RL1 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1020V9, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    10   4
  IL1RL1 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     10    4
  IL1RL1 WILD-TYPE  304   44
                               clus
vv                              IL1RL1 MUTATED IL1RL1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IL1RL1 MUTATED     9   0   0   2
  IL1RL1 WILD-TYPE 250   3  22  19
D1020V10, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              2               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"
D1020V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL1RL1 MUTATED                                  0     2
  IL1RL1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IL1RL1 MUTATED                           1     9
  IL1RL1 WILD-TYPE                        18   167
D1020V12, multiclass
                                  clus
vv                                 IL1RL1 MUTATED IL1RL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(1021) Variable = UGT1A1 MUTATION ANALYSIS
D1021V1, survival
                  sevent
clus2                0   1
  UGT1A1 MUTATED     4   7
  UGT1A1 WILD-TYPE 273  71
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
              11              344 
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
               7               71 
$`UGT1A1 MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6628 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-A01P 
       19.04       100.01        79.69         6.97        33.01        38.07 
TCGA-AY-4070 TCGA-AZ-6598 TCGA-CM-6161 TCGA-D5-5537 TCGA-D5-6537 
       16.31        49.41        15.02        45.40         4.80 

$`UGT1A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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           22.045 
[1] "4.8 - 100.0 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1021V2, continuous
                  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      62        1       22       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A1 MUTATED           1          0          1          1        0
  UGT1A1 WILD-TYPE        17          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT1A1 MUTATED           0         0
  UGT1A1 WILD-TYPE        12         1
D1021V3, multiclass
            clus
vv           UGT1A1 MUTATED UGT1A1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  UGT1A1 MUTATED     0   2   8   1
  UGT1A1 WILD-TYPE   9  65 241  40
D1021V4, multiclass
    clus
vv   UGT1A1 MUTATED UGT1A1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              8              241
  T4              1               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
  UGT1A1 MUTATED     7   2   2
  UGT1A1 WILD-TYPE 213  79  64
D1021V5, multiclass
    clus
vv   UGT1A1 MUTATED UGT1A1 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V6, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED     8   0
  UGT1A1 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED      8    0
  UGT1A1 WILD-TYPE  277   48
   clus
vv  UGT1A1 MUTATED UGT1A1 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1021V7, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED     5   6
  UGT1A1 WILD-TYPE 165 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED      5    6
  UGT1A1 WILD-TYPE  165  191
        clus
vv       UGT1A1 MUTATED UGT1A1 WILD-TYPE
  FEMALE              5              165
  MALE                6              191
[1] 2 2
[1] FALSE
D1021V8, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED    11   0
  UGT1A1 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED     11    0
  UGT1A1 WILD-TYPE  289    8
     clus
vv    UGT1A1 MUTATED UGT1A1 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1021V9, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED    10   1
  UGT1A1 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED     10    1
  UGT1A1 WILD-TYPE  304   47
                               clus
vv                              UGT1A1 MUTATED UGT1A1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UGT1A1 MUTATED     7   1   0   1
  UGT1A1 WILD-TYPE 252   2  22  20
D1021V10, multiclass
    clus
vv   UGT1A1 MUTATED UGT1A1 WILD-TYPE
  R0              7              252
  R1              1                2
  R2              0               22
  RX              1               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"
D1021V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT1A1 MUTATED                                  0     0
  UGT1A1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT1A1 MUTATED                           1     6
  UGT1A1 WILD-TYPE                        18   170
D1021V12, multiclass
                                  clus
vv                                 UGT1A1 MUTATED UGT1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = PTPRR MUTATION ANALYSIS
D1022V1, survival
                 sevent
clus2               0   1
  PTPRR MUTATED     7   3
  PTPRR WILD-TYPE 270  75
  PTPRR MUTATED PTPRR WILD-TYPE 
             10             345 
  PTPRR MUTATED PTPRR WILD-TYPE 
              3              75 
$`PTPRR MUTATED`
TCGA-AZ-6601 TCGA-A6-6141 TCGA-AA-3663 TCGA-AA-3845 TCGA-AZ-4315 TCGA-AZ-6599 
      100.01         8.38         6.97         0.00        58.39         6.77 
TCGA-CM-4743 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6538 
       23.05        12.00        14.04        17.13 

$`PTPRR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PTPRR MUTATED PTPRR WILD-TYPE 
              0               0 
  PTPRR MUTATED PTPRR WILD-TYPE 
         100.01          148.01 
  PTPRR MUTATED PTPRR WILD-TYPE 
          13.02           22.09 
[1] "0.0 - 100.0 (13.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1022V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRR MUTATED         2        0        2         4         0         0
  PTPRR WILD-TYPE      62        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRR MUTATED           0          0          2          0        0         0
  PTPRR WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  PTPRR MUTATED           0
  PTPRR WILD-TYPE         1
D1022V3, multiclass
            clus
vv           PTPRR MUTATED PTPRR WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PTPRR MUTATED     0   2   8   0
  PTPRR WILD-TYPE   9  65 241  41
D1022V4, multiclass
    clus
vv   PTPRR MUTATED PTPRR WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             0              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
  PTPRR MUTATED     8   1   1
  PTPRR WILD-TYPE 212  80  65
D1022V5, multiclass
    clus
vv   PTPRR MUTATED PTPRR WILD-TYPE
  N0             8             212
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V6, binary
                 cls
clus                0   1
  PTPRR MUTATED     9   0
  PTPRR WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRR MUTATED      9    0
  PTPRR WILD-TYPE  276   48
   clus
vv  PTPRR MUTATED PTPRR WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1022V7, binary
                 cls
clus                0   1
  PTPRR MUTATED     4   6
  PTPRR WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRR MUTATED      4    6
  PTPRR WILD-TYPE  166  191
        clus
vv       PTPRR MUTATED PTPRR WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1022V8, binary
                 cls
clus                0   1
  PTPRR MUTATED     9   0
  PTPRR WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRR MUTATED      9    0
  PTPRR WILD-TYPE  291    8
     clus
vv    PTPRR MUTATED PTPRR WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1022V9, binary
                 cls
clus                0   1
  PTPRR MUTATED     9   1
  PTPRR WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRR MUTATED      9    1
  PTPRR WILD-TYPE  305   47
                               clus
vv                              PTPRR MUTATED PTPRR WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRR MUTATED     7   0   0   0
  PTPRR WILD-TYPE 252   3  22  21
D1022V10, multiclass
    clus
vv   PTPRR MUTATED PTPRR WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1022V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRR MUTATED                                  0     0
  PTPRR WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRR MUTATED                           1     7
  PTPRR WILD-TYPE                        18   169
D1022V12, multiclass
                                  clus
vv                                 PTPRR MUTATED PTPRR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = STK11 MUTATION ANALYSIS
D1023V1, survival
                 sevent
clus2               0   1
  STK11 MUTATED    25   5
  STK11 WILD-TYPE 252  73
  STK11 MUTATED STK11 WILD-TYPE 
             30             325 
  STK11 MUTATED STK11 WILD-TYPE 
              5              73 
$`STK11 MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3713 TCGA-AD-6895 TCGA-AZ-6601 
       14.53         1.02         6.05        19.04        25.08       100.01 
TCGA-G4-6310 TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3660 TCGA-AU-3779 TCGA-AY-5543 
       63.62        35.80        22.06        78.08        14.50        33.01 
TCGA-AY-6197 TCGA-AZ-5407 TCGA-CA-6719 TCGA-CK-4950 TCGA-CM-4743 TCGA-CM-4752 
       21.44        88.21        14.30        85.45        23.05        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6533 
       22.03        22.98        30.08        45.40        19.59        25.48 
TCGA-D5-6923 TCGA-DM-A0XF TCGA-DM-A282 TCGA-G4-6293 TCGA-G4-6315 TCGA-G4-6626 
       12.43        38.20       139.17       133.18        61.91        46.75 

$`STK11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
       10.88       106.75         1.94        49.08         5.88        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        54.61        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         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       135.65        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
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-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 
       13.78 

  STK11 MUTATED STK11 WILD-TYPE 
           1.02            0.00 
  STK11 MUTATED STK11 WILD-TYPE 
         139.17          148.01 
  STK11 MUTATED STK11 WILD-TYPE 
          25.28           21.99 
[1] "1.0 - 139.2 (25.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1023V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK11 MUTATED         3        0        3        12         0         0
  STK11 WILD-TYPE      61        1       23        96         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK11 MUTATED           1          1          5          1        3         1
  STK11 WILD-TYPE        17          5         39         32       32        11
                 vv
clus              STAGE IVB
  STK11 MUTATED           0
  STK11 WILD-TYPE         1
D1023V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             12              96
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              1              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
  STK11 MUTATED     1   2  26   2
  STK11 WILD-TYPE   8  65 223  39
D1023V4, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            26             223
  T4             2              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
  STK11 MUTATED    19   9   3
  STK11 WILD-TYPE 201  72  63
D1023V5, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  N0            19             201
  N1             9              72
  N2             3              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"
D1023V6, binary
                 cls
clus                0   1
  STK11 MUTATED    24   4
  STK11 WILD-TYPE 261  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     24    4
  STK11 WILD-TYPE  261   44
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0            24             261
  1             4              44
[1] 2 2
[1] FALSE
D1023V7, binary
                 cls
clus                0   1
  STK11 MUTATED    15  16
  STK11 WILD-TYPE 155 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     15   16
  STK11 WILD-TYPE  155  181
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE            15             155
  MALE              16             181
[1] 2 2
[1] FALSE
D1023V8, binary
                 cls
clus                0   1
  STK11 MUTATED    25   2
  STK11 WILD-TYPE 275   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     25    2
  STK11 WILD-TYPE  275    6
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO             25             275
  YES             2               6
[1] 2 2
[1] FALSE
D1023V9, binary
                 cls
clus                0   1
  STK11 MUTATED    28   2
  STK11 WILD-TYPE 286  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     28    2
  STK11 WILD-TYPE  286   46
                               clus
vv                              STK11 MUTATED STK11 WILD-TYPE
  COLON ADENOCARCINOMA                     28             286
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK11 MUTATED    20   1   2   3
  STK11 WILD-TYPE 239   2  20  18
D1023V10, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0            20             239
  R1             1               2
  R2             2              20
  RX             3              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"
D1023V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK11 MUTATED                                  0     1
  STK11 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK11 MUTATED                           3    23
  STK11 WILD-TYPE                        16   153
D1023V12, multiclass
                                  clus
vv                                 STK11 MUTATED STK11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       23             153
[1] 4 2
[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 = AGFG2 MUTATION ANALYSIS
D1024V1, survival
                 sevent
clus2               0   1
  AGFG2 MUTATED     6   3
  AGFG2 WILD-TYPE 271  75
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              9             346 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              3              75 
$`AGFG2 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6586 TCGA-AA-3492 TCGA-AA-3518 
       19.04        19.04       100.01        35.80         3.02         1.02 
TCGA-AA-3663 TCGA-AA-3947 TCGA-CA-6717 
        6.97        33.01        12.76 

$`AGFG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.09 
[1] "1.0 - 100.0 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1024V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGFG2 MUTATED         0        0        4         3         1         0
  AGFG2 WILD-TYPE      64        1       22       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGFG2 MUTATED           0          0          0          0        1         0
  AGFG2 WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  AGFG2 MUTATED           0
  AGFG2 WILD-TYPE         1
D1024V3, multiclass
            clus
vv           AGFG2 MUTATED AGFG2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  AGFG2 MUTATED     0   0   8   1
  AGFG2 WILD-TYPE   9  67 241  40
D1024V4, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             8             241
  T4             1              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
  AGFG2 MUTATED     9   0   0
  AGFG2 WILD-TYPE 211  81  66
D1024V5, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  N0             9             211
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V6, binary
                 cls
clus                0   1
  AGFG2 MUTATED     8   1
  AGFG2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      8    1
  AGFG2 WILD-TYPE  277   47
   clus
vv  AGFG2 MUTATED AGFG2 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1024V7, binary
                 cls
clus                0   1
  AGFG2 MUTATED     4   5
  AGFG2 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      4    5
  AGFG2 WILD-TYPE  166  192
        clus
vv       AGFG2 MUTATED AGFG2 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1024V8, binary
                 cls
clus                0   1
  AGFG2 MUTATED     7   1
  AGFG2 WILD-TYPE 293   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      7    1
  AGFG2 WILD-TYPE  293    7
     clus
vv    AGFG2 MUTATED AGFG2 WILD-TYPE
  NO              7             293
  YES             1               7
[1] 2 2
[1] FALSE
D1024V9, binary
                 cls
clus                0   1
  AGFG2 MUTATED     7   2
  AGFG2 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      7    2
  AGFG2 WILD-TYPE  307   46
                               clus
vv                              AGFG2 MUTATED AGFG2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGFG2 MUTATED     6   0   1   1
  AGFG2 WILD-TYPE 253   3  21  20
D1024V10, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             1              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"
D1024V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGFG2 MUTATED                                  0     1
  AGFG2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGFG2 MUTATED                           0     2
  AGFG2 WILD-TYPE                        19   174
D1024V12, multiclass
                                  clus
vv                                 AGFG2 MUTATED AGFG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        2             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(1025) Variable = MFSD9 MUTATION ANALYSIS
D1025V1, survival
                 sevent
clus2               0   1
  MFSD9 MUTATED     8   3
  MFSD9 WILD-TYPE 269  75
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             11             344 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
              3              75 
$`MFSD9 MUTATED`
TCGA-AA-A024 TCGA-G4-6588 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AU-6004 
       39.06        26.17        19.66         3.02         1.02        27.09 
TCGA-CK-6747 TCGA-CM-4743 TCGA-DM-A28F TCGA-DM-A28H TCGA-G4-6299 
       82.95        23.05        35.97       117.07        74.56 

$`MFSD9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MFSD9 MUTATED MFSD9 WILD-TYPE 
           1.02            0.00 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
         117.07          148.01 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
          27.09           21.99 
[1] "1.0 - 117.1 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1025V2, continuous
                 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      63        1       24       103         8         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        18          6         43         30       35        12
                 vv
clus              STAGE IVB
  MFSD9 MUTATED           0
  MFSD9 WILD-TYPE         1
D1025V3, multiclass
            clus
vv           MFSD9 MUTATED MFSD9 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              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
  MFSD9 MUTATED     0   1  10   1
  MFSD9 WILD-TYPE   9  66 239  40
D1025V4, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             1              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
  MFSD9 MUTATED     8   2   2
  MFSD9 WILD-TYPE 212  79  64
D1025V5, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V6, binary
                 cls
clus                0   1
  MFSD9 MUTATED    10   0
  MFSD9 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED     10    0
  MFSD9 WILD-TYPE  275   48
   clus
vv  MFSD9 MUTATED MFSD9 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1025V7, binary
                 cls
clus                0   1
  MFSD9 MUTATED     6   6
  MFSD9 WILD-TYPE 164 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      6    6
  MFSD9 WILD-TYPE  164  191
        clus
vv       MFSD9 MUTATED MFSD9 WILD-TYPE
  FEMALE             6             164
  MALE               6             191
[1] 2 2
[1] FALSE
D1025V8, binary
                 cls
clus                0   1
  MFSD9 MUTATED     7   0
  MFSD9 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      7    0
  MFSD9 WILD-TYPE  293    8
     clus
vv    MFSD9 MUTATED MFSD9 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1025V9, binary
                 cls
clus                0   1
  MFSD9 MUTATED    10   2
  MFSD9 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED     10    2
  MFSD9 WILD-TYPE  304   46
                               clus
vv                              MFSD9 MUTATED MFSD9 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFSD9 MUTATED     9   0   0   1
  MFSD9 WILD-TYPE 250   3  22  20
D1025V10, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D1025V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFSD9 MUTATED                                  0     0
  MFSD9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFSD9 MUTATED                           0     8
  MFSD9 WILD-TYPE                        19   168
D1025V12, multiclass
                                  clus
vv                                 MFSD9 MUTATED MFSD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = C7ORF66 MUTATION ANALYSIS
D1026V1, survival
                   sevent
clus2                 0   1
  C7ORF66 MUTATED     6   0
  C7ORF66 WILD-TYPE 271  78
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                6               349 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                0                78 
$`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 

$`C7ORF66 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       29.03        16.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
            10.26              0.00 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
           135.65            148.01 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
           17.325            22.090 
[1] "10.3 - 135.7 (17.3)" "0.0 - 148.0 (22.1)" 
[1] "hr="     "9300000"
D1026V2, continuous
                   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      62        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF66 MUTATED           0          0          1          2        0
  C7ORF66 WILD-TYPE        18          6         43         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF66 MUTATED           0         0
  C7ORF66 WILD-TYPE        12         1
D1026V3, multiclass
            clus
vv           C7ORF66 MUTATED C7ORF66 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  C7ORF66 MUTATED     0   2   4   1
  C7ORF66 WILD-TYPE   9  65 245  40
D1026V4, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               4               245
  T4               1                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
  C7ORF66 MUTATED     4   2   1
  C7ORF66 WILD-TYPE 216  79  65
D1026V5, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  N0               4               216
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V6, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     6   0
  C7ORF66 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      6    0
  C7ORF66 WILD-TYPE  279   48
   clus
vv  C7ORF66 MUTATED C7ORF66 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1026V7, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     5   2
  C7ORF66 WILD-TYPE 165 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      5    2
  C7ORF66 WILD-TYPE  165  195
        clus
vv       C7ORF66 MUTATED C7ORF66 WILD-TYPE
  FEMALE               5               165
  MALE                 2               195
[1] 2 2
[1] FALSE
D1026V8, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     5   0
  C7ORF66 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      5    0
  C7ORF66 WILD-TYPE  295    8
     clus
vv    C7ORF66 MUTATED C7ORF66 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1026V9, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     4   2
  C7ORF66 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      4    2
  C7ORF66 WILD-TYPE  310   46
                               clus
vv                              C7ORF66 MUTATED C7ORF66 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF66 MUTATED     6   0   0   0
  C7ORF66 WILD-TYPE 253   3  22  21
D1026V10, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               0                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"
D1026V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF66 MUTATED                                  0     0
  C7ORF66 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF66 MUTATED                           1     5
  C7ORF66 WILD-TYPE                        18   171
D1026V12, multiclass
                                  clus
vv                                 C7ORF66 MUTATED C7ORF66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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    11   1
  MCART1 WILD-TYPE 266  77
  MCART1 MUTATED MCART1 WILD-TYPE 
              12              343 
  MCART1 MUTATED MCART1 WILD-TYPE 
               1               77 
$`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 

$`MCART1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MCART1 MUTATED MCART1 WILD-TYPE 
            7.04             0.00 
  MCART1 MUTATED MCART1 WILD-TYPE 
          140.38           148.01 
  MCART1 MUTATED MCART1 WILD-TYPE 
          35.275           21.990 
[1] "7.0 - 140.4 (35.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "5"  
D1027V2, continuous
                  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      61        1       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCART1 MUTATED           0          0          3          0        0
  MCART1 WILD-TYPE        18          6         41         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MCART1 MUTATED           0         0
  MCART1 WILD-TYPE        12         1
D1027V3, multiclass
            clus
vv           MCART1 MUTATED MCART1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MCART1 MUTATED     1   2   8   1
  MCART1 WILD-TYPE   8  65 241  40
D1027V4, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              8              241
  T4              1               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
  MCART1 MUTATED     9   3   0
  MCART1 WILD-TYPE 211  78  66
D1027V5, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  N0              9              211
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V6, binary
                  cls
clus                 0   1
  MCART1 MUTATED    12   0
  MCART1 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED     12    0
  MCART1 WILD-TYPE  273   48
   clus
vv  MCART1 MUTATED MCART1 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1027V7, binary
                  cls
clus                 0   1
  MCART1 MUTATED     7   5
  MCART1 WILD-TYPE 163 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED      7    5
  MCART1 WILD-TYPE  163  192
        clus
vv       MCART1 MUTATED MCART1 WILD-TYPE
  FEMALE              7              163
  MALE                5              192
[1] 2 2
[1] FALSE
D1027V8, binary
                  cls
clus                 0   1
  MCART1 MUTATED    10   0
  MCART1 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED     10    0
  MCART1 WILD-TYPE  290    8
     clus
vv    MCART1 MUTATED MCART1 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D1027V9, binary
                  cls
clus                 0   1
  MCART1 MUTATED     8   4
  MCART1 WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED      8    4
  MCART1 WILD-TYPE  306   44
                               clus
vv                              MCART1 MUTATED MCART1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MCART1 MUTATED     9   1   0   0
  MCART1 WILD-TYPE 250   2  22  21
D1027V10, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  R0              9              250
  R1              1                2
  R2              0               22
  RX              0               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"
D1027V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCART1 MUTATED                                  0     0
  MCART1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MCART1 MUTATED                           4     5
  MCART1 WILD-TYPE                        15   171
D1027V12, multiclass
                                  clus
vv                                 MCART1 MUTATED MCART1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                         5              171
[1] 4 2
[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 = P2RX7 MUTATION ANALYSIS
D1028V1, survival
                 sevent
clus2               0   1
  P2RX7 MUTATED     9   3
  P2RX7 WILD-TYPE 268  75
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             12             343 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
              3              75 
$`P2RX7 MUTATED`
TCGA-A6-4105 TCGA-AD-6895 TCGA-G4-6588 TCGA-AA-3966 TCGA-AA-A02J TCGA-CK-6747 
       14.53        25.08        26.17         2.01         5.03        82.95 
TCGA-CM-5863 TCGA-CM-6165 TCGA-D5-5538 TCGA-D5-6927 TCGA-DM-A1HA TCGA-DM-A28H 
       15.02        16.04        54.61         9.44       131.51       117.07 

$`P2RX7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
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-D5-5539 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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  P2RX7 MUTATED P2RX7 WILD-TYPE 
           2.01            0.00 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
         131.51          148.01 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
          20.56           22.06 
[1] "2.0 - 131.5 (20.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1028V2, continuous
                 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      64        1       26       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  P2RX7 MUTATED           0          0          3          2        1         0
  P2RX7 WILD-TYPE        18          6         41         31       34        12
                 vv
clus              STAGE IVB
  P2RX7 MUTATED           0
  P2RX7 WILD-TYPE         1
D1028V3, multiclass
            clus
vv           P2RX7 MUTATED P2RX7 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  P2RX7 MUTATED     0   0  12   0
  P2RX7 WILD-TYPE   9  67 237  41
D1028V4, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            12             237
  T4             0              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
  P2RX7 MUTATED     7   3   2
  P2RX7 WILD-TYPE 213  78  64
D1028V5, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V6, binary
                 cls
clus                0   1
  P2RX7 MUTATED    10   1
  P2RX7 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED     10    1
  P2RX7 WILD-TYPE  275   47
   clus
vv  P2RX7 MUTATED P2RX7 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1028V7, binary
                 cls
clus                0   1
  P2RX7 MUTATED     6   6
  P2RX7 WILD-TYPE 164 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED      6    6
  P2RX7 WILD-TYPE  164  191
        clus
vv       P2RX7 MUTATED P2RX7 WILD-TYPE
  FEMALE             6             164
  MALE               6             191
[1] 2 2
[1] FALSE
D1028V8, binary
                 cls
clus                0   1
  P2RX7 MUTATED     8   0
  P2RX7 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED      8    0
  P2RX7 WILD-TYPE  292    8
     clus
vv    P2RX7 MUTATED P2RX7 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1028V9, binary
                 cls
clus                0   1
  P2RX7 MUTATED    10   2
  P2RX7 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED     10    2
  P2RX7 WILD-TYPE  304   46
                               clus
vv                              P2RX7 MUTATED P2RX7 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  P2RX7 MUTATED     6   0   1   1
  P2RX7 WILD-TYPE 253   3  21  20
D1028V10, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             1              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"
D1028V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  P2RX7 MUTATED                                  0     0
  P2RX7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  P2RX7 MUTATED                           0    10
  P2RX7 WILD-TYPE                        19   166
D1028V12, multiclass
                                  clus
vv                                 P2RX7 MUTATED P2RX7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1029) Variable = SSX2IP MUTATION ANALYSIS
D1029V1, survival
                  sevent
clus2                0   1
  SSX2IP MUTATED     5   2
  SSX2IP WILD-TYPE 272  76
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               7              348 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               2               76 
$`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 
       19.59 

$`SSX2IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SSX2IP MUTATED SSX2IP WILD-TYPE 
            3.02             0.00 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
           62.79           148.01 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
          20.980           22.075 
[1] "3.0 - 62.8 (21.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1029V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SSX2IP MUTATED         1        0        3         1         1         0
  SSX2IP WILD-TYPE      63        1       23       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SSX2IP MUTATED           0          1          1          0        0
  SSX2IP WILD-TYPE        18          5         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SSX2IP MUTATED           0         0
  SSX2IP WILD-TYPE        12         1
D1029V3, multiclass
            clus
vv           SSX2IP MUTATED SSX2IP WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SSX2IP MUTATED     0   1   5   2
  SSX2IP WILD-TYPE   9  66 244  39
D1029V4, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              2               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
  SSX2IP MUTATED     6   2   0
  SSX2IP WILD-TYPE 214  79  66
D1029V5, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  N0              6              214
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V6, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     7   0
  SSX2IP WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      7    0
  SSX2IP WILD-TYPE  278   48
   clus
vv  SSX2IP MUTATED SSX2IP WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1029V7, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     4   4
  SSX2IP WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      4    4
  SSX2IP WILD-TYPE  166  193
        clus
vv       SSX2IP MUTATED SSX2IP WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D1029V8, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     7   0
  SSX2IP WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      7    0
  SSX2IP WILD-TYPE  293    8
     clus
vv    SSX2IP MUTATED SSX2IP WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1029V9, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     6   2
  SSX2IP WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      6    2
  SSX2IP WILD-TYPE  308   46
                               clus
vv                              SSX2IP MUTATED SSX2IP WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SSX2IP MUTATED     6   0   1   0
  SSX2IP WILD-TYPE 253   3  21  21
D1029V10, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              0               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"
D1029V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SSX2IP MUTATED                                  0     0
  SSX2IP WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SSX2IP MUTATED                           0     4
  SSX2IP WILD-TYPE                        19   172
D1029V12, multiclass
                                  clus
vv                                 SSX2IP MUTATED SSX2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = MRPS5 MUTATION ANALYSIS
D1030V1, survival
                 sevent
clus2               0   1
  MRPS5 MUTATED     7   4
  MRPS5 WILD-TYPE 270  74
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             11             344 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              4              74 
$`MRPS5 MUTATED`
TCGA-AA-3672 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6197 TCGA-AZ-6599 TCGA-AZ-6600 
        0.92         4.01        24.53        21.44         6.77        12.10 
TCGA-CA-5796 TCGA-CM-6165 TCGA-D5-6532 TCGA-D5-6537 TCGA-G4-6304 
       12.39        16.04        18.25         4.80        53.62 

$`MRPS5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  MRPS5 MUTATED MRPS5 WILD-TYPE 
           0.92            0.00 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          53.62          148.01 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          12.39           22.39 
[1] "0.9 - 53.6 (12.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.7"
D1030V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPS5 MUTATED         1        0        0         4         2         0
  MRPS5 WILD-TYPE      63        1       26       104         6         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        17          6         43         33       34        12
                 vv
clus              STAGE IVB
  MRPS5 MUTATED           0
  MRPS5 WILD-TYPE         1
D1030V3, multiclass
            clus
vv           MRPS5 MUTATED MRPS5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  MRPS5 MUTATED     1   1   6   3
  MRPS5 WILD-TYPE   8  66 243  38
D1030V4, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             6             243
  T4             3              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
  MRPS5 MUTATED     8   3   0
  MRPS5 WILD-TYPE 212  78  66
D1030V5, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V6, binary
                 cls
clus                0   1
  MRPS5 MUTATED     6   1
  MRPS5 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      6    1
  MRPS5 WILD-TYPE  279   47
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1030V7, binary
                 cls
clus                0   1
  MRPS5 MUTATED     3   8
  MRPS5 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      3    8
  MRPS5 WILD-TYPE  167  189
        clus
vv       MRPS5 MUTATED MRPS5 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1030V8, binary
                 cls
clus                0   1
  MRPS5 MUTATED    10   0
  MRPS5 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED     10    0
  MRPS5 WILD-TYPE  290    8
     clus
vv    MRPS5 MUTATED MRPS5 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1030V9, binary
                 cls
clus                0   1
  MRPS5 MUTATED     9   2
  MRPS5 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      9    2
  MRPS5 WILD-TYPE  305   46
                               clus
vv                              MRPS5 MUTATED MRPS5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MRPS5 MUTATED     8   0   0   0
  MRPS5 WILD-TYPE 251   3  22  21
D1030V10, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1030V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS5 MUTATED                                  0     1
  MRPS5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MRPS5 MUTATED                           1     7
  MRPS5 WILD-TYPE                        18   169
D1030V12, multiclass
                                  clus
vv                                 MRPS5 MUTATED MRPS5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = DUSP19 MUTATION ANALYSIS
D1031V1, survival
                  sevent
clus2                0   1
  DUSP19 MUTATED     6   3
  DUSP19 WILD-TYPE 271  75
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               9              346 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               3               75 
$`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        54.61 
TCGA-D5-6537 TCGA-D5-6923 TCGA-D5-6930 
        4.80        12.43        13.35 

$`DUSP19 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        10.06        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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-D5-6538 TCGA-D5-6539 
       25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  DUSP19 MUTATED DUSP19 WILD-TYPE 
            4.01             0.00 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
           58.39           148.01 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
          13.350           22.225 
[1] "4.0 - 58.4 (13.3)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.8"
D1031V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP19 MUTATED         1        0        0         5         1         0
  DUSP19 WILD-TYPE      63        1       26       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP19 MUTATED           0          0          2          0        0
  DUSP19 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  DUSP19 MUTATED           0         0
  DUSP19 WILD-TYPE        12         1
D1031V3, multiclass
            clus
vv           DUSP19 MUTATED DUSP19 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  DUSP19 MUTATED     0   1   7   1
  DUSP19 WILD-TYPE   9  66 242  40
D1031V4, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              1               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
  DUSP19 MUTATED     7   2   0
  DUSP19 WILD-TYPE 213  79  66
D1031V5, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V6, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     8   0
  DUSP19 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      8    0
  DUSP19 WILD-TYPE  277   48
   clus
vv  DUSP19 MUTATED DUSP19 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1031V7, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     2   7
  DUSP19 WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      2    7
  DUSP19 WILD-TYPE  168  190
        clus
vv       DUSP19 MUTATED DUSP19 WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D1031V8, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     8   0
  DUSP19 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      8    0
  DUSP19 WILD-TYPE  292    8
     clus
vv    DUSP19 MUTATED DUSP19 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1031V9, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     7   2
  DUSP19 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      7    2
  DUSP19 WILD-TYPE  307   46
                               clus
vv                              DUSP19 MUTATED DUSP19 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DUSP19 MUTATED     8   0   0   1
  DUSP19 WILD-TYPE 251   3  22  20
D1031V10, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              1               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"
D1031V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP19 MUTATED                                  0     1
  DUSP19 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DUSP19 MUTATED                           1     6
  DUSP19 WILD-TYPE                        18   170
D1031V12, multiclass
                                  clus
vv                                 DUSP19 MUTATED DUSP19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = STK35 MUTATION ANALYSIS
D1032V1, survival
                 sevent
clus2               0   1
  STK35 MUTATED     5   1
  STK35 WILD-TYPE 272  77
  STK35 MUTATED STK35 WILD-TYPE 
              6             349 
  STK35 MUTATED STK35 WILD-TYPE 
              1              77 
$`STK35 MUTATED`
TCGA-G4-6588 TCGA-A6-6651 TCGA-AA-3977 TCGA-AU-6004 TCGA-AY-6386 TCGA-F4-6570 
       26.17        21.76        25.02        27.09        17.82         6.18 

$`STK35 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.06 
[1] "6.2 - 27.1 (23.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1032V2, continuous
                 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      63        1       26       106         8         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  STK35 MUTATED           0
  STK35 WILD-TYPE         1
D1032V3, multiclass
            clus
vv           STK35 MUTATED STK35 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  STK35 MUTATED     0   2   4   0
  STK35 WILD-TYPE   9  65 245  41
D1032V4, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             0              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
  STK35 MUTATED     4   2   0
  STK35 WILD-TYPE 216  79  66
D1032V5, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V6, binary
                 cls
clus                0   1
  STK35 MUTATED     4   0
  STK35 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      4    0
  STK35 WILD-TYPE  281   48
   clus
vv  STK35 MUTATED STK35 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1032V7, binary
                 cls
clus                0   1
  STK35 MUTATED     5   1
  STK35 WILD-TYPE 165 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      5    1
  STK35 WILD-TYPE  165  196
        clus
vv       STK35 MUTATED STK35 WILD-TYPE
  FEMALE             5             165
  MALE               1             196
[1] 2 2
[1] FALSE
D1032V8, binary
                 cls
clus                0   1
  STK35 MUTATED     5   0
  STK35 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      5    0
  STK35 WILD-TYPE  295    8
     clus
vv    STK35 MUTATED STK35 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1032V9, binary
                 cls
clus                0   1
  STK35 MUTATED     6   0
  STK35 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      6    0
  STK35 WILD-TYPE  308   48
                               clus
vv                              STK35 MUTATED STK35 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK35 MUTATED     4   0   0   0
  STK35 WILD-TYPE 255   3  22  21
D1032V10, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1032V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK35 MUTATED                                  0     0
  STK35 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK35 MUTATED                           1     4
  STK35 WILD-TYPE                        18   172
D1032V12, multiclass
                                  clus
vv                                 STK35 MUTATED STK35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = CCDC110 MUTATION ANALYSIS
D1033V1, survival
                   sevent
clus2                 0   1
  CCDC110 MUTATED     7   4
  CCDC110 WILD-TYPE 270  74
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               11               344 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
                4                74 
$`CCDC110 MUTATED`
TCGA-AZ-6601 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3680 TCGA-AA-3977 TCGA-AA-A010 
      100.01        22.06        63.98        11.01        25.02        34.98 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6926 TCGA-F4-6570 
       49.41        12.76        15.02         9.04         6.18 

$`CCDC110 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCDC110 MUTATED CCDC110 WILD-TYPE 
             6.18              0.00 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
           100.01            148.01 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
            22.06             22.06 
[1] "6.2 - 100.0 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1033V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC110 MUTATED         0        0        3         5         2         0
  CCDC110 WILD-TYPE      64        1       23       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC110 MUTATED           0          0          1          0        1
  CCDC110 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC110 MUTATED           0         0
  CCDC110 WILD-TYPE        12         1
D1033V3, multiclass
            clus
vv           CCDC110 MUTATED CCDC110 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                5               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  CCDC110 MUTATED     0   1   8   4
  CCDC110 WILD-TYPE   9  66 241  37
D1033V4, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               8               241
  T4               4                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
  CCDC110 MUTATED    11   1   1
  CCDC110 WILD-TYPE 209  80  65
D1033V5, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  N0              11               209
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V6, binary
                   cls
clus                  0   1
  CCDC110 MUTATED     9   1
  CCDC110 WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED      9    1
  CCDC110 WILD-TYPE  276   47
   clus
vv  CCDC110 MUTATED CCDC110 WILD-TYPE
  0               9               276
  1               1                47
[1] 2 2
[1] FALSE
D1033V7, binary
                   cls
clus                  0   1
  CCDC110 MUTATED     8   5
  CCDC110 WILD-TYPE 162 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED      8    5
  CCDC110 WILD-TYPE  162  192
        clus
vv       CCDC110 MUTATED CCDC110 WILD-TYPE
  FEMALE               8               162
  MALE                 5               192
[1] 2 2
[1] FALSE
D1033V8, binary
                   cls
clus                  0   1
  CCDC110 MUTATED    10   1
  CCDC110 WILD-TYPE 290   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED     10    1
  CCDC110 WILD-TYPE  290    7
     clus
vv    CCDC110 MUTATED CCDC110 WILD-TYPE
  NO               10               290
  YES               1                 7
[1] 2 2
[1] FALSE
D1033V9, binary
                   cls
clus                  0   1
  CCDC110 MUTATED    12   1
  CCDC110 WILD-TYPE 302  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED     12    1
  CCDC110 WILD-TYPE  302   47
                               clus
vv                              CCDC110 MUTATED CCDC110 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC110 MUTATED     7   0   1   2
  CCDC110 WILD-TYPE 252   3  21  19
D1033V10, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               1                21
  RX               2                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"
D1033V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC110 MUTATED                                  0     1
  CCDC110 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC110 MUTATED                           0     7
  CCDC110 WILD-TYPE                        19   169
D1033V12, multiclass
                                  clus
vv                                 CCDC110 MUTATED CCDC110 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = RC3H2 MUTATION ANALYSIS
D1034V1, survival
                 sevent
clus2               0   1
  RC3H2 MUTATED     8   1
  RC3H2 WILD-TYPE 269  77
  RC3H2 MUTATED RC3H2 WILD-TYPE 
              9             346 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
              1              77 
$`RC3H2 MUTATED`
TCGA-G4-6586 TCGA-AA-3864 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6169 TCGA-CM-6674 
       35.80        53.00         2.01        23.05        13.02        12.95 
TCGA-D5-6541 TCGA-F4-6460 TCGA-F4-6806 
       15.58        31.96        41.42 

$`RC3H2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99        21.14        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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6569 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  RC3H2 MUTATED RC3H2 WILD-TYPE 
           2.01            0.00 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
          53.00          148.01 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
         23.050          22.045 
[1] "2.0 - 53.0 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1034V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RC3H2 MUTATED         1        0        1         5         0         0
  RC3H2 WILD-TYPE      63        1       25       103         8         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  RC3H2 MUTATED           0
  RC3H2 WILD-TYPE         1
D1034V3, multiclass
            clus
vv           RC3H2 MUTATED RC3H2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  RC3H2 MUTATED     0   1   8   0
  RC3H2 WILD-TYPE   9  66 241  41
D1034V4, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             0              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
  RC3H2 MUTATED     7   2   0
  RC3H2 WILD-TYPE 213  79  66
D1034V5, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V6, binary
                 cls
clus                0   1
  RC3H2 MUTATED     8   1
  RC3H2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      8    1
  RC3H2 WILD-TYPE  277   47
   clus
vv  RC3H2 MUTATED RC3H2 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1034V7, binary
                 cls
clus                0   1
  RC3H2 MUTATED     4   5
  RC3H2 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      4    5
  RC3H2 WILD-TYPE  166  192
        clus
vv       RC3H2 MUTATED RC3H2 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1034V8, binary
                 cls
clus                0   1
  RC3H2 MUTATED     9   0
  RC3H2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      9    0
  RC3H2 WILD-TYPE  291    8
     clus
vv    RC3H2 MUTATED RC3H2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1034V9, binary
                 cls
clus                0   1
  RC3H2 MUTATED     8   1
  RC3H2 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      8    1
  RC3H2 WILD-TYPE  306   47
                               clus
vv                              RC3H2 MUTATED RC3H2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RC3H2 MUTATED     8   0   0   1
  RC3H2 WILD-TYPE 251   3  22  20
D1034V10, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1034V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RC3H2 MUTATED                                  0     0
  RC3H2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RC3H2 MUTATED                           1     7
  RC3H2 WILD-TYPE                        18   169
D1034V12, multiclass
                                  clus
vv                                 RC3H2 MUTATED RC3H2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = LEO1 MUTATION ANALYSIS
D1035V1, survival
                sevent
clus2              0   1
  LEO1 MUTATED     8   2
  LEO1 WILD-TYPE 269  76
  LEO1 MUTATED LEO1 WILD-TYPE 
            10            345 
  LEO1 MUTATED LEO1 WILD-TYPE 
             2             76 
$`LEO1 MUTATED`
TCGA-AD-6895 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3864 
       25.08        23.87        20.12        20.28        63.98        53.00 
TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        4.01        58.39        49.41        12.76 

$`LEO1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       24.39        19.66         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LEO1 MUTATED LEO1 WILD-TYPE 
          4.01           0.00 
  LEO1 MUTATED LEO1 WILD-TYPE 
         63.98         148.01 
  LEO1 MUTATED LEO1 WILD-TYPE 
        24.475         22.030 
[1] "4.0 - 64.0 (24.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1035V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LEO1 MUTATED         0        0        3         3         2         0
  LEO1 WILD-TYPE      64        1       23       105         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEO1 MUTATED           0          0          2          0        0         0
  LEO1 WILD-TYPE        18          6         42         33       35        12
                vv
clus             STAGE IVB
  LEO1 MUTATED           0
  LEO1 WILD-TYPE         1
D1035V3, multiclass
            clus
vv           LEO1 MUTATED LEO1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  LEO1 MUTATED     0   0   8   2
  LEO1 WILD-TYPE   9  67 241  39
D1035V4, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            8            241
  T4            2             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
  LEO1 MUTATED     8   2   0
  LEO1 WILD-TYPE 212  79  66
D1035V5, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  N0            8            212
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V6, binary
                cls
clus               0   1
  LEO1 MUTATED     7   0
  LEO1 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      7    0
  LEO1 WILD-TYPE  278   48
   clus
vv  LEO1 MUTATED LEO1 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1035V7, binary
                cls
clus               0   1
  LEO1 MUTATED     2   8
  LEO1 WILD-TYPE 168 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      2    8
  LEO1 WILD-TYPE  168  189
        clus
vv       LEO1 MUTATED LEO1 WILD-TYPE
  FEMALE            2            168
  MALE              8            189
[1] 2 2
[1] FALSE
D1035V8, binary
                cls
clus               0   1
  LEO1 MUTATED     9   0
  LEO1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      9    0
  LEO1 WILD-TYPE  291    8
     clus
vv    LEO1 MUTATED LEO1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1035V9, binary
                cls
clus               0   1
  LEO1 MUTATED     7   3
  LEO1 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      7    3
  LEO1 WILD-TYPE  307   45
                               clus
vv                              LEO1 MUTATED LEO1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LEO1 MUTATED     5   0   0   1
  LEO1 WILD-TYPE 254   3  22  20
D1035V10, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1035V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEO1 MUTATED                                  0     1
  LEO1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LEO1 MUTATED                           0     6
  LEO1 WILD-TYPE                        19   170
D1035V12, multiclass
                                  clus
vv                                 LEO1 MUTATED LEO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = ANKRD23 MUTATION ANALYSIS
D1036V1, survival
                   sevent
clus2                 0   1
  ANKRD23 MUTATED     3   1
  ANKRD23 WILD-TYPE 274  77
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               351 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                1                77 
$`ANKRD23 MUTATED`
TCGA-G4-6628 TCGA-AA-3492 TCGA-CM-4743 TCGA-CM-6171 
       79.69         3.02        23.05        14.04 

$`ANKRD23 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
             3.02              0.00 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
            79.69            148.01 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
           18.545            22.060 
[1] "3.0 - 79.7 (18.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1036V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD23 MUTATED         2        0        1         1         0         0
  ANKRD23 WILD-TYPE      62        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD23 MUTATED           0          0          0          0        0
  ANKRD23 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD23 MUTATED           0         0
  ANKRD23 WILD-TYPE        12         1
D1036V3, multiclass
            clus
vv           ANKRD23 MUTATED ANKRD23 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ANKRD23 MUTATED     0   2   2   0
  ANKRD23 WILD-TYPE   9  65 247  41
D1036V4, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               2               247
  T4               0                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
  ANKRD23 MUTATED     4   0   0
  ANKRD23 WILD-TYPE 216  81  66
D1036V5, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  N0               4               216
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V6, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  281   48
   clus
vv  ANKRD23 MUTATED ANKRD23 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1036V7, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     2   2
  ANKRD23 WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      2    2
  ANKRD23 WILD-TYPE  168  195
        clus
vv       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D1036V8, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  296    8
     clus
vv    ANKRD23 MUTATED ANKRD23 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D1036V9, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  310   48
                               clus
vv                              ANKRD23 MUTATED ANKRD23 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD23 MUTATED     4   0   0   0
  ANKRD23 WILD-TYPE 255   3  22  21
D1036V10, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1036V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD23 MUTATED                                  0     0
  ANKRD23 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD23 MUTATED                           0     3
  ANKRD23 WILD-TYPE                        19   173
D1036V12, multiclass
                                  clus
vv                                 ANKRD23 MUTATED ANKRD23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = FBXL19 MUTATION ANALYSIS
D1037V1, survival
                  sevent
clus2                0   1
  FBXL19 MUTATED     5   1
  FBXL19 WILD-TYPE 272  77
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               6              349 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               1               77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.03 
[1] "13.2 - 133.2 (34.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.3"
D1037V2, continuous
                  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      62        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXL19 MUTATED           2          0          1          0        0
  FBXL19 WILD-TYPE        16          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXL19 MUTATED           1         0
  FBXL19 WILD-TYPE        11         1
D1037V3, multiclass
            clus
vv           FBXL19 MUTATED FBXL19 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  FBXL19 MUTATED     1   1   5   0
  FBXL19 WILD-TYPE   8  66 244  41
D1037V4, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              5              244
  T4              0               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
  FBXL19 MUTATED     3   3   1
  FBXL19 WILD-TYPE 217  78  65
D1037V5, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  N0              3              217
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V6, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     6   1
  FBXL19 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      6    1
  FBXL19 WILD-TYPE  279   47
   clus
vv  FBXL19 MUTATED FBXL19 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D1037V7, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     4   3
  FBXL19 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      4    3
  FBXL19 WILD-TYPE  166  194
        clus
vv       FBXL19 MUTATED FBXL19 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D1037V8, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     6   0
  FBXL19 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      6    0
  FBXL19 WILD-TYPE  294    8
     clus
vv    FBXL19 MUTATED FBXL19 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1037V9, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     6   1
  FBXL19 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      6    1
  FBXL19 WILD-TYPE  308   47
                               clus
vv                              FBXL19 MUTATED FBXL19 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXL19 MUTATED     7   0   0   0
  FBXL19 WILD-TYPE 252   3  22  21
D1037V10, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1037V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXL19 MUTATED                                  0     0
  FBXL19 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXL19 MUTATED                           2     3
  FBXL19 WILD-TYPE                        17   173
D1037V12, multiclass
                                  clus
vv                                 FBXL19 MUTATED FBXL19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         3              173
[1] 4 2
[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 = BFSP1 MUTATION ANALYSIS
D1038V1, survival
                 sevent
clus2               0   1
  BFSP1 MUTATED     4   3
  BFSP1 WILD-TYPE 273  75
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              7             348 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              3              75 
$`BFSP1 MUTATED`
TCGA-DM-A285 TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6654 TCGA-AZ-4616 TCGA-CA-5254 
        5.88        30.44         8.38        23.87         5.13        12.69 
TCGA-F4-6570 
        6.18 

$`BFSP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         1.41        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-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  BFSP1 MUTATED BFSP1 WILD-TYPE 
           5.13            0.00 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
          30.44          148.01 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
           8.38           22.09 
[1] "5.1 - 30.4 (8.4)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "3.9"
D1038V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BFSP1 MUTATED         1        0        0         4         0         0
  BFSP1 WILD-TYPE      63        1       26       104         8         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        18          6         43         33       33        12
                 vv
clus              STAGE IVB
  BFSP1 MUTATED           0
  BFSP1 WILD-TYPE         1
D1038V3, multiclass
            clus
vv           BFSP1 MUTATED BFSP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  BFSP1 MUTATED     0   1   7   0
  BFSP1 WILD-TYPE   9  66 242  41
D1038V4, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             0              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
  BFSP1 MUTATED     5   1   2
  BFSP1 WILD-TYPE 215  80  64
D1038V5, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V6, binary
                 cls
clus                0   1
  BFSP1 MUTATED     6   2
  BFSP1 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      6    2
  BFSP1 WILD-TYPE  279   46
   clus
vv  BFSP1 MUTATED BFSP1 WILD-TYPE
  0             6             279
  1             2              46
[1] 2 2
[1] FALSE
D1038V7, binary
                 cls
clus                0   1
  BFSP1 MUTATED     6   2
  BFSP1 WILD-TYPE 164 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      6    2
  BFSP1 WILD-TYPE  164  195
        clus
vv       BFSP1 MUTATED BFSP1 WILD-TYPE
  FEMALE             6             164
  MALE               2             195
[1] 2 2
[1] FALSE
D1038V8, binary
                 cls
clus                0   1
  BFSP1 MUTATED     6   0
  BFSP1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      6    0
  BFSP1 WILD-TYPE  294    8
     clus
vv    BFSP1 MUTATED BFSP1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1038V9, binary
                 cls
clus                0   1
  BFSP1 MUTATED     7   1
  BFSP1 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      7    1
  BFSP1 WILD-TYPE  307   47
                               clus
vv                              BFSP1 MUTATED BFSP1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BFSP1 MUTATED     3   0   0   1
  BFSP1 WILD-TYPE 256   3  22  20
D1038V10, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1038V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BFSP1 MUTATED                                  0     1
  BFSP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BFSP1 MUTATED                           1     5
  BFSP1 WILD-TYPE                        18   171
D1038V12, multiclass
                                  clus
vv                                 BFSP1 MUTATED BFSP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = C18ORF19 MUTATION ANALYSIS
D1039V1, survival
                    sevent
clus2                  0   1
  C18ORF19 MUTATED     7   1
  C18ORF19 WILD-TYPE 270  77
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 8                347 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 1                 77 
$`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        83.24        33.01 
TCGA-CM-5349 TCGA-D5-6930 
       30.08        13.35 

$`C18ORF19 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
              1.02               0.00 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             83.24             148.01 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             25.43              22.03 
[1] "1.0 - 83.2 (25.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1039V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C18ORF19 MUTATED         1        0        0         4         0         0
  C18ORF19 WILD-TYPE      63        1       26       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C18ORF19 MUTATED           0          0          2          0        0
  C18ORF19 WILD-TYPE        18          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C18ORF19 MUTATED           1         0
  C18ORF19 WILD-TYPE        11         1
D1039V3, multiclass
            clus
vv           C18ORF19 MUTATED C18ORF19 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  C18ORF19 MUTATED     0   1   6   1
  C18ORF19 WILD-TYPE   9  66 243  40
D1039V4, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                6                243
  T4                1                 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
  C18ORF19 MUTATED     5   3   0
  C18ORF19 WILD-TYPE 215  78  66
D1039V5, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  N0                5                215
  N1                3                 78
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1039V6, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     7   1
  C18ORF19 WILD-TYPE 278  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      7    1
  C18ORF19 WILD-TYPE  278   47
   clus
vv  C18ORF19 MUTATED C18ORF19 WILD-TYPE
  0                7                278
  1                1                 47
[1] 2 2
[1] FALSE
D1039V7, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     5   3
  C18ORF19 WILD-TYPE 165 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      5    3
  C18ORF19 WILD-TYPE  165  194
        clus
vv       C18ORF19 MUTATED C18ORF19 WILD-TYPE
  FEMALE                5                165
  MALE                  3                194
[1] 2 2
[1] FALSE
D1039V8, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     8   0
  C18ORF19 WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      8    0
  C18ORF19 WILD-TYPE  292    8
     clus
vv    C18ORF19 MUTATED C18ORF19 WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D1039V9, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     5   3
  C18ORF19 WILD-TYPE 309  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      5    3
  C18ORF19 WILD-TYPE  309   45
                               clus
vv                              C18ORF19 MUTATED C18ORF19 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C18ORF19 MUTATED     7   0   0   0
  C18ORF19 WILD-TYPE 252   3  22  21
D1039V10, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1039V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C18ORF19 MUTATED                                  0     1
  C18ORF19 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C18ORF19 MUTATED                           1     3
  C18ORF19 WILD-TYPE                        18   173
D1039V12, multiclass
                                  clus
vv                                 C18ORF19 MUTATED C18ORF19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           3                173
[1] 4 2
[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 = RNF20 MUTATION ANALYSIS
D1040V1, survival
                 sevent
clus2               0   1
  RNF20 MUTATED    15   3
  RNF20 WILD-TYPE 262  75
  RNF20 MUTATED RNF20 WILD-TYPE 
             18             337 
  RNF20 MUTATED RNF20 WILD-TYPE 
              3              75 
$`RNF20 MUTATED`
TCGA-AA-3543 TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
        0.99        10.88        79.69        23.87        20.12        19.66 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3947 TCGA-AA-A01I TCGA-AU-6004 TCGA-AY-6197 
       11.01        37.05        33.01        31.00        27.09        21.44 
TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6677 TCGA-D5-6928 TCGA-DM-A28H 
       49.41        37.02        12.00        11.08        11.64       117.07 

$`RNF20 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       15.02         5.98         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RNF20 MUTATED RNF20 WILD-TYPE 
           0.99            0.00 
  RNF20 MUTATED RNF20 WILD-TYPE 
         117.07          148.01 
  RNF20 MUTATED RNF20 WILD-TYPE 
         22.655          22.060 
[1] "1.0 - 117.1 (22.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1040V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF20 MUTATED         5        0        2         4         1         0
  RNF20 WILD-TYPE      59        1       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF20 MUTATED           0          0          2          2        1         0
  RNF20 WILD-TYPE        18          6         42         31       34        12
                 vv
clus              STAGE IVB
  RNF20 MUTATED           0
  RNF20 WILD-TYPE         1
D1040V3, multiclass
            clus
vv           RNF20 MUTATED RNF20 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  RNF20 MUTATED     0   5   9   4
  RNF20 WILD-TYPE   9  62 240  37
D1040V4, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             9             240
  T4             4              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
  RNF20 MUTATED    12   3   3
  RNF20 WILD-TYPE 208  78  63
D1040V5, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  N0            12             208
  N1             3              78
  N2             3              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"
D1040V6, binary
                 cls
clus                0   1
  RNF20 MUTATED    12   1
  RNF20 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     12    1
  RNF20 WILD-TYPE  273   47
   clus
vv  RNF20 MUTATED RNF20 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D1040V7, binary
                 cls
clus                0   1
  RNF20 MUTATED     7  11
  RNF20 WILD-TYPE 163 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED      7   11
  RNF20 WILD-TYPE  163  186
        clus
vv       RNF20 MUTATED RNF20 WILD-TYPE
  FEMALE             7             163
  MALE              11             186
[1] 2 2
[1] FALSE
D1040V8, binary
                 cls
clus                0   1
  RNF20 MUTATED    16   0
  RNF20 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     16    0
  RNF20 WILD-TYPE  284    8
     clus
vv    RNF20 MUTATED RNF20 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D1040V9, binary
                 cls
clus                0   1
  RNF20 MUTATED    12   6
  RNF20 WILD-TYPE 302  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     12    6
  RNF20 WILD-TYPE  302   42
                               clus
vv                              RNF20 MUTATED RNF20 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF20 MUTATED    12   0   1   0
  RNF20 WILD-TYPE 247   3  21  21
D1040V10, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             1              21
  RX             0              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"
D1040V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF20 MUTATED                                  0     0
  RNF20 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF20 MUTATED                           1    12
  RNF20 WILD-TYPE                        18   164
D1040V12, multiclass
                                  clus
vv                                 RNF20 MUTATED RNF20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = TRIM24 MUTATION ANALYSIS
D1041V1, survival
                  sevent
clus2                0   1
  TRIM24 MUTATED     7   9
  TRIM24 WILD-TYPE 270  69
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              16              339 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
               9               69 
$`TRIM24 MUTATED`
TCGA-G4-6628 TCGA-A6-6782 TCGA-AA-3811 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A02W 
       79.69        20.28        10.06        15.95         4.01        41.00 
TCGA-AD-5900 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6718 
       12.16        62.79         6.77        12.10        29.56        10.06 
TCGA-D5-6535 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-G4-6293 
       15.12        12.59         7.50       133.18 

$`TRIM24 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        19.66         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01         0.92        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6606 
        5.13        22.36        88.21        49.41         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-A1DB 
      130.65        92.75        49.91        13.32       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-F4-6459 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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TRIM24 MUTATED TRIM24 WILD-TYPE 
            4.01             0.00 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
          133.18           148.01 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
          13.855           22.360 
[1] "4.0 - 133.2 (13.9)" "0.0 - 148.0 (22.4)"
[1] "hr=" "2.7"
D1041V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM24 MUTATED         4        0        1         3         2         0
  TRIM24 WILD-TYPE      60        1       25       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM24 MUTATED           2          0          1          1        1
  TRIM24 WILD-TYPE        16          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM24 MUTATED           0         0
  TRIM24 WILD-TYPE        12         1
D1041V3, multiclass
            clus
vv           TRIM24 MUTATED TRIM24 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  TRIM24 MUTATED     0   5   9   3
  TRIM24 WILD-TYPE   9  62 240  38
D1041V4, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  T1              0                9
  T2              5               62
  T3              9              240
  T4              3               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
  TRIM24 MUTATED    10   5   2
  TRIM24 WILD-TYPE 210  76  64
D1041V5, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  N0             10              210
  N1              5               76
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1041V6, binary
                  cls
clus                 0   1
  TRIM24 MUTATED     9   1
  TRIM24 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED      9    1
  TRIM24 WILD-TYPE  276   47
   clus
vv  TRIM24 MUTATED TRIM24 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1041V7, binary
                  cls
clus                 0   1
  TRIM24 MUTATED     9   8
  TRIM24 WILD-TYPE 161 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED      9    8
  TRIM24 WILD-TYPE  161  189
        clus
vv       TRIM24 MUTATED TRIM24 WILD-TYPE
  FEMALE              9              161
  MALE                8              189
[1] 2 2
[1] FALSE
D1041V8, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    13   0
  TRIM24 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     13    0
  TRIM24 WILD-TYPE  287    8
     clus
vv    TRIM24 MUTATED TRIM24 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1041V9, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    15   2
  TRIM24 WILD-TYPE 299  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     15    2
  TRIM24 WILD-TYPE  299   46
                               clus
vv                              TRIM24 MUTATED TRIM24 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM24 MUTATED     8   0   0   2
  TRIM24 WILD-TYPE 251   3  22  19
D1041V10, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              2               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"
D1041V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM24 MUTATED                                  0     1
  TRIM24 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM24 MUTATED                           1    10
  TRIM24 WILD-TYPE                        18   166
D1041V12, multiclass
                                  clus
vv                                 TRIM24 MUTATED TRIM24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(1042) Variable = ODAM MUTATION ANALYSIS
D1042V1, survival
                sevent
clus2              0   1
  ODAM MUTATED     4   1
  ODAM WILD-TYPE 273  77
  ODAM MUTATED ODAM WILD-TYPE 
             5            350 
  ODAM MUTATED ODAM WILD-TYPE 
             1             77 
$`ODAM MUTATED`
TCGA-AA-3977 TCGA-CM-5348 TCGA-DM-A1D4 TCGA-DM-A28H TCGA-G4-6306 
       25.02        22.98        92.75       117.07        44.68 

$`ODAM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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-F4-6459 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ODAM MUTATED ODAM WILD-TYPE 
         22.98           0.00 
  ODAM MUTATED ODAM WILD-TYPE 
        117.07         148.01 
  ODAM MUTATED ODAM WILD-TYPE 
         44.68          21.99 
[1] "23.0 - 117.1 (44.7)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.3"
D1042V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ODAM MUTATED         0        0        0         1         0         0
  ODAM WILD-TYPE      64        1       26       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ODAM MUTATED           0          0          1          1        0         0
  ODAM WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  ODAM MUTATED           0
  ODAM WILD-TYPE         1
D1042V3, multiclass
            clus
vv           ODAM MUTATED ODAM WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  ODAM MUTATED     0   2   3   0
  ODAM WILD-TYPE   9  65 246  41
D1042V4, multiclass
    clus
vv   ODAM MUTATED ODAM WILD-TYPE
  T1            0              9
  T2            2             65
  T3            3            246
  T4            0             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
  ODAM MUTATED     3   1   1
  ODAM WILD-TYPE 217  80  65
D1042V5, multiclass
    clus
vv   ODAM MUTATED ODAM WILD-TYPE
  N0            3            217
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V6, binary
                cls
clus               0   1
  ODAM MUTATED     4   0
  ODAM WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      4    0
  ODAM WILD-TYPE  281   48
   clus
vv  ODAM MUTATED ODAM WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1042V7, binary
                cls
clus               0   1
  ODAM MUTATED     0   5
  ODAM WILD-TYPE 170 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      0    5
  ODAM WILD-TYPE  170  192
        clus
vv       ODAM MUTATED ODAM WILD-TYPE
  FEMALE            0            170
  MALE              5            192
[1] 2 2
[1] FALSE
D1042V8, binary
                cls
clus               0   1
  ODAM MUTATED     3   0
  ODAM WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      3    0
  ODAM WILD-TYPE  297    8
     clus
vv    ODAM MUTATED ODAM WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1042V9, binary
                cls
clus               0   1
  ODAM MUTATED     5   0
  ODAM WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      5    0
  ODAM WILD-TYPE  309   48
                               clus
vv                              ODAM MUTATED ODAM WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ODAM MUTATED     2   0   0   0
  ODAM WILD-TYPE 257   3  22  21
D1042V10, multiclass
[1] "Remove cluster labels:" "ODAM MUTATED"          
clus
  ODAM MUTATED ODAM WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     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-3527 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-2676     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-3502     TCGA-AA-3510 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660 
"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-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     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-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3975     TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00W     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-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4682 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
D1042V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ODAM MUTATED                                  0     0
  ODAM WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ODAM MUTATED                           0     4
  ODAM WILD-TYPE                        19   172
D1042V12, multiclass
                                  clus
vv                                 ODAM MUTATED ODAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = CDKL2 MUTATION ANALYSIS
D1043V1, survival
                 sevent
clus2               0   1
  CDKL2 MUTATED     9   1
  CDKL2 WILD-TYPE 268  77
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             10             345 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.09 
[1] "1.0 - 60.8 (16.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1043V2, continuous
                 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      64        1       25       103         7         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        18          6         42         32       35        11
                 vv
clus              STAGE IVB
  CDKL2 MUTATED           0
  CDKL2 WILD-TYPE         1
D1043V3, multiclass
            clus
vv           CDKL2 MUTATED CDKL2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  CDKL2 MUTATED     0   0   9   2
  CDKL2 WILD-TYPE   9  67 240  39
D1043V4, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             9             240
  T4             2              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
  CDKL2 MUTATED     7   3   1
  CDKL2 WILD-TYPE 213  78  65
D1043V5, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V6, binary
                 cls
clus                0   1
  CDKL2 MUTATED     9   1
  CDKL2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      9    1
  CDKL2 WILD-TYPE  276   47
   clus
vv  CDKL2 MUTATED CDKL2 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1043V7, binary
                 cls
clus                0   1
  CDKL2 MUTATED     7   4
  CDKL2 WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      7    4
  CDKL2 WILD-TYPE  163  193
        clus
vv       CDKL2 MUTATED CDKL2 WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D1043V8, binary
                 cls
clus                0   1
  CDKL2 MUTATED     8   0
  CDKL2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      8    0
  CDKL2 WILD-TYPE  292    8
     clus
vv    CDKL2 MUTATED CDKL2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1043V9, binary
                 cls
clus                0   1
  CDKL2 MUTATED     9   2
  CDKL2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      9    2
  CDKL2 WILD-TYPE  305   46
                               clus
vv                              CDKL2 MUTATED CDKL2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDKL2 MUTATED     8   0   0   2
  CDKL2 WILD-TYPE 251   3  22  19
D1043V10, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D1043V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKL2 MUTATED                                  0     1
  CDKL2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDKL2 MUTATED                           2     3
  CDKL2 WILD-TYPE                        17   173
D1043V12, multiclass
                                  clus
vv                                 CDKL2 MUTATED CDKL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        3             173
[1] 4 2
[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 = LRP2 MUTATION ANALYSIS
D1044V1, survival
                sevent
clus2              0   1
  LRP2 MUTATED    63  13
  LRP2 WILD-TYPE 214  65
  LRP2 MUTATED LRP2 WILD-TYPE 
            76            279 
  LRP2 MUTATED LRP2 WILD-TYPE 
            13             65 
$`LRP2 MUTATED`
TCGA-AA-3516 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-A00L 
       13.02         6.05         0.92        85.05        19.04        38.04 
TCGA-AD-6895 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5657 
       25.08       100.01        49.08        26.17        79.69        31.63 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6654 TCGA-A6-6780 
       22.06        32.71         8.38        25.08        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3845 
       19.66         1.02        29.95         6.97        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-A00N TCGA-AA-A00O 
       13.05        25.02        34.03        18.05         4.01        27.02 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A02O 
       34.98        38.07         1.02        35.01        33.04         0.92 
TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       12.16        21.44        58.39        49.41        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       14.30        15.62        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       15.02        15.02        14.04        14.04        11.01        13.05 
TCGA-CM-6677 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6540 
       11.08        56.09        20.19        18.25        25.48        16.14 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28G TCGA-DM-A28H 
       24.43        38.20       131.51       135.65        60.79       117.07 
TCGA-F4-6703 TCGA-F4-6854 TCGA-G4-6303 TCGA-G4-6304 
       47.87         0.53        65.85        53.62 

$`LRP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
        1.94         5.88        63.62        22.09        35.80        91.79 
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-A6-5656 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        32.91        30.44 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3489 
       25.18        21.76        24.69        24.39        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3837 TCGA-AA-3842 TCGA-AA-3846 
       25.02         1.02        17.98        38.99        37.02        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-3861 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        30.05        27.02        18.05         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        16.08        34.06 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       31.00         1.02         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       12.59        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 
       21.99        21.14        82.95         2.01       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        54.61 
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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
       13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28K 
       44.32       139.17        81.37       119.93        35.97        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        43.04        33.67        13.25        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
      133.18        74.56        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LRP2 MUTATED LRP2 WILD-TYPE 
             0              0 
  LRP2 MUTATED LRP2 WILD-TYPE 
        135.65         148.01 
  LRP2 MUTATED LRP2 WILD-TYPE 
         24.15          21.99 
[1] "0.0 - 135.7 (24.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1044V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRP2 MUTATED        10        0        8        25         4         1
  LRP2 WILD-TYPE      54        1       18        83         4         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRP2 MUTATED           5          1          9          7        3         1
  LRP2 WILD-TYPE        13          5         35         26       32        11
                vv
clus             STAGE IVB
  LRP2 MUTATED           1
  LRP2 WILD-TYPE         0
D1044V3, multiclass
            clus
vv           LRP2 MUTATED LRP2 WILD-TYPE
  STAGE I              10             54
  STAGE IA              0              1
  STAGE II              8             18
  STAGE IIA            25             83
  STAGE IIB             4              4
  STAGE IIC             1              0
  STAGE III             5             13
  STAGE IIIA            1              5
  STAGE IIIB            9             35
  STAGE IIIC            7             26
  STAGE IV              3             32
  STAGE IVA             1             11
  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     2  10  54  11
  LRP2 WILD-TYPE   7  57 195  30
D1044V4, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  T1            2              7
  T2           10             57
  T3           54            195
  T4           11             30
[1] 4 2
[1] TRUE
[1] "dimension 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    50  17  10
  LRP2 WILD-TYPE 170  64  56
D1044V5, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  N0           50            170
  N1           17             64
  N2           10             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V6, binary
                cls
clus               0   1
  LRP2 MUTATED    65   5
  LRP2 WILD-TYPE 220  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     65    5
  LRP2 WILD-TYPE  220   43
   clus
vv  LRP2 MUTATED LRP2 WILD-TYPE
  0           65            220
  1            5             43
[1] 2 2
[1] FALSE
D1044V7, binary
                cls
clus               0   1
  LRP2 MUTATED    34  43
  LRP2 WILD-TYPE 136 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     34   43
  LRP2 WILD-TYPE  136  154
        clus
vv       LRP2 MUTATED LRP2 WILD-TYPE
  FEMALE           34            136
  MALE             43            154
[1] 2 2
[1] FALSE
D1044V8, binary
                cls
clus               0   1
  LRP2 MUTATED    63   1
  LRP2 WILD-TYPE 237   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     63    1
  LRP2 WILD-TYPE  237    7
     clus
vv    LRP2 MUTATED LRP2 WILD-TYPE
  NO            63            237
  YES            1              7
[1] 2 2
[1] FALSE
D1044V9, binary
                cls
clus               0   1
  LRP2 MUTATED    61  14
  LRP2 WILD-TYPE 253  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     61   14
  LRP2 WILD-TYPE  253   34
                               clus
vv                              LRP2 MUTATED LRP2 WILD-TYPE
  COLON ADENOCARCINOMA                    61            253
  COLON MUCINOUS ADENOCARCINOMA           14             34
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LRP2 MUTATED    55   0   2   5
  LRP2 WILD-TYPE 204   3  20  16
D1044V10, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  R0           55            204
  R1            0              3
  R2            2             20
  RX            5             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"
D1044V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRP2 MUTATED                                  0     3
  LRP2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LRP2 MUTATED                           3    41
  LRP2 WILD-TYPE                        16   135
D1044V12, multiclass
                                  clus
vv                                 LRP2 MUTATED LRP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      41            135
[1] 4 2
[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 = KCNG4 MUTATION ANALYSIS
D1045V1, survival
                 sevent
clus2               0   1
  KCNG4 MUTATED     6   4
  KCNG4 WILD-TYPE 271  74
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             345 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
              4              74 
$`KCNG4 MUTATED`
TCGA-DM-A285 TCGA-A6-5665 TCGA-AA-3941 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6965 
        5.88        22.06        24.00        34.98        83.24        26.47 
TCGA-AY-6196 TCGA-D5-6536 TCGA-DM-A1D4 TCGA-DM-A1D7 
        0.20        17.85        92.75        13.32 

$`KCNG4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KCNG4 MUTATED KCNG4 WILD-TYPE 
            0.2             0.0 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
          92.75          148.01 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
          23.03           22.03 
[1] "0.2 - 92.8 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1045V2, continuous
                 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      64        1       26       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNG4 MUTATED           0          0          0          2        1         1
  KCNG4 WILD-TYPE        18          6         44         31       34        11
                 vv
clus              STAGE IVB
  KCNG4 MUTATED           0
  KCNG4 WILD-TYPE         1
D1045V3, multiclass
            clus
vv           KCNG4 MUTATED KCNG4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  KCNG4 MUTATED     0   0   7   3
  KCNG4 WILD-TYPE   9  67 242  38
D1045V4, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             3              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
  KCNG4 MUTATED     6   1   3
  KCNG4 WILD-TYPE 214  80  63
D1045V5, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             3              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"
D1045V6, binary
                 cls
clus                0   1
  KCNG4 MUTATED     7   2
  KCNG4 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      7    2
  KCNG4 WILD-TYPE  278   46
   clus
vv  KCNG4 MUTATED KCNG4 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D1045V7, binary
                 cls
clus                0   1
  KCNG4 MUTATED     4   6
  KCNG4 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      4    6
  KCNG4 WILD-TYPE  166  191
        clus
vv       KCNG4 MUTATED KCNG4 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1045V8, binary
                 cls
clus                0   1
  KCNG4 MUTATED     6   0
  KCNG4 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      6    0
  KCNG4 WILD-TYPE  294    8
     clus
vv    KCNG4 MUTATED KCNG4 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1045V9, binary
                 cls
clus                0   1
  KCNG4 MUTATED     7   2
  KCNG4 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      7    2
  KCNG4 WILD-TYPE  307   46
                               clus
vv                              KCNG4 MUTATED KCNG4 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNG4 MUTATED     6   1   0   0
  KCNG4 WILD-TYPE 253   2  22  21
D1045V10, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  R0             6             253
  R1             1               2
  R2             0              22
  RX             0              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"
D1045V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNG4 MUTATED                                  0     1
  KCNG4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNG4 MUTATED                           0     7
  KCNG4 WILD-TYPE                        19   169
D1045V12, multiclass
                                  clus
vv                                 KCNG4 MUTATED KCNG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = PAK7 MUTATION ANALYSIS
D1046V1, survival
                sevent
clus2              0   1
  PAK7 MUTATED    12   8
  PAK7 WILD-TYPE 265  70
  PAK7 MUTATED PAK7 WILD-TYPE 
            20            335 
  PAK7 MUTATED PAK7 WILD-TYPE 
             8             70 
$`PAK7 MUTATED`
TCGA-AA-3662 TCGA-AA-A024 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-A6-6141 
        6.05        39.06        49.08         5.88        22.09         8.38 
TCGA-AA-3815 TCGA-AA-3837 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 
       33.04        38.99         4.01        34.98        83.24        58.39 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-D5-6540 TCGA-D5-6541 TCGA-F4-6570 
       29.56         3.19        12.59        16.14        15.58         6.18 
TCGA-F4-6703 TCGA-G4-6307 
       47.87        55.04 

$`PAK7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        1.94        63.62        35.80        26.17        91.79        79.69 
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-A6-5656 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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        12.10         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PAK7 MUTATED PAK7 WILD-TYPE 
          3.19           0.00 
  PAK7 MUTATED PAK7 WILD-TYPE 
         83.24         148.01 
  PAK7 MUTATED PAK7 WILD-TYPE 
        25.825         22.030 
[1] "3.2 - 83.2 (25.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1046V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK7 MUTATED         2        0        1         9         2         0
  PAK7 WILD-TYPE      62        1       25        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK7 MUTATED           1          0          1          0        3         0
  PAK7 WILD-TYPE        17          6         43         33       32        12
                vv
clus             STAGE IVB
  PAK7 MUTATED           0
  PAK7 WILD-TYPE         1
D1046V3, multiclass
            clus
vv           PAK7 MUTATED PAK7 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             9             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              3             32
  STAGE IVA             0             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
  PAK7 MUTATED     0   4  12   4
  PAK7 WILD-TYPE   9  63 237  37
D1046V4, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           12            237
  T4            4             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
  PAK7 MUTATED    14   3   3
  PAK7 WILD-TYPE 206  78  63
D1046V5, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  N0           14            206
  N1            3             78
  N2            3             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"
D1046V6, binary
                cls
clus               0   1
  PAK7 MUTATED    14   3
  PAK7 WILD-TYPE 271  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     14    3
  PAK7 WILD-TYPE  271   45
   clus
vv  PAK7 MUTATED PAK7 WILD-TYPE
  0           14            271
  1            3             45
[1] 2 2
[1] FALSE
D1046V7, binary
                cls
clus               0   1
  PAK7 MUTATED     8  12
  PAK7 WILD-TYPE 162 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED      8   12
  PAK7 WILD-TYPE  162  185
        clus
vv       PAK7 MUTATED PAK7 WILD-TYPE
  FEMALE            8            162
  MALE             12            185
[1] 2 2
[1] FALSE
D1046V8, binary
                cls
clus               0   1
  PAK7 MUTATED    18   0
  PAK7 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     18    0
  PAK7 WILD-TYPE  282    8
     clus
vv    PAK7 MUTATED PAK7 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D1046V9, binary
                cls
clus               0   1
  PAK7 MUTATED    15   5
  PAK7 WILD-TYPE 299  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     15    5
  PAK7 WILD-TYPE  299   43
                               clus
vv                              PAK7 MUTATED PAK7 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAK7 MUTATED    14   0   1   1
  PAK7 WILD-TYPE 245   3  21  20
D1046V10, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            1             21
  RX            1             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"
D1046V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK7 MUTATED                                  0     2
  PAK7 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK7 MUTATED                           1    11
  PAK7 WILD-TYPE                        18   165
D1046V12, multiclass
                                  clus
vv                                 PAK7 MUTATED PAK7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(1047) Variable = CHD7 MUTATION ANALYSIS
D1047V1, survival
                sevent
clus2              0   1
  CHD7 MUTATED    30   5
  CHD7 WILD-TYPE 247  73
  CHD7 MUTATED CHD7 WILD-TYPE 
            35            320 
  CHD7 MUTATED CHD7 WILD-TYPE 
             5             73 
$`CHD7 MUTATED`
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6588 
        0.92        85.05        19.04        24.00        25.08        26.17 
TCGA-G4-6628 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3681 TCGA-AA-3815 
       79.69        32.75         3.02        63.98         5.98        33.04 
TCGA-AA-3861 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A010 TCGA-AA-A01K 
       30.05        26.01        25.02        13.94        34.98        31.00 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 
       83.24        27.09        58.39        49.41        12.76        15.62 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-6161 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-6538 
       23.05        22.98        15.02        12.95        10.06        17.13 
TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A0XF TCGA-DM-A1DB TCGA-G4-6309 
       16.14        11.64        38.20        44.32        85.48 

$`CHD7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       63.62        22.09        35.80        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02        11.01        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        38.04        19.00        30.02 
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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CHD7 MUTATED CHD7 WILD-TYPE 
          0.92           0.00 
  CHD7 MUTATED CHD7 WILD-TYPE 
         85.48         148.01 
  CHD7 MUTATED CHD7 WILD-TYPE 
         25.08          21.99 
[1] "0.9 - 85.5 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1047V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD7 MUTATED         4        0        4        14         3         0
  CHD7 WILD-TYPE      60        1       22        94         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD7 MUTATED           2          0          5          3        1         0
  CHD7 WILD-TYPE        16          6         39         30       34        12
                vv
clus             STAGE IVB
  CHD7 MUTATED           0
  CHD7 WILD-TYPE         1
D1047V3, multiclass
            clus
vv           CHD7 MUTATED CHD7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            14             94
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            5             39
  STAGE IIIC            3             30
  STAGE IV              1             34
  STAGE IVA             0             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
  CHD7 MUTATED     0   5  28   4
  CHD7 WILD-TYPE   9  62 221  37
D1047V4, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           28            221
  T4            4             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
  CHD7 MUTATED    27   6   4
  CHD7 WILD-TYPE 193  75  62
D1047V5, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  N0           27            193
  N1            6             75
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V6, binary
                cls
clus               0   1
  CHD7 MUTATED    33   1
  CHD7 WILD-TYPE 252  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     33    1
  CHD7 WILD-TYPE  252   47
   clus
vv  CHD7 MUTATED CHD7 WILD-TYPE
  0           33            252
  1            1             47
[1] 2 2
[1] FALSE
D1047V7, binary
                cls
clus               0   1
  CHD7 MUTATED    19  18
  CHD7 WILD-TYPE 151 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     19   18
  CHD7 WILD-TYPE  151  179
        clus
vv       CHD7 MUTATED CHD7 WILD-TYPE
  FEMALE           19            151
  MALE             18            179
[1] 2 2
[1] FALSE
D1047V8, binary
                cls
clus               0   1
  CHD7 MUTATED    30   1
  CHD7 WILD-TYPE 270   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     30    1
  CHD7 WILD-TYPE  270    7
     clus
vv    CHD7 MUTATED CHD7 WILD-TYPE
  NO            30            270
  YES            1              7
[1] 2 2
[1] FALSE
D1047V9, binary
                cls
clus               0   1
  CHD7 MUTATED    29   7
  CHD7 WILD-TYPE 285  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     29    7
  CHD7 WILD-TYPE  285   41
                               clus
vv                              CHD7 MUTATED CHD7 WILD-TYPE
  COLON ADENOCARCINOMA                    29            285
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD7 MUTATED    29   0   1   3
  CHD7 WILD-TYPE 230   3  21  18
D1047V10, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  R0           29            230
  R1            0              3
  R2            1             21
  RX            3             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"
D1047V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD7 MUTATED                                  0     2
  CHD7 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD7 MUTATED                           1    19
  CHD7 WILD-TYPE                        18   157
D1047V12, multiclass
                                  clus
vv                                 CHD7 MUTATED CHD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      19            157
[1] 4 2
[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 = ZNF585B MUTATION ANALYSIS
D1048V1, survival
                   sevent
clus2                 0   1
  ZNF585B MUTATED     4   3
  ZNF585B WILD-TYPE 273  75
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                7               348 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                3                75 
$`ZNF585B MUTATED`
TCGA-AA-3715 TCGA-AD-6895 TCGA-AA-A010 TCGA-CK-6747 TCGA-D5-6923 TCGA-F4-6460 
       19.04        25.08        34.98        82.95        12.43        31.96 
TCGA-F4-6570 
        6.18 

$`ZNF585B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF585B MUTATED ZNF585B WILD-TYPE 
             6.18              0.00 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
            82.95            148.01 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
           25.080            22.045 
[1] "6.2 - 83.0 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1048V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF585B MUTATED         1        0        1         2         1         0
  ZNF585B WILD-TYPE      63        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF585B MUTATED           0          0          2          0        0
  ZNF585B WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF585B MUTATED           0         0
  ZNF585B WILD-TYPE        12         1
D1048V3, multiclass
            clus
vv           ZNF585B MUTATED ZNF585B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ZNF585B MUTATED     0   1   5   1
  ZNF585B WILD-TYPE   9  66 244  40
D1048V4, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               1                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
  ZNF585B MUTATED     5   2   0
  ZNF585B WILD-TYPE 215  79  66
D1048V5, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  N0               5               215
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V6, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     6   0
  ZNF585B WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      6    0
  ZNF585B WILD-TYPE  279   48
   clus
vv  ZNF585B MUTATED ZNF585B WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1048V7, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     4   3
  ZNF585B WILD-TYPE 166 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      4    3
  ZNF585B WILD-TYPE  166  194
        clus
vv       ZNF585B MUTATED ZNF585B WILD-TYPE
  FEMALE               4               166
  MALE                 3               194
[1] 2 2
[1] FALSE
D1048V8, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     7   0
  ZNF585B WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      7    0
  ZNF585B WILD-TYPE  293    8
     clus
vv    ZNF585B MUTATED ZNF585B WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1048V9, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     7   0
  ZNF585B WILD-TYPE 307  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      7    0
  ZNF585B WILD-TYPE  307   48
                               clus
vv                              ZNF585B MUTATED ZNF585B WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF585B MUTATED     6   0   0   1
  ZNF585B WILD-TYPE 253   3  22  20
D1048V10, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D1048V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF585B MUTATED                                  0     0
  ZNF585B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF585B MUTATED                           0     5
  ZNF585B WILD-TYPE                        19   171
D1048V12, multiclass
                                  clus
vv                                 ZNF585B MUTATED ZNF585B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = NSUN2 MUTATION ANALYSIS
D1049V1, survival
                 sevent
clus2               0   1
  NSUN2 MUTATED     9   2
  NSUN2 WILD-TYPE 268  76
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             11             344 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
              2              76 
$`NSUN2 MUTATED`
TCGA-AD-6964 TCGA-A6-5659 TCGA-AA-3685 TCGA-AA-3833 TCGA-AA-3930 TCGA-AZ-4315 
       10.88        30.44        37.05        15.95         2.01        58.39 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6541 TCGA-F4-6856 TCGA-G4-6304 
       12.95        19.59        15.58        35.31        53.62 

$`NSUN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NSUN2 MUTATED NSUN2 WILD-TYPE 
           2.01            0.00 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
          58.39          148.01 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
         19.590          22.075 
[1] "2.0 - 58.4 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1049V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NSUN2 MUTATED         2        0        1         4         1         0
  NSUN2 WILD-TYPE      62        1       25       104         7         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        18          5         44         33       34        12
                 vv
clus              STAGE IVB
  NSUN2 MUTATED           0
  NSUN2 WILD-TYPE         1
D1049V3, multiclass
            clus
vv           NSUN2 MUTATED NSUN2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  NSUN2 MUTATED     0   2   7   2
  NSUN2 WILD-TYPE   9  65 242  39
D1049V4, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             2              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
  NSUN2 MUTATED     8   1   2
  NSUN2 WILD-TYPE 212  80  64
D1049V5, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V6, binary
                 cls
clus                0   1
  NSUN2 MUTATED     9   1
  NSUN2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED      9    1
  NSUN2 WILD-TYPE  276   47
   clus
vv  NSUN2 MUTATED NSUN2 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1049V7, binary
                 cls
clus                0   1
  NSUN2 MUTATED     2   9
  NSUN2 WILD-TYPE 168 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED      2    9
  NSUN2 WILD-TYPE  168  188
        clus
vv       NSUN2 MUTATED NSUN2 WILD-TYPE
  FEMALE             2             168
  MALE               9             188
[1] 2 2
[1] FALSE
D1049V8, binary
                 cls
clus                0   1
  NSUN2 MUTATED    11   0
  NSUN2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED     11    0
  NSUN2 WILD-TYPE  289    8
     clus
vv    NSUN2 MUTATED NSUN2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1049V9, binary
                 cls
clus                0   1
  NSUN2 MUTATED     9   2
  NSUN2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED      9    2
  NSUN2 WILD-TYPE  305   46
                               clus
vv                              NSUN2 MUTATED NSUN2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NSUN2 MUTATED     9   0   1   0
  NSUN2 WILD-TYPE 250   3  21  21
D1049V10, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             0              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"
D1049V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSUN2 MUTATED                                  0     0
  NSUN2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NSUN2 MUTATED                           0     8
  NSUN2 WILD-TYPE                        19   168
D1049V12, multiclass
                                  clus
vv                                 NSUN2 MUTATED NSUN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = CCNH MUTATION ANALYSIS
D1050V1, survival
                sevent
clus2              0   1
  CCNH MUTATED     6   1
  CCNH WILD-TYPE 271  77
  CCNH MUTATED CCNH WILD-TYPE 
             7            348 
  CCNH MUTATED CCNH WILD-TYPE 
             1             77 
$`CCNH MUTATED`
TCGA-G4-6628 TCGA-AA-3977 TCGA-AA-A00R TCGA-CM-6168 TCGA-D5-6536 TCGA-F4-6569 
       79.69        25.02         0.99        12.99        17.85        35.74 
TCGA-G4-6626 
       46.75 

$`CCNH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  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         22.045 
[1] "1.0 - 79.7 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1050V2, continuous
                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      61        1       26       105         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  CCNH MUTATED           0
  CCNH WILD-TYPE         1
D1050V3, multiclass
            clus
vv           CCNH MUTATED CCNH WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CCNH MUTATED     0   4   3   0
  CCNH WILD-TYPE   9  63 246  41
D1050V4, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  T1            0              9
  T2            4             63
  T3            3            246
  T4            0             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
  CCNH MUTATED     7   0   0
  CCNH WILD-TYPE 213  81  66
D1050V5, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  N0            7            213
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V6, binary
                cls
clus               0   1
  CCNH MUTATED     6   0
  CCNH WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      6    0
  CCNH WILD-TYPE  279   48
   clus
vv  CCNH MUTATED CCNH WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1050V7, binary
                cls
clus               0   1
  CCNH MUTATED     2   5
  CCNH WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      2    5
  CCNH WILD-TYPE  168  192
        clus
vv       CCNH MUTATED CCNH WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D1050V8, binary
                cls
clus               0   1
  CCNH MUTATED     6   0
  CCNH WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      6    0
  CCNH WILD-TYPE  294    8
     clus
vv    CCNH MUTATED CCNH WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1050V9, binary
                cls
clus               0   1
  CCNH MUTATED     7   0
  CCNH WILD-TYPE 307  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      7    0
  CCNH WILD-TYPE  307   48
                               clus
vv                              CCNH MUTATED CCNH WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCNH MUTATED     6   0   0   0
  CCNH WILD-TYPE 253   3  22  21
D1050V10, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D1050V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCNH MUTATED                                  0     0
  CCNH WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCNH MUTATED                           1     4
  CCNH WILD-TYPE                        18   172
D1050V12, multiclass
                                  clus
vv                                 CCNH MUTATED CCNH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = IVD MUTATION ANALYSIS
D1051V1, survival
               sevent
clus2             0   1
  IVD MUTATED     5   0
  IVD WILD-TYPE 272  78
  IVD MUTATED IVD WILD-TYPE 
            5           350 
  IVD MUTATED IVD WILD-TYPE 
            0            78 
$`IVD MUTATED`
TCGA-A6-6781 TCGA-AU-6004 TCGA-CA-6716 TCGA-D5-6539 TCGA-F4-6703 
       19.66        27.09        12.20        12.49        47.87 

$`IVD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  IVD MUTATED IVD WILD-TYPE 
         12.2           0.0 
  IVD MUTATED IVD WILD-TYPE 
        47.87        148.01 
  IVD MUTATED IVD WILD-TYPE 
       19.660        22.075 
[1] "12.2 - 47.9 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1051V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IVD MUTATED         1        0        0         2         0         0
  IVD WILD-TYPE      63        1       26       106         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVD MUTATED           0          0          0          1        0         0
  IVD WILD-TYPE        18          6         44         32       35        12
               vv
clus            STAGE IVB
  IVD MUTATED           0
  IVD WILD-TYPE         1
D1051V3, multiclass
            clus
vv           IVD MUTATED IVD WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            2           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  IVD MUTATED     0   1   3   1
  IVD WILD-TYPE   9  66 246  40
D1051V4, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  T1           0             9
  T2           1            66
  T3           3           246
  T4           1            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
  IVD MUTATED     4   1   0
  IVD WILD-TYPE 216  80  66
D1051V5, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  N0           4           216
  N1           1            80
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V6, binary
               cls
clus              0   1
  IVD MUTATED     4   0
  IVD WILD-TYPE 281  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      4    0
  IVD WILD-TYPE  281   48
   clus
vv  IVD MUTATED IVD WILD-TYPE
  0           4           281
  1           0            48
[1] 2 2
[1] FALSE
D1051V7, binary
               cls
clus              0   1
  IVD MUTATED     2   3
  IVD WILD-TYPE 168 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      2    3
  IVD WILD-TYPE  168  194
        clus
vv       IVD MUTATED IVD WILD-TYPE
  FEMALE           2           168
  MALE             3           194
[1] 2 2
[1] FALSE
D1051V8, binary
               cls
clus              0   1
  IVD MUTATED     4   0
  IVD WILD-TYPE 296   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      4    0
  IVD WILD-TYPE  296    8
     clus
vv    IVD MUTATED IVD WILD-TYPE
  NO            4           296
  YES           0             8
[1] 2 2
[1] FALSE
D1051V9, binary
               cls
clus              0   1
  IVD MUTATED     4   1
  IVD WILD-TYPE 310  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      4    1
  IVD WILD-TYPE  310   47
                               clus
vv                              IVD MUTATED IVD WILD-TYPE
  COLON ADENOCARCINOMA                    4           310
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  IVD MUTATED     4   0   0   1
  IVD WILD-TYPE 255   3  22  20
D1051V10, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  R0           4           255
  R1           0             3
  R2           0            22
  RX           1            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"
D1051V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IVD MUTATED                                  0     1
  IVD WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IVD MUTATED                           0     4
  IVD WILD-TYPE                        19   172
D1051V12, multiclass
                                  clus
vv                                 IVD MUTATED IVD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      4           172
[1] 4 2
[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 = PSMA2 MUTATION ANALYSIS
D1052V1, survival
                 sevent
clus2               0   1
  PSMA2 MUTATED     4   2
  PSMA2 WILD-TYPE 273  76
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             349 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              2              76 
$`PSMA2 MUTATED`
TCGA-AD-6895 TCGA-G4-6321 TCGA-AA-3492 TCGA-AA-A00A TCGA-CK-4950 TCGA-F4-6570 
       25.08        22.09         3.02        38.04        85.45         6.18 

$`PSMA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PSMA2 MUTATED PSMA2 WILD-TYPE 
           3.02            0.00 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
          85.45          148.01 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
         23.585          22.030 
[1] "3.0 - 85.5 (23.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1052V2, continuous
                 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      64        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMA2 MUTATED           1          0          2          0        0         0
  PSMA2 WILD-TYPE        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  PSMA2 MUTATED           0
  PSMA2 WILD-TYPE         1
D1052V3, multiclass
            clus
vv           PSMA2 MUTATED PSMA2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PSMA2 MUTATED     0   1   5   0
  PSMA2 WILD-TYPE   9  66 244  41
D1052V4, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             0              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
  PSMA2 MUTATED     3   3   0
  PSMA2 WILD-TYPE 217  78  66
D1052V5, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  N0             3             217
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V6, binary
                 cls
clus                0   1
  PSMA2 MUTATED     5   0
  PSMA2 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      5    0
  PSMA2 WILD-TYPE  280   48
   clus
vv  PSMA2 MUTATED PSMA2 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1052V7, binary
                 cls
clus                0   1
  PSMA2 MUTATED     4   2
  PSMA2 WILD-TYPE 166 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      4    2
  PSMA2 WILD-TYPE  166  195
        clus
vv       PSMA2 MUTATED PSMA2 WILD-TYPE
  FEMALE             4             166
  MALE               2             195
[1] 2 2
[1] FALSE
D1052V8, binary
                 cls
clus                0   1
  PSMA2 MUTATED     6   0
  PSMA2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      6    0
  PSMA2 WILD-TYPE  294    8
     clus
vv    PSMA2 MUTATED PSMA2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1052V9, binary
                 cls
clus                0   1
  PSMA2 MUTATED     5   1
  PSMA2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      5    1
  PSMA2 WILD-TYPE  309   47
                               clus
vv                              PSMA2 MUTATED PSMA2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMA2 MUTATED     5   1   0   0
  PSMA2 WILD-TYPE 254   2  22  21
D1052V10, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  R0             5             254
  R1             1               2
  R2             0              22
  RX             0              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"
D1052V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMA2 MUTATED                                  0     0
  PSMA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSMA2 MUTATED                           1     3
  PSMA2 WILD-TYPE                        18   173
D1052V12, multiclass
                                  clus
vv                                 PSMA2 MUTATED PSMA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = TUT1 MUTATION ANALYSIS
D1053V1, survival
                sevent
clus2              0   1
  TUT1 MUTATED     9   0
  TUT1 WILD-TYPE 268  78
  TUT1 MUTATED TUT1 WILD-TYPE 
             9            346 
  TUT1 MUTATED TUT1 WILD-TYPE 
             0             78 
$`TUT1 MUTATED`
TCGA-AA-3950 TCGA-A6-5661 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3837 
       24.00        33.53        20.12        19.66         1.02        38.99 
TCGA-AU-6004 TCGA-CM-5860 TCGA-D5-6529 
       27.09        32.02        20.19 

$`TUT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TUT1 MUTATED TUT1 WILD-TYPE 
          1.02           0.00 
  TUT1 MUTATED TUT1 WILD-TYPE 
         38.99         148.01 
  TUT1 MUTATED TUT1 WILD-TYPE 
        24.000         22.045 
[1] "1.0 - 39.0 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1053V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUT1 MUTATED         1        0        0         7         0         0
  TUT1 WILD-TYPE      63        1       26       101         8         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        18          6         44         32       35        12
                vv
clus             STAGE IVB
  TUT1 MUTATED           0
  TUT1 WILD-TYPE         1
D1053V3, multiclass
            clus
vv           TUT1 MUTATED TUT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TUT1 MUTATED     0   1   7   1
  TUT1 WILD-TYPE   9  66 242  40
D1053V4, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            1             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
  TUT1 MUTATED     8   1   0
  TUT1 WILD-TYPE 212  80  66
D1053V5, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  N0            8            212
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V6, binary
                cls
clus               0   1
  TUT1 MUTATED     7   0
  TUT1 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      7    0
  TUT1 WILD-TYPE  278   48
   clus
vv  TUT1 MUTATED TUT1 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1053V7, binary
                cls
clus               0   1
  TUT1 MUTATED     4   5
  TUT1 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      4    5
  TUT1 WILD-TYPE  166  192
        clus
vv       TUT1 MUTATED TUT1 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D1053V8, binary
                cls
clus               0   1
  TUT1 MUTATED     7   0
  TUT1 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      7    0
  TUT1 WILD-TYPE  293    8
     clus
vv    TUT1 MUTATED TUT1 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1053V9, binary
                cls
clus               0   1
  TUT1 MUTATED     5   4
  TUT1 WILD-TYPE 309  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      5    4
  TUT1 WILD-TYPE  309   44
                               clus
vv                              TUT1 MUTATED TUT1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TUT1 MUTATED     8   0   0   0
  TUT1 WILD-TYPE 251   3  22  21
D1053V10, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D1053V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUT1 MUTATED                                  0     0
  TUT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TUT1 MUTATED                           1     5
  TUT1 WILD-TYPE                        18   171
D1053V12, multiclass
                                  clus
vv                                 TUT1 MUTATED TUT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = AFF1 MUTATION ANALYSIS
D1054V1, survival
                sevent
clus2              0   1
  AFF1 MUTATED     7   5
  AFF1 WILD-TYPE 270  73
  AFF1 MUTATED AFF1 WILD-TYPE 
            12            343 
  AFF1 MUTATED AFF1 WILD-TYPE 
             5             73 
$`AFF1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6652 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N 
      100.01        26.17        24.69        27.02        25.02         4.01 
TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6170 TCGA-CM-6677 TCGA-D5-5537 
       21.44        12.76        21.14        15.02        11.08        45.40 

$`AFF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.060 
[1] "4.0 - 100.0 (23.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1054V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AFF1 MUTATED         2        0        1         5         1         0
  AFF1 WILD-TYPE      62        1       25       103         7         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        18          6         44         33       34        11
                vv
clus             STAGE IVB
  AFF1 MUTATED           0
  AFF1 WILD-TYPE         1
D1054V3, multiclass
            clus
vv           AFF1 MUTATED AFF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  AFF1 MUTATED     1   2   7   2
  AFF1 WILD-TYPE   8  65 242  39
D1054V4, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            7            242
  T4            2             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
  AFF1 MUTATED    10   0   2
  AFF1 WILD-TYPE 210  81  64
D1054V5, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  N0           10            210
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V6, binary
                cls
clus               0   1
  AFF1 MUTATED     7   2
  AFF1 WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED      7    2
  AFF1 WILD-TYPE  278   46
   clus
vv  AFF1 MUTATED AFF1 WILD-TYPE
  0            7            278
  1            2             46
[1] 2 2
[1] FALSE
D1054V7, binary
                cls
clus               0   1
  AFF1 MUTATED     4   8
  AFF1 WILD-TYPE 166 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED      4    8
  AFF1 WILD-TYPE  166  189
        clus
vv       AFF1 MUTATED AFF1 WILD-TYPE
  FEMALE            4            166
  MALE              8            189
[1] 2 2
[1] FALSE
D1054V8, binary
                cls
clus               0   1
  AFF1 MUTATED    11   0
  AFF1 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED     11    0
  AFF1 WILD-TYPE  289    8
     clus
vv    AFF1 MUTATED AFF1 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1054V9, binary
                cls
clus               0   1
  AFF1 MUTATED    10   2
  AFF1 WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED     10    2
  AFF1 WILD-TYPE  304   46
                               clus
vv                              AFF1 MUTATED AFF1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AFF1 MUTATED     5   0   1   3
  AFF1 WILD-TYPE 254   3  21  18
D1054V10, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            1             21
  RX            3             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"
D1054V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AFF1 MUTATED                                  0     1
  AFF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AFF1 MUTATED                           1     7
  AFF1 WILD-TYPE                        18   169
D1054V12, multiclass
                                  clus
vv                                 AFF1 MUTATED AFF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = KRTAP10-11 MUTATION ANALYSIS
D1055V1, survival
                      sevent
clus2                    0   1
  KRTAP10-11 MUTATED     4   1
  KRTAP10-11 WILD-TYPE 273  77
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   5                  350 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   1                   77 
$`KRTAP10-11 MUTATED`
TCGA-G4-6588 TCGA-A6-5660 TCGA-A6-6781 TCGA-AA-A010 TCGA-DM-A0XF 
       26.17        29.19        19.66        34.98        38.20 

$`KRTAP10-11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               19.66                 0.00 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               38.20               148.01 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               29.19                22.01 
[1] "19.7 - 38.2 (29.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1055V2, continuous
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRTAP10-11 MUTATED         0        0        0         1         1         0
  KRTAP10-11 WILD-TYPE      64        1       26       107         7         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        18          6         44         30       35
                      vv
clus                   STAGE IVA STAGE IVB
  KRTAP10-11 MUTATED           0         0
  KRTAP10-11 WILD-TYPE        12         1
D1055V3, multiclass
            clus
vv           KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  STAGE I                     0                   64
  STAGE IA                    0                    1
  STAGE II                    0                   26
  STAGE IIA                   1                  107
  STAGE IIB                   1                    7
  STAGE IIC                   0                    1
  STAGE III                   0                   18
  STAGE IIIA                  0                    6
  STAGE IIIB                  0                   44
  STAGE IIIC                  3                   30
  STAGE IV                    0                   35
  STAGE IVA                   0                   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
  KRTAP10-11 MUTATED     0   0   3   2
  KRTAP10-11 WILD-TYPE   9  67 246  39
D1055V4, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  T1                  0                    9
  T2                  0                   67
  T3                  3                  246
  T4                  2                   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
  KRTAP10-11 MUTATED     2   1   2
  KRTAP10-11 WILD-TYPE 218  80  64
D1055V5, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  N0                  2                  218
  N1                  1                   80
  N2                  2                   64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V6, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     4   0
  KRTAP10-11 WILD-TYPE 281  48
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      4    0
  KRTAP10-11 WILD-TYPE  281   48
   clus
vv  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  0                  4                  281
  1                  0                   48
[1] 2 2
[1] FALSE
D1055V7, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     3   2
  KRTAP10-11 WILD-TYPE 167 195
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      3    2
  KRTAP10-11 WILD-TYPE  167  195
        clus
vv       KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  FEMALE                  3                  167
  MALE                    2                  195
[1] 2 2
[1] FALSE
D1055V8, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     4   0
  KRTAP10-11 WILD-TYPE 296   8
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      4    0
  KRTAP10-11 WILD-TYPE  296    8
     clus
vv    KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  NO                   4                  296
  YES                  0                    8
[1] 2 2
[1] FALSE
D1055V9, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     3   1
  KRTAP10-11 WILD-TYPE 311  47
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      3    1
  KRTAP10-11 WILD-TYPE  311   47
                               clus
vv                              KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  COLON ADENOCARCINOMA                           3                  311
  COLON MUCINOUS ADENOCARCINOMA                  1                   47
[1] 2 2
[1] FALSE
                      vv
clus                    R0  R1  R2  RX
  KRTAP10-11 MUTATED     3   0   0   0
  KRTAP10-11 WILD-TYPE 256   3  22  21
D1055V10, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  R0                  3                  256
  R1                  0                    3
  R2                  0                   22
  RX                  0                   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"
D1055V11, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP10-11 MUTATED                                  0     0
  KRTAP10-11 WILD-TYPE                                1    10
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-11 MUTATED                           1     3
  KRTAP10-11 WILD-TYPE                        18   173
D1055V12, multiclass
                                  clus
vv                                 KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             0                   10
  BLACK OR AFRICAN AMERICAN                         1                   18
  WHITE                                             3                  173
[1] 4 2
[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 = CTCF MUTATION ANALYSIS
D1056V1, survival
                sevent
clus2              0   1
  CTCF MUTATED    14   3
  CTCF WILD-TYPE 263  75
  CTCF MUTATED CTCF WILD-TYPE 
            17            338 
  CTCF MUTATED CTCF WILD-TYPE 
             3             75 
$`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 
       22.98        15.02        12.39         9.44        85.48 

$`CTCF WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 
       61.02        78.08         6.97        54.02         2.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       124.27        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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CTCF MUTATED CTCF WILD-TYPE 
             0              0 
  CTCF MUTATED CTCF WILD-TYPE 
         85.48         148.01 
  CTCF MUTATED CTCF WILD-TYPE 
        19.000         22.225 
[1] "0.0 - 85.5 (19.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.1"
D1056V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTCF MUTATED         3        0        0         8         2         0
  CTCF WILD-TYPE      61        1       26       100         6         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        18          6         41         33       34        12
                vv
clus             STAGE IVB
  CTCF MUTATED           0
  CTCF WILD-TYPE         1
D1056V3, multiclass
            clus
vv           CTCF MUTATED CTCF WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  CTCF MUTATED     0   3  11   3
  CTCF WILD-TYPE   9  64 238  38
D1056V4, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  T1            0              9
  T2            3             64
  T3           11            238
  T4            3             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
  CTCF MUTATED    13   4   0
  CTCF WILD-TYPE 207  77  66
D1056V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0           13            207
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V6, binary
                cls
clus               0   1
  CTCF MUTATED    15   1
  CTCF WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15    1
  CTCF WILD-TYPE  270   47
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0           15            270
  1            1             47
[1] 2 2
[1] FALSE
D1056V7, binary
                cls
clus               0   1
  CTCF MUTATED    10   7
  CTCF WILD-TYPE 160 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     10    7
  CTCF WILD-TYPE  160  190
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE           10            160
  MALE              7            190
[1] 2 2
[1] FALSE
D1056V8, binary
                cls
clus               0   1
  CTCF MUTATED    15   0
  CTCF WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15    0
  CTCF WILD-TYPE  285    8
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D1056V9, binary
                cls
clus               0   1
  CTCF MUTATED    17   0
  CTCF WILD-TYPE 297  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     17    0
  CTCF WILD-TYPE  297   48
                               clus
vv                              CTCF MUTATED CTCF WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTCF MUTATED    15   0   0   1
  CTCF WILD-TYPE 244   3  22  20
D1056V10, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           15            244
  R1            0              3
  R2            0             22
  RX            1             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"
D1056V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCF MUTATED                                  0     1
  CTCF WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTCF MUTATED                           2     9
  CTCF WILD-TYPE                        17   167
D1056V12, multiclass
                                  clus
vv                                 CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       9            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(1057) Variable = STYK1 MUTATION ANALYSIS
D1057V1, survival
                 sevent
clus2               0   1
  STYK1 MUTATED     4   3
  STYK1 WILD-TYPE 273  75
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             348 
  STYK1 MUTATED STYK1 WILD-TYPE 
              3              75 
$`STYK1 MUTATED`
TCGA-AD-6964 TCGA-AZ-6608 TCGA-G4-6588 TCGA-AA-A01R TCGA-D5-6537 TCGA-D5-6538 
       10.88         1.94        26.17        35.01         4.80        17.13 
TCGA-G4-6307 
       55.04 

$`STYK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  STYK1 MUTATED STYK1 WILD-TYPE 
           1.94            0.00 
  STYK1 MUTATED STYK1 WILD-TYPE 
          55.04          148.01 
  STYK1 MUTATED STYK1 WILD-TYPE 
         17.130          22.075 
[1] "1.9 - 55.0 (17.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D1057V2, continuous
                 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      64        1       26       107         8         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        17          5         41         33       35        12
                 vv
clus              STAGE IVB
  STYK1 MUTATED           0
  STYK1 WILD-TYPE         1
D1057V3, multiclass
            clus
vv           STYK1 MUTATED STYK1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  STYK1 MUTATED     0   1   5   1
  STYK1 WILD-TYPE   9  66 244  40
D1057V4, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             1              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
  STYK1 MUTATED     1   3   3
  STYK1 WILD-TYPE 219  78  63
D1057V5, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  N0             1             219
  N1             3              78
  N2             3              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"
D1057V6, binary
                 cls
clus                0   1
  STYK1 MUTATED     5   0
  STYK1 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      5    0
  STYK1 WILD-TYPE  280   48
   clus
vv  STYK1 MUTATED STYK1 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1057V7, binary
                 cls
clus                0   1
  STYK1 MUTATED     4   3
  STYK1 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      4    3
  STYK1 WILD-TYPE  166  194
        clus
vv       STYK1 MUTATED STYK1 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1057V8, binary
                 cls
clus                0   1
  STYK1 MUTATED     6   1
  STYK1 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      6    1
  STYK1 WILD-TYPE  294    7
     clus
vv    STYK1 MUTATED STYK1 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D1057V9, binary
                 cls
clus                0   1
  STYK1 MUTATED     6   1
  STYK1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      6    1
  STYK1 WILD-TYPE  308   47
                               clus
vv                              STYK1 MUTATED STYK1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STYK1 MUTATED     5   0   0   0
  STYK1 WILD-TYPE 254   3  22  21
D1057V10, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1057V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STYK1 MUTATED                                  0     0
  STYK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STYK1 MUTATED                           0     6
  STYK1 WILD-TYPE                        19   170
D1057V12, multiclass
                                  clus
vv                                 STYK1 MUTATED STYK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = BCAP29 MUTATION ANALYSIS
D1058V1, survival
                  sevent
clus2                0   1
  BCAP29 MUTATED     7   0
  BCAP29 WILD-TYPE 270  78
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               7              348 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               0               78 
$`BCAP29 MUTATED`
TCGA-AA-3713 TCGA-AA-3977 TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-6675 
       19.04        25.02        12.16        12.76       148.01        13.05 
TCGA-DM-A28K 
       98.24 

$`BCAP29 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  BCAP29 MUTATED BCAP29 WILD-TYPE 
           12.16             0.00 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
          148.01           140.38 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
          19.040           22.075 
[1] "12.2 - 148.0 (19.0)" "0.0 - 140.4 (22.1)" 
[1] "hr="     "2.6e+07"
D1058V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCAP29 MUTATED         1        0        0         2         0         0
  BCAP29 WILD-TYPE      63        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCAP29 MUTATED           1          0          0          0        1
  BCAP29 WILD-TYPE        17          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  BCAP29 MUTATED           0         1
  BCAP29 WILD-TYPE        12         0
D1058V3, multiclass
            clus
vv           BCAP29 MUTATED BCAP29 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               12
  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   5   0
  BCAP29 WILD-TYPE   9  65 244  41
D1058V4, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              0               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
  BCAP29 MUTATED     5   1   1
  BCAP29 WILD-TYPE 215  80  65
D1058V5, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V6, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     3   2
  BCAP29 WILD-TYPE 282  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      3    2
  BCAP29 WILD-TYPE  282   46
   clus
vv  BCAP29 MUTATED BCAP29 WILD-TYPE
  0              3              282
  1              2               46
[1] 2 2
[1] FALSE
D1058V7, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     1   6
  BCAP29 WILD-TYPE 169 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      1    6
  BCAP29 WILD-TYPE  169  191
        clus
vv       BCAP29 MUTATED BCAP29 WILD-TYPE
  FEMALE              1              169
  MALE                6              191
[1] 2 2
[1] FALSE
D1058V8, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     5   1
  BCAP29 WILD-TYPE 295   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      5    1
  BCAP29 WILD-TYPE  295    7
     clus
vv    BCAP29 MUTATED BCAP29 WILD-TYPE
  NO               5              295
  YES              1                7
[1] 2 2
[1] FALSE
D1058V9, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     4   3
  BCAP29 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      4    3
  BCAP29 WILD-TYPE  310   45
                               clus
vv                              BCAP29 MUTATED BCAP29 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BCAP29 MUTATED     3   0   1   1
  BCAP29 WILD-TYPE 256   3  21  20
D1058V10, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              1               21
  RX              1               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"
D1058V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCAP29 MUTATED                                  0     1
  BCAP29 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCAP29 MUTATED                           1     3
  BCAP29 WILD-TYPE                        18   173
D1058V12, multiclass
                                  clus
vv                                 BCAP29 MUTATED BCAP29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = SERPINB7 MUTATION ANALYSIS
D1059V1, survival
                    sevent
clus2                  0   1
  SERPINB7 MUTATED     6   2
  SERPINB7 WILD-TYPE 271  76
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                347 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 2                 76 
$`SERPINB7 MUTATED`
TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3555 TCGA-AA-A010 TCGA-AZ-4315 
       79.69        22.06        23.87        29.95        34.98        58.39 
TCGA-AZ-6598 TCGA-F4-6460 
       49.41        31.96 

$`SERPINB7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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              21.99 
[1] "22.1 - 79.7 (33.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1059V2, continuous
                    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      63        1       25       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB7 MUTATED           0          0          2          0        0
  SERPINB7 WILD-TYPE        18          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINB7 MUTATED           0         0
  SERPINB7 WILD-TYPE        12         1
D1059V3, multiclass
            clus
vv           SERPINB7 MUTATED SERPINB7 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 3                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SERPINB7 MUTATED     0   1   6   1
  SERPINB7 WILD-TYPE   9  66 243  40
D1059V4, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                6                243
  T4                1                 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
  SERPINB7 MUTATED     6   2   0
  SERPINB7 WILD-TYPE 214  79  66
D1059V5, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  N0                6                214
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V6, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     7   0
  SERPINB7 WILD-TYPE 278  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      7    0
  SERPINB7 WILD-TYPE  278   48
   clus
vv  SERPINB7 MUTATED SERPINB7 WILD-TYPE
  0                7                278
  1                0                 48
[1] 2 2
[1] FALSE
D1059V7, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     6   2
  SERPINB7 WILD-TYPE 164 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      6    2
  SERPINB7 WILD-TYPE  164  195
        clus
vv       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  FEMALE                6                164
  MALE                  2                195
[1] 2 2
[1] FALSE
D1059V8, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     8   0
  SERPINB7 WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      8    0
  SERPINB7 WILD-TYPE  292    8
     clus
vv    SERPINB7 MUTATED SERPINB7 WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D1059V9, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     7   1
  SERPINB7 WILD-TYPE 307  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      7    1
  SERPINB7 WILD-TYPE  307   47
                               clus
vv                              SERPINB7 MUTATED SERPINB7 WILD-TYPE
  COLON ADENOCARCINOMA                         7                307
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SERPINB7 MUTATED     6   0   0   0
  SERPINB7 WILD-TYPE 253   3  22  21
D1059V10, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1059V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB7 MUTATED                                  0     0
  SERPINB7 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SERPINB7 MUTATED                           0     6
  SERPINB7 WILD-TYPE                        19   170
D1059V12, multiclass
                                  clus
vv                                 SERPINB7 MUTATED SERPINB7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = SPAST MUTATION ANALYSIS
D1060V1, survival
                 sevent
clus2               0   1
  SPAST MUTATED     5   4
  SPAST WILD-TYPE 272  74
  SPAST MUTATED SPAST WILD-TYPE 
              9             346 
  SPAST MUTATED SPAST WILD-TYPE 
              4              74 
$`SPAST MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AZ-4315 
       19.04       100.01        53.00        33.01        25.02        58.39 
TCGA-AZ-6603 TCGA-CA-6718 TCGA-G4-6309 
       29.56        10.06        85.48 

$`SPAST WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10         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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SPAST MUTATED SPAST WILD-TYPE 
          10.06            0.00 
  SPAST MUTATED SPAST WILD-TYPE 
         100.01          148.01 
  SPAST MUTATED SPAST WILD-TYPE 
          33.01           21.99 
[1] "10.1 - 100.0 (33.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.2"
D1060V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPAST MUTATED         0        0        3         2         1         0
  SPAST WILD-TYPE      64        1       23       106         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  SPAST MUTATED           0
  SPAST WILD-TYPE         1
D1060V3, multiclass
            clus
vv           SPAST MUTATED SPAST WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  SPAST MUTATED     0   2   6   1
  SPAST WILD-TYPE   9  65 243  40
D1060V4, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             1              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
  SPAST MUTATED     7   2   0
  SPAST WILD-TYPE 213  79  66
D1060V5, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  N0             7             213
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V6, binary
                 cls
clus                0   1
  SPAST MUTATED     7   0
  SPAST WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      7    0
  SPAST WILD-TYPE  278   48
   clus
vv  SPAST MUTATED SPAST WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1060V7, binary
                 cls
clus                0   1
  SPAST MUTATED     3   6
  SPAST WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      3    6
  SPAST WILD-TYPE  167  191
        clus
vv       SPAST MUTATED SPAST WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1060V8, binary
                 cls
clus                0   1
  SPAST MUTATED     9   0
  SPAST WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      9    0
  SPAST WILD-TYPE  291    8
     clus
vv    SPAST MUTATED SPAST WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1060V9, binary
                 cls
clus                0   1
  SPAST MUTATED     8   1
  SPAST WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      8    1
  SPAST WILD-TYPE  306   47
                               clus
vv                              SPAST MUTATED SPAST WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPAST MUTATED     5   0   0   1
  SPAST WILD-TYPE 254   3  22  20
D1060V10, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D1060V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPAST MUTATED                                  0     1
  SPAST WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPAST MUTATED                           1     3
  SPAST WILD-TYPE                        18   173
D1060V12, multiclass
                                  clus
vv                                 SPAST MUTATED SPAST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = NFKBIB MUTATION ANALYSIS
D1061V1, survival
                  sevent
clus2                0   1
  NFKBIB MUTATED     2   3
  NFKBIB WILD-TYPE 275  75
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              350 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               3               75 
$`NFKBIB MUTATED`
TCGA-G4-6588 TCGA-AA-3875 TCGA-AZ-6605 TCGA-DM-A1D7 TCGA-G4-6303 
       26.17        18.05         5.23        13.32        65.85 

$`NFKBIB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 
       31.07        30.05        53.00        17.03        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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           22.075 
[1] "5.2 - 65.8 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1061V2, continuous
                  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      63        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFKBIB MUTATED           0          0          1          0        1
  NFKBIB WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  NFKBIB MUTATED           0         0
  NFKBIB WILD-TYPE        12         1
D1061V3, multiclass
            clus
vv           NFKBIB MUTATED NFKBIB WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  NFKBIB MUTATED     1   0   3   1
  NFKBIB WILD-TYPE   8  67 246  40
D1061V4, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  T1              1                8
  T2              0               67
  T3              3              246
  T4              1               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
  NFKBIB MUTATED     3   2   0
  NFKBIB WILD-TYPE 217  79  66
D1061V5, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  N0              3              217
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V6, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     4   1
  NFKBIB WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      4    1
  NFKBIB WILD-TYPE  281   47
   clus
vv  NFKBIB MUTATED NFKBIB WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1061V7, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     3   2
  NFKBIB WILD-TYPE 167 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      3    2
  NFKBIB WILD-TYPE  167  195
        clus
vv       NFKBIB MUTATED NFKBIB WILD-TYPE
  FEMALE              3              167
  MALE                2              195
[1] 2 2
[1] FALSE
D1061V8, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     4   0
  NFKBIB WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      4    0
  NFKBIB WILD-TYPE  296    8
     clus
vv    NFKBIB MUTATED NFKBIB WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1061V9, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     4   0
  NFKBIB WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      4    0
  NFKBIB WILD-TYPE  310   48
                               clus
vv                              NFKBIB MUTATED NFKBIB WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NFKBIB MUTATED     3   0   0   0
  NFKBIB WILD-TYPE 256   3  22  21
D1061V10, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1061V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFKBIB MUTATED                                  0     0
  NFKBIB WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFKBIB MUTATED                           0     4
  NFKBIB WILD-TYPE                        19   172
D1061V12, multiclass
                                  clus
vv                                 NFKBIB MUTATED NFKBIB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = ARID5A MUTATION ANALYSIS
D1062V1, survival
                  sevent
clus2                0   1
  ARID5A MUTATED     6   1
  ARID5A WILD-TYPE 271  77
  ARID5A MUTATED ARID5A WILD-TYPE 
               7              348 
  ARID5A MUTATED ARID5A WILD-TYPE 
               1               77 
$`ARID5A MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-AA-3502 TCGA-AD-5900 TCGA-CA-6715 TCGA-CM-4743 
      100.01        79.69        35.01        12.16        12.59        23.05 
TCGA-CM-5861 
       15.02 

$`ARID5A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARID5A MUTATED ARID5A WILD-TYPE 
           12.16             0.00 
  ARID5A MUTATED ARID5A WILD-TYPE 
          100.01           148.01 
  ARID5A MUTATED ARID5A WILD-TYPE 
          23.050           22.045 
[1] "12.2 - 100.0 (23.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.2"
D1062V2, continuous
                  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      61        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID5A MUTATED           0          0          1          0        0
  ARID5A WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ARID5A MUTATED           0         0
  ARID5A WILD-TYPE        12         1
D1062V3, multiclass
            clus
vv           ARID5A MUTATED ARID5A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ARID5A MUTATED     0   3   5   0
  ARID5A WILD-TYPE   9  64 244  41
D1062V4, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              0               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
  ARID5A MUTATED     7   1   0
  ARID5A WILD-TYPE 213  80  66
D1062V5, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  N0              7              213
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V6, binary
                  cls
clus                 0   1
  ARID5A MUTATED     7   0
  ARID5A WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      7    0
  ARID5A WILD-TYPE  278   48
   clus
vv  ARID5A MUTATED ARID5A WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1062V7, binary
                  cls
clus                 0   1
  ARID5A MUTATED     2   6
  ARID5A WILD-TYPE 168 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      2    6
  ARID5A WILD-TYPE  168  191
        clus
vv       ARID5A MUTATED ARID5A WILD-TYPE
  FEMALE              2              168
  MALE                6              191
[1] 2 2
[1] FALSE
D1062V8, binary
                  cls
clus                 0   1
  ARID5A MUTATED     7   0
  ARID5A WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      7    0
  ARID5A WILD-TYPE  293    8
     clus
vv    ARID5A MUTATED ARID5A WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1062V9, binary
                  cls
clus                 0   1
  ARID5A MUTATED     7   1
  ARID5A WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      7    1
  ARID5A WILD-TYPE  307   47
                               clus
vv                              ARID5A MUTATED ARID5A WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID5A MUTATED     6   0   0   1
  ARID5A WILD-TYPE 253   3  22  20
D1062V10, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1062V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID5A MUTATED                                  0     1
  ARID5A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID5A MUTATED                           0     5
  ARID5A WILD-TYPE                        19   171
D1062V12, multiclass
                                  clus
vv                                 ARID5A MUTATED ARID5A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = CSNK2A2 MUTATION ANALYSIS
D1063V1, survival
                   sevent
clus2                 0   1
  CSNK2A2 MUTATED     4   2
  CSNK2A2 WILD-TYPE 273  76
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                6               349 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                2                76 
$`CSNK2A2 MUTATED`
TCGA-G4-6588 TCGA-AZ-6599 TCGA-CM-5868 TCGA-D5-6535 TCGA-D5-6927 TCGA-F4-6570 
       26.17         6.77        17.03        15.12         9.44         6.18 

$`CSNK2A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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             22.09 
[1] "6.2 - 26.2 (12.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1063V2, continuous
                   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      63        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK2A2 MUTATED           0          0          1          0        1
  CSNK2A2 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  CSNK2A2 MUTATED           1         0
  CSNK2A2 WILD-TYPE        11         1
D1063V3, multiclass
            clus
vv           CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                1                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
  CSNK2A2 MUTATED     0   1   4   2
  CSNK2A2 WILD-TYPE   9  66 245  39
D1063V4, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               2                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
  CSNK2A2 MUTATED     4   3   0
  CSNK2A2 WILD-TYPE 216  78  66
D1063V5, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  N0               4               216
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V6, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     3   2
  CSNK2A2 WILD-TYPE 282  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      3    2
  CSNK2A2 WILD-TYPE  282   46
   clus
vv  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  0               3               282
  1               2                46
[1] 2 2
[1] FALSE
D1063V7, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     5   2
  CSNK2A2 WILD-TYPE 165 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      5    2
  CSNK2A2 WILD-TYPE  165  195
        clus
vv       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  FEMALE               5               165
  MALE                 2               195
[1] 2 2
[1] FALSE
D1063V8, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     6   0
  CSNK2A2 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      6    0
  CSNK2A2 WILD-TYPE  294    8
     clus
vv    CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1063V9, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     7   0
  CSNK2A2 WILD-TYPE 307  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      7    0
  CSNK2A2 WILD-TYPE  307   48
                               clus
vv                              CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CSNK2A2 MUTATED     4   0   1   1
  CSNK2A2 WILD-TYPE 255   3  21  20
D1063V10, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               1                21
  RX               1                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"
D1063V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK2A2 MUTATED                                  0     0
  CSNK2A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CSNK2A2 MUTATED                           0     6
  CSNK2A2 WILD-TYPE                        19   170
D1063V12, multiclass
                                  clus
vv                                 CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = AK3L1 MUTATION ANALYSIS
D1064V1, survival
                 sevent
clus2               0   1
  AK3L1 MUTATED     3   0
  AK3L1 WILD-TYPE 274  78
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              3             352 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              0              78 
$`AK3L1 MUTATED`
TCGA-G4-6321 TCGA-A6-6781 TCGA-CM-6168 
       22.09        19.66        12.99 

$`AK3L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  AK3L1 MUTATED AK3L1 WILD-TYPE 
          12.99            0.00 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
          22.09          148.01 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
         19.660          22.075 
[1] "13.0 - 22.1 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1064V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AK3L1 MUTATED         0        0        0         1         0         0
  AK3L1 WILD-TYPE      64        1       26       107         8         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        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  AK3L1 MUTATED           0
  AK3L1 WILD-TYPE         1
D1064V3, multiclass
            clus
vv           AK3L1 MUTATED AK3L1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  AK3L1 MUTATED     0   1   1   1
  AK3L1 WILD-TYPE   9  66 248  40
D1064V4, multiclass
    clus
vv   AK3L1 MUTATED AK3L1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             1             248
  T4             1              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
  AK3L1 MUTATED     1   2   0
  AK3L1 WILD-TYPE 219  79  66
D1064V5, multiclass
    clus
vv   AK3L1 MUTATED AK3L1 WILD-TYPE
  N0             1             219
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V6, binary
                 cls
clus                0   1
  AK3L1 MUTATED     1   0
  AK3L1 WILD-TYPE 284  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      1    0
  AK3L1 WILD-TYPE  284   48
   clus
vv  AK3L1 MUTATED AK3L1 WILD-TYPE
  0             1             284
  1             0              48
[1] 2 2
[1] FALSE
D1064V7, binary
                 cls
clus                0   1
  AK3L1 MUTATED     2   1
  AK3L1 WILD-TYPE 168 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      2    1
  AK3L1 WILD-TYPE  168  196
        clus
vv       AK3L1 MUTATED AK3L1 WILD-TYPE
  FEMALE             2             168
  MALE               1             196
[1] 2 2
[1] FALSE
D1064V8, binary
                 cls
clus                0   1
  AK3L1 MUTATED     3   0
  AK3L1 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      3    0
  AK3L1 WILD-TYPE  297    8
     clus
vv    AK3L1 MUTATED AK3L1 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1064V9, binary
                 cls
clus                0   1
  AK3L1 MUTATED     2   1
  AK3L1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      2    1
  AK3L1 WILD-TYPE  312   47
                               clus
vv                              AK3L1 MUTATED AK3L1 WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AK3L1 MUTATED     3   0   0   0
  AK3L1 WILD-TYPE 256   3  22  21
D1064V10, multiclass
    clus
vv   AK3L1 MUTATED AK3L1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1064V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AK3L1 MUTATED                                  0     0
  AK3L1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AK3L1 MUTATED                           1     2
  AK3L1 WILD-TYPE                        18   174
D1064V12, multiclass
                                  clus
vv                                 AK3L1 MUTATED AK3L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(1065) Variable = IFITM3 MUTATION ANALYSIS
D1065V1, survival
                  sevent
clus2                0   1
  IFITM3 MUTATED     6   0
  IFITM3 WILD-TYPE 271  78
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               6              349 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               0               78 
$`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 

$`IFITM3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        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-D5-5541 
       10.06        12.03        45.40        54.61        19.59        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  IFITM3 MUTATED IFITM3 WILD-TYPE 
           16.04             0.00 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           56.09           148.01 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           25.76            22.06 
[1] "16.0 - 56.1 (25.8)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D1065V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFITM3 MUTATED         0        0        0         5         0         0
  IFITM3 WILD-TYPE      64        1       26       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM3 MUTATED           0          0          0          1        0
  IFITM3 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  IFITM3 MUTATED           0         0
  IFITM3 WILD-TYPE        12         1
D1065V3, multiclass
            clus
vv           IFITM3 MUTATED IFITM3 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  IFITM3 MUTATED     0   0   6   0
  IFITM3 WILD-TYPE   9  67 243  41
D1065V4, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              0               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
  IFITM3 MUTATED     5   0   1
  IFITM3 WILD-TYPE 215  81  65
D1065V5, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V6, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     4   0
  IFITM3 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      4    0
  IFITM3 WILD-TYPE  281   48
   clus
vv  IFITM3 MUTATED IFITM3 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1065V7, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     2   4
  IFITM3 WILD-TYPE 168 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      2    4
  IFITM3 WILD-TYPE  168  193
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  FEMALE              2              168
  MALE                4              193
[1] 2 2
[1] FALSE
D1065V8, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     6   0
  IFITM3 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      6    0
  IFITM3 WILD-TYPE  294    8
     clus
vv    IFITM3 MUTATED IFITM3 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1065V9, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     6   0
  IFITM3 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      6    0
  IFITM3 WILD-TYPE  308   48
                               clus
vv                              IFITM3 MUTATED IFITM3 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IFITM3 MUTATED     6   0   0   0
  IFITM3 WILD-TYPE 253   3  22  21
D1065V10, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1065V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFITM3 MUTATED                                  0     0
  IFITM3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFITM3 MUTATED                           0     6
  IFITM3 WILD-TYPE                        19   170
D1065V12, multiclass
                                  clus
vv                                 IFITM3 MUTATED IFITM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = ACTN1 MUTATION ANALYSIS
D1066V1, survival
                 sevent
clus2               0   1
  ACTN1 MUTATED     9   0
  ACTN1 WILD-TYPE 268  78
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              9             346 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              0              78 
$`ACTN1 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6196 
       19.66        63.98        53.00        34.98        35.01         0.20 
TCGA-CA-6717 TCGA-D5-6929 TCGA-F4-6808 
       12.76        13.41        33.67 

$`ACTN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6626 
       61.91        36.00        13.78        46.75 

  ACTN1 MUTATED ACTN1 WILD-TYPE 
            0.2             0.0 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
          63.98          148.01 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
         33.670          22.045 
[1] "0.2 - 64.0 (33.7)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1066V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTN1 MUTATED         1        0        2         1         1         0
  ACTN1 WILD-TYPE      63        1       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTN1 MUTATED           1          0          0          2        1         0
  ACTN1 WILD-TYPE        17          6         44         31       34        12
                 vv
clus              STAGE IVB
  ACTN1 MUTATED           0
  ACTN1 WILD-TYPE         1
D1066V3, multiclass
            clus
vv           ACTN1 MUTATED ACTN1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  ACTN1 MUTATED     1   0   6   2
  ACTN1 WILD-TYPE   8  67 243  39
D1066V4, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             6             243
  T4             2              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
  ACTN1 MUTATED     5   2   2
  ACTN1 WILD-TYPE 215  79  64
D1066V5, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V6, binary
                 cls
clus                0   1
  ACTN1 MUTATED     6   1
  ACTN1 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      6    1
  ACTN1 WILD-TYPE  279   47
   clus
vv  ACTN1 MUTATED ACTN1 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1066V7, binary
                 cls
clus                0   1
  ACTN1 MUTATED     3   6
  ACTN1 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      3    6
  ACTN1 WILD-TYPE  167  191
        clus
vv       ACTN1 MUTATED ACTN1 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1066V8, binary
                 cls
clus                0   1
  ACTN1 MUTATED     7   1
  ACTN1 WILD-TYPE 293   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      7    1
  ACTN1 WILD-TYPE  293    7
     clus
vv    ACTN1 MUTATED ACTN1 WILD-TYPE
  NO              7             293
  YES             1               7
[1] 2 2
[1] FALSE
D1066V9, binary
                 cls
clus                0   1
  ACTN1 MUTATED     5   4
  ACTN1 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      5    4
  ACTN1 WILD-TYPE  309   44
                               clus
vv                              ACTN1 MUTATED ACTN1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACTN1 MUTATED     8   0   0   1
  ACTN1 WILD-TYPE 251   3  22  20
D1066V10, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1066V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTN1 MUTATED                                  0     1
  ACTN1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACTN1 MUTATED                           0     4
  ACTN1 WILD-TYPE                        19   172
D1066V12, multiclass
                                  clus
vv                                 ACTN1 MUTATED ACTN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = FAM193A MUTATION ANALYSIS
D1067V1, survival
                   sevent
clus2                 0   1
  FAM193A MUTATED    14   3
  FAM193A WILD-TYPE 263  75
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               338 
  FAM193A MUTATED FAM193A WILD-TYPE 
                3                75 
$`FAM193A MUTATED`
TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3660 
       25.08        10.88        26.17        22.06        20.12        78.08 
TCGA-AA-3947 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 
       33.01        12.16        49.41        10.06        15.62        51.32 
TCGA-CM-5861 TCGA-CM-6169 TCGA-D5-6927 TCGA-D5-7000 TCGA-G4-6304 
       15.02        13.02         9.44        10.26        53.62 

$`FAM193A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        21.37        15.52       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  FAM193A MUTATED FAM193A WILD-TYPE 
             9.44              0.00 
  FAM193A MUTATED FAM193A WILD-TYPE 
            78.08            148.01 
  FAM193A MUTATED FAM193A WILD-TYPE 
            20.12             22.09 
[1] "9.4 - 78.1 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1067V2, continuous
                   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      62        1       24       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM193A MUTATED           0          0          1          1        0
  FAM193A WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM193A MUTATED           0         0
  FAM193A WILD-TYPE        12         1
D1067V3, multiclass
            clus
vv           FAM193A MUTATED FAM193A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                8               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM193A MUTATED     0   2  11   4
  FAM193A WILD-TYPE   9  65 238  37
D1067V4, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              11               238
  T4               4                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
  FAM193A MUTATED    14   1   2
  FAM193A WILD-TYPE 206  80  64
D1067V5, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  N0              14               206
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V6, binary
                   cls
clus                  0   1
  FAM193A MUTATED    12   0
  FAM193A WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     12    0
  FAM193A WILD-TYPE  273   48
   clus
vv  FAM193A MUTATED FAM193A WILD-TYPE
  0              12               273
  1               0                48
[1] 2 2
[1] FALSE
D1067V7, binary
                   cls
clus                  0   1
  FAM193A MUTATED    10   7
  FAM193A WILD-TYPE 160 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     10    7
  FAM193A WILD-TYPE  160  190
        clus
vv       FAM193A MUTATED FAM193A WILD-TYPE
  FEMALE              10               160
  MALE                 7               190
[1] 2 2
[1] FALSE
D1067V8, binary
                   cls
clus                  0   1
  FAM193A MUTATED    16   0
  FAM193A WILD-TYPE 284   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     16    0
  FAM193A WILD-TYPE  284    8
     clus
vv    FAM193A MUTATED FAM193A WILD-TYPE
  NO               16               284
  YES               0                 8
[1] 2 2
[1] FALSE
D1067V9, binary
                   cls
clus                  0   1
  FAM193A MUTATED    12   5
  FAM193A WILD-TYPE 302  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     12    5
  FAM193A WILD-TYPE  302   43
                               clus
vv                              FAM193A MUTATED FAM193A WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM193A MUTATED    11   0   0   3
  FAM193A WILD-TYPE 248   3  22  18
D1067V10, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  R0              11               248
  R1               0                 3
  R2               0                22
  RX               3                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"
D1067V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM193A MUTATED                                  0     1
  FAM193A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM193A MUTATED                           1    13
  FAM193A WILD-TYPE                        18   163
D1067V12, multiclass
                                  clus
vv                                 FAM193A MUTATED FAM193A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         13               163
[1] 4 2
[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 = TAF6 MUTATION ANALYSIS
D1068V1, survival
                sevent
clus2              0   1
  TAF6 MUTATED     6   3
  TAF6 WILD-TYPE 271  75
  TAF6 MUTATED TAF6 WILD-TYPE 
             9            346 
  TAF6 MUTATED TAF6 WILD-TYPE 
             3             75 
$`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        12.16        15.02        16.14 
TCGA-F4-6460 TCGA-G4-6307 TCGA-G4-6317 
       31.96        55.04        36.00 

$`TAF6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6569 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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  TAF6 MUTATED TAF6 WILD-TYPE 
          1.02           0.00 
  TAF6 MUTATED TAF6 WILD-TYPE 
         55.04         148.01 
  TAF6 MUTATED TAF6 WILD-TYPE 
         15.02          22.09 
[1] "1.0 - 55.0 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1068V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF6 MUTATED         3        0        0         1         1         0
  TAF6 WILD-TYPE      61        1       26       107         7         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        17          6         42         32       35        12
                vv
clus             STAGE IVB
  TAF6 MUTATED           0
  TAF6 WILD-TYPE         1
D1068V3, multiclass
            clus
vv           TAF6 MUTATED TAF6 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TAF6 MUTATED     0   3   5   1
  TAF6 WILD-TYPE   9  64 244  40
D1068V4, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            5            244
  T4            1             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
  TAF6 MUTATED     5   2   2
  TAF6 WILD-TYPE 215  79  64
D1068V5, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  N0            5            215
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V6, binary
                cls
clus               0   1
  TAF6 MUTATED     7   0
  TAF6 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      7    0
  TAF6 WILD-TYPE  278   48
   clus
vv  TAF6 MUTATED TAF6 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1068V7, binary
                cls
clus               0   1
  TAF6 MUTATED     6   3
  TAF6 WILD-TYPE 164 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      6    3
  TAF6 WILD-TYPE  164  194
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  FEMALE            6            164
  MALE              3            194
[1] 2 2
[1] FALSE
D1068V8, binary
                cls
clus               0   1
  TAF6 MUTATED     7   0
  TAF6 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      7    0
  TAF6 WILD-TYPE  293    8
     clus
vv    TAF6 MUTATED TAF6 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1068V9, binary
                cls
clus               0   1
  TAF6 MUTATED     5   4
  TAF6 WILD-TYPE 309  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      5    4
  TAF6 WILD-TYPE  309   44
                               clus
vv                              TAF6 MUTATED TAF6 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAF6 MUTATED     8   0   0   0
  TAF6 WILD-TYPE 251   3  22  21
D1068V10, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D1068V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF6 MUTATED                                  0     0
  TAF6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF6 MUTATED                           0     6
  TAF6 WILD-TYPE                        19   170
D1068V12, multiclass
                                  clus
vv                                 TAF6 MUTATED TAF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = CYP4F11 MUTATION ANALYSIS
D1069V1, survival
                   sevent
clus2                 0   1
  CYP4F11 MUTATED     4   2
  CYP4F11 WILD-TYPE 273  76
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               349 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                2                76 
$`CYP4F11 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-AA-A00N TCGA-AD-5900 TCGA-AY-6196 TCGA-CM-6171 
       19.04       100.01         4.01        12.16         0.20        14.04 

$`CYP4F11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
              0.2               0.0 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
           100.01            148.01 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
            13.10             22.09 
[1] "0.2 - 100.0 (13.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1069V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP4F11 MUTATED         2        0        1         0         1         0
  CYP4F11 WILD-TYPE      62        1       25       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4F11 MUTATED           0          0          0          1        1
  CYP4F11 WILD-TYPE        18          6         44         32       34
                   vv
clus                STAGE IVA STAGE IVB
  CYP4F11 MUTATED           0         0
  CYP4F11 WILD-TYPE        12         1
D1069V3, multiclass
            clus
vv           CYP4F11 MUTATED CYP4F11 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                0               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  CYP4F11 MUTATED     0   2   3   1
  CYP4F11 WILD-TYPE   9  65 246  40
D1069V4, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               3               246
  T4               1                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
  CYP4F11 MUTATED     5   0   1
  CYP4F11 WILD-TYPE 215  81  65
D1069V5, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  N0               5               215
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V6, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   1
  CYP4F11 WILD-TYPE 282  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    1
  CYP4F11 WILD-TYPE  282   47
   clus
vv  CYP4F11 MUTATED CYP4F11 WILD-TYPE
  0               3               282
  1               1                47
[1] 2 2
[1] FALSE
D1069V7, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     1   5
  CYP4F11 WILD-TYPE 169 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      1    5
  CYP4F11 WILD-TYPE  169  192
        clus
vv       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  FEMALE               1               169
  MALE                 5               192
[1] 2 2
[1] FALSE
D1069V8, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   1
  CYP4F11 WILD-TYPE 297   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    1
  CYP4F11 WILD-TYPE  297    7
     clus
vv    CYP4F11 MUTATED CYP4F11 WILD-TYPE
  NO                3               297
  YES               1                 7
[1] 2 2
[1] FALSE
D1069V9, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   3
  CYP4F11 WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    3
  CYP4F11 WILD-TYPE  311   45
                               clus
vv                              CYP4F11 MUTATED CYP4F11 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP4F11 MUTATED     4   0   1   0
  CYP4F11 WILD-TYPE 255   3  21  21
D1069V10, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               1                21
  RX               0                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"
D1069V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4F11 MUTATED                                  0     0
  CYP4F11 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP4F11 MUTATED                           0     4
  CYP4F11 WILD-TYPE                        19   172
D1069V12, multiclass
                                  clus
vv                                 CYP4F11 MUTATED CYP4F11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = MED13 MUTATION ANALYSIS
D1070V1, survival
                 sevent
clus2               0   1
  MED13 MUTATED    16   3
  MED13 WILD-TYPE 261  75
  MED13 MUTATED MED13 WILD-TYPE 
             19             336 
  MED13 MUTATED MED13 WILD-TYPE 
              3              75 
$`MED13 MUTATED`
TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3864 
       25.08        26.17        24.39        19.66        26.99        53.00 
TCGA-AA-3877 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-5543 TCGA-CA-6717 TCGA-CK-5913 
       31.00         4.01        34.98        33.01        12.76        51.32 
TCGA-CM-4746 TCGA-CM-5341 TCGA-D5-6928 TCGA-D5-6932 TCGA-F4-6570 TCGA-F4-6856 
       37.02        29.06        11.64        11.38         6.18        35.31 
TCGA-G4-6626 
       46.75 

$`MED13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
      124.27        23.05        20.02        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        13.41        13.35        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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  MED13 MUTATED MED13 WILD-TYPE 
           4.01            0.00 
  MED13 MUTATED MED13 WILD-TYPE 
          53.00          148.01 
  MED13 MUTATED MED13 WILD-TYPE 
          26.99           21.99 
[1] "4.0 - 53.0 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1070V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED13 MUTATED         4        0        1         8         3         0
  MED13 WILD-TYPE      60        1       25       100         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED13 MUTATED           0          1          1          1        0         1
  MED13 WILD-TYPE        18          5         43         32       35        11
                 vv
clus              STAGE IVB
  MED13 MUTATED           0
  MED13 WILD-TYPE         1
D1070V3, multiclass
            clus
vv           MED13 MUTATED MED13 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  MED13 MUTATED     1   4  11   4
  MED13 WILD-TYPE   8  63 238  37
D1070V4, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            11             238
  T4             4              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
  MED13 MUTATED    16   4   0
  MED13 WILD-TYPE 204  77  66
D1070V5, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  N0            16             204
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V6, binary
                 cls
clus                0   1
  MED13 MUTATED    16   1
  MED13 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     16    1
  MED13 WILD-TYPE  269   47
   clus
vv  MED13 MUTATED MED13 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D1070V7, binary
                 cls
clus                0   1
  MED13 MUTATED     9  11
  MED13 WILD-TYPE 161 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED      9   11
  MED13 WILD-TYPE  161  186
        clus
vv       MED13 MUTATED MED13 WILD-TYPE
  FEMALE             9             161
  MALE              11             186
[1] 2 2
[1] FALSE
D1070V8, binary
                 cls
clus                0   1
  MED13 MUTATED    18   0
  MED13 WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     18    0
  MED13 WILD-TYPE  282    8
     clus
vv    MED13 MUTATED MED13 WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D1070V9, binary
                 cls
clus                0   1
  MED13 MUTATED    14   6
  MED13 WILD-TYPE 300  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     14    6
  MED13 WILD-TYPE  300   42
                               clus
vv                              MED13 MUTATED MED13 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED13 MUTATED    16   0   0   3
  MED13 WILD-TYPE 243   3  22  18
D1070V10, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             3              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"
D1070V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED13 MUTATED                                  0     1
  MED13 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED13 MUTATED                           2    12
  MED13 WILD-TYPE                        17   164
D1070V12, multiclass
                                  clus
vv                                 MED13 MUTATED MED13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       12             164
[1] 4 2
[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 = DACT1 MUTATION ANALYSIS
D1071V1, survival
                 sevent
clus2               0   1
  DACT1 MUTATED     9   3
  DACT1 WILD-TYPE 268  75
  DACT1 MUTATED DACT1 WILD-TYPE 
             12             343 
  DACT1 MUTATED DACT1 WILD-TYPE 
              3              75 
$`DACT1 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-A00N 
       19.04        26.17        20.12        19.66        33.04         4.01 
TCGA-AA-A01P TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5348 TCGA-D5-6927 TCGA-DM-A28K 
       38.07        49.41        12.76        22.98         9.44        98.24 

$`DACT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DACT1 MUTATED DACT1 WILD-TYPE 
           4.01            0.00 
  DACT1 MUTATED DACT1 WILD-TYPE 
          98.24          148.01 
  DACT1 MUTATED DACT1 WILD-TYPE 
          21.55           22.06 
[1] "4.0 - 98.2 (21.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1071V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DACT1 MUTATED         0        0        2         7         2         0
  DACT1 WILD-TYPE      64        1       24       101         6         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        17          6         43         32       34        12
                 vv
clus              STAGE IVB
  DACT1 MUTATED           0
  DACT1 WILD-TYPE         1
D1071V3, multiclass
            clus
vv           DACT1 MUTATED DACT1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  DACT1 MUTATED     0   0  11   4
  DACT1 WILD-TYPE   9  67 238  37
D1071V4, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            11             238
  T4             4              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
  DACT1 MUTATED    12   3   0
  DACT1 WILD-TYPE 208  78  66
D1071V5, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  N0            12             208
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V6, binary
                 cls
clus                0   1
  DACT1 MUTATED    10   1
  DACT1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     10    1
  DACT1 WILD-TYPE  275   47
   clus
vv  DACT1 MUTATED DACT1 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1071V7, binary
                 cls
clus                0   1
  DACT1 MUTATED     7   8
  DACT1 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      7    8
  DACT1 WILD-TYPE  163  189
        clus
vv       DACT1 MUTATED DACT1 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D1071V8, binary
                 cls
clus                0   1
  DACT1 MUTATED     9   1
  DACT1 WILD-TYPE 291   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      9    1
  DACT1 WILD-TYPE  291    7
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  NO              9             291
  YES             1               7
[1] 2 2
[1] FALSE
D1071V9, binary
                 cls
clus                0   1
  DACT1 MUTATED    10   5
  DACT1 WILD-TYPE 304  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     10    5
  DACT1 WILD-TYPE  304   43
                               clus
vv                              DACT1 MUTATED DACT1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DACT1 MUTATED     9   0   1   2
  DACT1 WILD-TYPE 250   3  21  19
D1071V10, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             2              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"
D1071V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DACT1 MUTATED                                  0     1
  DACT1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DACT1 MUTATED                           0     8
  DACT1 WILD-TYPE                        19   168
D1071V12, multiclass
                                  clus
vv                                 DACT1 MUTATED DACT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = PTTG1IP MUTATION ANALYSIS
D1072V1, survival
                   sevent
clus2                 0   1
  PTTG1IP MUTATED     6   1
  PTTG1IP WILD-TYPE 271  77
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               348 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                1                77 
$`PTTG1IP MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3510 TCGA-CA-5255 TCGA-D5-6539 TCGA-DM-A1DB 
       26.17        79.69        63.98        12.36        12.49        44.32 
TCGA-G4-6304 
       53.62 

$`PTTG1IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
            12.36              0.00 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
            79.69            148.01 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
            44.32             22.01 
[1] "12.4 - 79.7 (44.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1072V2, continuous
                   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      63        1       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTTG1IP MUTATED           0          0          0          0        0
  PTTG1IP WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  PTTG1IP MUTATED           0         0
  PTTG1IP WILD-TYPE        12         1
D1072V3, multiclass
            clus
vv           PTTG1IP MUTATED PTTG1IP WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  PTTG1IP MUTATED     0   1   5   1
  PTTG1IP WILD-TYPE   9  66 244  40
D1072V4, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               1                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
  PTTG1IP MUTATED     7   0   0
  PTTG1IP WILD-TYPE 213  81  66
D1072V5, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  N0               7               213
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V6, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     7   0
  PTTG1IP WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      7    0
  PTTG1IP WILD-TYPE  278   48
   clus
vv  PTTG1IP MUTATED PTTG1IP WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D1072V7, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     3   4
  PTTG1IP WILD-TYPE 167 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      3    4
  PTTG1IP WILD-TYPE  167  193
        clus
vv       PTTG1IP MUTATED PTTG1IP WILD-TYPE
  FEMALE               3               167
  MALE                 4               193
[1] 2 2
[1] FALSE
D1072V8, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     5   1
  PTTG1IP WILD-TYPE 295   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      5    1
  PTTG1IP WILD-TYPE  295    7
     clus
vv    PTTG1IP MUTATED PTTG1IP WILD-TYPE
  NO                5               295
  YES               1                 7
[1] 2 2
[1] FALSE
D1072V9, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     7   0
  PTTG1IP WILD-TYPE 307  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      7    0
  PTTG1IP WILD-TYPE  307   48
                               clus
vv                              PTTG1IP MUTATED PTTG1IP WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PTTG1IP MUTATED     5   0   0   1
  PTTG1IP WILD-TYPE 254   3  22  20
D1072V10, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               1                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"
D1072V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTTG1IP MUTATED                                  0     1
  PTTG1IP WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PTTG1IP MUTATED                           0     5
  PTTG1IP WILD-TYPE                        19   171
D1072V12, multiclass
                                  clus
vv                                 PTTG1IP MUTATED PTTG1IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = ATP12A MUTATION ANALYSIS
D1073V1, survival
                  sevent
clus2                0   1
  ATP12A MUTATED    19   5
  ATP12A WILD-TYPE 258  73
  ATP12A MUTATED ATP12A WILD-TYPE 
              24              331 
  ATP12A MUTATED ATP12A WILD-TYPE 
               5               73 
$`ATP12A MUTATED`
TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3672 TCGA-G4-6628 TCGA-A6-5656 TCGA-A6-5661 
       19.07         0.99         0.92        79.69        32.91        33.53 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N 
       19.66         3.02        53.00        33.01        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6963 TCGA-AY-4071 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6161 
       34.98        27.42         0.95        15.62        23.05        15.02 
TCGA-CM-6675 TCGA-D5-6529 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-F4-6704 TCGA-G4-6307 
       13.05        20.19        49.91         7.50         1.55        55.04 

$`ATP12A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       37.05        36.03         8.05        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5662 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09        16.31        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-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 
       14.04        29.03        16.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A1DB TCGA-DM-A1HA 
       92.75        13.32        12.59       140.38        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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ATP12A MUTATED ATP12A WILD-TYPE 
            0.92             0.00 
  ATP12A MUTATED ATP12A WILD-TYPE 
           79.69           148.01 
  ATP12A MUTATED ATP12A WILD-TYPE 
          19.925           22.090 
[1] "0.9 - 79.7 (19.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1073V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP12A MUTATED         7        0        3         4         3         0
  ATP12A WILD-TYPE      57        1       23       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP12A MUTATED           1          0          1          4        0
  ATP12A WILD-TYPE        17          6         43         29       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP12A MUTATED           0         1
  ATP12A WILD-TYPE        12         0
D1073V3, multiclass
            clus
vv           ATP12A MUTATED ATP12A WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               4              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              4               29
  STAGE IV                0               35
  STAGE IVA               0               12
  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     1   7  12   6
  ATP12A WILD-TYPE   8  60 237  35
D1073V4, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  T1              1                8
  T2              7               60
  T3             12              237
  T4              6               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
  ATP12A MUTATED    19   3   4
  ATP12A WILD-TYPE 201  78  62
D1073V5, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  N0             19              201
  N1              3               78
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V6, binary
                  cls
clus                 0   1
  ATP12A MUTATED    19   1
  ATP12A WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     19    1
  ATP12A WILD-TYPE  266   47
   clus
vv  ATP12A MUTATED ATP12A WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D1073V7, binary
                  cls
clus                 0   1
  ATP12A MUTATED    11  15
  ATP12A WILD-TYPE 159 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     11   15
  ATP12A WILD-TYPE  159  182
        clus
vv       ATP12A MUTATED ATP12A WILD-TYPE
  FEMALE             11              159
  MALE               15              182
[1] 2 2
[1] FALSE
D1073V8, binary
                  cls
clus                 0   1
  ATP12A MUTATED    19   0
  ATP12A WILD-TYPE 281   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     19    0
  ATP12A WILD-TYPE  281    8
     clus
vv    ATP12A MUTATED ATP12A WILD-TYPE
  NO              19              281
  YES              0                8
[1] 2 2
[1] FALSE
D1073V9, binary
                  cls
clus                 0   1
  ATP12A MUTATED    18   7
  ATP12A WILD-TYPE 296  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     18    7
  ATP12A WILD-TYPE  296   41
                               clus
vv                              ATP12A MUTATED ATP12A WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP12A MUTATED    19   0   0   2
  ATP12A WILD-TYPE 240   3  22  19
D1073V10, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  R0             19              240
  R1              0                3
  R2              0               22
  RX              2               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"
D1073V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP12A MUTATED                                  1     0
  ATP12A WILD-TYPE                                0    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP12A MUTATED                           2    13
  ATP12A WILD-TYPE                        17   163
D1073V12, multiclass
                                  clus
vv                                 ATP12A MUTATED ATP12A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        13              163
[1] 4 2
[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 = DHX32 MUTATION ANALYSIS
D1074V1, survival
                 sevent
clus2               0   1
  DHX32 MUTATED     8   2
  DHX32 WILD-TYPE 269  76
  DHX32 MUTATED DHX32 WILD-TYPE 
             10             345 
  DHX32 MUTATED DHX32 WILD-TYPE 
              2              76 
$`DHX32 MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CM-6169 
       26.99        25.02        12.16        33.01        58.39        13.02 
TCGA-CM-6677 TCGA-D5-6931 TCGA-DM-A1D6 TCGA-F4-6809 
       11.08        12.00        49.91        13.25 

$`DHX32 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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        43.04 
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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DHX32 MUTATED DHX32 WILD-TYPE 
          11.08            0.00 
  DHX32 MUTATED DHX32 WILD-TYPE 
          58.39          148.01 
  DHX32 MUTATED DHX32 WILD-TYPE 
         19.135          22.060 
[1] "11.1 - 58.4 (19.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1074V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHX32 MUTATED         1        0        0         5         0         0
  DHX32 WILD-TYPE      63        1       26       103         8         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        18          6         44         32       35        10
                 vv
clus              STAGE IVB
  DHX32 MUTATED           0
  DHX32 WILD-TYPE         1
D1074V3, multiclass
            clus
vv           DHX32 MUTATED DHX32 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              2              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
  DHX32 MUTATED     0   2   7   1
  DHX32 WILD-TYPE   9  65 242  40
D1074V4, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             1              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
  DHX32 MUTATED     7   2   1
  DHX32 WILD-TYPE 213  79  65
D1074V5, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V6, binary
                 cls
clus                0   1
  DHX32 MUTATED     6   2
  DHX32 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      6    2
  DHX32 WILD-TYPE  279   46
   clus
vv  DHX32 MUTATED DHX32 WILD-TYPE
  0             6             279
  1             2              46
[1] 2 2
[1] FALSE
D1074V7, binary
                 cls
clus                0   1
  DHX32 MUTATED     4   6
  DHX32 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      4    6
  DHX32 WILD-TYPE  166  191
        clus
vv       DHX32 MUTATED DHX32 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1074V8, binary
                 cls
clus                0   1
  DHX32 MUTATED     9   0
  DHX32 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      9    0
  DHX32 WILD-TYPE  291    8
     clus
vv    DHX32 MUTATED DHX32 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1074V9, binary
                 cls
clus                0   1
  DHX32 MUTATED     8   2
  DHX32 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      8    2
  DHX32 WILD-TYPE  306   46
                               clus
vv                              DHX32 MUTATED DHX32 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHX32 MUTATED     8   0   0   0
  DHX32 WILD-TYPE 251   3  22  21
D1074V10, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1074V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHX32 MUTATED                                  0     0
  DHX32 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHX32 MUTATED                           2     6
  DHX32 WILD-TYPE                        17   170
D1074V12, multiclass
                                  clus
vv                                 DHX32 MUTATED DHX32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        6             170
[1] 4 2
[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 = SLITRK2 MUTATION ANALYSIS
D1075V1, survival
                   sevent
clus2                 0   1
  SLITRK2 MUTATED    16   4
  SLITRK2 WILD-TYPE 261  74
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               20               335 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
                4                74 
$`SLITRK2 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-A6-2678 TCGA-A6-5666 TCGA-AA-3492 
        0.92       100.01         1.94        42.28        32.71         3.02 
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 
       63.98        29.95        53.00        33.01        25.02        34.98 
TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5348 TCGA-D5-6532 
       27.09        12.76        10.06        51.32        22.98        18.25 
TCGA-D5-6930 TCGA-F4-6808 
       13.35        33.67 

$`SLITRK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
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-A6-6651 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-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
             0.92              0.00 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
           100.01            148.01 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
            28.52             21.99 
[1] "0.9 - 100.0 (28.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1075V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLITRK2 MUTATED         3        0        4         6         2         1
  SLITRK2 WILD-TYPE      61        1       22       102         6         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLITRK2 MUTATED           1          1          2          0        0
  SLITRK2 WILD-TYPE        17          5         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SLITRK2 MUTATED           0         0
  SLITRK2 WILD-TYPE        12         1
D1075V3, multiclass
            clus
vv           SLITRK2 MUTATED SLITRK2 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 4                22
  STAGE IIA                6               102
  STAGE IIB                2                 6
  STAGE IIC                1                 0
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLITRK2 MUTATED     1   4  13   3
  SLITRK2 WILD-TYPE   8  63 236  38
D1075V4, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  T1               1                 8
  T2               4                63
  T3              13               236
  T4               3                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
  SLITRK2 MUTATED    17   4   0
  SLITRK2 WILD-TYPE 203  77  66
D1075V5, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  N0              17               203
  N1               4                77
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V6, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    18   0
  SLITRK2 WILD-TYPE 267  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     18    0
  SLITRK2 WILD-TYPE  267   48
   clus
vv  SLITRK2 MUTATED SLITRK2 WILD-TYPE
  0              18               267
  1               0                48
[1] 2 2
[1] FALSE
D1075V7, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    10  11
  SLITRK2 WILD-TYPE 160 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     10   11
  SLITRK2 WILD-TYPE  160  186
        clus
vv       SLITRK2 MUTATED SLITRK2 WILD-TYPE
  FEMALE              10               160
  MALE                11               186
[1] 2 2
[1] FALSE
D1075V8, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    19   0
  SLITRK2 WILD-TYPE 281   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     19    0
  SLITRK2 WILD-TYPE  281    8
     clus
vv    SLITRK2 MUTATED SLITRK2 WILD-TYPE
  NO               19               281
  YES               0                 8
[1] 2 2
[1] FALSE
D1075V9, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    17   4
  SLITRK2 WILD-TYPE 297  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     17    4
  SLITRK2 WILD-TYPE  297   44
                               clus
vv                              SLITRK2 MUTATED SLITRK2 WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLITRK2 MUTATED    13   0   0   4
  SLITRK2 WILD-TYPE 246   3  22  17
D1075V10, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               4                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"
D1075V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLITRK2 MUTATED                                  0     2
  SLITRK2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLITRK2 MUTATED                           0    11
  SLITRK2 WILD-TYPE                        19   165
D1075V12, multiclass
                                  clus
vv                                 SLITRK2 MUTATED SLITRK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         11               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(1076) Variable = TMC8 MUTATION ANALYSIS
D1076V1, survival
                sevent
clus2              0   1
  TMC8 MUTATED     6   1
  TMC8 WILD-TYPE 271  77
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            348 
  TMC8 MUTATED TMC8 WILD-TYPE 
             1             77 
$`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        12.16        27.09        51.32 
TCGA-CM-6162 
       12.00 

$`TMC8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TMC8 MUTATED TMC8 WILD-TYPE 
          2.01           0.00 
  TMC8 MUTATED TMC8 WILD-TYPE 
         63.98         148.01 
  TMC8 MUTATED TMC8 WILD-TYPE 
        12.160         22.075 
[1] "2.0 - 64.0 (12.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1076V2, continuous
                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      62        1       24       106         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  TMC8 MUTATED           0
  TMC8 WILD-TYPE         1
D1076V3, multiclass
            clus
vv           TMC8 MUTATED TMC8 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TMC8 MUTATED     0   2   5   0
  TMC8 WILD-TYPE   9  65 244  41
D1076V4, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            0             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
  TMC8 MUTATED     6   1   0
  TMC8 WILD-TYPE 214  80  66
D1076V5, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V6, binary
                cls
clus               0   1
  TMC8 MUTATED     5   0
  TMC8 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      5    0
  TMC8 WILD-TYPE  280   48
   clus
vv  TMC8 MUTATED TMC8 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1076V7, binary
                cls
clus               0   1
  TMC8 MUTATED     5   2
  TMC8 WILD-TYPE 165 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      5    2
  TMC8 WILD-TYPE  165  195
        clus
vv       TMC8 MUTATED TMC8 WILD-TYPE
  FEMALE            5            165
  MALE              2            195
[1] 2 2
[1] FALSE
D1076V8, binary
                cls
clus               0   1
  TMC8 MUTATED     5   0
  TMC8 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      5    0
  TMC8 WILD-TYPE  295    8
     clus
vv    TMC8 MUTATED TMC8 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1076V9, binary
                cls
clus               0   1
  TMC8 MUTATED     4   3
  TMC8 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      4    3
  TMC8 WILD-TYPE  310   45
                               clus
vv                              TMC8 MUTATED TMC8 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TMC8 MUTATED     5   0   0   1
  TMC8 WILD-TYPE 254   3  22  20
D1076V10, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1076V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMC8 MUTATED                                  0     0
  TMC8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TMC8 MUTATED                           0     4
  TMC8 WILD-TYPE                        19   172
D1076V12, multiclass
                                  clus
vv                                 TMC8 MUTATED TMC8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = EMR3 MUTATION ANALYSIS
D1077V1, survival
                sevent
clus2              0   1
  EMR3 MUTATED    12   4
  EMR3 WILD-TYPE 265  74
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            339 
  EMR3 MUTATED EMR3 WILD-TYPE 
             4             74 
$`EMR3 MUTATED`
TCGA-A6-4105 TCGA-AA-3525 TCGA-AA-3870 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-2671 
       14.53         8.05        29.98        25.08        26.17        43.76 
TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A00N TCGA-AA-A010 
       22.06        35.01        63.98        26.99         4.01        34.98 
TCGA-AY-6196 TCGA-CM-4743 TCGA-CM-6172 TCGA-D5-6537 
        0.20        23.05        11.01         4.80 

$`EMR3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        3.02         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  EMR3 MUTATED EMR3 WILD-TYPE 
           0.2            0.0 
  EMR3 MUTATED EMR3 WILD-TYPE 
         63.98         148.01 
  EMR3 MUTATED EMR3 WILD-TYPE 
        24.065         21.990 
[1] "0.2 - 64.0 (24.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1077V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EMR3 MUTATED         1        0        1         5         2         0
  EMR3 WILD-TYPE      63        1       25       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EMR3 MUTATED           0          0          4          1        2         0
  EMR3 WILD-TYPE        18          6         40         32       33        12
                vv
clus             STAGE IVB
  EMR3 MUTATED           0
  EMR3 WILD-TYPE         1
D1077V3, multiclass
            clus
vv           EMR3 MUTATED EMR3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  EMR3 MUTATED     0   1  13   2
  EMR3 WILD-TYPE   9  66 236  39
D1077V4, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           13            236
  T4            2             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
  EMR3 MUTATED     9   4   3
  EMR3 WILD-TYPE 211  77  63
D1077V5, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  N0            9            211
  N1            4             77
  N2            3             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"
D1077V6, binary
                cls
clus               0   1
  EMR3 MUTATED    12   2
  EMR3 WILD-TYPE 273  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     12    2
  EMR3 WILD-TYPE  273   46
   clus
vv  EMR3 MUTATED EMR3 WILD-TYPE
  0           12            273
  1            2             46
[1] 2 2
[1] FALSE
D1077V7, binary
                cls
clus               0   1
  EMR3 MUTATED     6  10
  EMR3 WILD-TYPE 164 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED      6   10
  EMR3 WILD-TYPE  164  187
        clus
vv       EMR3 MUTATED EMR3 WILD-TYPE
  FEMALE            6            164
  MALE             10            187
[1] 2 2
[1] FALSE
D1077V8, binary
                cls
clus               0   1
  EMR3 MUTATED    13   0
  EMR3 WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     13    0
  EMR3 WILD-TYPE  287    8
     clus
vv    EMR3 MUTATED EMR3 WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D1077V9, binary
                cls
clus               0   1
  EMR3 MUTATED    14   2
  EMR3 WILD-TYPE 300  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     14    2
  EMR3 WILD-TYPE  300   46
                               clus
vv                              EMR3 MUTATED EMR3 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EMR3 MUTATED    15   0   0   0
  EMR3 WILD-TYPE 244   3  22  21
D1077V10, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  R0           15            244
  R1            0              3
  R2            0             22
  RX            0             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"
D1077V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMR3 MUTATED                                  0     0
  EMR3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMR3 MUTATED                           0     9
  EMR3 WILD-TYPE                        19   167
D1077V12, multiclass
                                  clus
vv                                 EMR3 MUTATED EMR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(1078) Variable = VPS33A MUTATION ANALYSIS
D1078V1, survival
                  sevent
clus2                0   1
  VPS33A MUTATED     6   1
  VPS33A WILD-TYPE 271  77
  VPS33A MUTATED VPS33A WILD-TYPE 
               7              348 
  VPS33A MUTATED VPS33A WILD-TYPE 
               1               77 
$`VPS33A MUTATED`
TCGA-AA-3525 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6588 TCGA-AA-3833 TCGA-AA-3845 
        8.05        24.00        25.08        26.17        15.95         0.00 
TCGA-AD-5900 
       12.16 

$`VPS33A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3837 TCGA-AA-3842 TCGA-AA-3846 
       25.02         1.02        17.98        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  VPS33A MUTATED VPS33A WILD-TYPE 
               0                0 
  VPS33A MUTATED VPS33A WILD-TYPE 
           26.17           148.01 
  VPS33A MUTATED VPS33A WILD-TYPE 
          15.950           22.075 
[1] "0.0 - 26.2 (15.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1078V2, continuous
                  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      63        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS33A MUTATED           0          0          2          0        0
  VPS33A WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  VPS33A MUTATED           0         0
  VPS33A WILD-TYPE        12         1
D1078V3, multiclass
            clus
vv           VPS33A MUTATED VPS33A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  VPS33A MUTATED     0   1   6   1
  VPS33A WILD-TYPE   9  66 243  40
D1078V4, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  T1              0                9
  T2              1               66
  T3              6              243
  T4              1               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
  VPS33A MUTATED     6   2   0
  VPS33A WILD-TYPE 214  79  66
D1078V5, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  N0              6              214
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V6, binary
                  cls
clus                 0   1
  VPS33A MUTATED     6   0
  VPS33A WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      6    0
  VPS33A WILD-TYPE  279   48
   clus
vv  VPS33A MUTATED VPS33A WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1078V7, binary
                  cls
clus                 0   1
  VPS33A MUTATED     5   3
  VPS33A WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      5    3
  VPS33A WILD-TYPE  165  194
        clus
vv       VPS33A MUTATED VPS33A WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1078V8, binary
                  cls
clus                 0   1
  VPS33A MUTATED     6   0
  VPS33A WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      6    0
  VPS33A WILD-TYPE  294    8
     clus
vv    VPS33A MUTATED VPS33A WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1078V9, binary
                  cls
clus                 0   1
  VPS33A MUTATED     6   2
  VPS33A WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      6    2
  VPS33A WILD-TYPE  308   46
                               clus
vv                              VPS33A MUTATED VPS33A WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  VPS33A MUTATED     7   0   0   1
  VPS33A WILD-TYPE 252   3  22  20
D1078V10, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1078V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS33A MUTATED                                  0     0
  VPS33A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS33A MUTATED                           0     4
  VPS33A WILD-TYPE                        19   172
D1078V12, multiclass
                                  clus
vv                                 VPS33A MUTATED VPS33A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = BRE MUTATION ANALYSIS
D1079V1, survival
               sevent
clus2             0   1
  BRE MUTATED     6   4
  BRE WILD-TYPE 271  74
  BRE MUTATED BRE WILD-TYPE 
           10           345 
  BRE MUTATED BRE WILD-TYPE 
            4            74 
$`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 
       37.02        13.02        11.08       133.18 

$`BRE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       88.21         6.77        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         22.03 
[1] "3.0 - 133.2 (27.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1079V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRE MUTATED         1        0        2         4         1         0
  BRE WILD-TYPE      63        1       24       104         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRE MUTATED           1          0          0          0        1         0
  BRE WILD-TYPE        17          6         44         33       34        12
               vv
clus            STAGE IVB
  BRE MUTATED           0
  BRE WILD-TYPE         1
D1079V3, multiclass
            clus
vv           BRE MUTATED BRE WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  BRE MUTATED     0   1   7   2
  BRE WILD-TYPE   9  66 242  39
D1079V4, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  T1           0             9
  T2           1            66
  T3           7           242
  T4           2            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
  BRE MUTATED     8   1   1
  BRE WILD-TYPE 212  80  65
D1079V5, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  N0           8           212
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V6, binary
               cls
clus              0   1
  BRE MUTATED     8   1
  BRE WILD-TYPE 277  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED      8    1
  BRE WILD-TYPE  277   47
   clus
vv  BRE MUTATED BRE WILD-TYPE
  0           8           277
  1           1            47
[1] 2 2
[1] FALSE
D1079V7, binary
               cls
clus              0   1
  BRE MUTATED     7   3
  BRE WILD-TYPE 163 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED      7    3
  BRE WILD-TYPE  163  194
        clus
vv       BRE MUTATED BRE WILD-TYPE
  FEMALE           7           163
  MALE             3           194
[1] 2 2
[1] FALSE
D1079V8, binary
               cls
clus              0   1
  BRE MUTATED    10   0
  BRE WILD-TYPE 290   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED     10    0
  BRE WILD-TYPE  290    8
     clus
vv    BRE MUTATED BRE WILD-TYPE
  NO           10           290
  YES           0             8
[1] 2 2
[1] FALSE
D1079V9, binary
               cls
clus              0   1
  BRE MUTATED    10   0
  BRE WILD-TYPE 304  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED     10    0
  BRE WILD-TYPE  304   48
                               clus
vv                              BRE MUTATED BRE WILD-TYPE
  COLON ADENOCARCINOMA                   10           304
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  BRE MUTATED     8   0   0   0
  BRE WILD-TYPE 251   3  22  21
D1079V10, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  R0           8           251
  R1           0             3
  R2           0            22
  RX           0            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"
D1079V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRE MUTATED                                  0     0
  BRE WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  BRE MUTATED                           2     6
  BRE WILD-TYPE                        17   170
D1079V12, multiclass
                                  clus
vv                                 BRE MUTATED BRE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                      6           170
[1] 4 2
[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 = NKTR MUTATION ANALYSIS
D1080V1, survival
                sevent
clus2              0   1
  NKTR MUTATED     7   6
  NKTR WILD-TYPE 270  72
  NKTR MUTATED NKTR WILD-TYPE 
            13            342 
  NKTR MUTATED NKTR WILD-TYPE 
             6             72 
$`NKTR MUTATED`
TCGA-AA-A00Z TCGA-AZ-6601 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 
       21.99       100.01         3.02        63.98         6.97        33.04 
TCGA-AA-3864 TCGA-AA-A00E TCGA-AD-6889 TCGA-D5-6532 TCGA-DM-A1D8 TCGA-DM-A28F 
       53.00        30.02        83.24        18.25        12.59        35.97 
TCGA-G4-6626 
       46.75 

$`NKTR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  NKTR MUTATED NKTR WILD-TYPE 
          3.02           0.00 
  NKTR MUTATED NKTR WILD-TYPE 
        100.01         148.01 
  NKTR MUTATED NKTR WILD-TYPE 
         33.04          22.01 
[1] "3.0 - 100.0 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1080V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NKTR MUTATED         0        0        5         6         0         0
  NKTR WILD-TYPE      64        1       21       102         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  NKTR MUTATED           0
  NKTR WILD-TYPE         1
D1080V3, multiclass
            clus
vv           NKTR MUTATED NKTR WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  NKTR MUTATED     0   0  13   0
  NKTR WILD-TYPE   9  67 236  41
D1080V4, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  T1            0              9
  T2            0             67
  T3           13            236
  T4            0             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
  NKTR MUTATED    11   2   0
  NKTR WILD-TYPE 209  79  66
D1080V5, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  N0           11            209
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V6, binary
                cls
clus               0   1
  NKTR MUTATED    12   0
  NKTR WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     12    0
  NKTR WILD-TYPE  273   48
   clus
vv  NKTR MUTATED NKTR WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D1080V7, binary
                cls
clus               0   1
  NKTR MUTATED     3  10
  NKTR WILD-TYPE 167 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      3   10
  NKTR WILD-TYPE  167  187
        clus
vv       NKTR MUTATED NKTR WILD-TYPE
  FEMALE            3            167
  MALE             10            187
[1] 2 2
[1] FALSE
D1080V8, binary
                cls
clus               0   1
  NKTR MUTATED    11   0
  NKTR WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     11    0
  NKTR WILD-TYPE  289    8
     clus
vv    NKTR MUTATED NKTR WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1080V9, binary
                cls
clus               0   1
  NKTR MUTATED    13   0
  NKTR WILD-TYPE 301  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     13    0
  NKTR WILD-TYPE  301   48
                               clus
vv                              NKTR MUTATED NKTR WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NKTR MUTATED    10   0   0   0
  NKTR WILD-TYPE 249   3  22  21
D1080V10, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            0             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"
D1080V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NKTR MUTATED                                  0     1
  NKTR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NKTR MUTATED                           0     5
  NKTR WILD-TYPE                        19   171
D1080V12, multiclass
                                  clus
vv                                 NKTR MUTATED NKTR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = ICA1 MUTATION ANALYSIS
D1081V1, survival
                sevent
clus2              0   1
  ICA1 MUTATED     6   0
  ICA1 WILD-TYPE 271  78
  ICA1 MUTATED ICA1 WILD-TYPE 
             6            349 
  ICA1 MUTATED ICA1 WILD-TYPE 
             0             78 
$`ICA1 MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-AA-3949 TCGA-CA-6717 TCGA-CM-5860 TCGA-D5-5540 
       24.00        25.08        26.01        12.76        32.02        56.09 

$`ICA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ICA1 MUTATED ICA1 WILD-TYPE 
         12.76           0.00 
  ICA1 MUTATED ICA1 WILD-TYPE 
         56.09         148.01 
  ICA1 MUTATED ICA1 WILD-TYPE 
        25.545         21.990 
[1] "12.8 - 56.1 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1081V2, continuous
                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      64        1       26       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ICA1 MUTATED           0          0          2          0        0         0
  ICA1 WILD-TYPE        18          6         42         33       35        12
                vv
clus             STAGE IVB
  ICA1 MUTATED           0
  ICA1 WILD-TYPE         1
D1081V3, multiclass
            clus
vv           ICA1 MUTATED ICA1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ICA1 MUTATED     0   0   6   0
  ICA1 WILD-TYPE   9  67 243  41
D1081V4, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            0             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
  ICA1 MUTATED     4   2   0
  ICA1 WILD-TYPE 216  79  66
D1081V5, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  N0            4            216
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V6, binary
                cls
clus               0   1
  ICA1 MUTATED     6   0
  ICA1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      6    0
  ICA1 WILD-TYPE  279   48
   clus
vv  ICA1 MUTATED ICA1 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1081V7, binary
                cls
clus               0   1
  ICA1 MUTATED     2   4
  ICA1 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      2    4
  ICA1 WILD-TYPE  168  193
        clus
vv       ICA1 MUTATED ICA1 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1081V8, binary
                cls
clus               0   1
  ICA1 MUTATED     6   0
  ICA1 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      6    0
  ICA1 WILD-TYPE  294    8
     clus
vv    ICA1 MUTATED ICA1 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1081V9, binary
                cls
clus               0   1
  ICA1 MUTATED     3   3
  ICA1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      3    3
  ICA1 WILD-TYPE  311   45
                               clus
vv                              ICA1 MUTATED ICA1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ICA1 MUTATED     5   0   0   1
  ICA1 WILD-TYPE 254   3  22  20
D1081V10, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1081V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ICA1 MUTATED                                  0     1
  ICA1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ICA1 MUTATED                           0     3
  ICA1 WILD-TYPE                        19   173
D1081V12, multiclass
                                  clus
vv                                 ICA1 MUTATED ICA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = ZFYVE16 MUTATION ANALYSIS
D1082V1, survival
                   sevent
clus2                 0   1
  ZFYVE16 MUTATED    14   1
  ZFYVE16 WILD-TYPE 263  77
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               15               340 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
                1                77 
$`ZFYVE16 MUTATED`
TCGA-AD-6895 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3667 TCGA-AA-3977 TCGA-AA-A00E 
       25.08        33.53        22.06        14.01        25.02        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 
        4.01        34.98        12.16        58.39        12.76        15.02 
TCGA-CM-6165 TCGA-D5-6540 TCGA-D5-6928 
       16.04        16.14        11.64 

$`ZFYVE16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
             4.01              0.00 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
            58.39            148.01 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
            16.14             22.09 
[1] "4.0 - 58.4 (16.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D1082V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFYVE16 MUTATED         3        0        0         9         3         0
  ZFYVE16 WILD-TYPE      61        1       26        99         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFYVE16 MUTATED           0          0          1          0        0
  ZFYVE16 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ZFYVE16 MUTATED           0         0
  ZFYVE16 WILD-TYPE        12         1
D1082V3, multiclass
            clus
vv           ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                9                99
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ZFYVE16 MUTATED     0   4  10   3
  ZFYVE16 WILD-TYPE   9  63 239  38
D1082V4, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3              10               239
  T4               3                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
  ZFYVE16 MUTATED    16   1   0
  ZFYVE16 WILD-TYPE 204  80  66
D1082V5, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  N0              16               204
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V6, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    14   0
  ZFYVE16 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     14    0
  ZFYVE16 WILD-TYPE  271   48
   clus
vv  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  0              14               271
  1               0                48
[1] 2 2
[1] FALSE
D1082V7, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED     7  10
  ZFYVE16 WILD-TYPE 163 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED      7   10
  ZFYVE16 WILD-TYPE  163  187
        clus
vv       ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  FEMALE               7               163
  MALE                10               187
[1] 2 2
[1] FALSE
D1082V8, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    14   0
  ZFYVE16 WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     14    0
  ZFYVE16 WILD-TYPE  286    8
     clus
vv    ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D1082V9, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    12   5
  ZFYVE16 WILD-TYPE 302  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     12    5
  ZFYVE16 WILD-TYPE  302   43
                               clus
vv                              ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFYVE16 MUTATED    14   0   0   2
  ZFYVE16 WILD-TYPE 245   3  22  19
D1082V10, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  R0              14               245
  R1               0                 3
  R2               0                22
  RX               2                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"
D1082V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFYVE16 MUTATED                                  0     1
  ZFYVE16 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFYVE16 MUTATED                           1     9
  ZFYVE16 WILD-TYPE                        18   167
D1082V12, multiclass
                                  clus
vv                                 ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          9               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(1083) Variable = RDBP MUTATION ANALYSIS
D1083V1, survival
                sevent
clus2              0   1
  RDBP MUTATED     6   0
  RDBP WILD-TYPE 271  78
  RDBP MUTATED RDBP WILD-TYPE 
             6            349 
  RDBP MUTATED RDBP WILD-TYPE 
             0             78 
$`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 

$`RDBP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RDBP MUTATED RDBP WILD-TYPE 
          6.97           0.00 
  RDBP MUTATED RDBP WILD-TYPE 
         51.32         148.01 
  RDBP MUTATED RDBP WILD-TYPE 
        22.915         22.060 
[1] "7.0 - 51.3 (22.9)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1083V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RDBP MUTATED         1        0        1         2         1         0
  RDBP WILD-TYPE      63        1       25       106         7         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  RDBP MUTATED           0
  RDBP WILD-TYPE         1
D1083V3, multiclass
            clus
vv           RDBP MUTATED RDBP WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RDBP MUTATED     0   1   4   1
  RDBP WILD-TYPE   9  66 245  40
D1083V4, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            1             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
  RDBP MUTATED     5   1   0
  RDBP WILD-TYPE 215  80  66
D1083V5, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  N0            5            215
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V6, binary
                cls
clus               0   1
  RDBP MUTATED     4   0
  RDBP WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      4    0
  RDBP WILD-TYPE  281   48
   clus
vv  RDBP MUTATED RDBP WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1083V7, binary
                cls
clus               0   1
  RDBP MUTATED     3   3
  RDBP WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      3    3
  RDBP WILD-TYPE  167  194
        clus
vv       RDBP MUTATED RDBP WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D1083V8, binary
                cls
clus               0   1
  RDBP MUTATED     6   0
  RDBP WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      6    0
  RDBP WILD-TYPE  294    8
     clus
vv    RDBP MUTATED RDBP WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1083V9, binary
                cls
clus               0   1
  RDBP MUTATED     4   2
  RDBP WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      4    2
  RDBP WILD-TYPE  310   46
                               clus
vv                              RDBP MUTATED RDBP WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RDBP MUTATED     4   0   0   1
  RDBP WILD-TYPE 255   3  22  20
D1083V10, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            1             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"
D1083V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RDBP MUTATED                                  0     0
  RDBP WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RDBP MUTATED                           0     5
  RDBP WILD-TYPE                        19   171
D1083V12, multiclass
                                  clus
vv                                 RDBP MUTATED RDBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = LMOD1 MUTATION ANALYSIS
D1084V1, survival
                 sevent
clus2               0   1
  LMOD1 MUTATED    10   2
  LMOD1 WILD-TYPE 267  76
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             12             343 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
              2              76 
$`LMOD1 MUTATED`
TCGA-AA-3672 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3947 TCGA-AZ-4315 TCGA-CA-6717 
        0.92         3.02        63.98        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        54.61        16.14         9.04 

$`LMOD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
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-D5-5537 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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  LMOD1 MUTATED LMOD1 WILD-TYPE 
           0.92            0.00 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
          63.98          148.01 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
          15.58           22.09 
[1] "0.9 - 64.0 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1084V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LMOD1 MUTATED         3        0        2         3         1         0
  LMOD1 WILD-TYPE      61        1       24       105         7         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        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  LMOD1 MUTATED           0
  LMOD1 WILD-TYPE         1
D1084V3, multiclass
            clus
vv           LMOD1 MUTATED LMOD1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LMOD1 MUTATED     0   3   7   2
  LMOD1 WILD-TYPE   9  64 242  39
D1084V4, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             7             242
  T4             2              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
  LMOD1 MUTATED     9   3   0
  LMOD1 WILD-TYPE 211  78  66
D1084V5, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  N0             9             211
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V6, binary
                 cls
clus                0   1
  LMOD1 MUTATED    12   0
  LMOD1 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED     12    0
  LMOD1 WILD-TYPE  273   48
   clus
vv  LMOD1 MUTATED LMOD1 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D1084V7, binary
                 cls
clus                0   1
  LMOD1 MUTATED     7   5
  LMOD1 WILD-TYPE 163 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED      7    5
  LMOD1 WILD-TYPE  163  192
        clus
vv       LMOD1 MUTATED LMOD1 WILD-TYPE
  FEMALE             7             163
  MALE               5             192
[1] 2 2
[1] FALSE
D1084V8, binary
                 cls
clus                0   1
  LMOD1 MUTATED    11   1
  LMOD1 WILD-TYPE 289   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED     11    1
  LMOD1 WILD-TYPE  289    7
     clus
vv    LMOD1 MUTATED LMOD1 WILD-TYPE
  NO             11             289
  YES             1               7
[1] 2 2
[1] FALSE
D1084V9, binary
                 cls
clus                0   1
  LMOD1 MUTATED     9   3
  LMOD1 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED      9    3
  LMOD1 WILD-TYPE  305   45
                               clus
vv                              LMOD1 MUTATED LMOD1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMOD1 MUTATED    11   0   0   1
  LMOD1 WILD-TYPE 248   3  22  20
D1084V10, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1084V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LMOD1 MUTATED                                  0     1
  LMOD1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LMOD1 MUTATED                           0     7
  LMOD1 WILD-TYPE                        19   169
D1084V12, multiclass
                                  clus
vv                                 LMOD1 MUTATED LMOD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = AP1G1 MUTATION ANALYSIS
D1085V1, survival
                 sevent
clus2               0   1
  AP1G1 MUTATED     7   3
  AP1G1 WILD-TYPE 270  75
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             10             345 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
              3              75 
$`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        12.59        12.76 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6929 TCGA-F4-6460 
       14.04        13.05        13.41        31.96 

$`AP1G1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  AP1G1 MUTATED AP1G1 WILD-TYPE 
           4.01            0.00 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
          58.39          148.01 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
         13.725          22.090 
[1] "4.0 - 58.4 (13.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1085V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP1G1 MUTATED         1        0        0         5         1         0
  AP1G1 WILD-TYPE      63        1       26       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP1G1 MUTATED           0          0          2          0        1         0
  AP1G1 WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  AP1G1 MUTATED           1
  AP1G1 WILD-TYPE         0
D1085V3, multiclass
            clus
vv           AP1G1 MUTATED AP1G1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              12
  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   1   9   1
  AP1G1 WILD-TYPE   9  66 240  40
D1085V4, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             1              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
  AP1G1 MUTATED     7   3   1
  AP1G1 WILD-TYPE 213  78  65
D1085V5, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V6, binary
                 cls
clus                0   1
  AP1G1 MUTATED     9   2
  AP1G1 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      9    2
  AP1G1 WILD-TYPE  276   46
   clus
vv  AP1G1 MUTATED AP1G1 WILD-TYPE
  0             9             276
  1             2              46
[1] 2 2
[1] FALSE
D1085V7, binary
                 cls
clus                0   1
  AP1G1 MUTATED     5   6
  AP1G1 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      5    6
  AP1G1 WILD-TYPE  165  191
        clus
vv       AP1G1 MUTATED AP1G1 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1085V8, binary
                 cls
clus                0   1
  AP1G1 MUTATED     9   0
  AP1G1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      9    0
  AP1G1 WILD-TYPE  291    8
     clus
vv    AP1G1 MUTATED AP1G1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1085V9, binary
                 cls
clus                0   1
  AP1G1 MUTATED     9   2
  AP1G1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      9    2
  AP1G1 WILD-TYPE  305   46
                               clus
vv                              AP1G1 MUTATED AP1G1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AP1G1 MUTATED     8   0   0   2
  AP1G1 WILD-TYPE 251   3  22  19
D1085V10, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D1085V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP1G1 MUTATED                                  0     2
  AP1G1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP1G1 MUTATED                           1     5
  AP1G1 WILD-TYPE                        18   171
D1085V12, multiclass
                                  clus
vv                                 AP1G1 MUTATED AP1G1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1086) Variable = TRPV2 MUTATION ANALYSIS
D1086V1, survival
                 sevent
clus2               0   1
  TRPV2 MUTATED     8   3
  TRPV2 WILD-TYPE 269  75
  TRPV2 MUTATED TRPV2 WILD-TYPE 
             11             344 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              3              75 
$`TRPV2 MUTATED`
TCGA-AA-3525 TCGA-AA-3672 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3845 
        8.05         0.92        79.69        46.65        20.12         0.00 
TCGA-AA-3949 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6718 TCGA-D5-6540 
       26.01        27.09        49.41        10.06        16.14 

$`TRPV2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       26.17        91.79        43.76        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TRPV2 MUTATED TRPV2 WILD-TYPE 
              0               0 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
          79.69          148.01 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
         20.120          22.075 
[1] "0.0 - 79.7 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1086V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPV2 MUTATED         3        0        1         3         0         0
  TRPV2 WILD-TYPE      61        1       25       105         8         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        17          6         41         33       35        12
                 vv
clus              STAGE IVB
  TRPV2 MUTATED           0
  TRPV2 WILD-TYPE         1
D1086V3, multiclass
            clus
vv           TRPV2 MUTATED TRPV2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  TRPV2 MUTATED     0   3   8   0
  TRPV2 WILD-TYPE   9  64 241  41
D1086V4, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             8             241
  T4             0              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
  TRPV2 MUTATED     7   4   0
  TRPV2 WILD-TYPE 213  77  66
D1086V5, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  N0             7             213
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V6, binary
                 cls
clus                0   1
  TRPV2 MUTATED     9   0
  TRPV2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      9    0
  TRPV2 WILD-TYPE  276   48
   clus
vv  TRPV2 MUTATED TRPV2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1086V7, binary
                 cls
clus                0   1
  TRPV2 MUTATED     6   5
  TRPV2 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      6    5
  TRPV2 WILD-TYPE  164  192
        clus
vv       TRPV2 MUTATED TRPV2 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D1086V8, binary
                 cls
clus                0   1
  TRPV2 MUTATED     9   0
  TRPV2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      9    0
  TRPV2 WILD-TYPE  291    8
     clus
vv    TRPV2 MUTATED TRPV2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1086V9, binary
                 cls
clus                0   1
  TRPV2 MUTATED     8   3
  TRPV2 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      8    3
  TRPV2 WILD-TYPE  306   45
                               clus
vv                              TRPV2 MUTATED TRPV2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRPV2 MUTATED     8   0   0   1
  TRPV2 WILD-TYPE 251   3  22  20
D1086V10, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1086V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPV2 MUTATED                                  0     1
  TRPV2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPV2 MUTATED                           0     6
  TRPV2 WILD-TYPE                        19   170
D1086V12, multiclass
                                  clus
vv                                 TRPV2 MUTATED TRPV2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ABLIM3 MUTATION ANALYSIS
D1087V1, survival
                  sevent
clus2                0   1
  ABLIM3 MUTATED     8   7
  ABLIM3 WILD-TYPE 269  71
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
              15              340 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
               7               71 
$`ABLIM3 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6888 TCGA-AD-6895 TCGA-AA-3526 
       13.02        19.04        19.04        15.52        25.08        19.07 
TCGA-AA-3710 TCGA-AA-3833 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       26.99        15.95        27.09        49.41        12.76        21.14 
TCGA-D5-6532 TCGA-DM-A28F TCGA-G4-6303 
       18.25        35.97        65.85 

$`ABLIM3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         1.02         9.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
           12.76             0.00 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
           65.85           148.01 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
           19.07            22.09 
[1] "12.8 - 65.8 (19.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1087V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABLIM3 MUTATED         3        0        2         5         0         0
  ABLIM3 WILD-TYPE      61        1       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABLIM3 MUTATED           1          0          3          0        2
  ABLIM3 WILD-TYPE        17          6         41         33       33
                  vv
clus               STAGE IVA STAGE IVB
  ABLIM3 MUTATED           0         0
  ABLIM3 WILD-TYPE        12         1
D1087V3, multiclass
            clus
vv           ABLIM3 MUTATED ABLIM3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  ABLIM3 MUTATED     1   2  13   0
  ABLIM3 WILD-TYPE   8  65 236  41
D1087V4, multiclass
    clus
vv   ABLIM3 MUTATED ABLIM3 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             13              236
  T4              0               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
  ABLIM3 MUTATED    11   4   1
  ABLIM3 WILD-TYPE 209  77  65
D1087V5, multiclass
    clus
vv   ABLIM3 MUTATED ABLIM3 WILD-TYPE
  N0             11              209
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V6, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED    13   2
  ABLIM3 WILD-TYPE 272  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED     13    2
  ABLIM3 WILD-TYPE  272   46
   clus
vv  ABLIM3 MUTATED ABLIM3 WILD-TYPE
  0             13              272
  1              2               46
[1] 2 2
[1] FALSE
D1087V7, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED     8   8
  ABLIM3 WILD-TYPE 162 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED      8    8
  ABLIM3 WILD-TYPE  162  189
        clus
vv       ABLIM3 MUTATED ABLIM3 WILD-TYPE
  FEMALE              8              162
  MALE                8              189
[1] 2 2
[1] FALSE
D1087V8, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED    12   1
  ABLIM3 WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED     12    1
  ABLIM3 WILD-TYPE  288    7
     clus
vv    ABLIM3 MUTATED ABLIM3 WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D1087V9, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED    14   2
  ABLIM3 WILD-TYPE 300  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED     14    2
  ABLIM3 WILD-TYPE  300   46
                               clus
vv                              ABLIM3 MUTATED ABLIM3 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ABLIM3 MUTATED    10   0   1   2
  ABLIM3 WILD-TYPE 249   3  21  19
D1087V10, multiclass
    clus
vv   ABLIM3 MUTATED ABLIM3 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              2               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"
D1087V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABLIM3 MUTATED                                  0     1
  ABLIM3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ABLIM3 MUTATED                           0     8
  ABLIM3 WILD-TYPE                        19   168
D1087V12, multiclass
                                  clus
vv                                 ABLIM3 MUTATED ABLIM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = STX7 MUTATION ANALYSIS
D1088V1, survival
                sevent
clus2              0   1
  STX7 MUTATED     2   1
  STX7 WILD-TYPE 275  77
  STX7 MUTATED STX7 WILD-TYPE 
             3            352 
  STX7 MUTATED STX7 WILD-TYPE 
             1             77 
$`STX7 MUTATED`
TCGA-AA-3815 TCGA-AA-A00N TCGA-CA-6717 
       33.04         4.01        12.76 

$`STX7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  STX7 MUTATED STX7 WILD-TYPE 
          4.01           0.00 
  STX7 MUTATED STX7 WILD-TYPE 
         33.04         148.01 
  STX7 MUTATED STX7 WILD-TYPE 
        12.760         22.075 
[1] "4.0 - 33.0 (12.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D1088V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STX7 MUTATED         0        0        0         3         1         0
  STX7 WILD-TYPE      64        1       26       105         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  STX7 MUTATED           0
  STX7 WILD-TYPE         1
D1088V3, multiclass
            clus
vv           STX7 MUTATED STX7 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  STX7 MUTATED     0   0   3   1
  STX7 WILD-TYPE   9  67 246  40
D1088V4, multiclass
    clus
vv   STX7 MUTATED STX7 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            3            246
  T4            1             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
  STX7 MUTATED     4   0   0
  STX7 WILD-TYPE 216  81  66
D1088V5, multiclass
    clus
vv   STX7 MUTATED STX7 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V6, binary
                cls
clus               0   1
  STX7 MUTATED     4   0
  STX7 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      4    0
  STX7 WILD-TYPE  281   48
   clus
vv  STX7 MUTATED STX7 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1088V7, binary
                cls
clus               0   1
  STX7 MUTATED     2   2
  STX7 WILD-TYPE 168 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      2    2
  STX7 WILD-TYPE  168  195
        clus
vv       STX7 MUTATED STX7 WILD-TYPE
  FEMALE            2            168
  MALE              2            195
[1] 2 2
[1] FALSE
D1088V8, binary
                cls
clus               0   1
  STX7 MUTATED     2   0
  STX7 WILD-TYPE 298   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      2    0
  STX7 WILD-TYPE  298    8
     clus
vv    STX7 MUTATED STX7 WILD-TYPE
  NO             2            298
  YES            0              8
[1] 2 2
[1] FALSE
D1088V9, binary
                cls
clus               0   1
  STX7 MUTATED     2   2
  STX7 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      2    2
  STX7 WILD-TYPE  312   46
                               clus
vv                              STX7 MUTATED STX7 WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  STX7 MUTATED     3   0   0   1
  STX7 WILD-TYPE 256   3  22  20
D1088V10, multiclass
    clus
vv   STX7 MUTATED STX7 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            1             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"
D1088V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STX7 MUTATED                                  0     1
  STX7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STX7 MUTATED                           0     0
  STX7 WILD-TYPE                        19   176
D1088V12, multiclass
[1] "Remove cluster labels:" "STX7 MUTATED"          
clus
  STX7 MUTATED STX7 WILD-TYPE 
             1            205 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-6600     TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-6607     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-5913     TCGA-CK-5914     TCGA-CK-5915 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6309     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6626 
"STX7 WILD-TYPE" 

Clustering(1089) Variable = LEPRE1 MUTATION ANALYSIS
D1089V1, survival
                  sevent
clus2                0   1
  LEPRE1 MUTATED     6   3
  LEPRE1 WILD-TYPE 271  75
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              346 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               3               75 
$`LEPRE1 MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-6781 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-5861 
       19.04        26.17        19.66        21.44        49.41        15.02 
TCGA-D5-6539 TCGA-F4-6570 TCGA-F4-6809 
       12.49         6.18        13.25 

$`LEPRE1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.225 
[1] "6.2 - 49.4 (19.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.9"
D1089V2, continuous
                  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      64        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEPRE1 MUTATED           0          0          0          1        1
  LEPRE1 WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  LEPRE1 MUTATED           1         0
  LEPRE1 WILD-TYPE        11         1
D1089V3, multiclass
            clus
vv           LEPRE1 MUTATED LEPRE1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  LEPRE1 MUTATED     0   0   8   1
  LEPRE1 WILD-TYPE   9  67 241  40
D1089V4, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              8              241
  T4              1               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
  LEPRE1 MUTATED     7   2   0
  LEPRE1 WILD-TYPE 213  79  66
D1089V5, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V6, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     4   2
  LEPRE1 WILD-TYPE 281  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      4    2
  LEPRE1 WILD-TYPE  281   46
   clus
vv  LEPRE1 MUTATED LEPRE1 WILD-TYPE
  0              4              281
  1              2               46
[1] 2 2
[1] FALSE
D1089V7, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     6   3
  LEPRE1 WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      6    3
  LEPRE1 WILD-TYPE  164  194
        clus
vv       LEPRE1 MUTATED LEPRE1 WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D1089V8, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     8   1
  LEPRE1 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      8    1
  LEPRE1 WILD-TYPE  292    7
     clus
vv    LEPRE1 MUTATED LEPRE1 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D1089V9, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     8   1
  LEPRE1 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      8    1
  LEPRE1 WILD-TYPE  306   47
                               clus
vv                              LEPRE1 MUTATED LEPRE1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LEPRE1 MUTATED     7   0   1   0
  LEPRE1 WILD-TYPE 252   3  21  21
D1089V10, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              1               21
  RX              0               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"
D1089V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEPRE1 MUTATED                                  0     0
  LEPRE1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LEPRE1 MUTATED                           0     8
  LEPRE1 WILD-TYPE                        19   168
D1089V12, multiclass
                                  clus
vv                                 LEPRE1 MUTATED LEPRE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = KIAA0240 MUTATION ANALYSIS
D1090V1, survival
                    sevent
clus2                  0   1
  KIAA0240 MUTATED     7   2
  KIAA0240 WILD-TYPE 270  76
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                346 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 2                 76 
$`KIAA0240 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3949 
       13.02        19.04        79.69        63.98         1.02        26.01 
TCGA-AA-A00N TCGA-CM-6171 TCGA-D5-6928 
        4.01        14.04        11.64 

$`KIAA0240 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
              1.02               0.00 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             79.69             148.01 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             14.04              22.09 
[1] "1.0 - 79.7 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1090V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0240 MUTATED         2        0        1         2         1         0
  KIAA0240 WILD-TYPE      62        1       25       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0240 MUTATED           1          0          1          0        1
  KIAA0240 WILD-TYPE        17          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0240 MUTATED           0         0
  KIAA0240 WILD-TYPE        12         1
D1090V3, multiclass
            clus
vv           KIAA0240 MUTATED KIAA0240 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 2                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  KIAA0240 MUTATED     0   2   6   1
  KIAA0240 WILD-TYPE   9  65 243  40
D1090V4, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                6                243
  T4                1                 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
  KIAA0240 MUTATED     7   1   1
  KIAA0240 WILD-TYPE 213  80  65
D1090V5, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  N0                7                213
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V6, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     8   1
  KIAA0240 WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      8    1
  KIAA0240 WILD-TYPE  277   47
   clus
vv  KIAA0240 MUTATED KIAA0240 WILD-TYPE
  0                8                277
  1                1                 47
[1] 2 2
[1] FALSE
D1090V7, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     4   5
  KIAA0240 WILD-TYPE 166 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      4    5
  KIAA0240 WILD-TYPE  166  192
        clus
vv       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  FEMALE                4                166
  MALE                  5                192
[1] 2 2
[1] FALSE
D1090V8, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     6   1
  KIAA0240 WILD-TYPE 294   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      6    1
  KIAA0240 WILD-TYPE  294    7
     clus
vv    KIAA0240 MUTATED KIAA0240 WILD-TYPE
  NO                 6                294
  YES                1                  7
[1] 2 2
[1] FALSE
D1090V9, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     5   4
  KIAA0240 WILD-TYPE 309  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      5    4
  KIAA0240 WILD-TYPE  309   44
                               clus
vv                              KIAA0240 MUTATED KIAA0240 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0240 MUTATED     7   0   1   0
  KIAA0240 WILD-TYPE 252   3  21  21
D1090V10, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D1090V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0240 MUTATED                                  0     0
  KIAA0240 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0240 MUTATED                           0     3
  KIAA0240 WILD-TYPE                        19   173
D1090V12, multiclass
                                  clus
vv                                 KIAA0240 MUTATED KIAA0240 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[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 = HLA-B MUTATION ANALYSIS
D1091V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    10   0
  HLA-B WILD-TYPE 267  78
  HLA-B MUTATED HLA-B WILD-TYPE 
             10             345 
  HLA-B MUTATED HLA-B WILD-TYPE 
              0              78 
$`HLA-B MUTATED`
TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3555 TCGA-AD-5900 TCGA-CK-4950 TCGA-CK-6751 
       26.17        22.06        29.95        12.16        85.45       124.27 
TCGA-D5-6920 TCGA-D5-6930 TCGA-D5-6931 TCGA-G4-6304 
       12.39        13.35        12.00        53.62 

$`HLA-B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       14.30         9.04         9.44        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  HLA-B MUTATED HLA-B WILD-TYPE 
             12               0 
  HLA-B MUTATED HLA-B WILD-TYPE 
         124.27          148.01 
  HLA-B MUTATED HLA-B WILD-TYPE 
         24.115          22.030 
[1] "12.0 - 124.3 (24.1)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1091V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HLA-B MUTATED         2        0        0         5         2         0
  HLA-B WILD-TYPE      62        1       26       103         6         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  HLA-B MUTATED           0
  HLA-B WILD-TYPE         1
D1091V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  HLA-B MUTATED     0   2   6   3
  HLA-B WILD-TYPE   9  65 243  38
D1091V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             3              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
  HLA-B MUTATED     9   1   1
  HLA-B WILD-TYPE 211  80  65
D1091V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V6, binary
                 cls
clus                0   1
  HLA-B MUTATED     8   0
  HLA-B WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      8    0
  HLA-B WILD-TYPE  277   48
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1091V7, binary
                 cls
clus                0   1
  HLA-B MUTATED     8   3
  HLA-B WILD-TYPE 162 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      8    3
  HLA-B WILD-TYPE  162  194
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             8             162
  MALE               3             194
[1] 2 2
[1] FALSE
D1091V8, binary
                 cls
clus                0   1
  HLA-B MUTATED    10   0
  HLA-B WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     10    0
  HLA-B WILD-TYPE  290    8
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1091V9, binary
                 cls
clus                0   1
  HLA-B MUTATED     6   5
  HLA-B WILD-TYPE 308  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      6    5
  HLA-B WILD-TYPE  308   43
                               clus
vv                              HLA-B MUTATED HLA-B WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED     8   1   0   2
  HLA-B WILD-TYPE 251   2  22  19
D1091V10, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             8             251
  R1             1               2
  R2             0              22
  RX             2              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"
D1091V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-B MUTATED                                  0     0
  HLA-B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED                           1     9
  HLA-B WILD-TYPE                        18   167
D1091V12, multiclass
                                  clus
vv                                 HLA-B MUTATED HLA-B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(1092) Variable = NEK1 MUTATION ANALYSIS
D1092V1, survival
                sevent
clus2              0   1
  NEK1 MUTATED    10   1
  NEK1 WILD-TYPE 267  77
  NEK1 MUTATED NEK1 WILD-TYPE 
            11            344 
  NEK1 MUTATED NEK1 WILD-TYPE 
             1             77 
$`NEK1 MUTATED`
TCGA-AA-3950 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       24.00        22.06        24.39        25.02        34.98        12.16 
TCGA-AU-6004 TCGA-CA-6717 TCGA-D5-6539 TCGA-D5-6931 TCGA-DM-A28F 
       27.09        12.76        12.49        12.00        35.97 

$`NEK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NEK1 MUTATED NEK1 WILD-TYPE 
            12              0 
  NEK1 MUTATED NEK1 WILD-TYPE 
         35.97         148.01 
  NEK1 MUTATED NEK1 WILD-TYPE 
         24.00          22.01 
[1] "12.0 - 36.0 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1092V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEK1 MUTATED         3        0        0         4         1         0
  NEK1 WILD-TYPE      61        1       26       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEK1 MUTATED           0          0          1          1        0         0
  NEK1 WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  NEK1 MUTATED           0
  NEK1 WILD-TYPE         1
D1092V3, multiclass
            clus
vv           NEK1 MUTATED NEK1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  NEK1 MUTATED     0   4   6   2
  NEK1 WILD-TYPE   9  63 243  39
D1092V4, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  T1            0              9
  T2            4             63
  T3            6            243
  T4            2             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
  NEK1 MUTATED    10   1   1
  NEK1 WILD-TYPE 210  80  65
D1092V5, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V6, binary
                cls
clus               0   1
  NEK1 MUTATED    10   0
  NEK1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED     10    0
  NEK1 WILD-TYPE  275   48
   clus
vv  NEK1 MUTATED NEK1 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1092V7, binary
                cls
clus               0   1
  NEK1 MUTATED     6   6
  NEK1 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED      6    6
  NEK1 WILD-TYPE  164  191
        clus
vv       NEK1 MUTATED NEK1 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D1092V8, binary
                cls
clus               0   1
  NEK1 MUTATED     9   0
  NEK1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED      9    0
  NEK1 WILD-TYPE  291    8
     clus
vv    NEK1 MUTATED NEK1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1092V9, binary
                cls
clus               0   1
  NEK1 MUTATED     9   3
  NEK1 WILD-TYPE 305  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED      9    3
  NEK1 WILD-TYPE  305   45
                               clus
vv                              NEK1 MUTATED NEK1 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEK1 MUTATED     8   0   0   1
  NEK1 WILD-TYPE 251   3  22  20
D1092V10, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D1092V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEK1 MUTATED                                  0     1
  NEK1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEK1 MUTATED                           0     7
  NEK1 WILD-TYPE                        19   169
D1092V12, multiclass
                                  clus
vv                                 NEK1 MUTATED NEK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = RNASEL MUTATION ANALYSIS
D1093V1, survival
                  sevent
clus2                0   1
  RNASEL MUTATED     8   4
  RNASEL WILD-TYPE 269  74
  RNASEL MUTATED RNASEL WILD-TYPE 
              12              343 
  RNASEL MUTATED RNASEL WILD-TYPE 
               4               74 
$`RNASEL MUTATED`
TCGA-AD-6895 TCGA-A6-3809 TCGA-AA-3517 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 
       25.08        32.75        38.99         4.01        12.16        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        10.13        33.67 

$`RNASEL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RNASEL MUTATED RNASEL WILD-TYPE 
            4.01             0.00 
  RNASEL MUTATED RNASEL WILD-TYPE 
           58.39           148.01 
  RNASEL MUTATED RNASEL WILD-TYPE 
           16.95            22.09 
[1] "4.0 - 58.4 (16.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1093V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNASEL MUTATED         3        0        0         4         2         0
  RNASEL WILD-TYPE      61        1       26       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASEL MUTATED           0          1          1          0        1
  RNASEL WILD-TYPE        18          5         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  RNASEL MUTATED           0         0
  RNASEL WILD-TYPE        12         1
D1093V3, multiclass
            clus
vv           RNASEL MUTATED RNASEL WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  RNASEL MUTATED     2   1   6   3
  RNASEL WILD-TYPE   7  66 243  38
D1093V4, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  T1              2                7
  T2              1               66
  T3              6              243
  T4              3               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
  RNASEL MUTATED     9   3   0
  RNASEL WILD-TYPE 211  78  66
D1093V5, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  N0              9              211
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V6, binary
                  cls
clus                 0   1
  RNASEL MUTATED    10   1
  RNASEL WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED     10    1
  RNASEL WILD-TYPE  275   47
   clus
vv  RNASEL MUTATED RNASEL WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D1093V7, binary
                  cls
clus                 0   1
  RNASEL MUTATED     3   9
  RNASEL WILD-TYPE 167 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      3    9
  RNASEL WILD-TYPE  167  188
        clus
vv       RNASEL MUTATED RNASEL WILD-TYPE
  FEMALE              3              167
  MALE                9              188
[1] 2 2
[1] FALSE
D1093V8, binary
                  cls
clus                 0   1
  RNASEL MUTATED    11   0
  RNASEL WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED     11    0
  RNASEL WILD-TYPE  289    8
     clus
vv    RNASEL MUTATED RNASEL WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1093V9, binary
                  cls
clus                 0   1
  RNASEL MUTATED     8   4
  RNASEL WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      8    4
  RNASEL WILD-TYPE  306   44
                               clus
vv                              RNASEL MUTATED RNASEL WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNASEL MUTATED     8   0   0   3
  RNASEL WILD-TYPE 251   3  22  18
D1093V10, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              3               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"
D1093V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNASEL MUTATED                                  0     2
  RNASEL WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNASEL MUTATED                           1     7
  RNASEL WILD-TYPE                        18   169
D1093V12, multiclass
                                  clus
vv                                 RNASEL MUTATED RNASEL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = ALCAM MUTATION ANALYSIS
D1094V1, survival
                 sevent
clus2               0   1
  ALCAM MUTATED     7   4
  ALCAM WILD-TYPE 270  74
  ALCAM MUTATED ALCAM WILD-TYPE 
             11             344 
  ALCAM MUTATED ALCAM WILD-TYPE 
              4              74 
$`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 
       10.06        12.43       131.51        65.85        61.91 

$`ALCAM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6317 
       74.56        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ALCAM MUTATED ALCAM WILD-TYPE 
           0.92            0.00 
  ALCAM MUTATED ALCAM WILD-TYPE 
         131.51          148.01 
  ALCAM MUTATED ALCAM WILD-TYPE 
         21.440          22.075 
[1] "0.9 - 131.5 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1094V2, continuous
                 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      63        1       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALCAM MUTATED           1          0          0          2        2         0
  ALCAM WILD-TYPE        17          6         44         31       33        12
                 vv
clus              STAGE IVB
  ALCAM MUTATED           0
  ALCAM WILD-TYPE         1
D1094V3, multiclass
            clus
vv           ALCAM MUTATED ALCAM WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  ALCAM MUTATED     0   1   9   1
  ALCAM WILD-TYPE   9  66 240  40
D1094V4, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             1              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
  ALCAM MUTATED     6   3   2
  ALCAM WILD-TYPE 214  78  64
D1094V5, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  N0             6             214
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1094V6, binary
                 cls
clus                0   1
  ALCAM MUTATED     6   2
  ALCAM WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      6    2
  ALCAM WILD-TYPE  279   46
   clus
vv  ALCAM MUTATED ALCAM WILD-TYPE
  0             6             279
  1             2              46
[1] 2 2
[1] FALSE
D1094V7, binary
                 cls
clus                0   1
  ALCAM MUTATED     3   8
  ALCAM WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      3    8
  ALCAM WILD-TYPE  167  189
        clus
vv       ALCAM MUTATED ALCAM WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1094V8, binary
                 cls
clus                0   1
  ALCAM MUTATED    10   0
  ALCAM WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED     10    0
  ALCAM WILD-TYPE  290    8
     clus
vv    ALCAM MUTATED ALCAM WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1094V9, binary
                 cls
clus                0   1
  ALCAM MUTATED     9   2
  ALCAM WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      9    2
  ALCAM WILD-TYPE  305   46
                               clus
vv                              ALCAM MUTATED ALCAM WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALCAM MUTATED     6   0   0   2
  ALCAM WILD-TYPE 253   3  22  19
D1094V10, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1094V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALCAM MUTATED                                  0     2
  ALCAM WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALCAM MUTATED                           0     7
  ALCAM WILD-TYPE                        19   169
D1094V12, multiclass
                                  clus
vv                                 ALCAM MUTATED ALCAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1095) Variable = SLC30A8 MUTATION ANALYSIS
D1095V1, survival
                   sevent
clus2                 0   1
  SLC30A8 MUTATED    10   3
  SLC30A8 WILD-TYPE 267  75
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               13               342 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
                3                75 
$`SLC30A8 MUTATED`
TCGA-A6-6649 TCGA-AA-3713 TCGA-A6-6648 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3869 
       24.16        19.04        25.18        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 
       61.91 

$`SLC30A8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
                0                 0 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
           124.27            148.01 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
            26.01             21.99 
[1] "0.0 - 124.3 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1095V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC30A8 MUTATED         1        0        1         5         0         0
  SLC30A8 WILD-TYPE      63        1       25       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC30A8 MUTATED           0          0          3          0        3
  SLC30A8 WILD-TYPE        18          6         41         33       32
                   vv
clus                STAGE IVA STAGE IVB
  SLC30A8 MUTATED           1         0
  SLC30A8 WILD-TYPE        11         1
D1095V3, multiclass
            clus
vv           SLC30A8 MUTATED SLC30A8 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               0                33
  STAGE IV                 3                32
  STAGE IVA                1                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
  SLC30A8 MUTATED     0   1  11   2
  SLC30A8 WILD-TYPE   9  66 238  39
D1095V4, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              11               238
  T4               2                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
  SLC30A8 MUTATED     9   4   1
  SLC30A8 WILD-TYPE 211  77  65
D1095V5, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  N0               9               211
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V6, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED     8   4
  SLC30A8 WILD-TYPE 277  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED      8    4
  SLC30A8 WILD-TYPE  277   44
   clus
vv  SLC30A8 MUTATED SLC30A8 WILD-TYPE
  0               8               277
  1               4                44
[1] 2 2
[1] FALSE
D1095V7, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED     8   6
  SLC30A8 WILD-TYPE 162 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED      8    6
  SLC30A8 WILD-TYPE  162  191
        clus
vv       SLC30A8 MUTATED SLC30A8 WILD-TYPE
  FEMALE               8               162
  MALE                 6               191
[1] 2 2
[1] FALSE
D1095V8, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED    10   1
  SLC30A8 WILD-TYPE 290   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED     10    1
  SLC30A8 WILD-TYPE  290    7
     clus
vv    SLC30A8 MUTATED SLC30A8 WILD-TYPE
  NO               10               290
  YES               1                 7
[1] 2 2
[1] FALSE
D1095V9, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED    10   4
  SLC30A8 WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED     10    4
  SLC30A8 WILD-TYPE  304   44
                               clus
vv                              SLC30A8 MUTATED SLC30A8 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC30A8 MUTATED     6   0   2   3
  SLC30A8 WILD-TYPE 253   3  20  18
D1095V10, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               2                20
  RX               3                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"
D1095V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC30A8 MUTATED                                  0     1
  SLC30A8 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC30A8 MUTATED                           0     6
  SLC30A8 WILD-TYPE                        19   170
D1095V12, multiclass
                                  clus
vv                                 SLC30A8 MUTATED SLC30A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1096) Variable = CREG2 MUTATION ANALYSIS
D1096V1, survival
                 sevent
clus2               0   1
  CREG2 MUTATED     3   2
  CREG2 WILD-TYPE 274  76
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             350 
  CREG2 MUTATED CREG2 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CREG2 MUTATED CREG2 WILD-TYPE 
          13.02            0.00 
  CREG2 MUTATED CREG2 WILD-TYPE 
          44.68          148.01 
  CREG2 MUTATED CREG2 WILD-TYPE 
          14.50           22.09 
[1] "13.0 - 44.7 (14.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1096V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CREG2 MUTATED         1        0        0         1         0         0
  CREG2 WILD-TYPE      63        1       26       107         8         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        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  CREG2 MUTATED           0
  CREG2 WILD-TYPE         1
D1096V3, multiclass
            clus
vv           CREG2 MUTATED CREG2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CREG2 MUTATED     0   2   3   0
  CREG2 WILD-TYPE   9  65 246  41
D1096V4, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             0              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
  CREG2 MUTATED     3   0   2
  CREG2 WILD-TYPE 217  81  64
D1096V5, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  N0             3             217
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V6, binary
                 cls
clus                0   1
  CREG2 MUTATED     5   0
  CREG2 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      5    0
  CREG2 WILD-TYPE  280   48
   clus
vv  CREG2 MUTATED CREG2 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1096V7, binary
                 cls
clus                0   1
  CREG2 MUTATED     3   2
  CREG2 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      3    2
  CREG2 WILD-TYPE  167  195
        clus
vv       CREG2 MUTATED CREG2 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1096V8, binary
                 cls
clus                0   1
  CREG2 MUTATED     5   0
  CREG2 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      5    0
  CREG2 WILD-TYPE  295    8
     clus
vv    CREG2 MUTATED CREG2 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1096V9, binary
                 cls
clus                0   1
  CREG2 MUTATED     4   1
  CREG2 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      4    1
  CREG2 WILD-TYPE  310   47
                               clus
vv                              CREG2 MUTATED CREG2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CREG2 MUTATED     4   0   0   0
  CREG2 WILD-TYPE 255   3  22  21
D1096V10, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1096V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREG2 MUTATED                                  0     0
  CREG2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CREG2 MUTATED                           0     3
  CREG2 WILD-TYPE                        19   173
D1096V12, multiclass
                                  clus
vv                                 CREG2 MUTATED CREG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = MSH4 MUTATION ANALYSIS
D1097V1, survival
                sevent
clus2              0   1
  MSH4 MUTATED     9   2
  MSH4 WILD-TYPE 268  76
  MSH4 MUTATED MSH4 WILD-TYPE 
            11            344 
  MSH4 MUTATED MSH4 WILD-TYPE 
             2             76 
$`MSH4 MUTATED`
TCGA-AZ-4681 TCGA-G4-6586 TCGA-A6-2678 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-4315 
      106.75        35.80        42.28        63.98        34.98        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-G4-6303 
       49.41        12.76       148.01        22.98        65.85 

$`MSH4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.90        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MSH4 MUTATED MSH4 WILD-TYPE 
         12.76           0.00 
  MSH4 MUTATED MSH4 WILD-TYPE 
        148.01         140.38 
  MSH4 MUTATED MSH4 WILD-TYPE 
         49.41          21.99 
[1] "12.8 - 148.0 (49.4)" "0.0 - 140.4 (22.0)" 
[1] "hr=" "2.4"
D1097V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH4 MUTATED         0        0        2         5         1         0
  MSH4 WILD-TYPE      64        1       24       103         7         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        17          6         42         33       34        12
                vv
clus             STAGE IVB
  MSH4 MUTATED           0
  MSH4 WILD-TYPE         1
D1097V3, multiclass
            clus
vv           MSH4 MUTATED MSH4 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  MSH4 MUTATED     0   0  11   1
  MSH4 WILD-TYPE   9  67 238  40
D1097V4, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  T1            0              9
  T2            0             67
  T3           11            238
  T4            1             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
  MSH4 MUTATED     8   4   0
  MSH4 WILD-TYPE 212  77  66
D1097V5, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  N0            8            212
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V6, binary
                cls
clus               0   1
  MSH4 MUTATED    10   1
  MSH4 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     10    1
  MSH4 WILD-TYPE  275   47
   clus
vv  MSH4 MUTATED MSH4 WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D1097V7, binary
                cls
clus               0   1
  MSH4 MUTATED     8   4
  MSH4 WILD-TYPE 162 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED      8    4
  MSH4 WILD-TYPE  162  193
        clus
vv       MSH4 MUTATED MSH4 WILD-TYPE
  FEMALE            8            162
  MALE              4            193
[1] 2 2
[1] FALSE
D1097V8, binary
                cls
clus               0   1
  MSH4 MUTATED    11   0
  MSH4 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     11    0
  MSH4 WILD-TYPE  289    8
     clus
vv    MSH4 MUTATED MSH4 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1097V9, binary
                cls
clus               0   1
  MSH4 MUTATED    11   1
  MSH4 WILD-TYPE 303  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     11    1
  MSH4 WILD-TYPE  303   47
                               clus
vv                              MSH4 MUTATED MSH4 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH4 MUTATED    10   0   0   1
  MSH4 WILD-TYPE 249   3  22  20
D1097V10, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D1097V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH4 MUTATED                                  0     1
  MSH4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH4 MUTATED                           0     8
  MSH4 WILD-TYPE                        19   168
D1097V12, multiclass
                                  clus
vv                                 MSH4 MUTATED MSH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = PANK3 MUTATION ANALYSIS
D1098V1, survival
                 sevent
clus2               0   1
  PANK3 MUTATED     5   1
  PANK3 WILD-TYPE 272  77
  PANK3 MUTATED PANK3 WILD-TYPE 
              6             349 
  PANK3 MUTATED PANK3 WILD-TYPE 
              1              77 
$`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        14.04         7.50 

$`PANK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PANK3 MUTATED PANK3 WILD-TYPE 
            7.5             0.0 
  PANK3 MUTATED PANK3 WILD-TYPE 
          46.65          148.01 
  PANK3 MUTATED PANK3 WILD-TYPE 
          31.56           22.03 
[1] "7.5 - 46.6 (31.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1098V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PANK3 MUTATED         1        0        0         2         1         0
  PANK3 WILD-TYPE      63        1       26       106         7         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  PANK3 MUTATED           0
  PANK3 WILD-TYPE         1
D1098V3, multiclass
            clus
vv           PANK3 MUTATED PANK3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  PANK3 MUTATED     1   0   4   1
  PANK3 WILD-TYPE   8  67 245  40
D1098V4, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             4             245
  T4             1              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
  PANK3 MUTATED     4   1   1
  PANK3 WILD-TYPE 216  80  65
D1098V5, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V6, binary
                 cls
clus                0   1
  PANK3 MUTATED     6   0
  PANK3 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      6    0
  PANK3 WILD-TYPE  279   48
   clus
vv  PANK3 MUTATED PANK3 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1098V7, binary
                 cls
clus                0   1
  PANK3 MUTATED     5   1
  PANK3 WILD-TYPE 165 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      5    1
  PANK3 WILD-TYPE  165  196
        clus
vv       PANK3 MUTATED PANK3 WILD-TYPE
  FEMALE             5             165
  MALE               1             196
[1] 2 2
[1] FALSE
D1098V8, binary
                 cls
clus                0   1
  PANK3 MUTATED     5   0
  PANK3 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      5    0
  PANK3 WILD-TYPE  295    8
     clus
vv    PANK3 MUTATED PANK3 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1098V9, binary
                 cls
clus                0   1
  PANK3 MUTATED     6   0
  PANK3 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      6    0
  PANK3 WILD-TYPE  308   48
                               clus
vv                              PANK3 MUTATED PANK3 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PANK3 MUTATED     5   0   0   0
  PANK3 WILD-TYPE 254   3  22  21
D1098V10, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1098V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PANK3 MUTATED                                  0     0
  PANK3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PANK3 MUTATED                           0     4
  PANK3 WILD-TYPE                        19   172
D1098V12, multiclass
                                  clus
vv                                 PANK3 MUTATED PANK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = DNMT1 MUTATION ANALYSIS
D1099V1, survival
                 sevent
clus2               0   1
  DNMT1 MUTATED    13   5
  DNMT1 WILD-TYPE 264  73
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             18             337 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
              5              73 
$`DNMT1 MUTATED`
TCGA-AA-3672 TCGA-A6-2683 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3845 TCGA-AA-3877 
        0.92        16.57         3.02        29.95         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 

$`DNMT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        42.28        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       20.98        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DNMT1 MUTATED DNMT1 WILD-TYPE 
              0               0 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          58.39          148.01 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
         16.355          22.090 
[1] "0.0 - 58.4 (16.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1099V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNMT1 MUTATED         2        0        3         8         2         0
  DNMT1 WILD-TYPE      62        1       23       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNMT1 MUTATED           1          0          1          0        1         0
  DNMT1 WILD-TYPE        17          6         43         33       34        12
                 vv
clus              STAGE IVB
  DNMT1 MUTATED           0
  DNMT1 WILD-TYPE         1
D1099V3, multiclass
            clus
vv           DNMT1 MUTATED DNMT1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  DNMT1 MUTATED     1   1  12   4
  DNMT1 WILD-TYPE   8  66 237  37
D1099V4, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            12             237
  T4             4              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
  DNMT1 MUTATED    16   2   0
  DNMT1 WILD-TYPE 204  79  66
D1099V5, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  N0            16             204
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V6, binary
                 cls
clus                0   1
  DNMT1 MUTATED    16   1
  DNMT1 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     16    1
  DNMT1 WILD-TYPE  269   47
   clus
vv  DNMT1 MUTATED DNMT1 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D1099V7, binary
                 cls
clus                0   1
  DNMT1 MUTATED    11   7
  DNMT1 WILD-TYPE 159 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     11    7
  DNMT1 WILD-TYPE  159  190
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  FEMALE            11             159
  MALE               7             190
[1] 2 2
[1] FALSE
D1099V8, binary
                 cls
clus                0   1
  DNMT1 MUTATED    14   0
  DNMT1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     14    0
  DNMT1 WILD-TYPE  286    8
     clus
vv    DNMT1 MUTATED DNMT1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1099V9, binary
                 cls
clus                0   1
  DNMT1 MUTATED    12   6
  DNMT1 WILD-TYPE 302  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     12    6
  DNMT1 WILD-TYPE  302   42
                               clus
vv                              DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNMT1 MUTATED    15   0   0   2
  DNMT1 WILD-TYPE 244   3  22  19
D1099V10, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             2              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"
D1099V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT1 MUTATED                                  0     1
  DNMT1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNMT1 MUTATED                           0     5
  DNMT1 WILD-TYPE                        19   171
D1099V12, multiclass
                                  clus
vv                                 DNMT1 MUTATED DNMT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = UCHL5 MUTATION ANALYSIS
D1100V1, survival
                 sevent
clus2               0   1
  UCHL5 MUTATED     2   2
  UCHL5 WILD-TYPE 275  76
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              4             351 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              2              76 
$`UCHL5 MUTATED`
TCGA-CK-5912 TCGA-AA-3510 TCGA-AZ-6606 TCGA-CM-4746 
       49.08        63.98        11.74        37.02 

$`UCHL5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  UCHL5 MUTATED UCHL5 WILD-TYPE 
          11.74            0.00 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
          63.98          148.01 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
          43.05           22.03 
[1] "11.7 - 64.0 (43.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1100V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UCHL5 MUTATED         2        0        1         0         0         0
  UCHL5 WILD-TYPE      62        1       25       108         8         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  UCHL5 MUTATED           0
  UCHL5 WILD-TYPE         1
D1100V3, multiclass
            clus
vv           UCHL5 MUTATED UCHL5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  UCHL5 MUTATED     0   2   1   1
  UCHL5 WILD-TYPE   9  65 248  40
D1100V4, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             1             248
  T4             1              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
  UCHL5 MUTATED     3   0   1
  UCHL5 WILD-TYPE 217  81  65
D1100V5, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  N0             3             217
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V6, binary
                 cls
clus                0   1
  UCHL5 MUTATED     2   1
  UCHL5 WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      2    1
  UCHL5 WILD-TYPE  283   47
   clus
vv  UCHL5 MUTATED UCHL5 WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D1100V7, binary
                 cls
clus                0   1
  UCHL5 MUTATED     0   4
  UCHL5 WILD-TYPE 170 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      0    4
  UCHL5 WILD-TYPE  170  193
        clus
vv       UCHL5 MUTATED UCHL5 WILD-TYPE
  FEMALE             0             170
  MALE               4             193
[1] 2 2
[1] FALSE
D1100V8, binary
                 cls
clus                0   1
  UCHL5 MUTATED     4   0
  UCHL5 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      4    0
  UCHL5 WILD-TYPE  296    8
     clus
vv    UCHL5 MUTATED UCHL5 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1100V9, binary
                 cls
clus                0   1
  UCHL5 MUTATED     4   0
  UCHL5 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      4    0
  UCHL5 WILD-TYPE  310   48
                               clus
vv                              UCHL5 MUTATED UCHL5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UCHL5 MUTATED     2   0   0   1
  UCHL5 WILD-TYPE 257   3  22  20
D1100V10, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             1              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"
D1100V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UCHL5 MUTATED                                  0     0
  UCHL5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UCHL5 MUTATED                           1     2
  UCHL5 WILD-TYPE                        18   174
D1100V12, multiclass
                                  clus
vv                                 UCHL5 MUTATED UCHL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(1101) Variable = HERC1 MUTATION ANALYSIS
D1101V1, survival
                 sevent
clus2               0   1
  HERC1 MUTATED    22   8
  HERC1 WILD-TYPE 255  70
  HERC1 MUTATED HERC1 WILD-TYPE 
             30             325 
  HERC1 MUTATED HERC1 WILD-TYPE 
              8              70 
$`HERC1 MUTATED`
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AD-6895 TCGA-A6-3809 TCGA-A6-5665 
       29.98        24.00         2.01        25.08        32.75        22.06 
TCGA-A6-5666 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3710 
       32.71        24.39        20.12        78.08         6.97        26.99 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-5900 
       33.01        25.02         4.01        34.98        14.01        12.16 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6751 TCGA-D5-6538 
       83.24        58.39        12.59        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 

$`HERC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6137 
       30.44        29.19        33.53        23.61        22.09        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-A6-6654 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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A28E TCGA-DM-A28G 
       44.32       131.51       135.65       139.17       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  HERC1 MUTATED HERC1 WILD-TYPE 
           2.01            0.00 
  HERC1 MUTATED HERC1 WILD-TYPE 
         124.27          148.01 
  HERC1 MUTATED HERC1 WILD-TYPE 
          25.05           21.99 
[1] "2.0 - 124.3 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1101V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HERC1 MUTATED         3        0        2        13         4         1
  HERC1 WILD-TYPE      61        1       24        95         4         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        18          6         40         32       33        12
                 vv
clus              STAGE IVB
  HERC1 MUTATED           0
  HERC1 WILD-TYPE         1
D1101V3, multiclass
            clus
vv           HERC1 MUTATED HERC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             13              95
  STAGE IIB              4               4
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  HERC1 MUTATED     0   4  21   6
  HERC1 WILD-TYPE   9  63 228  35
D1101V4, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            21             228
  T4             6              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
  HERC1 MUTATED    24   3   4
  HERC1 WILD-TYPE 196  78  62
D1101V5, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  N0            24             196
  N1             3              78
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V6, binary
                 cls
clus                0   1
  HERC1 MUTATED    25   2
  HERC1 WILD-TYPE 260  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     25    2
  HERC1 WILD-TYPE  260   46
   clus
vv  HERC1 MUTATED HERC1 WILD-TYPE
  0            25             260
  1             2              46
[1] 2 2
[1] FALSE
D1101V7, binary
                 cls
clus                0   1
  HERC1 MUTATED    13  18
  HERC1 WILD-TYPE 157 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     13   18
  HERC1 WILD-TYPE  157  179
        clus
vv       HERC1 MUTATED HERC1 WILD-TYPE
  FEMALE            13             157
  MALE              18             179
[1] 2 2
[1] FALSE
D1101V8, binary
                 cls
clus                0   1
  HERC1 MUTATED    24   0
  HERC1 WILD-TYPE 276   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     24    0
  HERC1 WILD-TYPE  276    8
     clus
vv    HERC1 MUTATED HERC1 WILD-TYPE
  NO             24             276
  YES             0               8
[1] 2 2
[1] FALSE
D1101V9, binary
                 cls
clus                0   1
  HERC1 MUTATED    23   8
  HERC1 WILD-TYPE 291  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     23    8
  HERC1 WILD-TYPE  291   40
                               clus
vv                              HERC1 MUTATED HERC1 WILD-TYPE
  COLON ADENOCARCINOMA                     23             291
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HERC1 MUTATED    21   0   1   2
  HERC1 WILD-TYPE 238   3  21  19
D1101V10, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  R0            21             238
  R1             0               3
  R2             1              21
  RX             2              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"
D1101V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HERC1 MUTATED                                  0     3
  HERC1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HERC1 MUTATED                           0    16
  HERC1 WILD-TYPE                        19   160
D1101V12, multiclass
                                  clus
vv                                 HERC1 MUTATED HERC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       16             160
[1] 4 2
[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 = PROM1 MUTATION ANALYSIS
D1102V1, survival
                 sevent
clus2               0   1
  PROM1 MUTATED    10   2
  PROM1 WILD-TYPE 267  76
  PROM1 MUTATED PROM1 WILD-TYPE 
             12             343 
  PROM1 MUTATED PROM1 WILD-TYPE 
              2              76 
$`PROM1 MUTATED`
TCGA-AD-6964 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-6653 TCGA-AA-3864 TCGA-AA-A010 
       10.88         1.94        26.17        24.39        53.00        34.98 
TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6930 TCGA-DM-A28H 
       14.04        14.04        11.01        18.25        13.35       117.07 

$`PROM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PROM1 MUTATED PROM1 WILD-TYPE 
           1.94            0.00 
  PROM1 MUTATED PROM1 WILD-TYPE 
         117.07          148.01 
  PROM1 MUTATED PROM1 WILD-TYPE 
         16.145          22.090 
[1] "1.9 - 117.1 (16.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1102V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PROM1 MUTATED         3        0        1         3         1         0
  PROM1 WILD-TYPE      61        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PROM1 MUTATED           0          1          1          1        0         0
  PROM1 WILD-TYPE        18          5         43         32       35        12
                 vv
clus              STAGE IVB
  PROM1 MUTATED           0
  PROM1 WILD-TYPE         1
D1102V3, multiclass
            clus
vv           PROM1 MUTATED PROM1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  PROM1 MUTATED     1   3   6   2
  PROM1 WILD-TYPE   8  64 243  39
D1102V4, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  T1             1               8
  T2             3              64
  T3             6             243
  T4             2              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
  PROM1 MUTATED     8   2   2
  PROM1 WILD-TYPE 212  79  64
D1102V5, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V6, binary
                 cls
clus                0   1
  PROM1 MUTATED    11   0
  PROM1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     11    0
  PROM1 WILD-TYPE  274   48
   clus
vv  PROM1 MUTATED PROM1 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1102V7, binary
                 cls
clus                0   1
  PROM1 MUTATED     5   7
  PROM1 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED      5    7
  PROM1 WILD-TYPE  165  190
        clus
vv       PROM1 MUTATED PROM1 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D1102V8, binary
                 cls
clus                0   1
  PROM1 MUTATED    11   0
  PROM1 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     11    0
  PROM1 WILD-TYPE  289    8
     clus
vv    PROM1 MUTATED PROM1 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1102V9, binary
                 cls
clus                0   1
  PROM1 MUTATED    11   1
  PROM1 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     11    1
  PROM1 WILD-TYPE  303   47
                               clus
vv                              PROM1 MUTATED PROM1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PROM1 MUTATED     8   0   0   0
  PROM1 WILD-TYPE 251   3  22  21
D1102V10, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1102V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PROM1 MUTATED                                  0     0
  PROM1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PROM1 MUTATED                           0    10
  PROM1 WILD-TYPE                        19   166
D1102V12, multiclass
                                  clus
vv                                 PROM1 MUTATED PROM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1103) Variable = TMCO6 MUTATION ANALYSIS
D1103V1, survival
                 sevent
clus2               0   1
  TMCO6 MUTATED     6   1
  TMCO6 WILD-TYPE 271  77
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             348 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              1              77 
$`TMCO6 MUTATED`
TCGA-AD-6895 TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-4746 
       25.08         1.02        33.01        34.98        49.41        37.02 
TCGA-G4-6307 
       55.04 

$`TMCO6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  TMCO6 MUTATED TMCO6 WILD-TYPE 
           1.02            0.00 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
          55.04          148.01 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
          34.98           21.99 
[1] "1.0 - 55.0 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1103V2, continuous
                 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      62        1       25       108         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMCO6 MUTATED           0          0          2          0        0         0
  TMCO6 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  TMCO6 MUTATED           0
  TMCO6 WILD-TYPE         1
D1103V3, multiclass
            clus
vv           TMCO6 MUTATED TMCO6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  TMCO6 MUTATED     0   2   3   2
  TMCO6 WILD-TYPE   9  65 246  39
D1103V4, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             2              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
  TMCO6 MUTATED     5   2   0
  TMCO6 WILD-TYPE 215  79  66
D1103V5, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V6, binary
                 cls
clus                0   1
  TMCO6 MUTATED     6   0
  TMCO6 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      6    0
  TMCO6 WILD-TYPE  279   48
   clus
vv  TMCO6 MUTATED TMCO6 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1103V7, binary
                 cls
clus                0   1
  TMCO6 MUTATED     5   2
  TMCO6 WILD-TYPE 165 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      5    2
  TMCO6 WILD-TYPE  165  195
        clus
vv       TMCO6 MUTATED TMCO6 WILD-TYPE
  FEMALE             5             165
  MALE               2             195
[1] 2 2
[1] FALSE
D1103V8, binary
                 cls
clus                0   1
  TMCO6 MUTATED     7   0
  TMCO6 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      7    0
  TMCO6 WILD-TYPE  293    8
     clus
vv    TMCO6 MUTATED TMCO6 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1103V9, binary
                 cls
clus                0   1
  TMCO6 MUTATED     5   2
  TMCO6 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      5    2
  TMCO6 WILD-TYPE  309   46
                               clus
vv                              TMCO6 MUTATED TMCO6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TMCO6 MUTATED     6   0   0   0
  TMCO6 WILD-TYPE 253   3  22  21
D1103V10, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1103V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMCO6 MUTATED                                  0     0
  TMCO6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMCO6 MUTATED                           1     3
  TMCO6 WILD-TYPE                        18   173
D1103V12, multiclass
                                  clus
vv                                 TMCO6 MUTATED TMCO6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = RAB38 MUTATION ANALYSIS
D1104V1, survival
                 sevent
clus2               0   1
  RAB38 MUTATED     2   3
  RAB38 WILD-TYPE 275  75
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             350 
  RAB38 MUTATED RAB38 WILD-TYPE 
              3              75 
$`RAB38 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AD-6890 TCGA-AZ-6598 TCGA-CM-5862 
       42.90        22.06        24.53        49.41         5.03 

$`RAB38 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RAB38 MUTATED RAB38 WILD-TYPE 
           5.03            0.00 
  RAB38 MUTATED RAB38 WILD-TYPE 
          49.41          148.01 
  RAB38 MUTATED RAB38 WILD-TYPE 
          24.53           22.01 
[1] "5.0 - 49.4 (24.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.7"
D1104V2, continuous
                 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      64        1       25       107         7         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        18          6         44         33       35        11
                 vv
clus              STAGE IVB
  RAB38 MUTATED           0
  RAB38 WILD-TYPE         1
D1104V3, multiclass
            clus
vv           RAB38 MUTATED RAB38 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  RAB38 MUTATED     1   0   3   1
  RAB38 WILD-TYPE   8  67 246  40
D1104V4, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             3             246
  T4             1              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
  RAB38 MUTATED     4   1   0
  RAB38 WILD-TYPE 216  80  66
D1104V5, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V6, binary
                 cls
clus                0   1
  RAB38 MUTATED     2   1
  RAB38 WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      2    1
  RAB38 WILD-TYPE  283   47
   clus
vv  RAB38 MUTATED RAB38 WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D1104V7, binary
                 cls
clus                0   1
  RAB38 MUTATED     3   2
  RAB38 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      3    2
  RAB38 WILD-TYPE  167  195
        clus
vv       RAB38 MUTATED RAB38 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1104V8, binary
                 cls
clus                0   1
  RAB38 MUTATED     5   0
  RAB38 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      5    0
  RAB38 WILD-TYPE  295    8
     clus
vv    RAB38 MUTATED RAB38 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1104V9, binary
                 cls
clus                0   1
  RAB38 MUTATED     5   0
  RAB38 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      5    0
  RAB38 WILD-TYPE  309   48
                               clus
vv                              RAB38 MUTATED RAB38 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RAB38 MUTATED     3   0   0   0
  RAB38 WILD-TYPE 256   3  22  21
D1104V10, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1104V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB38 MUTATED                                  0     0
  RAB38 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB38 MUTATED                           0     5
  RAB38 WILD-TYPE                        19   171
D1104V12, multiclass
                                  clus
vv                                 RAB38 MUTATED RAB38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = LRMP MUTATION ANALYSIS
D1105V1, survival
                sevent
clus2              0   1
  LRMP MUTATED     2   3
  LRMP WILD-TYPE 275  75
  LRMP MUTATED LRMP WILD-TYPE 
             5            350 
  LRMP MUTATED LRMP WILD-TYPE 
             3             75 
$`LRMP MUTATED`
TCGA-AA-3877 TCGA-AA-A00N TCGA-CA-6717 TCGA-DM-A0XF TCGA-DM-A1D7 
       31.00         4.01        12.76        38.20        13.32 

$`LRMP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LRMP MUTATED LRMP WILD-TYPE 
          4.01           0.00 
  LRMP MUTATED LRMP WILD-TYPE 
         38.20         148.01 
  LRMP MUTATED LRMP WILD-TYPE 
        13.320         22.075 
[1] "4.0 - 38.2 (13.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "4"  
D1105V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRMP MUTATED         1        0        0         2         1         0
  LRMP WILD-TYPE      63        1       26       106         7         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        18          6         44         32       35        12
                vv
clus             STAGE IVB
  LRMP MUTATED           0
  LRMP WILD-TYPE         1
D1105V3, multiclass
            clus
vv           LRMP MUTATED LRMP WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  LRMP MUTATED     1   0   3   1
  LRMP WILD-TYPE   8  67 246  40
D1105V4, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  T1            1              8
  T2            0             67
  T3            3            246
  T4            1             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
  LRMP MUTATED     4   0   1
  LRMP WILD-TYPE 216  81  65
D1105V5, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  N0            4            216
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V6, binary
                cls
clus               0   1
  LRMP MUTATED     5   0
  LRMP WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      5    0
  LRMP WILD-TYPE  280   48
   clus
vv  LRMP MUTATED LRMP WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1105V7, binary
                cls
clus               0   1
  LRMP MUTATED     2   3
  LRMP WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      2    3
  LRMP WILD-TYPE  168  194
        clus
vv       LRMP MUTATED LRMP WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D1105V8, binary
                cls
clus               0   1
  LRMP MUTATED     2   0
  LRMP WILD-TYPE 298   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      2    0
  LRMP WILD-TYPE  298    8
     clus
vv    LRMP MUTATED LRMP WILD-TYPE
  NO             2            298
  YES            0              8
[1] 2 2
[1] FALSE
D1105V9, binary
                cls
clus               0   1
  LRMP MUTATED     0   3
  LRMP WILD-TYPE 314  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      0    3
  LRMP WILD-TYPE  314   45
                               clus
vv                              LRMP MUTATED LRMP WILD-TYPE
  COLON ADENOCARCINOMA                     0            314
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LRMP MUTATED     2   0   0   1
  LRMP WILD-TYPE 257   3  22  20
D1105V10, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  R0            2            257
  R1            0              3
  R2            0             22
  RX            1             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"
D1105V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRMP MUTATED                                  0     1
  LRMP WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LRMP MUTATED                           0     2
  LRMP WILD-TYPE                        19   174
D1105V12, multiclass
                                  clus
vv                                 LRMP MUTATED LRMP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(1106) Variable = NHLRC2 MUTATION ANALYSIS
D1106V1, survival
                  sevent
clus2                0   1
  NHLRC2 MUTATED     7   1
  NHLRC2 WILD-TYPE 270  77
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               8              347 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               1               77 
$`NHLRC2 MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6965 TCGA-AY-5543 TCGA-CM-4746 
       63.98        35.01        83.24        26.47        33.01        37.02 
TCGA-D5-6536 TCGA-G4-6309 
       17.85        85.48 

$`NHLRC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 
       12.16        24.53         5.79        22.42        27.42        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
           17.85             0.00 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
           85.48           148.01 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
          36.015           21.990 
[1] "17.9 - 85.5 (36.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3"  
D1106V2, continuous
                  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      63        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHLRC2 MUTATED           1          0          1          1        0
  NHLRC2 WILD-TYPE        17          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  NHLRC2 MUTATED           1         0
  NHLRC2 WILD-TYPE        11         1
D1106V3, multiclass
            clus
vv           NHLRC2 MUTATED NHLRC2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  NHLRC2 MUTATED     0   1   7   1
  NHLRC2 WILD-TYPE   9  66 242  40
D1106V4, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              1               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
  NHLRC2 MUTATED     5   2   2
  NHLRC2 WILD-TYPE 215  79  64
D1106V5, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  N0              5              215
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V6, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     8   1
  NHLRC2 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      8    1
  NHLRC2 WILD-TYPE  277   47
   clus
vv  NHLRC2 MUTATED NHLRC2 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1106V7, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     3   6
  NHLRC2 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      3    6
  NHLRC2 WILD-TYPE  167  191
        clus
vv       NHLRC2 MUTATED NHLRC2 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D1106V8, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     7   1
  NHLRC2 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      7    1
  NHLRC2 WILD-TYPE  293    7
     clus
vv    NHLRC2 MUTATED NHLRC2 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D1106V9, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     8   1
  NHLRC2 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      8    1
  NHLRC2 WILD-TYPE  306   47
                               clus
vv                              NHLRC2 MUTATED NHLRC2 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NHLRC2 MUTATED     8   1   0   0
  NHLRC2 WILD-TYPE 251   2  22  21
D1106V10, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  R0              8              251
  R1              1                2
  R2              0               22
  RX              0               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"
D1106V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NHLRC2 MUTATED                                  0     1
  NHLRC2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NHLRC2 MUTATED                           3     2
  NHLRC2 WILD-TYPE                        16   174
D1106V12, multiclass
                                  clus
vv                                 NHLRC2 MUTATED NHLRC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         2              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(1107) Variable = DCBLD1 MUTATION ANALYSIS
D1107V1, survival
                  sevent
clus2                0   1
  DCBLD1 MUTATED     4   1
  DCBLD1 WILD-TYPE 273  77
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               5              350 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               1               77 
$`DCBLD1 MUTATED`
TCGA-AA-3697 TCGA-A6-6781 TCGA-AA-3977 TCGA-D5-6922 TCGA-DM-A28G 
       85.05        19.66        25.02        10.13        60.79 

$`DCBLD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
           10.13             0.00 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
           85.05           148.01 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
          25.020           22.045 
[1] "10.1 - 85.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1107V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCBLD1 MUTATED         0        0        1         1         0         0
  DCBLD1 WILD-TYPE      64        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCBLD1 MUTATED           0          1          0          1        0
  DCBLD1 WILD-TYPE        18          5         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  DCBLD1 MUTATED           0         0
  DCBLD1 WILD-TYPE        12         1
D1107V3, multiclass
            clus
vv           DCBLD1 MUTATED DCBLD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  DCBLD1 MUTATED     0   1   3   1
  DCBLD1 WILD-TYPE   9  66 246  40
D1107V4, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              3              246
  T4              1               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
  DCBLD1 MUTATED     3   2   0
  DCBLD1 WILD-TYPE 217  79  66
D1107V5, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  N0              3              217
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V6, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     3   0
  DCBLD1 WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      3    0
  DCBLD1 WILD-TYPE  282   48
   clus
vv  DCBLD1 MUTATED DCBLD1 WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D1107V7, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     0   5
  DCBLD1 WILD-TYPE 170 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      0    5
  DCBLD1 WILD-TYPE  170  192
        clus
vv       DCBLD1 MUTATED DCBLD1 WILD-TYPE
  FEMALE              0              170
  MALE                5              192
[1] 2 2
[1] FALSE
D1107V8, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     4   0
  DCBLD1 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      4    0
  DCBLD1 WILD-TYPE  296    8
     clus
vv    DCBLD1 MUTATED DCBLD1 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1107V9, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     4   1
  DCBLD1 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      4    1
  DCBLD1 WILD-TYPE  310   47
                               clus
vv                              DCBLD1 MUTATED DCBLD1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DCBLD1 MUTATED     3   0   0   0
  DCBLD1 WILD-TYPE 256   3  22  21
D1107V10, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1107V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCBLD1 MUTATED                                  0     0
  DCBLD1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DCBLD1 MUTATED                           0     3
  DCBLD1 WILD-TYPE                        19   173
D1107V12, multiclass
                                  clus
vv                                 DCBLD1 MUTATED DCBLD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = JAK1 MUTATION ANALYSIS
D1108V1, survival
                sevent
clus2              0   1
  JAK1 MUTATED    16   2
  JAK1 WILD-TYPE 261  76
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            337 
  JAK1 MUTATED JAK1 WILD-TYPE 
             2             76 
$`JAK1 MUTATED`
TCGA-AD-6895 TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5657 TCGA-A6-5665 
       25.08        10.88        35.80        79.69        31.63        22.06 
TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A01P TCGA-AY-6196 TCGA-AY-6197 
       19.66        26.99        25.02        38.07         0.20        21.44 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6928 
       12.76       148.01        15.62        23.05        14.04        11.64 

$`JAK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        21.37        15.52       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       10.06        14.30        17.56        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  JAK1 MUTATED JAK1 WILD-TYPE 
           0.2            0.0 
  JAK1 MUTATED JAK1 WILD-TYPE 
        148.01         140.38 
  JAK1 MUTATED JAK1 WILD-TYPE 
        22.555         22.030 
[1] "0.2 - 148.0 (22.6)" "0.0 - 140.4 (22.0)"
[1] "hr=" "2"  
D1108V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JAK1 MUTATED         2        0        0         7         0         0
  JAK1 WILD-TYPE      62        1       26       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK1 MUTATED           2          0          2          3        0         0
  JAK1 WILD-TYPE        16          6         42         30       35        12
                vv
clus             STAGE IVB
  JAK1 MUTATED           0
  JAK1 WILD-TYPE         1
D1108V3, multiclass
            clus
vv           JAK1 MUTATED JAK1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            3             30
  STAGE IV              0             35
  STAGE IVA             0             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
  JAK1 MUTATED     0   3  12   3
  JAK1 WILD-TYPE   9  64 237  38
D1108V4, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           12            237
  T4            3             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
  JAK1 MUTATED    10   5   3
  JAK1 WILD-TYPE 210  76  63
D1108V5, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  N0           10            210
  N1            5             76
  N2            3             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"
D1108V6, binary
                cls
clus               0   1
  JAK1 MUTATED    13   0
  JAK1 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     13    0
  JAK1 WILD-TYPE  272   48
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           13            272
  1            0             48
[1] 2 2
[1] FALSE
D1108V7, binary
                cls
clus               0   1
  JAK1 MUTATED     7  11
  JAK1 WILD-TYPE 163 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      7   11
  JAK1 WILD-TYPE  163  186
        clus
vv       JAK1 MUTATED JAK1 WILD-TYPE
  FEMALE            7            163
  MALE             11            186
[1] 2 2
[1] FALSE
D1108V8, binary
                cls
clus               0   1
  JAK1 MUTATED    16   0
  JAK1 WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     16    0
  JAK1 WILD-TYPE  284    8
     clus
vv    JAK1 MUTATED JAK1 WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D1108V9, binary
                cls
clus               0   1
  JAK1 MUTATED    13   5
  JAK1 WILD-TYPE 301  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     13    5
  JAK1 WILD-TYPE  301   43
                               clus
vv                              JAK1 MUTATED JAK1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  JAK1 MUTATED    14   0   0   2
  JAK1 WILD-TYPE 245   3  22  19
D1108V10, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            0             22
  RX            2             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"
D1108V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK1 MUTATED                                  0     1
  JAK1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK1 MUTATED                           1    13
  JAK1 WILD-TYPE                        18   163
D1108V12, multiclass
                                  clus
vv                                 JAK1 MUTATED JAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      13            163
[1] 4 2
[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 = PAK4 MUTATION ANALYSIS
D1109V1, survival
                sevent
clus2              0   1
  PAK4 MUTATED     6   0
  PAK4 WILD-TYPE 271  78
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            349 
  PAK4 MUTATED PAK4 WILD-TYPE 
             0             78 
$`PAK4 MUTATED`
TCGA-G4-6628 TCGA-AY-5543 TCGA-AY-6196 TCGA-CM-4743 TCGA-CM-6171 TCGA-DM-A1HB 
       79.69        33.01         0.20        23.05        14.04       135.65 

$`PAK4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PAK4 MUTATED PAK4 WILD-TYPE 
           0.2            0.0 
  PAK4 MUTATED PAK4 WILD-TYPE 
        135.65         148.01 
  PAK4 MUTATED PAK4 WILD-TYPE 
         28.03          22.03 
[1] "0.2 - 135.7 (28.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9400000"
D1109V2, continuous
                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      62        1       26       107         8         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        18          6         43         32       35        11
                vv
clus             STAGE IVB
  PAK4 MUTATED           0
  PAK4 WILD-TYPE         1
D1109V3, multiclass
            clus
vv           PAK4 MUTATED PAK4 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  PAK4 MUTATED     0   2   4   0
  PAK4 WILD-TYPE   9  65 245  41
D1109V4, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            4            245
  T4            0             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
  PAK4 MUTATED     3   2   1
  PAK4 WILD-TYPE 217  79  65
D1109V5, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  N0            3            217
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V6, binary
                cls
clus               0   1
  PAK4 MUTATED     4   1
  PAK4 WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      4    1
  PAK4 WILD-TYPE  281   47
   clus
vv  PAK4 MUTATED PAK4 WILD-TYPE
  0            4            281
  1            1             47
[1] 2 2
[1] FALSE
D1109V7, binary
                cls
clus               0   1
  PAK4 MUTATED     2   4
  PAK4 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      2    4
  PAK4 WILD-TYPE  168  193
        clus
vv       PAK4 MUTATED PAK4 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1109V8, binary
                cls
clus               0   1
  PAK4 MUTATED     4   0
  PAK4 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      4    0
  PAK4 WILD-TYPE  296    8
     clus
vv    PAK4 MUTATED PAK4 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1109V9, binary
                cls
clus               0   1
  PAK4 MUTATED     4   1
  PAK4 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      4    1
  PAK4 WILD-TYPE  310   47
                               clus
vv                              PAK4 MUTATED PAK4 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAK4 MUTATED     5   0   0   0
  PAK4 WILD-TYPE 254   3  22  21
D1109V10, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1109V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK4 MUTATED                                  0     0
  PAK4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK4 MUTATED                           1     5
  PAK4 WILD-TYPE                        18   171
D1109V12, multiclass
                                  clus
vv                                 PAK4 MUTATED PAK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = SNX2 MUTATION ANALYSIS
D1110V1, survival
                sevent
clus2              0   1
  SNX2 MUTATED     8   2
  SNX2 WILD-TYPE 269  76
  SNX2 MUTATED SNX2 WILD-TYPE 
            10            345 
  SNX2 MUTATED SNX2 WILD-TYPE 
             2             76 
$`SNX2 MUTATED`
TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3982 TCGA-AA-A010 
       79.69        19.66        63.98        10.06        27.02        34.98 
TCGA-AA-A02H TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6540 
        2.01        12.76        12.00        16.14 

$`SNX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SNX2 MUTATED SNX2 WILD-TYPE 
          2.01           0.00 
  SNX2 MUTATED SNX2 WILD-TYPE 
         79.69         148.01 
  SNX2 MUTATED SNX2 WILD-TYPE 
         17.90          22.09 
[1] "2.0 - 79.7 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1110V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNX2 MUTATED         2        0        1         1         2         0
  SNX2 WILD-TYPE      62        1       25       107         6         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        17          6         42         32       34        12
                vv
clus             STAGE IVB
  SNX2 MUTATED           0
  SNX2 WILD-TYPE         1
D1110V3, multiclass
            clus
vv           SNX2 MUTATED SNX2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  SNX2 MUTATED     0   2   6   3
  SNX2 WILD-TYPE   9  65 243  38
D1110V4, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            3             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
  SNX2 MUTATED     6   3   2
  SNX2 WILD-TYPE 214  78  64
D1110V5, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  N0            6            214
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V6, binary
                cls
clus               0   1
  SNX2 MUTATED     8   1
  SNX2 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      8    1
  SNX2 WILD-TYPE  277   47
   clus
vv  SNX2 MUTATED SNX2 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D1110V7, binary
                cls
clus               0   1
  SNX2 MUTATED     5   6
  SNX2 WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      5    6
  SNX2 WILD-TYPE  165  191
        clus
vv       SNX2 MUTATED SNX2 WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D1110V8, binary
                cls
clus               0   1
  SNX2 MUTATED     9   0
  SNX2 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      9    0
  SNX2 WILD-TYPE  291    8
     clus
vv    SNX2 MUTATED SNX2 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1110V9, binary
                cls
clus               0   1
  SNX2 MUTATED     7   4
  SNX2 WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      7    4
  SNX2 WILD-TYPE  307   44
                               clus
vv                              SNX2 MUTATED SNX2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SNX2 MUTATED     7   0   1   2
  SNX2 WILD-TYPE 252   3  21  19
D1110V10, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            2             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"
D1110V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNX2 MUTATED                                  0     1
  SNX2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SNX2 MUTATED                           0     5
  SNX2 WILD-TYPE                        19   171
D1110V12, multiclass
                                  clus
vv                                 SNX2 MUTATED SNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = LIMCH1 MUTATION ANALYSIS
D1111V1, survival
                  sevent
clus2                0   1
  LIMCH1 MUTATED    13   0
  LIMCH1 WILD-TYPE 264  78
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              13              342 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               0               78 
$`LIMCH1 MUTATED`
TCGA-AA-3672 TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3534 
        0.92        33.34        33.53        20.12        63.98        29.00 
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 
       19.59 

$`LIMCH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        34.65        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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            22.01 
[1] "0.9 - 64.0 (29.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D1111V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIMCH1 MUTATED         0        0        2         9         0         0
  LIMCH1 WILD-TYPE      64        1       24        99         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIMCH1 MUTATED           1          1          0          0        0
  LIMCH1 WILD-TYPE        17          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  LIMCH1 MUTATED           0         0
  LIMCH1 WILD-TYPE        12         1
D1111V3, multiclass
            clus
vv           LIMCH1 MUTATED LIMCH1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               9               99
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  LIMCH1 MUTATED     0   0  13   0
  LIMCH1 WILD-TYPE   9  67 236  41
D1111V4, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             13              236
  T4              0               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
  LIMCH1 MUTATED    11   2   0
  LIMCH1 WILD-TYPE 209  79  66
D1111V5, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  N0             11              209
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V6, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    12   0
  LIMCH1 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     12    0
  LIMCH1 WILD-TYPE  273   48
   clus
vv  LIMCH1 MUTATED LIMCH1 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1111V7, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED     5   8
  LIMCH1 WILD-TYPE 165 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED      5    8
  LIMCH1 WILD-TYPE  165  189
        clus
vv       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  FEMALE              5              165
  MALE                8              189
[1] 2 2
[1] FALSE
D1111V8, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    12   0
  LIMCH1 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     12    0
  LIMCH1 WILD-TYPE  288    8
     clus
vv    LIMCH1 MUTATED LIMCH1 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1111V9, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    10   3
  LIMCH1 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     10    3
  LIMCH1 WILD-TYPE  304   45
                               clus
vv                              LIMCH1 MUTATED LIMCH1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LIMCH1 MUTATED    11   0   0   1
  LIMCH1 WILD-TYPE 248   3  22  20
D1111V10, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              1               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"
D1111V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIMCH1 MUTATED                                  0     1
  LIMCH1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LIMCH1 MUTATED                           1     5
  LIMCH1 WILD-TYPE                        18   171
D1111V12, multiclass
                                  clus
vv                                 LIMCH1 MUTATED LIMCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = CD34 MUTATION ANALYSIS
D1112V1, survival
                sevent
clus2              0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 273  76
  CD34 MUTATED CD34 WILD-TYPE 
             6            349 
  CD34 MUTATED CD34 WILD-TYPE 
             2             76 
$`CD34 MUTATED`
TCGA-AA-3662 TCGA-AA-3489 TCGA-AA-3966 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 
        6.05         7.04         2.01        58.39        11.74        12.76 

$`CD34 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.09 
[1] "2.0 - 58.4 (9.4)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1112V2, continuous
                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      64        1       25       105         8         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        18          6         44         33       33        12
                vv
clus             STAGE IVB
  CD34 MUTATED           0
  CD34 WILD-TYPE         1
D1112V3, multiclass
            clus
vv           CD34 MUTATED CD34 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  CD34 MUTATED     0   0   4   2
  CD34 WILD-TYPE   9  67 245  39
D1112V4, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            4            245
  T4            2             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
  CD34 MUTATED     4   0   2
  CD34 WILD-TYPE 216  81  64
D1112V5, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V6, binary
                cls
clus               0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 281  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      4    2
  CD34 WILD-TYPE  281   46
   clus
vv  CD34 MUTATED CD34 WILD-TYPE
  0            4            281
  1            2             46
[1] 2 2
[1] FALSE
D1112V7, binary
                cls
clus               0   1
  CD34 MUTATED     2   4
  CD34 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      2    4
  CD34 WILD-TYPE  168  193
        clus
vv       CD34 MUTATED CD34 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1112V8, binary
                cls
clus               0   1
  CD34 MUTATED     5   0
  CD34 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      5    0
  CD34 WILD-TYPE  295    8
     clus
vv    CD34 MUTATED CD34 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1112V9, binary
                cls
clus               0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      4    2
  CD34 WILD-TYPE  310   46
                               clus
vv                              CD34 MUTATED CD34 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD34 MUTATED     2   0   1   1
  CD34 WILD-TYPE 257   3  21  20
D1112V10, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            1             21
  RX            1             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"
D1112V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD34 MUTATED                                  0     1
  CD34 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD34 MUTATED                           0     2
  CD34 WILD-TYPE                        19   174
D1112V12, multiclass
                                  clus
vv                                 CD34 MUTATED CD34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(1113) Variable = KIAA0564 MUTATION ANALYSIS
D1113V1, survival
                    sevent
clus2                  0   1
  KIAA0564 MUTATED    16   5
  KIAA0564 WILD-TYPE 261  73
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                21                334 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                 5                 73 
$`KIAA0564 MUTATED`
TCGA-AA-3525 TCGA-AA-3554 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-6653 TCGA-A6-6780 
        8.05        17.95        26.17        79.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       19.66        20.28         3.02        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 
       83.24        21.44        58.39        12.76        10.06        14.04 
TCGA-D5-6540 TCGA-DM-A1DB TCGA-DM-A1HA 
       16.14        44.32       131.51 

$`KIAA0564 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3489 TCGA-AA-3502 
       25.18        21.76        24.69        23.87         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.50       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
              3.02               0.00 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
            131.51             148.01 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
             20.28              22.09 
[1] "3.0 - 131.5 (20.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1113V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0564 MUTATED         4        0        1        10         3         0
  KIAA0564 WILD-TYPE      60        1       25        98         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0564 MUTATED           0          0          1          2        0
  KIAA0564 WILD-TYPE        18          6         43         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0564 MUTATED           0         0
  KIAA0564 WILD-TYPE        12         1
D1113V3, multiclass
            clus
vv           KIAA0564 MUTATED KIAA0564 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                10                 98
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                2                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA0564 MUTATED     0   5  13   4
  KIAA0564 WILD-TYPE   9  62 236  37
D1113V4, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  T1                0                  9
  T2                5                 62
  T3               13                236
  T4                4                 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
  KIAA0564 MUTATED    19   2   1
  KIAA0564 WILD-TYPE 201  79  65
D1113V5, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  N0               19                201
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V6, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    17   0
  KIAA0564 WILD-TYPE 268  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     17    0
  KIAA0564 WILD-TYPE  268   48
   clus
vv  KIAA0564 MUTATED KIAA0564 WILD-TYPE
  0               17                268
  1                0                 48
[1] 2 2
[1] FALSE
D1113V7, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED     6  16
  KIAA0564 WILD-TYPE 164 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED      6   16
  KIAA0564 WILD-TYPE  164  181
        clus
vv       KIAA0564 MUTATED KIAA0564 WILD-TYPE
  FEMALE                6                164
  MALE                 16                181
[1] 2 2
[1] FALSE
D1113V8, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    18   0
  KIAA0564 WILD-TYPE 282   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     18    0
  KIAA0564 WILD-TYPE  282    8
     clus
vv    KIAA0564 MUTATED KIAA0564 WILD-TYPE
  NO                18                282
  YES                0                  8
[1] 2 2
[1] FALSE
D1113V9, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    17   5
  KIAA0564 WILD-TYPE 297  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     17    5
  KIAA0564 WILD-TYPE  297   43
                               clus
vv                              KIAA0564 MUTATED KIAA0564 WILD-TYPE
  COLON ADENOCARCINOMA                        17                297
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0564 MUTATED    14   0   0   2
  KIAA0564 WILD-TYPE 245   3  22  19
D1113V10, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  R0               14                245
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1113V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0564 MUTATED                                  0     3
  KIAA0564 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0564 MUTATED                           0    12
  KIAA0564 WILD-TYPE                        19   164
D1113V12, multiclass
                                  clus
vv                                 KIAA0564 MUTATED KIAA0564 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          12                164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1114) Variable = CEACAM6 MUTATION ANALYSIS
D1114V1, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     2   2
  CEACAM6 WILD-TYPE 275  76
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               351 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                2                76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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            22.060 
[1] "6.2 - 133.2 (64.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1114V2, continuous
                   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      64        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEACAM6 MUTATED           1          0          0          1        1
  CEACAM6 WILD-TYPE        17          6         44         32       34
                   vv
clus                STAGE IVA STAGE IVB
  CEACAM6 MUTATED           0         0
  CEACAM6 WILD-TYPE        12         1
D1114V3, multiclass
            clus
vv           CEACAM6 MUTATED CEACAM6 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  CEACAM6 MUTATED     0   0   3   1
  CEACAM6 WILD-TYPE   9  67 246  40
D1114V4, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               3               246
  T4               1                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
  CEACAM6 MUTATED     1   2   1
  CEACAM6 WILD-TYPE 219  79  65
D1114V5, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  N0               1               219
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V6, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     3   1
  CEACAM6 WILD-TYPE 282  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      3    1
  CEACAM6 WILD-TYPE  282   47
   clus
vv  CEACAM6 MUTATED CEACAM6 WILD-TYPE
  0               3               282
  1               1                47
[1] 2 2
[1] FALSE
D1114V7, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     2   2
  CEACAM6 WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      2    2
  CEACAM6 WILD-TYPE  168  195
        clus
vv       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D1114V8, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     3   0
  CEACAM6 WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      3    0
  CEACAM6 WILD-TYPE  297    8
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D1114V9, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     4   0
  CEACAM6 WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      4    0
  CEACAM6 WILD-TYPE  310   48
                               clus
vv                              CEACAM6 MUTATED CEACAM6 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CEACAM6 MUTATED     2   0   0   0
  CEACAM6 WILD-TYPE 257   3  22  21
D1114V10, multiclass
[1] "Remove cluster labels:" "CEACAM6 MUTATED"       
clus
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        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-3527 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3662        TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AD-6895        TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-2676        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-3502        TCGA-AA-3510 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3561        TCGA-AA-3655        TCGA-AA-3660 
"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-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3815        TCGA-AA-3818 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3842        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-3861        TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3955 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3973 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3975        TCGA-AA-3984        TCGA-AA-3989        TCGA-AA-3994 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00N 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00W        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-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4682 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6703 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6315 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
D1114V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEACAM6 MUTATED                                  0     0
  CEACAM6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CEACAM6 MUTATED                           1     3
  CEACAM6 WILD-TYPE                        18   173
D1114V12, multiclass
                                  clus
vv                                 CEACAM6 MUTATED CEACAM6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = CASP4 MUTATION ANALYSIS
D1115V1, survival
                 sevent
clus2               0   1
  CASP4 MUTATED     6   2
  CASP4 WILD-TYPE 271  76
  CASP4 MUTATED CASP4 WILD-TYPE 
              8             347 
  CASP4 MUTATED CASP4 WILD-TYPE 
              2              76 
$`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 
       54.61        20.19 

$`CASP4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6676 TCGA-CM-6677 TCGA-CM-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-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CASP4 MUTATED CASP4 WILD-TYPE 
          12.76            0.00 
  CASP4 MUTATED CASP4 WILD-TYPE 
          54.61          148.01 
  CASP4 MUTATED CASP4 WILD-TYPE 
         20.815          22.090 
[1] "12.8 - 54.6 (20.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1115V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP4 MUTATED         0        0        0         3         0         0
  CASP4 WILD-TYPE      64        1       26       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP4 MUTATED           0          0          1          1        1         0
  CASP4 WILD-TYPE        18          6         43         32       34        12
                 vv
clus              STAGE IVB
  CASP4 MUTATED           1
  CASP4 WILD-TYPE         0
D1115V3, multiclass
            clus
vv           CASP4 MUTATED CASP4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              12
  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   1   6   1
  CASP4 WILD-TYPE   9  66 243  40
D1115V4, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             1              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
  CASP4 MUTATED     3   3   2
  CASP4 WILD-TYPE 217  78  64
D1115V5, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  N0             3             217
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V6, binary
                 cls
clus                0   1
  CASP4 MUTATED     4   2
  CASP4 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      4    2
  CASP4 WILD-TYPE  281   46
   clus
vv  CASP4 MUTATED CASP4 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D1115V7, binary
                 cls
clus                0   1
  CASP4 MUTATED     3   5
  CASP4 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      3    5
  CASP4 WILD-TYPE  167  192
        clus
vv       CASP4 MUTATED CASP4 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D1115V8, binary
                 cls
clus                0   1
  CASP4 MUTATED     7   0
  CASP4 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      7    0
  CASP4 WILD-TYPE  293    8
     clus
vv    CASP4 MUTATED CASP4 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1115V9, binary
                 cls
clus                0   1
  CASP4 MUTATED     6   2
  CASP4 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      6    2
  CASP4 WILD-TYPE  308   46
                               clus
vv                              CASP4 MUTATED CASP4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP4 MUTATED     4   0   1   2
  CASP4 WILD-TYPE 255   3  21  19
D1115V10, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             2              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"
D1115V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP4 MUTATED                                  0     1
  CASP4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP4 MUTATED                           1     5
  CASP4 WILD-TYPE                        18   171
D1115V12, multiclass
                                  clus
vv                                 CASP4 MUTATED CASP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = AKAP11 MUTATION ANALYSIS
D1116V1, survival
                  sevent
clus2                0   1
  AKAP11 MUTATED    16   5
  AKAP11 WILD-TYPE 261  73
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              21              334 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               5               73 
$`AKAP11 MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-A6-3809 TCGA-AA-3663 TCGA-AA-3861 TCGA-AA-A00E 
       24.00        25.08        32.75         6.97        30.05        30.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-6901 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        0.99        34.98        22.42        12.59        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        14.04        54.61        13.41 
TCGA-DM-A1DA TCGA-F4-6856 TCGA-G4-6307 
        7.50        35.31        55.04 

$`AKAP11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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-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-D5-5539 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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        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        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
            0.99             0.00 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           55.04           148.01 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
          22.420           22.045 
[1] "1.0 - 55.0 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1116V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP11 MUTATED         4        0        1         7         2         0
  AKAP11 WILD-TYPE      60        1       25       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP11 MUTATED           0          0          4          2        1
  AKAP11 WILD-TYPE        18          6         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  AKAP11 MUTATED           0         0
  AKAP11 WILD-TYPE        12         1
D1116V3, multiclass
            clus
vv           AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  AKAP11 MUTATED     2   2  15   3
  AKAP11 WILD-TYPE   7  65 234  38
D1116V4, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  T1              2                7
  T2              2               65
  T3             15              234
  T4              3               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
  AKAP11 MUTATED    15   5   2
  AKAP11 WILD-TYPE 205  76  64
D1116V5, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  N0             15              205
  N1              5               76
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V6, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    20   1
  AKAP11 WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     20    1
  AKAP11 WILD-TYPE  265   47
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0             20              265
  1              1               47
[1] 2 2
[1] FALSE
D1116V7, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    11  11
  AKAP11 WILD-TYPE 159 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     11   11
  AKAP11 WILD-TYPE  159  186
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  FEMALE             11              159
  MALE               11              186
[1] 2 2
[1] FALSE
D1116V8, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    18   0
  AKAP11 WILD-TYPE 282   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     18    0
  AKAP11 WILD-TYPE  282    8
     clus
vv    AKAP11 MUTATED AKAP11 WILD-TYPE
  NO              18              282
  YES              0                8
[1] 2 2
[1] FALSE
D1116V9, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    17   5
  AKAP11 WILD-TYPE 297  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     17    5
  AKAP11 WILD-TYPE  297   43
                               clus
vv                              AKAP11 MUTATED AKAP11 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKAP11 MUTATED    16   0   0   4
  AKAP11 WILD-TYPE 243   3  22  17
D1116V10, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  R0             16              243
  R1              0                3
  R2              0               22
  RX              4               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"
D1116V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP11 MUTATED                                  0     3
  AKAP11 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AKAP11 MUTATED                           0    12
  AKAP11 WILD-TYPE                        19   164
D1116V12, multiclass
                                  clus
vv                                 AKAP11 MUTATED AKAP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        12              164
[1] 4 2
[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 = OSMR MUTATION ANALYSIS
D1117V1, survival
                sevent
clus2              0   1
  OSMR MUTATED    13   7
  OSMR WILD-TYPE 264  71
  OSMR MUTATED OSMR WILD-TYPE 
            20            335 
  OSMR MUTATED OSMR WILD-TYPE 
             7             71 
$`OSMR MUTATED`
TCGA-AA-3972 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3818 
       50.99        22.06        19.66         3.02        63.98         0.99 
TCGA-AA-3864 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-6717 
       53.00         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 
      117.07        65.85 

$`OSMR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05        33.04        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        22.36 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        12.49        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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          22.52 
[1] "1.0 - 117.1 (17.5)" "0.0 - 148.0 (22.5)"
[1] "hr=" "1.6"
D1117V2, continuous
                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      60        1       23       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OSMR MUTATED           0          0          1          2        3         0
  OSMR WILD-TYPE        18          6         43         31       32        12
                vv
clus             STAGE IVB
  OSMR MUTATED           0
  OSMR WILD-TYPE         1
D1117V3, multiclass
            clus
vv           OSMR MUTATED OSMR WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              3             32
  STAGE IVA             0             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
  OSMR MUTATED     0   4  13   3
  OSMR WILD-TYPE   9  63 236  38
D1117V4, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  T1            0              9
  T2            4             63
  T3           13            236
  T4            3             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
  OSMR MUTATED    14   3   3
  OSMR WILD-TYPE 206  78  63
D1117V5, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  N0           14            206
  N1            3             78
  N2            3             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"
D1117V6, binary
                cls
clus               0   1
  OSMR MUTATED    14   3
  OSMR WILD-TYPE 271  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     14    3
  OSMR WILD-TYPE  271   45
   clus
vv  OSMR MUTATED OSMR WILD-TYPE
  0           14            271
  1            3             45
[1] 2 2
[1] FALSE
D1117V7, binary
                cls
clus               0   1
  OSMR MUTATED     6  14
  OSMR WILD-TYPE 164 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED      6   14
  OSMR WILD-TYPE  164  183
        clus
vv       OSMR MUTATED OSMR WILD-TYPE
  FEMALE            6            164
  MALE             14            183
[1] 2 2
[1] FALSE
D1117V8, binary
                cls
clus               0   1
  OSMR MUTATED    17   0
  OSMR WILD-TYPE 283   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     17    0
  OSMR WILD-TYPE  283    8
     clus
vv    OSMR MUTATED OSMR WILD-TYPE
  NO            17            283
  YES            0              8
[1] 2 2
[1] FALSE
D1117V9, binary
                cls
clus               0   1
  OSMR MUTATED    16   4
  OSMR WILD-TYPE 298  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     16    4
  OSMR WILD-TYPE  298   44
                               clus
vv                              OSMR MUTATED OSMR WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OSMR MUTATED    14   0   1   2
  OSMR WILD-TYPE 245   3  21  19
D1117V10, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  R0           14            245
  R1            0              3
  R2            1             21
  RX            2             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"
D1117V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSMR MUTATED                                  0     2
  OSMR WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OSMR MUTATED                           0    12
  OSMR WILD-TYPE                        19   164
D1117V12, multiclass
                                  clus
vv                                 OSMR MUTATED OSMR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      12            164
[1] 4 2
[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 = HDAC5 MUTATION ANALYSIS
D1118V1, survival
                 sevent
clus2               0   1
  HDAC5 MUTATED     6   5
  HDAC5 WILD-TYPE 271  73
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             11             344 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
              5              73 
$`HDAC5 MUTATED`
TCGA-AZ-6601 TCGA-AA-3492 TCGA-AA-A01R TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CK-5916 
      100.01         3.02        35.01        62.79        49.41        21.14 
TCGA-CM-5860 TCGA-D5-6930 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6315 
       32.02        13.35        47.87        35.31        61.91 

$`HDAC5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
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-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HDAC5 MUTATED HDAC5 WILD-TYPE 
           3.02            0.00 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
         100.01          148.01 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
          35.31           21.99 
[1] "3.0 - 100.0 (35.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1118V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HDAC5 MUTATED         2        0        4         3         0         0
  HDAC5 WILD-TYPE      62        1       22       105         8         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        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  HDAC5 MUTATED           0
  HDAC5 WILD-TYPE         1
D1118V3, multiclass
            clus
vv           HDAC5 MUTATED HDAC5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HDAC5 MUTATED     1   1   9   0
  HDAC5 WILD-TYPE   8  66 240  41
D1118V4, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             9             240
  T4             0              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
  HDAC5 MUTATED     9   1   1
  HDAC5 WILD-TYPE 211  80  65
D1118V5, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V6, binary
                 cls
clus                0   1
  HDAC5 MUTATED     8   1
  HDAC5 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      8    1
  HDAC5 WILD-TYPE  277   47
   clus
vv  HDAC5 MUTATED HDAC5 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1118V7, binary
                 cls
clus                0   1
  HDAC5 MUTATED     3   8
  HDAC5 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      3    8
  HDAC5 WILD-TYPE  167  189
        clus
vv       HDAC5 MUTATED HDAC5 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1118V8, binary
                 cls
clus                0   1
  HDAC5 MUTATED    10   1
  HDAC5 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED     10    1
  HDAC5 WILD-TYPE  290    7
     clus
vv    HDAC5 MUTATED HDAC5 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1118V9, binary
                 cls
clus                0   1
  HDAC5 MUTATED     8   3
  HDAC5 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      8    3
  HDAC5 WILD-TYPE  306   45
                               clus
vv                              HDAC5 MUTATED HDAC5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HDAC5 MUTATED     7   0   0   1
  HDAC5 WILD-TYPE 252   3  22  20
D1118V10, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1118V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC5 MUTATED                                  0     0
  HDAC5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HDAC5 MUTATED                           0     9
  HDAC5 WILD-TYPE                        19   167
D1118V12, multiclass
                                  clus
vv                                 HDAC5 MUTATED HDAC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(1119) Variable = NCR3 MUTATION ANALYSIS
D1119V1, survival
                sevent
clus2              0   1
  NCR3 MUTATED     3   1
  NCR3 WILD-TYPE 274  77
  NCR3 MUTATED NCR3 WILD-TYPE 
             4            351 
  NCR3 MUTATED NCR3 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NCR3 MUTATED NCR3 WILD-TYPE 
            12              0 
  NCR3 MUTATED NCR3 WILD-TYPE 
         53.00         148.01 
  NCR3 MUTATED NCR3 WILD-TYPE 
        32.515         22.060 
[1] "12.0 - 53.0 (32.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1119V2, continuous
                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      64        1       24       108         7         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        18          6         44         31       35        12
                vv
clus             STAGE IVB
  NCR3 MUTATED           0
  NCR3 WILD-TYPE         1
D1119V3, multiclass
            clus
vv           NCR3 MUTATED NCR3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             0            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  NCR3 MUTATED     0   0   2   3
  NCR3 WILD-TYPE   9  67 247  38
D1119V4, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            2            247
  T4            3             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
  NCR3 MUTATED     3   0   2
  NCR3 WILD-TYPE 217  81  64
D1119V5, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  N0            3            217
  N1            0             81
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V6, binary
                cls
clus               0   1
  NCR3 MUTATED     3   0
  NCR3 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      3    0
  NCR3 WILD-TYPE  282   48
   clus
vv  NCR3 MUTATED NCR3 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1119V7, binary
                cls
clus               0   1
  NCR3 MUTATED     3   2
  NCR3 WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      3    2
  NCR3 WILD-TYPE  167  195
        clus
vv       NCR3 MUTATED NCR3 WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D1119V8, binary
                cls
clus               0   1
  NCR3 MUTATED     3   0
  NCR3 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      3    0
  NCR3 WILD-TYPE  297    8
     clus
vv    NCR3 MUTATED NCR3 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1119V9, binary
                cls
clus               0   1
  NCR3 MUTATED     4   1
  NCR3 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      4    1
  NCR3 WILD-TYPE  310   47
                               clus
vv                              NCR3 MUTATED NCR3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NCR3 MUTATED     2   0   0   2
  NCR3 WILD-TYPE 257   3  22  19
D1119V10, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            0             22
  RX            2             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"
D1119V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCR3 MUTATED                                  0     0
  NCR3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NCR3 MUTATED                           0     4
  NCR3 WILD-TYPE                        19   172
D1119V12, multiclass
                                  clus
vv                                 NCR3 MUTATED NCR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = ORC4L MUTATION ANALYSIS
D1120V1, survival
                 sevent
clus2               0   1
  ORC4L MUTATED     4   2
  ORC4L WILD-TYPE 273  76
  ORC4L MUTATED ORC4L WILD-TYPE 
              6             349 
  ORC4L MUTATED ORC4L WILD-TYPE 
              2              76 
$`ORC4L MUTATED`
TCGA-G4-6628 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6606 TCGA-CK-6751 
       79.69        18.05         4.01        34.98        11.74       124.27 

$`ORC4L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ORC4L MUTATED ORC4L WILD-TYPE 
           4.01            0.00 
  ORC4L MUTATED ORC4L WILD-TYPE 
         124.27          148.01 
  ORC4L MUTATED ORC4L WILD-TYPE 
         26.515          22.060 
[1] "4.0 - 124.3 (26.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1120V2, continuous
                 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      62        1       26       108         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ORC4L MUTATED           0          0          1          0        1         0
  ORC4L WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  ORC4L MUTATED           0
  ORC4L WILD-TYPE         1
D1120V3, multiclass
            clus
vv           ORC4L MUTATED ORC4L WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ORC4L MUTATED     0   2   0   4
  ORC4L WILD-TYPE   9  65 249  37
D1120V4, multiclass
    clus
vv   ORC4L MUTATED ORC4L WILD-TYPE
  T1             0               9
  T2             2              65
  T3             0             249
  T4             4              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
  ORC4L MUTATED     4   1   1
  ORC4L WILD-TYPE 216  80  65
D1120V5, multiclass
    clus
vv   ORC4L MUTATED ORC4L WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V6, binary
                 cls
clus                0   1
  ORC4L MUTATED     4   1
  ORC4L WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      4    1
  ORC4L WILD-TYPE  281   47
   clus
vv  ORC4L MUTATED ORC4L WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1120V7, binary
                 cls
clus                0   1
  ORC4L MUTATED     2   4
  ORC4L WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      2    4
  ORC4L WILD-TYPE  168  193
        clus
vv       ORC4L MUTATED ORC4L WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D1120V8, binary
                 cls
clus                0   1
  ORC4L MUTATED     5   0
  ORC4L WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      5    0
  ORC4L WILD-TYPE  295    8
     clus
vv    ORC4L MUTATED ORC4L WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1120V9, binary
                 cls
clus                0   1
  ORC4L MUTATED     3   3
  ORC4L WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      3    3
  ORC4L WILD-TYPE  311   45
                               clus
vv                              ORC4L MUTATED ORC4L WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ORC4L MUTATED     4   0   0   1
  ORC4L WILD-TYPE 255   3  22  20
D1120V10, multiclass
    clus
vv   ORC4L MUTATED ORC4L WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1120V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ORC4L MUTATED                                  0     0
  ORC4L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ORC4L MUTATED                           0     3
  ORC4L WILD-TYPE                        19   173
D1120V12, multiclass
                                  clus
vv                                 ORC4L MUTATED ORC4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = SECISBP2 MUTATION ANALYSIS
D1121V1, survival
                    sevent
clus2                  0   1
  SECISBP2 MUTATED     6   1
  SECISBP2 WILD-TYPE 271  77
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 7                348 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 1                 77 
$`SECISBP2 MUTATED`
TCGA-G4-6588 TCGA-A6-2678 TCGA-A6-6648 TCGA-AA-A01R TCGA-AZ-6605 TCGA-CA-6717 
       26.17        42.28        25.18        35.01         5.23        12.76 
TCGA-DM-A28H 
      117.07 

$`SECISBP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        16.57        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
              5.23               0.00 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
            117.07             148.01 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
             26.17              22.01 
[1] "5.2 - 117.1 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1121V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SECISBP2 MUTATED         0        0        0         2         0         0
  SECISBP2 WILD-TYPE      64        1       26       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SECISBP2 MUTATED           1          0          2          1        0
  SECISBP2 WILD-TYPE        17          6         42         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  SECISBP2 MUTATED           1         0
  SECISBP2 WILD-TYPE        11         1
D1121V3, multiclass
            clus
vv           SECISBP2 MUTATED SECISBP2 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  SECISBP2 MUTATED     0   0   6   1
  SECISBP2 WILD-TYPE   9  67 243  40
D1121V4, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                6                243
  T4                1                 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
  SECISBP2 MUTATED     3   2   2
  SECISBP2 WILD-TYPE 217  79  64
D1121V5, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  N0                3                217
  N1                2                 79
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V6, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     6   1
  SECISBP2 WILD-TYPE 279  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      6    1
  SECISBP2 WILD-TYPE  279   47
   clus
vv  SECISBP2 MUTATED SECISBP2 WILD-TYPE
  0                6                279
  1                1                 47
[1] 2 2
[1] FALSE
D1121V7, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     2   5
  SECISBP2 WILD-TYPE 168 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      2    5
  SECISBP2 WILD-TYPE  168  192
        clus
vv       SECISBP2 MUTATED SECISBP2 WILD-TYPE
  FEMALE                2                168
  MALE                  5                192
[1] 2 2
[1] FALSE
D1121V8, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     5   1
  SECISBP2 WILD-TYPE 295   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      5    1
  SECISBP2 WILD-TYPE  295    7
     clus
vv    SECISBP2 MUTATED SECISBP2 WILD-TYPE
  NO                 5                295
  YES                1                  7
[1] 2 2
[1] FALSE
D1121V9, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     5   2
  SECISBP2 WILD-TYPE 309  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      5    2
  SECISBP2 WILD-TYPE  309   46
                               clus
vv                              SECISBP2 MUTATED SECISBP2 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SECISBP2 MUTATED     3   0   0   1
  SECISBP2 WILD-TYPE 256   3  22  20
D1121V10, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1121V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SECISBP2 MUTATED                                  0     1
  SECISBP2 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SECISBP2 MUTATED                           0     5
  SECISBP2 WILD-TYPE                        19   171
D1121V12, multiclass
                                  clus
vv                                 SECISBP2 MUTATED SECISBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = OR51T1 MUTATION ANALYSIS
D1122V1, survival
                  sevent
clus2                0   1
  OR51T1 MUTATED     7   3
  OR51T1 WILD-TYPE 270  75
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              10              345 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
               3               75 
$`OR51T1 MUTATED`
TCGA-AA-3697 TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-5864 TCGA-CM-6171 
       85.05        33.04        83.24        58.39        15.02        14.04 
TCGA-CM-6674 TCGA-D5-5538 TCGA-F4-6569 TCGA-G4-6626 
       12.95        54.61        35.74        46.75 

$`OR51T1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        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        14.04        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-D5-5539 
       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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  OR51T1 MUTATED OR51T1 WILD-TYPE 
           12.95             0.00 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
           85.05           148.01 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
          41.245           21.990 
[1] "12.9 - 85.0 (41.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1122V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51T1 MUTATED         3        0        1         6         0         0
  OR51T1 WILD-TYPE      61        1       25       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51T1 MUTATED           0          0          1          0        0
  OR51T1 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51T1 MUTATED           0         0
  OR51T1 WILD-TYPE        12         1
D1122V3, multiclass
            clus
vv           OR51T1 MUTATED OR51T1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  OR51T1 MUTATED     0   3   8   0
  OR51T1 WILD-TYPE   9  64 241  41
D1122V4, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              8              241
  T4              0               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
  OR51T1 MUTATED    10   1   0
  OR51T1 WILD-TYPE 210  80  66
D1122V5, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  N0             10              210
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1122V6, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    11   0
  OR51T1 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     11    0
  OR51T1 WILD-TYPE  274   48
   clus
vv  OR51T1 MUTATED OR51T1 WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D1122V7, binary
                  cls
clus                 0   1
  OR51T1 MUTATED     4   7
  OR51T1 WILD-TYPE 166 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED      4    7
  OR51T1 WILD-TYPE  166  190
        clus
vv       OR51T1 MUTATED OR51T1 WILD-TYPE
  FEMALE              4              166
  MALE                7              190
[1] 2 2
[1] FALSE
D1122V8, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    10   0
  OR51T1 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     10    0
  OR51T1 WILD-TYPE  290    8
     clus
vv    OR51T1 MUTATED OR51T1 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D1122V9, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    11   0
  OR51T1 WILD-TYPE 303  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     11    0
  OR51T1 WILD-TYPE  303   48
                               clus
vv                              OR51T1 MUTATED OR51T1 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51T1 MUTATED    11   0   0   0
  OR51T1 WILD-TYPE 248   3  22  21
D1122V10, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              0               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"
D1122V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51T1 MUTATED                                  0     1
  OR51T1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51T1 MUTATED                           0     7
  OR51T1 WILD-TYPE                        19   169
D1122V12, multiclass
                                  clus
vv                                 OR51T1 MUTATED OR51T1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = SNAPC2 MUTATION ANALYSIS
D1123V1, survival
                  sevent
clus2                0   1
  SNAPC2 MUTATED     4   2
  SNAPC2 WILD-TYPE 273  76
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              349 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2               76 
$`SNAPC2 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3663 TCGA-AA-3977 TCGA-AD-6889 TCGA-DM-A1HB 
       13.02        19.04         6.97        25.02        83.24       135.65 

$`SNAPC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.06 
[1] "7.0 - 135.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1123V2, continuous
                  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      64        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC2 MUTATED           1          0          1          0        1
  SNAPC2 WILD-TYPE        17          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  SNAPC2 MUTATED           0         0
  SNAPC2 WILD-TYPE        12         1
D1123V3, multiclass
            clus
vv           SNAPC2 MUTATED SNAPC2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  SNAPC2 MUTATED     0   1   5   0
  SNAPC2 WILD-TYPE   9  66 244  41
D1123V4, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              0               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
  SNAPC2 MUTATED     4   1   1
  SNAPC2 WILD-TYPE 216  80  65
D1123V5, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V6, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     4   1
  SNAPC2 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      4    1
  SNAPC2 WILD-TYPE  281   47
   clus
vv  SNAPC2 MUTATED SNAPC2 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1123V7, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     1   5
  SNAPC2 WILD-TYPE 169 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      1    5
  SNAPC2 WILD-TYPE  169  192
        clus
vv       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  FEMALE              1              169
  MALE                5              192
[1] 2 2
[1] FALSE
D1123V8, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     4   1
  SNAPC2 WILD-TYPE 296   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      4    1
  SNAPC2 WILD-TYPE  296    7
     clus
vv    SNAPC2 MUTATED SNAPC2 WILD-TYPE
  NO               4              296
  YES              1                7
[1] 2 2
[1] FALSE
D1123V9, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     4   1
  SNAPC2 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      4    1
  SNAPC2 WILD-TYPE  310   47
                               clus
vv                              SNAPC2 MUTATED SNAPC2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SNAPC2 MUTATED     2   0   1   0
  SNAPC2 WILD-TYPE 257   3  21  21
D1123V10, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              1               21
  RX              0               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"
D1123V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNAPC2 MUTATED                                  0     1
  SNAPC2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SNAPC2 MUTATED                           0     1
  SNAPC2 WILD-TYPE                        19   175
D1123V12, multiclass
[1] "Remove cluster labels:" "SNAPC2 MUTATED"        
clus
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6890       TCGA-AD-6899 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"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-5913       TCGA-CK-5914       TCGA-CK-5915 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 

Clustering(1124) Variable = ABHD2 MUTATION ANALYSIS
D1124V1, survival
                 sevent
clus2               0   1
  ABHD2 MUTATED     5   5
  ABHD2 WILD-TYPE 272  73
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             10             345 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
              5              73 
$`ABHD2 MUTATED`
TCGA-AA-3516 TCGA-AD-6964 TCGA-CK-5912 TCGA-G4-6628 TCGA-AA-A00J TCGA-AA-A00N 
       13.02        10.88        49.08        79.69        18.05         4.01 
TCGA-AD-6889 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5864 
       83.24        37.02        22.03        15.02 

$`ABHD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       23.05        20.02        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-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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ABHD2 MUTATED ABHD2 WILD-TYPE 
           4.01            0.00 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
          83.24          148.01 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
          20.04           22.09 
[1] "4.0 - 83.2 (20.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1124V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABHD2 MUTATED         4        0        0         1         1         0
  ABHD2 WILD-TYPE      60        1       26       107         7         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        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  ABHD2 MUTATED           0
  ABHD2 WILD-TYPE         1
D1124V3, multiclass
            clus
vv           ABHD2 MUTATED ABHD2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ABHD2 MUTATED     0   4   3   3
  ABHD2 WILD-TYPE   9  63 246  38
D1124V4, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             3             246
  T4             3              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
  ABHD2 MUTATED     6   2   2
  ABHD2 WILD-TYPE 214  79  64
D1124V5, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V6, binary
                 cls
clus                0   1
  ABHD2 MUTATED     8   0
  ABHD2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      8    0
  ABHD2 WILD-TYPE  277   48
   clus
vv  ABHD2 MUTATED ABHD2 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1124V7, binary
                 cls
clus                0   1
  ABHD2 MUTATED     2   8
  ABHD2 WILD-TYPE 168 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      2    8
  ABHD2 WILD-TYPE  168  189
        clus
vv       ABHD2 MUTATED ABHD2 WILD-TYPE
  FEMALE             2             168
  MALE               8             189
[1] 2 2
[1] FALSE
D1124V8, binary
                 cls
clus                0   1
  ABHD2 MUTATED     9   0
  ABHD2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      9    0
  ABHD2 WILD-TYPE  291    8
     clus
vv    ABHD2 MUTATED ABHD2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1124V9, binary
                 cls
clus                0   1
  ABHD2 MUTATED     7   3
  ABHD2 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      7    3
  ABHD2 WILD-TYPE  307   45
                               clus
vv                              ABHD2 MUTATED ABHD2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABHD2 MUTATED     7   0   0   1
  ABHD2 WILD-TYPE 252   3  22  20
D1124V10, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1124V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABHD2 MUTATED                                  0     1
  ABHD2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABHD2 MUTATED                           1     5
  ABHD2 WILD-TYPE                        18   171
D1124V12, multiclass
                                  clus
vv                                 ABHD2 MUTATED ABHD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = RNF38 MUTATION ANALYSIS
D1125V1, survival
                 sevent
clus2               0   1
  RNF38 MUTATED     3   2
  RNF38 WILD-TYPE 274  76
  RNF38 MUTATED RNF38 WILD-TYPE 
              5             350 
  RNF38 MUTATED RNF38 WILD-TYPE 
              2              76 
$`RNF38 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-A010 TCGA-AY-4071 TCGA-F4-6570 
       22.06        19.66        34.98         0.95         6.18 

$`RNF38 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RNF38 MUTATED RNF38 WILD-TYPE 
           0.95            0.00 
  RNF38 MUTATED RNF38 WILD-TYPE 
          34.98          148.01 
  RNF38 MUTATED RNF38 WILD-TYPE 
          19.66           22.09 
[1] "0.9 - 35.0 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.2"
D1125V2, continuous
                 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      63        1       26       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF38 MUTATED           0          0          0          1        0         0
  RNF38 WILD-TYPE        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  RNF38 MUTATED           0
  RNF38 WILD-TYPE         1
D1125V3, multiclass
            clus
vv           RNF38 MUTATED RNF38 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RNF38 MUTATED     1   0   2   2
  RNF38 WILD-TYPE   8  67 247  39
D1125V4, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             2             247
  T4             2              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
  RNF38 MUTATED     4   1   0
  RNF38 WILD-TYPE 216  80  66
D1125V5, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V6, binary
                 cls
clus                0   1
  RNF38 MUTATED     3   0
  RNF38 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      3    0
  RNF38 WILD-TYPE  282   48
   clus
vv  RNF38 MUTATED RNF38 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1125V7, binary
                 cls
clus                0   1
  RNF38 MUTATED     4   1
  RNF38 WILD-TYPE 166 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      4    1
  RNF38 WILD-TYPE  166  196
        clus
vv       RNF38 MUTATED RNF38 WILD-TYPE
  FEMALE             4             166
  MALE               1             196
[1] 2 2
[1] FALSE
D1125V8, binary
                 cls
clus                0   1
  RNF38 MUTATED     5   0
  RNF38 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      5    0
  RNF38 WILD-TYPE  295    8
     clus
vv    RNF38 MUTATED RNF38 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1125V9, binary
                 cls
clus                0   1
  RNF38 MUTATED     3   1
  RNF38 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      3    1
  RNF38 WILD-TYPE  311   47
                               clus
vv                              RNF38 MUTATED RNF38 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF38 MUTATED     5   0   0   0
  RNF38 WILD-TYPE 254   3  22  21
D1125V10, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1125V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF38 MUTATED                                  0     0
  RNF38 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF38 MUTATED                           0     4
  RNF38 WILD-TYPE                        19   172
D1125V12, multiclass
                                  clus
vv                                 RNF38 MUTATED RNF38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = FGD4 MUTATION ANALYSIS
D1126V1, survival
                sevent
clus2              0   1
  FGD4 MUTATED     4   0
  FGD4 WILD-TYPE 273  78
  FGD4 MUTATED FGD4 WILD-TYPE 
             4            351 
  FGD4 MUTATED FGD4 WILD-TYPE 
             0             78 
$`FGD4 MUTATED`
TCGA-CM-4746 TCGA-D5-6533 TCGA-F4-6703 TCGA-G4-6306 
       37.02        25.48        47.87        44.68 

$`FGD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        53.62        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FGD4 MUTATED FGD4 WILD-TYPE 
         25.48           0.00 
  FGD4 MUTATED FGD4 WILD-TYPE 
         47.87         148.01 
  FGD4 MUTATED FGD4 WILD-TYPE 
         40.85          21.99 
[1] "25.5 - 47.9 (40.9)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1126V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGD4 MUTATED         1        0        0         2         0         0
  FGD4 WILD-TYPE      63        1       26       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGD4 MUTATED           0          0          0          0        0         0
  FGD4 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  FGD4 MUTATED           0
  FGD4 WILD-TYPE         1
D1126V3, multiclass
            clus
vv           FGD4 MUTATED FGD4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  FGD4 MUTATED     0   2   2   1
  FGD4 WILD-TYPE   9  65 247  40
D1126V4, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            2            247
  T4            1             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
  FGD4 MUTATED     5   0   0
  FGD4 WILD-TYPE 215  81  66
D1126V5, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V6, binary
                cls
clus               0   1
  FGD4 MUTATED     5   0
  FGD4 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      5    0
  FGD4 WILD-TYPE  280   48
   clus
vv  FGD4 MUTATED FGD4 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1126V7, binary
                cls
clus               0   1
  FGD4 MUTATED     2   3
  FGD4 WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      2    3
  FGD4 WILD-TYPE  168  194
        clus
vv       FGD4 MUTATED FGD4 WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D1126V8, binary
                cls
clus               0   1
  FGD4 MUTATED     4   0
  FGD4 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      4    0
  FGD4 WILD-TYPE  296    8
     clus
vv    FGD4 MUTATED FGD4 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1126V9, binary
                cls
clus               0   1
  FGD4 MUTATED     5   0
  FGD4 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      5    0
  FGD4 WILD-TYPE  309   48
                               clus
vv                              FGD4 MUTATED FGD4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FGD4 MUTATED     5   0   0   0
  FGD4 WILD-TYPE 254   3  22  21
D1126V10, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1126V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGD4 MUTATED                                  0     0
  FGD4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FGD4 MUTATED                           1     3
  FGD4 WILD-TYPE                        18   173
D1126V12, multiclass
                                  clus
vv                                 FGD4 MUTATED FGD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = IRS4 MUTATION ANALYSIS
D1127V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED    18   7
  IRS4 WILD-TYPE 259  71
  IRS4 MUTATED IRS4 WILD-TYPE 
            25            330 
  IRS4 MUTATED IRS4 WILD-TYPE 
             7             71 
$`IRS4 MUTATED`
TCGA-AA-3713 TCGA-AA-3979 TCGA-AZ-6601 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5657 
       19.04        24.00       100.01        46.65        42.90        31.63 
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3811 
       33.53        22.06        63.98         6.97         5.03        10.06 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01Q TCGA-AD-6889 TCGA-AD-6965 
       25.02         4.01         0.99         1.02        83.24        26.47 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6171 
       58.39        49.41        15.02        15.02        15.02        14.04 
TCGA-G4-6315 
       61.91 

$`IRS4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       91.79        79.69        43.76        43.76        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-A6-5666 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-5864 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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  IRS4 MUTATED IRS4 WILD-TYPE 
          0.99           0.00 
  IRS4 MUTATED IRS4 WILD-TYPE 
        100.01         148.01 
  IRS4 MUTATED IRS4 WILD-TYPE 
         24.00          22.01 
[1] "1.0 - 100.0 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1127V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRS4 MUTATED         3        0        6         6         3         0
  IRS4 WILD-TYPE      61        1       20       102         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRS4 MUTATED           1          0          3          1        3         0
  IRS4 WILD-TYPE        17          6         41         32       32        12
                vv
clus             STAGE IVB
  IRS4 MUTATED           0
  IRS4 WILD-TYPE         1
D1127V3, multiclass
            clus
vv           IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA             6            102
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              3             32
  STAGE IVA             0             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
  IRS4 MUTATED     0   4  18   5
  IRS4 WILD-TYPE   9  63 231  36
D1127V4, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           18            231
  T4            5             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
  IRS4 MUTATED    20   5   2
  IRS4 WILD-TYPE 200  76  64
D1127V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0           20            200
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V6, binary
                cls
clus               0   1
  IRS4 MUTATED    21   3
  IRS4 WILD-TYPE 264  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     21    3
  IRS4 WILD-TYPE  264   45
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           21            264
  1            3             45
[1] 2 2
[1] FALSE
D1127V7, binary
                cls
clus               0   1
  IRS4 MUTATED    15  12
  IRS4 WILD-TYPE 155 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     15   12
  IRS4 WILD-TYPE  155  185
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE           15            155
  MALE             12            185
[1] 2 2
[1] FALSE
D1127V8, binary
                cls
clus               0   1
  IRS4 MUTATED    21   1
  IRS4 WILD-TYPE 279   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     21    1
  IRS4 WILD-TYPE  279    7
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO            21            279
  YES            1              7
[1] 2 2
[1] FALSE
D1127V9, binary
                cls
clus               0   1
  IRS4 MUTATED    25   2
  IRS4 WILD-TYPE 289  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     25    2
  IRS4 WILD-TYPE  289   46
                               clus
vv                              IRS4 MUTATED IRS4 WILD-TYPE
  COLON ADENOCARCINOMA                    25            289
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRS4 MUTATED    20   1   2   1
  IRS4 WILD-TYPE 239   2  20  20
D1127V10, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0           20            239
  R1            1              2
  R2            2             20
  RX            1             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"
D1127V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRS4 MUTATED                                  0     1
  IRS4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED                           2    13
  IRS4 WILD-TYPE                        17   163
D1127V12, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      13            163
[1] 4 2
[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 = GABRA6 MUTATION ANALYSIS
D1128V1, survival
                  sevent
clus2                0   1
  GABRA6 MUTATED    17   2
  GABRA6 WILD-TYPE 260  76
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              19              336 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
               2               76 
$`GABRA6 MUTATED`
TCGA-AA-3715 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6588 TCGA-AA-3510 TCGA-AA-3663 
       19.04         5.88        63.62        26.17        63.98         6.97 
TCGA-AA-3681 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-5407 TCGA-CK-6751 
        5.98        53.00        34.98        33.01        88.21       124.27 
TCGA-CM-6164 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-F4-6703 
       29.03        12.43        11.64        13.35        12.00        47.87 
TCGA-G4-6304 
       53.62 

$`GABRA6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
      100.01         1.94        49.08        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01        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 
       14.04        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04         9.44        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GABRA6 MUTATED GABRA6 WILD-TYPE 
            5.88             0.00 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
          124.27           148.01 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
           29.03            22.01 
[1] "5.9 - 124.3 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.9"
D1128V2, continuous
                  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      61        1       22       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRA6 MUTATED           1          0          1          1        1
  GABRA6 WILD-TYPE        17          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  GABRA6 MUTATED           1         0
  GABRA6 WILD-TYPE        11         1
D1128V3, multiclass
            clus
vv           GABRA6 MUTATED GABRA6 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               5              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  GABRA6 MUTATED     1   2  13   3
  GABRA6 WILD-TYPE   8  65 236  38
D1128V4, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             13              236
  T4              3               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
  GABRA6 MUTATED    14   3   2
  GABRA6 WILD-TYPE 206  78  64
D1128V5, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  N0             14              206
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V6, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    16   2
  GABRA6 WILD-TYPE 269  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     16    2
  GABRA6 WILD-TYPE  269   46
   clus
vv  GABRA6 MUTATED GABRA6 WILD-TYPE
  0             16              269
  1              2               46
[1] 2 2
[1] FALSE
D1128V7, binary
                  cls
clus                 0   1
  GABRA6 MUTATED     9  10
  GABRA6 WILD-TYPE 161 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED      9   10
  GABRA6 WILD-TYPE  161  187
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  FEMALE              9              161
  MALE               10              187
[1] 2 2
[1] FALSE
D1128V8, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    17   1
  GABRA6 WILD-TYPE 283   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     17    1
  GABRA6 WILD-TYPE  283    7
     clus
vv    GABRA6 MUTATED GABRA6 WILD-TYPE
  NO              17              283
  YES              1                7
[1] 2 2
[1] FALSE
D1128V9, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    15   4
  GABRA6 WILD-TYPE 299  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     15    4
  GABRA6 WILD-TYPE  299   44
                               clus
vv                              GABRA6 MUTATED GABRA6 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GABRA6 MUTATED    16   0   0   1
  GABRA6 WILD-TYPE 243   3  22  20
D1128V10, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  R0             16              243
  R1              0                3
  R2              0               22
  RX              1               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"
D1128V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRA6 MUTATED                                  0     0
  GABRA6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GABRA6 MUTATED                           1    12
  GABRA6 WILD-TYPE                        18   164
D1128V12, multiclass
                                  clus
vv                                 GABRA6 MUTATED GABRA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = HECTD2 MUTATION ANALYSIS
D1129V1, survival
                  sevent
clus2                0   1
  HECTD2 MUTATED     6   3
  HECTD2 WILD-TYPE 271  75
  HECTD2 MUTATED HECTD2 WILD-TYPE 
               9              346 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
               3               75 
$`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        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6927 
       12.76        10.06         9.44 

$`HECTD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  HECTD2 MUTATED HECTD2 WILD-TYPE 
            4.01             0.00 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
           34.98           148.01 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
           12.39            22.09 
[1] "4.0 - 35.0 (12.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D1129V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HECTD2 MUTATED         0        0        0         7         2         0
  HECTD2 WILD-TYPE      64        1       26       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HECTD2 MUTATED           0          0          0          0        1
  HECTD2 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  HECTD2 MUTATED           0         0
  HECTD2 WILD-TYPE        12         1
D1129V3, multiclass
            clus
vv           HECTD2 MUTATED HECTD2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  HECTD2 MUTATED     0   0   7   3
  HECTD2 WILD-TYPE   9  67 242  38
D1129V4, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              3               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
  HECTD2 MUTATED     9   0   1
  HECTD2 WILD-TYPE 211  81  65
D1129V5, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V6, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     9   1
  HECTD2 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      9    1
  HECTD2 WILD-TYPE  276   47
   clus
vv  HECTD2 MUTATED HECTD2 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1129V7, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     4   6
  HECTD2 WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      4    6
  HECTD2 WILD-TYPE  166  191
        clus
vv       HECTD2 MUTATED HECTD2 WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D1129V8, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     8   0
  HECTD2 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      8    0
  HECTD2 WILD-TYPE  292    8
     clus
vv    HECTD2 MUTATED HECTD2 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1129V9, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     6   4
  HECTD2 WILD-TYPE 308  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      6    4
  HECTD2 WILD-TYPE  308   44
                               clus
vv                              HECTD2 MUTATED HECTD2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HECTD2 MUTATED     7   0   0   2
  HECTD2 WILD-TYPE 252   3  22  19
D1129V10, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D1129V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HECTD2 MUTATED                                  0     3
  HECTD2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HECTD2 MUTATED                           0     2
  HECTD2 WILD-TYPE                        19   174
D1129V12, multiclass
                                  clus
vv                                 HECTD2 MUTATED HECTD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1130) Variable = ARHGAP11A MUTATION ANALYSIS
D1130V1, survival
                     sevent
clus2                   0   1
  ARHGAP11A MUTATED    10   3
  ARHGAP11A WILD-TYPE 267  75
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 13                 342 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                  3                  75 
$`ARHGAP11A MUTATED`
TCGA-AA-3662 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3977 
        6.05        10.88       100.01        20.12        19.66        25.02 
TCGA-AA-A01X TCGA-AD-6889 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6166 
       26.01        83.24        27.09        12.76        22.98        21.99 
TCGA-D5-5541 
       55.92 

$`ARHGAP11A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6167 TCGA-CM-6168 
       12.00        14.04        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-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        19.59        56.09        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
               6.05                0.00 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
             100.01              148.01 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
             22.980              22.045 
[1] "6.0 - 100.0 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1130V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP11A MUTATED         2        0        1         4         0         0
  ARHGAP11A WILD-TYPE      62        1       25       104         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP11A MUTATED           1          0          2          1        1
  ARHGAP11A WILD-TYPE        17          6         42         32       34
                     vv
clus                  STAGE IVA STAGE IVB
  ARHGAP11A MUTATED           0         0
  ARHGAP11A WILD-TYPE        12         1
D1130V3, multiclass
            clus
vv           ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  4                 104
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  1                  17
  STAGE IIIA                 0                   6
  STAGE IIIB                 2                  42
  STAGE IIIC                 1                  32
  STAGE IV                   1                  34
  STAGE IVA                  0                  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
  ARHGAP11A MUTATED     0   4   7   3
  ARHGAP11A WILD-TYPE   9  63 242  38
D1130V4, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  T1                 0                   9
  T2                 4                  63
  T3                 7                 242
  T4                 3                  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
  ARHGAP11A MUTATED     8   4   2
  ARHGAP11A WILD-TYPE 212  77  64
D1130V5, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  N0                 8                 212
  N1                 4                  77
  N2                 2                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V6, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED     9   1
  ARHGAP11A WILD-TYPE 276  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED      9    1
  ARHGAP11A WILD-TYPE  276   47
   clus
vv  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  0                 9                 276
  1                 1                  47
[1] 2 2
[1] FALSE
D1130V7, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED     5   9
  ARHGAP11A WILD-TYPE 165 188
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED      5    9
  ARHGAP11A WILD-TYPE  165  188
        clus
vv       ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  FEMALE                 5                 165
  MALE                   9                 188
[1] 2 2
[1] FALSE
D1130V8, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED    12   0
  ARHGAP11A WILD-TYPE 288   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED     12    0
  ARHGAP11A WILD-TYPE  288    8
     clus
vv    ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  NO                 12                 288
  YES                 0                   8
[1] 2 2
[1] FALSE
D1130V9, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED    11   3
  ARHGAP11A WILD-TYPE 303  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED     11    3
  ARHGAP11A WILD-TYPE  303   45
                               clus
vv                              ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  COLON ADENOCARCINOMA                         11                 303
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  ARHGAP11A MUTATED     7   0   1   2
  ARHGAP11A WILD-TYPE 252   3  21  19
D1130V10, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  R0                 7                 252
  R1                 0                   3
  R2                 1                  21
  RX                 2                  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"
D1130V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP11A MUTATED                                  0     2
  ARHGAP11A WILD-TYPE                                1     8
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP11A MUTATED                           0     8
  ARHGAP11A WILD-TYPE                        19   168
D1130V12, multiclass
                                  clus
vv                                 ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            2                   8
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            8                 168
[1] 4 2
[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 = OR4A16 MUTATION ANALYSIS
D1131V1, survival
                  sevent
clus2                0   1
  OR4A16 MUTATED    10   3
  OR4A16 WILD-TYPE 267  75
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              13              342 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
               3               75 
$`OR4A16 MUTATED`
TCGA-AA-3950 TCGA-AZ-6608 TCGA-AA-3510 TCGA-AA-A02J TCGA-CA-6717 TCGA-CM-4743 
       24.00         1.94        63.98         5.03        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 
       13.25 

$`OR4A16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O 
       37.02        51.98        39.98         2.01        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  OR4A16 MUTATED OR4A16 WILD-TYPE 
            1.94             0.00 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
          119.70           148.01 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
           15.02            22.09 
[1] "1.9 - 119.7 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1131V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4A16 MUTATED         1        0        1         8         0         0
  OR4A16 WILD-TYPE      63        1       25       100         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4A16 MUTATED           0          1          1          0        1
  OR4A16 WILD-TYPE        18          5         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  OR4A16 MUTATED           1         0
  OR4A16 WILD-TYPE        11         1
D1131V3, multiclass
            clus
vv           OR4A16 MUTATED OR4A16 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  OR4A16 MUTATED     0   2  12   0
  OR4A16 WILD-TYPE   9  65 237  41
D1131V4, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             12              237
  T4              0               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
  OR4A16 MUTATED    11   3   0
  OR4A16 WILD-TYPE 209  78  66
D1131V5, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  N0             11              209
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V6, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    12   2
  OR4A16 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     12    2
  OR4A16 WILD-TYPE  273   46
   clus
vv  OR4A16 MUTATED OR4A16 WILD-TYPE
  0             12              273
  1              2               46
[1] 2 2
[1] FALSE
D1131V7, binary
                  cls
clus                 0   1
  OR4A16 MUTATED     9   5
  OR4A16 WILD-TYPE 161 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED      9    5
  OR4A16 WILD-TYPE  161  192
        clus
vv       OR4A16 MUTATED OR4A16 WILD-TYPE
  FEMALE              9              161
  MALE                5              192
[1] 2 2
[1] FALSE
D1131V8, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    11   0
  OR4A16 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     11    0
  OR4A16 WILD-TYPE  289    8
     clus
vv    OR4A16 MUTATED OR4A16 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1131V9, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    11   3
  OR4A16 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     11    3
  OR4A16 WILD-TYPE  303   45
                               clus
vv                              OR4A16 MUTATED OR4A16 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR4A16 MUTATED    10   0   1   1
  OR4A16 WILD-TYPE 249   3  21  20
D1131V10, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              1               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"
D1131V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4A16 MUTATED                                  0     1
  OR4A16 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4A16 MUTATED                           0     9
  OR4A16 WILD-TYPE                        19   167
D1131V12, multiclass
                                  clus
vv                                 OR4A16 MUTATED OR4A16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         9              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(1132) Variable = TSHZ1 MUTATION ANALYSIS
D1132V1, survival
                 sevent
clus2               0   1
  TSHZ1 MUTATED    10   2
  TSHZ1 WILD-TYPE 267  76
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             12             343 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
              2              76 
$`TSHZ1 MUTATED`
TCGA-AA-3697 TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3821 TCGA-AA-3877 
       85.05        79.69        33.53        20.12         1.02        31.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6928 
        4.01        34.98        21.44        58.39        49.41        11.64 

$`TSHZ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
           1.02            0.00 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
          85.05          148.01 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
         32.265          22.030 
[1] "1.0 - 85.0 (32.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1132V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSHZ1 MUTATED         3        0        2         5         2         0
  TSHZ1 WILD-TYPE      61        1       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSHZ1 MUTATED           0          0          0          0        0         0
  TSHZ1 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  TSHZ1 MUTATED           0
  TSHZ1 WILD-TYPE         1
D1132V3, multiclass
            clus
vv           TSHZ1 MUTATED TSHZ1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  TSHZ1 MUTATED     1   2   7   2
  TSHZ1 WILD-TYPE   8  65 242  39
D1132V4, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             2              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
  TSHZ1 MUTATED    12   0   0
  TSHZ1 WILD-TYPE 208  81  66
D1132V5, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  N0            12             208
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V6, binary
                 cls
clus                0   1
  TSHZ1 MUTATED     9   0
  TSHZ1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED      9    0
  TSHZ1 WILD-TYPE  276   48
   clus
vv  TSHZ1 MUTATED TSHZ1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1132V7, binary
                 cls
clus                0   1
  TSHZ1 MUTATED     5   7
  TSHZ1 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED      5    7
  TSHZ1 WILD-TYPE  165  190
        clus
vv       TSHZ1 MUTATED TSHZ1 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D1132V8, binary
                 cls
clus                0   1
  TSHZ1 MUTATED    11   0
  TSHZ1 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED     11    0
  TSHZ1 WILD-TYPE  289    8
     clus
vv    TSHZ1 MUTATED TSHZ1 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1132V9, binary
                 cls
clus                0   1
  TSHZ1 MUTATED     7   5
  TSHZ1 WILD-TYPE 307  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED      7    5
  TSHZ1 WILD-TYPE  307   43
                               clus
vv                              TSHZ1 MUTATED TSHZ1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TSHZ1 MUTATED    10   0   0   0
  TSHZ1 WILD-TYPE 249   3  22  21
D1132V10, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D1132V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSHZ1 MUTATED                                  0     0
  TSHZ1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TSHZ1 MUTATED                           1     6
  TSHZ1 WILD-TYPE                        18   170
D1132V12, multiclass
                                  clus
vv                                 TSHZ1 MUTATED TSHZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = URGCP MUTATION ANALYSIS
D1133V1, survival
                 sevent
clus2               0   1
  URGCP MUTATED    12   3
  URGCP WILD-TYPE 265  75
  URGCP MUTATED URGCP WILD-TYPE 
             15             340 
  URGCP MUTATED URGCP WILD-TYPE 
              3              75 
$`URGCP MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3655 TCGA-AA-3977 
       10.88       100.01        22.06        22.52        61.02        25.02 
TCGA-AA-A01D TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6167 
       10.98        58.39        12.20        12.76        22.03        14.99 
TCGA-CM-6172 TCGA-D5-6927 TCGA-G4-6309 
       11.01         9.44        85.48 

$`URGCP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       23.61        22.09        32.71        27.09         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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6168 
       12.00        14.04        29.03        16.04        21.99        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  URGCP MUTATED URGCP WILD-TYPE 
           9.44            0.00 
  URGCP MUTATED URGCP WILD-TYPE 
         100.01          148.01 
  URGCP MUTATED URGCP WILD-TYPE 
          22.03           22.09 
[1] "9.4 - 100.0 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1133V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  URGCP MUTATED         1        0        2         5         0         0
  URGCP WILD-TYPE      63        1       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  URGCP MUTATED           0          0          3          2        0         0
  URGCP WILD-TYPE        18          6         41         31       35        12
                 vv
clus              STAGE IVB
  URGCP MUTATED           0
  URGCP WILD-TYPE         1
D1133V3, multiclass
            clus
vv           URGCP MUTATED URGCP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  URGCP MUTATED     0   2  12   1
  URGCP WILD-TYPE   9  65 237  40
D1133V4, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  T1             0               9
  T2             2              65
  T3            12             237
  T4             1              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
  URGCP MUTATED     9   3   3
  URGCP WILD-TYPE 211  78  63
D1133V5, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  N0             9             211
  N1             3              78
  N2             3              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"
D1133V6, binary
                 cls
clus                0   1
  URGCP MUTATED    13   0
  URGCP WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     13    0
  URGCP WILD-TYPE  272   48
   clus
vv  URGCP MUTATED URGCP WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D1133V7, binary
                 cls
clus                0   1
  URGCP MUTATED     6   9
  URGCP WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED      6    9
  URGCP WILD-TYPE  164  188
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D1133V8, binary
                 cls
clus                0   1
  URGCP MUTATED    15   0
  URGCP WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     15    0
  URGCP WILD-TYPE  285    8
     clus
vv    URGCP MUTATED URGCP WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D1133V9, binary
                 cls
clus                0   1
  URGCP MUTATED    13   2
  URGCP WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     13    2
  URGCP WILD-TYPE  301   46
                               clus
vv                              URGCP MUTATED URGCP WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  URGCP MUTATED     9   0   0   2
  URGCP WILD-TYPE 250   3  22  19
D1133V10, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D1133V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  URGCP MUTATED                                  0     2
  URGCP WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  URGCP MUTATED                           2     8
  URGCP WILD-TYPE                        17   168
D1133V12, multiclass
                                  clus
vv                                 URGCP MUTATED URGCP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = FRMD6 MUTATION ANALYSIS
D1134V1, survival
                 sevent
clus2               0   1
  FRMD6 MUTATED     8   1
  FRMD6 WILD-TYPE 269  77
  FRMD6 MUTATED FRMD6 WILD-TYPE 
              9             346 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
              1              77 
$`FRMD6 MUTATED`
TCGA-G4-6321 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 
       22.09        23.61        22.06         6.97        34.98        12.16 
TCGA-AY-6386 TCGA-AZ-6598 TCGA-CM-5348 
       17.82        49.41        22.98 

$`FRMD6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FRMD6 MUTATED FRMD6 WILD-TYPE 
           6.97            0.00 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
          49.41          148.01 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
          22.09           22.01 
[1] "7.0 - 49.4 (22.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1134V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRMD6 MUTATED         1        0        2         1         2         0
  FRMD6 WILD-TYPE      63        1       24       107         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRMD6 MUTATED           1          0          2          0        0         1
  FRMD6 WILD-TYPE        17          6         42         33       35        11
                 vv
clus              STAGE IVB
  FRMD6 MUTATED           0
  FRMD6 WILD-TYPE         1
D1134V3, multiclass
            clus
vv           FRMD6 MUTATED FRMD6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  FRMD6 MUTATED     0   2   6   2
  FRMD6 WILD-TYPE   9  65 243  39
D1134V4, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  FRMD6 MUTATED     6   3   1
  FRMD6 WILD-TYPE 214  78  65
D1134V5, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  N0             6             214
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V6, binary
                 cls
clus                0   1
  FRMD6 MUTATED     5   1
  FRMD6 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      5    1
  FRMD6 WILD-TYPE  280   47
   clus
vv  FRMD6 MUTATED FRMD6 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D1134V7, binary
                 cls
clus                0   1
  FRMD6 MUTATED     6   4
  FRMD6 WILD-TYPE 164 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      6    4
  FRMD6 WILD-TYPE  164  193
        clus
vv       FRMD6 MUTATED FRMD6 WILD-TYPE
  FEMALE             6             164
  MALE               4             193
[1] 2 2
[1] FALSE
D1134V8, binary
                 cls
clus                0   1
  FRMD6 MUTATED     9   0
  FRMD6 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      9    0
  FRMD6 WILD-TYPE  291    8
     clus
vv    FRMD6 MUTATED FRMD6 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1134V9, binary
                 cls
clus                0   1
  FRMD6 MUTATED     9   1
  FRMD6 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      9    1
  FRMD6 WILD-TYPE  305   47
                               clus
vv                              FRMD6 MUTATED FRMD6 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FRMD6 MUTATED     7   0   0   1
  FRMD6 WILD-TYPE 252   3  22  20
D1134V10, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1134V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRMD6 MUTATED                                  0     0
  FRMD6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FRMD6 MUTATED                           1     7
  FRMD6 WILD-TYPE                        18   169
D1134V12, multiclass
                                  clus
vv                                 FRMD6 MUTATED FRMD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = CPS1 MUTATION ANALYSIS
D1135V1, survival
                sevent
clus2              0   1
  CPS1 MUTATED    22   7
  CPS1 WILD-TYPE 255  71
  CPS1 MUTATED CPS1 WILD-TYPE 
            29            326 
  CPS1 MUTATED CPS1 WILD-TYPE 
             7             71 
$`CPS1 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-5660 TCGA-A6-5665 
       13.02         0.92        22.09        79.69        29.19        22.06 
TCGA-AA-3811 TCGA-AA-3861 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 
       10.06        30.05        33.01        21.99        25.02        34.98 
TCGA-AA-A01K TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       31.00        83.24        58.39        12.76        10.06        23.05 
TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6537 
       37.02        15.02        13.02        11.01        55.92         4.80 
TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-G4-6299 TCGA-G4-6307 
       13.35        38.20        49.91        74.56        55.04 

$`CPS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5666 
       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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CPS1 MUTATED CPS1 WILD-TYPE 
          0.92           0.00 
  CPS1 MUTATED CPS1 WILD-TYPE 
         83.24         148.01 
  CPS1 MUTATED CPS1 WILD-TYPE 
         25.02          21.99 
[1] "0.9 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1135V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPS1 MUTATED         3        0        0        12         2         0
  CPS1 WILD-TYPE      61        1       26        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPS1 MUTATED           4          0          4          4        0         0
  CPS1 WILD-TYPE        14          6         40         29       35        12
                vv
clus             STAGE IVB
  CPS1 MUTATED           0
  CPS1 WILD-TYPE         1
D1135V3, multiclass
            clus
vv           CPS1 MUTATED CPS1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA            12             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             14
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            4             29
  STAGE IV              0             35
  STAGE IVA             0             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
  CPS1 MUTATED     0   5  23   2
  CPS1 WILD-TYPE   9  62 226  39
D1135V4, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           23            226
  T4            2             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
  CPS1 MUTATED    18   6   6
  CPS1 WILD-TYPE 202  75  60
D1135V5, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  N0           18            202
  N1            6             75
  N2            6             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V6, binary
                cls
clus               0   1
  CPS1 MUTATED    27   0
  CPS1 WILD-TYPE 258  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     27    0
  CPS1 WILD-TYPE  258   48
   clus
vv  CPS1 MUTATED CPS1 WILD-TYPE
  0           27            258
  1            0             48
[1] 2 2
[1] FALSE
D1135V7, binary
                cls
clus               0   1
  CPS1 MUTATED    14  16
  CPS1 WILD-TYPE 156 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     14   16
  CPS1 WILD-TYPE  156  181
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  FEMALE           14            156
  MALE             16            181
[1] 2 2
[1] FALSE
D1135V8, binary
                cls
clus               0   1
  CPS1 MUTATED    27   0
  CPS1 WILD-TYPE 273   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     27    0
  CPS1 WILD-TYPE  273    8
     clus
vv    CPS1 MUTATED CPS1 WILD-TYPE
  NO            27            273
  YES            0              8
[1] 2 2
[1] FALSE
D1135V9, binary
                cls
clus               0   1
  CPS1 MUTATED    24   5
  CPS1 WILD-TYPE 290  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     24    5
  CPS1 WILD-TYPE  290   43
                               clus
vv                              CPS1 MUTATED CPS1 WILD-TYPE
  COLON ADENOCARCINOMA                    24            290
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CPS1 MUTATED    23   0   0   2
  CPS1 WILD-TYPE 236   3  22  19
D1135V10, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  R0           23            236
  R1            0              3
  R2            0             22
  RX            2             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"
D1135V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPS1 MUTATED                                  0     3
  CPS1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CPS1 MUTATED                           3    14
  CPS1 WILD-TYPE                        16   162
D1135V12, multiclass
                                  clus
vv                                 CPS1 MUTATED CPS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      14            162
[1] 4 2
[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 = TUBB4 MUTATION ANALYSIS
D1136V1, survival
                 sevent
clus2               0   1
  TUBB4 MUTATED     3   0
  TUBB4 WILD-TYPE 274  78
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              3             352 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              0              78 
$`TUBB4 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-D5-6930 
       22.06        53.00        13.35 

$`TUBB4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TUBB4 MUTATED TUBB4 WILD-TYPE 
          13.35            0.00 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          53.00          148.01 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          22.06           22.06 
[1] "13.3 - 53.0 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1136V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUBB4 MUTATED         0        0        1         2         1         0
  TUBB4 WILD-TYPE      64        1       25       106         7         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  TUBB4 MUTATED           0
  TUBB4 WILD-TYPE         1
D1136V3, multiclass
            clus
vv           TUBB4 MUTATED TUBB4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TUBB4 MUTATED     0   0   3   2
  TUBB4 WILD-TYPE   9  67 246  39
D1136V4, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             2              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
  TUBB4 MUTATED     4   0   1
  TUBB4 WILD-TYPE 216  81  65
D1136V5, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V6, binary
                 cls
clus                0   1
  TUBB4 MUTATED     3   1
  TUBB4 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      3    1
  TUBB4 WILD-TYPE  282   47
   clus
vv  TUBB4 MUTATED TUBB4 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D1136V7, binary
                 cls
clus                0   1
  TUBB4 MUTATED     3   2
  TUBB4 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      3    2
  TUBB4 WILD-TYPE  167  195
        clus
vv       TUBB4 MUTATED TUBB4 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1136V8, binary
                 cls
clus                0   1
  TUBB4 MUTATED     3   0
  TUBB4 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      3    0
  TUBB4 WILD-TYPE  297    8
     clus
vv    TUBB4 MUTATED TUBB4 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1136V9, binary
                 cls
clus                0   1
  TUBB4 MUTATED     3   2
  TUBB4 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      3    2
  TUBB4 WILD-TYPE  311   46
                               clus
vv                              TUBB4 MUTATED TUBB4 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TUBB4 MUTATED     3   0   1   1
  TUBB4 WILD-TYPE 256   3  21  20
D1136V10, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             1              21
  RX             1              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"
D1136V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBB4 MUTATED                                  0     0
  TUBB4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TUBB4 MUTATED                           0     3
  TUBB4 WILD-TYPE                        19   173
D1136V12, multiclass
                                  clus
vv                                 TUBB4 MUTATED TUBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = USF1 MUTATION ANALYSIS
D1137V1, survival
                sevent
clus2              0   1
  USF1 MUTATED     4   1
  USF1 WILD-TYPE 273  77
  USF1 MUTATED USF1 WILD-TYPE 
             5            350 
  USF1 MUTATED USF1 WILD-TYPE 
             1             77 
$`USF1 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-5407 TCGA-AZ-6598 
       33.01        34.98        12.16        88.21        49.41 

$`USF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  USF1 MUTATED USF1 WILD-TYPE 
         12.16           0.00 
  USF1 MUTATED USF1 WILD-TYPE 
         88.21         148.01 
  USF1 MUTATED USF1 WILD-TYPE 
         34.98          22.01 
[1] "12.2 - 88.2 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1137V2, continuous
                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      62        1       25       108         6         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  USF1 MUTATED           0
  USF1 WILD-TYPE         1
D1137V3, multiclass
            clus
vv           USF1 MUTATED USF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             0            108
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  USF1 MUTATED     1   1   1   2
  USF1 WILD-TYPE   8  66 248  39
D1137V4, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            1            248
  T4            2             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
  USF1 MUTATED     5   0   0
  USF1 WILD-TYPE 215  81  66
D1137V5, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V6, binary
                cls
clus               0   1
  USF1 MUTATED     3   0
  USF1 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      3    0
  USF1 WILD-TYPE  282   48
   clus
vv  USF1 MUTATED USF1 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1137V7, binary
                cls
clus               0   1
  USF1 MUTATED     4   1
  USF1 WILD-TYPE 166 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      4    1
  USF1 WILD-TYPE  166  196
        clus
vv       USF1 MUTATED USF1 WILD-TYPE
  FEMALE            4            166
  MALE              1            196
[1] 2 2
[1] FALSE
D1137V8, binary
                cls
clus               0   1
  USF1 MUTATED     5   0
  USF1 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      5    0
  USF1 WILD-TYPE  295    8
     clus
vv    USF1 MUTATED USF1 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1137V9, binary
                cls
clus               0   1
  USF1 MUTATED     3   2
  USF1 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      3    2
  USF1 WILD-TYPE  311   46
                               clus
vv                              USF1 MUTATED USF1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  USF1 MUTATED     3   0   0   0
  USF1 WILD-TYPE 256   3  22  21
D1137V10, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1137V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USF1 MUTATED                                  0     0
  USF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USF1 MUTATED                           0     3
  USF1 WILD-TYPE                        19   173
D1137V12, multiclass
                                  clus
vv                                 USF1 MUTATED USF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = TM7SF4 MUTATION ANALYSIS
D1138V1, survival
                  sevent
clus2                0   1
  TM7SF4 MUTATED     6   1
  TM7SF4 WILD-TYPE 271  77
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              348 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               1               77 
$`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        12.16        37.02         4.80 
TCGA-D5-6928 
       11.64 

$`TM7SF4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
             4.8              0.0 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
           37.02           148.01 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
          25.180           22.045 
[1] "4.8 - 37.0 (25.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1138V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TM7SF4 MUTATED         2        0        0         1         2         0
  TM7SF4 WILD-TYPE      62        1       26       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM7SF4 MUTATED           0          0          1          0        0
  TM7SF4 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TM7SF4 MUTATED           1         0
  TM7SF4 WILD-TYPE        11         1
D1138V3, multiclass
            clus
vv           TM7SF4 MUTATED TM7SF4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  TM7SF4 MUTATED     0   2   3   2
  TM7SF4 WILD-TYPE   9  65 246  39
D1138V4, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              3              246
  T4              2               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
  TM7SF4 MUTATED     6   1   0
  TM7SF4 WILD-TYPE 214  80  66
D1138V5, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V6, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     4   1
  TM7SF4 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      4    1
  TM7SF4 WILD-TYPE  281   47
   clus
vv  TM7SF4 MUTATED TM7SF4 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1138V7, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     2   5
  TM7SF4 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      2    5
  TM7SF4 WILD-TYPE  168  192
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1138V8, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     7   0
  TM7SF4 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      7    0
  TM7SF4 WILD-TYPE  293    8
     clus
vv    TM7SF4 MUTATED TM7SF4 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1138V9, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     4   3
  TM7SF4 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      4    3
  TM7SF4 WILD-TYPE  310   45
                               clus
vv                              TM7SF4 MUTATED TM7SF4 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TM7SF4 MUTATED     6   0   0   0
  TM7SF4 WILD-TYPE 253   3  22  21
D1138V10, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1138V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TM7SF4 MUTATED                                  0     0
  TM7SF4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TM7SF4 MUTATED                           1     5
  TM7SF4 WILD-TYPE                        18   171
D1138V12, multiclass
                                  clus
vv                                 TM7SF4 MUTATED TM7SF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = PPP1R12A MUTATION ANALYSIS
D1139V1, survival
                    sevent
clus2                  0   1
  PPP1R12A MUTATED     9   4
  PPP1R12A WILD-TYPE 268  74
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                13                342 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                 4                 74 
$`PPP1R12A MUTATED`
TCGA-AZ-6608 TCGA-A6-2671 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3845 TCGA-AA-3864 
        1.94        43.76        19.66        35.01         0.00        53.00 
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 
       33.67 

$`PPP1R12A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 
       23.87        20.12        20.28         7.04         3.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95         2.01        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        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        43.04        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                 0                  0 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
            131.51             148.01 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
             35.01              22.01 
[1] "0.0 - 131.5 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1139V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP1R12A MUTATED         3        0        1         4         0         0
  PPP1R12A WILD-TYPE      61        1       25       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12A MUTATED           0          1          0          2        1
  PPP1R12A WILD-TYPE        18          5         44         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  PPP1R12A MUTATED           0         0
  PPP1R12A WILD-TYPE        12         1
D1139V3, multiclass
            clus
vv           PPP1R12A MUTATED PPP1R12A WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                0                 44
  STAGE IIIC                2                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  PPP1R12A MUTATED     1   3   8   1
  PPP1R12A WILD-TYPE   8  64 241  40
D1139V4, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  T1                1                  8
  T2                3                 64
  T3                8                241
  T4                1                 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
  PPP1R12A MUTATED     9   2   2
  PPP1R12A WILD-TYPE 211  79  64
D1139V5, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  N0                9                211
  N1                2                 79
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V6, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED     9   1
  PPP1R12A WILD-TYPE 276  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED      9    1
  PPP1R12A WILD-TYPE  276   47
   clus
vv  PPP1R12A MUTATED PPP1R12A WILD-TYPE
  0                9                276
  1                1                 47
[1] 2 2
[1] FALSE
D1139V7, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED     6   7
  PPP1R12A WILD-TYPE 164 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED      6    7
  PPP1R12A WILD-TYPE  164  190
        clus
vv       PPP1R12A MUTATED PPP1R12A WILD-TYPE
  FEMALE                6                164
  MALE                  7                190
[1] 2 2
[1] FALSE
D1139V8, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED    11   0
  PPP1R12A WILD-TYPE 289   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED     11    0
  PPP1R12A WILD-TYPE  289    8
     clus
vv    PPP1R12A MUTATED PPP1R12A WILD-TYPE
  NO                11                289
  YES                0                  8
[1] 2 2
[1] FALSE
D1139V9, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED    11   2
  PPP1R12A WILD-TYPE 303  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED     11    2
  PPP1R12A WILD-TYPE  303   46
                               clus
vv                              PPP1R12A MUTATED PPP1R12A WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPP1R12A MUTATED     8   0   0   3
  PPP1R12A WILD-TYPE 251   3  22  18
D1139V10, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  R0                8                251
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D1139V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP1R12A MUTATED                                  0     1
  PPP1R12A WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PPP1R12A MUTATED                           0     9
  PPP1R12A WILD-TYPE                        19   167
D1139V12, multiclass
                                  clus
vv                                 PPP1R12A MUTATED PPP1R12A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           9                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(1140) Variable = APOBEC4 MUTATION ANALYSIS
D1140V1, survival
                   sevent
clus2                 0   1
  APOBEC4 MUTATED     6   1
  APOBEC4 WILD-TYPE 271  77
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                7               348 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                1                77 
$`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 
       85.48 

$`APOBEC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            10.06              0.00 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            85.48            148.01 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            29.95             22.01 
[1] "10.1 - 85.5 (29.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1140V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APOBEC4 MUTATED         0        0        0         5         1         0
  APOBEC4 WILD-TYPE      64        1       26       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APOBEC4 MUTATED           0          0          1          0        0
  APOBEC4 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  APOBEC4 MUTATED           0         0
  APOBEC4 WILD-TYPE        12         1
D1140V3, multiclass
            clus
vv           APOBEC4 MUTATED APOBEC4 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  APOBEC4 MUTATED     0   0   6   1
  APOBEC4 WILD-TYPE   9  67 243  40
D1140V4, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               6               243
  T4               1                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
  APOBEC4 MUTATED     6   1   0
  APOBEC4 WILD-TYPE 214  80  66
D1140V5, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  N0               6               214
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V6, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     7   0
  APOBEC4 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      7    0
  APOBEC4 WILD-TYPE  278   48
   clus
vv  APOBEC4 MUTATED APOBEC4 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D1140V7, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     5   2
  APOBEC4 WILD-TYPE 165 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      5    2
  APOBEC4 WILD-TYPE  165  195
        clus
vv       APOBEC4 MUTATED APOBEC4 WILD-TYPE
  FEMALE               5               165
  MALE                 2               195
[1] 2 2
[1] FALSE
D1140V8, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     7   0
  APOBEC4 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      7    0
  APOBEC4 WILD-TYPE  293    8
     clus
vv    APOBEC4 MUTATED APOBEC4 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1140V9, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     5   2
  APOBEC4 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      5    2
  APOBEC4 WILD-TYPE  309   46
                               clus
vv                              APOBEC4 MUTATED APOBEC4 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  APOBEC4 MUTATED     5   0   0   2
  APOBEC4 WILD-TYPE 254   3  22  19
D1140V10, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               2                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"
D1140V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOBEC4 MUTATED                                  0     2
  APOBEC4 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  APOBEC4 MUTATED                           1     1
  APOBEC4 WILD-TYPE                        18   175
D1140V12, multiclass
                                  clus
vv                                 APOBEC4 MUTATED APOBEC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          1               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(1141) Variable = SPOPL MUTATION ANALYSIS
D1141V1, survival
                 sevent
clus2               0   1
  SPOPL MUTATED     8   2
  SPOPL WILD-TYPE 269  76
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             345 
  SPOPL MUTATED SPOPL WILD-TYPE 
              2              76 
$`SPOPL MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-AA-3666 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6716 
        0.92        35.80         2.01        58.39        29.56        12.20 
TCGA-D5-6532 TCGA-D5-6541 TCGA-DM-A28E TCGA-F4-6704 
       18.25        15.58       119.93         1.55 

$`SPOPL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28F 
       44.32       131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.090 
[1] "0.9 - 119.9 (16.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1141V2, continuous
                 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      64        1       26       102         8         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        16          6         44         32       35        12
                 vv
clus              STAGE IVB
  SPOPL MUTATED           0
  SPOPL WILD-TYPE         1
D1141V3, multiclass
            clus
vv           SPOPL MUTATED SPOPL WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  SPOPL MUTATED     0   1   9   0
  SPOPL WILD-TYPE   9  66 240  41
D1141V4, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             0              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
  SPOPL MUTATED     6   3   1
  SPOPL WILD-TYPE 214  78  65
D1141V5, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  N0             6             214
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V6, binary
                 cls
clus                0   1
  SPOPL MUTATED     8   0
  SPOPL WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      8    0
  SPOPL WILD-TYPE  277   48
   clus
vv  SPOPL MUTATED SPOPL WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1141V7, binary
                 cls
clus                0   1
  SPOPL MUTATED     4   6
  SPOPL WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      4    6
  SPOPL WILD-TYPE  166  191
        clus
vv       SPOPL MUTATED SPOPL WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1141V8, binary
                 cls
clus                0   1
  SPOPL MUTATED     7   0
  SPOPL WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      7    0
  SPOPL WILD-TYPE  293    8
     clus
vv    SPOPL MUTATED SPOPL WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1141V9, binary
                 cls
clus                0   1
  SPOPL MUTATED     9   1
  SPOPL WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      9    1
  SPOPL WILD-TYPE  305   47
                               clus
vv                              SPOPL MUTATED SPOPL WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPOPL MUTATED     7   0   0   1
  SPOPL WILD-TYPE 252   3  22  20
D1141V10, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1141V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPOPL MUTATED                                  1     1
  SPOPL WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPOPL MUTATED                           0     6
  SPOPL WILD-TYPE                        19   170
D1141V12, multiclass
                                  clus
vv                                 SPOPL MUTATED SPOPL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = GPR98 MUTATION ANALYSIS
D1142V1, survival
                 sevent
clus2               0   1
  GPR98 MUTATED    48  12
  GPR98 WILD-TYPE 229  66
  GPR98 MUTATED GPR98 WILD-TYPE 
             60             295 
  GPR98 MUTATED GPR98 WILD-TYPE 
             12              66 
$`GPR98 MUTATED`
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-CK-5912 
        0.92        85.05        19.04        24.00        25.08        49.08 
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6651 
       35.80        26.17        32.75        29.19        22.06        21.76 
TCGA-A6-6654 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3819 TCGA-AA-3833 
       23.87         7.04         3.02         6.97        25.02        15.95 
TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 
        0.00        53.00        31.00        24.00        20.98         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AU-3779 
       25.02         4.01        34.98        35.01        83.24        14.50 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       21.44        58.39         5.13        62.79        49.41         6.77 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5349 
       12.76        10.06       124.27        23.05        37.02        30.08 
TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5541 TCGA-D5-6535 
       15.02        14.04        12.95        11.01        55.92        15.12 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1HB TCGA-DM-A28H 
        9.44        11.64        13.35        11.38       135.65       117.07 
TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
        6.18        35.31        44.68        55.04        85.48        61.91 

$`GPR98 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 
       10.88       106.75       100.01         1.94         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
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-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3502 
       24.69        24.39        20.12        19.66        20.28        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        38.99        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       31.07        30.05        17.03        27.02        18.05         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 
        0.95        33.01         0.20        17.82         1.41        22.36 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        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        12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 
       12.43        14.30         9.04        13.41        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 
      133.18        74.56        65.85        53.62        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GPR98 MUTATED GPR98 WILD-TYPE 
              0               0 
  GPR98 MUTATED GPR98 WILD-TYPE 
         135.65          148.01 
  GPR98 MUTATED GPR98 WILD-TYPE 
         23.935          21.990 
[1] "0.0 - 135.7 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1142V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR98 MUTATED         7        0        7        24         3         0
  GPR98 WILD-TYPE      57        1       19        84         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR98 MUTATED           2          0          9          2        3         2
  GPR98 WILD-TYPE        16          6         35         31       32        10
                 vv
clus              STAGE IVB
  GPR98 MUTATED           0
  GPR98 WILD-TYPE         1
D1142V3, multiclass
            clus
vv           GPR98 MUTATED GPR98 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               7              19
  STAGE IIA             24              84
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             9              35
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              2              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
  GPR98 MUTATED     1   9  46   5
  GPR98 WILD-TYPE   8  58 203  36
D1142V4, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  T1             1               8
  T2             9              58
  T3            46             203
  T4             5              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
  GPR98 MUTATED    44  12   5
  GPR98 WILD-TYPE 176  69  61
D1142V5, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  N0            44             176
  N1            12              69
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V6, binary
                 cls
clus                0   1
  GPR98 MUTATED    47   5
  GPR98 WILD-TYPE 238  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     47    5
  GPR98 WILD-TYPE  238   43
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0            47             238
  1             5              43
[1] 2 2
[1] FALSE
D1142V7, binary
                 cls
clus                0   1
  GPR98 MUTATED    28  33
  GPR98 WILD-TYPE 142 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     28   33
  GPR98 WILD-TYPE  142  164
        clus
vv       GPR98 MUTATED GPR98 WILD-TYPE
  FEMALE            28             142
  MALE              33             164
[1] 2 2
[1] FALSE
D1142V8, binary
                 cls
clus                0   1
  GPR98 MUTATED    53   2
  GPR98 WILD-TYPE 247   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     53    2
  GPR98 WILD-TYPE  247    6
     clus
vv    GPR98 MUTATED GPR98 WILD-TYPE
  NO             53             247
  YES             2               6
[1] 2 2
[1] FALSE
D1142V9, binary
                 cls
clus                0   1
  GPR98 MUTATED    48  12
  GPR98 WILD-TYPE 266  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     48   12
  GPR98 WILD-TYPE  266   36
                               clus
vv                              GPR98 MUTATED GPR98 WILD-TYPE
  COLON ADENOCARCINOMA                     48             266
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR98 MUTATED    44   0   1   5
  GPR98 WILD-TYPE 215   3  21  16
D1142V10, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  R0            44             215
  R1             0               3
  R2             1              21
  RX             5              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"
D1142V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR98 MUTATED                                  0     3
  GPR98 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR98 MUTATED                           3    35
  GPR98 WILD-TYPE                        16   141
D1142V12, multiclass
                                  clus
vv                                 GPR98 MUTATED GPR98 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       35             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(1143) Variable = TMEM41B MUTATION ANALYSIS
D1143V1, survival
                   sevent
clus2                 0   1
  TMEM41B MUTATED     4   0
  TMEM41B WILD-TYPE 273  78
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               351 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                0                78 
$`TMEM41B MUTATED`
TCGA-AA-3543 TCGA-AY-6197 TCGA-CM-6162 TCGA-CM-6164 
        0.99        21.44        12.00        29.03 

$`TMEM41B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6165 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             0.99              0.00 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            29.03            148.01 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            16.72             22.09 
[1] "1.0 - 29.0 (16.7)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1143V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM41B MUTATED         1        0        0         2         0         0
  TMEM41B WILD-TYPE      63        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41B MUTATED           0          0          1          0        0
  TMEM41B WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  TMEM41B MUTATED           0         0
  TMEM41B WILD-TYPE        12         1
D1143V3, multiclass
            clus
vv           TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  TMEM41B MUTATED     0   1   3   0
  TMEM41B WILD-TYPE   9  66 246  41
D1143V4, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               0                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
  TMEM41B MUTATED     3   1   0
  TMEM41B WILD-TYPE 217  80  66
D1143V5, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  N0               3               217
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V6, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     3   0
  TMEM41B WILD-TYPE 282  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      3    0
  TMEM41B WILD-TYPE  282   48
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               3               282
  1               0                48
[1] 2 2
[1] FALSE
D1143V7, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     2   2
  TMEM41B WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    2
  TMEM41B WILD-TYPE  168  195
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D1143V8, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     4   0
  TMEM41B WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      4    0
  TMEM41B WILD-TYPE  296    8
     clus
vv    TMEM41B MUTATED TMEM41B WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D1143V9, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     2   2
  TMEM41B WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    2
  TMEM41B WILD-TYPE  312   46
                               clus
vv                              TMEM41B MUTATED TMEM41B WILD-TYPE
  COLON ADENOCARCINOMA                        2               312
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM41B MUTATED     4   0   0   0
  TMEM41B WILD-TYPE 255   3  22  21
D1143V10, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1143V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM41B MUTATED                                  0     0
  TMEM41B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM41B MUTATED                           0     3
  TMEM41B WILD-TYPE                        19   173
D1143V12, multiclass
                                  clus
vv                                 TMEM41B MUTATED TMEM41B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = RGS3 MUTATION ANALYSIS
D1144V1, survival
                sevent
clus2              0   1
  RGS3 MUTATED    11   3
  RGS3 WILD-TYPE 266  75
  RGS3 MUTATED RGS3 WILD-TYPE 
            14            341 
  RGS3 MUTATED RGS3 WILD-TYPE 
             3             75 
$`RGS3 MUTATED`
TCGA-AA-3713 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 
       19.04         8.38        63.98         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 
      119.93        35.31 

$`RGS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.99        82.95         2.01        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RGS3 MUTATED RGS3 WILD-TYPE 
             0              0 
  RGS3 MUTATED RGS3 WILD-TYPE 
        124.27         148.01 
  RGS3 MUTATED RGS3 WILD-TYPE 
         20.09          22.09 
[1] "0.0 - 124.3 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1144V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RGS3 MUTATED         5        0        2         5         2         0
  RGS3 WILD-TYPE      59        1       24       103         6         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        18          6         44         33       34        12
                vv
clus             STAGE IVB
  RGS3 MUTATED           0
  RGS3 WILD-TYPE         1
D1144V3, multiclass
            clus
vv           RGS3 MUTATED RGS3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  RGS3 MUTATED     1   4   8   2
  RGS3 WILD-TYPE   8  63 241  39
D1144V4, multiclass
    clus
vv   RGS3 MUTATED RGS3 WILD-TYPE
  T1            1              8
  T2            4             63
  T3            8            241
  T4            2             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
  RGS3 MUTATED    15   0   0
  RGS3 WILD-TYPE 205  81  66
D1144V5, multiclass
    clus
vv   RGS3 MUTATED RGS3 WILD-TYPE
  N0           15            205
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V6, binary
                cls
clus               0   1
  RGS3 MUTATED    12   1
  RGS3 WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED     12    1
  RGS3 WILD-TYPE  273   47
   clus
vv  RGS3 MUTATED RGS3 WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D1144V7, binary
                cls
clus               0   1
  RGS3 MUTATED     8   7
  RGS3 WILD-TYPE 162 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED      8    7
  RGS3 WILD-TYPE  162  190
        clus
vv       RGS3 MUTATED RGS3 WILD-TYPE
  FEMALE            8            162
  MALE              7            190
[1] 2 2
[1] FALSE
D1144V8, binary
                cls
clus               0   1
  RGS3 MUTATED     9   1
  RGS3 WILD-TYPE 291   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED      9    1
  RGS3 WILD-TYPE  291    7
     clus
vv    RGS3 MUTATED RGS3 WILD-TYPE
  NO             9            291
  YES            1              7
[1] 2 2
[1] FALSE
D1144V9, binary
                cls
clus               0   1
  RGS3 MUTATED    10   4
  RGS3 WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED     10    4
  RGS3 WILD-TYPE  304   44
                               clus
vv                              RGS3 MUTATED RGS3 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RGS3 MUTATED     8   0   1   3
  RGS3 WILD-TYPE 251   3  21  18
D1144V10, multiclass
    clus
vv   RGS3 MUTATED RGS3 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            3             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"
D1144V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGS3 MUTATED                                  0     0
  RGS3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RGS3 MUTATED                           1     7
  RGS3 WILD-TYPE                        18   169
D1144V12, multiclass
                                  clus
vv                                 RGS3 MUTATED RGS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = FAM119A MUTATION ANALYSIS
D1145V1, survival
                   sevent
clus2                 0   1
  FAM119A MUTATED     3   2
  FAM119A WILD-TYPE 274  76
  FAM119A MUTATED FAM119A WILD-TYPE 
                5               350 
  FAM119A MUTATED FAM119A WILD-TYPE 
                2                76 
$`FAM119A MUTATED`
TCGA-AD-6895 TCGA-AA-3977 TCGA-AA-A00N TCGA-AU-3779 TCGA-AZ-6599 
       25.08        25.02         4.01        14.50         6.77 

$`FAM119A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FAM119A MUTATED FAM119A WILD-TYPE 
             4.01              0.00 
  FAM119A MUTATED FAM119A WILD-TYPE 
            25.08            148.01 
  FAM119A MUTATED FAM119A WILD-TYPE 
           14.500            22.075 
[1] "4.0 - 25.1 (14.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D1145V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM119A MUTATED         1        0        0         1         1         0
  FAM119A WILD-TYPE      63        1       26       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM119A MUTATED           0          0          1          0        0
  FAM119A WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM119A MUTATED           0         0
  FAM119A WILD-TYPE        12         1
D1145V3, multiclass
            clus
vv           FAM119A MUTATED FAM119A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM119A MUTATED     0   2   2   1
  FAM119A WILD-TYPE   9  65 247  40
D1145V4, multiclass
    clus
vv   FAM119A MUTATED FAM119A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               2               247
  T4               1                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
  FAM119A MUTATED     4   1   0
  FAM119A WILD-TYPE 216  80  66
D1145V5, multiclass
    clus
vv   FAM119A MUTATED FAM119A WILD-TYPE
  N0               4               216
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V6, binary
                   cls
clus                  0   1
  FAM119A MUTATED     3   0
  FAM119A WILD-TYPE 282  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      3    0
  FAM119A WILD-TYPE  282   48
   clus
vv  FAM119A MUTATED FAM119A WILD-TYPE
  0               3               282
  1               0                48
[1] 2 2
[1] FALSE
D1145V7, binary
                   cls
clus                  0   1
  FAM119A MUTATED     1   4
  FAM119A WILD-TYPE 169 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      1    4
  FAM119A WILD-TYPE  169  193
        clus
vv       FAM119A MUTATED FAM119A WILD-TYPE
  FEMALE               1               169
  MALE                 4               193
[1] 2 2
[1] FALSE
D1145V8, binary
                   cls
clus                  0   1
  FAM119A MUTATED     4   0
  FAM119A WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      4    0
  FAM119A WILD-TYPE  296    8
     clus
vv    FAM119A MUTATED FAM119A WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D1145V9, binary
                   cls
clus                  0   1
  FAM119A MUTATED     4   1
  FAM119A WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      4    1
  FAM119A WILD-TYPE  310   47
                               clus
vv                              FAM119A MUTATED FAM119A WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM119A MUTATED     3   0   0   0
  FAM119A WILD-TYPE 256   3  22  21
D1145V10, multiclass
    clus
vv   FAM119A MUTATED FAM119A WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D1145V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM119A MUTATED                                  0     0
  FAM119A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM119A MUTATED                           0     3
  FAM119A WILD-TYPE                        19   173
D1145V12, multiclass
                                  clus
vv                                 FAM119A MUTATED FAM119A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = TRIM45 MUTATION ANALYSIS
D1146V1, survival
                  sevent
clus2                0   1
  TRIM45 MUTATED    12   2
  TRIM45 WILD-TYPE 265  76
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              341 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
               2               76 
$`TRIM45 MUTATED`
TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3518 TCGA-AA-3811 
       25.08        26.17        46.65        20.12         1.02        10.06 
TCGA-AA-3864 TCGA-AA-A00J TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-5861 
       53.00        18.05        12.76        23.05        30.08        15.02 
TCGA-DM-A28K TCGA-F4-6570 
       98.24         6.18 

$`TRIM45 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TRIM45 MUTATED TRIM45 WILD-TYPE 
            1.02             0.00 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
           98.24           148.01 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
          21.585           22.060 
[1] "1.0 - 98.2 (21.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1146V2, continuous
                  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      64        1       25        99         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM45 MUTATED           1          0          3          0        0
  TRIM45 WILD-TYPE        17          6         41         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM45 MUTATED           0         0
  TRIM45 WILD-TYPE        12         1
D1146V3, multiclass
            clus
vv           TRIM45 MUTATED TRIM45 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               9               99
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TRIM45 MUTATED     0   0  13   1
  TRIM45 WILD-TYPE   9  67 236  40
D1146V4, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             13              236
  T4              1               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
  TRIM45 MUTATED    10   3   1
  TRIM45 WILD-TYPE 210  78  65
D1146V5, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  N0             10              210
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V6, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    13   0
  TRIM45 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     13    0
  TRIM45 WILD-TYPE  272   48
   clus
vv  TRIM45 MUTATED TRIM45 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D1146V7, binary
                  cls
clus                 0   1
  TRIM45 MUTATED     7   7
  TRIM45 WILD-TYPE 163 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED      7    7
  TRIM45 WILD-TYPE  163  190
        clus
vv       TRIM45 MUTATED TRIM45 WILD-TYPE
  FEMALE              7              163
  MALE                7              190
[1] 2 2
[1] FALSE
D1146V8, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    12   0
  TRIM45 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     12    0
  TRIM45 WILD-TYPE  288    8
     clus
vv    TRIM45 MUTATED TRIM45 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1146V9, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    10   4
  TRIM45 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     10    4
  TRIM45 WILD-TYPE  304   44
                               clus
vv                              TRIM45 MUTATED TRIM45 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM45 MUTATED    11   0   0   1
  TRIM45 WILD-TYPE 248   3  22  20
D1146V10, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              1               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"
D1146V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM45 MUTATED                                  0     1
  TRIM45 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM45 MUTATED                           0     9
  TRIM45 WILD-TYPE                        19   167
D1146V12, multiclass
                                  clus
vv                                 TRIM45 MUTATED TRIM45 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         9              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(1147) Variable = MAGEA4 MUTATION ANALYSIS
D1147V1, survival
                  sevent
clus2                0   1
  MAGEA4 MUTATED     2   3
  MAGEA4 WILD-TYPE 275  75
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               5              350 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               3               75 
$`MAGEA4 MUTATED`
TCGA-AA-3496 TCGA-G4-6588 TCGA-AZ-6598 TCGA-CA-6718 TCGA-F4-6459 
        1.02        26.17        49.41        10.06         8.61 

$`MAGEA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
            1.02             0.00 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
           49.41           148.01 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
          10.060           22.075 
[1] "1.0 - 49.4 (10.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.8"
D1147V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEA4 MUTATED         0        0        2         2         0         0
  MAGEA4 WILD-TYPE      64        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEA4 MUTATED           0          0          1          0        1
  MAGEA4 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  MAGEA4 MUTATED           0         0
  MAGEA4 WILD-TYPE        12         1
D1147V3, multiclass
            clus
vv           MAGEA4 MUTATED MAGEA4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  MAGEA4 MUTATED     0   0   6   0
  MAGEA4 WILD-TYPE   9  67 243  41
D1147V4, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              0               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
  MAGEA4 MUTATED     4   0   2
  MAGEA4 WILD-TYPE 216  81  64
D1147V5, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  N0              4              216
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V6, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     4   1
  MAGEA4 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      4    1
  MAGEA4 WILD-TYPE  281   47
   clus
vv  MAGEA4 MUTATED MAGEA4 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1147V7, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     5   1
  MAGEA4 WILD-TYPE 165 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      5    1
  MAGEA4 WILD-TYPE  165  196
        clus
vv       MAGEA4 MUTATED MAGEA4 WILD-TYPE
  FEMALE              5              165
  MALE                1              196
[1] 2 2
[1] FALSE
D1147V8, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     4   0
  MAGEA4 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      4    0
  MAGEA4 WILD-TYPE  296    8
     clus
vv    MAGEA4 MUTATED MAGEA4 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1147V9, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     6   0
  MAGEA4 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      6    0
  MAGEA4 WILD-TYPE  308   48
                               clus
vv                              MAGEA4 MUTATED MAGEA4 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGEA4 MUTATED     3   0   1   1
  MAGEA4 WILD-TYPE 256   3  21  20
D1147V10, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              1               21
  RX              1               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"
D1147V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEA4 MUTATED                                  0     1
  MAGEA4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEA4 MUTATED                           0     3
  MAGEA4 WILD-TYPE                        19   173
D1147V12, multiclass
                                  clus
vv                                 MAGEA4 MUTATED MAGEA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = MANF MUTATION ANALYSIS
D1148V1, survival
                sevent
clus2              0   1
  MANF MUTATED     3   1
  MANF WILD-TYPE 274  77
  MANF MUTATED MANF WILD-TYPE 
             4            351 
  MANF MUTATED MANF WILD-TYPE 
             1             77 
$`MANF MUTATED`
TCGA-AD-6964 TCGA-A6-3809 TCGA-AU-6004 TCGA-AY-6197 
       10.88        32.75        27.09        21.44 

$`MANF WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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         22.060 
[1] "10.9 - 32.8 (24.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1148V2, continuous
                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      63        1       26       107         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  MANF MUTATED           0
  MANF WILD-TYPE         1
D1148V3, multiclass
            clus
vv           MANF MUTATED MANF WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MANF MUTATED     0   1   1   2
  MANF WILD-TYPE   9  66 248  39
D1148V4, multiclass
    clus
vv   MANF MUTATED MANF WILD-TYPE
  T1            0              9
  T2            1             66
  T3            1            248
  T4            2             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
  MANF MUTATED     3   0   1
  MANF WILD-TYPE 217  81  65
D1148V5, multiclass
    clus
vv   MANF MUTATED MANF WILD-TYPE
  N0            3            217
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V6, binary
                cls
clus               0   1
  MANF MUTATED     2   0
  MANF WILD-TYPE 283  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      2    0
  MANF WILD-TYPE  283   48
   clus
vv  MANF MUTATED MANF WILD-TYPE
  0            2            283
  1            0             48
[1] 2 2
[1] FALSE
D1148V7, binary
                cls
clus               0   1
  MANF MUTATED     2   2
  MANF WILD-TYPE 168 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      2    2
  MANF WILD-TYPE  168  195
        clus
vv       MANF MUTATED MANF WILD-TYPE
  FEMALE            2            168
  MALE              2            195
[1] 2 2
[1] FALSE
D1148V8, binary
                cls
clus               0   1
  MANF MUTATED     3   0
  MANF WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      3    0
  MANF WILD-TYPE  297    8
     clus
vv    MANF MUTATED MANF WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1148V9, binary
                cls
clus               0   1
  MANF MUTATED     3   1
  MANF WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      3    1
  MANF WILD-TYPE  311   47
                               clus
vv                              MANF MUTATED MANF WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MANF MUTATED     3   0   0   0
  MANF WILD-TYPE 256   3  22  21
D1148V10, multiclass
    clus
vv   MANF MUTATED MANF WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1148V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MANF MUTATED                                  0     0
  MANF WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MANF MUTATED                           0     4
  MANF WILD-TYPE                        19   172
D1148V12, multiclass
                                  clus
vv                                 MANF MUTATED MANF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = TBC1D10C MUTATION ANALYSIS
D1149V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     6   2
  TBC1D10C WILD-TYPE 271  76
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                347 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 2                 76 
$`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 
        6.18        74.56 

$`TBC1D10C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.02               0.00 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             74.56             148.01 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             19.35              22.06 
[1] "1.0 - 74.6 (19.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1149V2, continuous
                    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      63        1       26       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D10C MUTATED           0          0          1          1        0
  TBC1D10C WILD-TYPE        18          6         43         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  TBC1D10C MUTATED           0         0
  TBC1D10C WILD-TYPE        12         1
D1149V3, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  TBC1D10C MUTATED     0   1   7   0
  TBC1D10C WILD-TYPE   9  66 242  41
D1149V4, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                7                242
  T4                0                 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
  TBC1D10C MUTATED     5   1   2
  TBC1D10C WILD-TYPE 215  80  64
D1149V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                5                215
  N1                1                 80
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V6, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     7   0
  TBC1D10C WILD-TYPE 278  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      7    0
  TBC1D10C WILD-TYPE  278   48
   clus
vv  TBC1D10C MUTATED TBC1D10C WILD-TYPE
  0                7                278
  1                0                 48
[1] 2 2
[1] FALSE
D1149V7, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     6   2
  TBC1D10C WILD-TYPE 164 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      6    2
  TBC1D10C WILD-TYPE  164  195
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  FEMALE                6                164
  MALE                  2                195
[1] 2 2
[1] FALSE
D1149V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     8   0
  TBC1D10C WILD-TYPE 292   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      8    0
  TBC1D10C WILD-TYPE  292    8
     clus
vv    TBC1D10C MUTATED TBC1D10C WILD-TYPE
  NO                 8                292
  YES                0                  8
[1] 2 2
[1] FALSE
D1149V9, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     6   2
  TBC1D10C WILD-TYPE 308  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      6    2
  TBC1D10C WILD-TYPE  308   46
                               clus
vv                              TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON ADENOCARCINOMA                         6                308
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TBC1D10C MUTATED     6   0   0   2
  TBC1D10C WILD-TYPE 253   3  22  19
D1149V10, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1149V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBC1D10C MUTATED                                  0     1
  TBC1D10C WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TBC1D10C MUTATED                           1     4
  TBC1D10C WILD-TYPE                        18   172
D1149V12, multiclass
                                  clus
vv                                 TBC1D10C MUTATED TBC1D10C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                172
[1] 4 2
[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 = DPF3 MUTATION ANALYSIS
D1150V1, survival
                sevent
clus2              0   1
  DPF3 MUTATED     4   1
  DPF3 WILD-TYPE 273  77
  DPF3 MUTATED DPF3 WILD-TYPE 
             5            350 
  DPF3 MUTATED DPF3 WILD-TYPE 
             1             77 
$`DPF3 MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-6674 
        3.02         6.97        34.98        12.16        12.95 

$`DPF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DPF3 MUTATED DPF3 WILD-TYPE 
          3.02           0.00 
  DPF3 MUTATED DPF3 WILD-TYPE 
         34.98         148.01 
  DPF3 MUTATED DPF3 WILD-TYPE 
         12.16          22.09 
[1] "3.0 - 35.0 (12.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1150V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPF3 MUTATED         1        0        2         1         1         0
  DPF3 WILD-TYPE      63        1       24       107         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DPF3 MUTATED           0          0          0          0        0         0
  DPF3 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  DPF3 MUTATED           0
  DPF3 WILD-TYPE         1
D1150V3, multiclass
            clus
vv           DPF3 MUTATED DPF3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  DPF3 MUTATED     0   1   3   1
  DPF3 WILD-TYPE   9  66 246  40
D1150V4, multiclass
    clus
vv   DPF3 MUTATED DPF3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            1             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
  DPF3 MUTATED     5   0   0
  DPF3 WILD-TYPE 215  81  66
D1150V5, multiclass
    clus
vv   DPF3 MUTATED DPF3 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V6, binary
                cls
clus               0   1
  DPF3 MUTATED     4   0
  DPF3 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      4    0
  DPF3 WILD-TYPE  281   48
   clus
vv  DPF3 MUTATED DPF3 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1150V7, binary
                cls
clus               0   1
  DPF3 MUTATED     2   3
  DPF3 WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      2    3
  DPF3 WILD-TYPE  168  194
        clus
vv       DPF3 MUTATED DPF3 WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D1150V8, binary
                cls
clus               0   1
  DPF3 MUTATED     5   0
  DPF3 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      5    0
  DPF3 WILD-TYPE  295    8
     clus
vv    DPF3 MUTATED DPF3 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1150V9, binary
                cls
clus               0   1
  DPF3 MUTATED     4   1
  DPF3 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      4    1
  DPF3 WILD-TYPE  310   47
                               clus
vv                              DPF3 MUTATED DPF3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DPF3 MUTATED     5   0   0   0
  DPF3 WILD-TYPE 254   3  22  21
D1150V10, multiclass
    clus
vv   DPF3 MUTATED DPF3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1150V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPF3 MUTATED                                  0     0
  DPF3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DPF3 MUTATED                           0     2
  DPF3 WILD-TYPE                        19   174
D1150V12, multiclass
[1] "Remove cluster labels:" "DPF3 MUTATED"          
clus
  DPF3 MUTATED DPF3 WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6651     TCGA-A6-6652 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6899 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 

Clustering(1151) Variable = DBF4B MUTATION ANALYSIS
D1151V1, survival
                 sevent
clus2               0   1
  DBF4B MUTATED     5   1
  DBF4B WILD-TYPE 272  77
  DBF4B MUTATED DBF4B WILD-TYPE 
              6             349 
  DBF4B MUTATED DBF4B WILD-TYPE 
              1              77 
$`DBF4B MUTATED`
TCGA-AA-3715 TCGA-A6-5656 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6930 
       19.04        32.91        34.98        12.76        14.04        13.35 

$`DBF4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DBF4B MUTATED DBF4B WILD-TYPE 
          12.76            0.00 
  DBF4B MUTATED DBF4B WILD-TYPE 
          34.98          148.01 
  DBF4B MUTATED DBF4B WILD-TYPE 
          16.54           22.09 
[1] "12.8 - 35.0 (16.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1151V2, continuous
                 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      62        1       25       105         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  DBF4B MUTATED           0
  DBF4B WILD-TYPE         1
D1151V3, multiclass
            clus
vv           DBF4B MUTATED DBF4B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DBF4B MUTATED     0   2   4   1
  DBF4B WILD-TYPE   9  65 245  40
D1151V4, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             1              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
  DBF4B MUTATED     7   0   0
  DBF4B WILD-TYPE 213  81  66
D1151V5, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V6, binary
                 cls
clus                0   1
  DBF4B MUTATED     7   0
  DBF4B WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      7    0
  DBF4B WILD-TYPE  278   48
   clus
vv  DBF4B MUTATED DBF4B WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1151V7, binary
                 cls
clus                0   1
  DBF4B MUTATED     3   4
  DBF4B WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      3    4
  DBF4B WILD-TYPE  167  193
        clus
vv       DBF4B MUTATED DBF4B WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1151V8, binary
                 cls
clus                0   1
  DBF4B MUTATED     6   0
  DBF4B WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      6    0
  DBF4B WILD-TYPE  294    8
     clus
vv    DBF4B MUTATED DBF4B WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1151V9, binary
                 cls
clus                0   1
  DBF4B MUTATED     5   2
  DBF4B WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      5    2
  DBF4B WILD-TYPE  309   46
                               clus
vv                              DBF4B MUTATED DBF4B WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DBF4B MUTATED     5   0   0   1
  DBF4B WILD-TYPE 254   3  22  20
D1151V10, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D1151V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DBF4B MUTATED                                  0     1
  DBF4B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DBF4B MUTATED                           0     3
  DBF4B WILD-TYPE                        19   173
D1151V12, multiclass
                                  clus
vv                                 DBF4B MUTATED DBF4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = AKAP7 MUTATION ANALYSIS
D1152V1, survival
                 sevent
clus2               0   1
  AKAP7 MUTATED     4   1
  AKAP7 WILD-TYPE 273  77
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              5             350 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              1              77 
$`AKAP7 MUTATED`
TCGA-A6-2671 TCGA-A6-5665 TCGA-AA-A010 TCGA-AD-5900 TCGA-CK-4948 
       43.76        22.06        34.98        12.16       148.01 

$`AKAP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        79.69        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  AKAP7 MUTATED AKAP7 WILD-TYPE 
          12.16            0.00 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
         148.01          140.38 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
          34.98           22.01 
[1] "12.2 - 148.0 (35.0)" "0.0 - 140.4 (22.0)" 
[1] "hr=" "1.6"
D1152V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP7 MUTATED         1        0        0         1         1         0
  AKAP7 WILD-TYPE      63        1       26       107         7         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        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  AKAP7 MUTATED           0
  AKAP7 WILD-TYPE         1
D1152V3, multiclass
            clus
vv           AKAP7 MUTATED AKAP7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  AKAP7 MUTATED     0   1   3   1
  AKAP7 WILD-TYPE   9  66 246  40
D1152V4, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             3             246
  T4             1              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
  AKAP7 MUTATED     3   1   1
  AKAP7 WILD-TYPE 217  80  65
D1152V5, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V6, binary
                 cls
clus                0   1
  AKAP7 MUTATED     3   1
  AKAP7 WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      3    1
  AKAP7 WILD-TYPE  282   47
   clus
vv  AKAP7 MUTATED AKAP7 WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D1152V7, binary
                 cls
clus                0   1
  AKAP7 MUTATED     3   2
  AKAP7 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      3    2
  AKAP7 WILD-TYPE  167  195
        clus
vv       AKAP7 MUTATED AKAP7 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1152V8, binary
                 cls
clus                0   1
  AKAP7 MUTATED     5   0
  AKAP7 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      5    0
  AKAP7 WILD-TYPE  295    8
     clus
vv    AKAP7 MUTATED AKAP7 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1152V9, binary
                 cls
clus                0   1
  AKAP7 MUTATED     4   1
  AKAP7 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      4    1
  AKAP7 WILD-TYPE  310   47
                               clus
vv                              AKAP7 MUTATED AKAP7 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AKAP7 MUTATED     5   0   0   0
  AKAP7 WILD-TYPE 254   3  22  21
D1152V10, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1152V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP7 MUTATED                                  0     0
  AKAP7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP7 MUTATED                           0     4
  AKAP7 WILD-TYPE                        19   172
D1152V12, multiclass
                                  clus
vv                                 AKAP7 MUTATED AKAP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = RNF215 MUTATION ANALYSIS
D1153V1, survival
                  sevent
clus2                0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 274  78
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              352 
  RNF215 MUTATED RNF215 WILD-TYPE 
               0               78 
$`RNF215 MUTATED`
TCGA-G4-6586 TCGA-CA-5796 TCGA-CM-6163 
       35.80        12.39        14.04 

$`RNF215 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  RNF215 MUTATED RNF215 WILD-TYPE 
           12.39             0.00 
  RNF215 MUTATED RNF215 WILD-TYPE 
           35.80           148.01 
  RNF215 MUTATED RNF215 WILD-TYPE 
          14.040           22.075 
[1] "12.4 - 35.8 (14.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1153V2, continuous
                  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      63        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF215 MUTATED           0          0          0          0        0
  RNF215 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF215 MUTATED           0         0
  RNF215 WILD-TYPE        12         1
D1153V3, multiclass
            clus
vv           RNF215 MUTATED RNF215 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  RNF215 MUTATED     1   0   2   0
  RNF215 WILD-TYPE   8  67 247  41
D1153V4, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              2              247
  T4              0               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
  RNF215 MUTATED     3   0   0
  RNF215 WILD-TYPE 217  81  66
D1153V5, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  N0              3              217
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V6, binary
                  cls
clus                 0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      3    0
  RNF215 WILD-TYPE  282   48
   clus
vv  RNF215 MUTATED RNF215 WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D1153V7, binary
                  cls
clus                 0   1
  RNF215 MUTATED     2   1
  RNF215 WILD-TYPE 168 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      2    1
  RNF215 WILD-TYPE  168  196
        clus
vv       RNF215 MUTATED RNF215 WILD-TYPE
  FEMALE              2              168
  MALE                1              196
[1] 2 2
[1] FALSE
D1153V8, binary
                  cls
clus                 0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      3    0
  RNF215 WILD-TYPE  297    8
     clus
vv    RNF215 MUTATED RNF215 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1153V9, binary
                  cls
clus                 0   1
  RNF215 MUTATED     2   1
  RNF215 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      2    1
  RNF215 WILD-TYPE  312   47
                               clus
vv                              RNF215 MUTATED RNF215 WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF215 MUTATED     3   0   0   0
  RNF215 WILD-TYPE 256   3  22  21
D1153V10, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1153V11, continuous
[1] "Remove cluster labels:" "RNF215 MUTATED"        
clus
  RNF215 MUTATED RNF215 WILD-TYPE 
               2              344 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3516       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-3527       TCGA-AA-3530 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6964       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-DM-A285 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6588       TCGA-G4-6625 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-2676       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-A6-5656 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660       TCGA-A6-5661 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665       TCGA-A6-5666 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652       TCGA-A6-6653 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       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-3544 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3663 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       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-3693       TCGA-AA-3695 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3811 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3861 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       TCGA-AA-3872 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3941 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3977       TCGA-AA-3980       TCGA-AA-3982 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N       TCGA-AA-A00O 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"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-6889 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963 
"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-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-CA-6715       TCGA-CK-4947       TCGA-CK-4948 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6164 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806       TCGA-F4-6807 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"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     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF215 MUTATED                           0     2
  RNF215 WILD-TYPE                        19   174
D1153V12, multiclass
                                  clus
vv                                 RNF215 MUTATED RNF215 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1154) Variable = KIRREL2 MUTATION ANALYSIS
D1154V1, survival
                   sevent
clus2                 0   1
  KIRREL2 MUTATED    11   1
  KIRREL2 WILD-TYPE 266  77
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               12               343 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                1                77 
$`KIRREL2 MUTATED`
TCGA-AA-3715 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 
       19.04        26.17        33.53        22.06        19.66         6.97 
TCGA-AA-3831 TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-4743 TCGA-D5-6540 
       17.98        53.00        34.98        12.16        23.05        16.14 

$`KIRREL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
             6.97              0.00 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            53.00            148.01 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            20.86             22.09 
[1] "7.0 - 53.0 (20.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1154V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIRREL2 MUTATED         2        0        3         5         1         0
  KIRREL2 WILD-TYPE      62        1       23       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL2 MUTATED           0          0          0          1        0
  KIRREL2 WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  KIRREL2 MUTATED           0         0
  KIRREL2 WILD-TYPE        12         1
D1154V3, multiclass
            clus
vv           KIRREL2 MUTATED KIRREL2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  KIRREL2 MUTATED     0   2   8   2
  KIRREL2 WILD-TYPE   9  65 241  39
D1154V4, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               8               241
  T4               2                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
  KIRREL2 MUTATED    11   1   0
  KIRREL2 WILD-TYPE 209  80  66
D1154V5, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  N0              11               209
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V6, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    10   0
  KIRREL2 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     10    0
  KIRREL2 WILD-TYPE  275   48
   clus
vv  KIRREL2 MUTATED KIRREL2 WILD-TYPE
  0              10               275
  1               0                48
[1] 2 2
[1] FALSE
D1154V7, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     4   8
  KIRREL2 WILD-TYPE 166 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      4    8
  KIRREL2 WILD-TYPE  166  189
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  FEMALE               4               166
  MALE                 8               189
[1] 2 2
[1] FALSE
D1154V8, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    12   0
  KIRREL2 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     12    0
  KIRREL2 WILD-TYPE  288    8
     clus
vv    KIRREL2 MUTATED KIRREL2 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D1154V9, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     9   3
  KIRREL2 WILD-TYPE 305  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      9    3
  KIRREL2 WILD-TYPE  305   45
                               clus
vv                              KIRREL2 MUTATED KIRREL2 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KIRREL2 MUTATED    12   0   0   0
  KIRREL2 WILD-TYPE 247   3  22  21
D1154V10, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               0                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"
D1154V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIRREL2 MUTATED                                  0     0
  KIRREL2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  KIRREL2 MUTATED                           1     6
  KIRREL2 WILD-TYPE                        18   170
D1154V12, multiclass
                                  clus
vv                                 KIRREL2 MUTATED KIRREL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[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 = METTL5 MUTATION ANALYSIS
D1155V1, survival
                  sevent
clus2                0   1
  METTL5 MUTATED     3   1
  METTL5 WILD-TYPE 274  77
  METTL5 MUTATED METTL5 WILD-TYPE 
               4              351 
  METTL5 MUTATED METTL5 WILD-TYPE 
               1               77 
$`METTL5 MUTATED`
TCGA-AA-3710 TCGA-AD-6889 TCGA-CM-5860 TCGA-CM-6171 
       26.99        83.24        32.02        14.04 

$`METTL5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  METTL5 MUTATED METTL5 WILD-TYPE 
           14.04             0.00 
  METTL5 MUTATED METTL5 WILD-TYPE 
           83.24           148.01 
  METTL5 MUTATED METTL5 WILD-TYPE 
          29.505           22.030 
[1] "14.0 - 83.2 (29.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1155V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METTL5 MUTATED         1        0        0         3         0         0
  METTL5 WILD-TYPE      63        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL5 MUTATED           1          0          0          0        0
  METTL5 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  METTL5 MUTATED           0         0
  METTL5 WILD-TYPE        12         1
D1155V3, multiclass
            clus
vv           METTL5 MUTATED METTL5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  METTL5 MUTATED     0   1   4   0
  METTL5 WILD-TYPE   9  66 245  41
D1155V4, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              0               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
  METTL5 MUTATED     4   0   1
  METTL5 WILD-TYPE 216  81  65
D1155V5, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  N0              4              216
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1155V6, binary
                  cls
clus                 0   1
  METTL5 MUTATED     5   0
  METTL5 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      5    0
  METTL5 WILD-TYPE  280   48
   clus
vv  METTL5 MUTATED METTL5 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1155V7, binary
                  cls
clus                 0   1
  METTL5 MUTATED     2   3
  METTL5 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      2    3
  METTL5 WILD-TYPE  168  194
        clus
vv       METTL5 MUTATED METTL5 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D1155V8, binary
                  cls
clus                 0   1
  METTL5 MUTATED     4   0
  METTL5 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      4    0
  METTL5 WILD-TYPE  296    8
     clus
vv    METTL5 MUTATED METTL5 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1155V9, binary
                  cls
clus                 0   1
  METTL5 MUTATED     5   0
  METTL5 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      5    0
  METTL5 WILD-TYPE  309   48
                               clus
vv                              METTL5 MUTATED METTL5 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  METTL5 MUTATED     5   0   0   0
  METTL5 WILD-TYPE 254   3  22  21
D1155V10, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1155V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METTL5 MUTATED                                  0     1
  METTL5 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  METTL5 MUTATED                           0     2
  METTL5 WILD-TYPE                        19   174
D1155V12, multiclass
                                  clus
vv                                 METTL5 MUTATED METTL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1156) Variable = CCR8 MUTATION ANALYSIS
D1156V1, survival
                sevent
clus2              0   1
  CCR8 MUTATED     3   4
  CCR8 WILD-TYPE 274  74
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            348 
  CCR8 MUTATED CCR8 WILD-TYPE 
             4             74 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6605 
       62.79        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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         22.075 
[1] "2.0 - 92.8 (14.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3"  
D1156V2, continuous
                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      64        1       26       104         7         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        18          6         44         33       34        12
                vv
clus             STAGE IVB
  CCR8 MUTATED           0
  CCR8 WILD-TYPE         1
D1156V3, multiclass
            clus
vv           CCR8 MUTATED CCR8 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  CCR8 MUTATED     0   1   4   2
  CCR8 WILD-TYPE   9  66 245  39
D1156V4, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            2             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
  CCR8 MUTATED     5   1   1
  CCR8 WILD-TYPE 215  80  65
D1156V5, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V6, binary
                cls
clus               0   1
  CCR8 MUTATED     5   1
  CCR8 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      5    1
  CCR8 WILD-TYPE  280   47
   clus
vv  CCR8 MUTATED CCR8 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D1156V7, binary
                cls
clus               0   1
  CCR8 MUTATED     3   4
  CCR8 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      3    4
  CCR8 WILD-TYPE  167  193
        clus
vv       CCR8 MUTATED CCR8 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D1156V8, binary
                cls
clus               0   1
  CCR8 MUTATED     4   0
  CCR8 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      4    0
  CCR8 WILD-TYPE  296    8
     clus
vv    CCR8 MUTATED CCR8 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1156V9, binary
                cls
clus               0   1
  CCR8 MUTATED     4   3
  CCR8 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      4    3
  CCR8 WILD-TYPE  310   45
                               clus
vv                              CCR8 MUTATED CCR8 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCR8 MUTATED     3   0   0   0
  CCR8 WILD-TYPE 256   3  22  21
D1156V10, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1156V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCR8 MUTATED                                  0     0
  CCR8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCR8 MUTATED                           0     4
  CCR8 WILD-TYPE                        19   172
D1156V12, multiclass
                                  clus
vv                                 CCR8 MUTATED CCR8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = OR5AK2 MUTATION ANALYSIS
D1157V1, survival
                  sevent
clus2                0   1
  OR5AK2 MUTATED     5   4
  OR5AK2 WILD-TYPE 272  74
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              346 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               4               74 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         1.41        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.075 
[1] "1.0 - 98.2 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1157V2, continuous
                  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      63        1       24       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5AK2 MUTATED           0          0          0          0        1
  OR5AK2 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  OR5AK2 MUTATED           0         0
  OR5AK2 WILD-TYPE        12         1
D1157V3, multiclass
            clus
vv           OR5AK2 MUTATED OR5AK2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  OR5AK2 MUTATED     1   0   6   2
  OR5AK2 WILD-TYPE   8  67 243  39
D1157V4, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              6              243
  T4              2               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
  OR5AK2 MUTATED     8   0   1
  OR5AK2 WILD-TYPE 212  81  65
D1157V5, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1157V6, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     8   1
  OR5AK2 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      8    1
  OR5AK2 WILD-TYPE  277   47
   clus
vv  OR5AK2 MUTATED OR5AK2 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1157V7, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     5   4
  OR5AK2 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      5    4
  OR5AK2 WILD-TYPE  165  193
        clus
vv       OR5AK2 MUTATED OR5AK2 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1157V8, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     6   0
  OR5AK2 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      6    0
  OR5AK2 WILD-TYPE  294    8
     clus
vv    OR5AK2 MUTATED OR5AK2 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1157V9, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     6   2
  OR5AK2 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      6    2
  OR5AK2 WILD-TYPE  308   46
                               clus
vv                              OR5AK2 MUTATED OR5AK2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR5AK2 MUTATED     5   0   0   1
  OR5AK2 WILD-TYPE 254   3  22  20
D1157V10, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D1157V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5AK2 MUTATED                                  0     1
  OR5AK2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR5AK2 MUTATED                           0     4
  OR5AK2 WILD-TYPE                        19   172
D1157V12, multiclass
                                  clus
vv                                 OR5AK2 MUTATED OR5AK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1158) Variable = NTRK2 MUTATION ANALYSIS
D1158V1, survival
                 sevent
clus2               0   1
  NTRK2 MUTATED    17   5
  NTRK2 WILD-TYPE 260  73
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             22             333 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
              5              73 
$`NTRK2 MUTATED`
TCGA-AD-6895 TCGA-A6-3810 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3492 
       25.08        36.53        23.61        22.06        32.71         3.02 
TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AU-6004 TCGA-AZ-6598 
       63.98         4.01        34.98        14.01        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        14.04        29.03        16.04        15.58 
TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6315 
       10.13        13.35        44.32        61.91 

$`NTRK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.91        31.63        30.44        29.19        33.53 
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-A6-6651 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-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-6166 TCGA-CM-6167 
       15.02        17.03        15.02        12.00        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14         7.53        12.39        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NTRK2 MUTATED NTRK2 WILD-TYPE 
           3.02            0.00 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
          63.98          148.01 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
         23.295          21.990 
[1] "3.0 - 64.0 (23.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1158V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTRK2 MUTATED         2        0        3         8         3         1
  NTRK2 WILD-TYPE      62        1       23       100         5         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTRK2 MUTATED           0          1          2          0        2         1
  NTRK2 WILD-TYPE        18          5         42         33       33        11
                 vv
clus              STAGE IVB
  NTRK2 MUTATED           0
  NTRK2 WILD-TYPE         1
D1158V3, multiclass
            clus
vv           NTRK2 MUTATED NTRK2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              1              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
  NTRK2 MUTATED     1   1  16   5
  NTRK2 WILD-TYPE   8  66 233  36
D1158V4, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  T1             1               8
  T2             1              66
  T3            16             233
  T4             5              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
  NTRK2 MUTATED    17   4   2
  NTRK2 WILD-TYPE 203  77  64
D1158V5, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  N0            17             203
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V6, binary
                 cls
clus                0   1
  NTRK2 MUTATED    18   3
  NTRK2 WILD-TYPE 267  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     18    3
  NTRK2 WILD-TYPE  267   45
   clus
vv  NTRK2 MUTATED NTRK2 WILD-TYPE
  0            18             267
  1             3              45
[1] 2 2
[1] FALSE
D1158V7, binary
                 cls
clus                0   1
  NTRK2 MUTATED     7  16
  NTRK2 WILD-TYPE 163 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED      7   16
  NTRK2 WILD-TYPE  163  181
        clus
vv       NTRK2 MUTATED NTRK2 WILD-TYPE
  FEMALE             7             163
  MALE              16             181
[1] 2 2
[1] FALSE
D1158V8, binary
                 cls
clus                0   1
  NTRK2 MUTATED    19   0
  NTRK2 WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     19    0
  NTRK2 WILD-TYPE  281    8
     clus
vv    NTRK2 MUTATED NTRK2 WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D1158V9, binary
                 cls
clus                0   1
  NTRK2 MUTATED    20   3
  NTRK2 WILD-TYPE 294  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     20    3
  NTRK2 WILD-TYPE  294   45
                               clus
vv                              NTRK2 MUTATED NTRK2 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NTRK2 MUTATED    16   0   1   2
  NTRK2 WILD-TYPE 243   3  21  19
D1158V10, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             1              21
  RX             2              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"
D1158V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTRK2 MUTATED                                  0     1
  NTRK2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTRK2 MUTATED                           0    17
  NTRK2 WILD-TYPE                        19   159
D1158V12, multiclass
                                  clus
vv                                 NTRK2 MUTATED NTRK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       17             159
[1] 4 2
[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 = SMARCB1 MUTATION ANALYSIS
D1159V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED    17   5
  SMARCB1 WILD-TYPE 260  73
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               22               333 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5                73 
$`SMARCB1 MUTATED`
TCGA-AA-3713 TCGA-G4-6321 TCGA-G4-6588 TCGA-AA-3542 TCGA-AA-3663 TCGA-AA-A010 
       19.04        22.09        26.17        12.99         6.97        34.98 
TCGA-AA-A02W TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-4746 TCGA-CM-5344 
       41.00        14.50        58.39         6.77        37.02        22.03 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D7 
       11.01        12.95         4.80        16.14        11.64        13.32 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6317 TCGA-G4-6626 
      133.18        65.85        36.00        46.75 

$`SMARCB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        22.36 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6323 
       85.48        61.91        13.78 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              4.8               0.0 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           133.18            148.01 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           20.535            22.090 
[1] "4.8 - 133.2 (20.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1159V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMARCB1 MUTATED         5        0        1         7         1         0
  SMARCB1 WILD-TYPE      59        1       25       101         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCB1 MUTATED           2          0          3          2        2
  SMARCB1 WILD-TYPE        16          6         41         31       33
                   vv
clus                STAGE IVA STAGE IVB
  SMARCB1 MUTATED           0         0
  SMARCB1 WILD-TYPE        12         1
D1159V3, multiclass
            clus
vv           SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                7               101
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               2                31
  STAGE IV                 2                33
  STAGE IVA                0                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
  SMARCB1 MUTATED     0   6  16   1
  SMARCB1 WILD-TYPE   9  61 233  40
D1159V4, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1               0                 9
  T2               6                61
  T3              16               233
  T4               1                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
  SMARCB1 MUTATED    15   6   2
  SMARCB1 WILD-TYPE 205  75  64
D1159V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0              15               205
  N1               6                75
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    16   2
  SMARCB1 WILD-TYPE 269  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     16    2
  SMARCB1 WILD-TYPE  269   46
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0              16               269
  1               2                46
[1] 2 2
[1] FALSE
D1159V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    10  13
  SMARCB1 WILD-TYPE 160 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     10   13
  SMARCB1 WILD-TYPE  160  184
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE              10               160
  MALE                13               184
[1] 2 2
[1] FALSE
D1159V8, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    20   1
  SMARCB1 WILD-TYPE 280   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     20    1
  SMARCB1 WILD-TYPE  280    7
     clus
vv    SMARCB1 MUTATED SMARCB1 WILD-TYPE
  NO               20               280
  YES               1                 7
[1] 2 2
[1] FALSE
D1159V9, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    20   2
  SMARCB1 WILD-TYPE 294  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     20    2
  SMARCB1 WILD-TYPE  294   46
                               clus
vv                              SMARCB1 MUTATED SMARCB1 WILD-TYPE
  COLON ADENOCARCINOMA                       20               294
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SMARCB1 MUTATED    19   0   1   1
  SMARCB1 WILD-TYPE 240   3  21  20
D1159V10, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  R0              19               240
  R1               0                 3
  R2               1                21
  RX               1                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"
D1159V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           1    17
  SMARCB1 WILD-TYPE                        18   159
D1159V12, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         17               159
[1] 4 2
[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 = ERCC6 MUTATION ANALYSIS
D1160V1, survival
                 sevent
clus2               0   1
  ERCC6 MUTATED    21   6
  ERCC6 WILD-TYPE 256  72
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             27             328 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              6              72 
$`ERCC6 MUTATED`
TCGA-AA-3496 TCGA-AA-3554 TCGA-AA-3697 TCGA-AD-6964 TCGA-G4-6586 TCGA-A6-2676 
        1.02        17.95        85.05        10.88        35.80        42.90 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3666 
       22.06         8.38        24.69        63.98         6.97         2.01 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 
       25.02        18.05         4.01        34.98        21.44        58.39 
TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-DM-A1HA TCGA-DM-A28H 
       12.76        51.32        16.14        92.75       131.51       117.07 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6303 
       47.87        35.31        65.85 

$`ERCC6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.52        25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        78.08        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ERCC6 MUTATED ERCC6 WILD-TYPE 
           1.02            0.00 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
         131.51          148.01 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
          25.02           21.99 
[1] "1.0 - 131.5 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1160V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC6 MUTATED         2        0        5        10         3         0
  ERCC6 WILD-TYPE      62        1       21        98         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC6 MUTATED           1          0          1          2        1         1
  ERCC6 WILD-TYPE        17          6         43         31       34        11
                 vv
clus              STAGE IVB
  ERCC6 MUTATED           0
  ERCC6 WILD-TYPE         1
D1160V3, multiclass
            clus
vv           ERCC6 MUTATED ERCC6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             10              98
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  ERCC6 MUTATED     0   3  19   6
  ERCC6 WILD-TYPE   9  64 230  35
D1160V4, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            19             230
  T4             6              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
  ERCC6 MUTATED    22   3   3
  ERCC6 WILD-TYPE 198  78  63
D1160V5, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  N0            22             198
  N1             3              78
  N2             3              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"
D1160V6, binary
                 cls
clus                0   1
  ERCC6 MUTATED    22   2
  ERCC6 WILD-TYPE 263  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     22    2
  ERCC6 WILD-TYPE  263   46
   clus
vv  ERCC6 MUTATED ERCC6 WILD-TYPE
  0            22             263
  1             2              46
[1] 2 2
[1] FALSE
D1160V7, binary
                 cls
clus                0   1
  ERCC6 MUTATED     9  19
  ERCC6 WILD-TYPE 161 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED      9   19
  ERCC6 WILD-TYPE  161  178
        clus
vv       ERCC6 MUTATED ERCC6 WILD-TYPE
  FEMALE             9             161
  MALE              19             178
[1] 2 2
[1] FALSE
D1160V8, binary
                 cls
clus                0   1
  ERCC6 MUTATED    21   0
  ERCC6 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     21    0
  ERCC6 WILD-TYPE  279    8
     clus
vv    ERCC6 MUTATED ERCC6 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D1160V9, binary
                 cls
clus                0   1
  ERCC6 MUTATED    23   5
  ERCC6 WILD-TYPE 291  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     23    5
  ERCC6 WILD-TYPE  291   43
                               clus
vv                              ERCC6 MUTATED ERCC6 WILD-TYPE
  COLON ADENOCARCINOMA                     23             291
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERCC6 MUTATED    19   0   0   2
  ERCC6 WILD-TYPE 240   3  22  19
D1160V10, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             0              22
  RX             2              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"
D1160V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC6 MUTATED                                  0     1
  ERCC6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERCC6 MUTATED                           2    14
  ERCC6 WILD-TYPE                        17   162
D1160V12, multiclass
                                  clus
vv                                 ERCC6 MUTATED ERCC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       14             162
[1] 4 2
[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 = RARG MUTATION ANALYSIS
D1161V1, survival
                sevent
clus2              0   1
  RARG MUTATED     6   3
  RARG WILD-TYPE 271  75
  RARG MUTATED RARG WILD-TYPE 
             9            346 
  RARG MUTATED RARG WILD-TYPE 
             3             75 
$`RARG MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3518 TCGA-AA-3968 TCGA-AA-A00J TCGA-AA-A02J 
       13.02        19.04         1.02        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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         22.225 
[1] "1.0 - 55.0 (18.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.8"
D1161V2, continuous
                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      63        1       25       106         8         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        17          6         41         33       33        12
                vv
clus             STAGE IVB
  RARG MUTATED           0
  RARG WILD-TYPE         1
D1161V3, multiclass
            clus
vv           RARG MUTATED RARG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  RARG MUTATED     0   1   8   1
  RARG WILD-TYPE   9  66 241  40
D1161V4, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            1             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
  RARG MUTATED     6   3   1
  RARG WILD-TYPE 214  78  65
D1161V5, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  N0            6            214
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V6, binary
                cls
clus               0   1
  RARG MUTATED     7   2
  RARG WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      7    2
  RARG WILD-TYPE  278   46
   clus
vv  RARG MUTATED RARG WILD-TYPE
  0            7            278
  1            2             46
[1] 2 2
[1] FALSE
D1161V7, binary
                cls
clus               0   1
  RARG MUTATED     8   2
  RARG WILD-TYPE 162 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      8    2
  RARG WILD-TYPE  162  195
        clus
vv       RARG MUTATED RARG WILD-TYPE
  FEMALE            8            162
  MALE              2            195
[1] 2 2
[1] FALSE
D1161V8, binary
                cls
clus               0   1
  RARG MUTATED     6   1
  RARG WILD-TYPE 294   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      6    1
  RARG WILD-TYPE  294    7
     clus
vv    RARG MUTATED RARG WILD-TYPE
  NO             6            294
  YES            1              7
[1] 2 2
[1] FALSE
D1161V9, binary
                cls
clus               0   1
  RARG MUTATED     8   2
  RARG WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      8    2
  RARG WILD-TYPE  306   46
                               clus
vv                              RARG MUTATED RARG WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RARG MUTATED     6   0   2   0
  RARG WILD-TYPE 253   3  20  21
D1161V10, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  R0            6            253
  R1            0              3
  R2            2             20
  RX            0             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"
D1161V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RARG MUTATED                                  0     0
  RARG WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RARG MUTATED                           1     2
  RARG WILD-TYPE                        18   174
D1161V12, multiclass
                                  clus
vv                                 RARG MUTATED RARG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(1162) Variable = HEPH MUTATION ANALYSIS
D1162V1, survival
                sevent
clus2              0   1
  HEPH MUTATED    12   3
  HEPH WILD-TYPE 265  75
  HEPH MUTATED HEPH WILD-TYPE 
            15            340 
  HEPH MUTATED HEPH WILD-TYPE 
             3             75 
$`HEPH MUTATED`
TCGA-G4-6321 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-A00N 
       22.09        31.63        30.44        33.53        61.02         4.01 
TCGA-AZ-4315 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-5538 TCGA-D5-5541 
       58.39        15.62        23.05        15.02        54.61        55.92 
TCGA-DM-A1D8 TCGA-DM-A28H TCGA-F4-6856 
       12.59       117.07        35.31 

$`HEPH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.75        36.53        32.91        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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-4744 
       21.99        21.14        82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        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-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  HEPH MUTATED HEPH WILD-TYPE 
          4.01           0.00 
  HEPH MUTATED HEPH WILD-TYPE 
        117.07         148.01 
  HEPH MUTATED HEPH WILD-TYPE 
         31.63          21.99 
[1] "4.0 - 117.1 (31.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1162V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEPH MUTATED         2        0        1         4         1         0
  HEPH WILD-TYPE      62        1       25       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HEPH MUTATED           1          0          3          2        0         0
  HEPH WILD-TYPE        17          6         41         31       35        12
                vv
clus             STAGE IVB
  HEPH MUTATED           0
  HEPH WILD-TYPE         1
D1162V3, multiclass
            clus
vv           HEPH MUTATED HEPH WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  HEPH MUTATED     0   3  10   2
  HEPH WILD-TYPE   9  64 239  39
D1162V4, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  T1            0              9
  T2            3             64
  T3           10            239
  T4            2             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
  HEPH MUTATED     8   5   2
  HEPH WILD-TYPE 212  76  64
D1162V5, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  N0            8            212
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V6, binary
                cls
clus               0   1
  HEPH MUTATED    13   0
  HEPH WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     13    0
  HEPH WILD-TYPE  272   48
   clus
vv  HEPH MUTATED HEPH WILD-TYPE
  0           13            272
  1            0             48
[1] 2 2
[1] FALSE
D1162V7, binary
                cls
clus               0   1
  HEPH MUTATED     6   9
  HEPH WILD-TYPE 164 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED      6    9
  HEPH WILD-TYPE  164  188
        clus
vv       HEPH MUTATED HEPH WILD-TYPE
  FEMALE            6            164
  MALE              9            188
[1] 2 2
[1] FALSE
D1162V8, binary
                cls
clus               0   1
  HEPH MUTATED    11   0
  HEPH WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     11    0
  HEPH WILD-TYPE  289    8
     clus
vv    HEPH MUTATED HEPH WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1162V9, binary
                cls
clus               0   1
  HEPH MUTATED    12   3
  HEPH WILD-TYPE 302  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     12    3
  HEPH WILD-TYPE  302   45
                               clus
vv                              HEPH MUTATED HEPH WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HEPH MUTATED    12   0   0   1
  HEPH WILD-TYPE 247   3  22  20
D1162V10, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            1             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"
D1162V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEPH MUTATED                                  0     0
  HEPH WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HEPH MUTATED                           2    11
  HEPH WILD-TYPE                        17   165
D1162V12, multiclass
                                  clus
vv                                 HEPH MUTATED HEPH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      11            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(1163) Variable = RASGRF2 MUTATION ANALYSIS
D1163V1, survival
                   sevent
clus2                 0   1
  RASGRF2 MUTATED    14   3
  RASGRF2 WILD-TYPE 263  75
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
               17               338 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                3                75 
$`RASGRF2 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5662 TCGA-AA-3510 
       24.00       100.01        35.80        26.17        23.61        63.98 
TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
       31.00        25.02         4.01        34.98        58.39        12.76 
TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5349 TCGA-D5-6535 TCGA-DM-A28E 
       10.06        23.05        30.08        15.12       119.93 

$`RASGRF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5664 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
             4.01              0.00 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
           119.93            148.01 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
            26.17             21.99 
[1] "4.0 - 119.9 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1163V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASGRF2 MUTATED         1        0        2         9         2         0
  RASGRF2 WILD-TYPE      63        1       24        99         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASGRF2 MUTATED           0          0          1          0        0
  RASGRF2 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  RASGRF2 MUTATED           1         0
  RASGRF2 WILD-TYPE        11         1
D1163V3, multiclass
            clus
vv           RASGRF2 MUTATED RASGRF2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                9                99
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  RASGRF2 MUTATED     1   1  13   2
  RASGRF2 WILD-TYPE   8  66 236  39
D1163V4, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3              13               236
  T4               2                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
  RASGRF2 MUTATED    15   1   1
  RASGRF2 WILD-TYPE 205  80  65
D1163V5, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  N0              15               205
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V6, binary
                   cls
clus                  0   1
  RASGRF2 MUTATED    14   1
  RASGRF2 WILD-TYPE 271  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED     14    1
  RASGRF2 WILD-TYPE  271   47
   clus
vv  RASGRF2 MUTATED RASGRF2 WILD-TYPE
  0              14               271
  1               1                47
[1] 2 2
[1] FALSE
D1163V7, binary
                   cls
clus                  0   1
  RASGRF2 MUTATED     8   9
  RASGRF2 WILD-TYPE 162 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED      8    9
  RASGRF2 WILD-TYPE  162  188
        clus
vv       RASGRF2 MUTATED RASGRF2 WILD-TYPE
  FEMALE               8               162
  MALE                 9               188
[1] 2 2
[1] FALSE
D1163V8, binary
                   cls
clus                  0   1
  RASGRF2 MUTATED    15   0
  RASGRF2 WILD-TYPE 285   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED     15    0
  RASGRF2 WILD-TYPE  285    8
     clus
vv    RASGRF2 MUTATED RASGRF2 WILD-TYPE
  NO               15               285
  YES               0                 8
[1] 2 2
[1] FALSE
D1163V9, binary
                   cls
clus                  0   1
  RASGRF2 MUTATED    13   4
  RASGRF2 WILD-TYPE 301  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED     13    4
  RASGRF2 WILD-TYPE  301   44
                               clus
vv                              RASGRF2 MUTATED RASGRF2 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RASGRF2 MUTATED    10   0   0   3
  RASGRF2 WILD-TYPE 249   3  22  18
D1163V10, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               3                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"
D1163V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASGRF2 MUTATED                                  0     2
  RASGRF2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RASGRF2 MUTATED                           0     9
  RASGRF2 WILD-TYPE                        19   167
D1163V12, multiclass
                                  clus
vv                                 RASGRF2 MUTATED RASGRF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          9               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(1164) Variable = LCN9 MUTATION ANALYSIS
D1164V1, survival
                sevent
clus2              0   1
  LCN9 MUTATED     2   1
  LCN9 WILD-TYPE 275  77
  LCN9 MUTATED LCN9 WILD-TYPE 
             3            352 
  LCN9 MUTATED LCN9 WILD-TYPE 
             1             77 
$`LCN9 MUTATED`
TCGA-AZ-6608 TCGA-CK-4950 TCGA-D5-6534 
        1.94        85.45        43.27 

$`LCN9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LCN9 MUTATED LCN9 WILD-TYPE 
          1.94           0.00 
  LCN9 MUTATED LCN9 WILD-TYPE 
         85.45         148.01 
  LCN9 MUTATED LCN9 WILD-TYPE 
        43.270         22.045 
[1] "1.9 - 85.5 (43.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1164V2, continuous
                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      64        1       26       106         8         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        18          5         43         33       35        12
                vv
clus             STAGE IVB
  LCN9 MUTATED           0
  LCN9 WILD-TYPE         1
D1164V3, multiclass
            clus
vv           LCN9 MUTATED LCN9 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  LCN9 MUTATED     0   1   3   0
  LCN9 WILD-TYPE   9  66 246  41
D1164V4, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            0             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
  LCN9 MUTATED     2   2   0
  LCN9 WILD-TYPE 218  79  66
D1164V5, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  N0            2            218
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V6, binary
                cls
clus               0   1
  LCN9 MUTATED     4   0
  LCN9 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      4    0
  LCN9 WILD-TYPE  281   48
   clus
vv  LCN9 MUTATED LCN9 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1164V7, binary
                cls
clus               0   1
  LCN9 MUTATED     4   0
  LCN9 WILD-TYPE 166 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      4    0
  LCN9 WILD-TYPE  166  197
        clus
vv       LCN9 MUTATED LCN9 WILD-TYPE
  FEMALE            4            166
  MALE              0            197
[1] 2 2
[1] FALSE
D1164V8, binary
                cls
clus               0   1
  LCN9 MUTATED     3   0
  LCN9 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      3    0
  LCN9 WILD-TYPE  297    8
     clus
vv    LCN9 MUTATED LCN9 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1164V9, binary
                cls
clus               0   1
  LCN9 MUTATED     2   2
  LCN9 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      2    2
  LCN9 WILD-TYPE  312   46
                               clus
vv                              LCN9 MUTATED LCN9 WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LCN9 MUTATED     2   1   0   0
  LCN9 WILD-TYPE 257   2  22  21
D1164V10, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  R0            2            257
  R1            1              2
  R2            0             22
  RX            0             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"
D1164V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCN9 MUTATED                                  0     0
  LCN9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LCN9 MUTATED                           1     2
  LCN9 WILD-TYPE                        18   174
D1164V12, multiclass
                                  clus
vv                                 LCN9 MUTATED LCN9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(1165) Variable = DST MUTATION ANALYSIS
D1165V1, survival
               sevent
clus2             0   1
  DST MUTATED    50  14
  DST WILD-TYPE 227  64
  DST MUTATED DST WILD-TYPE 
           64           291 
  DST MUTATED DST WILD-TYPE 
           14            64 
$`DST MUTATED`
TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3672 TCGA-AD-6964 TCGA-G4-6310 TCGA-G4-6588 
       24.16         1.02         0.92        10.88        63.62        26.17 
TCGA-G4-6628 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5661 
       79.69        42.90        33.34        36.53        32.91        33.53 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 
       21.76        24.39        20.12        19.66         3.02        63.98 
TCGA-AA-3660 TCGA-AA-3667 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3941 TCGA-AA-3966 
       78.08        14.01         1.02         0.00        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AU-3779 
       25.02         4.01        34.98        35.01        12.16        14.50 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 
       27.09         0.20        21.44        58.39        88.21         6.77 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       12.69        12.76        10.06        21.99        21.14        82.95 
TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 
       37.02        29.06        32.02        15.02        12.00        21.99 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       45.40        54.61        16.14        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6460 
       11.38        49.91       131.51       135.65        35.97        31.96 
TCGA-F4-6703 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       47.87        65.85        53.62        85.48 

$`DST WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
        5.88        22.09        35.80        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5657 
       43.76        42.28        16.57        34.65        32.75        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-A6-6652 
       27.09        22.52         8.38        25.08        25.18        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       23.87        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        27.42        26.47        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       33.01        17.82         1.41         5.13        22.36        62.79 
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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 
       17.56       148.01        85.45        15.62        51.32         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
      124.27        23.05        20.02        25.02        13.02        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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        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-D5-5539 
       11.08        11.08        11.01        10.06        12.03        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        9.44        12.00        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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       44.32       139.17        81.37       119.93        60.79       117.07 
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        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 
       35.31       133.18        74.56        44.68        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DST MUTATED DST WILD-TYPE 
            0             0 
  DST MUTATED DST WILD-TYPE 
       135.65        148.01 
  DST MUTATED DST WILD-TYPE 
       24.275        21.990 
[1] "0.0 - 135.7 (24.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1165V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DST MUTATED        13        0        5        23         4         0
  DST WILD-TYPE      51        1       21        85         4         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DST MUTATED           2          1         10          3        2         1
  DST WILD-TYPE        16          5         34         30       33        11
               vv
clus            STAGE IVB
  DST MUTATED           0
  DST WILD-TYPE         1
D1165V3, multiclass
            clus
vv           DST MUTATED DST WILD-TYPE
  STAGE I             13            51
  STAGE IA             0             1
  STAGE II             5            21
  STAGE IIA           23            85
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            2            16
  STAGE IIIA           1             5
  STAGE IIIB          10            34
  STAGE IIIC           3            30
  STAGE IV             2            33
  STAGE IVA            1            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
  DST MUTATED     2  13  43   8
  DST WILD-TYPE   7  54 206  33
D1165V4, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  T1           2             7
  T2          13            54
  T3          43           206
  T4           8            33
[1] 4 2
[1] TRUE
[1] "dimension 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    45  16   5
  DST WILD-TYPE 175  65  61
D1165V5, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  N0          45           175
  N1          16            65
  N2           5            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V6, binary
               cls
clus              0   1
  DST MUTATED    51   3
  DST WILD-TYPE 234  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     51    3
  DST WILD-TYPE  234   45
   clus
vv  DST MUTATED DST WILD-TYPE
  0          51           234
  1           3            45
[1] 2 2
[1] FALSE
D1165V7, binary
               cls
clus              0   1
  DST MUTATED    32  34
  DST WILD-TYPE 138 163
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     32   34
  DST WILD-TYPE  138  163
        clus
vv       DST MUTATED DST WILD-TYPE
  FEMALE          32           138
  MALE            34           163
[1] 2 2
[1] FALSE
D1165V8, binary
               cls
clus              0   1
  DST MUTATED    51   2
  DST WILD-TYPE 249   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     51    2
  DST WILD-TYPE  249    6
     clus
vv    DST MUTATED DST WILD-TYPE
  NO           51           249
  YES           2             6
[1] 2 2
[1] FALSE
D1165V9, binary
               cls
clus              0   1
  DST MUTATED    51  14
  DST WILD-TYPE 263  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     51   14
  DST WILD-TYPE  263   34
                               clus
vv                              DST MUTATED DST WILD-TYPE
  COLON ADENOCARCINOMA                   51           263
  COLON MUCINOUS ADENOCARCINOMA          14            34
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  DST MUTATED    45   0   0   7
  DST WILD-TYPE 214   3  22  14
D1165V10, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  R0          45           214
  R1           0             3
  R2           0            22
  RX           7            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"
D1165V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DST MUTATED                                  0     3
  DST WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DST MUTATED                           3    44
  DST WILD-TYPE                        16   132
D1165V12, multiclass
                                  clus
vv                                 DST MUTATED DST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             7
  BLACK OR AFRICAN AMERICAN                  3            16
  WHITE                                     44           132
[1] 4 2
[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 = FBXO38 MUTATION ANALYSIS
D1166V1, survival
                  sevent
clus2                0   1
  FBXO38 MUTATED    11   6
  FBXO38 WILD-TYPE 266  72
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              17              338 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
               6               72 
$`FBXO38 MUTATED`
TCGA-AA-3554 TCGA-AA-3713 TCGA-AD-6964 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3666 
       17.95        19.04        10.88        22.06        19.66         2.01 
TCGA-AA-3811 TCGA-AA-A00N TCGA-AD-6963 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       10.06         4.01        27.42        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        25.48        98.24 

$`FBXO38 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FBXO38 MUTATED FBXO38 WILD-TYPE 
            2.01             0.00 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
           98.24           148.01 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
           17.95            22.47 
[1] "2.0 - 98.2 (17.9)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "2"  
D1166V2, continuous
                  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      63        1       26       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO38 MUTATED           2          0          0          2        1
  FBXO38 WILD-TYPE        16          6         44         31       34
                  vv
clus               STAGE IVA STAGE IVB
  FBXO38 MUTATED           0         0
  FBXO38 WILD-TYPE        12         1
D1166V3, multiclass
            clus
vv           FBXO38 MUTATED FBXO38 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  FBXO38 MUTATED     1   0  11   6
  FBXO38 WILD-TYPE   8  67 238  35
D1166V4, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  T1              1                8
  T2              0               67
  T3             11              238
  T4              6               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
  FBXO38 MUTATED    13   2   3
  FBXO38 WILD-TYPE 207  79  63
D1166V5, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  N0             13              207
  N1              2               79
  N2              3               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"
D1166V6, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    13   1
  FBXO38 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     13    1
  FBXO38 WILD-TYPE  272   47
   clus
vv  FBXO38 MUTATED FBXO38 WILD-TYPE
  0             13              272
  1              1               47
[1] 2 2
[1] FALSE
D1166V7, binary
                  cls
clus                 0   1
  FBXO38 MUTATED     8  10
  FBXO38 WILD-TYPE 162 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED      8   10
  FBXO38 WILD-TYPE  162  187
        clus
vv       FBXO38 MUTATED FBXO38 WILD-TYPE
  FEMALE              8              162
  MALE               10              187
[1] 2 2
[1] FALSE
D1166V8, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    12   1
  FBXO38 WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     12    1
  FBXO38 WILD-TYPE  288    7
     clus
vv    FBXO38 MUTATED FBXO38 WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D1166V9, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    13   5
  FBXO38 WILD-TYPE 301  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     13    5
  FBXO38 WILD-TYPE  301   43
                               clus
vv                              FBXO38 MUTATED FBXO38 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXO38 MUTATED     9   0   1   5
  FBXO38 WILD-TYPE 250   3  21  16
D1166V10, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              5               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"
D1166V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO38 MUTATED                                  0     2
  FBXO38 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO38 MUTATED                           1    10
  FBXO38 WILD-TYPE                        18   166
D1166V12, multiclass
                                  clus
vv                                 FBXO38 MUTATED FBXO38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(1167) Variable = STAT3 MUTATION ANALYSIS
D1167V1, survival
                 sevent
clus2               0   1
  STAT3 MUTATED     8   1
  STAT3 WILD-TYPE 269  77
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             346 
  STAT3 MUTATED STAT3 WILD-TYPE 
              1              77 
$`STAT3 MUTATED`
TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6532 
       79.69        63.98        34.98        12.16        14.50        18.25 
TCGA-D5-6536 TCGA-DM-A1HA TCGA-F4-6570 
       17.85       131.51         6.18 

$`STAT3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50        44.32       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  STAT3 MUTATED STAT3 WILD-TYPE 
           6.18            0.00 
  STAT3 MUTATED STAT3 WILD-TYPE 
         131.51          148.01 
  STAT3 MUTATED STAT3 WILD-TYPE 
         18.250          22.075 
[1] "6.2 - 131.5 (18.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1167V2, continuous
                 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      62        1       25       104         7         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  STAT3 MUTATED           0
  STAT3 WILD-TYPE         1
D1167V3, multiclass
            clus
vv           STAT3 MUTATED STAT3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  STAT3 MUTATED     0   2   6   1
  STAT3 WILD-TYPE   9  65 243  40
D1167V4, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             1              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
  STAT3 MUTATED     8   0   1
  STAT3 WILD-TYPE 212  81  65
D1167V5, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V6, binary
                 cls
clus                0   1
  STAT3 MUTATED     8   0
  STAT3 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      8    0
  STAT3 WILD-TYPE  277   48
   clus
vv  STAT3 MUTATED STAT3 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1167V7, binary
                 cls
clus                0   1
  STAT3 MUTATED     3   6
  STAT3 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      3    6
  STAT3 WILD-TYPE  167  191
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1167V8, binary
                 cls
clus                0   1
  STAT3 MUTATED     8   0
  STAT3 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      8    0
  STAT3 WILD-TYPE  292    8
     clus
vv    STAT3 MUTATED STAT3 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1167V9, binary
                 cls
clus                0   1
  STAT3 MUTATED     8   1
  STAT3 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      8    1
  STAT3 WILD-TYPE  306   47
                               clus
vv                              STAT3 MUTATED STAT3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAT3 MUTATED     8   0   0   0
  STAT3 WILD-TYPE 251   3  22  21
D1167V10, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1167V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAT3 MUTATED                                  0     0
  STAT3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAT3 MUTATED                           0     7
  STAT3 WILD-TYPE                        19   169
D1167V12, multiclass
                                  clus
vv                                 STAT3 MUTATED STAT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = ATP11C MUTATION ANALYSIS
D1168V1, survival
                  sevent
clus2                0   1
  ATP11C MUTATED    18   6
  ATP11C WILD-TYPE 259  72
  ATP11C MUTATED ATP11C WILD-TYPE 
              24              331 
  ATP11C MUTATED ATP11C WILD-TYPE 
               6               72 
$`ATP11C MUTATED`
TCGA-A6-4105 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6654 
       14.53       100.01        35.80        26.17        33.53        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3660 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3980 
       19.66        20.28        78.08        33.01        25.02        27.02 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6600 
        4.01         0.99        34.98        21.44        58.39        12.10 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-D5-6535 TCGA-DM-A1HA TCGA-DM-A28F 
       12.76        10.06        17.56        15.12       131.51        35.97 

$`ATP11C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3492 
       21.76        24.69        24.39        20.12         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       18.05        27.02        42.02        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ATP11C MUTATED ATP11C WILD-TYPE 
            0.99             0.00 
  ATP11C MUTATED ATP11C WILD-TYPE 
          131.51           148.01 
  ATP11C MUTATED ATP11C WILD-TYPE 
          24.445           22.030 
[1] "1.0 - 131.5 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1168V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP11C MUTATED         2        0        2         9         4         0
  ATP11C WILD-TYPE      62        1       24        99         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11C MUTATED           0          0          4          2        1
  ATP11C WILD-TYPE        18          6         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ATP11C MUTATED           0         0
  ATP11C WILD-TYPE        12         1
D1168V3, multiclass
            clus
vv           ATP11C MUTATED ATP11C WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               9               99
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  ATP11C MUTATED     0   3  15   7
  ATP11C WILD-TYPE   9  64 234  34
D1168V4, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  T1              0                9
  T2              3               64
  T3             15              234
  T4              7               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
  ATP11C MUTATED    18   6   1
  ATP11C WILD-TYPE 202  75  65
D1168V5, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  N0             18              202
  N1              6               75
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V6, binary
                  cls
clus                 0   1
  ATP11C MUTATED    19   1
  ATP11C WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     19    1
  ATP11C WILD-TYPE  266   47
   clus
vv  ATP11C MUTATED ATP11C WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D1168V7, binary
                  cls
clus                 0   1
  ATP11C MUTATED    12  13
  ATP11C WILD-TYPE 158 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     12   13
  ATP11C WILD-TYPE  158  184
        clus
vv       ATP11C MUTATED ATP11C WILD-TYPE
  FEMALE             12              158
  MALE               13              184
[1] 2 2
[1] FALSE
D1168V8, binary
                  cls
clus                 0   1
  ATP11C MUTATED    20   0
  ATP11C WILD-TYPE 280   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     20    0
  ATP11C WILD-TYPE  280    8
     clus
vv    ATP11C MUTATED ATP11C WILD-TYPE
  NO              20              280
  YES              0                8
[1] 2 2
[1] FALSE
D1168V9, binary
                  cls
clus                 0   1
  ATP11C MUTATED    21   4
  ATP11C WILD-TYPE 293  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     21    4
  ATP11C WILD-TYPE  293   44
                               clus
vv                              ATP11C MUTATED ATP11C WILD-TYPE
  COLON ADENOCARCINOMA                      21              293
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP11C MUTATED    12   0   0   4
  ATP11C WILD-TYPE 247   3  22  17
D1168V10, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              4               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"
D1168V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP11C MUTATED                                  0     2
  ATP11C WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP11C MUTATED                           2    13
  ATP11C WILD-TYPE                        17   163
D1168V12, multiclass
                                  clus
vv                                 ATP11C MUTATED ATP11C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        13              163
[1] 4 2
[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 = IRF6 MUTATION ANALYSIS
D1169V1, survival
                sevent
clus2              0   1
  IRF6 MUTATED     2   4
  IRF6 WILD-TYPE 275  74
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            349 
  IRF6 MUTATED IRF6 WILD-TYPE 
             4             74 
$`IRF6 MUTATED`
TCGA-AA-3715 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-A00N TCGA-D5-5538 TCGA-DM-A1DA 
       19.04         8.38        63.98         4.01        54.61         7.50 

$`IRF6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  IRF6 MUTATED IRF6 WILD-TYPE 
          4.01           0.00 
  IRF6 MUTATED IRF6 WILD-TYPE 
         63.98         148.01 
  IRF6 MUTATED IRF6 WILD-TYPE 
         13.71          22.09 
[1] "4.0 - 64.0 (13.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D1169V2, continuous
                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      64        1       24       107         7         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  IRF6 MUTATED           0
  IRF6 WILD-TYPE         1
D1169V3, multiclass
            clus
vv           IRF6 MUTATED IRF6 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  IRF6 MUTATED     0   0   5   1
  IRF6 WILD-TYPE   9  67 244  40
D1169V4, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            1             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
  IRF6 MUTATED     4   1   1
  IRF6 WILD-TYPE 216  80  65
D1169V5, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V6, binary
                cls
clus               0   1
  IRF6 MUTATED     6   0
  IRF6 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      6    0
  IRF6 WILD-TYPE  279   48
   clus
vv  IRF6 MUTATED IRF6 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1169V7, binary
                cls
clus               0   1
  IRF6 MUTATED     2   4
  IRF6 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      2    4
  IRF6 WILD-TYPE  168  193
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1169V8, binary
                cls
clus               0   1
  IRF6 MUTATED     4   0
  IRF6 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      4    0
  IRF6 WILD-TYPE  296    8
     clus
vv    IRF6 MUTATED IRF6 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1169V9, binary
                cls
clus               0   1
  IRF6 MUTATED     5   1
  IRF6 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      5    1
  IRF6 WILD-TYPE  309   47
                               clus
vv                              IRF6 MUTATED IRF6 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRF6 MUTATED     4   0   0   0
  IRF6 WILD-TYPE 255   3  22  21
D1169V10, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D1169V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRF6 MUTATED                                  0     0
  IRF6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRF6 MUTATED                           1     2
  IRF6 WILD-TYPE                        18   174
D1169V12, multiclass
                                  clus
vv                                 IRF6 MUTATED IRF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(1170) Variable = DNAJC11 MUTATION ANALYSIS
D1170V1, survival
                   sevent
clus2                 0   1
  DNAJC11 MUTATED     7   1
  DNAJC11 WILD-TYPE 270  77
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                8               347 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                1                77 
$`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        13.41 
TCGA-F4-6570 TCGA-G4-6307 
        6.18        55.04 

$`DNAJC11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
             2.01              0.00 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
            55.04            148.01 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
            18.23             22.09 
[1] "2.0 - 55.0 (18.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1170V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC11 MUTATED         1        0        0         5         0         0
  DNAJC11 WILD-TYPE      63        1       26       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC11 MUTATED           1          0          1          0        1
  DNAJC11 WILD-TYPE        17          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC11 MUTATED           0         0
  DNAJC11 WILD-TYPE        12         1
D1170V3, multiclass
            clus
vv           DNAJC11 MUTATED DNAJC11 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  DNAJC11 MUTATED     0   1   8   0
  DNAJC11 WILD-TYPE   9  66 241  41
D1170V4, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               8               241
  T4               0                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
  DNAJC11 MUTATED     6   2   1
  DNAJC11 WILD-TYPE 214  79  65
D1170V5, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  N0               6               214
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V6, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     7   1
  DNAJC11 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      7    1
  DNAJC11 WILD-TYPE  278   47
   clus
vv  DNAJC11 MUTATED DNAJC11 WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D1170V7, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     7   2
  DNAJC11 WILD-TYPE 163 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      7    2
  DNAJC11 WILD-TYPE  163  195
        clus
vv       DNAJC11 MUTATED DNAJC11 WILD-TYPE
  FEMALE               7               163
  MALE                 2               195
[1] 2 2
[1] FALSE
D1170V8, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     6   1
  DNAJC11 WILD-TYPE 294   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      6    1
  DNAJC11 WILD-TYPE  294    7
     clus
vv    DNAJC11 MUTATED DNAJC11 WILD-TYPE
  NO                6               294
  YES               1                 7
[1] 2 2
[1] FALSE
D1170V9, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     6   3
  DNAJC11 WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      6    3
  DNAJC11 WILD-TYPE  308   45
                               clus
vv                              DNAJC11 MUTATED DNAJC11 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DNAJC11 MUTATED     8   0   0   0
  DNAJC11 WILD-TYPE 251   3  22  21
D1170V10, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               0                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"
D1170V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC11 MUTATED                                  0     0
  DNAJC11 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJC11 MUTATED                           0     5
  DNAJC11 WILD-TYPE                        19   171
D1170V12, multiclass
                                  clus
vv                                 DNAJC11 MUTATED DNAJC11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1171) Variable = CLDN10 MUTATION ANALYSIS
D1171V1, survival
                  sevent
clus2                0   1
  CLDN10 MUTATED     8   3
  CLDN10 WILD-TYPE 269  75
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              11              344 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
               3               75 
$`CLDN10 MUTATED`
TCGA-AA-3715 TCGA-A6-6781 TCGA-AA-3510 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4746 
       19.04        19.66        63.98        27.09        49.41        37.02 
TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6856 
       13.41       119.70       119.93         6.18        35.31 

$`CLDN10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.35 
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-A28C TCGA-DM-A28F 
       44.32       131.51       135.65       139.17        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-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CLDN10 MUTATED CLDN10 WILD-TYPE 
            6.18             0.00 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
          119.93           148.01 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
           35.31            22.01 
[1] "6.2 - 119.9 (35.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1171V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLDN10 MUTATED         3        0        3         3         0         0
  CLDN10 WILD-TYPE      61        1       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN10 MUTATED           0          0          0          1        1
  CLDN10 WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CLDN10 MUTATED           0         0
  CLDN10 WILD-TYPE        12         1
D1171V3, multiclass
            clus
vv           CLDN10 MUTATED CLDN10 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CLDN10 MUTATED     0   3   7   1
  CLDN10 WILD-TYPE   9  64 242  40
D1171V4, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              7              242
  T4              1               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
  CLDN10 MUTATED     9   2   0
  CLDN10 WILD-TYPE 211  79  66
D1171V5, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  N0              9              211
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V6, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     8   1
  CLDN10 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      8    1
  CLDN10 WILD-TYPE  277   47
   clus
vv  CLDN10 MUTATED CLDN10 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1171V7, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     6   5
  CLDN10 WILD-TYPE 164 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      6    5
  CLDN10 WILD-TYPE  164  192
        clus
vv       CLDN10 MUTATED CLDN10 WILD-TYPE
  FEMALE              6              164
  MALE                5              192
[1] 2 2
[1] FALSE
D1171V8, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     8   0
  CLDN10 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      8    0
  CLDN10 WILD-TYPE  292    8
     clus
vv    CLDN10 MUTATED CLDN10 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1171V9, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     9   2
  CLDN10 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      9    2
  CLDN10 WILD-TYPE  305   46
                               clus
vv                              CLDN10 MUTATED CLDN10 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLDN10 MUTATED     8   0   0   0
  CLDN10 WILD-TYPE 251   3  22  21
D1171V10, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              0               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"
D1171V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLDN10 MUTATED                                  0     0
  CLDN10 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLDN10 MUTATED                           1     8
  CLDN10 WILD-TYPE                        18   168
D1171V12, multiclass
                                  clus
vv                                 CLDN10 MUTATED CLDN10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = IGSF5 MUTATION ANALYSIS
D1172V1, survival
                 sevent
clus2               0   1
  IGSF5 MUTATED     9   4
  IGSF5 WILD-TYPE 268  74
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             13             342 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
              4              74 
$`IGSF5 MUTATED`
TCGA-AA-3713 TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-3517 TCGA-AA-3542 TCGA-AA-3815 
       19.04        42.90        20.12        38.99        12.99        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 
        6.18 

$`IGSF5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       18.05        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IGSF5 MUTATED IGSF5 WILD-TYPE 
           0.99            0.00 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
          51.32          148.01 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
          19.04           22.09 
[1] "1.0 - 51.3 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1172V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGSF5 MUTATED         2        0        0         7         2         0
  IGSF5 WILD-TYPE      62        1       26       101         6         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        18          6         44         32       33        12
                 vv
clus              STAGE IVB
  IGSF5 MUTATED           0
  IGSF5 WILD-TYPE         1
D1172V3, multiclass
            clus
vv           IGSF5 MUTATED IGSF5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  IGSF5 MUTATED     0   2   9   3
  IGSF5 WILD-TYPE   9  65 240  38
D1172V4, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             3              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
  IGSF5 MUTATED    12   1   1
  IGSF5 WILD-TYPE 208  80  65
D1172V5, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V6, binary
                 cls
clus                0   1
  IGSF5 MUTATED    10   2
  IGSF5 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     10    2
  IGSF5 WILD-TYPE  275   46
   clus
vv  IGSF5 MUTATED IGSF5 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D1172V7, binary
                 cls
clus                0   1
  IGSF5 MUTATED     7   7
  IGSF5 WILD-TYPE 163 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED      7    7
  IGSF5 WILD-TYPE  163  190
        clus
vv       IGSF5 MUTATED IGSF5 WILD-TYPE
  FEMALE             7             163
  MALE               7             190
[1] 2 2
[1] FALSE
D1172V8, binary
                 cls
clus                0   1
  IGSF5 MUTATED    10   1
  IGSF5 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     10    1
  IGSF5 WILD-TYPE  290    7
     clus
vv    IGSF5 MUTATED IGSF5 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1172V9, binary
                 cls
clus                0   1
  IGSF5 MUTATED    12   2
  IGSF5 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     12    2
  IGSF5 WILD-TYPE  302   46
                               clus
vv                              IGSF5 MUTATED IGSF5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IGSF5 MUTATED    10   0   1   1
  IGSF5 WILD-TYPE 249   3  21  20
D1172V10, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             1              21
  RX             1              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"
D1172V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGSF5 MUTATED                                  0     0
  IGSF5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGSF5 MUTATED                           3     4
  IGSF5 WILD-TYPE                        16   172
D1172V12, multiclass
                                  clus
vv                                 IGSF5 MUTATED IGSF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        4             172
[1] 4 2
[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 = PCSK5 MUTATION ANALYSIS
D1173V1, survival
                 sevent
clus2               0   1
  PCSK5 MUTATED    12   2
  PCSK5 WILD-TYPE 265  76
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             14             341 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              2              76 
$`PCSK5 MUTATED`
TCGA-G4-6588 TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3866 TCGA-AA-3947 
       26.17        25.08        24.39         1.02        17.03        33.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AY-5543 TCGA-CM-6163 TCGA-D5-6532 
        4.01        34.98        18.05        33.01        14.04        18.25 
TCGA-D5-6930 TCGA-DM-A282 
       13.35       139.17 

$`PCSK5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       22.52         8.38        25.18        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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PCSK5 MUTATED PCSK5 WILD-TYPE 
           1.02            0.00 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
         139.17          148.01 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
          21.32           22.06 
[1] "1.0 - 139.2 (21.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1173V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCSK5 MUTATED         3        0        0         5         3         0
  PCSK5 WILD-TYPE      61        1       26       103         5         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        17          6         44         33       35        10
                 vv
clus              STAGE IVB
  PCSK5 MUTATED           0
  PCSK5 WILD-TYPE         1
D1173V3, multiclass
            clus
vv           PCSK5 MUTATED PCSK5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              2              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
  PCSK5 MUTATED     1   2   8   3
  PCSK5 WILD-TYPE   8  65 241  38
D1173V4, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             8             241
  T4             3              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
  PCSK5 MUTATED    11   2   1
  PCSK5 WILD-TYPE 209  79  65
D1173V5, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V6, binary
                 cls
clus                0   1
  PCSK5 MUTATED    12   2
  PCSK5 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     12    2
  PCSK5 WILD-TYPE  273   46
   clus
vv  PCSK5 MUTATED PCSK5 WILD-TYPE
  0            12             273
  1             2              46
[1] 2 2
[1] FALSE
D1173V7, binary
                 cls
clus                0   1
  PCSK5 MUTATED     9   5
  PCSK5 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      9    5
  PCSK5 WILD-TYPE  161  192
        clus
vv       PCSK5 MUTATED PCSK5 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D1173V8, binary
                 cls
clus                0   1
  PCSK5 MUTATED    11   0
  PCSK5 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     11    0
  PCSK5 WILD-TYPE  289    8
     clus
vv    PCSK5 MUTATED PCSK5 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1173V9, binary
                 cls
clus                0   1
  PCSK5 MUTATED    10   4
  PCSK5 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     10    4
  PCSK5 WILD-TYPE  304   44
                               clus
vv                              PCSK5 MUTATED PCSK5 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCSK5 MUTATED    11   0   0   0
  PCSK5 WILD-TYPE 248   3  22  21
D1173V10, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D1173V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCSK5 MUTATED                                  0     0
  PCSK5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCSK5 MUTATED                           1     7
  PCSK5 WILD-TYPE                        18   169
D1173V12, multiclass
                                  clus
vv                                 PCSK5 MUTATED PCSK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = DDHD2 MUTATION ANALYSIS
D1174V1, survival
                 sevent
clus2               0   1
  DDHD2 MUTATED     6   3
  DDHD2 WILD-TYPE 271  75
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              9             346 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              3              75 
$`DDHD2 MUTATED`
TCGA-AA-3715 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3947 TCGA-AZ-6599 TCGA-CK-5913 
       19.04        19.66        29.95        33.01         6.77        51.32 
TCGA-CM-6161 TCGA-D5-6923 TCGA-G4-6626 
       15.02        12.43        46.75 

$`DDHD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  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          22.075 
[1] "6.8 - 51.3 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1174V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDHD2 MUTATED         3        0        1         3         1         0
  DDHD2 WILD-TYPE      61        1       25       105         7         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  DDHD2 MUTATED           0
  DDHD2 WILD-TYPE         1
D1174V3, multiclass
            clus
vv           DDHD2 MUTATED DDHD2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  DDHD2 MUTATED     0   3   4   2
  DDHD2 WILD-TYPE   9  64 245  39
D1174V4, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             4             245
  T4             2              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
  DDHD2 MUTATED     8   1   0
  DDHD2 WILD-TYPE 212  80  66
D1174V5, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V6, binary
                 cls
clus                0   1
  DDHD2 MUTATED     6   0
  DDHD2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      6    0
  DDHD2 WILD-TYPE  279   48
   clus
vv  DDHD2 MUTATED DDHD2 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1174V7, binary
                 cls
clus                0   1
  DDHD2 MUTATED     4   5
  DDHD2 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      4    5
  DDHD2 WILD-TYPE  166  192
        clus
vv       DDHD2 MUTATED DDHD2 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1174V8, binary
                 cls
clus                0   1
  DDHD2 MUTATED     9   0
  DDHD2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      9    0
  DDHD2 WILD-TYPE  291    8
     clus
vv    DDHD2 MUTATED DDHD2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1174V9, binary
                 cls
clus                0   1
  DDHD2 MUTATED     6   3
  DDHD2 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      6    3
  DDHD2 WILD-TYPE  308   45
                               clus
vv                              DDHD2 MUTATED DDHD2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDHD2 MUTATED     7   0   0   1
  DDHD2 WILD-TYPE 252   3  22  20
D1174V10, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1174V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDHD2 MUTATED                                  0     0
  DDHD2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDHD2 MUTATED                           0     6
  DDHD2 WILD-TYPE                        19   170
D1174V12, multiclass
                                  clus
vv                                 DDHD2 MUTATED DDHD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = SPAG7 MUTATION ANALYSIS
D1175V1, survival
                 sevent
clus2               0   1
  SPAG7 MUTATED     2   1
  SPAG7 WILD-TYPE 275  77
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             352 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              1              77 
$`SPAG7 MUTATED`
TCGA-AY-6386 TCGA-AZ-6598 TCGA-D5-5540 
       17.82        49.41        56.09 

$`SPAG7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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          22.045 
[1] "17.8 - 56.1 (49.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1175V2, continuous
                 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      64        1       25       107         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  SPAG7 MUTATED           0
  SPAG7 WILD-TYPE         1
D1175V3, multiclass
            clus
vv           SPAG7 MUTATED SPAG7 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  SPAG7 MUTATED     0   0   3   0
  SPAG7 WILD-TYPE   9  67 246  41
D1175V4, multiclass
    clus
vv   SPAG7 MUTATED SPAG7 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             0              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
  SPAG7 MUTATED     2   1   0
  SPAG7 WILD-TYPE 218  80  66
D1175V5, multiclass
    clus
vv   SPAG7 MUTATED SPAG7 WILD-TYPE
  N0             2             218
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V6, binary
                 cls
clus                0   1
  SPAG7 MUTATED     2   0
  SPAG7 WILD-TYPE 283  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      2    0
  SPAG7 WILD-TYPE  283   48
   clus
vv  SPAG7 MUTATED SPAG7 WILD-TYPE
  0             2             283
  1             0              48
[1] 2 2
[1] FALSE
D1175V7, binary
                 cls
clus                0   1
  SPAG7 MUTATED     2   1
  SPAG7 WILD-TYPE 168 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      2    1
  SPAG7 WILD-TYPE  168  196
        clus
vv       SPAG7 MUTATED SPAG7 WILD-TYPE
  FEMALE             2             168
  MALE               1             196
[1] 2 2
[1] FALSE
D1175V8, binary
                 cls
clus                0   1
  SPAG7 MUTATED     3   0
  SPAG7 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      3    0
  SPAG7 WILD-TYPE  297    8
     clus
vv    SPAG7 MUTATED SPAG7 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1175V9, binary
                 cls
clus                0   1
  SPAG7 MUTATED     3   0
  SPAG7 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      3    0
  SPAG7 WILD-TYPE  311   48
                               clus
vv                              SPAG7 MUTATED SPAG7 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPAG7 MUTATED     2   0   0   0
  SPAG7 WILD-TYPE 257   3  22  21
D1175V10, multiclass
[1] "Remove cluster labels:" "SPAG7 MUTATED"         
clus
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              2             303 
     TCGA-A6-2677      TCGA-AA-3496      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-3527 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AD-6895      TCGA-AZ-4681      TCGA-CK-5912      TCGA-G4-6310 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-2676      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-3502      TCGA-AA-3510 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3526      TCGA-AA-3529      TCGA-AA-3532 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3544 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3553      TCGA-AA-3555 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3561      TCGA-AA-3655      TCGA-AA-3660 
"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-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3815      TCGA-AA-3818 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      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-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3955 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3975      TCGA-AA-3984      TCGA-AA-3989      TCGA-AA-3994 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00N 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00W      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-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AZ-4315      TCGA-AZ-4682      TCGA-CA-5254 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6315 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
D1175V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPAG7 MUTATED                                  0     0
  SPAG7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPAG7 MUTATED                           1     2
  SPAG7 WILD-TYPE                        18   174
D1175V12, multiclass
                                  clus
vv                                 SPAG7 MUTATED SPAG7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(1176) Variable = RARRES3 MUTATION ANALYSIS
D1176V1, survival
                   sevent
clus2                 0   1
  RARRES3 MUTATED     4   1
  RARRES3 WILD-TYPE 273  77
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               350 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                1                77 
$`RARRES3 MUTATED`
TCGA-AA-3710 TCGA-AY-6196 TCGA-CA-5797 TCGA-CM-6168 TCGA-DM-A1DA 
       26.99         0.20        12.59        12.99         7.50 

$`RARRES3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RARRES3 MUTATED RARRES3 WILD-TYPE 
              0.2               0.0 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
            26.99            148.01 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
            12.59             22.09 
[1] "0.2 - 27.0 (12.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1176V2, continuous
                   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      64        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RARRES3 MUTATED           0          0          0          2        0
  RARRES3 WILD-TYPE        18          6         44         31       35
                   vv
clus                STAGE IVA STAGE IVB
  RARRES3 MUTATED           0         0
  RARRES3 WILD-TYPE        12         1
D1176V3, multiclass
            clus
vv           RARRES3 MUTATED RARRES3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  RARRES3 MUTATED     0   0   5   0
  RARRES3 WILD-TYPE   9  67 244  41
D1176V4, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  RARRES3 MUTATED     3   0   2
  RARRES3 WILD-TYPE 217  81  64
D1176V5, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  N0               3               217
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V6, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     4   0
  RARRES3 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      4    0
  RARRES3 WILD-TYPE  281   48
   clus
vv  RARRES3 MUTATED RARRES3 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1176V7, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     3   2
  RARRES3 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      3    2
  RARRES3 WILD-TYPE  167  195
        clus
vv       RARRES3 MUTATED RARRES3 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1176V8, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     3   0
  RARRES3 WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      3    0
  RARRES3 WILD-TYPE  297    8
     clus
vv    RARRES3 MUTATED RARRES3 WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D1176V9, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     4   1
  RARRES3 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      4    1
  RARRES3 WILD-TYPE  310   47
                               clus
vv                              RARRES3 MUTATED RARRES3 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RARRES3 MUTATED     4   0   0   0
  RARRES3 WILD-TYPE 255   3  22  21
D1176V10, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1176V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RARRES3 MUTATED                                  0     1
  RARRES3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RARRES3 MUTATED                           1     2
  RARRES3 WILD-TYPE                        18   174
D1176V12, multiclass
                                  clus
vv                                 RARRES3 MUTATED RARRES3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          2               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(1177) Variable = TRAF3IP1 MUTATION ANALYSIS
D1177V1, survival
                    sevent
clus2                  0   1
  TRAF3IP1 MUTATED     5   1
  TRAF3IP1 WILD-TYPE 272  77
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 6                349 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 1                 77 
$`TRAF3IP1 MUTATED`
TCGA-AD-6964 TCGA-A6-6781 TCGA-AA-A010 TCGA-CA-6717 TCGA-D5-5539 TCGA-F4-6856 
       10.88        19.66        34.98        12.76        19.59        35.31 

$`TRAF3IP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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        54.61        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
             10.88               0.00 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
             35.31             148.01 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
            19.625             22.090 
[1] "10.9 - 35.3 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1177V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAF3IP1 MUTATED         1        0        0         1         1         0
  TRAF3IP1 WILD-TYPE      63        1       26       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAF3IP1 MUTATED           0          1          0          1        0
  TRAF3IP1 WILD-TYPE        18          5         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  TRAF3IP1 MUTATED           0         0
  TRAF3IP1 WILD-TYPE        12         1
D1177V3, multiclass
            clus
vv           TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 1                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  TRAF3IP1 MUTATED     0   1   2   3
  TRAF3IP1 WILD-TYPE   9  66 247  38
D1177V4, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                2                247
  T4                3                 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
  TRAF3IP1 MUTATED     3   2   1
  TRAF3IP1 WILD-TYPE 217  79  65
D1177V5, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  N0                3                217
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V6, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     4   0
  TRAF3IP1 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      4    0
  TRAF3IP1 WILD-TYPE  281   48
   clus
vv  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D1177V7, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     1   5
  TRAF3IP1 WILD-TYPE 169 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      1    5
  TRAF3IP1 WILD-TYPE  169  192
        clus
vv       TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  FEMALE                1                169
  MALE                  5                192
[1] 2 2
[1] FALSE
D1177V8, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     6   0
  TRAF3IP1 WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      6    0
  TRAF3IP1 WILD-TYPE  294    8
     clus
vv    TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D1177V9, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     2   4
  TRAF3IP1 WILD-TYPE 312  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      2    4
  TRAF3IP1 WILD-TYPE  312   44
                               clus
vv                              TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  COLON ADENOCARCINOMA                         2                312
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TRAF3IP1 MUTATED     4   0   0   1
  TRAF3IP1 WILD-TYPE 255   3  22  20
D1177V10, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  R0                4                255
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1177V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAF3IP1 MUTATED                                  0     1
  TRAF3IP1 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TRAF3IP1 MUTATED                           0     4
  TRAF3IP1 WILD-TYPE                        19   172
D1177V12, multiclass
                                  clus
vv                                 TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = C14ORF50 MUTATION ANALYSIS
D1178V1, survival
                    sevent
clus2                  0   1
  C14ORF50 MUTATED     3   2
  C14ORF50 WILD-TYPE 274  76
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 5                350 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 2                 76 
$`C14ORF50 MUTATED`
TCGA-AA-3543 TCGA-AA-3492 TCGA-AA-3837 TCGA-AA-3994 TCGA-CK-5916 
        0.99         3.02        38.99        27.02        21.14 

$`C14ORF50 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        13.94        38.04        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
              0.99               0.00 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
             38.99             148.01 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
            21.140             22.075 
[1] "1.0 - 39.0 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.9"
D1178V2, continuous
                    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      62        1       25       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF50 MUTATED           0          0          1          0        0
  C14ORF50 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF50 MUTATED           0         0
  C14ORF50 WILD-TYPE        12         1
D1178V3, multiclass
            clus
vv           C14ORF50 MUTATED C14ORF50 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 1                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C14ORF50 MUTATED     1   1   3   1
  C14ORF50 WILD-TYPE   8  66 246  40
D1178V4, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  T1                1                  8
  T2                1                 66
  T3                3                246
  T4                1                 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
  C14ORF50 MUTATED     5   1   0
  C14ORF50 WILD-TYPE 215  80  66
D1178V5, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  N0                5                215
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V6, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     5   0
  C14ORF50 WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      5    0
  C14ORF50 WILD-TYPE  280   48
   clus
vv  C14ORF50 MUTATED C14ORF50 WILD-TYPE
  0                5                280
  1                0                 48
[1] 2 2
[1] FALSE
D1178V7, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     3   3
  C14ORF50 WILD-TYPE 167 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      3    3
  C14ORF50 WILD-TYPE  167  194
        clus
vv       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  FEMALE                3                167
  MALE                  3                194
[1] 2 2
[1] FALSE
D1178V8, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     5   0
  C14ORF50 WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      5    0
  C14ORF50 WILD-TYPE  295    8
     clus
vv    C14ORF50 MUTATED C14ORF50 WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D1178V9, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     3   3
  C14ORF50 WILD-TYPE 311  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      3    3
  C14ORF50 WILD-TYPE  311   45
                               clus
vv                              C14ORF50 MUTATED C14ORF50 WILD-TYPE
  COLON ADENOCARCINOMA                         3                311
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C14ORF50 MUTATED     4   0   0   2
  C14ORF50 WILD-TYPE 255   3  22  19
D1178V10, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  R0                4                255
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1178V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF50 MUTATED                                  0     0
  C14ORF50 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF50 MUTATED                           0     2
  C14ORF50 WILD-TYPE                        19   174
D1178V12, multiclass
[1] "Remove cluster labels:" "C14ORF50 MUTATED"      
clus
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 

Clustering(1179) Variable = ALAS1 MUTATION ANALYSIS
D1179V1, survival
                 sevent
clus2               0   1
  ALAS1 MUTATED     6   1
  ALAS1 WILD-TYPE 271  77
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              7             348 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              1              77 
$`ALAS1 MUTATED`
TCGA-G4-6588 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-CK-5913 TCGA-D5-5538 
       26.17         1.02        25.02        34.98        51.32        54.61 
TCGA-D5-6930 
       13.35 

$`ALAS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ALAS1 MUTATED ALAS1 WILD-TYPE 
           1.02            0.00 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
          54.61          148.01 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
          26.17           22.01 
[1] "1.0 - 54.6 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1179V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALAS1 MUTATED         2        0        1         3         1         0
  ALAS1 WILD-TYPE      62        1       25       105         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  ALAS1 MUTATED           0
  ALAS1 WILD-TYPE         1
D1179V3, multiclass
            clus
vv           ALAS1 MUTATED ALAS1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ALAS1 MUTATED     0   3   4   2
  ALAS1 WILD-TYPE   9  64 245  39
D1179V4, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             4             245
  T4             2              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
  ALAS1 MUTATED     8   1   0
  ALAS1 WILD-TYPE 212  80  66
D1179V5, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V6, binary
                 cls
clus                0   1
  ALAS1 MUTATED     6   0
  ALAS1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      6    0
  ALAS1 WILD-TYPE  279   48
   clus
vv  ALAS1 MUTATED ALAS1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1179V7, binary
                 cls
clus                0   1
  ALAS1 MUTATED     6   3
  ALAS1 WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      6    3
  ALAS1 WILD-TYPE  164  194
        clus
vv       ALAS1 MUTATED ALAS1 WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D1179V8, binary
                 cls
clus                0   1
  ALAS1 MUTATED     7   0
  ALAS1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      7    0
  ALAS1 WILD-TYPE  293    8
     clus
vv    ALAS1 MUTATED ALAS1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1179V9, binary
                 cls
clus                0   1
  ALAS1 MUTATED     7   2
  ALAS1 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      7    2
  ALAS1 WILD-TYPE  307   46
                               clus
vv                              ALAS1 MUTATED ALAS1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALAS1 MUTATED     6   0   0   2
  ALAS1 WILD-TYPE 253   3  22  19
D1179V10, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1179V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALAS1 MUTATED                                  0     0
  ALAS1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALAS1 MUTATED                           0     5
  ALAS1 WILD-TYPE                        19   171
D1179V12, multiclass
                                  clus
vv                                 ALAS1 MUTATED ALAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = FAM151A MUTATION ANALYSIS
D1180V1, survival
                   sevent
clus2                 0   1
  FAM151A MUTATED     4   2
  FAM151A WILD-TYPE 273  76
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               349 
  FAM151A MUTATED FAM151A WILD-TYPE 
                2                76 
$`FAM151A MUTATED`
TCGA-AZ-6601 TCGA-A6-6780 TCGA-AA-3811 TCGA-CA-6717 TCGA-D5-6540 TCGA-F4-6856 
      100.01        20.12        10.06        12.76        16.14        35.31 

$`FAM151A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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             22.09 
[1] "10.1 - 100.0 (18.1)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.3"
D1180V2, continuous
                   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      62        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM151A MUTATED           1          0          0          0        0
  FAM151A WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM151A MUTATED           0         0
  FAM151A WILD-TYPE        12         1
D1180V3, multiclass
            clus
vv           FAM151A MUTATED FAM151A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM151A MUTATED     0   2   4   0
  FAM151A WILD-TYPE   9  65 245  41
D1180V4, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               4               245
  T4               0                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
  FAM151A MUTATED     5   0   1
  FAM151A WILD-TYPE 215  81  65
D1180V5, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  N0               5               215
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V6, binary
                   cls
clus                  0   1
  FAM151A MUTATED     5   0
  FAM151A WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      5    0
  FAM151A WILD-TYPE  280   48
   clus
vv  FAM151A MUTATED FAM151A WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1180V7, binary
                   cls
clus                  0   1
  FAM151A MUTATED     1   5
  FAM151A WILD-TYPE 169 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      1    5
  FAM151A WILD-TYPE  169  192
        clus
vv       FAM151A MUTATED FAM151A WILD-TYPE
  FEMALE               1               169
  MALE                 5               192
[1] 2 2
[1] FALSE
D1180V8, binary
                   cls
clus                  0   1
  FAM151A MUTATED     6   0
  FAM151A WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      6    0
  FAM151A WILD-TYPE  294    8
     clus
vv    FAM151A MUTATED FAM151A WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1180V9, binary
                   cls
clus                  0   1
  FAM151A MUTATED     2   4
  FAM151A WILD-TYPE 312  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      2    4
  FAM151A WILD-TYPE  312   44
                               clus
vv                              FAM151A MUTATED FAM151A WILD-TYPE
  COLON ADENOCARCINOMA                        2               312
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM151A MUTATED     3   0   0   1
  FAM151A WILD-TYPE 256   3  22  20
D1180V10, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               1                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"
D1180V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM151A MUTATED                                  0     1
  FAM151A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM151A MUTATED                           0     4
  FAM151A WILD-TYPE                        19   172
D1180V12, multiclass
                                  clus
vv                                 FAM151A MUTATED FAM151A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = SYNGR4 MUTATION ANALYSIS
D1181V1, survival
                  sevent
clus2                0   1
  SYNGR4 MUTATED     4   1
  SYNGR4 WILD-TYPE 273  77
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               5              350 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               1               77 
$`SYNGR4 MUTATED`
TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 TCGA-D5-5539 
       19.66         4.01        12.16        58.39        19.59 

$`SYNGR4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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        54.61        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
            4.01             0.00 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
           58.39           148.01 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
           19.59            22.09 
[1] "4.0 - 58.4 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1181V2, continuous
                  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      63        1       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNGR4 MUTATED           0          1          0          1        0
  SYNGR4 WILD-TYPE        18          5         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  SYNGR4 MUTATED           0         0
  SYNGR4 WILD-TYPE        12         1
D1181V3, multiclass
            clus
vv           SYNGR4 MUTATED SYNGR4 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  SYNGR4 MUTATED     0   1   3   2
  SYNGR4 WILD-TYPE   9  66 246  39
D1181V4, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              3              246
  T4              2               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
  SYNGR4 MUTATED     4   2   0
  SYNGR4 WILD-TYPE 216  79  66
D1181V5, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  N0              4              216
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V6, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     4   0
  SYNGR4 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      4    0
  SYNGR4 WILD-TYPE  281   48
   clus
vv  SYNGR4 MUTATED SYNGR4 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1181V7, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     0   6
  SYNGR4 WILD-TYPE 170 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      0    6
  SYNGR4 WILD-TYPE  170  191
        clus
vv       SYNGR4 MUTATED SYNGR4 WILD-TYPE
  FEMALE              0              170
  MALE                6              191
[1] 2 2
[1] FALSE
D1181V8, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     4   0
  SYNGR4 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      4    0
  SYNGR4 WILD-TYPE  296    8
     clus
vv    SYNGR4 MUTATED SYNGR4 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1181V9, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     2   4
  SYNGR4 WILD-TYPE 312  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      2    4
  SYNGR4 WILD-TYPE  312   44
                               clus
vv                              SYNGR4 MUTATED SYNGR4 WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SYNGR4 MUTATED     6   0   0   0
  SYNGR4 WILD-TYPE 253   3  22  21
D1181V10, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1181V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNGR4 MUTATED                                  0     0
  SYNGR4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SYNGR4 MUTATED                           0     4
  SYNGR4 WILD-TYPE                        19   172
D1181V12, multiclass
                                  clus
vv                                 SYNGR4 MUTATED SYNGR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = ADH7 MUTATION ANALYSIS
D1182V1, survival
                sevent
clus2              0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 270  78
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            348 
  ADH7 MUTATED ADH7 WILD-TYPE 
             0             78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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         22.045 
[1] "12.2 - 58.4 (29.9)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1182V2, continuous
                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      63        1       26       103         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ADH7 MUTATED           0
  ADH7 WILD-TYPE         1
D1182V3, multiclass
            clus
vv           ADH7 MUTATED ADH7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ADH7 MUTATED     0   1   5   1
  ADH7 WILD-TYPE   9  66 244  40
D1182V4, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            1             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
  ADH7 MUTATED     7   0   0
  ADH7 WILD-TYPE 213  81  66
D1182V5, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  N0            7            213
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V6, binary
                cls
clus               0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      7    0
  ADH7 WILD-TYPE  278   48
   clus
vv  ADH7 MUTATED ADH7 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1182V7, binary
                cls
clus               0   1
  ADH7 MUTATED     4   3
  ADH7 WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      4    3
  ADH7 WILD-TYPE  166  194
        clus
vv       ADH7 MUTATED ADH7 WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D1182V8, binary
                cls
clus               0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      7    0
  ADH7 WILD-TYPE  293    8
     clus
vv    ADH7 MUTATED ADH7 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1182V9, binary
                cls
clus               0   1
  ADH7 MUTATED     6   1
  ADH7 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      6    1
  ADH7 WILD-TYPE  308   47
                               clus
vv                              ADH7 MUTATED ADH7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ADH7 MUTATED     6   0   0   1
  ADH7 WILD-TYPE 253   3  22  20
D1182V10, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D1182V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADH7 MUTATED                                  0     1
  ADH7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ADH7 MUTATED                           0     3
  ADH7 WILD-TYPE                        19   173
D1182V12, multiclass
                                  clus
vv                                 ADH7 MUTATED ADH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = KLF3 MUTATION ANALYSIS
D1183V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED     4   1
  KLF3 WILD-TYPE 273  77
  KLF3 MUTATED KLF3 WILD-TYPE 
             5            350 
  KLF3 MUTATED KLF3 WILD-TYPE 
             1             77 
$`KLF3 MUTATED`
TCGA-AD-6895 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3930 TCGA-AZ-4315 
       25.08        22.06         6.97         2.01        58.39 

$`KLF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       53.00        17.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KLF3 MUTATED KLF3 WILD-TYPE 
          2.01           0.00 
  KLF3 MUTATED KLF3 WILD-TYPE 
         58.39         148.01 
  KLF3 MUTATED KLF3 WILD-TYPE 
         22.06          22.06 
[1] "2.0 - 58.4 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1183V2, continuous
                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      64        1       25       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF3 MUTATED           0          0          1          0        1         0
  KLF3 WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  KLF3 MUTATED           0
  KLF3 WILD-TYPE         1
D1183V3, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  KLF3 MUTATED     0   0   6   1
  KLF3 WILD-TYPE   9  67 243  40
D1183V4, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            1             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
  KLF3 MUTATED     5   1   1
  KLF3 WILD-TYPE 215  80  65
D1183V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V6, binary
                cls
clus               0   1
  KLF3 MUTATED     5   1
  KLF3 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      5    1
  KLF3 WILD-TYPE  280   47
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D1183V7, binary
                cls
clus               0   1
  KLF3 MUTATED     3   4
  KLF3 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      3    4
  KLF3 WILD-TYPE  167  193
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D1183V8, binary
                cls
clus               0   1
  KLF3 MUTATED     5   0
  KLF3 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      5    0
  KLF3 WILD-TYPE  295    8
     clus
vv    KLF3 MUTATED KLF3 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1183V9, binary
                cls
clus               0   1
  KLF3 MUTATED     7   0
  KLF3 WILD-TYPE 307  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      7    0
  KLF3 WILD-TYPE  307   48
                               clus
vv                              KLF3 MUTATED KLF3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLF3 MUTATED     5   0   1   1
  KLF3 WILD-TYPE 254   3  21  20
D1183V10, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            1             21
  RX            1             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"
D1183V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF3 MUTATED                                  0     0
  KLF3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLF3 MUTATED                           0     4
  KLF3 WILD-TYPE                        19   172
D1183V12, multiclass
                                  clus
vv                                 KLF3 MUTATED KLF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = ARHGAP28 MUTATION ANALYSIS
D1184V1, survival
                    sevent
clus2                  0   1
  ARHGAP28 MUTATED    11   2
  ARHGAP28 WILD-TYPE 266  76
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                13                342 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                 2                 76 
$`ARHGAP28 MUTATED`
TCGA-AA-3554 TCGA-AA-3715 TCGA-G4-6628 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3947 
       17.95        19.04        79.69        24.39        19.66        33.01 
TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-4743 TCGA-CM-5861 
       26.01        18.05        34.98        83.24        23.05        15.02 
TCGA-CM-6674 
       12.95 

$`ARHGAP28 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 
       27.02        18.05        31.00         2.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
             12.95               0.00 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
             83.24             148.01 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
            23.050             22.045 
[1] "12.9 - 83.2 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1184V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP28 MUTATED         2        0        1         5         2         0
  ARHGAP28 WILD-TYPE      62        1       25       103         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP28 MUTATED           0          0          2          1        0
  ARHGAP28 WILD-TYPE        18          6         42         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP28 MUTATED           0         0
  ARHGAP28 WILD-TYPE        12         1
D1184V3, multiclass
            clus
vv           ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  ARHGAP28 MUTATED     0   2   7   4
  ARHGAP28 WILD-TYPE   9  65 242  37
D1184V4, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                7                242
  T4                4                 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
  ARHGAP28 MUTATED    10   3   0
  ARHGAP28 WILD-TYPE 210  78  66
D1184V5, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  N0               10                210
  N1                3                 78
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V6, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED    12   0
  ARHGAP28 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED     12    0
  ARHGAP28 WILD-TYPE  273   48
   clus
vv  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  0               12                273
  1                0                 48
[1] 2 2
[1] FALSE
D1184V7, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED     5   8
  ARHGAP28 WILD-TYPE 165 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED      5    8
  ARHGAP28 WILD-TYPE  165  189
        clus
vv       ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  FEMALE                5                165
  MALE                  8                189
[1] 2 2
[1] FALSE
D1184V8, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED    13   0
  ARHGAP28 WILD-TYPE 287   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED     13    0
  ARHGAP28 WILD-TYPE  287    8
     clus
vv    ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  NO                13                287
  YES                0                  8
[1] 2 2
[1] FALSE
D1184V9, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED     9   4
  ARHGAP28 WILD-TYPE 305  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED      9    4
  ARHGAP28 WILD-TYPE  305   44
                               clus
vv                              ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP28 MUTATED    12   0   0   0
  ARHGAP28 WILD-TYPE 247   3  22  21
D1184V10, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  R0               12                247
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1184V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP28 MUTATED                                  0     1
  ARHGAP28 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP28 MUTATED                           0     6
  ARHGAP28 WILD-TYPE                        19   170
D1184V12, multiclass
                                  clus
vv                                 ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1185) Variable = SLC38A5 MUTATION ANALYSIS
D1185V1, survival
                   sevent
clus2                 0   1
  SLC38A5 MUTATED     5   1
  SLC38A5 WILD-TYPE 272  77
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                6               349 
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.90        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        85.45        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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             22.09 
[1] "5.2 - 51.3 (18.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1185V2, continuous
                   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      64        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A5 MUTATED           0          0          2          1        0
  SLC38A5 WILD-TYPE        18          6         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC38A5 MUTATED           0         0
  SLC38A5 WILD-TYPE        12         1
D1185V3, multiclass
            clus
vv           SLC38A5 MUTATED SLC38A5 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC38A5 MUTATED     0   0   4   2
  SLC38A5 WILD-TYPE   9  67 245  39
D1185V4, multiclass
    clus
vv   SLC38A5 MUTATED SLC38A5 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               4               245
  T4               2                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
  SLC38A5 MUTATED     3   2   1
  SLC38A5 WILD-TYPE 217  79  65
D1185V5, multiclass
    clus
vv   SLC38A5 MUTATED SLC38A5 WILD-TYPE
  N0               3               217
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V6, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   0
  SLC38A5 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    0
  SLC38A5 WILD-TYPE  280   48
   clus
vv  SLC38A5 MUTATED SLC38A5 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1185V7, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   1
  SLC38A5 WILD-TYPE 165 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    1
  SLC38A5 WILD-TYPE  165  196
        clus
vv       SLC38A5 MUTATED SLC38A5 WILD-TYPE
  FEMALE               5               165
  MALE                 1               196
[1] 2 2
[1] FALSE
D1185V8, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   0
  SLC38A5 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    0
  SLC38A5 WILD-TYPE  295    8
     clus
vv    SLC38A5 MUTATED SLC38A5 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1185V9, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   1
  SLC38A5 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    1
  SLC38A5 WILD-TYPE  309   47
                               clus
vv                              SLC38A5 MUTATED SLC38A5 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC38A5 MUTATED     3   0   0   2
  SLC38A5 WILD-TYPE 256   3  22  19
D1185V10, multiclass
    clus
vv   SLC38A5 MUTATED SLC38A5 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               2                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"
D1185V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC38A5 MUTATED                                  0     0
  SLC38A5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC38A5 MUTATED                           0     6
  SLC38A5 WILD-TYPE                        19   170
D1185V12, multiclass
                                  clus
vv                                 SLC38A5 MUTATED SLC38A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = HIST1H1A MUTATION ANALYSIS
D1186V1, survival
                    sevent
clus2                  0   1
  HIST1H1A MUTATED     6   3
  HIST1H1A WILD-TYPE 271  75
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                346 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 3                 75 
$`HIST1H1A MUTATED`
TCGA-AA-A024 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3710 
       39.06         1.94        26.17         8.38         3.02        26.99 
TCGA-AA-A01R TCGA-AZ-4315 TCGA-F4-6855 
       35.01        58.39        47.41 

$`HIST1H1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
              1.94               0.00 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
             58.39             148.01 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
             26.99              22.01 
[1] "1.9 - 58.4 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1186V2, continuous
                    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      64        1       24       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1A MUTATED           1          1          0          0        0
  HIST1H1A WILD-TYPE        17          5         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1A MUTATED           0         0
  HIST1H1A WILD-TYPE        12         1
D1186V3, multiclass
            clus
vv           HIST1H1A MUTATED HIST1H1A WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 5                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                1                  5
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  HIST1H1A MUTATED     0   1   8   0
  HIST1H1A WILD-TYPE   9  66 241  41
D1186V4, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                8                241
  T4                0                 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
  HIST1H1A MUTATED     7   1   1
  HIST1H1A WILD-TYPE 213  80  65
D1186V5, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  N0                7                213
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V6, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     9   0
  HIST1H1A WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      9    0
  HIST1H1A WILD-TYPE  276   48
   clus
vv  HIST1H1A MUTATED HIST1H1A WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D1186V7, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     5   4
  HIST1H1A WILD-TYPE 165 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      5    4
  HIST1H1A WILD-TYPE  165  193
        clus
vv       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  FEMALE                5                165
  MALE                  4                193
[1] 2 2
[1] FALSE
D1186V8, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     8   1
  HIST1H1A WILD-TYPE 292   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      8    1
  HIST1H1A WILD-TYPE  292    7
     clus
vv    HIST1H1A MUTATED HIST1H1A WILD-TYPE
  NO                 8                292
  YES                1                  7
[1] 2 2
[1] FALSE
D1186V9, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     7   2
  HIST1H1A WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      7    2
  HIST1H1A WILD-TYPE  307   46
                               clus
vv                              HIST1H1A MUTATED HIST1H1A WILD-TYPE
  COLON ADENOCARCINOMA                         7                307
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1A MUTATED     7   0   0   0
  HIST1H1A WILD-TYPE 252   3  22  21
D1186V10, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1186V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1A MUTATED                                  0     0
  HIST1H1A WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1A MUTATED                           1     4
  HIST1H1A WILD-TYPE                        18   172
D1186V12, multiclass
                                  clus
vv                                 HIST1H1A MUTATED HIST1H1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                172
[1] 4 2
[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 = OR7D4 MUTATION ANALYSIS
D1187V1, survival
                 sevent
clus2               0   1
  OR7D4 MUTATED     6   2
  OR7D4 WILD-TYPE 271  76
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              8             347 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              2              76 
$`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 
      139.17        31.96 

$`OR7D4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04         3.02        35.01         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
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-A28F TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR7D4 MUTATED OR7D4 WILD-TYPE 
              0               0 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
         139.17          148.01 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
          31.99           22.03 
[1] "0.0 - 139.2 (32.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1187V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR7D4 MUTATED         1        0        2         5         0         0
  OR7D4 WILD-TYPE      63        1       24       103         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  OR7D4 MUTATED           0
  OR7D4 WILD-TYPE         1
D1187V3, multiclass
            clus
vv           OR7D4 MUTATED OR7D4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR7D4 MUTATED     0   1   7   1
  OR7D4 WILD-TYPE   9  66 242  40
D1187V4, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             1              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
  OR7D4 MUTATED     8   1   0
  OR7D4 WILD-TYPE 212  80  66
D1187V5, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V6, binary
                 cls
clus                0   1
  OR7D4 MUTATED     7   0
  OR7D4 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      7    0
  OR7D4 WILD-TYPE  278   48
   clus
vv  OR7D4 MUTATED OR7D4 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1187V7, binary
                 cls
clus                0   1
  OR7D4 MUTATED     4   5
  OR7D4 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      4    5
  OR7D4 WILD-TYPE  166  192
        clus
vv       OR7D4 MUTATED OR7D4 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1187V8, binary
                 cls
clus                0   1
  OR7D4 MUTATED     6   0
  OR7D4 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      6    0
  OR7D4 WILD-TYPE  294    8
     clus
vv    OR7D4 MUTATED OR7D4 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1187V9, binary
                 cls
clus                0   1
  OR7D4 MUTATED     8   1
  OR7D4 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      8    1
  OR7D4 WILD-TYPE  306   47
                               clus
vv                              OR7D4 MUTATED OR7D4 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR7D4 MUTATED     5   0   0   3
  OR7D4 WILD-TYPE 254   3  22  18
D1187V10, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             3              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"
D1187V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR7D4 MUTATED                                  0     1
  OR7D4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR7D4 MUTATED                           0     5
  OR7D4 WILD-TYPE                        19   171
D1187V12, multiclass
                                  clus
vv                                 OR7D4 MUTATED OR7D4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = OSR1 MUTATION ANALYSIS
D1188V1, survival
                sevent
clus2              0   1
  OSR1 MUTATED     3   1
  OSR1 WILD-TYPE 274  77
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            351 
  OSR1 MUTATED OSR1 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       61.91        36.00        13.78 

  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          22.03 
[1] "15.0 - 133.2 (66.1)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2"  
D1188V2, continuous
                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      64        1       26       107         8         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        17          6         42         33       35        12
                vv
clus             STAGE IVB
  OSR1 MUTATED           0
  OSR1 WILD-TYPE         1
D1188V3, multiclass
            clus
vv           OSR1 MUTATED OSR1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  OSR1 MUTATED     0   0   4   0
  OSR1 WILD-TYPE   9  67 245  41
D1188V4, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            4            245
  T4            0             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
  OSR1 MUTATED     1   3   0
  OSR1 WILD-TYPE 219  78  66
D1188V5, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  N0            1            219
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V6, binary
                cls
clus               0   1
  OSR1 MUTATED     4   0
  OSR1 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      4    0
  OSR1 WILD-TYPE  281   48
   clus
vv  OSR1 MUTATED OSR1 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1188V7, binary
                cls
clus               0   1
  OSR1 MUTATED     3   1
  OSR1 WILD-TYPE 167 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      3    1
  OSR1 WILD-TYPE  167  196
        clus
vv       OSR1 MUTATED OSR1 WILD-TYPE
  FEMALE            3            167
  MALE              1            196
[1] 2 2
[1] FALSE
D1188V8, binary
                cls
clus               0   1
  OSR1 MUTATED     4   0
  OSR1 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      4    0
  OSR1 WILD-TYPE  296    8
     clus
vv    OSR1 MUTATED OSR1 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1188V9, binary
                cls
clus               0   1
  OSR1 MUTATED     2   2
  OSR1 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      2    2
  OSR1 WILD-TYPE  312   46
                               clus
vv                              OSR1 MUTATED OSR1 WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OSR1 MUTATED     3   1   0   0
  OSR1 WILD-TYPE 256   2  22  21
D1188V10, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  R0            3            256
  R1            1              2
  R2            0             22
  RX            0             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"
D1188V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSR1 MUTATED                                  0     0
  OSR1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OSR1 MUTATED                           1     3
  OSR1 WILD-TYPE                        18   173
D1188V12, multiclass
                                  clus
vv                                 OSR1 MUTATED OSR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = MAP2 MUTATION ANALYSIS
D1189V1, survival
                sevent
clus2              0   1
  MAP2 MUTATED    26   9
  MAP2 WILD-TYPE 251  69
  MAP2 MUTATED MAP2 WILD-TYPE 
            35            320 
  MAP2 MUTATED MAP2 WILD-TYPE 
             9             69 
$`MAP2 MUTATED`
TCGA-AA-3525 TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-2671 TCGA-A6-2672 
        8.05        24.00        10.88       100.01        43.76        46.65 
TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3518 
       29.19        22.06        19.66         3.02        63.98         1.02 
TCGA-AA-3663 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3852 TCGA-AA-3949 TCGA-AA-3980 
        6.97         0.99        25.02         0.00        26.01        27.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-5900 TCGA-AD-6965 
       18.05         4.01        34.98        37.02        12.16        26.47 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-6167 TCGA-CM-6171 
       58.39        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 
       11.08        56.09         6.18        35.31        13.78 

$`MAP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       79.69        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        33.04         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
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        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
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-G4-6626 
       36.00        46.75 

  MAP2 MUTATED MAP2 WILD-TYPE 
             0              0 
  MAP2 MUTATED MAP2 WILD-TYPE 
        100.01         148.01 
  MAP2 MUTATED MAP2 WILD-TYPE 
         19.66          22.09 
[1] "0.0 - 100.0 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1189V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP2 MUTATED         5        1        5        12         2         0
  MAP2 WILD-TYPE      59        0       21        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP2 MUTATED           0          0          5          4        1         0
  MAP2 WILD-TYPE        18          6         39         29       34        12
                vv
clus             STAGE IVB
  MAP2 MUTATED           0
  MAP2 WILD-TYPE         1
D1189V3, multiclass
            clus
vv           MAP2 MUTATED MAP2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              1              0
  STAGE II              5             21
  STAGE IIA            12             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            5             39
  STAGE IIIC            4             29
  STAGE IV              1             34
  STAGE IVA             0             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
  MAP2 MUTATED     0   5  24   6
  MAP2 WILD-TYPE   9  62 225  35
D1189V4, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  T1            0              9
  T2            5             62
  T3           24            225
  T4            6             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
  MAP2 MUTATED    25   6   5
  MAP2 WILD-TYPE 195  75  61
D1189V5, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  N0           25            195
  N1            6             75
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V6, binary
                cls
clus               0   1
  MAP2 MUTATED    31   1
  MAP2 WILD-TYPE 254  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     31    1
  MAP2 WILD-TYPE  254   47
   clus
vv  MAP2 MUTATED MAP2 WILD-TYPE
  0           31            254
  1            1             47
[1] 2 2
[1] FALSE
D1189V7, binary
                cls
clus               0   1
  MAP2 MUTATED    15  21
  MAP2 WILD-TYPE 155 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     15   21
  MAP2 WILD-TYPE  155  176
        clus
vv       MAP2 MUTATED MAP2 WILD-TYPE
  FEMALE           15            155
  MALE             21            176
[1] 2 2
[1] FALSE
D1189V8, binary
                cls
clus               0   1
  MAP2 MUTATED    31   0
  MAP2 WILD-TYPE 269   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     31    0
  MAP2 WILD-TYPE  269    8
     clus
vv    MAP2 MUTATED MAP2 WILD-TYPE
  NO            31            269
  YES            0              8
[1] 2 2
[1] FALSE
D1189V9, binary
                cls
clus               0   1
  MAP2 MUTATED    26  10
  MAP2 WILD-TYPE 288  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     26   10
  MAP2 WILD-TYPE  288   38
                               clus
vv                              MAP2 MUTATED MAP2 WILD-TYPE
  COLON ADENOCARCINOMA                    26            288
  COLON MUCINOUS ADENOCARCINOMA           10             38
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAP2 MUTATED    28   2   0   2
  MAP2 WILD-TYPE 231   1  22  19
D1189V10, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  R0           28            231
  R1            2              1
  R2            0             22
  RX            2             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"
D1189V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP2 MUTATED                                  0     2
  MAP2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAP2 MUTATED                           4    14
  MAP2 WILD-TYPE                        15   162
D1189V12, multiclass
                                  clus
vv                                 MAP2 MUTATED MAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      14            162
[1] 4 2
[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 = UPF2 MUTATION ANALYSIS
D1190V1, survival
                sevent
clus2              0   1
  UPF2 MUTATED    10   5
  UPF2 WILD-TYPE 267  73
  UPF2 MUTATED UPF2 WILD-TYPE 
            15            340 
  UPF2 MUTATED UPF2 WILD-TYPE 
             5             73 
$`UPF2 MUTATED`
TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3713 TCGA-AZ-6601 TCGA-A6-2676 TCGA-A6-5661 
        8.05         6.05        19.04       100.01        42.90        33.53 
TCGA-A6-5665 TCGA-AA-3818 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02Y TCGA-AZ-4315 
       22.06         0.99        25.02         4.01        39.98        58.39 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6162 
       12.76        21.14        12.00 

$`UPF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        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-A6-5662 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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  UPF2 MUTATED UPF2 WILD-TYPE 
          0.99           0.00 
  UPF2 MUTATED UPF2 WILD-TYPE 
        100.01         148.01 
  UPF2 MUTATED UPF2 WILD-TYPE 
         21.14          22.09 
[1] "1.0 - 100.0 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1190V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UPF2 MUTATED         2        0        1         5         3         0
  UPF2 WILD-TYPE      62        1       25       103         5         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        18          6         42         33       33        12
                vv
clus             STAGE IVB
  UPF2 MUTATED           0
  UPF2 WILD-TYPE         1
D1190V3, multiclass
            clus
vv           UPF2 MUTATED UPF2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  UPF2 MUTATED     1   2   9   4
  UPF2 WILD-TYPE   8  65 240  37
D1190V4, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            9            240
  T4            4             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
  UPF2 MUTATED    13   2   1
  UPF2 WILD-TYPE 207  79  65
D1190V5, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  N0           13            207
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V6, binary
                cls
clus               0   1
  UPF2 MUTATED    12   2
  UPF2 WILD-TYPE 273  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     12    2
  UPF2 WILD-TYPE  273   46
   clus
vv  UPF2 MUTATED UPF2 WILD-TYPE
  0           12            273
  1            2             46
[1] 2 2
[1] FALSE
D1190V7, binary
                cls
clus               0   1
  UPF2 MUTATED     8   8
  UPF2 WILD-TYPE 162 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED      8    8
  UPF2 WILD-TYPE  162  189
        clus
vv       UPF2 MUTATED UPF2 WILD-TYPE
  FEMALE            8            162
  MALE              8            189
[1] 2 2
[1] FALSE
D1190V8, binary
                cls
clus               0   1
  UPF2 MUTATED    12   1
  UPF2 WILD-TYPE 288   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     12    1
  UPF2 WILD-TYPE  288    7
     clus
vv    UPF2 MUTATED UPF2 WILD-TYPE
  NO            12            288
  YES            1              7
[1] 2 2
[1] FALSE
D1190V9, binary
                cls
clus               0   1
  UPF2 MUTATED    13   3
  UPF2 WILD-TYPE 301  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     13    3
  UPF2 WILD-TYPE  301   45
                               clus
vv                              UPF2 MUTATED UPF2 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UPF2 MUTATED     9   0   2   3
  UPF2 WILD-TYPE 250   3  20  18
D1190V10, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            2             20
  RX            3             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"
D1190V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UPF2 MUTATED                                  0     1
  UPF2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UPF2 MUTATED                           1     7
  UPF2 WILD-TYPE                        18   169
D1190V12, multiclass
                                  clus
vv                                 UPF2 MUTATED UPF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = MFSD6 MUTATION ANALYSIS
D1191V1, survival
                 sevent
clus2               0   1
  MFSD6 MUTATED     6   1
  MFSD6 WILD-TYPE 271  77
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              7             348 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              1              77 
$`MFSD6 MUTATED`
TCGA-A6-5662 TCGA-AA-3949 TCGA-AD-5900 TCGA-AZ-4616 TCGA-D5-6533 TCGA-D5-6539 
       23.61        26.01        12.16         5.13        25.48        12.49 
TCGA-F4-6808 
       33.67 

$`MFSD6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82        58.39         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MFSD6 MUTATED MFSD6 WILD-TYPE 
           5.13            0.00 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
          33.67          148.01 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
         23.610          22.045 
[1] "5.1 - 33.7 (23.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1191V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFSD6 MUTATED         2        0        0         0         0         0
  MFSD6 WILD-TYPE      62        1       26       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFSD6 MUTATED           0          0          1          0        1         1
  MFSD6 WILD-TYPE        18          6         43         33       34        11
                 vv
clus              STAGE IVB
  MFSD6 MUTATED           0
  MFSD6 WILD-TYPE         1
D1191V3, multiclass
            clus
vv           MFSD6 MUTATED MFSD6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  MFSD6 MUTATED     1   1   4   1
  MFSD6 WILD-TYPE   8  66 245  40
D1191V4, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             4             245
  T4             1              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
  MFSD6 MUTATED     4   1   2
  MFSD6 WILD-TYPE 216  80  64
D1191V5, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V6, binary
                 cls
clus                0   1
  MFSD6 MUTATED     4   2
  MFSD6 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      4    2
  MFSD6 WILD-TYPE  281   46
   clus
vv  MFSD6 MUTATED MFSD6 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D1191V7, binary
                 cls
clus                0   1
  MFSD6 MUTATED     5   2
  MFSD6 WILD-TYPE 165 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      5    2
  MFSD6 WILD-TYPE  165  195
        clus
vv       MFSD6 MUTATED MFSD6 WILD-TYPE
  FEMALE             5             165
  MALE               2             195
[1] 2 2
[1] FALSE
D1191V8, binary
                 cls
clus                0   1
  MFSD6 MUTATED     7   0
  MFSD6 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      7    0
  MFSD6 WILD-TYPE  293    8
     clus
vv    MFSD6 MUTATED MFSD6 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1191V9, binary
                 cls
clus                0   1
  MFSD6 MUTATED     5   2
  MFSD6 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      5    2
  MFSD6 WILD-TYPE  309   46
                               clus
vv                              MFSD6 MUTATED MFSD6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFSD6 MUTATED     5   0   0   0
  MFSD6 WILD-TYPE 254   3  22  21
D1191V10, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1191V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFSD6 MUTATED                                  0     0
  MFSD6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFSD6 MUTATED                           0     6
  MFSD6 WILD-TYPE                        19   170
D1191V12, multiclass
                                  clus
vv                                 MFSD6 MUTATED MFSD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = CACNA1D MUTATION ANALYSIS
D1192V1, survival
                   sevent
clus2                 0   1
  CACNA1D MUTATED    14   7
  CACNA1D WILD-TYPE 263  71
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               21               334 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
                7                71 
$`CACNA1D MUTATED`
TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-6780 TCGA-A6-6781 
       25.08       100.01        26.17        42.90        20.12        19.66 
TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 
       18.05        34.98        35.01        12.16        27.09        58.39 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5916 
       88.21        49.41        12.76        10.06        51.32        21.14 
TCGA-DM-A0XD TCGA-DM-A1DA TCGA-G4-6309 
       24.43         7.50        85.48 

$`CACNA1D WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        15.62        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CACNA1D MUTATED CACNA1D WILD-TYPE 
              7.5               0.0 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
           100.01            148.01 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
            26.17             21.99 
[1] "7.5 - 100.0 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1192V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CACNA1D MUTATED         4        0        3         8         2         0
  CACNA1D WILD-TYPE      60        1       23       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNA1D MUTATED           1          0          2          2        0
  CACNA1D WILD-TYPE        17          6         42         31       35
                   vv
clus                STAGE IVA STAGE IVB
  CACNA1D MUTATED           0         0
  CACNA1D WILD-TYPE        12         1
D1192V3, multiclass
            clus
vv           CACNA1D MUTATED CACNA1D WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                8               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  CACNA1D MUTATED     2   2  14   4
  CACNA1D WILD-TYPE   7  65 235  37
D1192V4, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  T1               2                 7
  T2               2                65
  T3              14               235
  T4               4                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
  CACNA1D MUTATED    17   3   2
  CACNA1D WILD-TYPE 203  78  64
D1192V5, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  N0              17               203
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V6, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    17   0
  CACNA1D WILD-TYPE 268  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     17    0
  CACNA1D WILD-TYPE  268   48
   clus
vv  CACNA1D MUTATED CACNA1D WILD-TYPE
  0              17               268
  1               0                48
[1] 2 2
[1] FALSE
D1192V7, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    11  11
  CACNA1D WILD-TYPE 159 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     11   11
  CACNA1D WILD-TYPE  159  186
        clus
vv       CACNA1D MUTATED CACNA1D WILD-TYPE
  FEMALE              11               159
  MALE                11               186
[1] 2 2
[1] FALSE
D1192V8, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    16   1
  CACNA1D WILD-TYPE 284   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     16    1
  CACNA1D WILD-TYPE  284    7
     clus
vv    CACNA1D MUTATED CACNA1D WILD-TYPE
  NO               16               284
  YES               1                 7
[1] 2 2
[1] FALSE
D1192V9, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    17   5
  CACNA1D WILD-TYPE 297  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     17    5
  CACNA1D WILD-TYPE  297   43
                               clus
vv                              CACNA1D MUTATED CACNA1D WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CACNA1D MUTATED    12   0   0   4
  CACNA1D WILD-TYPE 247   3  22  17
D1192V10, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               4                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"
D1192V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1D MUTATED                                  0     2
  CACNA1D WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1D MUTATED                           1    15
  CACNA1D WILD-TYPE                        18   161
D1192V12, multiclass
                                  clus
vv                                 CACNA1D MUTATED CACNA1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         15               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(1193) Variable = OR9Q1 MUTATION ANALYSIS
D1193V1, survival
                 sevent
clus2               0   1
  OR9Q1 MUTATED     3   3
  OR9Q1 WILD-TYPE 274  75
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             349 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              3              75 
$`OR9Q1 MUTATED`
TCGA-AA-3713 TCGA-AD-6889 TCGA-CK-4952 TCGA-CM-6674 TCGA-DM-A1DB TCGA-F4-6570 
       19.04        83.24        15.62        12.95        44.32         6.18 

$`OR9Q1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
           6.18            0.00 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
          83.24          148.01 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
          17.33           22.09 
[1] "6.2 - 83.2 (17.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1193V2, continuous
                 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      64        1       26       104         8         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        18          6         44         32       34        12
                 vv
clus              STAGE IVB
  OR9Q1 MUTATED           0
  OR9Q1 WILD-TYPE         1
D1193V3, multiclass
            clus
vv           OR9Q1 MUTATED OR9Q1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  OR9Q1 MUTATED     0   0   5   1
  OR9Q1 WILD-TYPE   9  67 244  40
D1193V4, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             1              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
  OR9Q1 MUTATED     5   0   1
  OR9Q1 WILD-TYPE 215  81  65
D1193V5, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V6, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     5   1
  OR9Q1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      5    1
  OR9Q1 WILD-TYPE  280   47
   clus
vv  OR9Q1 MUTATED OR9Q1 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D1193V7, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     2   4
  OR9Q1 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      2    4
  OR9Q1 WILD-TYPE  168  193
        clus
vv       OR9Q1 MUTATED OR9Q1 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D1193V8, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     3   1
  OR9Q1 WILD-TYPE 297   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      3    1
  OR9Q1 WILD-TYPE  297    7
     clus
vv    OR9Q1 MUTATED OR9Q1 WILD-TYPE
  NO              3             297
  YES             1               7
[1] 2 2
[1] FALSE
D1193V9, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     5   1
  OR9Q1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      5    1
  OR9Q1 WILD-TYPE  309   47
                               clus
vv                              OR9Q1 MUTATED OR9Q1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR9Q1 MUTATED     3   0   1   1
  OR9Q1 WILD-TYPE 256   3  21  20
D1193V10, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             1              21
  RX             1              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"
D1193V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR9Q1 MUTATED                                  0     1
  OR9Q1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR9Q1 MUTATED                           0     4
  OR9Q1 WILD-TYPE                        19   172
D1193V12, multiclass
                                  clus
vv                                 OR9Q1 MUTATED OR9Q1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SSRP1 MUTATION ANALYSIS
D1194V1, survival
                 sevent
clus2               0   1
  SSRP1 MUTATED    11   1
  SSRP1 WILD-TYPE 266  77
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             12             343 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
              1              77 
$`SSRP1 MUTATED`
TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3966 TCGA-AU-6004 
       10.88        79.69        24.39         6.97         2.01        27.09 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6674 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6323 
       12.00        21.99        12.95        53.62        55.04        13.78 

$`SSRP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
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-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 
       74.56        65.85        44.68        85.48        61.91        36.00 
TCGA-G4-6626 
       46.75 

  SSRP1 MUTATED SSRP1 WILD-TYPE 
           2.01            0.00 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
          79.69          148.01 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
         17.885          22.090 
[1] "2.0 - 79.7 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D1194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SSRP1 MUTATED         4        1        1         2         1         0
  SSRP1 WILD-TYPE      60        0       25       106         7         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        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  SSRP1 MUTATED           0
  SSRP1 WILD-TYPE         1
D1194V3, multiclass
            clus
vv           SSRP1 MUTATED SSRP1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  SSRP1 MUTATED     0   4   6   2
  SSRP1 WILD-TYPE   9  63 243  39
D1194V4, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             6             243
  T4             2              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
  SSRP1 MUTATED     9   2   2
  SSRP1 WILD-TYPE 211  79  64
D1194V5, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1194V6, binary
                 cls
clus                0   1
  SSRP1 MUTATED    11   0
  SSRP1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     11    0
  SSRP1 WILD-TYPE  274   48
   clus
vv  SSRP1 MUTATED SSRP1 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1194V7, binary
                 cls
clus                0   1
  SSRP1 MUTATED     6   7
  SSRP1 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED      6    7
  SSRP1 WILD-TYPE  164  190
        clus
vv       SSRP1 MUTATED SSRP1 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1194V8, binary
                 cls
clus                0   1
  SSRP1 MUTATED    10   0
  SSRP1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     10    0
  SSRP1 WILD-TYPE  290    8
     clus
vv    SSRP1 MUTATED SSRP1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1194V9, binary
                 cls
clus                0   1
  SSRP1 MUTATED    11   2
  SSRP1 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     11    2
  SSRP1 WILD-TYPE  303   46
                               clus
vv                              SSRP1 MUTATED SSRP1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SSRP1 MUTATED    10   0   0   0
  SSRP1 WILD-TYPE 249   3  22  21
D1194V10, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D1194V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SSRP1 MUTATED                                  0     0
  SSRP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SSRP1 MUTATED                           1     9
  SSRP1 WILD-TYPE                        18   167
D1194V12, multiclass
                                  clus
vv                                 SSRP1 MUTATED SSRP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(1195) Variable = ST6GALNAC3 MUTATION ANALYSIS
D1195V1, survival
                      sevent
clus2                    0   1
  ST6GALNAC3 MUTATED     9   3
  ST6GALNAC3 WILD-TYPE 268  75
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  12                  343 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                   3                   75 
$`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 

$`ST6GALNAC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.52         8.38        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        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-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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                4.01                 0.00 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
               38.07               148.01 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
              17.195               22.090 
[1] "4.0 - 38.1 (17.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1195V2, continuous
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST6GALNAC3 MUTATED         1        0        0         5         1         0
  ST6GALNAC3 WILD-TYPE      63        1       26       103         7         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST6GALNAC3 MUTATED           1          0          1          1        0
  ST6GALNAC3 WILD-TYPE        17          6         43         32       35
                      vv
clus                   STAGE IVA STAGE IVB
  ST6GALNAC3 MUTATED           2         0
  ST6GALNAC3 WILD-TYPE        10         1
D1195V3, multiclass
            clus
vv           ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  STAGE I                     1                   63
  STAGE IA                    0                    1
  STAGE II                    0                   26
  STAGE IIA                   5                  103
  STAGE IIB                   1                    7
  STAGE IIC                   0                    1
  STAGE III                   1                   17
  STAGE IIIA                  0                    6
  STAGE IIIB                  1                   43
  STAGE IIIC                  1                   32
  STAGE IV                    0                   35
  STAGE IVA                   2                   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
  ST6GALNAC3 MUTATED     0   1  10   1
  ST6GALNAC3 WILD-TYPE   9  66 239  40
D1195V4, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  T1                  0                    9
  T2                  1                   66
  T3                 10                  239
  T4                  1                   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
  ST6GALNAC3 MUTATED     8   3   1
  ST6GALNAC3 WILD-TYPE 212  78  65
D1195V5, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  N0                  8                  212
  N1                  3                   78
  N2                  1                   65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1195V6, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED    10   2
  ST6GALNAC3 WILD-TYPE 275  46
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED     10    2
  ST6GALNAC3 WILD-TYPE  275   46
   clus
vv  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  0                 10                  275
  1                  2                   46
[1] 2 2
[1] FALSE
D1195V7, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED     4   8
  ST6GALNAC3 WILD-TYPE 166 189
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED      4    8
  ST6GALNAC3 WILD-TYPE  166  189
        clus
vv       ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  FEMALE                  4                  166
  MALE                    8                  189
[1] 2 2
[1] FALSE
D1195V8, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED    11   0
  ST6GALNAC3 WILD-TYPE 289   8
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED     11    0
  ST6GALNAC3 WILD-TYPE  289    8
     clus
vv    ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  NO                  11                  289
  YES                  0                    8
[1] 2 2
[1] FALSE
D1195V9, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED     9   3
  ST6GALNAC3 WILD-TYPE 305  45
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED      9    3
  ST6GALNAC3 WILD-TYPE  305   45
                               clus
vv                              ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  COLON ADENOCARCINOMA                           9                  305
  COLON MUCINOUS ADENOCARCINOMA                  3                   45
[1] 2 2
[1] FALSE
                      vv
clus                    R0  R1  R2  RX
  ST6GALNAC3 MUTATED     8   0   0   2
  ST6GALNAC3 WILD-TYPE 251   3  22  19
D1195V10, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  R0                  8                  251
  R1                  0                    3
  R2                  0                   22
  RX                  2                   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"
D1195V11, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST6GALNAC3 MUTATED                                  0     2
  ST6GALNAC3 WILD-TYPE                                1     8
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  ST6GALNAC3 MUTATED                           2     6
  ST6GALNAC3 WILD-TYPE                        17   170
D1195V12, multiclass
                                  clus
vv                                 ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             2                    8
  BLACK OR AFRICAN AMERICAN                         2                   17
  WHITE                                             6                  170
[1] 4 2
[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 = TCF7L2 MUTATION ANALYSIS
D1196V1, survival
                  sevent
clus2                0   1
  TCF7L2 MUTATED    19   1
  TCF7L2 WILD-TYPE 258  77
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              20              335 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               1               77 
$`TCF7L2 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3955 
        0.92       100.01        19.66         6.97        50.04        20.98 
TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01I TCGA-AU-6004 TCGA-AY-6197 
       25.02        18.05        34.98        31.00        27.09        21.44 
TCGA-AZ-4315 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6165 TCGA-CM-6171 
       58.39        17.56        30.08        15.02        16.04        14.04 
TCGA-D5-6922 TCGA-DM-A282 
       10.13       139.17 

$`TCF7L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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-6166 TCGA-CM-6167 
       15.02        12.00        14.04        29.03        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            0.92             0.00 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
          139.17           148.01 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           21.21            22.09 
[1] "0.9 - 139.2 (21.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "5.3"
D1196V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCF7L2 MUTATED         3        0        4         8         1         0
  TCF7L2 WILD-TYPE      61        1       22       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCF7L2 MUTATED           1          1          2          1        1
  TCF7L2 WILD-TYPE        17          5         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  TCF7L2 MUTATED           0         0
  TCF7L2 WILD-TYPE        12         1
D1196V3, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  TCF7L2 MUTATED     0   5  14   4
  TCF7L2 WILD-TYPE   9  62 235  37
D1196V4, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0                9
  T2              5               62
  T3             14              235
  T4              4               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
  TCF7L2 MUTATED    17   4   2
  TCF7L2 WILD-TYPE 203  77  64
D1196V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0             17              203
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1196V6, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    19   1
  TCF7L2 WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     19    1
  TCF7L2 WILD-TYPE  266   47
   clus
vv  TCF7L2 MUTATED TCF7L2 WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D1196V7, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    12  11
  TCF7L2 WILD-TYPE 158 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     12   11
  TCF7L2 WILD-TYPE  158  186
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE             12              158
  MALE               11              186
[1] 2 2
[1] FALSE
D1196V8, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    17   0
  TCF7L2 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     17    0
  TCF7L2 WILD-TYPE  283    8
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D1196V9, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    22   1
  TCF7L2 WILD-TYPE 292  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     22    1
  TCF7L2 WILD-TYPE  292   47
                               clus
vv                              TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON ADENOCARCINOMA                      22              292
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCF7L2 MUTATED    18   0   1   1
  TCF7L2 WILD-TYPE 241   3  21  20
D1196V10, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0             18              241
  R1              0                3
  R2              1               21
  RX              1               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"
D1196V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCF7L2 MUTATED                                  0     0
  TCF7L2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCF7L2 MUTATED                           0    12
  TCF7L2 WILD-TYPE                        19   164
D1196V12, multiclass
                                  clus
vv                                 TCF7L2 MUTATED TCF7L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        12              164
[1] 4 2
[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 = PACS2 MUTATION ANALYSIS
D1197V1, survival
                 sevent
clus2               0   1
  PACS2 MUTATED     4   1
  PACS2 WILD-TYPE 273  77
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             350 
  PACS2 MUTATED PACS2 WILD-TYPE 
              1              77 
$`PACS2 MUTATED`
TCGA-AD-5900 TCGA-CK-5913 TCGA-CK-6747 TCGA-CM-6674 TCGA-F4-6570 
       12.16        51.32        82.95        12.95         6.18 

$`PACS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PACS2 MUTATED PACS2 WILD-TYPE 
           6.18            0.00 
  PACS2 MUTATED PACS2 WILD-TYPE 
          82.95          148.01 
  PACS2 MUTATED PACS2 WILD-TYPE 
         12.950          22.075 
[1] "6.2 - 83.0 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1197V2, continuous
                 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      63        1       26       104         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  PACS2 MUTATED           0
  PACS2 WILD-TYPE         1
D1197V3, multiclass
            clus
vv           PACS2 MUTATED PACS2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PACS2 MUTATED     0   1   4   0
  PACS2 WILD-TYPE   9  66 245  41
D1197V4, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             0              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
  PACS2 MUTATED     5   0   0
  PACS2 WILD-TYPE 215  81  66
D1197V5, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1197V6, binary
                 cls
clus                0   1
  PACS2 MUTATED     2   0
  PACS2 WILD-TYPE 283  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      2    0
  PACS2 WILD-TYPE  283   48
   clus
vv  PACS2 MUTATED PACS2 WILD-TYPE
  0             2             283
  1             0              48
[1] 2 2
[1] FALSE
D1197V7, binary
                 cls
clus                0   1
  PACS2 MUTATED     3   2
  PACS2 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      3    2
  PACS2 WILD-TYPE  167  195
        clus
vv       PACS2 MUTATED PACS2 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1197V8, binary
                 cls
clus                0   1
  PACS2 MUTATED     5   0
  PACS2 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      5    0
  PACS2 WILD-TYPE  295    8
     clus
vv    PACS2 MUTATED PACS2 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1197V9, binary
                 cls
clus                0   1
  PACS2 MUTATED     4   1
  PACS2 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      4    1
  PACS2 WILD-TYPE  310   47
                               clus
vv                              PACS2 MUTATED PACS2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PACS2 MUTATED     3   0   0   2
  PACS2 WILD-TYPE 256   3  22  19
D1197V10, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             2              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"
D1197V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PACS2 MUTATED                                  0     0
  PACS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PACS2 MUTATED                           0     5
  PACS2 WILD-TYPE                        19   171
D1197V12, multiclass
                                  clus
vv                                 PACS2 MUTATED PACS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = STAT5B MUTATION ANALYSIS
D1198V1, survival
                  sevent
clus2                0   1
  STAT5B MUTATED    10   2
  STAT5B WILD-TYPE 267  76
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              343 
  STAT5B MUTATED STAT5B WILD-TYPE 
               2               76 
$`STAT5B MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3815 
       24.00        79.69        32.75        24.39        20.12        33.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6717 TCGA-G4-6303 
        4.01        34.98        27.09         0.20        12.76        65.85 

$`STAT5B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6781 
       25.08        25.18        21.76        24.69        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       26.47        14.50        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  STAT5B MUTATED STAT5B WILD-TYPE 
             0.2              0.0 
  STAT5B MUTATED STAT5B WILD-TYPE 
           79.69           148.01 
  STAT5B MUTATED STAT5B WILD-TYPE 
           25.74            21.99 
[1] "0.2 - 79.7 (25.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1198V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAT5B MUTATED         3        0        0         4         3         0
  STAT5B WILD-TYPE      61        1       26       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAT5B MUTATED           0          0          0          1        1
  STAT5B WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  STAT5B MUTATED           0         0
  STAT5B WILD-TYPE        12         1
D1198V3, multiclass
            clus
vv           STAT5B MUTATED STAT5B WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  STAT5B MUTATED     0   3   6   3
  STAT5B WILD-TYPE   9  64 243  38
D1198V4, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  T1              0                9
  T2              3               64
  T3              6              243
  T4              3               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
  STAT5B MUTATED    10   1   1
  STAT5B WILD-TYPE 210  80  65
D1198V5, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  N0             10              210
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1198V6, binary
                  cls
clus                 0   1
  STAT5B MUTATED     9   1
  STAT5B WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      9    1
  STAT5B WILD-TYPE  276   47
   clus
vv  STAT5B MUTATED STAT5B WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1198V7, binary
                  cls
clus                 0   1
  STAT5B MUTATED     6   6
  STAT5B WILD-TYPE 164 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      6    6
  STAT5B WILD-TYPE  164  191
        clus
vv       STAT5B MUTATED STAT5B WILD-TYPE
  FEMALE              6              164
  MALE                6              191
[1] 2 2
[1] FALSE
D1198V8, binary
                  cls
clus                 0   1
  STAT5B MUTATED     9   0
  STAT5B WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      9    0
  STAT5B WILD-TYPE  291    8
     clus
vv    STAT5B MUTATED STAT5B WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1198V9, binary
                  cls
clus                 0   1
  STAT5B MUTATED     6   6
  STAT5B WILD-TYPE 308  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      6    6
  STAT5B WILD-TYPE  308   42
                               clus
vv                              STAT5B MUTATED STAT5B WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  STAT5B MUTATED     9   0   0   1
  STAT5B WILD-TYPE 250   3  22  20
D1198V10, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D1198V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAT5B MUTATED                                  0     1
  STAT5B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STAT5B MUTATED                           0     7
  STAT5B WILD-TYPE                        19   169
D1198V12, multiclass
                                  clus
vv                                 STAT5B MUTATED STAT5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = ZNF622 MUTATION ANALYSIS
D1199V1, survival
                  sevent
clus2                0   1
  ZNF622 MUTATED     4   3
  ZNF622 WILD-TYPE 273  75
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               7              348 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               3               75 
$`ZNF622 MUTATED`
TCGA-AA-3715 TCGA-AA-3663 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6679 TCGA-D5-6923 
       19.04         6.97        15.62        21.14        10.06        12.43 
TCGA-DM-A0XD 
       24.43 

$`ZNF622 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF622 MUTATED ZNF622 WILD-TYPE 
            6.97             0.00 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
           24.43           148.01 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
          15.620           22.225 
[1] "7.0 - 24.4 (15.6)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "3.2"
D1199V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF622 MUTATED         2        0        2         2         0         0
  ZNF622 WILD-TYPE      62        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF622 MUTATED           0          0          0          1        0
  ZNF622 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF622 MUTATED           0         0
  ZNF622 WILD-TYPE        12         1
D1199V3, multiclass
            clus
vv           ZNF622 MUTATED ZNF622 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF622 MUTATED     1   1   4   1
  ZNF622 WILD-TYPE   8  66 245  40
D1199V4, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              4              245
  T4              1               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
  ZNF622 MUTATED     6   0   1
  ZNF622 WILD-TYPE 214  81  65
D1199V5, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1199V6, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     7   0
  ZNF622 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      7    0
  ZNF622 WILD-TYPE  278   48
   clus
vv  ZNF622 MUTATED ZNF622 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1199V7, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     2   5
  ZNF622 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      2    5
  ZNF622 WILD-TYPE  168  192
        clus
vv       ZNF622 MUTATED ZNF622 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1199V8, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     5   0
  ZNF622 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      5    0
  ZNF622 WILD-TYPE  295    8
     clus
vv    ZNF622 MUTATED ZNF622 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1199V9, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     6   1
  ZNF622 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      6    1
  ZNF622 WILD-TYPE  308   47
                               clus
vv                              ZNF622 MUTATED ZNF622 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF622 MUTATED     4   0   0   2
  ZNF622 WILD-TYPE 255   3  22  19
D1199V10, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              2               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"
D1199V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF622 MUTATED                                  0     0
  ZNF622 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF622 MUTATED                           0     5
  ZNF622 WILD-TYPE                        19   171
D1199V12, multiclass
                                  clus
vv                                 ZNF622 MUTATED ZNF622 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = ABCB6 MUTATION ANALYSIS
D1200V1, survival
                 sevent
clus2               0   1
  ABCB6 MUTATED     4   3
  ABCB6 WILD-TYPE 273  75
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              7             348 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              3              75 
$`ABCB6 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-AA-3696 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AZ-6600 
        0.92       100.01         5.03         1.02        14.50        12.10 
TCGA-D5-6927 
        9.44 

$`ABCB6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ABCB6 MUTATED ABCB6 WILD-TYPE 
           0.92            0.00 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
         100.01          148.01 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
          9.440          22.225 
[1] "0.9 - 100.0 (9.4)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.5"
D1200V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCB6 MUTATED         0        0        2         2         0         0
  ABCB6 WILD-TYPE      64        1       24       106         8         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        17          6         44         33       33        12
                 vv
clus              STAGE IVB
  ABCB6 MUTATED           0
  ABCB6 WILD-TYPE         1
D1200V3, multiclass
            clus
vv           ABCB6 MUTATED ABCB6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  ABCB6 MUTATED     0   0   6   1
  ABCB6 WILD-TYPE   9  67 243  40
D1200V4, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  ABCB6 MUTATED     4   3   0
  ABCB6 WILD-TYPE 216  78  66
D1200V5, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  N0             4             216
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1200V6, binary
                 cls
clus                0   1
  ABCB6 MUTATED     5   2
  ABCB6 WILD-TYPE 280  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      5    2
  ABCB6 WILD-TYPE  280   46
   clus
vv  ABCB6 MUTATED ABCB6 WILD-TYPE
  0             5             280
  1             2              46
[1] 2 2
[1] FALSE
D1200V7, binary
                 cls
clus                0   1
  ABCB6 MUTATED     4   3
  ABCB6 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      4    3
  ABCB6 WILD-TYPE  166  194
        clus
vv       ABCB6 MUTATED ABCB6 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1200V8, binary
                 cls
clus                0   1
  ABCB6 MUTATED     6   0
  ABCB6 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      6    0
  ABCB6 WILD-TYPE  294    8
     clus
vv    ABCB6 MUTATED ABCB6 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1200V9, binary
                 cls
clus                0   1
  ABCB6 MUTATED     7   0
  ABCB6 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      7    0
  ABCB6 WILD-TYPE  307   48
                               clus
vv                              ABCB6 MUTATED ABCB6 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCB6 MUTATED     4   0   1   0
  ABCB6 WILD-TYPE 255   3  21  21
D1200V10, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D1200V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCB6 MUTATED                                  0     0
  ABCB6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCB6 MUTATED                           1     3
  ABCB6 WILD-TYPE                        18   173
D1200V12, multiclass
                                  clus
vv                                 ABCB6 MUTATED ABCB6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = ZKSCAN1 MUTATION ANALYSIS
D1201V1, survival
                   sevent
clus2                 0   1
  ZKSCAN1 MUTATED     5   2
  ZKSCAN1 WILD-TYPE 272  76
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               348 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                2                76 
$`ZKSCAN1 MUTATED`
TCGA-AA-3516 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3864 TCGA-AA-A00J TCGA-AD-5900 
       13.02         3.02         1.02        53.00        18.05        12.16 
TCGA-G4-6293 
      133.18 

$`ZKSCAN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
             1.02              0.00 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
           133.18            148.01 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            13.02             22.09 
[1] "1.0 - 133.2 (13.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1201V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZKSCAN1 MUTATED         1        0        2         1         0         0
  ZKSCAN1 WILD-TYPE      63        1       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN1 MUTATED           2          0          1          0        0
  ZKSCAN1 WILD-TYPE        16          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ZKSCAN1 MUTATED           0         0
  ZKSCAN1 WILD-TYPE        12         1
D1201V3, multiclass
            clus
vv           ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ZKSCAN1 MUTATED     0   1   5   1
  ZKSCAN1 WILD-TYPE   9  66 244  40
D1201V4, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               1                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
  ZKSCAN1 MUTATED     4   2   1
  ZKSCAN1 WILD-TYPE 216  79  65
D1201V5, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  N0               4               216
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1201V6, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     6   0
  ZKSCAN1 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      6    0
  ZKSCAN1 WILD-TYPE  279   48
   clus
vv  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1201V7, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     4   3
  ZKSCAN1 WILD-TYPE 166 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      4    3
  ZKSCAN1 WILD-TYPE  166  194
        clus
vv       ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  FEMALE               4               166
  MALE                 3               194
[1] 2 2
[1] FALSE
D1201V8, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     6   0
  ZKSCAN1 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      6    0
  ZKSCAN1 WILD-TYPE  294    8
     clus
vv    ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1201V9, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     4   3
  ZKSCAN1 WILD-TYPE 310  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      4    3
  ZKSCAN1 WILD-TYPE  310   45
                               clus
vv                              ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN1 MUTATED     6   0   0   0
  ZKSCAN1 WILD-TYPE 253   3  22  21
D1201V10, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               0                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"
D1201V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZKSCAN1 MUTATED                                  0     0
  ZKSCAN1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZKSCAN1 MUTATED                           0     2
  ZKSCAN1 WILD-TYPE                        19   174
D1201V12, multiclass
[1] "Remove cluster labels:" "ZKSCAN1 MUTATED"       
clus
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6899 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965        TCGA-AU-3779 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"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-5913        TCGA-CK-5914        TCGA-CK-5915 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6299        TCGA-G4-6303 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 

Clustering(1202) Variable = C10ORF119 MUTATION ANALYSIS
D1202V1, survival
                     sevent
clus2                   0   1
  C10ORF119 MUTATED     6   2
  C10ORF119 WILD-TYPE 271  76
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  8                 347 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  2                  76 
$`C10ORF119 MUTATED`
TCGA-AD-6964 TCGA-G4-6628 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-4315 
       10.88        79.69        20.12        78.08        34.98        58.39 
TCGA-CM-5344 TCGA-DM-A1D4 
       22.03        92.75 

$`C10ORF119 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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              21.990 
[1] "10.9 - 92.8 (46.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1202V2, continuous
                     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      63        1       25       104         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF119 MUTATED           0          0          1          0        0
  C10ORF119 WILD-TYPE        18          6         43         33       35
                     vv
clus                  STAGE IVA STAGE IVB
  C10ORF119 MUTATED           0         0
  C10ORF119 WILD-TYPE        12         1
D1202V3, multiclass
            clus
vv           C10ORF119 MUTATED C10ORF119 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  4                 104
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 1                  43
  STAGE IIIC                 0                  33
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C10ORF119 MUTATED     0   1   6   2
  C10ORF119 WILD-TYPE   9  66 243  39
D1202V4, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 6                 243
  T4                 2                  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
  C10ORF119 MUTATED     7   1   1
  C10ORF119 WILD-TYPE 213  80  65
D1202V5, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  N0                 7                 213
  N1                 1                  80
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1202V6, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     7   0
  C10ORF119 WILD-TYPE 278  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      7    0
  C10ORF119 WILD-TYPE  278   48
   clus
vv  C10ORF119 MUTATED C10ORF119 WILD-TYPE
  0                 7                 278
  1                 0                  48
[1] 2 2
[1] FALSE
D1202V7, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     4   5
  C10ORF119 WILD-TYPE 166 192
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      4    5
  C10ORF119 WILD-TYPE  166  192
        clus
vv       C10ORF119 MUTATED C10ORF119 WILD-TYPE
  FEMALE                 4                 166
  MALE                   5                 192
[1] 2 2
[1] FALSE
D1202V8, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     7   0
  C10ORF119 WILD-TYPE 293   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      7    0
  C10ORF119 WILD-TYPE  293    8
     clus
vv    C10ORF119 MUTATED C10ORF119 WILD-TYPE
  NO                  7                 293
  YES                 0                   8
[1] 2 2
[1] FALSE
D1202V9, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     8   1
  C10ORF119 WILD-TYPE 306  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      8    1
  C10ORF119 WILD-TYPE  306   47
                               clus
vv                              C10ORF119 MUTATED C10ORF119 WILD-TYPE
  COLON ADENOCARCINOMA                          8                 306
  COLON MUCINOUS ADENOCARCINOMA                 1                  47
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C10ORF119 MUTATED     6   0   0   0
  C10ORF119 WILD-TYPE 253   3  22  21
D1202V10, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  R0                 6                 253
  R1                 0                   3
  R2                 0                  22
  RX                 0                  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"
D1202V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF119 MUTATED                                  0     0
  C10ORF119 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C10ORF119 MUTATED                           0     6
  C10ORF119 WILD-TYPE                        19   170
D1202V12, multiclass
                                  clus
vv                                 C10ORF119 MUTATED C10ORF119 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            6                 170
[1] 4 2
[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 = CLTCL1 MUTATION ANALYSIS
D1203V1, survival
                  sevent
clus2                0   1
  CLTCL1 MUTATED    15   2
  CLTCL1 WILD-TYPE 262  76
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              17              338 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
               2               76 
$`CLTCL1 MUTATED`
TCGA-AA-3713 TCGA-AA-3972 TCGA-G4-6588 TCGA-AA-3660 TCGA-AA-3818 TCGA-AA-3877 
       19.04        50.99        26.17        78.08         0.99        31.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4950 
       25.02        34.98        12.16         6.77        12.76        85.45 
TCGA-CM-5348 TCGA-D5-6928 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 
       22.98        11.64        33.67        55.04        61.91 

$`CLTCL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
        5.03        26.99        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6317 
       74.56        65.85        53.62        44.68        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
            0.99             0.00 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
           85.45           148.01 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
           26.17            21.99 
[1] "1.0 - 85.5 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1203V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLTCL1 MUTATED         4        0        1         5         1         0
  CLTCL1 WILD-TYPE      60        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLTCL1 MUTATED           0          0          3          0        3
  CLTCL1 WILD-TYPE        18          6         41         33       32
                  vv
clus               STAGE IVA STAGE IVB
  CLTCL1 MUTATED           0         0
  CLTCL1 WILD-TYPE        12         1
D1203V3, multiclass
            clus
vv           CLTCL1 MUTATED CLTCL1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                3               32
  STAGE IVA               0               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
  CLTCL1 MUTATED     2   3  12   1
  CLTCL1 WILD-TYPE   7  64 237  40
D1203V4, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  T1              2                7
  T2              3               64
  T3             12              237
  T4              1               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
  CLTCL1 MUTATED    13   5   0
  CLTCL1 WILD-TYPE 207  76  66
D1203V5, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  N0             13              207
  N1              5               76
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1203V6, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    12   3
  CLTCL1 WILD-TYPE 273  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     12    3
  CLTCL1 WILD-TYPE  273   45
   clus
vv  CLTCL1 MUTATED CLTCL1 WILD-TYPE
  0             12              273
  1              3               45
[1] 2 2
[1] FALSE
D1203V7, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED     9   9
  CLTCL1 WILD-TYPE 161 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED      9    9
  CLTCL1 WILD-TYPE  161  188
        clus
vv       CLTCL1 MUTATED CLTCL1 WILD-TYPE
  FEMALE              9              161
  MALE                9              188
[1] 2 2
[1] FALSE
D1203V8, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    15   1
  CLTCL1 WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     15    1
  CLTCL1 WILD-TYPE  285    7
     clus
vv    CLTCL1 MUTATED CLTCL1 WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D1203V9, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    13   5
  CLTCL1 WILD-TYPE 301  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     13    5
  CLTCL1 WILD-TYPE  301   43
                               clus
vv                              CLTCL1 MUTATED CLTCL1 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLTCL1 MUTATED    12   1   2   1
  CLTCL1 WILD-TYPE 247   2  20  20
D1203V10, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  R0             12              247
  R1              1                2
  R2              2               20
  RX              1               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"
D1203V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLTCL1 MUTATED                                  0     1
  CLTCL1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLTCL1 MUTATED                           1     8
  CLTCL1 WILD-TYPE                        18   168
D1203V12, multiclass
                                  clus
vv                                 CLTCL1 MUTATED CLTCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = GFRA4 MUTATION ANALYSIS
D1204V1, survival
                 sevent
clus2               0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 274  78
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             352 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              0              78 
$`GFRA4 MUTATED`
TCGA-AA-3510 TCGA-AA-3864 TCGA-G4-6304 
       63.98        53.00        53.62 

$`GFRA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GFRA4 MUTATED GFRA4 WILD-TYPE 
             53               0 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
          63.98          148.01 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
          53.62           22.01 
[1] "53.0 - 64.0 (53.6)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9400000"
D1204V2, continuous
                 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      64        1       24       108         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  GFRA4 MUTATED           0
  GFRA4 WILD-TYPE         1
D1204V3, multiclass
            clus
vv           GFRA4 MUTATED GFRA4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              0             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GFRA4 MUTATED     0   0   2   1
  GFRA4 WILD-TYPE   9  67 247  40
D1204V4, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             2             247
  T4             1              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
  GFRA4 MUTATED     3   0   0
  GFRA4 WILD-TYPE 217  81  66
D1204V5, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  N0             3             217
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1204V6, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  282   48
   clus
vv  GFRA4 MUTATED GFRA4 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1204V7, binary
                 cls
clus                0   1
  GFRA4 MUTATED     1   2
  GFRA4 WILD-TYPE 169 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      1    2
  GFRA4 WILD-TYPE  169  195
        clus
vv       GFRA4 MUTATED GFRA4 WILD-TYPE
  FEMALE             1             169
  MALE               2             195
[1] 2 2
[1] FALSE
D1204V8, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  297    8
     clus
vv    GFRA4 MUTATED GFRA4 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1204V9, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  311   48
                               clus
vv                              GFRA4 MUTATED GFRA4 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GFRA4 MUTATED     3   0   0   0
  GFRA4 WILD-TYPE 256   3  22  21
D1204V10, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1204V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFRA4 MUTATED                                  0     0
  GFRA4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GFRA4 MUTATED                           0     1
  GFRA4 WILD-TYPE                        19   175
D1204V12, multiclass
[1] "Remove cluster labels:" "GFRA4 MUTATED"         
clus
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              1             205 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6607      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-5913      TCGA-CK-5914 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6306      TCGA-G4-6307 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6626 
"GFRA4 WILD-TYPE" 

Clustering(1205) Variable = CYP3A7 MUTATION ANALYSIS
D1205V1, survival
                  sevent
clus2                0   1
  CYP3A7 MUTATED     8   2
  CYP3A7 WILD-TYPE 269  76
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              10              345 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
               2               76 
$`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 
       12.76        12.00       117.07        13.78 

$`CYP3A7 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        46.75 

  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
               0                0 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          117.07           148.01 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          24.675           22.030 
[1] "0.0 - 117.1 (24.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1205V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP3A7 MUTATED         0        1        2         2         1         0
  CYP3A7 WILD-TYPE      64        0       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP3A7 MUTATED           0          0          1          2        0
  CYP3A7 WILD-TYPE        18          6         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CYP3A7 MUTATED           0         0
  CYP3A7 WILD-TYPE        12         1
D1205V3, multiclass
            clus
vv           CYP3A7 MUTATED CYP3A7 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  CYP3A7 MUTATED     0   1   7   1
  CYP3A7 WILD-TYPE   9  66 242  40
D1205V4, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              1               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
  CYP3A7 MUTATED     7   1   2
  CYP3A7 WILD-TYPE 213  80  64
D1205V5, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1205V6, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     8   0
  CYP3A7 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      8    0
  CYP3A7 WILD-TYPE  277   48
   clus
vv  CYP3A7 MUTATED CYP3A7 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1205V7, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     4   6
  CYP3A7 WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      4    6
  CYP3A7 WILD-TYPE  166  191
        clus
vv       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D1205V8, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     8   0
  CYP3A7 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      8    0
  CYP3A7 WILD-TYPE  292    8
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1205V9, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     8   2
  CYP3A7 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      8    2
  CYP3A7 WILD-TYPE  306   46
                               clus
vv                              CYP3A7 MUTATED CYP3A7 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CYP3A7 MUTATED     7   0   0   1
  CYP3A7 WILD-TYPE 252   3  22  20
D1205V10, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1205V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP3A7 MUTATED                                  0     1
  CYP3A7 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP3A7 MUTATED                           1     3
  CYP3A7 WILD-TYPE                        18   173
D1205V12, multiclass
                                  clus
vv                                 CYP3A7 MUTATED CYP3A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = THRAP3 MUTATION ANALYSIS
D1206V1, survival
                  sevent
clus2                0   1
  THRAP3 MUTATED     8   3
  THRAP3 WILD-TYPE 269  75
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              11              344 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
               3               75 
$`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 
       12.76        23.05        16.14        14.30        47.87 

$`THRAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  THRAP3 MUTATED THRAP3 WILD-TYPE 
               0                0 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
           47.87           148.01 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
          14.300           22.225 
[1] "0.0 - 47.9 (14.3)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.1"
D1206V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THRAP3 MUTATED         2        0        1         6         1         0
  THRAP3 WILD-TYPE      62        1       25       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THRAP3 MUTATED           0          0          1          0        0
  THRAP3 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  THRAP3 MUTATED           0         0
  THRAP3 WILD-TYPE        12         1
D1206V3, multiclass
            clus
vv           THRAP3 MUTATED THRAP3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  THRAP3 MUTATED     0   2   8   1
  THRAP3 WILD-TYPE   9  65 241  40
D1206V4, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              8              241
  T4              1               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
  THRAP3 MUTATED    10   1   0
  THRAP3 WILD-TYPE 210  80  66
D1206V5, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  N0             10              210
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1206V6, binary
                  cls
clus                 0   1
  THRAP3 MUTATED    11   0
  THRAP3 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED     11    0
  THRAP3 WILD-TYPE  274   48
   clus
vv  THRAP3 MUTATED THRAP3 WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D1206V7, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     5   6
  THRAP3 WILD-TYPE 165 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      5    6
  THRAP3 WILD-TYPE  165  191
        clus
vv       THRAP3 MUTATED THRAP3 WILD-TYPE
  FEMALE              5              165
  MALE                6              191
[1] 2 2
[1] FALSE
D1206V8, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     9   0
  THRAP3 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      9    0
  THRAP3 WILD-TYPE  291    8
     clus
vv    THRAP3 MUTATED THRAP3 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1206V9, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     7   4
  THRAP3 WILD-TYPE 307  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      7    4
  THRAP3 WILD-TYPE  307   44
                               clus
vv                              THRAP3 MUTATED THRAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  THRAP3 MUTATED    10   0   0   1
  THRAP3 WILD-TYPE 249   3  22  20
D1206V10, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              1               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"
D1206V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THRAP3 MUTATED                                  0     1
  THRAP3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  THRAP3 MUTATED                           1     4
  THRAP3 WILD-TYPE                        18   172
D1206V12, multiclass
                                  clus
vv                                 THRAP3 MUTATED THRAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = DNAH8 MUTATION ANALYSIS
D1207V1, survival
                 sevent
clus2               0   1
  DNAH8 MUTATED    47  10
  DNAH8 WILD-TYPE 230  68
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             57             298 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             10              68 
$`DNAH8 MUTATED`
TCGA-A6-4105 TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6964 TCGA-G4-6588 TCGA-G4-6628 
       14.53         0.92        19.04        10.88        26.17        79.69 
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       43.76        32.75        36.53        29.19        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3861 TCGA-AA-3864 
        8.38        24.39        19.66        63.98        30.05        53.00 
TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A00E 
       33.01        34.03         2.01        34.06        25.02        30.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AU-3779 
       18.05         4.01        34.98        35.01        83.24        14.50 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-5797 TCGA-CA-6716 
       21.44        58.39        22.36        49.41        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-5344 TCGA-CM-6161 TCGA-CM-6168 
       12.76        10.06        85.45        22.03        15.02        12.99 
TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D9 
       14.04        54.61        12.49         9.04        11.38       140.38 
TCGA-DM-A1HA TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 
      131.51         6.18        47.87        43.04        33.67        35.31 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       53.62        44.68        55.04 

$`DNAH8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2672 
        5.88        63.62        22.09        35.80        91.79        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 
       32.91        31.63        30.44        33.53        23.61        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A28C 
       12.59         7.50        44.32       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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
       31.96        35.74         1.55        34.42        41.42        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6309 
        0.53        47.41       133.18        74.56        65.85        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  DNAH8 MUTATED DNAH8 WILD-TYPE 
           0.92            0.00 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
         140.38          148.01 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
         26.170          21.565 
[1] "0.9 - 140.4 (26.2)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1.5"
D1207V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH8 MUTATED         7        0        3        23         6         0
  DNAH8 WILD-TYPE      57        1       23        85         2         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH8 MUTATED           2          0          6          5        2         1
  DNAH8 WILD-TYPE        16          6         38         28       33        11
                 vv
clus              STAGE IVB
  DNAH8 MUTATED           0
  DNAH8 WILD-TYPE         1
D1207V3, multiclass
            clus
vv           DNAH8 MUTATED DNAH8 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             23              85
  STAGE IIB              6               2
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             5              28
  STAGE IV               2              33
  STAGE IVA              1              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
  DNAH8 MUTATED     1   8  39  11
  DNAH8 WILD-TYPE   8  59 210  30
D1207V4, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  T1             1               8
  T2             8              59
  T3            39             210
  T4            11              30
[1] 4 2
[1] TRUE
[1] "dimension 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    44   8   7
  DNAH8 WILD-TYPE 176  73  59
D1207V5, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  N0            44             176
  N1             8              73
  N2             7              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1207V6, binary
                 cls
clus                0   1
  DNAH8 MUTATED    49   3
  DNAH8 WILD-TYPE 236  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     49    3
  DNAH8 WILD-TYPE  236   45
   clus
vv  DNAH8 MUTATED DNAH8 WILD-TYPE
  0            49             236
  1             3              45
[1] 2 2
[1] FALSE
D1207V7, binary
                 cls
clus                0   1
  DNAH8 MUTATED    24  35
  DNAH8 WILD-TYPE 146 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     24   35
  DNAH8 WILD-TYPE  146  162
        clus
vv       DNAH8 MUTATED DNAH8 WILD-TYPE
  FEMALE            24             146
  MALE              35             162
[1] 2 2
[1] FALSE
D1207V8, binary
                 cls
clus                0   1
  DNAH8 MUTATED    50   3
  DNAH8 WILD-TYPE 250   5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     50    3
  DNAH8 WILD-TYPE  250    5
     clus
vv    DNAH8 MUTATED DNAH8 WILD-TYPE
  NO             50             250
  YES             3               5
[1] 2 2
[1] FALSE
D1207V9, binary
                 cls
clus                0   1
  DNAH8 MUTATED    49  10
  DNAH8 WILD-TYPE 265  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     49   10
  DNAH8 WILD-TYPE  265   38
                               clus
vv                              DNAH8 MUTATED DNAH8 WILD-TYPE
  COLON ADENOCARCINOMA                     49             265
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNAH8 MUTATED    42   1   1   4
  DNAH8 WILD-TYPE 217   2  21  17
D1207V10, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  R0            42             217
  R1             1               2
  R2             1              21
  RX             4              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"
D1207V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH8 MUTATED                                  0     5
  DNAH8 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNAH8 MUTATED                           5    33
  DNAH8 WILD-TYPE                        14   143
D1207V12, multiclass
                                  clus
vv                                 DNAH8 MUTATED DNAH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        5               5
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       33             143
[1] 4 2
[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 = PDGFC MUTATION ANALYSIS
D1208V1, survival
                 sevent
clus2               0   1
  PDGFC MUTATED     7   2
  PDGFC WILD-TYPE 270  76
  PDGFC MUTATED PDGFC WILD-TYPE 
              9             346 
  PDGFC MUTATED PDGFC WILD-TYPE 
              2              76 
$`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 
        1.41        12.99        44.68 

$`PDGFC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PDGFC MUTATED PDGFC WILD-TYPE 
           1.41            0.00 
  PDGFC MUTATED PDGFC WILD-TYPE 
          44.68          148.01 
  PDGFC MUTATED PDGFC WILD-TYPE 
          22.06           22.06 
[1] "1.4 - 44.7 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1208V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDGFC MUTATED         0        0        0         3         1         0
  PDGFC WILD-TYPE      64        1       26       105         7         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        18          6         44         32       33        12
                 vv
clus              STAGE IVB
  PDGFC MUTATED           0
  PDGFC WILD-TYPE         1
D1208V3, multiclass
            clus
vv           PDGFC MUTATED PDGFC WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  PDGFC MUTATED     0   1   4   4
  PDGFC WILD-TYPE   9  66 245  37
D1208V4, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             4              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
  PDGFC MUTATED     6   1   2
  PDGFC WILD-TYPE 214  80  64
D1208V5, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  N0             6             214
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1208V6, binary
                 cls
clus                0   1
  PDGFC MUTATED     5   2
  PDGFC WILD-TYPE 280  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      5    2
  PDGFC WILD-TYPE  280   46
   clus
vv  PDGFC MUTATED PDGFC WILD-TYPE
  0             5             280
  1             2              46
[1] 2 2
[1] FALSE
D1208V7, binary
                 cls
clus                0   1
  PDGFC MUTATED     4   5
  PDGFC WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      4    5
  PDGFC WILD-TYPE  166  192
        clus
vv       PDGFC MUTATED PDGFC WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1208V8, binary
                 cls
clus                0   1
  PDGFC MUTATED     9   0
  PDGFC WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      9    0
  PDGFC WILD-TYPE  291    8
     clus
vv    PDGFC MUTATED PDGFC WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1208V9, binary
                 cls
clus                0   1
  PDGFC MUTATED     8   1
  PDGFC WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      8    1
  PDGFC WILD-TYPE  306   47
                               clus
vv                              PDGFC MUTATED PDGFC WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PDGFC MUTATED     6   0   1   0
  PDGFC WILD-TYPE 253   3  21  21
D1208V10, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             0              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"
D1208V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDGFC MUTATED                                  0     0
  PDGFC WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDGFC MUTATED                           1     5
  PDGFC WILD-TYPE                        18   171
D1208V12, multiclass
                                  clus
vv                                 PDGFC MUTATED PDGFC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = STAG2 MUTATION ANALYSIS
D1209V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED    11   1
  STAG2 WILD-TYPE 266  77
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             343 
  STAG2 MUTATED STAG2 WILD-TYPE 
              1              77 
$`STAG2 MUTATED`
TCGA-AA-3496 TCGA-AZ-6601 TCGA-A6-2678 TCGA-A6-5662 TCGA-A6-5666 TCGA-AA-3510 
        1.02       100.01        42.28        23.61        32.71        63.98 
TCGA-AA-3555 TCGA-AA-3821 TCGA-AA-A010 TCGA-CK-4948 TCGA-CM-6678 TCGA-G4-6317 
       29.95         1.02        34.98       148.01        11.01        36.00 

$`STAG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.90        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  STAG2 MUTATED STAG2 WILD-TYPE 
           1.02            0.00 
  STAG2 MUTATED STAG2 WILD-TYPE 
         148.01          140.38 
  STAG2 MUTATED STAG2 WILD-TYPE 
         33.845          21.990 
[1] "1.0 - 148.0 (33.8)" "0.0 - 140.4 (22.0)"
[1] "hr=" "3.8"
D1209V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAG2 MUTATED         1        0        3         2         1         1
  STAG2 WILD-TYPE      63        1       23       106         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAG2 MUTATED           1          0          1          1        0         2
  STAG2 WILD-TYPE        17          6         43         32       35        10
                 vv
clus              STAGE IVB
  STAG2 MUTATED           0
  STAG2 WILD-TYPE         1
D1209V3, multiclass
            clus
vv           STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              2              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
  STAG2 MUTATED     0   1   9   3
  STAG2 WILD-TYPE   9  66 240  38
D1209V4, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             3              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
  STAG2 MUTATED     8   3   2
  STAG2 WILD-TYPE 212  78  64
D1209V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1209V6, binary
                 cls
clus                0   1
  STAG2 MUTATED    10   2
  STAG2 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     10    2
  STAG2 WILD-TYPE  275   46
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D1209V7, binary
                 cls
clus                0   1
  STAG2 MUTATED     9   4
  STAG2 WILD-TYPE 161 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      9    4
  STAG2 WILD-TYPE  161  193
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             9             161
  MALE               4             193
[1] 2 2
[1] FALSE
D1209V8, binary
                 cls
clus                0   1
  STAG2 MUTATED    11   0
  STAG2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     11    0
  STAG2 WILD-TYPE  289    8
     clus
vv    STAG2 MUTATED STAG2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1209V9, binary
                 cls
clus                0   1
  STAG2 MUTATED    11   2
  STAG2 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     11    2
  STAG2 WILD-TYPE  303   46
                               clus
vv                              STAG2 MUTATED STAG2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAG2 MUTATED    10   0   0   0
  STAG2 WILD-TYPE 249   3  22  21
D1209V10, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D1209V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAG2 MUTATED                                  0     0
  STAG2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED                           0     7
  STAG2 WILD-TYPE                        19   169
D1209V12, multiclass
                                  clus
vv                                 STAG2 MUTATED STAG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = CNOT10 MUTATION ANALYSIS
D1210V1, survival
                  sevent
clus2                0   1
  CNOT10 MUTATED     6   3
  CNOT10 WILD-TYPE 271  75
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               9              346 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               3               75 
$`CNOT10 MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 
      100.01        35.80         4.01        34.98        35.01        58.39 
TCGA-AZ-4616 TCGA-CA-6717 TCGA-G4-6317 
        5.13        12.76        36.00 

$`CNOT10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  CNOT10 MUTATED CNOT10 WILD-TYPE 
            4.01             0.00 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
          100.01           148.01 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
           35.01            22.01 
[1] "4.0 - 100.0 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1210V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNOT10 MUTATED         0        0        1         3         2         0
  CNOT10 WILD-TYPE      64        1       25       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNOT10 MUTATED           1          0          0          1        1
  CNOT10 WILD-TYPE        17          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CNOT10 MUTATED           0         0
  CNOT10 WILD-TYPE        12         1
D1210V3, multiclass
            clus
vv           CNOT10 MUTATED CNOT10 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CNOT10 MUTATED     0   0   7   2
  CNOT10 WILD-TYPE   9  67 242  39
D1210V4, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              2               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
  CNOT10 MUTATED     6   0   3
  CNOT10 WILD-TYPE 214  81  63
D1210V5, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              3               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"
D1210V6, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     7   1
  CNOT10 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      7    1
  CNOT10 WILD-TYPE  278   47
   clus
vv  CNOT10 MUTATED CNOT10 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D1210V7, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     4   5
  CNOT10 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      4    5
  CNOT10 WILD-TYPE  166  192
        clus
vv       CNOT10 MUTATED CNOT10 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D1210V8, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     7   1
  CNOT10 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      7    1
  CNOT10 WILD-TYPE  293    7
     clus
vv    CNOT10 MUTATED CNOT10 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D1210V9, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     6   3
  CNOT10 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      6    3
  CNOT10 WILD-TYPE  308   45
                               clus
vv                              CNOT10 MUTATED CNOT10 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CNOT10 MUTATED     6   0   0   1
  CNOT10 WILD-TYPE 253   3  22  20
D1210V10, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1210V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNOT10 MUTATED                                  0     1
  CNOT10 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CNOT10 MUTATED                           0     5
  CNOT10 WILD-TYPE                        19   171
D1210V12, multiclass
                                  clus
vv                                 CNOT10 MUTATED CNOT10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = RSPO2 MUTATION ANALYSIS
D1211V1, survival
                 sevent
clus2               0   1
  RSPO2 MUTATED    12   4
  RSPO2 WILD-TYPE 265  74
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             16             339 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
              4              74 
$`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        12.39        10.06        30.08        12.03        13.41 
TCGA-DM-A1D4 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 
       92.75       117.07        98.24         6.18 

$`RSPO2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        29.56        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.36        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        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-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      119.93        35.97        60.79         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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  RSPO2 MUTATED RSPO2 WILD-TYPE 
           5.23            0.00 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
         117.07          148.01 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
         26.975          22.030 
[1] "5.2 - 117.1 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1211V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RSPO2 MUTATED         2        0        0         7         2         0
  RSPO2 WILD-TYPE      62        1       26       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RSPO2 MUTATED           0          0          4          1        1         0
  RSPO2 WILD-TYPE        18          6         40         32       34        12
                 vv
clus              STAGE IVB
  RSPO2 MUTATED           0
  RSPO2 WILD-TYPE         1
D1211V3, multiclass
            clus
vv           RSPO2 MUTATED RSPO2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  RSPO2 MUTATED     0   2  12   3
  RSPO2 WILD-TYPE   9  65 237  38
D1211V4, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            12             237
  T4             3              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
  RSPO2 MUTATED    11   4   2
  RSPO2 WILD-TYPE 209  77  64
D1211V5, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  N0            11             209
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1211V6, binary
                 cls
clus                0   1
  RSPO2 MUTATED    15   1
  RSPO2 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     15    1
  RSPO2 WILD-TYPE  270   47
   clus
vv  RSPO2 MUTATED RSPO2 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D1211V7, binary
                 cls
clus                0   1
  RSPO2 MUTATED    10   7
  RSPO2 WILD-TYPE 160 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     10    7
  RSPO2 WILD-TYPE  160  190
        clus
vv       RSPO2 MUTATED RSPO2 WILD-TYPE
  FEMALE            10             160
  MALE               7             190
[1] 2 2
[1] FALSE
D1211V8, binary
                 cls
clus                0   1
  RSPO2 MUTATED    13   0
  RSPO2 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     13    0
  RSPO2 WILD-TYPE  287    8
     clus
vv    RSPO2 MUTATED RSPO2 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D1211V9, binary
                 cls
clus                0   1
  RSPO2 MUTATED    14   3
  RSPO2 WILD-TYPE 300  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     14    3
  RSPO2 WILD-TYPE  300   45
                               clus
vv                              RSPO2 MUTATED RSPO2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RSPO2 MUTATED    10   0   0   1
  RSPO2 WILD-TYPE 249   3  22  20
D1211V10, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             1              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"
D1211V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RSPO2 MUTATED                                  0     2
  RSPO2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RSPO2 MUTATED                           0    11
  RSPO2 WILD-TYPE                        19   165
D1211V12, multiclass
                                  clus
vv                                 RSPO2 MUTATED RSPO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(1212) Variable = LPAR6 MUTATION ANALYSIS
D1212V1, survival
                 sevent
clus2               0   1
  LPAR6 MUTATED     4   2
  LPAR6 WILD-TYPE 273  76
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              6             349 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              2              76 
$`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 

$`LPAR6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  LPAR6 MUTATED LPAR6 WILD-TYPE 
           4.01            0.00 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
          58.39          148.01 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
          17.23           22.09 
[1] "4.0 - 58.4 (17.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1212V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPAR6 MUTATED         1        0        0         4         1         0
  LPAR6 WILD-TYPE      63        1       26       104         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  LPAR6 MUTATED           0
  LPAR6 WILD-TYPE         1
D1212V3, multiclass
            clus
vv           LPAR6 MUTATED LPAR6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LPAR6 MUTATED     0   1   5   1
  LPAR6 WILD-TYPE   9  66 244  40
D1212V4, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             1              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
  LPAR6 MUTATED     7   0   0
  LPAR6 WILD-TYPE 213  81  66
D1212V5, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1212V6, binary
                 cls
clus                0   1
  LPAR6 MUTATED     4   0
  LPAR6 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      4    0
  LPAR6 WILD-TYPE  281   48
   clus
vv  LPAR6 MUTATED LPAR6 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1212V7, binary
                 cls
clus                0   1
  LPAR6 MUTATED     0   7
  LPAR6 WILD-TYPE 170 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      0    7
  LPAR6 WILD-TYPE  170  190
        clus
vv       LPAR6 MUTATED LPAR6 WILD-TYPE
  FEMALE             0             170
  MALE               7             190
[1] 2 2
[1] FALSE
D1212V8, binary
                 cls
clus                0   1
  LPAR6 MUTATED     5   0
  LPAR6 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      5    0
  LPAR6 WILD-TYPE  295    8
     clus
vv    LPAR6 MUTATED LPAR6 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1212V9, binary
                 cls
clus                0   1
  LPAR6 MUTATED     6   1
  LPAR6 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      6    1
  LPAR6 WILD-TYPE  308   47
                               clus
vv                              LPAR6 MUTATED LPAR6 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LPAR6 MUTATED     4   0   0   2
  LPAR6 WILD-TYPE 255   3  22  19
D1212V10, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             2              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"
D1212V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPAR6 MUTATED                                  0     1
  LPAR6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LPAR6 MUTATED                           1     4
  LPAR6 WILD-TYPE                        18   172
D1212V12, multiclass
                                  clus
vv                                 LPAR6 MUTATED LPAR6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = FAM175A MUTATION ANALYSIS
D1213V1, survival
                   sevent
clus2                 0   1
  FAM175A MUTATED     6   2
  FAM175A WILD-TYPE 271  76
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               347 
  FAM175A MUTATED FAM175A WILD-TYPE 
                2                76 
$`FAM175A MUTATED`
TCGA-G4-6586 TCGA-A6-5664 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-6599 
       35.80        22.09         4.01        34.98         1.02         6.77 
TCGA-DM-A28E TCGA-G4-6309 
      119.93        85.48 

$`FAM175A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  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            22.030 
[1] "1.0 - 119.9 (28.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1213V2, continuous
                   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      63        1       25       106         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM175A MUTATED           0          0          1          1        0
  FAM175A WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM175A MUTATED           0         0
  FAM175A WILD-TYPE        12         1
D1213V3, multiclass
            clus
vv           FAM175A MUTATED FAM175A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM175A MUTATED     0   1   4   3
  FAM175A WILD-TYPE   9  66 245  38
D1213V4, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               3                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
  FAM175A MUTATED     6   1   1
  FAM175A WILD-TYPE 214  80  65
D1213V5, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  N0               6               214
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1213V6, binary
                   cls
clus                  0   1
  FAM175A MUTATED     6   0
  FAM175A WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      6    0
  FAM175A WILD-TYPE  279   48
   clus
vv  FAM175A MUTATED FAM175A WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1213V7, binary
                   cls
clus                  0   1
  FAM175A MUTATED     5   3
  FAM175A WILD-TYPE 165 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      5    3
  FAM175A WILD-TYPE  165  194
        clus
vv       FAM175A MUTATED FAM175A WILD-TYPE
  FEMALE               5               165
  MALE                 3               194
[1] 2 2
[1] FALSE
D1213V8, binary
                   cls
clus                  0   1
  FAM175A MUTATED     5   0
  FAM175A WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      5    0
  FAM175A WILD-TYPE  295    8
     clus
vv    FAM175A MUTATED FAM175A WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1213V9, binary
                   cls
clus                  0   1
  FAM175A MUTATED     7   1
  FAM175A WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      7    1
  FAM175A WILD-TYPE  307   47
                               clus
vv                              FAM175A MUTATED FAM175A WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM175A MUTATED     5   0   0   0
  FAM175A WILD-TYPE 254   3  22  21
D1213V10, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1213V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM175A MUTATED                                  0     0
  FAM175A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM175A MUTATED                           2     3
  FAM175A WILD-TYPE                        17   173
D1213V12, multiclass
                                  clus
vv                                 FAM175A MUTATED FAM175A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          3               173
[1] 4 2
[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 = SLC8A3 MUTATION ANALYSIS
D1214V1, survival
                  sevent
clus2                0   1
  SLC8A3 MUTATED    12   0
  SLC8A3 WILD-TYPE 265  78
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
              12              343 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
               0               78 
$`SLC8A3 MUTATED`
TCGA-AA-3522 TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3864 
       37.05        46.65        22.06        63.98         1.02        53.00 
TCGA-AA-3968 TCGA-AZ-4315 TCGA-CM-6172 TCGA-D5-6928 TCGA-G4-6299 TCGA-G4-6306 
       21.99        58.39        11.01        11.64        74.56        44.68 

$`SLC8A3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
            1.02             0.00 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
           74.56           148.01 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
          40.865           21.990 
[1] "1.0 - 74.6 (40.9)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "2.7e+07"
D1214V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC8A3 MUTATED         1        0        2         5         0         0
  SLC8A3 WILD-TYPE      63        1       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC8A3 MUTATED           0          0          2          1        0
  SLC8A3 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC8A3 MUTATED           0         0
  SLC8A3 WILD-TYPE        12         1
D1214V3, multiclass
            clus
vv           SLC8A3 MUTATED SLC8A3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  SLC8A3 MUTATED     0   2  10   0
  SLC8A3 WILD-TYPE   9  65 239  41
D1214V4, multiclass
    clus
vv   SLC8A3 MUTATED SLC8A3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              0               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
  SLC8A3 MUTATED     9   2   1
  SLC8A3 WILD-TYPE 211  79  65
D1214V5, multiclass
    clus
vv   SLC8A3 MUTATED SLC8A3 WILD-TYPE
  N0              9              211
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1214V6, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED    12   0
  SLC8A3 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED     12    0
  SLC8A3 WILD-TYPE  273   48
   clus
vv  SLC8A3 MUTATED SLC8A3 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1214V7, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED     5   7
  SLC8A3 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED      5    7
  SLC8A3 WILD-TYPE  165  190
        clus
vv       SLC8A3 MUTATED SLC8A3 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D1214V8, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED    11   0
  SLC8A3 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED     11    0
  SLC8A3 WILD-TYPE  289    8
     clus
vv    SLC8A3 MUTATED SLC8A3 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1214V9, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED    11   1
  SLC8A3 WILD-TYPE 303  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED     11    1
  SLC8A3 WILD-TYPE  303   47
                               clus
vv                              SLC8A3 MUTATED SLC8A3 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC8A3 MUTATED    12   0   0   0
  SLC8A3 WILD-TYPE 247   3  22  21
D1214V10, multiclass
    clus
vv   SLC8A3 MUTATED SLC8A3 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              0               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"
D1214V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC8A3 MUTATED                                  0     0
  SLC8A3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC8A3 MUTATED                           0     7
  SLC8A3 WILD-TYPE                        19   169
D1214V12, multiclass
                                  clus
vv                                 SLC8A3 MUTATED SLC8A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = A1CF MUTATION ANALYSIS
D1215V1, survival
                sevent
clus2              0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 270  78
  A1CF MUTATED A1CF WILD-TYPE 
             7            348 
  A1CF MUTATED A1CF WILD-TYPE 
             0             78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       33.34        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  A1CF MUTATED A1CF WILD-TYPE 
         11.08           0.00 
  A1CF MUTATED A1CF WILD-TYPE 
         55.04         148.01 
  A1CF MUTATED A1CF WILD-TYPE 
         29.19          22.01 
[1] "11.1 - 55.0 (29.2)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1215V2, continuous
                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      63        1       26       105         7         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  A1CF MUTATED           0
  A1CF WILD-TYPE         1
D1215V3, multiclass
            clus
vv           A1CF MUTATED A1CF WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  A1CF MUTATED     0   2   5   1
  A1CF WILD-TYPE   9  65 244  40
D1215V4, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            1             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
  A1CF MUTATED     6   1   1
  A1CF WILD-TYPE 214  80  65
D1215V5, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  N0            6            214
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1215V6, binary
                cls
clus               0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      7    0
  A1CF WILD-TYPE  278   48
   clus
vv  A1CF MUTATED A1CF WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1215V7, binary
                cls
clus               0   1
  A1CF MUTATED     3   5
  A1CF WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      3    5
  A1CF WILD-TYPE  167  192
        clus
vv       A1CF MUTATED A1CF WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D1215V8, binary
                cls
clus               0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      7    0
  A1CF WILD-TYPE  293    8
     clus
vv    A1CF MUTATED A1CF WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1215V9, binary
                cls
clus               0   1
  A1CF MUTATED     6   2
  A1CF WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      6    2
  A1CF WILD-TYPE  308   46
                               clus
vv                              A1CF MUTATED A1CF WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  A1CF MUTATED     5   0   0   1
  A1CF WILD-TYPE 254   3  22  20
D1215V10, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1215V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  A1CF MUTATED                                  0     1
  A1CF WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  A1CF MUTATED                           1     4
  A1CF WILD-TYPE                        18   172
D1215V12, multiclass
                                  clus
vv                                 A1CF MUTATED A1CF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = ARHGEF1 MUTATION ANALYSIS
D1216V1, survival
                   sevent
clus2                 0   1
  ARHGEF1 MUTATED     9   4
  ARHGEF1 WILD-TYPE 268  74
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               13               342 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
                4                74 
$`ARHGEF1 MUTATED`
TCGA-AA-3986 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-3811 
       19.07        26.17        22.06         8.38        78.08        10.06 
TCGA-AA-3815 TCGA-AA-3977 TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5916 TCGA-F4-6570 
       33.04        25.02        83.24        27.09        21.14         6.18 
TCGA-G4-6306 
       44.68 

$`ARHGEF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        24.00        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
             6.18              0.00 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
            83.24            148.01 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
            25.02             22.01 
[1] "6.2 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1216V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF1 MUTATED         3        0        1         6         0         0
  ARHGEF1 WILD-TYPE      61        1       25       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF1 MUTATED           1          0          0          0        0
  ARHGEF1 WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF1 MUTATED           0         0
  ARHGEF1 WILD-TYPE        12         1
D1216V3, multiclass
            clus
vv           ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                6               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ARHGEF1 MUTATED     1   4   8   0
  ARHGEF1 WILD-TYPE   8  63 241  41
D1216V4, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  T1               1                 8
  T2               4                63
  T3               8               241
  T4               0                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
  ARHGEF1 MUTATED    12   0   1
  ARHGEF1 WILD-TYPE 208  81  65
D1216V5, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  N0              12               208
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1216V6, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    12   0
  ARHGEF1 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     12    0
  ARHGEF1 WILD-TYPE  273   48
   clus
vv  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  0              12               273
  1               0                48
[1] 2 2
[1] FALSE
D1216V7, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED     8   5
  ARHGEF1 WILD-TYPE 162 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED      8    5
  ARHGEF1 WILD-TYPE  162  192
        clus
vv       ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  FEMALE               8               162
  MALE                 5               192
[1] 2 2
[1] FALSE
D1216V8, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    12   0
  ARHGEF1 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     12    0
  ARHGEF1 WILD-TYPE  288    8
     clus
vv    ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D1216V9, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    13   0
  ARHGEF1 WILD-TYPE 301  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     13    0
  ARHGEF1 WILD-TYPE  301   48
                               clus
vv                              ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGEF1 MUTATED    10   0   0   1
  ARHGEF1 WILD-TYPE 249   3  22  20
D1216V10, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               1                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"
D1216V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF1 MUTATED                                  0     1
  ARHGEF1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF1 MUTATED                           1     6
  ARHGEF1 WILD-TYPE                        18   170
D1216V12, multiclass
                                  clus
vv                                 ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[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 = ZNF559 MUTATION ANALYSIS
D1217V1, survival
                  sevent
clus2                0   1
  ZNF559 MUTATED    12   3
  ZNF559 WILD-TYPE 265  75
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              15              340 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
               3               75 
$`ZNF559 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-A6-3810 TCGA-A6-6141 TCGA-AA-3710 TCGA-AA-A00A 
        0.92        19.04        36.53         8.38        26.99        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 
       21.99        35.97        35.31 

$`ZNF559 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF559 MUTATED ZNF559 WILD-TYPE 
            0.92             0.00 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
           58.39           148.01 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
          21.990           22.075 
[1] "0.9 - 58.4 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1217V2, continuous
                  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      62        1       25       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF559 MUTATED           1          0          2          0        0
  ZNF559 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF559 MUTATED           0         0
  ZNF559 WILD-TYPE        12         1
D1217V3, multiclass
            clus
vv           ZNF559 MUTATED ZNF559 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF559 MUTATED     0   2  11   2
  ZNF559 WILD-TYPE   9  65 238  39
D1217V4, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             11              238
  T4              2               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
  ZNF559 MUTATED    12   3   0
  ZNF559 WILD-TYPE 208  78  66
D1217V5, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  N0             12              208
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1217V6, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    14   0
  ZNF559 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     14    0
  ZNF559 WILD-TYPE  271   48
   clus
vv  ZNF559 MUTATED ZNF559 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D1217V7, binary
                  cls
clus                 0   1
  ZNF559 MUTATED     4  11
  ZNF559 WILD-TYPE 166 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED      4   11
  ZNF559 WILD-TYPE  166  186
        clus
vv       ZNF559 MUTATED ZNF559 WILD-TYPE
  FEMALE              4              166
  MALE               11              186
[1] 2 2
[1] FALSE
D1217V8, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    14   0
  ZNF559 WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     14    0
  ZNF559 WILD-TYPE  286    8
     clus
vv    ZNF559 MUTATED ZNF559 WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D1217V9, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    12   3
  ZNF559 WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     12    3
  ZNF559 WILD-TYPE  302   45
                               clus
vv                              ZNF559 MUTATED ZNF559 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF559 MUTATED    11   0   0   2
  ZNF559 WILD-TYPE 248   3  22  19
D1217V10, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              2               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"
D1217V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF559 MUTATED                                  0     2
  ZNF559 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF559 MUTATED                           1     6
  ZNF559 WILD-TYPE                        18   170
D1217V12, multiclass
                                  clus
vv                                 ZNF559 MUTATED ZNF559 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = EPHA7 MUTATION ANALYSIS
D1218V1, survival
                 sevent
clus2               0   1
  EPHA7 MUTATED    24  10
  EPHA7 WILD-TYPE 253  68
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             34             321 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             10              68 
$`EPHA7 MUTATED`
TCGA-AA-3496 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6964 TCGA-G4-6321 TCGA-A6-3809 
        1.02        19.04        19.04        10.88        22.09        32.75 
TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3858 
        3.02        29.95         6.97        26.99        33.04        31.07 
TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6196 
        2.01         4.01        34.98        12.16        22.42         0.20 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-6751 
       58.39         5.23        12.76        10.06        17.56       124.27 
TCGA-CM-5349 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 
       30.08        12.00        14.04        17.85        12.49        15.58 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A28G 
       13.35        49.91         7.50        60.79 

$`EPHA7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        35.80        26.17        91.79        79.69 
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-A6-3810 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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        27.42        26.47        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
       12.39        12.59        12.59        12.20        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  EPHA7 MUTATED EPHA7 WILD-TYPE 
            0.2             0.0 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
         124.27          148.01 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
          16.57           22.98 
[1] "0.2 - 124.3 (16.6)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1.7"
D1218V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA7 MUTATED         4        0        4        13         3         0
  EPHA7 WILD-TYPE      60        1       22        95         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA7 MUTATED           2          0          3          2        1         0
  EPHA7 WILD-TYPE        16          6         41         31       34        12
                 vv
clus              STAGE IVB
  EPHA7 MUTATED           0
  EPHA7 WILD-TYPE         1
D1218V3, multiclass
            clus
vv           EPHA7 MUTATED EPHA7 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             13              95
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  EPHA7 MUTATED     0   5  24   6
  EPHA7 WILD-TYPE   9  62 225  35
D1218V4, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            24             225
  T4             6              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
  EPHA7 MUTATED    27   4   4
  EPHA7 WILD-TYPE 193  77  62
D1218V5, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  N0            27             193
  N1             4              77
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1218V6, binary
                 cls
clus                0   1
  EPHA7 MUTATED    28   1
  EPHA7 WILD-TYPE 257  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     28    1
  EPHA7 WILD-TYPE  257   47
   clus
vv  EPHA7 MUTATED EPHA7 WILD-TYPE
  0            28             257
  1             1              47
[1] 2 2
[1] FALSE
D1218V7, binary
                 cls
clus                0   1
  EPHA7 MUTATED    16  19
  EPHA7 WILD-TYPE 154 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     16   19
  EPHA7 WILD-TYPE  154  178
        clus
vv       EPHA7 MUTATED EPHA7 WILD-TYPE
  FEMALE            16             154
  MALE              19             178
[1] 2 2
[1] FALSE
D1218V8, binary
                 cls
clus                0   1
  EPHA7 MUTATED    26   1
  EPHA7 WILD-TYPE 274   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     26    1
  EPHA7 WILD-TYPE  274    7
     clus
vv    EPHA7 MUTATED EPHA7 WILD-TYPE
  NO             26             274
  YES             1               7
[1] 2 2
[1] FALSE
D1218V9, binary
                 cls
clus                0   1
  EPHA7 MUTATED    24  11
  EPHA7 WILD-TYPE 290  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     24   11
  EPHA7 WILD-TYPE  290   37
                               clus
vv                              EPHA7 MUTATED EPHA7 WILD-TYPE
  COLON ADENOCARCINOMA                     24             290
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA7 MUTATED    23   0   1   4
  EPHA7 WILD-TYPE 236   3  21  17
D1218V10, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  R0            23             236
  R1             0               3
  R2             1              21
  RX             4              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"
D1218V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA7 MUTATED                                  0     2
  EPHA7 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA7 MUTATED                           0    20
  EPHA7 WILD-TYPE                        19   156
D1218V12, multiclass
                                  clus
vv                                 EPHA7 MUTATED EPHA7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       20             156
[1] 4 2
[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 = KCTD9 MUTATION ANALYSIS
D1219V1, survival
                 sevent
clus2               0   1
  KCTD9 MUTATED     5   0
  KCTD9 WILD-TYPE 272  78
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             350 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              0              78 
$`KCTD9 MUTATED`
TCGA-G4-6628 TCGA-A6-6781 TCGA-AD-5900 TCGA-CM-6162 TCGA-CM-6674 
       79.69        19.66        12.16        12.00        12.95 

$`KCTD9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KCTD9 MUTATED KCTD9 WILD-TYPE 
             12               0 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          79.69          148.01 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          12.95           22.09 
[1] "12.0 - 79.7 (12.9)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1219V2, continuous
                 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      62        1       26       107         8         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  KCTD9 MUTATED           0
  KCTD9 WILD-TYPE         1
D1219V3, multiclass
            clus
vv           KCTD9 MUTATED KCTD9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  KCTD9 MUTATED     0   2   2   1
  KCTD9 WILD-TYPE   9  65 247  40
D1219V4, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             2             247
  T4             1              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
  KCTD9 MUTATED     3   2   0
  KCTD9 WILD-TYPE 217  79  66
D1219V5, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  N0             3             217
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1219V6, binary
                 cls
clus                0   1
  KCTD9 MUTATED     3   0
  KCTD9 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      3    0
  KCTD9 WILD-TYPE  282   48
   clus
vv  KCTD9 MUTATED KCTD9 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1219V7, binary
                 cls
clus                0   1
  KCTD9 MUTATED     1   4
  KCTD9 WILD-TYPE 169 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      1    4
  KCTD9 WILD-TYPE  169  193
        clus
vv       KCTD9 MUTATED KCTD9 WILD-TYPE
  FEMALE             1             169
  MALE               4             193
[1] 2 2
[1] FALSE
D1219V8, binary
                 cls
clus                0   1
  KCTD9 MUTATED     5   0
  KCTD9 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      5    0
  KCTD9 WILD-TYPE  295    8
     clus
vv    KCTD9 MUTATED KCTD9 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1219V9, binary
                 cls
clus                0   1
  KCTD9 MUTATED     2   3
  KCTD9 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      2    3
  KCTD9 WILD-TYPE  312   45
                               clus
vv                              KCTD9 MUTATED KCTD9 WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCTD9 MUTATED     5   0   0   0
  KCTD9 WILD-TYPE 254   3  22  21
D1219V10, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1219V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD9 MUTATED                                  0     0
  KCTD9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCTD9 MUTATED                           0     5
  KCTD9 WILD-TYPE                        19   171
D1219V12, multiclass
                                  clus
vv                                 KCTD9 MUTATED KCTD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = CD47 MUTATION ANALYSIS
D1220V1, survival
                sevent
clus2              0   1
  CD47 MUTATED     6   0
  CD47 WILD-TYPE 271  78
  CD47 MUTATED CD47 WILD-TYPE 
             6            349 
  CD47 MUTATED CD47 WILD-TYPE 
             0             78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.090 
[1] "12.8 - 35.0 (16.3)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1220V2, continuous
                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      64        1       25       106         6         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        17          6         44         32       35        11
                vv
clus             STAGE IVB
  CD47 MUTATED           0
  CD47 WILD-TYPE         1
D1220V3, multiclass
            clus
vv           CD47 MUTATED CD47 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  CD47 MUTATED     0   0   3   5
  CD47 WILD-TYPE   9  67 246  36
D1220V4, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            3            246
  T4            5             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
  CD47 MUTATED     5   1   2
  CD47 WILD-TYPE 215  80  64
D1220V5, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1220V6, binary
                cls
clus               0   1
  CD47 MUTATED     7   1
  CD47 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      7    1
  CD47 WILD-TYPE  278   47
   clus
vv  CD47 MUTATED CD47 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D1220V7, binary
                cls
clus               0   1
  CD47 MUTATED     5   3
  CD47 WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      5    3
  CD47 WILD-TYPE  165  194
        clus
vv       CD47 MUTATED CD47 WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D1220V8, binary
                cls
clus               0   1
  CD47 MUTATED     5   0
  CD47 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      5    0
  CD47 WILD-TYPE  295    8
     clus
vv    CD47 MUTATED CD47 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1220V9, binary
                cls
clus               0   1
  CD47 MUTATED     5   3
  CD47 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      5    3
  CD47 WILD-TYPE  309   45
                               clus
vv                              CD47 MUTATED CD47 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD47 MUTATED     6   0   0   2
  CD47 WILD-TYPE 253   3  22  19
D1220V10, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            2             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"
D1220V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD47 MUTATED                                  0     1
  CD47 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD47 MUTATED                           0     3
  CD47 WILD-TYPE                        19   173
D1220V12, multiclass
                                  clus
vv                                 CD47 MUTATED CD47 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = PTPRB MUTATION ANALYSIS
D1221V1, survival
                 sevent
clus2               0   1
  PTPRB MUTATED    14   1
  PTPRB WILD-TYPE 263  77
  PTPRB MUTATED PTPRB WILD-TYPE 
             15             340 
  PTPRB MUTATED PTPRB WILD-TYPE 
              1              77 
$`PTPRB MUTATED`
TCGA-AA-3713 TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3864 
       19.04        30.44        24.39        63.98         0.00        53.00 
TCGA-AA-3949 TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6928 
       26.01        27.09         0.20        12.76        23.05        11.64 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-G4-6293 
       13.35       130.65       133.18 

$`PTPRB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PTPRB MUTATED PTPRB WILD-TYPE 
              0               0 
  PTPRB MUTATED PTPRB WILD-TYPE 
         133.18          148.01 
  PTPRB MUTATED PTPRB WILD-TYPE 
          24.39           22.01 
[1] "0.0 - 133.2 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "4.3"
D1221V2, continuous
                 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      60        1       24       101         8         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        17          6         43         32       34        12
                 vv
clus              STAGE IVB
  PTPRB MUTATED           0
  PTPRB WILD-TYPE         1
D1221V3, multiclass
            clus
vv           PTPRB MUTATED PTPRB WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  PTPRB MUTATED     0   4  13   0
  PTPRB WILD-TYPE   9  63 236  41
D1221V4, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  T1             0               9
  T2             4              63
  T3            13             236
  T4             0              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
  PTPRB MUTATED    14   2   1
  PTPRB WILD-TYPE 206  79  65
D1221V5, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  N0            14             206
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1221V6, binary
                 cls
clus                0   1
  PTPRB MUTATED    14   1
  PTPRB WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     14    1
  PTPRB WILD-TYPE  271   47
   clus
vv  PTPRB MUTATED PTPRB WILD-TYPE
  0            14             271
  1             1              47
[1] 2 2
[1] FALSE
D1221V7, binary
                 cls
clus                0   1
  PTPRB MUTATED     6  11
  PTPRB WILD-TYPE 164 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED      6   11
  PTPRB WILD-TYPE  164  186
        clus
vv       PTPRB MUTATED PTPRB WILD-TYPE
  FEMALE             6             164
  MALE              11             186
[1] 2 2
[1] FALSE
D1221V8, binary
                 cls
clus                0   1
  PTPRB MUTATED    10   1
  PTPRB WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     10    1
  PTPRB WILD-TYPE  290    7
     clus
vv    PTPRB MUTATED PTPRB WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1221V9, binary
                 cls
clus                0   1
  PTPRB MUTATED    12   5
  PTPRB WILD-TYPE 302  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     12    5
  PTPRB WILD-TYPE  302   43
                               clus
vv                              PTPRB MUTATED PTPRB WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRB MUTATED    12   0   1   2
  PTPRB WILD-TYPE 247   3  21  19
D1221V10, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  R0            12             247
  R1             0               3
  R2             1              21
  RX             2              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"
D1221V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRB MUTATED                                  0     1
  PTPRB WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRB MUTATED                           0    10
  PTPRB WILD-TYPE                        19   166
D1221V12, multiclass
                                  clus
vv                                 PTPRB MUTATED PTPRB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1222) Variable = GPR113 MUTATION ANALYSIS
D1222V1, survival
                  sevent
clus2                0   1
  GPR113 MUTATED    12   1
  GPR113 WILD-TYPE 265  77
  GPR113 MUTATED GPR113 WILD-TYPE 
              13              342 
  GPR113 MUTATED GPR113 WILD-TYPE 
               1               77 
$`GPR113 MUTATED`
TCGA-AZ-6601 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3519 TCGA-AA-3663 TCGA-AA-3710 
      100.01        33.53        63.98         9.07         6.97        26.99 
TCGA-AA-3877 TCGA-AA-3966 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4743 TCGA-D5-6532 
       31.00         2.01        12.76        15.62        23.05        18.25 
TCGA-D5-6928 
       11.64 

$`GPR113 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 
       35.01         6.97         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GPR113 MUTATED GPR113 WILD-TYPE 
            2.01             0.00 
  GPR113 MUTATED GPR113 WILD-TYPE 
          100.01           148.01 
  GPR113 MUTATED GPR113 WILD-TYPE 
          18.250           22.075 
[1] "2.0 - 100.0 (18.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3"  
D1222V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR113 MUTATED         1        0        3         7         1         0
  GPR113 WILD-TYPE      63        1       23       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR113 MUTATED           1          0          0          1        0
  GPR113 WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR113 MUTATED           0         0
  GPR113 WILD-TYPE        12         1
D1222V3, multiclass
            clus
vv           GPR113 MUTATED GPR113 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  GPR113 MUTATED     1   0  11   2
  GPR113 WILD-TYPE   8  67 238  39
D1222V4, multiclass
    clus
vv   GPR113 MUTATED GPR113 WILD-TYPE
  T1              1                8
  T2              0               67
  T3             11              238
  T4              2               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
  GPR113 MUTATED    12   1   1
  GPR113 WILD-TYPE 208  80  65
D1222V5, multiclass
    clus
vv   GPR113 MUTATED GPR113 WILD-TYPE
  N0             12              208
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1222V6, binary
                  cls
clus                 0   1
  GPR113 MUTATED    13   0
  GPR113 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR113 MUTATED     13    0
  GPR113 WILD-TYPE  272   48
   clus
vv  GPR113 MUTATED GPR113 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D1222V7, binary
                  cls
clus                 0   1
  GPR113 MUTATED     6   8
  GPR113 WILD-TYPE 164 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR113 MUTATED      6    8
  GPR113 WILD-TYPE  164  189
        clus
vv       GPR113 MUTATED GPR113 WILD-TYPE
  FEMALE              6              164
  MALE                8              189
[1] 2 2
[1] FALSE
D1222V8, binary
                  cls
clus                 0   1
  GPR113 MUTATED    11   0
  GPR113 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR113 MUTATED     11    0
  GPR113 WILD-TYPE  289    8
     clus
vv    GPR113 MUTATED GPR113 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1222V9, binary
                  cls
clus                 0   1
  GPR113 MUTATED     9   5
  GPR113 WILD-TYPE 305  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR113 MUTATED      9    5
  GPR113 WILD-TYPE  305   43
                               clus
vv                              GPR113 MUTATED GPR113 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR113 MUTATED     9   0   0   3
  GPR113 WILD-TYPE 250   3  22  18
D1222V10, multiclass
    clus
vv   GPR113 MUTATED GPR113 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              3               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"
D1222V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR113 MUTATED                                  0     1
  GPR113 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR113 MUTATED                           1     6
  GPR113 WILD-TYPE                        18   170
D1222V12, multiclass
                                  clus
vv                                 GPR113 MUTATED GPR113 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = KIAA1407 MUTATION ANALYSIS
D1223V1, survival
                    sevent
clus2                  0   1
  KIAA1407 MUTATED     8   3
  KIAA1407 WILD-TYPE 269  75
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                11                344 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                 3                 75 
$`KIAA1407 MUTATED`
TCGA-AA-3697 TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 
       85.05        23.87        26.99        33.04        25.02        34.98 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6718 TCGA-CM-6171 TCGA-CM-6676 
       49.41         5.23        10.06        14.04        11.08 

$`KIAA1407 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
              5.23               0.00 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
             85.05             148.01 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
             25.02              22.01 
[1] "5.2 - 85.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1223V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1407 MUTATED         2        0        2         3         1         0
  KIAA1407 WILD-TYPE      62        1       24       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1407 MUTATED           0          0          2          0        0
  KIAA1407 WILD-TYPE        18          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1407 MUTATED           0         0
  KIAA1407 WILD-TYPE        12         1
D1223V3, multiclass
            clus
vv           KIAA1407 MUTATED KIAA1407 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 3                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA1407 MUTATED     0   3   6   2
  KIAA1407 WILD-TYPE   9  64 243  39
D1223V4, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3                6                243
  T4                2                 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
  KIAA1407 MUTATED     9   2   0
  KIAA1407 WILD-TYPE 211  79  66
D1223V5, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  N0                9                211
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1223V6, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED     9   0
  KIAA1407 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED      9    0
  KIAA1407 WILD-TYPE  276   48
   clus
vv  KIAA1407 MUTATED KIAA1407 WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D1223V7, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED     6   5
  KIAA1407 WILD-TYPE 164 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED      6    5
  KIAA1407 WILD-TYPE  164  192
        clus
vv       KIAA1407 MUTATED KIAA1407 WILD-TYPE
  FEMALE                6                164
  MALE                  5                192
[1] 2 2
[1] FALSE
D1223V8, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED    11   0
  KIAA1407 WILD-TYPE 289   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED     11    0
  KIAA1407 WILD-TYPE  289    8
     clus
vv    KIAA1407 MUTATED KIAA1407 WILD-TYPE
  NO                11                289
  YES                0                  8
[1] 2 2
[1] FALSE
D1223V9, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED    11   0
  KIAA1407 WILD-TYPE 303  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED     11    0
  KIAA1407 WILD-TYPE  303   48
                               clus
vv                              KIAA1407 MUTATED KIAA1407 WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1407 MUTATED     6   0   0   1
  KIAA1407 WILD-TYPE 253   3  22  20
D1223V10, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1223V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1407 MUTATED                                  0     1
  KIAA1407 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1407 MUTATED                           0     5
  KIAA1407 WILD-TYPE                        19   171
D1223V12, multiclass
                                  clus
vv                                 KIAA1407 MUTATED KIAA1407 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = PCDH20 MUTATION ANALYSIS
D1224V1, survival
                  sevent
clus2                0   1
  PCDH20 MUTATED    12   8
  PCDH20 WILD-TYPE 265  70
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              20              335 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
               8               70 
$`PCDH20 MUTATED`
TCGA-A6-6649 TCGA-AA-3672 TCGA-G4-6628 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3850 
       24.16         0.92        79.69        20.28         3.02         0.00 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 
       33.01        25.02        34.98        27.09        58.39        49.41 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5864 TCGA-D5-5537 TCGA-DM-A1D8 TCGA-DM-A1DA 
       10.06        51.32        15.02        45.40        12.59         7.50 
TCGA-G4-6293 TCGA-G4-6626 
      133.18        46.75 

$`PCDH20 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.12        19.66         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32       140.38        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        13.78 

  PCDH20 MUTATED PCDH20 WILD-TYPE 
               0                0 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
          133.18           148.01 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
          26.055           21.990 
[1] "0.0 - 133.2 (26.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1224V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH20 MUTATED         4        0        3         5         3         0
  PCDH20 WILD-TYPE      60        1       23       103         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH20 MUTATED           2          0          1          1        0
  PCDH20 WILD-TYPE        16          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  PCDH20 MUTATED           0         0
  PCDH20 WILD-TYPE        12         1
D1224V3, multiclass
            clus
vv           PCDH20 MUTATED PCDH20 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               5              103
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  PCDH20 MUTATED     0   5  13   3
  PCDH20 WILD-TYPE   9  62 236  38
D1224V4, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  T1              0                9
  T2              5               62
  T3             13              236
  T4              3               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
  PCDH20 MUTATED    15   4   2
  PCDH20 WILD-TYPE 205  77  64
D1224V5, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  N0             15              205
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1224V6, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    15   0
  PCDH20 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     15    0
  PCDH20 WILD-TYPE  270   48
   clus
vv  PCDH20 MUTATED PCDH20 WILD-TYPE
  0             15              270
  1              0               48
[1] 2 2
[1] FALSE
D1224V7, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    10  11
  PCDH20 WILD-TYPE 160 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     10   11
  PCDH20 WILD-TYPE  160  186
        clus
vv       PCDH20 MUTATED PCDH20 WILD-TYPE
  FEMALE             10              160
  MALE               11              186
[1] 2 2
[1] FALSE
D1224V8, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    16   0
  PCDH20 WILD-TYPE 284   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     16    0
  PCDH20 WILD-TYPE  284    8
     clus
vv    PCDH20 MUTATED PCDH20 WILD-TYPE
  NO              16              284
  YES              0                8
[1] 2 2
[1] FALSE
D1224V9, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    20   1
  PCDH20 WILD-TYPE 294  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     20    1
  PCDH20 WILD-TYPE  294   47
                               clus
vv                              PCDH20 MUTATED PCDH20 WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PCDH20 MUTATED    12   0   0   3
  PCDH20 WILD-TYPE 247   3  22  18
D1224V10, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              3               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"
D1224V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH20 MUTATED                                  0     1
  PCDH20 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PCDH20 MUTATED                           0    13
  PCDH20 WILD-TYPE                        19   163
D1224V12, multiclass
                                  clus
vv                                 PCDH20 MUTATED PCDH20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        13              163
[1] 4 2
[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 = ADH1B MUTATION ANALYSIS
D1225V1, survival
                 sevent
clus2               0   1
  ADH1B MUTATED     4   3
  ADH1B WILD-TYPE 273  75
  ADH1B MUTATED ADH1B WILD-TYPE 
              7             348 
  ADH1B MUTATED ADH1B WILD-TYPE 
              3              75 
$`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 
        6.18 

$`ADH1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02H TCGA-AA-A02J 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ADH1B MUTATED ADH1B WILD-TYPE 
           5.03            0.00 
  ADH1B MUTATED ADH1B WILD-TYPE 
          51.32          148.01 
  ADH1B MUTATED ADH1B WILD-TYPE 
         16.140          22.075 
[1] "5.0 - 51.3 (16.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1225V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADH1B MUTATED         2        0        0         2         0         0
  ADH1B WILD-TYPE      62        1       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADH1B MUTATED           1          0          0          0        1         1
  ADH1B WILD-TYPE        17          6         44         33       34        11
                 vv
clus              STAGE IVB
  ADH1B MUTATED           0
  ADH1B WILD-TYPE         1
D1225V3, multiclass
            clus
vv           ADH1B MUTATED ADH1B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  ADH1B MUTATED     0   2   5   0
  ADH1B WILD-TYPE   9  65 244  41
D1225V4, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             0              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
  ADH1B MUTATED     4   2   1
  ADH1B WILD-TYPE 216  79  65
D1225V5, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  N0             4             216
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1225V6, binary
                 cls
clus                0   1
  ADH1B MUTATED     4   2
  ADH1B WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      4    2
  ADH1B WILD-TYPE  281   46
   clus
vv  ADH1B MUTATED ADH1B WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D1225V7, binary
                 cls
clus                0   1
  ADH1B MUTATED     4   3
  ADH1B WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      4    3
  ADH1B WILD-TYPE  166  194
        clus
vv       ADH1B MUTATED ADH1B WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1225V8, binary
                 cls
clus                0   1
  ADH1B MUTATED     7   0
  ADH1B WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      7    0
  ADH1B WILD-TYPE  293    8
     clus
vv    ADH1B MUTATED ADH1B WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1225V9, binary
                 cls
clus                0   1
  ADH1B MUTATED     5   2
  ADH1B WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      5    2
  ADH1B WILD-TYPE  309   46
                               clus
vv                              ADH1B MUTATED ADH1B WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ADH1B MUTATED     4   0   1   1
  ADH1B WILD-TYPE 255   3  21  20
D1225V10, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             1              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"
D1225V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADH1B MUTATED                                  0     0
  ADH1B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADH1B MUTATED                           1     4
  ADH1B WILD-TYPE                        18   172
D1225V12, multiclass
                                  clus
vv                                 ADH1B MUTATED ADH1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = TGIF1 MUTATION ANALYSIS
D1226V1, survival
                 sevent
clus2               0   1
  TGIF1 MUTATED     6   2
  TGIF1 WILD-TYPE 271  76
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              8             347 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              2              76 
$`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        12.39         9.44 
TCGA-D5-6932 TCGA-DM-A28C 
       11.38        81.37 

$`TGIF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3850 
       15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-A28E 
        7.50        44.32       131.51       135.65       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TGIF1 MUTATED TGIF1 WILD-TYPE 
           9.44            0.00 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
          81.37          148.01 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
         12.295          22.090 
[1] "9.4 - 81.4 (12.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1226V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGIF1 MUTATED         1        0        1         6         0         0
  TGIF1 WILD-TYPE      63        1       25       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TGIF1 MUTATED           0          0          0          1        0         0
  TGIF1 WILD-TYPE        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  TGIF1 MUTATED           0
  TGIF1 WILD-TYPE         1
D1226V3, multiclass
            clus
vv           TGIF1 MUTATED TGIF1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TGIF1 MUTATED     0   1   8   0
  TGIF1 WILD-TYPE   9  66 241  41
D1226V4, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             0              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
  TGIF1 MUTATED     8   0   1
  TGIF1 WILD-TYPE 212  81  65
D1226V5, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1226V6, binary
                 cls
clus                0   1
  TGIF1 MUTATED     8   0
  TGIF1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      8    0
  TGIF1 WILD-TYPE  277   48
   clus
vv  TGIF1 MUTATED TGIF1 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1226V7, binary
                 cls
clus                0   1
  TGIF1 MUTATED     2   7
  TGIF1 WILD-TYPE 168 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      2    7
  TGIF1 WILD-TYPE  168  190
        clus
vv       TGIF1 MUTATED TGIF1 WILD-TYPE
  FEMALE             2             168
  MALE               7             190
[1] 2 2
[1] FALSE
D1226V8, binary
                 cls
clus                0   1
  TGIF1 MUTATED     7   0
  TGIF1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      7    0
  TGIF1 WILD-TYPE  293    8
     clus
vv    TGIF1 MUTATED TGIF1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1226V9, binary
                 cls
clus                0   1
  TGIF1 MUTATED     9   0
  TGIF1 WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      9    0
  TGIF1 WILD-TYPE  305   48
                               clus
vv                              TGIF1 MUTATED TGIF1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TGIF1 MUTATED     6   0   0   2
  TGIF1 WILD-TYPE 253   3  22  19
D1226V10, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1226V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGIF1 MUTATED                                  0     1
  TGIF1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TGIF1 MUTATED                           0     6
  TGIF1 WILD-TYPE                        19   170
D1226V12, multiclass
                                  clus
vv                                 TGIF1 MUTATED TGIF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = IGFBP3 MUTATION ANALYSIS
D1227V1, survival
                  sevent
clus2                0   1
  IGFBP3 MUTATED     4   2
  IGFBP3 WILD-TYPE 273  76
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               6              349 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               2               76 
$`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 

$`IGFBP3 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
            2.01             0.00 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
           58.39           148.01 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
           18.08            22.09 
[1] "2.0 - 58.4 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1227V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFBP3 MUTATED         1        0        0         3         0         0
  IGFBP3 WILD-TYPE      63        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP3 MUTATED           0          0          0          1        0
  IGFBP3 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  IGFBP3 MUTATED           1         0
  IGFBP3 WILD-TYPE        11         1
D1227V3, multiclass
            clus
vv           IGFBP3 MUTATED IGFBP3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  IGFBP3 MUTATED     1   0   4   1
  IGFBP3 WILD-TYPE   8  67 245  40
D1227V4, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              4              245
  T4              1               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
  IGFBP3 MUTATED     4   1   1
  IGFBP3 WILD-TYPE 216  80  65
D1227V5, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1227V6, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     5   1
  IGFBP3 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      5    1
  IGFBP3 WILD-TYPE  280   47
   clus
vv  IGFBP3 MUTATED IGFBP3 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D1227V7, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     5   1
  IGFBP3 WILD-TYPE 165 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      5    1
  IGFBP3 WILD-TYPE  165  196
        clus
vv       IGFBP3 MUTATED IGFBP3 WILD-TYPE
  FEMALE              5              165
  MALE                1              196
[1] 2 2
[1] FALSE
D1227V8, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     5   0
  IGFBP3 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      5    0
  IGFBP3 WILD-TYPE  295    8
     clus
vv    IGFBP3 MUTATED IGFBP3 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1227V9, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     5   1
  IGFBP3 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      5    1
  IGFBP3 WILD-TYPE  309   47
                               clus
vv                              IGFBP3 MUTATED IGFBP3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IGFBP3 MUTATED     4   0   0   1
  IGFBP3 WILD-TYPE 255   3  22  20
D1227V10, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D1227V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFBP3 MUTATED                                  0     0
  IGFBP3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IGFBP3 MUTATED                           0     5
  IGFBP3 WILD-TYPE                        19   171
D1227V12, multiclass
                                  clus
vv                                 IGFBP3 MUTATED IGFBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = POPDC3 MUTATION ANALYSIS
D1228V1, survival
                  sevent
clus2                0   1
  POPDC3 MUTATED     4   1
  POPDC3 WILD-TYPE 273  77
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               5              350 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               1               77 
$`POPDC3 MUTATED`
TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-6599 
        8.38        29.95        78.08        34.98         6.77 

$`POPDC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  POPDC3 MUTATED POPDC3 WILD-TYPE 
            6.77             0.00 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
           78.08           148.01 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
          29.950           22.045 
[1] "6.8 - 78.1 (29.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1228V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POPDC3 MUTATED         1        0        1         3         1         0
  POPDC3 WILD-TYPE      63        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POPDC3 MUTATED           0          0          0          0        0
  POPDC3 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  POPDC3 MUTATED           0         0
  POPDC3 WILD-TYPE        12         1
D1228V3, multiclass
            clus
vv           POPDC3 MUTATED POPDC3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  POPDC3 MUTATED     0   1   4   1
  POPDC3 WILD-TYPE   9  66 245  40
D1228V4, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              1               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
  POPDC3 MUTATED     6   0   0
  POPDC3 WILD-TYPE 214  81  66
D1228V5, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1228V6, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     5   0
  POPDC3 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      5    0
  POPDC3 WILD-TYPE  280   48
   clus
vv  POPDC3 MUTATED POPDC3 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1228V7, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     4   2
  POPDC3 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      4    2
  POPDC3 WILD-TYPE  166  195
        clus
vv       POPDC3 MUTATED POPDC3 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D1228V8, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     5   0
  POPDC3 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      5    0
  POPDC3 WILD-TYPE  295    8
     clus
vv    POPDC3 MUTATED POPDC3 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1228V9, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     5   1
  POPDC3 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      5    1
  POPDC3 WILD-TYPE  309   47
                               clus
vv                              POPDC3 MUTATED POPDC3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  POPDC3 MUTATED     4   0   0   0
  POPDC3 WILD-TYPE 255   3  22  21
D1228V10, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D1228V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POPDC3 MUTATED                                  0     0
  POPDC3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  POPDC3 MUTATED                           1     1
  POPDC3 WILD-TYPE                        18   175
D1228V12, multiclass
[1] "Remove cluster labels:" "POPDC3 MUTATED"        
clus
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6142 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652       TCGA-A6-6653 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6600       TCGA-AZ-6603 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-CA-5254 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 

Clustering(1229) Variable = SNRNP200 MUTATION ANALYSIS
D1229V1, survival
                    sevent
clus2                  0   1
  SNRNP200 MUTATED    17   2
  SNRNP200 WILD-TYPE 260  76
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                19                336 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                 2                 76 
$`SNRNP200 MUTATED`
TCGA-AA-3554 TCGA-AA-A00L TCGA-G4-6321 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3685 
       17.95        38.04        22.09        23.87        20.12        37.05 
TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-A00N TCGA-AY-5543 TCGA-CA-5796 TCGA-CA-6717 
       10.06         1.02         4.01        33.01        12.39        12.76 
TCGA-CM-5348 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6536 TCGA-F4-6806 TCGA-G4-6304 
       22.98        12.95        25.48        17.85        41.42        53.62 
TCGA-G4-6307 
       55.04 

$`SNRNP200 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        24.00        19.07        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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-5797 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
              1.02               0.00 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
             55.04             148.01 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
            22.090             22.045 
[1] "1.0 - 55.0 (22.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1229V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNRNP200 MUTATED         2        0        1         8         2         0
  SNRNP200 WILD-TYPE      62        1       25       100         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNRNP200 MUTATED           2          0          3          0        0
  SNRNP200 WILD-TYPE        16          6         41         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SNRNP200 MUTATED           1         0
  SNRNP200 WILD-TYPE        11         1
D1229V3, multiclass
            clus
vv           SNRNP200 MUTATED SNRNP200 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 8                100
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  SNRNP200 MUTATED     0   3  14   3
  SNRNP200 WILD-TYPE   9  64 235  38
D1229V4, multiclass
    clus
vv   SNRNP200 MUTATED SNRNP200 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3               14                235
  T4                3                 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
  SNRNP200 MUTATED    14   5   1
  SNRNP200 WILD-TYPE 206  76  65
D1229V5, multiclass
    clus
vv   SNRNP200 MUTATED SNRNP200 WILD-TYPE
  N0               14                206
  N1                5                 76
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1229V6, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    17   1
  SNRNP200 WILD-TYPE 268  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     17    1
  SNRNP200 WILD-TYPE  268   47
   clus
vv  SNRNP200 MUTATED SNRNP200 WILD-TYPE
  0               17                268
  1                1                 47
[1] 2 2
[1] FALSE
D1229V7, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    12   8
  SNRNP200 WILD-TYPE 158 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     12    8
  SNRNP200 WILD-TYPE  158  189
        clus
vv       SNRNP200 MUTATED SNRNP200 WILD-TYPE
  FEMALE               12                158
  MALE                  8                189
[1] 2 2
[1] FALSE
D1229V8, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    18   0
  SNRNP200 WILD-TYPE 282   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     18    0
  SNRNP200 WILD-TYPE  282    8
     clus
vv    SNRNP200 MUTATED SNRNP200 WILD-TYPE
  NO                18                282
  YES                0                  8
[1] 2 2
[1] FALSE
D1229V9, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    15   5
  SNRNP200 WILD-TYPE 299  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     15    5
  SNRNP200 WILD-TYPE  299   43
                               clus
vv                              SNRNP200 MUTATED SNRNP200 WILD-TYPE
  COLON ADENOCARCINOMA                        15                299
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SNRNP200 MUTATED    17   0   0   1
  SNRNP200 WILD-TYPE 242   3  22  20
D1229V10, multiclass
    clus
vv   SNRNP200 MUTATED SNRNP200 WILD-TYPE
  R0               17                242
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1229V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNRNP200 MUTATED                                  0     2
  SNRNP200 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SNRNP200 MUTATED                           1    10
  SNRNP200 WILD-TYPE                        18   166
D1229V12, multiclass
                                  clus
vv                                 SNRNP200 MUTATED SNRNP200 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          10                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(1230) Variable = BEND2 MUTATION ANALYSIS
D1230V1, survival
                 sevent
clus2               0   1
  BEND2 MUTATED    17   4
  BEND2 WILD-TYPE 260  74
  BEND2 MUTATED BEND2 WILD-TYPE 
             21             334 
  BEND2 MUTATED BEND2 WILD-TYPE 
              4              74 
$`BEND2 MUTATED`
TCGA-AA-3516 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3514 TCGA-AA-3666 TCGA-AA-3710 
       13.02        32.75        32.71         1.02         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        21.99        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       18.05         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10         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        12.36        12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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          22.045 
[1] "1.0 - 119.9 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1230V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BEND2 MUTATED         2        0        0         8         2         1
  BEND2 WILD-TYPE      62        1       26       100         6         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        15          6         40         32       35        12
                 vv
clus              STAGE IVB
  BEND2 MUTATED           0
  BEND2 WILD-TYPE         1
D1230V3, multiclass
            clus
vv           BEND2 MUTATED BEND2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  BEND2 MUTATED     1   3  14   5
  BEND2 WILD-TYPE   8  64 235  36
D1230V4, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            14             235
  T4             5              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
  BEND2 MUTATED    14   6   3
  BEND2 WILD-TYPE 206  75  63
D1230V5, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  N0            14             206
  N1             6              75
  N2             3              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"
D1230V6, binary
                 cls
clus                0   1
  BEND2 MUTATED    20   0
  BEND2 WILD-TYPE 265  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     20    0
  BEND2 WILD-TYPE  265   48
   clus
vv  BEND2 MUTATED BEND2 WILD-TYPE
  0            20             265
  1             0              48
[1] 2 2
[1] FALSE
D1230V7, binary
                 cls
clus                0   1
  BEND2 MUTATED    10  13
  BEND2 WILD-TYPE 160 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     10   13
  BEND2 WILD-TYPE  160  184
        clus
vv       BEND2 MUTATED BEND2 WILD-TYPE
  FEMALE            10             160
  MALE              13             184
[1] 2 2
[1] FALSE
D1230V8, binary
                 cls
clus                0   1
  BEND2 MUTATED    18   0
  BEND2 WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     18    0
  BEND2 WILD-TYPE  282    8
     clus
vv    BEND2 MUTATED BEND2 WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D1230V9, binary
                 cls
clus                0   1
  BEND2 MUTATED    16   7
  BEND2 WILD-TYPE 298  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     16    7
  BEND2 WILD-TYPE  298   41
                               clus
vv                              BEND2 MUTATED BEND2 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BEND2 MUTATED    16   0   0   3
  BEND2 WILD-TYPE 243   3  22  18
D1230V10, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             3              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"
D1230V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BEND2 MUTATED                                  0     2
  BEND2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BEND2 MUTATED                           0    12
  BEND2 WILD-TYPE                        19   164
D1230V12, multiclass
                                  clus
vv                                 BEND2 MUTATED BEND2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = MAP3K13 MUTATION ANALYSIS
D1231V1, survival
                   sevent
clus2                 0   1
  MAP3K13 MUTATED    13   5
  MAP3K13 WILD-TYPE 264  73
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
               18               337 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
                5                73 
$`MAP3K13 MUTATED`
TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3811 TCGA-AA-3864 
       24.00        35.80         8.38        24.39        10.06        53.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6599 
       33.01        26.01        25.02         4.01        34.98         6.77 
TCGA-AZ-6606 TCGA-CM-4746 TCGA-CM-6170 TCGA-CM-6680 TCGA-DM-A1D9 TCGA-F4-6570 
       11.74        37.02        15.02        12.03       140.38         6.18 

$`MAP3K13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       49.41        12.10        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-6717 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
             4.01              0.00 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
           140.38            148.01 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
           24.195            22.030 
[1] "4.0 - 140.4 (24.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1231V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP3K13 MUTATED         4        0        1         5         3         0
  MAP3K13 WILD-TYPE      60        1       25       103         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K13 MUTATED           1          0          2          0        1
  MAP3K13 WILD-TYPE        17          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  MAP3K13 MUTATED           0         0
  MAP3K13 WILD-TYPE        12         1
D1231V3, multiclass
            clus
vv           MAP3K13 MUTATED MAP3K13 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  MAP3K13 MUTATED     0   5   9   4
  MAP3K13 WILD-TYPE   9  62 240  37
D1231V4, multiclass
    clus
vv   MAP3K13 MUTATED MAP3K13 WILD-TYPE
  T1               0                 9
  T2               5                62
  T3               9               240
  T4               4                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
  MAP3K13 MUTATED    14   1   3
  MAP3K13 WILD-TYPE 206  80  63
D1231V5, multiclass
    clus
vv   MAP3K13 MUTATED MAP3K13 WILD-TYPE
  N0              14               206
  N1               1                80
  N2               3                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"
D1231V6, binary
                   cls
clus                  0   1
  MAP3K13 MUTATED    15   1
  MAP3K13 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K13 MUTATED     15    1
  MAP3K13 WILD-TYPE  270   47
   clus
vv  MAP3K13 MUTATED MAP3K13 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D1231V7, binary
                   cls
clus                  0   1
  MAP3K13 MUTATED    10   8
  MAP3K13 WILD-TYPE 160 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K13 MUTATED     10    8
  MAP3K13 WILD-TYPE  160  189
        clus
vv       MAP3K13 MUTATED MAP3K13 WILD-TYPE
  FEMALE              10               160
  MALE                 8               189
[1] 2 2
[1] FALSE
D1231V8, binary
                   cls
clus                  0   1
  MAP3K13 MUTATED    16   0
  MAP3K13 WILD-TYPE 284   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K13 MUTATED     16    0
  MAP3K13 WILD-TYPE  284    8
     clus
vv    MAP3K13 MUTATED MAP3K13 WILD-TYPE
  NO               16               284
  YES               0                 8
[1] 2 2
[1] FALSE
D1231V9, binary
                   cls
clus                  0   1
  MAP3K13 MUTATED    14   4
  MAP3K13 WILD-TYPE 300  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K13 MUTATED     14    4
  MAP3K13 WILD-TYPE  300   44
                               clus
vv                              MAP3K13 MUTATED MAP3K13 WILD-TYPE
  COLON ADENOCARCINOMA                       14               300
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  MAP3K13 MUTATED    12   0   0   0
  MAP3K13 WILD-TYPE 247   3  22  21
D1231V10, multiclass
    clus
vv   MAP3K13 MUTATED MAP3K13 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               0                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"
D1231V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP3K13 MUTATED                                  0     0
  MAP3K13 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MAP3K13 MUTATED                           2     8
  MAP3K13 WILD-TYPE                        17   168
D1231V12, multiclass
                                  clus
vv                                 MAP3K13 MUTATED MAP3K13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          8               168
[1] 4 2
[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 = ADAMTS16 MUTATION ANALYSIS
D1232V1, survival
                    sevent
clus2                  0   1
  ADAMTS16 MUTATED    22   7
  ADAMTS16 WILD-TYPE 255  71
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                29                326 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                 7                 71 
$`ADAMTS16 MUTATED`
TCGA-AA-3939 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3510 
       12.99        26.17        79.69        32.71        35.01        63.98 
TCGA-AA-3815 TCGA-AA-3854 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       33.04        36.03        20.98        25.02         4.01        34.98 
TCGA-AA-A01I TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6719 
       31.00         0.95        21.44        58.39        12.10        14.30 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6165 
       15.62        21.14        23.05        22.98        12.00        16.04 
TCGA-CM-6171 TCGA-D5-6537 TCGA-DM-A28C TCGA-DM-A28H TCGA-G4-6303 
       14.04         4.80        81.37       117.07        65.85 

$`ADAMTS16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-3511 TCGA-AA-3514 
       19.66        20.28         7.04         3.02         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       27.42        26.47        14.50        27.09        16.31        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32        21.99        82.95         2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F 
       44.32       131.51       135.65       139.17       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
              0.95               0.00 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
            117.07             148.01 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
             23.05              22.01 
[1] "0.9 - 117.1 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1232V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTS16 MUTATED         7        0        1        10         2         1
  ADAMTS16 WILD-TYPE      57        1       25        98         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS16 MUTATED           0          0          4          2        2
  ADAMTS16 WILD-TYPE        18          6         40         31       33
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTS16 MUTATED           0         0
  ADAMTS16 WILD-TYPE        12         1
D1232V3, multiclass
            clus
vv           ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  STAGE I                   7                 57
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                10                 98
  STAGE IIB                 2                  6
  STAGE IIC                 1                  0
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                4                 40
  STAGE IIIC                2                 31
  STAGE IV                  2                 33
  STAGE IVA                 0                 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
  ADAMTS16 MUTATED     2   7  16   5
  ADAMTS16 WILD-TYPE   7  60 233  36
D1232V4, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  T1                2                  7
  T2                7                 60
  T3               16                233
  T4                5                 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
  ADAMTS16 MUTATED    22   5   3
  ADAMTS16 WILD-TYPE 198  76  63
D1232V5, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  N0               22                198
  N1                5                 76
  N2                3                 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"
D1232V6, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    24   2
  ADAMTS16 WILD-TYPE 261  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     24    2
  ADAMTS16 WILD-TYPE  261   46
   clus
vv  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  0               24                261
  1                2                 46
[1] 2 2
[1] FALSE
D1232V7, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    11  19
  ADAMTS16 WILD-TYPE 159 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     11   19
  ADAMTS16 WILD-TYPE  159  178
        clus
vv       ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  FEMALE               11                159
  MALE                 19                178
[1] 2 2
[1] FALSE
D1232V8, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    25   0
  ADAMTS16 WILD-TYPE 275   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     25    0
  ADAMTS16 WILD-TYPE  275    8
     clus
vv    ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  NO                25                275
  YES                0                  8
[1] 2 2
[1] FALSE
D1232V9, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    25   4
  ADAMTS16 WILD-TYPE 289  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     25    4
  ADAMTS16 WILD-TYPE  289   44
                               clus
vv                              ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  COLON ADENOCARCINOMA                        25                289
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ADAMTS16 MUTATED    22   0   0   3
  ADAMTS16 WILD-TYPE 237   3  22  18
D1232V10, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  R0               22                237
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D1232V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS16 MUTATED                                  0     1
  ADAMTS16 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS16 MUTATED                           1    17
  ADAMTS16 WILD-TYPE                        18   159
D1232V12, multiclass
                                  clus
vv                                 ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          17                159
[1] 4 2
[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 = MAP3K10 MUTATION ANALYSIS
D1233V1, survival
                   sevent
clus2                 0   1
  MAP3K10 MUTATED     8   2
  MAP3K10 WILD-TYPE 269  76
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
               10               345 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
                2                76 
$`MAP3K10 MUTATED`
TCGA-AD-6964 TCGA-G4-6628 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3947 TCGA-D5-6535 
       10.88        79.69         6.97         1.02        33.01        15.12 
TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D6 TCGA-DM-A1HB 
       16.14        11.64        49.91       135.65 

$`MAP3K10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
             1.02              0.00 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
           135.65            148.01 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
            15.63             22.09 
[1] "1.0 - 135.7 (15.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1233V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP3K10 MUTATED         3        0        1         2         1         0
  MAP3K10 WILD-TYPE      61        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K10 MUTATED           0          0          2          0        0
  MAP3K10 WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  MAP3K10 MUTATED           0         0
  MAP3K10 WILD-TYPE        12         1
D1233V3, multiclass
            clus
vv           MAP3K10 MUTATED MAP3K10 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  MAP3K10 MUTATED     0   3   5   2
  MAP3K10 WILD-TYPE   9  64 244  39
D1233V4, multiclass
    clus
vv   MAP3K10 MUTATED MAP3K10 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               5               244
  T4               2                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
  MAP3K10 MUTATED     7   2   1
  MAP3K10 WILD-TYPE 213  79  65
D1233V5, multiclass
    clus
vv   MAP3K10 MUTATED MAP3K10 WILD-TYPE
  N0               7               213
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1233V6, binary
                   cls
clus                  0   1
  MAP3K10 MUTATED     8   0
  MAP3K10 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K10 MUTATED      8    0
  MAP3K10 WILD-TYPE  277   48
   clus
vv  MAP3K10 MUTATED MAP3K10 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D1233V7, binary
                   cls
clus                  0   1
  MAP3K10 MUTATED     3   7
  MAP3K10 WILD-TYPE 167 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K10 MUTATED      3    7
  MAP3K10 WILD-TYPE  167  190
        clus
vv       MAP3K10 MUTATED MAP3K10 WILD-TYPE
  FEMALE               3               167
  MALE                 7               190
[1] 2 2
[1] FALSE
D1233V8, binary
                   cls
clus                  0   1
  MAP3K10 MUTATED     8   0
  MAP3K10 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K10 MUTATED      8    0
  MAP3K10 WILD-TYPE  292    8
     clus
vv    MAP3K10 MUTATED MAP3K10 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1233V9, binary
                   cls
clus                  0   1
  MAP3K10 MUTATED     4   5
  MAP3K10 WILD-TYPE 310  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K10 MUTATED      4    5
  MAP3K10 WILD-TYPE  310   43
                               clus
vv                              MAP3K10 MUTATED MAP3K10 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  MAP3K10 MUTATED     6   0   0   1
  MAP3K10 WILD-TYPE 253   3  22  20
D1233V10, multiclass
    clus
vv   MAP3K10 MUTATED MAP3K10 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D1233V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP3K10 MUTATED                                  0     0
  MAP3K10 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MAP3K10 MUTATED                           0     7
  MAP3K10 WILD-TYPE                        19   169
D1233V12, multiclass
                                  clus
vv                                 MAP3K10 MUTATED MAP3K10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = RUNX2 MUTATION ANALYSIS
D1234V1, survival
                 sevent
clus2               0   1
  RUNX2 MUTATED     5   2
  RUNX2 WILD-TYPE 272  76
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              7             348 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              2              76 
$`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        12.16        27.09        21.14 
TCGA-F4-6570 
        6.18 

$`RUNX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RUNX2 MUTATED RUNX2 WILD-TYPE 
           6.18            0.00 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          53.00          148.01 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
         26.990          22.045 
[1] "6.2 - 53.0 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1234V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUNX2 MUTATED         3        0        1         3         1         0
  RUNX2 WILD-TYPE      61        1       25       105         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  RUNX2 MUTATED           0
  RUNX2 WILD-TYPE         1
D1234V3, multiclass
            clus
vv           RUNX2 MUTATED RUNX2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RUNX2 MUTATED     1   2   4   1
  RUNX2 WILD-TYPE   8  65 245  40
D1234V4, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             4             245
  T4             1              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
  RUNX2 MUTATED     8   0   0
  RUNX2 WILD-TYPE 212  81  66
D1234V5, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1234V6, binary
                 cls
clus                0   1
  RUNX2 MUTATED     7   0
  RUNX2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      7    0
  RUNX2 WILD-TYPE  278   48
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1234V7, binary
                 cls
clus                0   1
  RUNX2 MUTATED     6   2
  RUNX2 WILD-TYPE 164 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      6    2
  RUNX2 WILD-TYPE  164  195
        clus
vv       RUNX2 MUTATED RUNX2 WILD-TYPE
  FEMALE             6             164
  MALE               2             195
[1] 2 2
[1] FALSE
D1234V8, binary
                 cls
clus                0   1
  RUNX2 MUTATED     6   0
  RUNX2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      6    0
  RUNX2 WILD-TYPE  294    8
     clus
vv    RUNX2 MUTATED RUNX2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1234V9, binary
                 cls
clus                0   1
  RUNX2 MUTATED     6   2
  RUNX2 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      6    2
  RUNX2 WILD-TYPE  308   46
                               clus
vv                              RUNX2 MUTATED RUNX2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUNX2 MUTATED     7   0   0   1
  RUNX2 WILD-TYPE 252   3  22  20
D1234V10, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1234V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUNX2 MUTATED                                  0     0
  RUNX2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUNX2 MUTATED                           0     5
  RUNX2 WILD-TYPE                        19   171
D1234V12, multiclass
                                  clus
vv                                 RUNX2 MUTATED RUNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = SMARCA1 MUTATION ANALYSIS
D1235V1, survival
                   sevent
clus2                 0   1
  SMARCA1 MUTATED    13   5
  SMARCA1 WILD-TYPE 264  73
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               18               337 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
                5                73 
$`SMARCA1 MUTATED`
TCGA-AD-6964 TCGA-G4-6586 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3529 
       10.88        35.80        32.75        22.06        19.66         0.00 
TCGA-AA-3555 TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A01P TCGA-AU-3779 TCGA-AY-6197 
       29.95        25.02        18.05        38.07        14.50        21.44 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-5861 TCGA-D5-6536 TCGA-DM-A28G 
        6.77        12.76        82.95        15.02        17.85        60.79 

$`SMARCA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 
        1.02        38.99         1.02         9.07        19.07        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        26.47        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
                0                 0 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
            82.95            148.01 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
            20.55             22.09 
[1] "0.0 - 83.0 (20.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1235V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMARCA1 MUTATED         1        0        1        11         1         0
  SMARCA1 WILD-TYPE      63        1       25        97         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA1 MUTATED           1          0          0          2        0
  SMARCA1 WILD-TYPE        17          6         44         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SMARCA1 MUTATED           0         0
  SMARCA1 WILD-TYPE        12         1
D1235V3, multiclass
            clus
vv           SMARCA1 MUTATED SMARCA1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA               11                97
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  SMARCA1 MUTATED     0   2  13   4
  SMARCA1 WILD-TYPE   9  65 236  37
D1235V4, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              13               236
  T4               4                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
  SMARCA1 MUTATED    15   2   2
  SMARCA1 WILD-TYPE 205  79  64
D1235V5, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  N0              15               205
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1235V6, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    13   0
  SMARCA1 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     13    0
  SMARCA1 WILD-TYPE  272   48
   clus
vv  SMARCA1 MUTATED SMARCA1 WILD-TYPE
  0              13               272
  1               0                48
[1] 2 2
[1] FALSE
D1235V7, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    10   9
  SMARCA1 WILD-TYPE 160 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     10    9
  SMARCA1 WILD-TYPE  160  188
        clus
vv       SMARCA1 MUTATED SMARCA1 WILD-TYPE
  FEMALE              10               160
  MALE                 9               188
[1] 2 2
[1] FALSE
D1235V8, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    15   0
  SMARCA1 WILD-TYPE 285   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     15    0
  SMARCA1 WILD-TYPE  285    8
     clus
vv    SMARCA1 MUTATED SMARCA1 WILD-TYPE
  NO               15               285
  YES               0                 8
[1] 2 2
[1] FALSE
D1235V9, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    15   4
  SMARCA1 WILD-TYPE 299  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     15    4
  SMARCA1 WILD-TYPE  299   44
                               clus
vv                              SMARCA1 MUTATED SMARCA1 WILD-TYPE
  COLON ADENOCARCINOMA                       15               299
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SMARCA1 MUTATED    13   0   0   2
  SMARCA1 WILD-TYPE 246   3  22  19
D1235V10, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               2                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"
D1235V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA1 MUTATED                                  0     1
  SMARCA1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA1 MUTATED                           0    12
  SMARCA1 WILD-TYPE                        19   164
D1235V12, multiclass
                                  clus
vv                                 SMARCA1 MUTATED SMARCA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         12               164
[1] 4 2
[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 = ZNF41 MUTATION ANALYSIS
D1236V1, survival
                 sevent
clus2               0   1
  ZNF41 MUTATED     8   1
  ZNF41 WILD-TYPE 269  77
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              9             346 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              1              77 
$`ZNF41 MUTATED`
TCGA-AA-3939 TCGA-AA-3549 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CK-4947 TCGA-CK-6747 
       12.99        21.01        34.98        49.41        17.56        82.95 
TCGA-CM-4752 TCGA-D5-6532 TCGA-D5-6533 
       13.02        18.25        25.48 

$`ZNF41 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 
       26.01        12.99        14.01        33.99        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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-D5-6540 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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF41 MUTATED ZNF41 WILD-TYPE 
          12.99            0.00 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
          82.95          148.01 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
         21.010          22.075 
[1] "13.0 - 83.0 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1236V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF41 MUTATED         1        0        1         4         1         0
  ZNF41 WILD-TYPE      63        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF41 MUTATED           0          0          1          0        0         0
  ZNF41 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  ZNF41 MUTATED           0
  ZNF41 WILD-TYPE         1
D1236V3, multiclass
            clus
vv           ZNF41 MUTATED ZNF41 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ZNF41 MUTATED     0   1   5   3
  ZNF41 WILD-TYPE   9  66 244  38
D1236V4, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             3              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
  ZNF41 MUTATED     8   1   0
  ZNF41 WILD-TYPE 212  80  66
D1236V5, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1236V6, binary
                 cls
clus                0   1
  ZNF41 MUTATED     7   0
  ZNF41 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      7    0
  ZNF41 WILD-TYPE  278   48
   clus
vv  ZNF41 MUTATED ZNF41 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1236V7, binary
                 cls
clus                0   1
  ZNF41 MUTATED     5   4
  ZNF41 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      5    4
  ZNF41 WILD-TYPE  165  193
        clus
vv       ZNF41 MUTATED ZNF41 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1236V8, binary
                 cls
clus                0   1
  ZNF41 MUTATED     8   1
  ZNF41 WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      8    1
  ZNF41 WILD-TYPE  292    7
     clus
vv    ZNF41 MUTATED ZNF41 WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D1236V9, binary
                 cls
clus                0   1
  ZNF41 MUTATED     9   0
  ZNF41 WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      9    0
  ZNF41 WILD-TYPE  305   48
                               clus
vv                              ZNF41 MUTATED ZNF41 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZNF41 MUTATED     6   0   0   2
  ZNF41 WILD-TYPE 253   3  22  19
D1236V10, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1236V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF41 MUTATED                                  0     0
  ZNF41 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF41 MUTATED                           1     5
  ZNF41 WILD-TYPE                        18   171
D1236V12, multiclass
                                  clus
vv                                 ZNF41 MUTATED ZNF41 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = CD79A MUTATION ANALYSIS
D1237V1, survival
                 sevent
clus2               0   1
  CD79A MUTATED     5   1
  CD79A WILD-TYPE 272  77
  CD79A MUTATED CD79A WILD-TYPE 
              6             349 
  CD79A MUTATED CD79A WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.03 
[1] "12.0 - 53.0 (28.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1237V2, continuous
                 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      64        1       25       106         6         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  CD79A MUTATED           0
  CD79A WILD-TYPE         1
D1237V3, multiclass
            clus
vv           CD79A MUTATED CD79A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CD79A MUTATED     0   0   4   2
  CD79A WILD-TYPE   9  67 245  39
D1237V4, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             2              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
  CD79A MUTATED     5   0   1
  CD79A WILD-TYPE 215  81  65
D1237V5, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  N0             5             215
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1237V6, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  279   48
   clus
vv  CD79A MUTATED CD79A WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1237V7, binary
                 cls
clus                0   1
  CD79A MUTATED     3   3
  CD79A WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      3    3
  CD79A WILD-TYPE  167  194
        clus
vv       CD79A MUTATED CD79A WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1237V8, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  294    8
     clus
vv    CD79A MUTATED CD79A WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1237V9, binary
                 cls
clus                0   1
  CD79A MUTATED     5   1
  CD79A WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      5    1
  CD79A WILD-TYPE  309   47
                               clus
vv                              CD79A MUTATED CD79A WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CD79A MUTATED     6   0   0   0
  CD79A WILD-TYPE 253   3  22  21
D1237V10, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1237V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD79A MUTATED                                  0     0
  CD79A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD79A MUTATED                           1     3
  CD79A WILD-TYPE                        18   173
D1237V12, multiclass
                                  clus
vv                                 CD79A MUTATED CD79A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = TBX4 MUTATION ANALYSIS
D1238V1, survival
                sevent
clus2              0   1
  TBX4 MUTATED     7   4
  TBX4 WILD-TYPE 270  74
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            344 
  TBX4 MUTATED TBX4 WILD-TYPE 
             4             74 
$`TBX4 MUTATED`
TCGA-AZ-6601 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3877 
      100.01        33.53        24.39         3.02        53.00        31.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-5407 TCGA-CA-5254 TCGA-CA-6718 
        4.01        34.98        88.21        12.69        10.06 

$`TBX4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TBX4 MUTATED TBX4 WILD-TYPE 
          3.02           0.00 
  TBX4 MUTATED TBX4 WILD-TYPE 
        100.01         148.01 
  TBX4 MUTATED TBX4 WILD-TYPE 
         31.00          22.01 
[1] "3.0 - 100.0 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1238V2, continuous
                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      61        1       23       105         6         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  TBX4 MUTATED           0
  TBX4 WILD-TYPE         1
D1238V3, multiclass
            clus
vv           TBX4 MUTATED TBX4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TBX4 MUTATED     2   1   6   2
  TBX4 WILD-TYPE   7  66 243  39
D1238V4, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  T1            2              7
  T2            1             66
  T3            6            243
  T4            2             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
  TBX4 MUTATED    11   0   0
  TBX4 WILD-TYPE 209  81  66
D1238V5, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  N0           11            209
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1238V6, binary
                cls
clus               0   1
  TBX4 MUTATED    11   0
  TBX4 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     11    0
  TBX4 WILD-TYPE  274   48
   clus
vv  TBX4 MUTATED TBX4 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D1238V7, binary
                cls
clus               0   1
  TBX4 MUTATED     6   5
  TBX4 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      6    5
  TBX4 WILD-TYPE  164  192
        clus
vv       TBX4 MUTATED TBX4 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D1238V8, binary
                cls
clus               0   1
  TBX4 MUTATED    10   0
  TBX4 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     10    0
  TBX4 WILD-TYPE  290    8
     clus
vv    TBX4 MUTATED TBX4 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1238V9, binary
                cls
clus               0   1
  TBX4 MUTATED     9   2
  TBX4 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      9    2
  TBX4 WILD-TYPE  305   46
                               clus
vv                              TBX4 MUTATED TBX4 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TBX4 MUTATED     6   0   0   2
  TBX4 WILD-TYPE 253   3  22  19
D1238V10, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            2             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"
D1238V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBX4 MUTATED                                  0     2
  TBX4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TBX4 MUTATED                           1     3
  TBX4 WILD-TYPE                        18   173
D1238V12, multiclass
                                  clus
vv                                 TBX4 MUTATED TBX4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = EPSTI1 MUTATION ANALYSIS
D1239V1, survival
                  sevent
clus2                0   1
  EPSTI1 MUTATED     6   1
  EPSTI1 WILD-TYPE 271  77
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               7              348 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               1               77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
           12.76             0.00 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
           58.39           148.01 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
           33.67            21.99 
[1] "12.8 - 58.4 (33.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1239V2, continuous
                  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      62        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPSTI1 MUTATED           0          0          0          0        0
  EPSTI1 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  EPSTI1 MUTATED           0         0
  EPSTI1 WILD-TYPE        12         1
D1239V3, multiclass
            clus
vv           EPSTI1 MUTATED EPSTI1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  EPSTI1 MUTATED     1   2   3   1
  EPSTI1 WILD-TYPE   8  65 246  40
D1239V4, multiclass
    clus
vv   EPSTI1 MUTATED EPSTI1 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              3              246
  T4              1               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
  EPSTI1 MUTATED     7   0   0
  EPSTI1 WILD-TYPE 213  81  66
D1239V5, multiclass
    clus
vv   EPSTI1 MUTATED EPSTI1 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1239V6, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     5   0
  EPSTI1 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      5    0
  EPSTI1 WILD-TYPE  280   48
   clus
vv  EPSTI1 MUTATED EPSTI1 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1239V7, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     3   4
  EPSTI1 WILD-TYPE 167 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      3    4
  EPSTI1 WILD-TYPE  167  193
        clus
vv       EPSTI1 MUTATED EPSTI1 WILD-TYPE
  FEMALE              3              167
  MALE                4              193
[1] 2 2
[1] FALSE
D1239V8, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     7   0
  EPSTI1 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      7    0
  EPSTI1 WILD-TYPE  293    8
     clus
vv    EPSTI1 MUTATED EPSTI1 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1239V9, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     5   2
  EPSTI1 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      5    2
  EPSTI1 WILD-TYPE  309   46
                               clus
vv                              EPSTI1 MUTATED EPSTI1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EPSTI1 MUTATED     4   0   0   1
  EPSTI1 WILD-TYPE 255   3  22  20
D1239V10, multiclass
    clus
vv   EPSTI1 MUTATED EPSTI1 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D1239V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPSTI1 MUTATED                                  0     1
  EPSTI1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EPSTI1 MUTATED                           1     4
  EPSTI1 WILD-TYPE                        18   172
D1239V12, multiclass
                                  clus
vv                                 EPSTI1 MUTATED EPSTI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = TSPAN7 MUTATION ANALYSIS
D1240V1, survival
                  sevent
clus2                0   1
  TSPAN7 MUTATED     6   3
  TSPAN7 WILD-TYPE 271  75
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               9              346 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               3               75 
$`TSPAN7 MUTATED`
TCGA-DM-A285 TCGA-A6-5661 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-3966 
        5.88        33.53        23.87         3.02         0.00         2.01 
TCGA-AD-5900 TCGA-AU-6004 TCGA-D5-6930 
       12.16        27.09        13.35 

$`TSPAN7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               0                0 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
           33.53           148.01 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
           12.16            22.09 
[1] "0.0 - 33.5 (12.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D1240V2, continuous
                  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      62        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TSPAN7 MUTATED           0          0          1          0        1
  TSPAN7 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  TSPAN7 MUTATED           0         0
  TSPAN7 WILD-TYPE        12         1
D1240V3, multiclass
            clus
vv           TSPAN7 MUTATED TSPAN7 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  TSPAN7 MUTATED     0   2   7   0
  TSPAN7 WILD-TYPE   9  65 242  41
D1240V4, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              0               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
  TSPAN7 MUTATED     7   1   1
  TSPAN7 WILD-TYPE 213  80  65
D1240V5, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1240V6, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     7   1
  TSPAN7 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      7    1
  TSPAN7 WILD-TYPE  278   47
   clus
vv  TSPAN7 MUTATED TSPAN7 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D1240V7, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     7   2
  TSPAN7 WILD-TYPE 163 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      7    2
  TSPAN7 WILD-TYPE  163  195
        clus
vv       TSPAN7 MUTATED TSPAN7 WILD-TYPE
  FEMALE              7              163
  MALE                2              195
[1] 2 2
[1] FALSE
D1240V8, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     5   0
  TSPAN7 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      5    0
  TSPAN7 WILD-TYPE  295    8
     clus
vv    TSPAN7 MUTATED TSPAN7 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1240V9, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     5   4
  TSPAN7 WILD-TYPE 309  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      5    4
  TSPAN7 WILD-TYPE  309   44
                               clus
vv                              TSPAN7 MUTATED TSPAN7 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TSPAN7 MUTATED     6   0   0   0
  TSPAN7 WILD-TYPE 253   3  22  21
D1240V10, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1240V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSPAN7 MUTATED                                  0     0
  TSPAN7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TSPAN7 MUTATED                           1     5
  TSPAN7 WILD-TYPE                        18   171
D1240V12, multiclass
                                  clus
vv                                 TSPAN7 MUTATED TSPAN7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 264  72
  MED14 MUTATED MED14 WILD-TYPE 
             19             336 
  MED14 MUTATED MED14 WILD-TYPE 
              6              72 
$`MED14 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3518 TCGA-AA-3534 
       13.02         0.92        19.04        24.00         1.02        29.00 
TCGA-AA-3947 TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-5913 
       33.01        12.16        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        88.21         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       47.87        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  MED14 MUTATED MED14 WILD-TYPE 
           0.92            0.00 
  MED14 MUTATED MED14 WILD-TYPE 
         124.27          148.01 
  MED14 MUTATED MED14 WILD-TYPE 
          13.02           22.09 
[1] "0.9 - 124.3 (13.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1241V2, continuous
                 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      62        1       24       101         7         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        16          6         42         32       34        11
                 vv
clus              STAGE IVB
  MED14 MUTATED           0
  MED14 WILD-TYPE         1
D1241V3, multiclass
            clus
vv           MED14 MUTATED MED14 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  MED14 MUTATED     0   2  14   3
  MED14 WILD-TYPE   9  65 235  38
D1241V4, multiclass
    clus
vv   MED14 MUTATED MED14 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            14             235
  T4             3              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
  MED14 MUTATED    12   4   3
  MED14 WILD-TYPE 208  77  63
D1241V5, multiclass
    clus
vv   MED14 MUTATED MED14 WILD-TYPE
  N0            12             208
  N1             4              77
  N2             3              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"
D1241V6, binary
                 cls
clus                0   1
  MED14 MUTATED    12   2
  MED14 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     12    2
  MED14 WILD-TYPE  273   46
   clus
vv  MED14 MUTATED MED14 WILD-TYPE
  0            12             273
  1             2              46
[1] 2 2
[1] FALSE
D1241V7, binary
                 cls
clus                0   1
  MED14 MUTATED    14   5
  MED14 WILD-TYPE 156 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     14    5
  MED14 WILD-TYPE  156  192
        clus
vv       MED14 MUTATED MED14 WILD-TYPE
  FEMALE            14             156
  MALE               5             192
[1] 2 2
[1] FALSE
D1241V8, binary
                 cls
clus                0   1
  MED14 MUTATED    17   0
  MED14 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     17    0
  MED14 WILD-TYPE  283    8
     clus
vv    MED14 MUTATED MED14 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D1241V9, binary
                 cls
clus                0   1
  MED14 MUTATED    12   7
  MED14 WILD-TYPE 302  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     12    7
  MED14 WILD-TYPE  302   41
                               clus
vv                              MED14 MUTATED MED14 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED14 MUTATED    13   0   0   3
  MED14 WILD-TYPE 246   3  22  18
D1241V10, multiclass
    clus
vv   MED14 MUTATED MED14 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             3              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"
D1241V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED14 MUTATED                                  1     1
  MED14 WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED14 MUTATED                           1     9
  MED14 WILD-TYPE                        18   167
D1241V12, multiclass
                                  clus
vv                                 MED14 MUTATED MED14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(1242) Variable = DOCK7 MUTATION ANALYSIS
D1242V1, survival
                 sevent
clus2               0   1
  DOCK7 MUTATED    15   2
  DOCK7 WILD-TYPE 262  76
  DOCK7 MUTATED DOCK7 WILD-TYPE 
             17             338 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
              2              76 
$`DOCK7 MUTATED`
TCGA-AD-6895 TCGA-G4-6310 TCGA-G4-6628 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3710 
       25.08        63.62        79.69        22.06         1.02        26.99 
TCGA-AA-3956 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-4950 
       34.03        18.05         4.01        34.98        58.39        85.45 
TCGA-CK-5916 TCGA-CM-4746 TCGA-D5-6927 TCGA-D5-6929 TCGA-DM-A1HB 
       21.14        37.02         9.44        13.41       135.65 

$`DOCK7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DOCK7 MUTATED DOCK7 WILD-TYPE 
           1.02            0.00 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
         135.65          148.01 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
          26.99           21.99 
[1] "1.0 - 135.7 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D1242V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK7 MUTATED         3        0        0         6         2         0
  DOCK7 WILD-TYPE      61        1       26       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK7 MUTATED           0          0          5          0        1         0
  DOCK7 WILD-TYPE        18          6         39         33       34        12
                 vv
clus              STAGE IVB
  DOCK7 MUTATED           0
  DOCK7 WILD-TYPE         1
D1242V3, multiclass
            clus
vv           DOCK7 MUTATED DOCK7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  DOCK7 MUTATED     1   2  11   3
  DOCK7 WILD-TYPE   8  65 238  38
D1242V4, multiclass
    clus
vv   DOCK7 MUTATED DOCK7 WILD-TYPE
  T1             1               8
  T2             2              65
  T3            11             238
  T4             3              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
  DOCK7 MUTATED    11   6   0
  DOCK7 WILD-TYPE 209  75  66
D1242V5, multiclass
    clus
vv   DOCK7 MUTATED DOCK7 WILD-TYPE
  N0            11             209
  N1             6              75
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1242V6, binary
                 cls
clus                0   1
  DOCK7 MUTATED    16   1
  DOCK7 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK7 MUTATED     16    1
  DOCK7 WILD-TYPE  269   47
   clus
vv  DOCK7 MUTATED DOCK7 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D1242V7, binary
                 cls
clus                0   1
  DOCK7 MUTATED     7  10
  DOCK7 WILD-TYPE 163 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK7 MUTATED      7   10
  DOCK7 WILD-TYPE  163  187
        clus
vv       DOCK7 MUTATED DOCK7 WILD-TYPE
  FEMALE             7             163
  MALE              10             187
[1] 2 2
[1] FALSE
D1242V8, binary
                 cls
clus                0   1
  DOCK7 MUTATED    13   1
  DOCK7 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK7 MUTATED     13    1
  DOCK7 WILD-TYPE  287    7
     clus
vv    DOCK7 MUTATED DOCK7 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D1242V9, binary
                 cls
clus                0   1
  DOCK7 MUTATED    13   3
  DOCK7 WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK7 MUTATED     13    3
  DOCK7 WILD-TYPE  301   45
                               clus
vv                              DOCK7 MUTATED DOCK7 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK7 MUTATED    14   1   0   1
  DOCK7 WILD-TYPE 245   2  22  20
D1242V10, multiclass
    clus
vv   DOCK7 MUTATED DOCK7 WILD-TYPE
  R0            14             245
  R1             1               2
  R2             0              22
  RX             1              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"
D1242V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK7 MUTATED                                  0     0
  DOCK7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK7 MUTATED                           2     9
  DOCK7 WILD-TYPE                        17   167
D1242V12, multiclass
                                  clus
vv                                 DOCK7 MUTATED DOCK7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(1243) Variable = DBF4 MUTATION ANALYSIS
D1243V1, survival
                sevent
clus2              0   1
  DBF4 MUTATED     5   1
  DBF4 WILD-TYPE 272  77
  DBF4 MUTATED DBF4 WILD-TYPE 
             6            349 
  DBF4 MUTATED DBF4 WILD-TYPE 
             1             77 
$`DBF4 MUTATED`
TCGA-A6-3809 TCGA-AA-3663 TCGA-AA-A00J TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-7000 
       32.75         6.97        18.05        12.76        10.06        10.26 

$`DBF4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DBF4 MUTATED DBF4 WILD-TYPE 
          6.97           0.00 
  DBF4 MUTATED DBF4 WILD-TYPE 
         32.75         148.01 
  DBF4 MUTATED DBF4 WILD-TYPE 
         11.51          22.09 
[1] "7.0 - 32.8 (11.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1243V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DBF4 MUTATED         1        0        1         3         1         0
  DBF4 WILD-TYPE      63        1       25       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DBF4 MUTATED           0          0          1          0        0         0
  DBF4 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  DBF4 MUTATED           0
  DBF4 WILD-TYPE         1
D1243V3, multiclass
            clus
vv           DBF4 MUTATED DBF4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  DBF4 MUTATED     0   1   4   2
  DBF4 WILD-TYPE   9  66 245  39
D1243V4, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            2             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
  DBF4 MUTATED     6   1   0
  DBF4 WILD-TYPE 214  80  66
D1243V5, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1243V6, binary
                cls
clus               0   1
  DBF4 MUTATED     7   0
  DBF4 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      7    0
  DBF4 WILD-TYPE  278   48
   clus
vv  DBF4 MUTATED DBF4 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1243V7, binary
                cls
clus               0   1
  DBF4 MUTATED     3   4
  DBF4 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      3    4
  DBF4 WILD-TYPE  167  193
        clus
vv       DBF4 MUTATED DBF4 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D1243V8, binary
                cls
clus               0   1
  DBF4 MUTATED     6   0
  DBF4 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      6    0
  DBF4 WILD-TYPE  294    8
     clus
vv    DBF4 MUTATED DBF4 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1243V9, binary
                cls
clus               0   1
  DBF4 MUTATED     3   4
  DBF4 WILD-TYPE 311  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      3    4
  DBF4 WILD-TYPE  311   44
                               clus
vv                              DBF4 MUTATED DBF4 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DBF4 MUTATED     5   0   0   2
  DBF4 WILD-TYPE 254   3  22  19
D1243V10, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            2             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"
D1243V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DBF4 MUTATED                                  0     2
  DBF4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DBF4 MUTATED                           0     2
  DBF4 WILD-TYPE                        19   174
D1243V12, multiclass
                                  clus
vv                                 DBF4 MUTATED DBF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(1244) Variable = OR13C5 MUTATION ANALYSIS
D1244V1, survival
                  sevent
clus2                0   1
  OR13C5 MUTATED     9   2
  OR13C5 WILD-TYPE 268  76
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              11              344 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
               2               76 
$`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        12.59        12.59 
TCGA-CM-4752 TCGA-CM-6171 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D8 
       13.02        14.04        16.14        13.35        12.59 

$`OR13C5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 
        5.23        11.74        12.69        12.36        12.39        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OR13C5 MUTATED OR13C5 WILD-TYPE 
            3.19             0.00 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
           33.04           148.01 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
          13.350           22.225 
[1] "3.2 - 33.0 (13.3)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D1244V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR13C5 MUTATED         2        0        0         4         0         0
  OR13C5 WILD-TYPE      62        1       26       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR13C5 MUTATED           0          0          3          0        1
  OR13C5 WILD-TYPE        18          6         41         33       34
                  vv
clus               STAGE IVA STAGE IVB
  OR13C5 MUTATED           0         0
  OR13C5 WILD-TYPE        12         1
D1244V3, multiclass
            clus
vv           OR13C5 MUTATED OR13C5 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  OR13C5 MUTATED     0   2   8   1
  OR13C5 WILD-TYPE   9  65 241  40
D1244V4, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              8              241
  T4              1               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
  OR13C5 MUTATED     6   4   1
  OR13C5 WILD-TYPE 214  77  65
D1244V5, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  N0              6              214
  N1              4               77
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1244V6, binary
                  cls
clus                 0   1
  OR13C5 MUTATED     9   1
  OR13C5 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED      9    1
  OR13C5 WILD-TYPE  276   47
   clus
vv  OR13C5 MUTATED OR13C5 WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1244V7, binary
                  cls
clus                 0   1
  OR13C5 MUTATED     3   8
  OR13C5 WILD-TYPE 167 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED      3    8
  OR13C5 WILD-TYPE  167  189
        clus
vv       OR13C5 MUTATED OR13C5 WILD-TYPE
  FEMALE              3              167
  MALE                8              189
[1] 2 2
[1] FALSE
D1244V8, binary
                  cls
clus                 0   1
  OR13C5 MUTATED    10   0
  OR13C5 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED     10    0
  OR13C5 WILD-TYPE  290    8
     clus
vv    OR13C5 MUTATED OR13C5 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D1244V9, binary
                  cls
clus                 0   1
  OR13C5 MUTATED     9   2
  OR13C5 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED      9    2
  OR13C5 WILD-TYPE  305   46
                               clus
vv                              OR13C5 MUTATED OR13C5 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR13C5 MUTATED     7   0   0   1
  OR13C5 WILD-TYPE 252   3  22  20
D1244V10, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1244V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR13C5 MUTATED                                  0     2
  OR13C5 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR13C5 MUTATED                           2     5
  OR13C5 WILD-TYPE                        17   171
D1244V12, multiclass
                                  clus
vv                                 OR13C5 MUTATED OR13C5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         5              171
[1] 4 2
[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 = GOLIM4 MUTATION ANALYSIS
D1245V1, survival
                  sevent
clus2                0   1
  GOLIM4 MUTATED     6   3
  GOLIM4 WILD-TYPE 271  75
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               9              346 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               3               75 
$`GOLIM4 MUTATED`
TCGA-AA-3516 TCGA-AZ-6601 TCGA-A6-3810 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A00J 
       13.02       100.01        36.53        63.98        26.99        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-DM-A1HB 
        4.01        34.98       135.65 

$`GOLIM4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
            4.01             0.00 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
          135.65           148.01 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
           34.98            22.01 
[1] "4.0 - 135.7 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1245V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLIM4 MUTATED         0        0        2         2         2         0
  GOLIM4 WILD-TYPE      64        1       24       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLIM4 MUTATED           1          0          2          0        0
  GOLIM4 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  GOLIM4 MUTATED           0         0
  GOLIM4 WILD-TYPE        12         1
D1245V3, multiclass
            clus
vv           GOLIM4 MUTATED GOLIM4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  GOLIM4 MUTATED     0   0   6   3
  GOLIM4 WILD-TYPE   9  67 243  38
D1245V4, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              3               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
  GOLIM4 MUTATED     6   2   1
  GOLIM4 WILD-TYPE 214  79  65
D1245V5, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  N0              6              214
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1245V6, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     9   0
  GOLIM4 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      9    0
  GOLIM4 WILD-TYPE  276   48
   clus
vv  GOLIM4 MUTATED GOLIM4 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1245V7, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     3   6
  GOLIM4 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      3    6
  GOLIM4 WILD-TYPE  167  191
        clus
vv       GOLIM4 MUTATED GOLIM4 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D1245V8, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     7   0
  GOLIM4 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      7    0
  GOLIM4 WILD-TYPE  293    8
     clus
vv    GOLIM4 MUTATED GOLIM4 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1245V9, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     5   3
  GOLIM4 WILD-TYPE 309  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      5    3
  GOLIM4 WILD-TYPE  309   45
                               clus
vv                              GOLIM4 MUTATED GOLIM4 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GOLIM4 MUTATED     6   0   0   0
  GOLIM4 WILD-TYPE 253   3  22  21
D1245V10, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1245V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLIM4 MUTATED                                  0     0
  GOLIM4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GOLIM4 MUTATED                           0     3
  GOLIM4 WILD-TYPE                        19   173
D1245V12, multiclass
                                  clus
vv                                 GOLIM4 MUTATED GOLIM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = IRGQ MUTATION ANALYSIS
D1246V1, survival
                sevent
clus2              0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 274  78
  IRGQ MUTATED IRGQ WILD-TYPE 
             3            352 
  IRGQ MUTATED IRGQ WILD-TYPE 
             0             78 
$`IRGQ MUTATED`
TCGA-AA-3672 TCGA-G4-6588 TCGA-A6-6653 
        0.92        26.17        24.39 

$`IRGQ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  IRGQ MUTATED IRGQ WILD-TYPE 
          0.92           0.00 
  IRGQ MUTATED IRGQ WILD-TYPE 
         26.17         148.01 
  IRGQ MUTATED IRGQ WILD-TYPE 
        24.390         22.045 
[1] "0.9 - 26.2 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1246V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRGQ MUTATED         1        0        0         1         0         0
  IRGQ WILD-TYPE      63        1       26       107         8         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        17          6         44         33       35        12
                vv
clus             STAGE IVB
  IRGQ MUTATED           0
  IRGQ WILD-TYPE         1
D1246V3, multiclass
            clus
vv           IRGQ MUTATED IRGQ WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  IRGQ MUTATED     0   1   2   0
  IRGQ WILD-TYPE   9  66 247  41
D1246V4, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            0             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
  IRGQ MUTATED     2   1   0
  IRGQ WILD-TYPE 218  80  66
D1246V5, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  N0            2            218
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1246V6, binary
                cls
clus               0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      3    0
  IRGQ WILD-TYPE  282   48
   clus
vv  IRGQ MUTATED IRGQ WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1246V7, binary
                cls
clus               0   1
  IRGQ MUTATED     2   1
  IRGQ WILD-TYPE 168 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      2    1
  IRGQ WILD-TYPE  168  196
        clus
vv       IRGQ MUTATED IRGQ WILD-TYPE
  FEMALE            2            168
  MALE              1            196
[1] 2 2
[1] FALSE
D1246V8, binary
                cls
clus               0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      3    0
  IRGQ WILD-TYPE  297    8
     clus
vv    IRGQ MUTATED IRGQ WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1246V9, binary
                cls
clus               0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      3    0
  IRGQ WILD-TYPE  311   48
                               clus
vv                              IRGQ MUTATED IRGQ WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRGQ MUTATED     2   0   0   0
  IRGQ WILD-TYPE 257   3  22  21
D1246V10, multiclass
[1] "Remove cluster labels:" "IRGQ MUTATED"          
clus
  IRGQ MUTATED IRGQ WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     TCGA-AA-3520     TCGA-AA-3521 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3527 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3697 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814     TCGA-AA-3844 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870     TCGA-AA-3939 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972     TCGA-AA-3976 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L     TCGA-AA-A00Z 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6895 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310     TCGA-G4-6321 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-3810     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5661 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5665     TCGA-A6-6781     TCGA-AA-3489     TCGA-AA-3492 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3502     TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3517     TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3526 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3542     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3555     TCGA-AA-3558     TCGA-AA-3561 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3663     TCGA-AA-3664 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3673     TCGA-AA-3678 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3811     TCGA-AA-3812 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3861     TCGA-AA-3864 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872     TCGA-AA-3875 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3941     TCGA-AA-3947 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3984 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A010 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01V 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022     TCGA-AA-A029 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6965 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5913 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
D1246V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRGQ MUTATED                                  0     0
  IRGQ WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRGQ MUTATED                           0     2
  IRGQ WILD-TYPE                        19   174
D1246V12, multiclass
[1] "Remove cluster labels:" "IRGQ MUTATED"          
clus
  IRGQ MUTATED IRGQ WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6625 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5656 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660     TCGA-A6-5661 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665     TCGA-A6-5666 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141     TCGA-A6-6142 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-6648     TCGA-A6-6651     TCGA-A6-6652     TCGA-A6-6654 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-6780     TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6899     TCGA-AD-6901 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6603 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-CA-5254 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 

Clustering(1247) Variable = CYP2C9 MUTATION ANALYSIS
D1247V1, survival
                  sevent
clus2                0   1
  CYP2C9 MUTATED     6   0
  CYP2C9 WILD-TYPE 271  78
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               6              349 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               0               78 
$`CYP2C9 MUTATED`
TCGA-AA-3697 TCGA-G4-6588 TCGA-AA-3947 TCGA-AA-A01Q TCGA-D5-6532 TCGA-G4-6306 
       85.05        26.17        33.01         1.02        18.25        44.68 

$`CYP2C9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
            1.02             0.00 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
           85.05           148.01 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
           29.59            22.03 
[1] "1.0 - 85.0 (29.6)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1247V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP2C9 MUTATED         0        0        3         3         1         0
  CYP2C9 WILD-TYPE      64        1       23       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP2C9 MUTATED           0          0          0          0        0
  CYP2C9 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CYP2C9 MUTATED           0         0
  CYP2C9 WILD-TYPE        12         1
D1247V3, multiclass
            clus
vv           CYP2C9 MUTATED CYP2C9 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CYP2C9 MUTATED     0   1   6   1
  CYP2C9 WILD-TYPE   9  66 243  40
D1247V4, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              6              243
  T4              1               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
  CYP2C9 MUTATED     8   0   0
  CYP2C9 WILD-TYPE 212  81  66
D1247V5, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1247V6, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     8   0
  CYP2C9 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      8    0
  CYP2C9 WILD-TYPE  277   48
   clus
vv  CYP2C9 MUTATED CYP2C9 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1247V7, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     4   4
  CYP2C9 WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      4    4
  CYP2C9 WILD-TYPE  166  193
        clus
vv       CYP2C9 MUTATED CYP2C9 WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D1247V8, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     5   0
  CYP2C9 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      5    0
  CYP2C9 WILD-TYPE  295    8
     clus
vv    CYP2C9 MUTATED CYP2C9 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1247V9, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     7   1
  CYP2C9 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      7    1
  CYP2C9 WILD-TYPE  307   47
                               clus
vv                              CYP2C9 MUTATED CYP2C9 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CYP2C9 MUTATED     8   0   0   0
  CYP2C9 WILD-TYPE 251   3  22  21
D1247V10, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              0               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"
D1247V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP2C9 MUTATED                                  0     0
  CYP2C9 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP2C9 MUTATED                           0     3
  CYP2C9 WILD-TYPE                        19   173
D1247V12, multiclass
                                  clus
vv                                 CYP2C9 MUTATED CYP2C9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = IL6R MUTATION ANALYSIS
D1248V1, survival
                sevent
clus2              0   1
  IL6R MUTATED     6   1
  IL6R WILD-TYPE 271  77
  IL6R MUTATED IL6R WILD-TYPE 
             7            348 
  IL6R MUTATED IL6R WILD-TYPE 
             1             77 
$`IL6R MUTATED`
TCGA-AA-3715 TCGA-AD-6895 TCGA-AA-3510 TCGA-AA-3864 TCGA-D5-6928 TCGA-DM-A1HB 
       19.04        25.08        63.98        53.00        11.64       135.65 
TCGA-DM-A282 
      139.17 

$`IL6R WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28C 
       12.59       140.38         7.50        44.32       131.51        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IL6R MUTATED IL6R WILD-TYPE 
         11.64           0.00 
  IL6R MUTATED IL6R WILD-TYPE 
        139.17         148.01 
  IL6R MUTATED IL6R WILD-TYPE 
         53.00          22.01 
[1] "11.6 - 139.2 (53.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.2"
D1248V2, continuous
                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      64        1       23       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL6R MUTATED           0          0          2          0        0         0
  IL6R WILD-TYPE        18          6         42         33       35        12
                vv
clus             STAGE IVB
  IL6R MUTATED           0
  IL6R WILD-TYPE         1
D1248V3, multiclass
            clus
vv           IL6R MUTATED IL6R WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  IL6R MUTATED     0   0   7   0
  IL6R WILD-TYPE   9  67 242  41
D1248V4, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  T1            0              9
  T2            0             67
  T3            7            242
  T4            0             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
  IL6R MUTATED     5   2   0
  IL6R WILD-TYPE 215  79  66
D1248V5, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  N0            5            215
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1248V6, binary
                cls
clus               0   1
  IL6R MUTATED     7   0
  IL6R WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      7    0
  IL6R WILD-TYPE  278   48
   clus
vv  IL6R MUTATED IL6R WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1248V7, binary
                cls
clus               0   1
  IL6R MUTATED     1   6
  IL6R WILD-TYPE 169 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      1    6
  IL6R WILD-TYPE  169  191
        clus
vv       IL6R MUTATED IL6R WILD-TYPE
  FEMALE            1            169
  MALE              6            191
[1] 2 2
[1] FALSE
D1248V8, binary
                cls
clus               0   1
  IL6R MUTATED     5   0
  IL6R WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      5    0
  IL6R WILD-TYPE  295    8
     clus
vv    IL6R MUTATED IL6R WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1248V9, binary
                cls
clus               0   1
  IL6R MUTATED     5   1
  IL6R WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      5    1
  IL6R WILD-TYPE  309   47
                               clus
vv                              IL6R MUTATED IL6R WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IL6R MUTATED     5   0   0   0
  IL6R WILD-TYPE 254   3  22  21
D1248V10, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1248V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL6R MUTATED                                  0     0
  IL6R WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IL6R MUTATED                           0     4
  IL6R WILD-TYPE                        19   172
D1248V12, multiclass
                                  clus
vv                                 IL6R MUTATED IL6R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = ZNF235 MUTATION ANALYSIS
D1249V1, survival
                  sevent
clus2                0   1
  ZNF235 MUTATED     6   2
  ZNF235 WILD-TYPE 271  76
  ZNF235 MUTATED ZNF235 WILD-TYPE 
               8              347 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
               2               76 
$`ZNF235 MUTATED`
TCGA-AA-3496 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3492 TCGA-CM-5344 
        1.02        36.00        19.04        14.93         3.02        22.03 
TCGA-CM-5349 TCGA-F4-6807 
       30.08        43.04 

$`ZNF235 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.00        85.05        19.04        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6808 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF235 MUTATED ZNF235 WILD-TYPE 
            1.02             0.00 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
           43.04           148.01 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
          20.535           22.090 
[1] "1.0 - 43.0 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1249V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF235 MUTATED         0        0        2         2         0         0
  ZNF235 WILD-TYPE      64        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF235 MUTATED           0          0          1          2        2
  ZNF235 WILD-TYPE        18          6         43         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF235 MUTATED           0         0
  ZNF235 WILD-TYPE        12         1
D1249V3, multiclass
            clus
vv           ZNF235 MUTATED ZNF235 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                2               33
  STAGE IVA               0               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
  ZNF235 MUTATED     0   0   9   0
  ZNF235 WILD-TYPE   9  67 240  41
D1249V4, multiclass
    clus
vv   ZNF235 MUTATED ZNF235 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              9              240
  T4              0               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
  ZNF235 MUTATED     5   1   3
  ZNF235 WILD-TYPE 215  80  63
D1249V5, multiclass
    clus
vv   ZNF235 MUTATED ZNF235 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              3               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"
D1249V6, binary
                  cls
clus                 0   1
  ZNF235 MUTATED     7   2
  ZNF235 WILD-TYPE 278  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF235 MUTATED      7    2
  ZNF235 WILD-TYPE  278   46
   clus
vv  ZNF235 MUTATED ZNF235 WILD-TYPE
  0              7              278
  1              2               46
[1] 2 2
[1] FALSE
D1249V7, binary
                  cls
clus                 0   1
  ZNF235 MUTATED     8   1
  ZNF235 WILD-TYPE 162 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF235 MUTATED      8    1
  ZNF235 WILD-TYPE  162  196
        clus
vv       ZNF235 MUTATED ZNF235 WILD-TYPE
  FEMALE              8              162
  MALE                1              196
[1] 2 2
[1] FALSE
D1249V8, binary
                  cls
clus                 0   1
  ZNF235 MUTATED     4   3
  ZNF235 WILD-TYPE 296   5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF235 MUTATED      4    3
  ZNF235 WILD-TYPE  296    5
     clus
vv    ZNF235 MUTATED ZNF235 WILD-TYPE
  NO               4              296
  YES              3                5
[1] 2 2
[1] FALSE
D1249V9, binary
                  cls
clus                 0   1
  ZNF235 MUTATED     8   1
  ZNF235 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF235 MUTATED      8    1
  ZNF235 WILD-TYPE  306   47
                               clus
vv                              ZNF235 MUTATED ZNF235 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF235 MUTATED     7   0   2   0
  ZNF235 WILD-TYPE 252   3  20  21
D1249V10, multiclass
    clus
vv   ZNF235 MUTATED ZNF235 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              2               20
  RX              0               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"
D1249V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF235 MUTATED                                  0     0
  ZNF235 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF235 MUTATED                           0     3
  ZNF235 WILD-TYPE                        19   173
D1249V12, multiclass
                                  clus
vv                                 ZNF235 MUTATED ZNF235 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = C20ORF151 MUTATION ANALYSIS
D1250V1, survival
                     sevent
clus2                   0   1
  C20ORF151 MUTATED     8   1
  C20ORF151 WILD-TYPE 269  77
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                  9                 346 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                  1                  77 
$`C20ORF151 MUTATED`
TCGA-AA-3713 TCGA-AA-A01R TCGA-AA-A01S TCGA-AD-6889 TCGA-AY-6196 TCGA-CM-6674 
       19.04        35.01         1.02        83.24         0.20        12.95 
TCGA-CM-6676 TCGA-D5-6928 TCGA-F4-6855 
       11.08        11.64        47.41 

$`C20ORF151 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        33.04         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                0.2                 0.0 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
              83.24              148.01 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
              12.95               22.09 
[1] "0.2 - 83.2 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1250V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF151 MUTATED         1        0        0         4         0         0
  C20ORF151 WILD-TYPE      63        1       26       104         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF151 MUTATED           2          0          0          1        1
  C20ORF151 WILD-TYPE        16          6         44         32       34
                     vv
clus                  STAGE IVA STAGE IVB
  C20ORF151 MUTATED           0         0
  C20ORF151 WILD-TYPE        12         1
D1250V3, multiclass
            clus
vv           C20ORF151 MUTATED C20ORF151 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  26
  STAGE IIA                  4                 104
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  2                  16
  STAGE IIIA                 0                   6
  STAGE IIIB                 0                  44
  STAGE IIIC                 1                  32
  STAGE IV                   1                  34
  STAGE IVA                  0                  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
  C20ORF151 MUTATED     0   1   8   0
  C20ORF151 WILD-TYPE   9  66 241  41
D1250V4, multiclass
    clus
vv   C20ORF151 MUTATED C20ORF151 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 8                 241
  T4                 0                  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
  C20ORF151 MUTATED     6   1   2
  C20ORF151 WILD-TYPE 214  80  64
D1250V5, multiclass
    clus
vv   C20ORF151 MUTATED C20ORF151 WILD-TYPE
  N0                 6                 214
  N1                 1                  80
  N2                 2                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1250V6, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     7   1
  C20ORF151 WILD-TYPE 278  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      7    1
  C20ORF151 WILD-TYPE  278   47
   clus
vv  C20ORF151 MUTATED C20ORF151 WILD-TYPE
  0                 7                 278
  1                 1                  47
[1] 2 2
[1] FALSE
D1250V7, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     2   7
  C20ORF151 WILD-TYPE 168 190
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      2    7
  C20ORF151 WILD-TYPE  168  190
        clus
vv       C20ORF151 MUTATED C20ORF151 WILD-TYPE
  FEMALE                 2                 168
  MALE                   7                 190
[1] 2 2
[1] FALSE
D1250V8, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     5   2
  C20ORF151 WILD-TYPE 295   6
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      5    2
  C20ORF151 WILD-TYPE  295    6
     clus
vv    C20ORF151 MUTATED C20ORF151 WILD-TYPE
  NO                  5                 295
  YES                 2                   6
[1] 2 2
[1] FALSE
D1250V9, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     6   3
  C20ORF151 WILD-TYPE 308  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      6    3
  C20ORF151 WILD-TYPE  308   45
                               clus
vv                              C20ORF151 MUTATED C20ORF151 WILD-TYPE
  COLON ADENOCARCINOMA                          6                 308
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C20ORF151 MUTATED     8   0   1   0
  C20ORF151 WILD-TYPE 251   3  21  21
D1250V10, multiclass
    clus
vv   C20ORF151 MUTATED C20ORF151 WILD-TYPE
  R0                 8                 251
  R1                 0                   3
  R2                 1                  21
  RX                 0                  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"
D1250V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF151 MUTATED                                  0     1
  C20ORF151 WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C20ORF151 MUTATED                           0     5
  C20ORF151 WILD-TYPE                        19   171
D1250V12, multiclass
                                  clus
vv                                 C20ORF151 MUTATED C20ORF151 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                   9
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            5                 171
[1] 4 2
[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 = CEPT1 MUTATION ANALYSIS
D1251V1, survival
                 sevent
clus2               0   1
  CEPT1 MUTATED     4   1
  CEPT1 WILD-TYPE 273  77
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              5             350 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              1              77 
$`CEPT1 MUTATED`
TCGA-G4-6586 TCGA-AA-3877 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A1D9 
       35.80        31.00        12.76        10.06       140.38 

$`CEPT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CEPT1 MUTATED CEPT1 WILD-TYPE 
          10.06            0.00 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
         140.38          148.01 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
         31.000          22.045 
[1] "10.1 - 140.4 (31.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.5"
D1251V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEPT1 MUTATED         1        0        0         4         0         0
  CEPT1 WILD-TYPE      63        1       26       104         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  CEPT1 MUTATED           0
  CEPT1 WILD-TYPE         1
D1251V3, multiclass
            clus
vv           CEPT1 MUTATED CEPT1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CEPT1 MUTATED     1   0   4   0
  CEPT1 WILD-TYPE   8  67 245  41
D1251V4, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             4             245
  T4             0              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
  CEPT1 MUTATED     5   0   0
  CEPT1 WILD-TYPE 215  81  66
D1251V5, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1251V6, binary
                 cls
clus                0   1
  CEPT1 MUTATED     5   0
  CEPT1 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      5    0
  CEPT1 WILD-TYPE  280   48
   clus
vv  CEPT1 MUTATED CEPT1 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1251V7, binary
                 cls
clus                0   1
  CEPT1 MUTATED     3   2
  CEPT1 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      3    2
  CEPT1 WILD-TYPE  167  195
        clus
vv       CEPT1 MUTATED CEPT1 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1251V8, binary
                 cls
clus                0   1
  CEPT1 MUTATED     4   0
  CEPT1 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      4    0
  CEPT1 WILD-TYPE  296    8
     clus
vv    CEPT1 MUTATED CEPT1 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1251V9, binary
                 cls
clus                0   1
  CEPT1 MUTATED     3   2
  CEPT1 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      3    2
  CEPT1 WILD-TYPE  311   46
                               clus
vv                              CEPT1 MUTATED CEPT1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CEPT1 MUTATED     2   0   0   2
  CEPT1 WILD-TYPE 257   3  22  19
D1251V10, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             2              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"
D1251V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEPT1 MUTATED                                  0     2
  CEPT1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CEPT1 MUTATED                           0     2
  CEPT1 WILD-TYPE                        19   174
D1251V12, multiclass
                                  clus
vv                                 CEPT1 MUTATED CEPT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        2             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(1252) Variable = GGNBP2 MUTATION ANALYSIS
D1252V1, survival
                  sevent
clus2                0   1
  GGNBP2 MUTATED     8   2
  GGNBP2 WILD-TYPE 269  76
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              10              345 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
               2               76 
$`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 
       13.02        11.08       119.93         6.18 

$`GGNBP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28F 
       44.32       131.51       135.65       139.17        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-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.060 
[1] "4.0 - 148.0 (24.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.5"
D1252V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGNBP2 MUTATED         1        0        0         6         3         0
  GGNBP2 WILD-TYPE      63        1       26       102         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GGNBP2 MUTATED           1          0          0          0        0
  GGNBP2 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  GGNBP2 MUTATED           0         0
  GGNBP2 WILD-TYPE        12         1
D1252V3, multiclass
            clus
vv           GGNBP2 MUTATED GGNBP2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  GGNBP2 MUTATED     0   1   7   3
  GGNBP2 WILD-TYPE   9  66 242  38
D1252V4, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              3               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
  GGNBP2 MUTATED    10   1   0
  GGNBP2 WILD-TYPE 210  80  66
D1252V5, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  N0             10              210
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1252V6, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     9   0
  GGNBP2 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      9    0
  GGNBP2 WILD-TYPE  276   48
   clus
vv  GGNBP2 MUTATED GGNBP2 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1252V7, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     7   4
  GGNBP2 WILD-TYPE 163 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      7    4
  GGNBP2 WILD-TYPE  163  193
        clus
vv       GGNBP2 MUTATED GGNBP2 WILD-TYPE
  FEMALE              7              163
  MALE                4              193
[1] 2 2
[1] FALSE
D1252V8, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     7   0
  GGNBP2 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      7    0
  GGNBP2 WILD-TYPE  293    8
     clus
vv    GGNBP2 MUTATED GGNBP2 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1252V9, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED    10   1
  GGNBP2 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED     10    1
  GGNBP2 WILD-TYPE  304   47
                               clus
vv                              GGNBP2 MUTATED GGNBP2 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GGNBP2 MUTATED     9   0   0   1
  GGNBP2 WILD-TYPE 250   3  22  20
D1252V10, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D1252V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGNBP2 MUTATED                                  0     0
  GGNBP2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GGNBP2 MUTATED                           1     8
  GGNBP2 WILD-TYPE                        18   168
D1252V12, multiclass
                                  clus
vv                                 GGNBP2 MUTATED GGNBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = CTCFL MUTATION ANALYSIS
D1253V1, survival
                 sevent
clus2               0   1
  CTCFL MUTATED    10   4
  CTCFL WILD-TYPE 267  74
  CTCFL MUTATED CTCFL WILD-TYPE 
             14             341 
  CTCFL MUTATED CTCFL WILD-TYPE 
              4              74 
$`CTCFL MUTATED`
TCGA-AA-3672 TCGA-A6-6141 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N 
        0.92         8.38        33.04        15.95        25.02         4.01 
TCGA-AA-A01R TCGA-AY-6196 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-5537 
       35.01         0.20        12.76        10.06        14.04        45.40 
TCGA-DM-A1DB TCGA-G4-6323 
       44.32        13.78 

$`CTCFL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  CTCFL MUTATED CTCFL WILD-TYPE 
            0.2             0.0 
  CTCFL MUTATED CTCFL WILD-TYPE 
          45.40          148.01 
  CTCFL MUTATED CTCFL WILD-TYPE 
          13.91           22.09 
[1] "0.2 - 45.4 (13.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1253V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTCFL MUTATED         1        1        0         8         1         0
  CTCFL WILD-TYPE      63        0       26       100         7         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        16          6         44         32       35        12
                 vv
clus              STAGE IVB
  CTCFL MUTATED           0
  CTCFL WILD-TYPE         1
D1253V3, multiclass
            clus
vv           CTCFL MUTATED CTCFL WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               0              26
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CTCFL MUTATED     0   2  11   1
  CTCFL WILD-TYPE   9  65 238  40
D1253V4, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  T1             0               9
  T2             2              65
  T3            11             238
  T4             1              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
  CTCFL MUTATED    11   1   3
  CTCFL WILD-TYPE 209  80  63
D1253V5, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  N0            11             209
  N1             1              80
  N2             3              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"
D1253V6, binary
                 cls
clus                0   1
  CTCFL MUTATED    11   0
  CTCFL WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     11    0
  CTCFL WILD-TYPE  274   48
   clus
vv  CTCFL MUTATED CTCFL WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1253V7, binary
                 cls
clus                0   1
  CTCFL MUTATED     5  10
  CTCFL WILD-TYPE 165 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED      5   10
  CTCFL WILD-TYPE  165  187
        clus
vv       CTCFL MUTATED CTCFL WILD-TYPE
  FEMALE             5             165
  MALE              10             187
[1] 2 2
[1] FALSE
D1253V8, binary
                 cls
clus                0   1
  CTCFL MUTATED    10   1
  CTCFL WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     10    1
  CTCFL WILD-TYPE  290    7
     clus
vv    CTCFL MUTATED CTCFL WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1253V9, binary
                 cls
clus                0   1
  CTCFL MUTATED    11   4
  CTCFL WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     11    4
  CTCFL WILD-TYPE  303   44
                               clus
vv                              CTCFL MUTATED CTCFL WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CTCFL MUTATED     9   0   0   3
  CTCFL WILD-TYPE 250   3  22  18
D1253V10, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             3              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"
D1253V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCFL MUTATED                                  0     2
  CTCFL WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CTCFL MUTATED                           2     4
  CTCFL WILD-TYPE                        17   172
D1253V12, multiclass
                                  clus
vv                                 CTCFL MUTATED CTCFL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = SLC16A1 MUTATION ANALYSIS
D1254V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     5   2
  SLC16A1 WILD-TYPE 272  76
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               348 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                2                76 
$`SLC16A1 MUTATED`
TCGA-AA-3715 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3966 TCGA-CA-6717 TCGA-CK-5916 
       19.04        22.06         6.97         2.01        12.76        21.14 
TCGA-G4-6293 
      133.18 

$`SLC16A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             2.01              0.00 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           133.18            148.01 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           19.040            22.225 
[1] "2.0 - 133.2 (19.0)" "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D1254V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC16A1 MUTATED         1        0        2         3         0         0
  SLC16A1 WILD-TYPE      63        1       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A1 MUTATED           1          0          0          0        0
  SLC16A1 WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A1 MUTATED           0         0
  SLC16A1 WILD-TYPE        12         1
D1254V3, multiclass
            clus
vv           SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC16A1 MUTATED     1   0   6   0
  SLC16A1 WILD-TYPE   8  67 243  41
D1254V4, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T1               1                 8
  T2               0                67
  T3               6               243
  T4               0                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
  SLC16A1 MUTATED     6   1   0
  SLC16A1 WILD-TYPE 214  80  66
D1254V5, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  N0               6               214
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1254V6, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     7   0
  SLC16A1 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      7    0
  SLC16A1 WILD-TYPE  278   48
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D1254V7, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     4   3
  SLC16A1 WILD-TYPE 166 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      4    3
  SLC16A1 WILD-TYPE  166  194
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  FEMALE               4               166
  MALE                 3               194
[1] 2 2
[1] FALSE
D1254V8, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     6   0
  SLC16A1 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      6    0
  SLC16A1 WILD-TYPE  294    8
     clus
vv    SLC16A1 MUTATED SLC16A1 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1254V9, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     5   2
  SLC16A1 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      5    2
  SLC16A1 WILD-TYPE  309   46
                               clus
vv                              SLC16A1 MUTATED SLC16A1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC16A1 MUTATED     4   0   0   2
  SLC16A1 WILD-TYPE 255   3  22  19
D1254V10, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               2                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"
D1254V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A1 MUTATED                                  0     1
  SLC16A1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A1 MUTATED                           0     3
  SLC16A1 WILD-TYPE                        19   173
D1254V12, multiclass
                                  clus
vv                                 SLC16A1 MUTATED SLC16A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = MAP2K4 MUTATION ANALYSIS
D1255V1, survival
                  sevent
clus2                0   1
  MAP2K4 MUTATED    19   9
  MAP2K4 WILD-TYPE 258  69
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              28              327 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               9               69 
$`MAP2K4 MUTATED`
TCGA-AA-3672 TCGA-AA-3952 TCGA-AA-3986 TCGA-AD-6548 TCGA-G4-6628 TCGA-A6-5666 
        0.92         2.01        19.07        21.37        79.69        32.71 
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3966 
        8.38         3.02         0.00        30.05        53.00         2.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6899 TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-6598 
        4.01        34.98         5.79        22.42         0.20        49.41 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-6171 
       12.20        10.06        17.56       148.01        15.62        14.04 
TCGA-CM-6172 TCGA-D5-6535 TCGA-D5-6539 TCGA-DM-A1DA 
       11.01        15.12        12.49         7.50 

$`MAP2K4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 
       31.07        24.03        29.98        12.99        24.00        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 
       26.01        24.00        38.04        21.99        39.06        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5656 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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3866 
        0.00        36.03        32.05         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       12.16        83.24        24.53        27.42        26.47        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-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-6717 
       12.69        12.36        12.39        12.59        12.59        12.76 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       14.30        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               0                0 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
          148.01           140.38 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
          13.265           23.010 
[1] "0.0 - 148.0 (13.3)" "0.0 - 140.4 (23.0)"
[1] "hr=" "2"  
D1255V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP2K4 MUTATED         4        0        3         7         3         1
  MAP2K4 WILD-TYPE      60        1       23       101         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K4 MUTATED           2          0          3          5        0
  MAP2K4 WILD-TYPE        16          6         41         28       35
                  vv
clus               STAGE IVA STAGE IVB
  MAP2K4 MUTATED           0         0
  MAP2K4 WILD-TYPE        12         1
D1255V3, multiclass
            clus
vv           MAP2K4 MUTATED MAP2K4 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               7              101
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              5               28
  STAGE IV                0               35
  STAGE IVA               0               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
  MAP2K4 MUTATED     0   4  19   7
  MAP2K4 WILD-TYPE   9  63 230  34
D1255V4, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             19              230
  T4              7               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
  MAP2K4 MUTATED    20   5   5
  MAP2K4 WILD-TYPE 200  76  61
D1255V5, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  N0             20              200
  N1              5               76
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1255V6, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    24   0
  MAP2K4 WILD-TYPE 261  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     24    0
  MAP2K4 WILD-TYPE  261   48
   clus
vv  MAP2K4 MUTATED MAP2K4 WILD-TYPE
  0             24              261
  1              0               48
[1] 2 2
[1] FALSE
D1255V7, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    17  13
  MAP2K4 WILD-TYPE 153 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     17   13
  MAP2K4 WILD-TYPE  153  184
        clus
vv       MAP2K4 MUTATED MAP2K4 WILD-TYPE
  FEMALE             17              153
  MALE               13              184
[1] 2 2
[1] FALSE
D1255V8, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    21   0
  MAP2K4 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     21    0
  MAP2K4 WILD-TYPE  279    8
     clus
vv    MAP2K4 MUTATED MAP2K4 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D1255V9, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    25   5
  MAP2K4 WILD-TYPE 289  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     25    5
  MAP2K4 WILD-TYPE  289   43
                               clus
vv                              MAP2K4 MUTATED MAP2K4 WILD-TYPE
  COLON ADENOCARCINOMA                      25              289
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP2K4 MUTATED    17   0   0   6
  MAP2K4 WILD-TYPE 242   3  22  15
D1255V10, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              0               22
  RX              6               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"
D1255V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP2K4 MUTATED                                  0     2
  MAP2K4 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP2K4 MUTATED                           1    16
  MAP2K4 WILD-TYPE                        18   160
D1255V12, multiclass
                                  clus
vv                                 MAP2K4 MUTATED MAP2K4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        16              160
[1] 4 2
[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 = DUSP9 MUTATION ANALYSIS
D1256V1, survival
                 sevent
clus2               0   1
  DUSP9 MUTATED     8   1
  DUSP9 WILD-TYPE 269  77
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             346 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              1              77 
$`DUSP9 MUTATED`
TCGA-G4-6588 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3655 TCGA-AA-3821 TCGA-CM-4743 
       26.17        24.69        20.28        61.02         1.02        23.05 
TCGA-D5-6534 TCGA-D5-6930 TCGA-G4-6303 
       43.27        13.35        65.85 

$`DUSP9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        21.76        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  DUSP9 MUTATED DUSP9 WILD-TYPE 
           1.02            0.00 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          65.85          148.01 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          24.69           22.01 
[1] "1.0 - 65.8 (24.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1256V2, continuous
                 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      63        1       25       104         7         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        18          6         44         33       34        11
                 vv
clus              STAGE IVB
  DUSP9 MUTATED           0
  DUSP9 WILD-TYPE         1
D1256V3, multiclass
            clus
vv           DUSP9 MUTATED DUSP9 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  DUSP9 MUTATED     0   1   7   1
  DUSP9 WILD-TYPE   9  66 242  40
D1256V4, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             1              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
  DUSP9 MUTATED     8   1   0
  DUSP9 WILD-TYPE 212  80  66
D1256V5, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1256V6, binary
                 cls
clus                0   1
  DUSP9 MUTATED     6   2
  DUSP9 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      6    2
  DUSP9 WILD-TYPE  279   46
   clus
vv  DUSP9 MUTATED DUSP9 WILD-TYPE
  0             6             279
  1             2              46
[1] 2 2
[1] FALSE
D1256V7, binary
                 cls
clus                0   1
  DUSP9 MUTATED     4   5
  DUSP9 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      4    5
  DUSP9 WILD-TYPE  166  192
        clus
vv       DUSP9 MUTATED DUSP9 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1256V8, binary
                 cls
clus                0   1
  DUSP9 MUTATED     9   0
  DUSP9 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      9    0
  DUSP9 WILD-TYPE  291    8
     clus
vv    DUSP9 MUTATED DUSP9 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1256V9, binary
                 cls
clus                0   1
  DUSP9 MUTATED     6   3
  DUSP9 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      6    3
  DUSP9 WILD-TYPE  308   45
                               clus
vv                              DUSP9 MUTATED DUSP9 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DUSP9 MUTATED     7   0   0   0
  DUSP9 WILD-TYPE 252   3  22  21
D1256V10, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1256V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP9 MUTATED                                  0     0
  DUSP9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DUSP9 MUTATED                           1     6
  DUSP9 WILD-TYPE                        18   170
D1256V12, multiclass
                                  clus
vv                                 DUSP9 MUTATED DUSP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = BRD2 MUTATION ANALYSIS
D1257V1, survival
                sevent
clus2              0   1
  BRD2 MUTATED     7   2
  BRD2 WILD-TYPE 270  76
  BRD2 MUTATED BRD2 WILD-TYPE 
             9            346 
  BRD2 MUTATED BRD2 WILD-TYPE 
             2             76 
$`BRD2 MUTATED`
TCGA-G4-6588 TCGA-A6-3809 TCGA-AA-3821 TCGA-AZ-6599 TCGA-CM-4743 TCGA-CM-4746 
       26.17        32.75         1.02         6.77        23.05        37.02 
TCGA-D5-6924 TCGA-DM-A0X9 TCGA-G4-6626 
       14.30       119.70        46.75 

$`BRD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
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-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  BRD2 MUTATED BRD2 WILD-TYPE 
          1.02           0.00 
  BRD2 MUTATED BRD2 WILD-TYPE 
        119.70         148.01 
  BRD2 MUTATED BRD2 WILD-TYPE 
         26.17          22.01 
[1] "1.0 - 119.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1257V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRD2 MUTATED         3        0        0         6         2         0
  BRD2 WILD-TYPE      61        1       26       102         6         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  BRD2 MUTATED           0
  BRD2 WILD-TYPE         1
D1257V3, multiclass
            clus
vv           BRD2 MUTATED BRD2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  BRD2 MUTATED     0   3   6   2
  BRD2 WILD-TYPE   9  64 243  39
D1257V4, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            6            243
  T4            2             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
  BRD2 MUTATED    11   0   0
  BRD2 WILD-TYPE 209  81  66
D1257V5, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  N0           11            209
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1257V6, binary
                cls
clus               0   1
  BRD2 MUTATED     9   0
  BRD2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      9    0
  BRD2 WILD-TYPE  276   48
   clus
vv  BRD2 MUTATED BRD2 WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D1257V7, binary
                cls
clus               0   1
  BRD2 MUTATED     6   5
  BRD2 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      6    5
  BRD2 WILD-TYPE  164  192
        clus
vv       BRD2 MUTATED BRD2 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D1257V8, binary
                cls
clus               0   1
  BRD2 MUTATED     8   0
  BRD2 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      8    0
  BRD2 WILD-TYPE  292    8
     clus
vv    BRD2 MUTATED BRD2 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1257V9, binary
                cls
clus               0   1
  BRD2 MUTATED     9   2
  BRD2 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      9    2
  BRD2 WILD-TYPE  305   46
                               clus
vv                              BRD2 MUTATED BRD2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRD2 MUTATED     8   0   0   1
  BRD2 WILD-TYPE 251   3  22  20
D1257V10, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D1257V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD2 MUTATED                                  0     0
  BRD2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD2 MUTATED                           1     8
  BRD2 WILD-TYPE                        18   168
D1257V12, multiclass
                                  clus
vv                                 BRD2 MUTATED BRD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = AP4B1 MUTATION ANALYSIS
D1258V1, survival
                 sevent
clus2               0   1
  AP4B1 MUTATED    10   2
  AP4B1 WILD-TYPE 267  76
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             12             343 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              2              76 
$`AP4B1 MUTATED`
TCGA-AA-3713 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 
       19.04        22.06        20.12        63.98        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          21.990 
[1] "15.6 - 64.0 (23.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1258V2, continuous
                 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      64        1       25       102         7         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        18          6         43         32       34        12
                 vv
clus              STAGE IVB
  AP4B1 MUTATED           0
  AP4B1 WILD-TYPE         1
D1258V3, multiclass
            clus
vv           AP4B1 MUTATED AP4B1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  AP4B1 MUTATED     0   1   9   2
  AP4B1 WILD-TYPE   9  66 240  39
D1258V4, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             2              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
  AP4B1 MUTATED    10   1   1
  AP4B1 WILD-TYPE 210  80  65
D1258V5, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1258V6, binary
                 cls
clus                0   1
  AP4B1 MUTATED     9   1
  AP4B1 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      9    1
  AP4B1 WILD-TYPE  276   47
   clus
vv  AP4B1 MUTATED AP4B1 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1258V7, binary
                 cls
clus                0   1
  AP4B1 MUTATED     4   8
  AP4B1 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      4    8
  AP4B1 WILD-TYPE  166  189
        clus
vv       AP4B1 MUTATED AP4B1 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D1258V8, binary
                 cls
clus                0   1
  AP4B1 MUTATED     8   1
  AP4B1 WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      8    1
  AP4B1 WILD-TYPE  292    7
     clus
vv    AP4B1 MUTATED AP4B1 WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D1258V9, binary
                 cls
clus                0   1
  AP4B1 MUTATED    10   2
  AP4B1 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED     10    2
  AP4B1 WILD-TYPE  304   46
                               clus
vv                              AP4B1 MUTATED AP4B1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AP4B1 MUTATED     6   0   1   1
  AP4B1 WILD-TYPE 253   3  21  20
D1258V10, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             1              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"
D1258V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP4B1 MUTATED                                  0     0
  AP4B1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP4B1 MUTATED                           0     8
  AP4B1 WILD-TYPE                        19   168
D1258V12, multiclass
                                  clus
vv                                 AP4B1 MUTATED AP4B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = NTNG1 MUTATION ANALYSIS
D1259V1, survival
                 sevent
clus2               0   1
  NTNG1 MUTATED    11   3
  NTNG1 WILD-TYPE 266  75
  NTNG1 MUTATED NTNG1 WILD-TYPE 
             14             341 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
              3              75 
$`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 
       35.74        85.48 

$`NTNG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  NTNG1 MUTATED NTNG1 WILD-TYPE 
           5.79            0.00 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
         135.65          148.01 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
         30.475          21.990 
[1] "5.8 - 135.7 (30.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1259V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTNG1 MUTATED         1        0        2         5         0         0
  NTNG1 WILD-TYPE      63        1       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTNG1 MUTATED           0          0          3          3        0         0
  NTNG1 WILD-TYPE        18          6         41         30       35        12
                 vv
clus              STAGE IVB
  NTNG1 MUTATED           0
  NTNG1 WILD-TYPE         1
D1259V3, multiclass
            clus
vv           NTNG1 MUTATED NTNG1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             3              30
  STAGE IV               0              35
  STAGE IVA              0              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
  NTNG1 MUTATED     0   1  12   1
  NTNG1 WILD-TYPE   9  66 237  40
D1259V4, multiclass
    clus
vv   NTNG1 MUTATED NTNG1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            12             237
  T4             1              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
  NTNG1 MUTATED     8   3   3
  NTNG1 WILD-TYPE 212  78  63
D1259V5, multiclass
    clus
vv   NTNG1 MUTATED NTNG1 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             3              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"
D1259V6, binary
                 cls
clus                0   1
  NTNG1 MUTATED    13   0
  NTNG1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED     13    0
  NTNG1 WILD-TYPE  272   48
   clus
vv  NTNG1 MUTATED NTNG1 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D1259V7, binary
                 cls
clus                0   1
  NTNG1 MUTATED     8   6
  NTNG1 WILD-TYPE 162 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED      8    6
  NTNG1 WILD-TYPE  162  191
        clus
vv       NTNG1 MUTATED NTNG1 WILD-TYPE
  FEMALE             8             162
  MALE               6             191
[1] 2 2
[1] FALSE
D1259V8, binary
                 cls
clus                0   1
  NTNG1 MUTATED    12   0
  NTNG1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED     12    0
  NTNG1 WILD-TYPE  288    8
     clus
vv    NTNG1 MUTATED NTNG1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1259V9, binary
                 cls
clus                0   1
  NTNG1 MUTATED    11   2
  NTNG1 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED     11    2
  NTNG1 WILD-TYPE  303   46
                               clus
vv                              NTNG1 MUTATED NTNG1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NTNG1 MUTATED    10   0   0   0
  NTNG1 WILD-TYPE 249   3  22  21
D1259V10, multiclass
    clus
vv   NTNG1 MUTATED NTNG1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D1259V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTNG1 MUTATED                                  0     0
  NTNG1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTNG1 MUTATED                           2     8
  NTNG1 WILD-TYPE                        17   168
D1259V12, multiclass
                                  clus
vv                                 NTNG1 MUTATED NTNG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        8             168
[1] 4 2
[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 = LGALS9C MUTATION ANALYSIS
D1260V1, survival
                   sevent
clus2                 0   1
  LGALS9C MUTATED     4   1
  LGALS9C WILD-TYPE 273  77
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                5               350 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                1                77 
$`LGALS9C MUTATED`
TCGA-G4-6586 TCGA-AA-3511 TCGA-AZ-6599 TCGA-CM-6164 TCGA-CM-6674 
       35.80         6.97         6.77        29.03        12.95 

$`LGALS9C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LGALS9C MUTATED LGALS9C WILD-TYPE 
             6.77              0.00 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
            35.80            148.01 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
           12.950            22.075 
[1] "6.8 - 35.8 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1260V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LGALS9C MUTATED         1        0        1         3         0         0
  LGALS9C WILD-TYPE      63        1       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LGALS9C MUTATED           0          0          0          0        0
  LGALS9C WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  LGALS9C MUTATED           0         0
  LGALS9C WILD-TYPE        12         1
D1260V3, multiclass
            clus
vv           LGALS9C MUTATED LGALS9C WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  LGALS9C MUTATED     0   1   3   1
  LGALS9C WILD-TYPE   9  66 246  40
D1260V4, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               1                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
  LGALS9C MUTATED     5   0   0
  LGALS9C WILD-TYPE 215  81  66
D1260V5, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  N0               5               215
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1260V6, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     4   0
  LGALS9C WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      4    0
  LGALS9C WILD-TYPE  281   48
   clus
vv  LGALS9C MUTATED LGALS9C WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1260V7, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     2   3
  LGALS9C WILD-TYPE 168 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      2    3
  LGALS9C WILD-TYPE  168  194
        clus
vv       LGALS9C MUTATED LGALS9C WILD-TYPE
  FEMALE               2               168
  MALE                 3               194
[1] 2 2
[1] FALSE
D1260V8, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     5   0
  LGALS9C WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      5    0
  LGALS9C WILD-TYPE  295    8
     clus
vv    LGALS9C MUTATED LGALS9C WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1260V9, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     5   0
  LGALS9C WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      5    0
  LGALS9C WILD-TYPE  309   48
                               clus
vv                              LGALS9C MUTATED LGALS9C WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  LGALS9C MUTATED     4   0   0   0
  LGALS9C WILD-TYPE 255   3  22  21
D1260V10, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1260V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGALS9C MUTATED                                  0     0
  LGALS9C WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LGALS9C MUTATED                           0     4
  LGALS9C WILD-TYPE                        19   172
D1260V12, multiclass
                                  clus
vv                                 LGALS9C MUTATED LGALS9C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = CHMP4C MUTATION ANALYSIS
D1261V1, survival
                  sevent
clus2                0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 275  77
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               3              352 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               1               77 
$`CHMP4C MUTATED`
TCGA-AU-6004 TCGA-AZ-6606 TCGA-CK-4952 
       27.09        11.74        15.62 

$`CHMP4C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CHMP4C MUTATED CHMP4C WILD-TYPE 
           11.74             0.00 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
           27.09           148.01 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
          15.620           22.075 
[1] "11.7 - 27.1 (15.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1261V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHMP4C MUTATED         1        0        0         0         0         0
  CHMP4C WILD-TYPE      63        1       26       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP4C MUTATED           0          0          0          1        1
  CHMP4C WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CHMP4C MUTATED           0         0
  CHMP4C WILD-TYPE        12         1
D1261V3, multiclass
            clus
vv           CHMP4C MUTATED CHMP4C WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CHMP4C MUTATED     0   1   0   2
  CHMP4C WILD-TYPE   9  66 249  39
D1261V4, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  T1              0                9
  T2              1               66
  T3              0              249
  T4              2               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
  CHMP4C MUTATED     1   0   2
  CHMP4C WILD-TYPE 219  81  64
D1261V5, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  N0              1              219
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1261V6, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 283  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    1
  CHMP4C WILD-TYPE  283   47
   clus
vv  CHMP4C MUTATED CHMP4C WILD-TYPE
  0              2              283
  1              1               47
[1] 2 2
[1] FALSE
D1261V7, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 168 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    1
  CHMP4C WILD-TYPE  168  196
        clus
vv       CHMP4C MUTATED CHMP4C WILD-TYPE
  FEMALE              2              168
  MALE                1              196
[1] 2 2
[1] FALSE
D1261V8, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     1   0
  CHMP4C WILD-TYPE 299   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      1    0
  CHMP4C WILD-TYPE  299    8
     clus
vv    CHMP4C MUTATED CHMP4C WILD-TYPE
  NO               1              299
  YES              0                8
[1] 2 2
[1] FALSE
D1261V9, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    1
  CHMP4C WILD-TYPE  312   47
                               clus
vv                              CHMP4C MUTATED CHMP4C WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHMP4C MUTATED     1   0   0   1
  CHMP4C WILD-TYPE 258   3  22  20
D1261V10, multiclass
[1] "Remove cluster labels:" "CHMP4C MUTATED"        
clus
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               2              303 
      TCGA-A6-2677       TCGA-AA-3496       TCGA-AA-3520       TCGA-AA-3521 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6965       TCGA-AU-3779       TCGA-AY-4070 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682       TCGA-CA-5254 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-5913 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
D1261V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHMP4C MUTATED                                  0     0
  CHMP4C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHMP4C MUTATED                           0     3
  CHMP4C WILD-TYPE                        19   173
D1261V12, multiclass
                                  clus
vv                                 CHMP4C MUTATED CHMP4C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ZNF630 MUTATION ANALYSIS
D1262V1, survival
                  sevent
clus2                0   1
  ZNF630 MUTATED     6   0
  ZNF630 WILD-TYPE 271  78
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               6              349 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               0               78 
$`ZNF630 MUTATED`
TCGA-AZ-4681 TCGA-G4-6588 TCGA-AA-3555 TCGA-AZ-4315 TCGA-CM-6164 TCGA-D5-5540 
      106.75        26.17        29.95        58.39        29.03        56.09 

$`ZNF630 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZNF630 MUTATED ZNF630 WILD-TYPE 
           26.17             0.00 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
          106.75           148.01 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
           43.02            21.99 
[1] "26.2 - 106.8 (43.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1262V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF630 MUTATED         0        0        0         7         0         0
  ZNF630 WILD-TYPE      64        1       26       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF630 MUTATED           0          0          0          0        0
  ZNF630 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF630 MUTATED           0         0
  ZNF630 WILD-TYPE        12         1
D1262V3, multiclass
            clus
vv           ZNF630 MUTATED ZNF630 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF630 MUTATED     0   0   7   0
  ZNF630 WILD-TYPE   9  67 242  41
D1262V4, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              0               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
  ZNF630 MUTATED     7   0   0
  ZNF630 WILD-TYPE 213  81  66
D1262V5, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1262V6, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     7   0
  ZNF630 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      7    0
  ZNF630 WILD-TYPE  278   48
   clus
vv  ZNF630 MUTATED ZNF630 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1262V7, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     5   2
  ZNF630 WILD-TYPE 165 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      5    2
  ZNF630 WILD-TYPE  165  195
        clus
vv       ZNF630 MUTATED ZNF630 WILD-TYPE
  FEMALE              5              165
  MALE                2              195
[1] 2 2
[1] FALSE
D1262V8, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     6   0
  ZNF630 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      6    0
  ZNF630 WILD-TYPE  294    8
     clus
vv    ZNF630 MUTATED ZNF630 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1262V9, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     6   1
  ZNF630 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      6    1
  ZNF630 WILD-TYPE  308   47
                               clus
vv                              ZNF630 MUTATED ZNF630 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF630 MUTATED     7   0   0   0
  ZNF630 WILD-TYPE 252   3  22  21
D1262V10, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1262V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF630 MUTATED                                  0     0
  ZNF630 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF630 MUTATED                           0     5
  ZNF630 WILD-TYPE                        19   171
D1262V12, multiclass
                                  clus
vv                                 ZNF630 MUTATED ZNF630 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = PTPDC1 MUTATION ANALYSIS
D1263V1, survival
                  sevent
clus2                0   1
  PTPDC1 MUTATED     7   1
  PTPDC1 WILD-TYPE 270  77
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               8              347 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               1               77 
$`PTPDC1 MUTATED`
TCGA-AA-3554 TCGA-AD-6895 TCGA-G4-6588 TCGA-AA-3553 TCGA-AU-6004 TCGA-CM-4743 
       17.95        25.08        26.17        24.00        27.09        23.05 
TCGA-CM-6675 TCGA-DM-A1DA 
       13.05         7.50 

$`PTPDC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
             7.5              0.0 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
           27.09           148.01 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
          23.525           22.030 
[1] "7.5 - 27.1 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1263V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPDC1 MUTATED         2        0        0         3         0         0
  PTPDC1 WILD-TYPE      62        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPDC1 MUTATED           0          0          1          1        0
  PTPDC1 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  PTPDC1 MUTATED           0         1
  PTPDC1 WILD-TYPE        12         0
D1263V3, multiclass
            clus
vv           PTPDC1 MUTATED PTPDC1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               12
  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   2   6   0
  PTPDC1 WILD-TYPE   9  65 243  41
D1263V4, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              6              243
  T4              0               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
  PTPDC1 MUTATED     5   1   2
  PTPDC1 WILD-TYPE 215  80  64
D1263V5, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1263V6, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     7   1
  PTPDC1 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      7    1
  PTPDC1 WILD-TYPE  278   47
   clus
vv  PTPDC1 MUTATED PTPDC1 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D1263V7, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     5   3
  PTPDC1 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      5    3
  PTPDC1 WILD-TYPE  165  194
        clus
vv       PTPDC1 MUTATED PTPDC1 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1263V8, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     6   0
  PTPDC1 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      6    0
  PTPDC1 WILD-TYPE  294    8
     clus
vv    PTPDC1 MUTATED PTPDC1 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1263V9, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     8   0
  PTPDC1 WILD-TYPE 306  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      8    0
  PTPDC1 WILD-TYPE  306   48
                               clus
vv                              PTPDC1 MUTATED PTPDC1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPDC1 MUTATED     7   0   0   0
  PTPDC1 WILD-TYPE 252   3  22  21
D1263V10, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1263V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPDC1 MUTATED                                  0     0
  PTPDC1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPDC1 MUTATED                           1     5
  PTPDC1 WILD-TYPE                        18   171
D1263V12, multiclass
                                  clus
vv                                 PTPDC1 MUTATED PTPDC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = DMXL2 MUTATION ANALYSIS
D1264V1, survival
                 sevent
clus2               0   1
  DMXL2 MUTATED    22   9
  DMXL2 WILD-TYPE 255  69
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             31             324 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
              9              69 
$`DMXL2 MUTATED`
TCGA-AA-3496 TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6588 
        1.02        17.95         6.05        19.04       100.01        26.17 
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3555 
       42.90        32.75        22.06        20.28        63.98        29.95 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N 
       15.95        37.02        53.00        27.02        25.02         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4323 TCGA-CA-6717 TCGA-CA-6718 
       34.98        12.16        21.44         1.41        12.76        10.06 
TCGA-CK-5916 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A28E TCGA-F4-6460 TCGA-G4-6293 
       21.14        12.95        11.64       119.93        31.96       133.18 
TCGA-G4-6303 
       65.85 

$`DMXL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       63.62        22.09        35.80        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 TCGA-AA-3511 
       20.12        19.66         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       17.98        38.99         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-3861 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       30.05        17.03        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82        58.39         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        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        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G 
      131.51       135.65       139.17        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DMXL2 MUTATED DMXL2 WILD-TYPE 
           1.02            0.00 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
         133.18          148.01 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
          22.06           22.06 
[1] "1.0 - 133.2 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1264V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DMXL2 MUTATED         2        0        4        12         6         0
  DMXL2 WILD-TYPE      62        1       22        96         2         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        17          5         43         33       30        12
                 vv
clus              STAGE IVB
  DMXL2 MUTATED           0
  DMXL2 WILD-TYPE         1
D1264V3, multiclass
            clus
vv           DMXL2 MUTATED DMXL2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             12              96
  STAGE IIB              6               2
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               5              30
  STAGE IVA              0              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
  DMXL2 MUTATED     1   3  20   9
  DMXL2 WILD-TYPE   8  64 229  32
D1264V4, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            20             229
  T4             9              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
  DMXL2 MUTATED    26   4   3
  DMXL2 WILD-TYPE 194  77  63
D1264V5, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  N0            26             194
  N1             4              77
  N2             3              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"
D1264V6, binary
                 cls
clus                0   1
  DMXL2 MUTATED    23   5
  DMXL2 WILD-TYPE 262  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     23    5
  DMXL2 WILD-TYPE  262   43
   clus
vv  DMXL2 MUTATED DMXL2 WILD-TYPE
  0            23             262
  1             5              43
[1] 2 2
[1] FALSE
D1264V7, binary
                 cls
clus                0   1
  DMXL2 MUTATED    17  16
  DMXL2 WILD-TYPE 153 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     17   16
  DMXL2 WILD-TYPE  153  181
        clus
vv       DMXL2 MUTATED DMXL2 WILD-TYPE
  FEMALE            17             153
  MALE              16             181
[1] 2 2
[1] FALSE
D1264V8, binary
                 cls
clus                0   1
  DMXL2 MUTATED    27   1
  DMXL2 WILD-TYPE 273   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     27    1
  DMXL2 WILD-TYPE  273    7
     clus
vv    DMXL2 MUTATED DMXL2 WILD-TYPE
  NO             27             273
  YES             1               7
[1] 2 2
[1] FALSE
D1264V9, binary
                 cls
clus                0   1
  DMXL2 MUTATED    27   6
  DMXL2 WILD-TYPE 287  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     27    6
  DMXL2 WILD-TYPE  287   42
                               clus
vv                              DMXL2 MUTATED DMXL2 WILD-TYPE
  COLON ADENOCARCINOMA                     27             287
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DMXL2 MUTATED    21   0   3   4
  DMXL2 WILD-TYPE 238   3  19  17
D1264V10, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  R0            21             238
  R1             0               3
  R2             3              19
  RX             4              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"
D1264V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DMXL2 MUTATED                                  0     2
  DMXL2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DMXL2 MUTATED                           0    17
  DMXL2 WILD-TYPE                        19   159
D1264V12, multiclass
                                  clus
vv                                 DMXL2 MUTATED DMXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       17             159
[1] 4 2
[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 = DIAPH3 MUTATION ANALYSIS
D1265V1, survival
                  sevent
clus2                0   1
  DIAPH3 MUTATED    13   2
  DIAPH3 WILD-TYPE 264  76
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              15              340 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               2               76 
$`DIAPH3 MUTATED`
TCGA-AA-3662 TCGA-G4-6310 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3977 TCGA-AD-6899 
        6.05        63.62        20.12         7.04        25.02         5.79 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6929 
       12.76        51.32        23.05        14.04        12.95        13.41 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6306 
       47.41       133.18        44.68 

$`DIAPH3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        19.66        20.28         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
            5.79             0.00 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          133.18           148.01 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          20.120           22.075 
[1] "5.8 - 133.2 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1265V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIAPH3 MUTATED         1        0        1         7         0         0
  DIAPH3 WILD-TYPE      63        1       25       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIAPH3 MUTATED           1          0          1          1        2
  DIAPH3 WILD-TYPE        17          6         43         32       33
                  vv
clus               STAGE IVA STAGE IVB
  DIAPH3 MUTATED           0         0
  DIAPH3 WILD-TYPE        12         1
D1265V3, multiclass
            clus
vv           DIAPH3 MUTATED DIAPH3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               0               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
  DIAPH3 MUTATED     0   3  11   2
  DIAPH3 WILD-TYPE   9  64 238  39
D1265V4, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             11              238
  T4              2               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
  DIAPH3 MUTATED    11   3   2
  DIAPH3 WILD-TYPE 209  78  64
D1265V5, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  N0             11              209
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1265V6, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    10   2
  DIAPH3 WILD-TYPE 275  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     10    2
  DIAPH3 WILD-TYPE  275   46
   clus
vv  DIAPH3 MUTATED DIAPH3 WILD-TYPE
  0             10              275
  1              2               46
[1] 2 2
[1] FALSE
D1265V7, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED     7   9
  DIAPH3 WILD-TYPE 163 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      7    9
  DIAPH3 WILD-TYPE  163  188
        clus
vv       DIAPH3 MUTATED DIAPH3 WILD-TYPE
  FEMALE              7              163
  MALE                9              188
[1] 2 2
[1] FALSE
D1265V8, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    14   1
  DIAPH3 WILD-TYPE 286   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     14    1
  DIAPH3 WILD-TYPE  286    7
     clus
vv    DIAPH3 MUTATED DIAPH3 WILD-TYPE
  NO              14              286
  YES              1                7
[1] 2 2
[1] FALSE
D1265V9, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    13   3
  DIAPH3 WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     13    3
  DIAPH3 WILD-TYPE  301   45
                               clus
vv                              DIAPH3 MUTATED DIAPH3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DIAPH3 MUTATED    10   0   1   2
  DIAPH3 WILD-TYPE 249   3  21  19
D1265V10, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              2               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"
D1265V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIAPH3 MUTATED                                  0     1
  DIAPH3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DIAPH3 MUTATED                           0    11
  DIAPH3 WILD-TYPE                        19   165
D1265V12, multiclass
                                  clus
vv                                 DIAPH3 MUTATED DIAPH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        11              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(1266) Variable = KLF11 MUTATION ANALYSIS
D1266V1, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     5   1
  KLF11 WILD-TYPE 272  77
  KLF11 MUTATED KLF11 WILD-TYPE 
              6             349 
  KLF11 MUTATED KLF11 WILD-TYPE 
              1              77 
$`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 

$`KLF11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KLF11 MUTATED KLF11 WILD-TYPE 
           6.05            0.00 
  KLF11 MUTATED KLF11 WILD-TYPE 
          62.79          148.01 
  KLF11 MUTATED KLF11 WILD-TYPE 
         17.305          22.090 
[1] "6.0 - 62.8 (17.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1266V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF11 MUTATED         1        0        1         2         1         0
  KLF11 WILD-TYPE      63        1       25       106         7         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        18          5         44         33       34        12
                 vv
clus              STAGE IVB
  KLF11 MUTATED           0
  KLF11 WILD-TYPE         1
D1266V3, multiclass
            clus
vv           KLF11 MUTATED KLF11 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  KLF11 MUTATED     1   0   4   2
  KLF11 WILD-TYPE   8  67 245  39
D1266V4, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             4             245
  T4             2              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
  KLF11 MUTATED     5   1   1
  KLF11 WILD-TYPE 215  80  65
D1266V5, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1266V6, binary
                 cls
clus                0   1
  KLF11 MUTATED     4   1
  KLF11 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      4    1
  KLF11 WILD-TYPE  281   47
   clus
vv  KLF11 MUTATED KLF11 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1266V7, binary
                 cls
clus                0   1
  KLF11 MUTATED     4   3
  KLF11 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      4    3
  KLF11 WILD-TYPE  166  194
        clus
vv       KLF11 MUTATED KLF11 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1266V8, binary
                 cls
clus                0   1
  KLF11 MUTATED     6   0
  KLF11 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      6    0
  KLF11 WILD-TYPE  294    8
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1266V9, binary
                 cls
clus                0   1
  KLF11 MUTATED     4   3
  KLF11 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      4    3
  KLF11 WILD-TYPE  310   45
                               clus
vv                              KLF11 MUTATED KLF11 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLF11 MUTATED     3   0   1   2
  KLF11 WILD-TYPE 256   3  21  19
D1266V10, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             1              21
  RX             2              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"
D1266V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF11 MUTATED                                  0     1
  KLF11 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLF11 MUTATED                           0     4
  KLF11 WILD-TYPE                        19   172
D1266V12, multiclass
                                  clus
vv                                 KLF11 MUTATED KLF11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = TAX1BP1 MUTATION ANALYSIS
D1267V1, survival
                   sevent
clus2                 0   1
  TAX1BP1 MUTATED     8   4
  TAX1BP1 WILD-TYPE 269  74
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               12               343 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                4                74 
$`TAX1BP1 MUTATED`
TCGA-AZ-6601 TCGA-A6-5665 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-6598 
      100.01        22.06        53.00        34.98         0.95        49.41 
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 

$`TAX1BP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       15.62        21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
             0.95              0.00 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
           135.65            148.01 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
           29.015            21.990 
[1] "0.9 - 135.7 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1267V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAX1BP1 MUTATED         3        0        3         4         1         0
  TAX1BP1 WILD-TYPE      61        1       23       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAX1BP1 MUTATED           0          0          1          0        0
  TAX1BP1 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  TAX1BP1 MUTATED           0         0
  TAX1BP1 WILD-TYPE        12         1
D1267V3, multiclass
            clus
vv           TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  TAX1BP1 MUTATED     2   1   8   1
  TAX1BP1 WILD-TYPE   7  66 241  40
D1267V4, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  T1               2                 7
  T2               1                66
  T3               8               241
  T4               1                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
  TAX1BP1 MUTATED    11   1   0
  TAX1BP1 WILD-TYPE 209  80  66
D1267V5, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  N0              11               209
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1267V6, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     9   0
  TAX1BP1 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      9    0
  TAX1BP1 WILD-TYPE  276   48
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D1267V7, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     6   6
  TAX1BP1 WILD-TYPE 164 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      6    6
  TAX1BP1 WILD-TYPE  164  191
        clus
vv       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  FEMALE               6               164
  MALE                 6               191
[1] 2 2
[1] FALSE
D1267V8, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED    11   0
  TAX1BP1 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED     11    0
  TAX1BP1 WILD-TYPE  289    8
     clus
vv    TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D1267V9, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     9   1
  TAX1BP1 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      9    1
  TAX1BP1 WILD-TYPE  305   47
                               clus
vv                              TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TAX1BP1 MUTATED     7   0   0   2
  TAX1BP1 WILD-TYPE 252   3  22  19
D1267V10, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               2                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"
D1267V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAX1BP1 MUTATED                                  0     0
  TAX1BP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TAX1BP1 MUTATED                           0    10
  TAX1BP1 WILD-TYPE                        19   166
D1267V12, multiclass
                                  clus
vv                                 TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         10               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(1268) Variable = MCM9 MUTATION ANALYSIS
D1268V1, survival
                sevent
clus2              0   1
  MCM9 MUTATED     6   1
  MCM9 WILD-TYPE 271  77
  MCM9 MUTATED MCM9 WILD-TYPE 
             7            348 
  MCM9 MUTATED MCM9 WILD-TYPE 
             1             77 
$`MCM9 MUTATED`
TCGA-AA-3662 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A010 TCGA-AZ-5403 TCGA-CA-6717 
        6.05        63.98        53.00        34.98        62.79        12.76 
TCGA-D5-6541 
       15.58 

$`MCM9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MCM9 MUTATED MCM9 WILD-TYPE 
          6.05           0.00 
  MCM9 MUTATED MCM9 WILD-TYPE 
         63.98         148.01 
  MCM9 MUTATED MCM9 WILD-TYPE 
        34.980         22.045 
[1] "6.0 - 64.0 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1268V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCM9 MUTATED         0        0        3         2         1         0
  MCM9 WILD-TYPE      64        1       23       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCM9 MUTATED           0          0          0          0        1         0
  MCM9 WILD-TYPE        18          6         44         33       34        12
                vv
clus             STAGE IVB
  MCM9 MUTATED           0
  MCM9 WILD-TYPE         1
D1268V3, multiclass
            clus
vv           MCM9 MUTATED MCM9 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  MCM9 MUTATED     0   0   5   2
  MCM9 WILD-TYPE   9  67 244  39
D1268V4, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            2             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
  MCM9 MUTATED     6   0   1
  MCM9 WILD-TYPE 214  81  65
D1268V5, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1268V6, binary
                cls
clus               0   1
  MCM9 MUTATED     5   1
  MCM9 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      5    1
  MCM9 WILD-TYPE  280   47
   clus
vv  MCM9 MUTATED MCM9 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D1268V7, binary
                cls
clus               0   1
  MCM9 MUTATED     2   5
  MCM9 WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    5
  MCM9 WILD-TYPE  168  192
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D1268V8, binary
                cls
clus               0   1
  MCM9 MUTATED     7   0
  MCM9 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      7    0
  MCM9 WILD-TYPE  293    8
     clus
vv    MCM9 MUTATED MCM9 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1268V9, binary
                cls
clus               0   1
  MCM9 MUTATED     6   1
  MCM9 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      6    1
  MCM9 WILD-TYPE  308   47
                               clus
vv                              MCM9 MUTATED MCM9 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MCM9 MUTATED     4   0   1   1
  MCM9 WILD-TYPE 255   3  21  20
D1268V10, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            1             21
  RX            1             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"
D1268V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM9 MUTATED                                  0     1
  MCM9 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCM9 MUTATED                           0     2
  MCM9 WILD-TYPE                        19   174
D1268V12, multiclass
                                  clus
vv                                 MCM9 MUTATED MCM9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(1269) Variable = SBDS MUTATION ANALYSIS
D1269V1, survival
                sevent
clus2              0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 275  77
  SBDS MUTATED SBDS WILD-TYPE 
             3            352 
  SBDS MUTATED SBDS WILD-TYPE 
             1             77 
$`SBDS MUTATED`
TCGA-AA-3660 TCGA-D5-6926 TCGA-G4-6303 
       78.08         9.04        65.85 

$`SBDS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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         22.045 
[1] "9.0 - 78.1 (65.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1269V2, continuous
                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      64        1       25       108         8         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  SBDS MUTATED           0
  SBDS WILD-TYPE         1
D1269V3, multiclass
            clus
vv           SBDS MUTATED SBDS WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  SBDS MUTATED     0   0   2   1
  SBDS WILD-TYPE   9  67 247  40
D1269V4, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  T1            0              9
  T2            0             67
  T3            2            247
  T4            1             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
  SBDS MUTATED     1   2   0
  SBDS WILD-TYPE 219  79  66
D1269V5, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  N0            1            219
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1269V6, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 283  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  283   47
   clus
vv  SBDS MUTATED SBDS WILD-TYPE
  0            2            283
  1            1             47
[1] 2 2
[1] FALSE
D1269V7, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 168 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  168  196
        clus
vv       SBDS MUTATED SBDS WILD-TYPE
  FEMALE            2            168
  MALE              1            196
[1] 2 2
[1] FALSE
D1269V8, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 298   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  298    7
     clus
vv    SBDS MUTATED SBDS WILD-TYPE
  NO             2            298
  YES            1              7
[1] 2 2
[1] FALSE
D1269V9, binary
                cls
clus               0   1
  SBDS MUTATED     3   0
  SBDS WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      3    0
  SBDS WILD-TYPE  311   48
                               clus
vv                              SBDS MUTATED SBDS WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SBDS MUTATED     3   0   0   0
  SBDS WILD-TYPE 256   3  22  21
D1269V10, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1269V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBDS MUTATED                                  0     0
  SBDS WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBDS MUTATED                           0     2
  SBDS WILD-TYPE                        19   174
D1269V12, multiclass
[1] "Remove cluster labels:" "SBDS MUTATED"          
clus
  SBDS MUTATED SBDS WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6600     TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6607     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-5913     TCGA-CK-5914 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 

Clustering(1270) Variable = ANXA11 MUTATION ANALYSIS
D1270V1, survival
                  sevent
clus2                0   1
  ANXA11 MUTATED     5   2
  ANXA11 WILD-TYPE 272  76
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               7              348 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               2               76 
$`ANXA11 MUTATED`
TCGA-AA-3516 TCGA-AA-3531 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-A010 TCGA-AZ-4315 
       13.02        34.03        24.39         3.02        34.98        58.39 
TCGA-CM-5861 
       15.02 

$`ANXA11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ANXA11 MUTATED ANXA11 WILD-TYPE 
            3.02             0.00 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
           58.39           148.01 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
          24.390           22.045 
[1] "3.0 - 58.4 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1270V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANXA11 MUTATED         1        0        1         3         1         0
  ANXA11 WILD-TYPE      63        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANXA11 MUTATED           1          0          0          0        0
  ANXA11 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ANXA11 MUTATED           0         0
  ANXA11 WILD-TYPE        12         1
D1270V3, multiclass
            clus
vv           ANXA11 MUTATED ANXA11 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ANXA11 MUTATED     0   1   5   1
  ANXA11 WILD-TYPE   9  66 244  40
D1270V4, multiclass
    clus
vv   ANXA11 MUTATED ANXA11 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              1               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
  ANXA11 MUTATED     6   0   1
  ANXA11 WILD-TYPE 214  81  65
D1270V5, multiclass
    clus
vv   ANXA11 MUTATED ANXA11 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1270V6, binary
                  cls
clus                 0   1
  ANXA11 MUTATED     7   0
  ANXA11 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANXA11 MUTATED      7    0
  ANXA11 WILD-TYPE  278   48
   clus
vv  ANXA11 MUTATED ANXA11 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1270V7, binary
                  cls
clus                 0   1
  ANXA11 MUTATED     5   2
  ANXA11 WILD-TYPE 165 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANXA11 MUTATED      5    2
  ANXA11 WILD-TYPE  165  195
        clus
vv       ANXA11 MUTATED ANXA11 WILD-TYPE
  FEMALE              5              165
  MALE                2              195
[1] 2 2
[1] FALSE
D1270V8, binary
                  cls
clus                 0   1
  ANXA11 MUTATED     7   0
  ANXA11 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANXA11 MUTATED      7    0
  ANXA11 WILD-TYPE  293    8
     clus
vv    ANXA11 MUTATED ANXA11 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1270V9, binary
                  cls
clus                 0   1
  ANXA11 MUTATED     6   1
  ANXA11 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANXA11 MUTATED      6    1
  ANXA11 WILD-TYPE  308   47
                               clus
vv                              ANXA11 MUTATED ANXA11 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ANXA11 MUTATED     5   0   0   0
  ANXA11 WILD-TYPE 254   3  22  21
D1270V10, multiclass
    clus
vv   ANXA11 MUTATED ANXA11 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1270V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANXA11 MUTATED                                  0     0
  ANXA11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANXA11 MUTATED                           0     3
  ANXA11 WILD-TYPE                        19   173
D1270V12, multiclass
                                  clus
vv                                 ANXA11 MUTATED ANXA11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = OR2A5 MUTATION ANALYSIS
D1271V1, survival
                 sevent
clus2               0   1
  OR2A5 MUTATED     7   1
  OR2A5 WILD-TYPE 270  77
  OR2A5 MUTATED OR2A5 WILD-TYPE 
              8             347 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
              1              77 
$`OR2A5 MUTATED`
TCGA-AA-3713 TCGA-G4-6628 TCGA-AA-3947 TCGA-AA-3977 TCGA-CA-6717 TCGA-CM-5349 
       19.04        79.69        33.01        25.02        12.76        30.08 
TCGA-CM-6676 TCGA-DM-A0XF 
       11.08        38.20 

$`OR2A5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR2A5 MUTATED OR2A5 WILD-TYPE 
          11.08            0.00 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
          79.69          148.01 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
          27.55           22.03 
[1] "11.1 - 79.7 (27.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1271V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2A5 MUTATED         2        0        0         3         1         0
  OR2A5 WILD-TYPE      62        1       26       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2A5 MUTATED           0          0          0          1        2         0
  OR2A5 WILD-TYPE        18          6         44         32       33        12
                 vv
clus              STAGE IVB
  OR2A5 MUTATED           0
  OR2A5 WILD-TYPE         1
D1271V3, multiclass
            clus
vv           OR2A5 MUTATED OR2A5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  OR2A5 MUTATED     0   3   6   1
  OR2A5 WILD-TYPE   9  64 243  40
D1271V4, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             6             243
  T4             1              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
  OR2A5 MUTATED     8   0   2
  OR2A5 WILD-TYPE 212  81  64
D1271V5, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1271V6, binary
                 cls
clus                0   1
  OR2A5 MUTATED     7   2
  OR2A5 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      7    2
  OR2A5 WILD-TYPE  278   46
   clus
vv  OR2A5 MUTATED OR2A5 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D1271V7, binary
                 cls
clus                0   1
  OR2A5 MUTATED     5   5
  OR2A5 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      5    5
  OR2A5 WILD-TYPE  165  192
        clus
vv       OR2A5 MUTATED OR2A5 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1271V8, binary
                 cls
clus                0   1
  OR2A5 MUTATED     6   1
  OR2A5 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      6    1
  OR2A5 WILD-TYPE  294    7
     clus
vv    OR2A5 MUTATED OR2A5 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D1271V9, binary
                 cls
clus                0   1
  OR2A5 MUTATED     7   2
  OR2A5 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      7    2
  OR2A5 WILD-TYPE  307   46
                               clus
vv                              OR2A5 MUTATED OR2A5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2A5 MUTATED     5   0   2   1
  OR2A5 WILD-TYPE 254   3  20  20
D1271V10, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             2              20
  RX             1              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"
D1271V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2A5 MUTATED                                  0     1
  OR2A5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2A5 MUTATED                           0     4
  OR2A5 WILD-TYPE                        19   172
D1271V12, multiclass
                                  clus
vv                                 OR2A5 MUTATED OR2A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SLC45A2 MUTATION ANALYSIS
D1272V1, survival
                   sevent
clus2                 0   1
  SLC45A2 MUTATED     7   2
  SLC45A2 WILD-TYPE 270  76
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                9               346 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                2                76 
$`SLC45A2 MUTATED`
TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-A00D TCGA-AD-6899 
       26.17        33.53        14.01         2.01        19.00         5.79 
TCGA-CK-4948 TCGA-D5-6529 TCGA-D5-6541 
      148.01        20.19        15.58 

$`SLC45A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
             2.01              0.00 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
           148.01            140.38 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
            19.00             22.09 
[1] "2.0 - 148.0 (19.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D1272V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC45A2 MUTATED         2        0        0         4         0         0
  SLC45A2 WILD-TYPE      62        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC45A2 MUTATED           2          0          0          1        0
  SLC45A2 WILD-TYPE        16          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC45A2 MUTATED           0         0
  SLC45A2 WILD-TYPE        12         1
D1272V3, multiclass
            clus
vv           SLC45A2 MUTATED SLC45A2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC45A2 MUTATED     0   2   6   1
  SLC45A2 WILD-TYPE   9  65 243  40
D1272V4, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               6               243
  T4               1                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
  SLC45A2 MUTATED     6   2   1
  SLC45A2 WILD-TYPE 214  79  65
D1272V5, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  N0               6               214
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1272V6, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     8   0
  SLC45A2 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      8    0
  SLC45A2 WILD-TYPE  277   48
   clus
vv  SLC45A2 MUTATED SLC45A2 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D1272V7, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     3   6
  SLC45A2 WILD-TYPE 167 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      3    6
  SLC45A2 WILD-TYPE  167  191
        clus
vv       SLC45A2 MUTATED SLC45A2 WILD-TYPE
  FEMALE               3               167
  MALE                 6               191
[1] 2 2
[1] FALSE
D1272V8, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     8   0
  SLC45A2 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      8    0
  SLC45A2 WILD-TYPE  292    8
     clus
vv    SLC45A2 MUTATED SLC45A2 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1272V9, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     8   1
  SLC45A2 WILD-TYPE 306  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      8    1
  SLC45A2 WILD-TYPE  306   47
                               clus
vv                              SLC45A2 MUTATED SLC45A2 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC45A2 MUTATED     8   0   0   0
  SLC45A2 WILD-TYPE 251   3  22  21
D1272V10, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               0                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"
D1272V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC45A2 MUTATED                                  0     0
  SLC45A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC45A2 MUTATED                           1     5
  SLC45A2 WILD-TYPE                        18   171
D1272V12, multiclass
                                  clus
vv                                 SLC45A2 MUTATED SLC45A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = SYNJ1 MUTATION ANALYSIS
D1273V1, survival
                 sevent
clus2               0   1
  SYNJ1 MUTATED    11   4
  SYNJ1 WILD-TYPE 266  74
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             15             340 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
              4              74 
$`SYNJ1 MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3710 
        0.92        25.08        79.69         3.02        29.95        26.99 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
       25.02        34.98        49.41        12.10        12.76        10.06 
TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6168 
       32.02        15.02        12.99 

$`SYNJ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        88.21         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
           0.92            0.00 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
          79.69          148.01 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
         25.020          22.045 
[1] "0.9 - 79.7 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1273V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNJ1 MUTATED         2        0        2         7         1         0
  SYNJ1 WILD-TYPE      62        1       24       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNJ1 MUTATED           1          0          1          0        1         0
  SYNJ1 WILD-TYPE        17          6         43         33       34        12
                 vv
clus              STAGE IVB
  SYNJ1 MUTATED           0
  SYNJ1 WILD-TYPE         1
D1273V3, multiclass
            clus
vv           SYNJ1 MUTATED SYNJ1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  SYNJ1 MUTATED     0   3  11   2
  SYNJ1 WILD-TYPE   9  64 238  39
D1273V4, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            11             238
  T4             2              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
  SYNJ1 MUTATED    13   3   0
  SYNJ1 WILD-TYPE 207  78  66
D1273V5, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  N0            13             207
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1273V6, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    13   1
  SYNJ1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     13    1
  SYNJ1 WILD-TYPE  272   47
   clus
vv  SYNJ1 MUTATED SYNJ1 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D1273V7, binary
                 cls
clus                0   1
  SYNJ1 MUTATED     9   7
  SYNJ1 WILD-TYPE 161 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED      9    7
  SYNJ1 WILD-TYPE  161  190
        clus
vv       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  FEMALE             9             161
  MALE               7             190
[1] 2 2
[1] FALSE
D1273V8, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    15   0
  SYNJ1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     15    0
  SYNJ1 WILD-TYPE  285    8
     clus
vv    SYNJ1 MUTATED SYNJ1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D1273V9, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    14   2
  SYNJ1 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     14    2
  SYNJ1 WILD-TYPE  300   46
                               clus
vv                              SYNJ1 MUTATED SYNJ1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNJ1 MUTATED    11   0   0   2
  SYNJ1 WILD-TYPE 248   3  22  19
D1273V10, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             2              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"
D1273V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNJ1 MUTATED                                  0     2
  SYNJ1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYNJ1 MUTATED                           2     5
  SYNJ1 WILD-TYPE                        17   171
D1273V12, multiclass
                                  clus
vv                                 SYNJ1 MUTATED SYNJ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = SLC9A2 MUTATION ANALYSIS
D1274V1, survival
                  sevent
clus2                0   1
  SLC9A2 MUTATED     7   2
  SLC9A2 WILD-TYPE 270  76
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               9              346 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               2               76 
$`SLC9A2 MUTATED`
TCGA-AA-3821 TCGA-AA-3949 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-6717 
        1.02        26.01        83.24        58.39         3.19        12.76 
TCGA-CK-4950 TCGA-CM-5861 TCGA-F4-6807 
       85.45        15.02        43.04 

$`SLC9A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
            1.02             0.00 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
           85.45           148.01 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
          26.010           22.045 
[1] "1.0 - 85.5 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1274V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC9A2 MUTATED         1        0        0         4         1         0
  SLC9A2 WILD-TYPE      63        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A2 MUTATED           0          0          2          1        1
  SLC9A2 WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  SLC9A2 MUTATED           0         0
  SLC9A2 WILD-TYPE        12         1
D1274V3, multiclass
            clus
vv           SLC9A2 MUTATED SLC9A2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  SLC9A2 MUTATED     0   1   7   2
  SLC9A2 WILD-TYPE   9  66 242  39
D1274V4, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              2               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
  SLC9A2 MUTATED     6   2   2
  SLC9A2 WILD-TYPE 214  79  64
D1274V5, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  N0              6              214
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1274V6, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     8   1
  SLC9A2 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      8    1
  SLC9A2 WILD-TYPE  277   47
   clus
vv  SLC9A2 MUTATED SLC9A2 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1274V7, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     6   4
  SLC9A2 WILD-TYPE 164 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      6    4
  SLC9A2 WILD-TYPE  164  193
        clus
vv       SLC9A2 MUTATED SLC9A2 WILD-TYPE
  FEMALE              6              164
  MALE                4              193
[1] 2 2
[1] FALSE
D1274V8, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     9   0
  SLC9A2 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      9    0
  SLC9A2 WILD-TYPE  291    8
     clus
vv    SLC9A2 MUTATED SLC9A2 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1274V9, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     6   4
  SLC9A2 WILD-TYPE 308  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      6    4
  SLC9A2 WILD-TYPE  308   44
                               clus
vv                              SLC9A2 MUTATED SLC9A2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC9A2 MUTATED     6   1   0   2
  SLC9A2 WILD-TYPE 253   2  22  19
D1274V10, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  R0              6              253
  R1              1                2
  R2              0               22
  RX              2               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"
D1274V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A2 MUTATED                                  0     2
  SLC9A2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC9A2 MUTATED                           1     5
  SLC9A2 WILD-TYPE                        18   171
D1274V12, multiclass
                                  clus
vv                                 SLC9A2 MUTATED SLC9A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = DUSP7 MUTATION ANALYSIS
D1275V1, survival
                 sevent
clus2               0   1
  DUSP7 MUTATED     5   1
  DUSP7 WILD-TYPE 272  77
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              6             349 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              1              77 
$`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 

$`DUSP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DUSP7 MUTATED DUSP7 WILD-TYPE 
              0               0 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
          78.08          148.01 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
         19.855          22.090 
[1] "0.0 - 78.1 (19.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1275V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP7 MUTATED         1        0        2         1         0         0
  DUSP7 WILD-TYPE      63        1       24       107         8         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        18          5         44         32       35        12
                 vv
clus              STAGE IVB
  DUSP7 MUTATED           0
  DUSP7 WILD-TYPE         1
D1275V3, multiclass
            clus
vv           DUSP7 MUTATED DUSP7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  DUSP7 MUTATED     0   1   5   0
  DUSP7 WILD-TYPE   9  66 244  41
D1275V4, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             0              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
  DUSP7 MUTATED     4   1   1
  DUSP7 WILD-TYPE 216  80  65
D1275V5, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1275V6, binary
                 cls
clus                0   1
  DUSP7 MUTATED     5   0
  DUSP7 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      5    0
  DUSP7 WILD-TYPE  280   48
   clus
vv  DUSP7 MUTATED DUSP7 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1275V7, binary
                 cls
clus                0   1
  DUSP7 MUTATED     3   3
  DUSP7 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      3    3
  DUSP7 WILD-TYPE  167  194
        clus
vv       DUSP7 MUTATED DUSP7 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1275V8, binary
                 cls
clus                0   1
  DUSP7 MUTATED     5   0
  DUSP7 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      5    0
  DUSP7 WILD-TYPE  295    8
     clus
vv    DUSP7 MUTATED DUSP7 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1275V9, binary
                 cls
clus                0   1
  DUSP7 MUTATED     4   2
  DUSP7 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      4    2
  DUSP7 WILD-TYPE  310   46
                               clus
vv                              DUSP7 MUTATED DUSP7 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DUSP7 MUTATED     5   0   0   0
  DUSP7 WILD-TYPE 254   3  22  21
D1275V10, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1275V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP7 MUTATED                                  0     0
  DUSP7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DUSP7 MUTATED                           0     3
  DUSP7 WILD-TYPE                        19   173
D1275V12, multiclass
                                  clus
vv                                 DUSP7 MUTATED DUSP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = EFCAB4B MUTATION ANALYSIS
D1276V1, survival
                   sevent
clus2                 0   1
  EFCAB4B MUTATED     4   1
  EFCAB4B WILD-TYPE 273  77
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                5               350 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                1                77 
$`EFCAB4B MUTATED`
TCGA-AA-3821 TCGA-CA-5796 TCGA-CK-4950 TCGA-CM-6171 TCGA-F4-6459 
        1.02        12.39        85.45        14.04         8.61 

$`EFCAB4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
             1.02              0.00 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
            85.45            148.01 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
            12.39             22.09 
[1] "1.0 - 85.5 (12.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1276V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFCAB4B MUTATED         2        0        0         1         0         0
  EFCAB4B WILD-TYPE      62        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFCAB4B MUTATED           0          0          2          0        0
  EFCAB4B WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  EFCAB4B MUTATED           0         0
  EFCAB4B WILD-TYPE        12         1
D1276V3, multiclass
            clus
vv           EFCAB4B MUTATED EFCAB4B WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  EFCAB4B MUTATED     0   2   3   0
  EFCAB4B WILD-TYPE   9  65 246  41
D1276V4, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               3               246
  T4               0                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
  EFCAB4B MUTATED     3   1   1
  EFCAB4B WILD-TYPE 217  80  65
D1276V5, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  N0               3               217
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1276V6, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     5   0
  EFCAB4B WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      5    0
  EFCAB4B WILD-TYPE  280   48
   clus
vv  EFCAB4B MUTATED EFCAB4B WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1276V7, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     5   0
  EFCAB4B WILD-TYPE 165 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      5    0
  EFCAB4B WILD-TYPE  165  197
        clus
vv       EFCAB4B MUTATED EFCAB4B WILD-TYPE
  FEMALE               5               165
  MALE                 0               197
[1] 2 2
[1] FALSE
D1276V8, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     5   0
  EFCAB4B WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      5    0
  EFCAB4B WILD-TYPE  295    8
     clus
vv    EFCAB4B MUTATED EFCAB4B WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1276V9, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     2   3
  EFCAB4B WILD-TYPE 312  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      2    3
  EFCAB4B WILD-TYPE  312   45
                               clus
vv                              EFCAB4B MUTATED EFCAB4B WILD-TYPE
  COLON ADENOCARCINOMA                        2               312
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EFCAB4B MUTATED     4   1   0   0
  EFCAB4B WILD-TYPE 255   2  22  21
D1276V10, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  R0               4               255
  R1               1                 2
  R2               0                22
  RX               0                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"
D1276V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFCAB4B MUTATED                                  0     1
  EFCAB4B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EFCAB4B MUTATED                           1     2
  EFCAB4B WILD-TYPE                        18   174
D1276V12, multiclass
                                  clus
vv                                 EFCAB4B MUTATED EFCAB4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          2               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(1277) Variable = PAK1 MUTATION ANALYSIS
D1277V1, survival
                sevent
clus2              0   1
  PAK1 MUTATED     8   0
  PAK1 WILD-TYPE 269  78
  PAK1 MUTATED PAK1 WILD-TYPE 
             8            347 
  PAK1 MUTATED PAK1 WILD-TYPE 
             0             78 
$`PAK1 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
       26.17        79.69        33.01        34.98        58.39        12.76 
TCGA-D5-6539 TCGA-DM-A28H 
       12.49       117.07 

$`PAK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PAK1 MUTATED PAK1 WILD-TYPE 
         12.49           0.00 
  PAK1 MUTATED PAK1 WILD-TYPE 
        117.07         148.01 
  PAK1 MUTATED PAK1 WILD-TYPE 
        33.995         21.990 
[1] "12.5 - 117.1 (34.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1277V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK1 MUTATED         1        0        1         4         2         0
  PAK1 WILD-TYPE      63        1       25       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK1 MUTATED           0          0          0          1        0         0
  PAK1 WILD-TYPE        18          6         44         32       35        12
                vv
clus             STAGE IVB
  PAK1 MUTATED           0
  PAK1 WILD-TYPE         1
D1277V3, multiclass
            clus
vv           PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  PAK1 MUTATED     0   1   6   3
  PAK1 WILD-TYPE   9  66 243  38
D1277V4, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            3             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
  PAK1 MUTATED     9   0   1
  PAK1 WILD-TYPE 211  81  65
D1277V5, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  N0            9            211
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1277V6, binary
                cls
clus               0   1
  PAK1 MUTATED    10   0
  PAK1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED     10    0
  PAK1 WILD-TYPE  275   48
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1277V7, binary
                cls
clus               0   1
  PAK1 MUTATED     6   4
  PAK1 WILD-TYPE 164 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      6    4
  PAK1 WILD-TYPE  164  193
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  FEMALE            6            164
  MALE              4            193
[1] 2 2
[1] FALSE
D1277V8, binary
                cls
clus               0   1
  PAK1 MUTATED     7   0
  PAK1 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      7    0
  PAK1 WILD-TYPE  293    8
     clus
vv    PAK1 MUTATED PAK1 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1277V9, binary
                cls
clus               0   1
  PAK1 MUTATED     8   2
  PAK1 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      8    2
  PAK1 WILD-TYPE  306   46
                               clus
vv                              PAK1 MUTATED PAK1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAK1 MUTATED     8   0   0   1
  PAK1 WILD-TYPE 251   3  22  20
D1277V10, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D1277V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK1 MUTATED                                  0     1
  PAK1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK1 MUTATED                           0     5
  PAK1 WILD-TYPE                        19   171
D1277V12, multiclass
                                  clus
vv                                 PAK1 MUTATED PAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = OR4N4 MUTATION ANALYSIS
D1278V1, survival
                 sevent
clus2               0   1
  OR4N4 MUTATED     7   5
  OR4N4 WILD-TYPE 270  73
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             12             343 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
              5              73 
$`OR4N4 MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-6137 TCGA-AA-3655 TCGA-AA-A00N TCGA-AA-A010 
       19.04        35.80        27.09        61.02         4.01        34.98 
TCGA-CM-6162 TCGA-CM-6676 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6303 
       12.00        11.08        38.20       135.65        31.96        65.85 

$`OR4N4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  OR4N4 MUTATED OR4N4 WILD-TYPE 
           4.01            0.00 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
         135.65          148.01 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
          33.47           21.99 
[1] "4.0 - 135.7 (33.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1278V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4N4 MUTATED         1        0        2         1         2         0
  OR4N4 WILD-TYPE      63        1       24       107         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4N4 MUTATED           0          0          4          1        1         0
  OR4N4 WILD-TYPE        18          6         40         32       34        12
                 vv
clus              STAGE IVB
  OR4N4 MUTATED           0
  OR4N4 WILD-TYPE         1
D1278V3, multiclass
            clus
vv           OR4N4 MUTATED OR4N4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  OR4N4 MUTATED     0   1   9   2
  OR4N4 WILD-TYPE   9  66 240  39
D1278V4, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             2              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
  OR4N4 MUTATED     6   5   1
  OR4N4 WILD-TYPE 214  76  65
D1278V5, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  N0             6             214
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1278V6, binary
                 cls
clus                0   1
  OR4N4 MUTATED    11   1
  OR4N4 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED     11    1
  OR4N4 WILD-TYPE  274   47
   clus
vv  OR4N4 MUTATED OR4N4 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D1278V7, binary
                 cls
clus                0   1
  OR4N4 MUTATED     6   6
  OR4N4 WILD-TYPE 164 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED      6    6
  OR4N4 WILD-TYPE  164  191
        clus
vv       OR4N4 MUTATED OR4N4 WILD-TYPE
  FEMALE             6             164
  MALE               6             191
[1] 2 2
[1] FALSE
D1278V8, binary
                 cls
clus                0   1
  OR4N4 MUTATED     9   0
  OR4N4 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED      9    0
  OR4N4 WILD-TYPE  291    8
     clus
vv    OR4N4 MUTATED OR4N4 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1278V9, binary
                 cls
clus                0   1
  OR4N4 MUTATED     8   2
  OR4N4 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED      8    2
  OR4N4 WILD-TYPE  306   46
                               clus
vv                              OR4N4 MUTATED OR4N4 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4N4 MUTATED     9   0   0   0
  OR4N4 WILD-TYPE 250   3  22  21
D1278V10, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1278V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4N4 MUTATED                                  0     0
  OR4N4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4N4 MUTATED                           0     8
  OR4N4 WILD-TYPE                        19   168
D1278V12, multiclass
                                  clus
vv                                 OR4N4 MUTATED OR4N4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = IFI44 MUTATION ANALYSIS
D1279V1, survival
                 sevent
clus2               0   1
  IFI44 MUTATED     7   1
  IFI44 WILD-TYPE 270  77
  IFI44 MUTATED IFI44 WILD-TYPE 
              8             347 
  IFI44 MUTATED IFI44 WILD-TYPE 
              1              77 
$`IFI44 MUTATED`
TCGA-G4-6321 TCGA-A6-2672 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 
       22.09        46.65        25.02        58.39        88.21        12.76 
TCGA-D5-6533 TCGA-DM-A0XF 
       25.48        38.20 

$`IFI44 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  IFI44 MUTATED IFI44 WILD-TYPE 
          12.76            0.00 
  IFI44 MUTATED IFI44 WILD-TYPE 
          88.21          148.01 
  IFI44 MUTATED IFI44 WILD-TYPE 
          31.84           21.99 
[1] "12.8 - 88.2 (31.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D1279V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFI44 MUTATED         1        0        0         2         0         0
  IFI44 WILD-TYPE      63        1       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFI44 MUTATED           1          0          1          1        0         0
  IFI44 WILD-TYPE        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  IFI44 MUTATED           0
  IFI44 WILD-TYPE         1
D1279V3, multiclass
            clus
vv           IFI44 MUTATED IFI44 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  IFI44 MUTATED     1   2   4   1
  IFI44 WILD-TYPE   8  65 245  40
D1279V4, multiclass
    clus
vv   IFI44 MUTATED IFI44 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             4             245
  T4             1              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
  IFI44 MUTATED     5   2   1
  IFI44 WILD-TYPE 215  79  65
D1279V5, multiclass
    clus
vv   IFI44 MUTATED IFI44 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1279V6, binary
                 cls
clus                0   1
  IFI44 MUTATED     6   0
  IFI44 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      6    0
  IFI44 WILD-TYPE  279   48
   clus
vv  IFI44 MUTATED IFI44 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1279V7, binary
                 cls
clus                0   1
  IFI44 MUTATED     5   3
  IFI44 WILD-TYPE 165 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      5    3
  IFI44 WILD-TYPE  165  194
        clus
vv       IFI44 MUTATED IFI44 WILD-TYPE
  FEMALE             5             165
  MALE               3             194
[1] 2 2
[1] FALSE
D1279V8, binary
                 cls
clus                0   1
  IFI44 MUTATED     7   0
  IFI44 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      7    0
  IFI44 WILD-TYPE  293    8
     clus
vv    IFI44 MUTATED IFI44 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1279V9, binary
                 cls
clus                0   1
  IFI44 MUTATED     6   1
  IFI44 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      6    1
  IFI44 WILD-TYPE  308   47
                               clus
vv                              IFI44 MUTATED IFI44 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IFI44 MUTATED     4   0   0   1
  IFI44 WILD-TYPE 255   3  22  20
D1279V10, multiclass
    clus
vv   IFI44 MUTATED IFI44 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1279V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFI44 MUTATED                                  0     1
  IFI44 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFI44 MUTATED                           0     6
  IFI44 WILD-TYPE                        19   170
D1279V12, multiclass
                                  clus
vv                                 IFI44 MUTATED IFI44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = IPPK MUTATION ANALYSIS
D1280V1, survival
                sevent
clus2              0   1
  IPPK MUTATED     8   1
  IPPK WILD-TYPE 269  77
  IPPK MUTATED IPPK WILD-TYPE 
             9            346 
  IPPK MUTATED IPPK WILD-TYPE 
             1             77 
$`IPPK MUTATED`
TCGA-AZ-6601 TCGA-A6-6780 TCGA-AA-3542 TCGA-AA-3864 TCGA-CA-6717 TCGA-CM-5349 
      100.01        20.12        12.99        53.00        12.76        30.08 
TCGA-CM-6674 TCGA-D5-6533 TCGA-G4-6304 
       12.95        25.48        53.62 

$`IPPK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  IPPK MUTATED IPPK WILD-TYPE 
         12.76           0.00 
  IPPK MUTATED IPPK WILD-TYPE 
        100.01         148.01 
  IPPK MUTATED IPPK WILD-TYPE 
        25.480         22.045 
[1] "12.8 - 100.0 (25.5)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.7"
D1280V2, continuous
                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      64        1       24       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPPK MUTATED           0          0          0          1        0         0
  IPPK WILD-TYPE        18          6         44         32       35        12
                vv
clus             STAGE IVB
  IPPK MUTATED           0
  IPPK WILD-TYPE         1
D1280V3, multiclass
            clus
vv           IPPK MUTATED IPPK WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  IPPK MUTATED     0   0   7   2
  IPPK WILD-TYPE   9  67 242  39
D1280V4, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  T1            0              9
  T2            0             67
  T3            7            242
  T4            2             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
  IPPK MUTATED     8   0   1
  IPPK WILD-TYPE 212  81  65
D1280V5, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  N0            8            212
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1280V6, binary
                cls
clus               0   1
  IPPK MUTATED     8   0
  IPPK WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      8    0
  IPPK WILD-TYPE  277   48
   clus
vv  IPPK MUTATED IPPK WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1280V7, binary
                cls
clus               0   1
  IPPK MUTATED     3   6
  IPPK WILD-TYPE 167 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      3    6
  IPPK WILD-TYPE  167  191
        clus
vv       IPPK MUTATED IPPK WILD-TYPE
  FEMALE            3            167
  MALE              6            191
[1] 2 2
[1] FALSE
D1280V8, binary
                cls
clus               0   1
  IPPK MUTATED     9   0
  IPPK WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      9    0
  IPPK WILD-TYPE  291    8
     clus
vv    IPPK MUTATED IPPK WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1280V9, binary
                cls
clus               0   1
  IPPK MUTATED     7   2
  IPPK WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      7    2
  IPPK WILD-TYPE  307   46
                               clus
vv                              IPPK MUTATED IPPK WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IPPK MUTATED     6   0   0   1
  IPPK WILD-TYPE 253   3  22  20
D1280V10, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D1280V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IPPK MUTATED                                  0     1
  IPPK WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IPPK MUTATED                           0     6
  IPPK WILD-TYPE                        19   170
D1280V12, multiclass
                                  clus
vv                                 IPPK MUTATED IPPK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = SPATA16 MUTATION ANALYSIS
D1281V1, survival
                   sevent
clus2                 0   1
  SPATA16 MUTATED     7   5
  SPATA16 WILD-TYPE 270  73
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               343 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
                5                73 
$`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        83.24        12.76        44.32        85.48 

$`SPATA16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 
       46.65        43.76        42.28        16.57        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-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       34.98        15.02        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         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SPATA16 MUTATED SPATA16 WILD-TYPE 
                0                 0 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
            85.48            148.01 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
            26.38             22.06 
[1] "0.0 - 85.5 (26.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1281V2, continuous
                   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      63        1       26       102         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA16 MUTATED           0          0          2          1        0
  SPATA16 WILD-TYPE        18          6         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SPATA16 MUTATED           0         0
  SPATA16 WILD-TYPE        12         1
D1281V3, multiclass
            clus
vv           SPATA16 MUTATED SPATA16 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                6               102
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SPATA16 MUTATED     0   1   9   2
  SPATA16 WILD-TYPE   9  66 240  39
D1281V4, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               9               240
  T4               2                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
  SPATA16 MUTATED     9   2   1
  SPATA16 WILD-TYPE 211  79  65
D1281V5, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  N0               9               211
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1281V6, binary
                   cls
clus                  0   1
  SPATA16 MUTATED    11   0
  SPATA16 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED     11    0
  SPATA16 WILD-TYPE  274   48
   clus
vv  SPATA16 MUTATED SPATA16 WILD-TYPE
  0              11               274
  1               0                48
[1] 2 2
[1] FALSE
D1281V7, binary
                   cls
clus                  0   1
  SPATA16 MUTATED     7   5
  SPATA16 WILD-TYPE 163 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED      7    5
  SPATA16 WILD-TYPE  163  192
        clus
vv       SPATA16 MUTATED SPATA16 WILD-TYPE
  FEMALE               7               163
  MALE                 5               192
[1] 2 2
[1] FALSE
D1281V8, binary
                   cls
clus                  0   1
  SPATA16 MUTATED     7   0
  SPATA16 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED      7    0
  SPATA16 WILD-TYPE  293    8
     clus
vv    SPATA16 MUTATED SPATA16 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1281V9, binary
                   cls
clus                  0   1
  SPATA16 MUTATED     9   3
  SPATA16 WILD-TYPE 305  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED      9    3
  SPATA16 WILD-TYPE  305   45
                               clus
vv                              SPATA16 MUTATED SPATA16 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SPATA16 MUTATED     8   0   0   1
  SPATA16 WILD-TYPE 251   3  22  20
D1281V10, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               1                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"
D1281V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPATA16 MUTATED                                  0     2
  SPATA16 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPATA16 MUTATED                           1     4
  SPATA16 WILD-TYPE                        18   172
D1281V12, multiclass
                                  clus
vv                                 SPATA16 MUTATED SPATA16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = ACAN MUTATION ANALYSIS
D1282V1, survival
                sevent
clus2              0   1
  ACAN MUTATED    18   8
  ACAN WILD-TYPE 259  70
  ACAN MUTATED ACAN WILD-TYPE 
            26            329 
  ACAN MUTATED ACAN WILD-TYPE 
             8             70 
$`ACAN MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5665 
        0.92        19.04        19.04       100.01        26.17        22.06 
TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3930 TCGA-AA-A00N 
        3.02        26.99        36.03        30.05         2.01         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6965 TCGA-AZ-4616 TCGA-CA-6717 TCGA-CA-6718 
       34.98        12.16        26.47         5.13        12.76        10.06 
TCGA-CK-4952 TCGA-CM-4746 TCGA-CM-5348 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       15.62        37.02        22.98        43.27        17.85         4.80 
TCGA-D5-6541 TCGA-D5-6931 
       15.58        12.00 

$`ACAN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82        58.39         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       55.92        20.19        18.25        25.48        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ACAN MUTATED ACAN WILD-TYPE 
          0.92           0.00 
  ACAN MUTATED ACAN WILD-TYPE 
        100.01         148.01 
  ACAN MUTATED ACAN WILD-TYPE 
        18.445         22.360 
[1] "0.9 - 100.0 (18.4)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.9"
D1282V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACAN MUTATED         3        0        3        10         2         0
  ACAN WILD-TYPE      61        1       23        98         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAN MUTATED           1          0          2          3        3         0
  ACAN WILD-TYPE        17          6         42         30       32        12
                vv
clus             STAGE IVB
  ACAN MUTATED           0
  ACAN WILD-TYPE         1
D1282V3, multiclass
            clus
vv           ACAN MUTATED ACAN WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            10             98
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            3             30
  STAGE IV              3             32
  STAGE IVA             0             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
  ACAN MUTATED     0   3  19   5
  ACAN WILD-TYPE   9  64 230  36
D1282V4, multiclass
    clus
vv   ACAN MUTATED ACAN WILD-TYPE
  T1            0              9
  T2            3             64
  T3           19            230
  T4            5             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
  ACAN MUTATED    19   3   5
  ACAN WILD-TYPE 201  78  61
D1282V5, multiclass
    clus
vv   ACAN MUTATED ACAN WILD-TYPE
  N0           19            201
  N1            3             78
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1282V6, binary
                cls
clus               0   1
  ACAN MUTATED    22   3
  ACAN WILD-TYPE 263  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACAN MUTATED     22    3
  ACAN WILD-TYPE  263   45
   clus
vv  ACAN MUTATED ACAN WILD-TYPE
  0           22            263
  1            3             45
[1] 2 2
[1] FALSE
D1282V7, binary
                cls
clus               0   1
  ACAN MUTATED    11  16
  ACAN WILD-TYPE 159 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACAN MUTATED     11   16
  ACAN WILD-TYPE  159  181
        clus
vv       ACAN MUTATED ACAN WILD-TYPE
  FEMALE           11            159
  MALE             16            181
[1] 2 2
[1] FALSE
D1282V8, binary
                cls
clus               0   1
  ACAN MUTATED    23   1
  ACAN WILD-TYPE 277   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACAN MUTATED     23    1
  ACAN WILD-TYPE  277    7
     clus
vv    ACAN MUTATED ACAN WILD-TYPE
  NO            23            277
  YES            1              7
[1] 2 2
[1] FALSE
D1282V9, binary
                cls
clus               0   1
  ACAN MUTATED    21   6
  ACAN WILD-TYPE 293  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACAN MUTATED     21    6
  ACAN WILD-TYPE  293   42
                               clus
vv                              ACAN MUTATED ACAN WILD-TYPE
  COLON ADENOCARCINOMA                    21            293
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ACAN MUTATED    19   1   2   3
  ACAN WILD-TYPE 240   2  20  18
D1282V10, multiclass
    clus
vv   ACAN MUTATED ACAN WILD-TYPE
  R0           19            240
  R1            1              2
  R2            2             20
  RX            3             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"
D1282V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACAN MUTATED                                  0     2
  ACAN WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ACAN MUTATED                           1    13
  ACAN WILD-TYPE                        18   163
D1282V12, multiclass
                                  clus
vv                                 ACAN MUTATED ACAN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      13            163
[1] 4 2
[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 = C16ORF88 MUTATION ANALYSIS
D1283V1, survival
                    sevent
clus2                  0   1
  C16ORF88 MUTATED     7   0
  C16ORF88 WILD-TYPE 270  78
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 7                348 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 0                 78 
$`C16ORF88 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3673 TCGA-AA-A01R TCGA-CM-4743 TCGA-CM-5861 
       22.06        20.12        50.04        35.01        23.05        15.02 
TCGA-F4-6856 
       35.31 

$`C16ORF88 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
             15.02               0.00 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
             50.04             148.01 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
             23.05              22.01 
[1] "15.0 - 50.0 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1283V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C16ORF88 MUTATED         1        0        1         4         0         0
  C16ORF88 WILD-TYPE      63        1       25       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF88 MUTATED           1          0          0          0        0
  C16ORF88 WILD-TYPE        17          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C16ORF88 MUTATED           0         0
  C16ORF88 WILD-TYPE        12         1
D1283V3, multiclass
            clus
vv           C16ORF88 MUTATED C16ORF88 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C16ORF88 MUTATED     0   1   6   0
  C16ORF88 WILD-TYPE   9  66 243  41
D1283V4, multiclass
    clus
vv   C16ORF88 MUTATED C16ORF88 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                6                243
  T4                0                 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
  C16ORF88 MUTATED     6   0   1
  C16ORF88 WILD-TYPE 214  81  65
D1283V5, multiclass
    clus
vv   C16ORF88 MUTATED C16ORF88 WILD-TYPE
  N0                6                214
  N1                0                 81
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1283V6, binary
                    cls
clus                   0   1
  C16ORF88 MUTATED     6   0
  C16ORF88 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF88 MUTATED      6    0
  C16ORF88 WILD-TYPE  279   48
   clus
vv  C16ORF88 MUTATED C16ORF88 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D1283V7, binary
                    cls
clus                   0   1
  C16ORF88 MUTATED     3   4
  C16ORF88 WILD-TYPE 167 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF88 MUTATED      3    4
  C16ORF88 WILD-TYPE  167  193
        clus
vv       C16ORF88 MUTATED C16ORF88 WILD-TYPE
  FEMALE                3                167
  MALE                  4                193
[1] 2 2
[1] FALSE
D1283V8, binary
                    cls
clus                   0   1
  C16ORF88 MUTATED     6   1
  C16ORF88 WILD-TYPE 294   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF88 MUTATED      6    1
  C16ORF88 WILD-TYPE  294    7
     clus
vv    C16ORF88 MUTATED C16ORF88 WILD-TYPE
  NO                 6                294
  YES                1                  7
[1] 2 2
[1] FALSE
D1283V9, binary
                    cls
clus                   0   1
  C16ORF88 MUTATED     4   3
  C16ORF88 WILD-TYPE 310  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF88 MUTATED      4    3
  C16ORF88 WILD-TYPE  310   45
                               clus
vv                              C16ORF88 MUTATED C16ORF88 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C16ORF88 MUTATED     6   0   0   0
  C16ORF88 WILD-TYPE 253   3  22  21
D1283V10, multiclass
    clus
vv   C16ORF88 MUTATED C16ORF88 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1283V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C16ORF88 MUTATED                                  0     0
  C16ORF88 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C16ORF88 MUTATED                           0     5
  C16ORF88 WILD-TYPE                        19   171
D1283V12, multiclass
                                  clus
vv                                 C16ORF88 MUTATED C16ORF88 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = ABCG2 MUTATION ANALYSIS
D1284V1, survival
                 sevent
clus2               0   1
  ABCG2 MUTATED    11   1
  ABCG2 WILD-TYPE 266  77
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             12             343 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
              1              77 
$`ABCG2 MUTATED`
TCGA-AA-3672 TCGA-G4-6628 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A02J 
        0.92        79.69        25.02        38.04        34.98         5.03 
TCGA-AD-6965 TCGA-CA-6717 TCGA-D5-6540 TCGA-D5-6922 TCGA-G4-6306 TCGA-G4-6317 
       26.47        12.76        16.14        10.13        44.68        36.00 

$`ABCG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6323 
       65.85        53.62        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  ABCG2 MUTATED ABCG2 WILD-TYPE 
           0.92            0.00 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
          79.69          148.01 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
         25.745          22.030 
[1] "0.9 - 79.7 (25.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D1284V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCG2 MUTATED         2        0        0         2         1         0
  ABCG2 WILD-TYPE      62        1       26       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCG2 MUTATED           1          1          0          2        1         0
  ABCG2 WILD-TYPE        17          5         44         31       34        12
                 vv
clus              STAGE IVB
  ABCG2 MUTATED           0
  ABCG2 WILD-TYPE         1
D1284V3, multiclass
            clus
vv           ABCG2 MUTATED ABCG2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  ABCG2 MUTATED     0   4   6   2
  ABCG2 WILD-TYPE   9  63 243  39
D1284V4, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             6             243
  T4             2              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
  ABCG2 MUTATED     8   2   2
  ABCG2 WILD-TYPE 212  79  64
D1284V5, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1284V6, binary
                 cls
clus                0   1
  ABCG2 MUTATED     9   1
  ABCG2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED      9    1
  ABCG2 WILD-TYPE  276   47
   clus
vv  ABCG2 MUTATED ABCG2 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1284V7, binary
                 cls
clus                0   1
  ABCG2 MUTATED     4   8
  ABCG2 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED      4    8
  ABCG2 WILD-TYPE  166  189
        clus
vv       ABCG2 MUTATED ABCG2 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D1284V8, binary
                 cls
clus                0   1
  ABCG2 MUTATED    11   0
  ABCG2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED     11    0
  ABCG2 WILD-TYPE  289    8
     clus
vv    ABCG2 MUTATED ABCG2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1284V9, binary
                 cls
clus                0   1
  ABCG2 MUTATED    10   2
  ABCG2 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED     10    2
  ABCG2 WILD-TYPE  304   46
                               clus
vv                              ABCG2 MUTATED ABCG2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCG2 MUTATED     8   1   1   1
  ABCG2 WILD-TYPE 251   2  21  20
D1284V10, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  R0             8             251
  R1             1               2
  R2             1              21
  RX             1              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"
D1284V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCG2 MUTATED                                  0     1
  ABCG2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCG2 MUTATED                           0     6
  ABCG2 WILD-TYPE                        19   170
D1284V12, multiclass
                                  clus
vv                                 ABCG2 MUTATED ABCG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = EPC1 MUTATION ANALYSIS
D1285V1, survival
                sevent
clus2              0   1
  EPC1 MUTATED     7   6
  EPC1 WILD-TYPE 270  72
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            342 
  EPC1 MUTATED EPC1 WILD-TYPE 
             6             72 
$`EPC1 MUTATED`
TCGA-AZ-6608 TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-A010 TCGA-AZ-6598 
        1.94        42.90        30.44        19.66        34.98        49.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5860 
        6.77        12.76        10.06        17.56        30.08        32.02 
TCGA-G4-6303 
       65.85 

$`EPC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 
       25.02        13.02        29.06        22.03        22.98        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  EPC1 MUTATED EPC1 WILD-TYPE 
          1.94           0.00 
  EPC1 MUTATED EPC1 WILD-TYPE 
         65.85         148.01 
  EPC1 MUTATED EPC1 WILD-TYPE 
        30.080         22.045 
[1] "1.9 - 65.8 (30.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1285V2, continuous
                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      62        1       25       104         6         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        18          5         43         32       34        12
                vv
clus             STAGE IVB
  EPC1 MUTATED           0
  EPC1 WILD-TYPE         1
D1285V3, multiclass
            clus
vv           EPC1 MUTATED EPC1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  EPC1 MUTATED     0   3   6   4
  EPC1 WILD-TYPE   9  64 243  37
D1285V4, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            6            243
  T4            4             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
  EPC1 MUTATED     9   4   0
  EPC1 WILD-TYPE 211  77  66
D1285V5, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  N0            9            211
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1285V6, binary
                cls
clus               0   1
  EPC1 MUTATED     9   1
  EPC1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED      9    1
  EPC1 WILD-TYPE  276   47
   clus
vv  EPC1 MUTATED EPC1 WILD-TYPE
  0            9            276
  1            1             47
[1] 2 2
[1] FALSE
D1285V7, binary
                cls
clus               0   1
  EPC1 MUTATED     7   6
  EPC1 WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED      7    6
  EPC1 WILD-TYPE  163  191
        clus
vv       EPC1 MUTATED EPC1 WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D1285V8, binary
                cls
clus               0   1
  EPC1 MUTATED    13   0
  EPC1 WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED     13    0
  EPC1 WILD-TYPE  287    8
     clus
vv    EPC1 MUTATED EPC1 WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D1285V9, binary
                cls
clus               0   1
  EPC1 MUTATED    11   2
  EPC1 WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED     11    2
  EPC1 WILD-TYPE  303   46
                               clus
vv                              EPC1 MUTATED EPC1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EPC1 MUTATED     7   0   0   3
  EPC1 WILD-TYPE 252   3  22  18
D1285V10, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            3             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"
D1285V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPC1 MUTATED                                  0     2
  EPC1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EPC1 MUTATED                           0    10
  EPC1 WILD-TYPE                        19   166
D1285V12, multiclass
                                  clus
vv                                 EPC1 MUTATED EPC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(1286) Variable = PTPN3 MUTATION ANALYSIS
D1286V1, survival
                 sevent
clus2               0   1
  PTPN3 MUTATED    12   2
  PTPN3 WILD-TYPE 265  76
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             14             341 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
              2              76 
$`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        12.16        14.50 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
       21.44        49.41        21.99        12.00        21.99        14.04 
TCGA-D5-6539 TCGA-G4-6315 
       12.49        61.91 

$`PTPN3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        26.01        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6167 
       17.03        15.02        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  PTPN3 MUTATED PTPN3 WILD-TYPE 
           4.01            0.00 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
          61.91          148.01 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
         16.275          22.420 
[1] "4.0 - 61.9 (16.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.3"
D1286V2, continuous
                 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      61        1       25       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPN3 MUTATED           0          0          3          1        1         0
  PTPN3 WILD-TYPE        18          6         41         32       34        12
                 vv
clus              STAGE IVB
  PTPN3 MUTATED           0
  PTPN3 WILD-TYPE         1
D1286V3, multiclass
            clus
vv           PTPN3 MUTATED PTPN3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  PTPN3 MUTATED     0   3   9   3
  PTPN3 WILD-TYPE   9  64 240  38
D1286V4, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             3              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
  PTPN3 MUTATED    10   4   1
  PTPN3 WILD-TYPE 210  77  65
D1286V5, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  N0            10             210
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1286V6, binary
                 cls
clus                0   1
  PTPN3 MUTATED    10   1
  PTPN3 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     10    1
  PTPN3 WILD-TYPE  275   47
   clus
vv  PTPN3 MUTATED PTPN3 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1286V7, binary
                 cls
clus                0   1
  PTPN3 MUTATED     8   7
  PTPN3 WILD-TYPE 162 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED      8    7
  PTPN3 WILD-TYPE  162  190
        clus
vv       PTPN3 MUTATED PTPN3 WILD-TYPE
  FEMALE             8             162
  MALE               7             190
[1] 2 2
[1] FALSE
D1286V8, binary
                 cls
clus                0   1
  PTPN3 MUTATED    12   0
  PTPN3 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     12    0
  PTPN3 WILD-TYPE  288    8
     clus
vv    PTPN3 MUTATED PTPN3 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1286V9, binary
                 cls
clus                0   1
  PTPN3 MUTATED    11   4
  PTPN3 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     11    4
  PTPN3 WILD-TYPE  303   44
                               clus
vv                              PTPN3 MUTATED PTPN3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPN3 MUTATED    13   0   0   1
  PTPN3 WILD-TYPE 246   3  22  20
D1286V10, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             1              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"
D1286V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN3 MUTATED                                  0     0
  PTPN3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPN3 MUTATED                           0    10
  PTPN3 WILD-TYPE                        19   166
D1286V12, multiclass
                                  clus
vv                                 PTPN3 MUTATED PTPN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1287) Variable = DGKH MUTATION ANALYSIS
D1287V1, survival
                sevent
clus2              0   1
  DGKH MUTATED    12   3
  DGKH WILD-TYPE 265  75
  DGKH MUTATED DGKH WILD-TYPE 
            15            340 
  DGKH MUTATED DGKH WILD-TYPE 
             3             75 
$`DGKH MUTATED`
TCGA-AA-3554 TCGA-AD-6895 TCGA-AZ-6608 TCGA-AA-3511 TCGA-AA-3544 TCGA-AA-3815 
       17.95        25.08         1.94         6.97        14.01        33.04 
TCGA-AA-3977 TCGA-AA-A01P TCGA-AZ-6600 TCGA-CK-6751 TCGA-CM-5864 TCGA-D5-6536 
       25.02        38.07        12.10       124.27        15.02        17.85 
TCGA-DM-A1D0 TCGA-F4-6807 TCGA-G4-6304 
      130.65        43.04        53.62 

$`DGKH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6808 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-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  DGKH MUTATED DGKH WILD-TYPE 
          1.94           0.00 
  DGKH MUTATED DGKH WILD-TYPE 
        130.65         148.01 
  DGKH MUTATED DGKH WILD-TYPE 
        25.020         22.045 
[1] "1.9 - 130.7 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1287V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DGKH MUTATED         3        0        1         4         1         0
  DGKH WILD-TYPE      61        1       25       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DGKH MUTATED           1          1          1          1        1         0
  DGKH WILD-TYPE        17          5         43         32       34        12
                vv
clus             STAGE IVB
  DGKH MUTATED           0
  DGKH WILD-TYPE         1
D1287V3, multiclass
            clus
vv           DGKH MUTATED DGKH WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  DGKH MUTATED     0   5   7   3
  DGKH WILD-TYPE   9  62 242  38
D1287V4, multiclass
    clus
vv   DGKH MUTATED DGKH WILD-TYPE
  T1            0              9
  T2            5             62
  T3            7            242
  T4            3             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
  DGKH MUTATED    10   4   1
  DGKH WILD-TYPE 210  77  65
D1287V5, multiclass
    clus
vv   DGKH MUTATED DGKH WILD-TYPE
  N0           10            210
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1287V6, binary
                cls
clus               0   1
  DGKH MUTATED    12   1
  DGKH WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED     12    1
  DGKH WILD-TYPE  273   47
   clus
vv  DGKH MUTATED DGKH WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D1287V7, binary
                cls
clus               0   1
  DGKH MUTATED     8   7
  DGKH WILD-TYPE 162 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED      8    7
  DGKH WILD-TYPE  162  190
        clus
vv       DGKH MUTATED DGKH WILD-TYPE
  FEMALE            8            162
  MALE              7            190
[1] 2 2
[1] FALSE
D1287V8, binary
                cls
clus               0   1
  DGKH MUTATED    14   0
  DGKH WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED     14    0
  DGKH WILD-TYPE  286    8
     clus
vv    DGKH MUTATED DGKH WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1287V9, binary
                cls
clus               0   1
  DGKH MUTATED    14   1
  DGKH WILD-TYPE 300  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED     14    1
  DGKH WILD-TYPE  300   47
                               clus
vv                              DGKH MUTATED DGKH WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DGKH MUTATED    10   0   0   1
  DGKH WILD-TYPE 249   3  22  20
D1287V10, multiclass
    clus
vv   DGKH MUTATED DGKH WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D1287V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DGKH MUTATED                                  0     0
  DGKH WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DGKH MUTATED                           1     8
  DGKH WILD-TYPE                        18   168
D1287V12, multiclass
                                  clus
vv                                 DGKH MUTATED DGKH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = LEMD1 MUTATION ANALYSIS
D1288V1, survival
                 sevent
clus2               0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 274  78
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             352 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              0              78 
$`LEMD1 MUTATED`
TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-5665 
       25.08        26.17        22.06 

$`LEMD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LEMD1 MUTATED LEMD1 WILD-TYPE 
          22.06            0.00 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
          26.17          148.01 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
          25.08           22.01 
[1] "22.1 - 26.2 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1288V2, continuous
                 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      64        1       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEMD1 MUTATED           0          0          1          0        0         0
  LEMD1 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  LEMD1 MUTATED           0
  LEMD1 WILD-TYPE         1
D1288V3, multiclass
            clus
vv           LEMD1 MUTATED LEMD1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LEMD1 MUTATED     0   0   3   0
  LEMD1 WILD-TYPE   9  67 246  41
D1288V4, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             0              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
  LEMD1 MUTATED     2   1   0
  LEMD1 WILD-TYPE 218  80  66
D1288V5, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  N0             2             218
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1288V6, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    0
  LEMD1 WILD-TYPE  282   48
   clus
vv  LEMD1 MUTATED LEMD1 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1288V7, binary
                 cls
clus                0   1
  LEMD1 MUTATED     2   1
  LEMD1 WILD-TYPE 168 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      2    1
  LEMD1 WILD-TYPE  168  196
        clus
vv       LEMD1 MUTATED LEMD1 WILD-TYPE
  FEMALE             2             168
  MALE               1             196
[1] 2 2
[1] FALSE
D1288V8, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    0
  LEMD1 WILD-TYPE  297    8
     clus
vv    LEMD1 MUTATED LEMD1 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1288V9, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    0
  LEMD1 WILD-TYPE  311   48
                               clus
vv                              LEMD1 MUTATED LEMD1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LEMD1 MUTATED     3   0   0   0
  LEMD1 WILD-TYPE 256   3  22  21
D1288V10, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1288V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEMD1 MUTATED                                  0     0
  LEMD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LEMD1 MUTATED                           0     3
  LEMD1 WILD-TYPE                        19   173
D1288V12, multiclass
                                  clus
vv                                 LEMD1 MUTATED LEMD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = ABCD4 MUTATION ANALYSIS
D1289V1, survival
                 sevent
clus2               0   1
  ABCD4 MUTATED     9   1
  ABCD4 WILD-TYPE 268  77
  ABCD4 MUTATED ABCD4 WILD-TYPE 
             10             345 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
              1              77 
$`ABCD4 MUTATED`
TCGA-AA-3672 TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 
        0.92        26.17        79.69         6.97        53.00        31.00 
TCGA-AA-A00E TCGA-CK-4950 TCGA-D5-6930 TCGA-F4-6570 
       30.02        85.45        13.35         6.18 

$`ABCD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.030 
[1] "0.9 - 85.5 (28.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D1289V2, continuous
                 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      62        1       24       104         8         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  ABCD4 MUTATED           0
  ABCD4 WILD-TYPE         1
D1289V3, multiclass
            clus
vv           ABCD4 MUTATED ABCD4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ABCD4 MUTATED     1   1   8   0
  ABCD4 WILD-TYPE   8  66 241  41
D1289V4, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             8             241
  T4             0              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
  ABCD4 MUTATED     8   2   0
  ABCD4 WILD-TYPE 212  79  66
D1289V5, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1289V6, binary
                 cls
clus                0   1
  ABCD4 MUTATED    10   0
  ABCD4 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED     10    0
  ABCD4 WILD-TYPE  275   48
   clus
vv  ABCD4 MUTATED ABCD4 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1289V7, binary
                 cls
clus                0   1
  ABCD4 MUTATED     5   5
  ABCD4 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      5    5
  ABCD4 WILD-TYPE  165  192
        clus
vv       ABCD4 MUTATED ABCD4 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1289V8, binary
                 cls
clus                0   1
  ABCD4 MUTATED    10   0
  ABCD4 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED     10    0
  ABCD4 WILD-TYPE  290    8
     clus
vv    ABCD4 MUTATED ABCD4 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1289V9, binary
                 cls
clus                0   1
  ABCD4 MUTATED     7   3
  ABCD4 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      7    3
  ABCD4 WILD-TYPE  307   45
                               clus
vv                              ABCD4 MUTATED ABCD4 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCD4 MUTATED     9   1   0   0
  ABCD4 WILD-TYPE 250   2  22  21
D1289V10, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  R0             9             250
  R1             1               2
  R2             0              22
  RX             0              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"
D1289V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCD4 MUTATED                                  0     0
  ABCD4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCD4 MUTATED                           1     4
  ABCD4 WILD-TYPE                        18   172
D1289V12, multiclass
                                  clus
vv                                 ABCD4 MUTATED ABCD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = HCLS1 MUTATION ANALYSIS
D1290V1, survival
                 sevent
clus2               0   1
  HCLS1 MUTATED    13   2
  HCLS1 WILD-TYPE 264  76
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             340 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
              2              76 
$`HCLS1 MUTATED`
TCGA-AA-3516 TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3548 
       13.02       100.01        26.17         6.97         1.02        33.99 
TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A010 TCGA-AZ-4315 
        6.97        25.02        18.05        18.05        34.98        58.39 
TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6930 
       12.76        15.02        13.35 

$`HCLS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
       63.98         1.02        38.99         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 
       29.00        29.00        26.01        12.99        14.01        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.09 
[1] "1.0 - 100.0 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1290V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HCLS1 MUTATED         0        0        3         7         1         0
  HCLS1 WILD-TYPE      64        1       23       101         7         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        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  HCLS1 MUTATED           0
  HCLS1 WILD-TYPE         1
D1290V3, multiclass
            clus
vv           HCLS1 MUTATED HCLS1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  HCLS1 MUTATED     0   1  11   3
  HCLS1 WILD-TYPE   9  66 238  38
D1290V4, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             3              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
  HCLS1 MUTATED    12   1   2
  HCLS1 WILD-TYPE 208  80  64
D1290V5, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1290V6, binary
                 cls
clus                0   1
  HCLS1 MUTATED    14   0
  HCLS1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     14    0
  HCLS1 WILD-TYPE  271   48
   clus
vv  HCLS1 MUTATED HCLS1 WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D1290V7, binary
                 cls
clus                0   1
  HCLS1 MUTATED     6   9
  HCLS1 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED      6    9
  HCLS1 WILD-TYPE  164  188
        clus
vv       HCLS1 MUTATED HCLS1 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D1290V8, binary
                 cls
clus                0   1
  HCLS1 MUTATED    13   0
  HCLS1 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     13    0
  HCLS1 WILD-TYPE  287    8
     clus
vv    HCLS1 MUTATED HCLS1 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D1290V9, binary
                 cls
clus                0   1
  HCLS1 MUTATED    11   4
  HCLS1 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     11    4
  HCLS1 WILD-TYPE  303   44
                               clus
vv                              HCLS1 MUTATED HCLS1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HCLS1 MUTATED    11   0   0   1
  HCLS1 WILD-TYPE 248   3  22  20
D1290V10, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1290V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCLS1 MUTATED                                  0     1
  HCLS1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HCLS1 MUTATED                           0     5
  HCLS1 WILD-TYPE                        19   171
D1290V12, multiclass
                                  clus
vv                                 HCLS1 MUTATED HCLS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = SULT1C4 MUTATION ANALYSIS
D1291V1, survival
                   sevent
clus2                 0   1
  SULT1C4 MUTATED     2   1
  SULT1C4 WILD-TYPE 275  77
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               352 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                1                77 
$`SULT1C4 MUTATED`
TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-A00N 
       19.07        29.95         4.01 

$`SULT1C4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02         9.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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            22.075 
[1] "4.0 - 29.9 (19.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D1291V2, continuous
                   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      63        1       26       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT1C4 MUTATED           0          0          0          0        0
  SULT1C4 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SULT1C4 MUTATED           0         0
  SULT1C4 WILD-TYPE        12         1
D1291V3, multiclass
            clus
vv           SULT1C4 MUTATED SULT1C4 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SULT1C4 MUTATED     0   1   1   1
  SULT1C4 WILD-TYPE   9  66 248  40
D1291V4, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               1               248
  T4               1                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
  SULT1C4 MUTATED     3   0   0
  SULT1C4 WILD-TYPE 217  81  66
D1291V5, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  N0               3               217
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1291V6, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     3   0
  SULT1C4 WILD-TYPE 282  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      3    0
  SULT1C4 WILD-TYPE  282   48
   clus
vv  SULT1C4 MUTATED SULT1C4 WILD-TYPE
  0               3               282
  1               0                48
[1] 2 2
[1] FALSE
D1291V7, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     1   2
  SULT1C4 WILD-TYPE 169 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      1    2
  SULT1C4 WILD-TYPE  169  195
        clus
vv       SULT1C4 MUTATED SULT1C4 WILD-TYPE
  FEMALE               1               169
  MALE                 2               195
[1] 2 2
[1] FALSE
D1291V8, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     2   0
  SULT1C4 WILD-TYPE 298   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      2    0
  SULT1C4 WILD-TYPE  298    8
     clus
vv    SULT1C4 MUTATED SULT1C4 WILD-TYPE
  NO                2               298
  YES               0                 8
[1] 2 2
[1] FALSE
D1291V9, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     1   2
  SULT1C4 WILD-TYPE 313  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      1    2
  SULT1C4 WILD-TYPE  313   46
                               clus
vv                              SULT1C4 MUTATED SULT1C4 WILD-TYPE
  COLON ADENOCARCINOMA                        1               313
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SULT1C4 MUTATED     3   0   0   0
  SULT1C4 WILD-TYPE 256   3  22  21
D1291V10, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D1291V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULT1C4 MUTATED                                  0     0
  SULT1C4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SULT1C4 MUTATED                           0     0
  SULT1C4 WILD-TYPE                        19   176
D1291V12, multiclass

Clustering(1292) Variable = TRAF2 MUTATION ANALYSIS
D1292V1, survival
                 sevent
clus2               0   1
  TRAF2 MUTATED     5   2
  TRAF2 WILD-TYPE 272  76
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              7             348 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              2              76 
$`TRAF2 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3502 TCGA-AY-6386 TCGA-AZ-5407 TCGA-CA-6718 
        6.05        19.04        35.01        17.82        88.21        10.06 
TCGA-D5-6540 
       16.14 

$`TRAF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TRAF2 MUTATED TRAF2 WILD-TYPE 
           6.05            0.00 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
          88.21          148.01 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
          17.82           22.09 
[1] "6.0 - 88.2 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1292V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAF2 MUTATED         3        0        1         1         0         0
  TRAF2 WILD-TYPE      61        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRAF2 MUTATED           0          0          1          0        1         0
  TRAF2 WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  TRAF2 MUTATED           0
  TRAF2 WILD-TYPE         1
D1292V3, multiclass
            clus
vv           TRAF2 MUTATED TRAF2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TRAF2 MUTATED     1   2   3   1
  TRAF2 WILD-TYPE   8  65 246  40
D1292V4, multiclass
    clus
vv   TRAF2 MUTATED TRAF2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             3             246
  T4             1              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
  TRAF2 MUTATED     5   1   1
  TRAF2 WILD-TYPE 215  80  65
D1292V5, multiclass
    clus
vv   TRAF2 MUTATED TRAF2 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1292V6, binary
                 cls
clus                0   1
  TRAF2 MUTATED     6   1
  TRAF2 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF2 MUTATED      6    1
  TRAF2 WILD-TYPE  279   47
   clus
vv  TRAF2 MUTATED TRAF2 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1292V7, binary
                 cls
clus                0   1
  TRAF2 MUTATED     3   4
  TRAF2 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF2 MUTATED      3    4
  TRAF2 WILD-TYPE  167  193
        clus
vv       TRAF2 MUTATED TRAF2 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1292V8, binary
                 cls
clus                0   1
  TRAF2 MUTATED     7   0
  TRAF2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF2 MUTATED      7    0
  TRAF2 WILD-TYPE  293    8
     clus
vv    TRAF2 MUTATED TRAF2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1292V9, binary
                 cls
clus                0   1
  TRAF2 MUTATED     6   1
  TRAF2 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF2 MUTATED      6    1
  TRAF2 WILD-TYPE  308   47
                               clus
vv                              TRAF2 MUTATED TRAF2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRAF2 MUTATED     4   0   1   1
  TRAF2 WILD-TYPE 255   3  21  20
D1292V10, multiclass
    clus
vv   TRAF2 MUTATED TRAF2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             1              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"
D1292V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAF2 MUTATED                                  0     1
  TRAF2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRAF2 MUTATED                           1     2
  TRAF2 WILD-TYPE                        18   174
D1292V12, multiclass
                                  clus
vv                                 TRAF2 MUTATED TRAF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(1293) Variable = ZNF564 MUTATION ANALYSIS
D1293V1, survival
                  sevent
clus2                0   1
  ZNF564 MUTATED     6   3
  ZNF564 WILD-TYPE 271  75
  ZNF564 MUTATED ZNF564 WILD-TYPE 
               9              346 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
               3               75 
$`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 
       15.62        15.02        49.91 

$`ZNF564 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF564 MUTATED ZNF564 WILD-TYPE 
            4.01             0.00 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
           53.00           148.01 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
           15.02            22.09 
[1] "4.0 - 53.0 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1293V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF564 MUTATED         1        0        2         4         2         0
  ZNF564 WILD-TYPE      63        1       24       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF564 MUTATED           0          0          0          1        0
  ZNF564 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF564 MUTATED           0         0
  ZNF564 WILD-TYPE        12         1
D1293V3, multiclass
            clus
vv           ZNF564 MUTATED ZNF564 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF564 MUTATED     0   1   6   3
  ZNF564 WILD-TYPE   9  66 243  38
D1293V4, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              6              243
  T4              3               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
  ZNF564 MUTATED     9   0   1
  ZNF564 WILD-TYPE 211  81  65
D1293V5, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1293V6, binary
                  cls
clus                 0   1
  ZNF564 MUTATED    10   0
  ZNF564 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED     10    0
  ZNF564 WILD-TYPE  275   48
   clus
vv  ZNF564 MUTATED ZNF564 WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D1293V7, binary
                  cls
clus                 0   1
  ZNF564 MUTATED     3   7
  ZNF564 WILD-TYPE 167 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED      3    7
  ZNF564 WILD-TYPE  167  190
        clus
vv       ZNF564 MUTATED ZNF564 WILD-TYPE
  FEMALE              3              167
  MALE                7              190
[1] 2 2
[1] FALSE
D1293V8, binary
                  cls
clus                 0   1
  ZNF564 MUTATED     6   0
  ZNF564 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED      6    0
  ZNF564 WILD-TYPE  294    8
     clus
vv    ZNF564 MUTATED ZNF564 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1293V9, binary
                  cls
clus                 0   1
  ZNF564 MUTATED     6   4
  ZNF564 WILD-TYPE 308  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED      6    4
  ZNF564 WILD-TYPE  308   44
                               clus
vv                              ZNF564 MUTATED ZNF564 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF564 MUTATED     6   0   0   3
  ZNF564 WILD-TYPE 253   3  22  18
D1293V10, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              3               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"
D1293V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF564 MUTATED                                  0     2
  ZNF564 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF564 MUTATED                           0     3
  ZNF564 WILD-TYPE                        19   173
D1293V12, multiclass
                                  clus
vv                                 ZNF564 MUTATED ZNF564 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = JMJD1C MUTATION ANALYSIS
D1294V1, survival
                  sevent
clus2                0   1
  JMJD1C MUTATED    22   1
  JMJD1C WILD-TYPE 255  77
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              23              332 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               1               77 
$`JMJD1C MUTATED`
TCGA-AA-3672 TCGA-AD-6964 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3866 TCGA-AA-3949 
        0.92        10.88        19.66        63.98        17.03        26.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01K TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       25.02        34.98        31.00        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 
       17.13        15.58        11.64       133.18        13.78 

$`JMJD1C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6626 
       36.00        46.75 

  JMJD1C MUTATED JMJD1C WILD-TYPE 
            0.92             0.00 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
          133.18           148.01 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
           17.13            22.47 
[1] "0.9 - 133.2 (17.1)" "0.0 - 148.0 (22.5)"
[1] "hr=" "5"  
D1294V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JMJD1C MUTATED         2        1        1         8         1         0
  JMJD1C WILD-TYPE      62        0       25       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JMJD1C MUTATED           2          0          3          3        0
  JMJD1C WILD-TYPE        16          6         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  JMJD1C MUTATED           1         0
  JMJD1C WILD-TYPE        11         1
D1294V3, multiclass
            clus
vv           JMJD1C MUTATED JMJD1C WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                1               25
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              3               30
  STAGE IV                0               35
  STAGE IVA               1               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
  JMJD1C MUTATED     0   3  15   5
  JMJD1C WILD-TYPE   9  64 234  36
D1294V4, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  T1              0                9
  T2              3               64
  T3             15              234
  T4              5               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
  JMJD1C MUTATED    14   6   4
  JMJD1C WILD-TYPE 206  75  62
D1294V5, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  N0             14              206
  N1              6               75
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1294V6, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    18   1
  JMJD1C WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     18    1
  JMJD1C WILD-TYPE  267   47
   clus
vv  JMJD1C MUTATED JMJD1C WILD-TYPE
  0             18              267
  1              1               47
[1] 2 2
[1] FALSE
D1294V7, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    11  13
  JMJD1C WILD-TYPE 159 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     11   13
  JMJD1C WILD-TYPE  159  184
        clus
vv       JMJD1C MUTATED JMJD1C WILD-TYPE
  FEMALE             11              159
  MALE               13              184
[1] 2 2
[1] FALSE
D1294V8, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    22   0
  JMJD1C WILD-TYPE 278   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     22    0
  JMJD1C WILD-TYPE  278    8
     clus
vv    JMJD1C MUTATED JMJD1C WILD-TYPE
  NO              22              278
  YES              0                8
[1] 2 2
[1] FALSE
D1294V9, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    19   5
  JMJD1C WILD-TYPE 295  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     19    5
  JMJD1C WILD-TYPE  295   43
                               clus
vv                              JMJD1C MUTATED JMJD1C WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  JMJD1C MUTATED    20   0   0   2
  JMJD1C WILD-TYPE 239   3  22  19
D1294V10, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  R0             20              239
  R1              0                3
  R2              0               22
  RX              2               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"
D1294V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JMJD1C MUTATED                                  0     1
  JMJD1C WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  JMJD1C MUTATED                           3    12
  JMJD1C WILD-TYPE                        16   164
D1294V12, multiclass
                                  clus
vv                                 JMJD1C MUTATED JMJD1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        12              164
[1] 4 2
[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 = CCDC111 MUTATION ANALYSIS
D1295V1, survival
                   sevent
clus2                 0   1
  CCDC111 MUTATED     4   3
  CCDC111 WILD-TYPE 273  75
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                7               348 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                3                75 
$`CCDC111 MUTATED`
TCGA-AA-3660 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-CM-6168 
       78.08        34.98        83.24         5.79        58.39        12.99 
TCGA-DM-A0XD 
       24.43 

$`CCDC111 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       12.16        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CCDC111 MUTATED CCDC111 WILD-TYPE 
             5.79              0.00 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
            83.24            148.01 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
            34.98             22.01 
[1] "5.8 - 83.2 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1295V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC111 MUTATED         0        0        1         4         1         0
  CCDC111 WILD-TYPE      64        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC111 MUTATED           0          0          0          1        0
  CCDC111 WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  CCDC111 MUTATED           0         0
  CCDC111 WILD-TYPE        12         1
D1295V3, multiclass
            clus
vv           CCDC111 MUTATED CCDC111 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  CCDC111 MUTATED     0   0   5   2
  CCDC111 WILD-TYPE   9  67 244  39
D1295V4, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               2                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
  CCDC111 MUTATED     6   0   1
  CCDC111 WILD-TYPE 214  81  65
D1295V5, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  N0               6               214
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1295V6, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     6   0
  CCDC111 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      6    0
  CCDC111 WILD-TYPE  279   48
   clus
vv  CCDC111 MUTATED CCDC111 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1295V7, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     3   4
  CCDC111 WILD-TYPE 167 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      3    4
  CCDC111 WILD-TYPE  167  193
        clus
vv       CCDC111 MUTATED CCDC111 WILD-TYPE
  FEMALE               3               167
  MALE                 4               193
[1] 2 2
[1] FALSE
D1295V8, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     6   0
  CCDC111 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      6    0
  CCDC111 WILD-TYPE  294    8
     clus
vv    CCDC111 MUTATED CCDC111 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1295V9, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     6   1
  CCDC111 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      6    1
  CCDC111 WILD-TYPE  308   47
                               clus
vv                              CCDC111 MUTATED CCDC111 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC111 MUTATED     5   0   0   0
  CCDC111 WILD-TYPE 254   3  22  21
D1295V10, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1295V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC111 MUTATED                                  0     1
  CCDC111 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC111 MUTATED                           1     3
  CCDC111 WILD-TYPE                        18   173
D1295V12, multiclass
                                  clus
vv                                 CCDC111 MUTATED CCDC111 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = PAK2 MUTATION ANALYSIS
D1296V1, survival
                sevent
clus2              0   1
  PAK2 MUTATED     9   1
  PAK2 WILD-TYPE 268  77
  PAK2 MUTATED PAK2 WILD-TYPE 
            10            345 
  PAK2 MUTATED PAK2 WILD-TYPE 
             1             77 
$`PAK2 MUTATED`
TCGA-G4-6586 TCGA-A6-2672 TCGA-A6-6781 TCGA-CK-4948 TCGA-CM-4752 TCGA-CM-5868 
       35.80        46.65        19.66       148.01        13.02        17.03 
TCGA-CM-6171 TCGA-D5-6931 TCGA-F4-6570 TCGA-G4-6293 
       14.04        12.00         6.18       133.18 

$`PAK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       22.09        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PAK2 MUTATED PAK2 WILD-TYPE 
          6.18           0.00 
  PAK2 MUTATED PAK2 WILD-TYPE 
        148.01         140.38 
  PAK2 MUTATED PAK2 WILD-TYPE 
        18.345         22.090 
[1] "6.2 - 148.0 (18.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "3.1"
D1296V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK2 MUTATED         1        0        0         3         0         0
  PAK2 WILD-TYPE      63        1       26       105         8         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        16          6         43         31       35        11
                vv
clus             STAGE IVB
  PAK2 MUTATED           0
  PAK2 WILD-TYPE         1
D1296V3, multiclass
            clus
vv           PAK2 MUTATED PAK2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             1             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
  PAK2 MUTATED     0   1   6   3
  PAK2 WILD-TYPE   9  66 243  38
D1296V4, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            3             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
  PAK2 MUTATED     4   5   1
  PAK2 WILD-TYPE 216  76  65
D1296V5, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  N0            4            216
  N1            5             76
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1296V6, binary
                cls
clus               0   1
  PAK2 MUTATED     8   1
  PAK2 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      8    1
  PAK2 WILD-TYPE  277   47
   clus
vv  PAK2 MUTATED PAK2 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D1296V7, binary
                cls
clus               0   1
  PAK2 MUTATED     7   3
  PAK2 WILD-TYPE 163 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      7    3
  PAK2 WILD-TYPE  163  194
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  FEMALE            7            163
  MALE              3            194
[1] 2 2
[1] FALSE
D1296V8, binary
                cls
clus               0   1
  PAK2 MUTATED    10   0
  PAK2 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED     10    0
  PAK2 WILD-TYPE  290    8
     clus
vv    PAK2 MUTATED PAK2 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1296V9, binary
                cls
clus               0   1
  PAK2 MUTATED     9   1
  PAK2 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      9    1
  PAK2 WILD-TYPE  305   47
                               clus
vv                              PAK2 MUTATED PAK2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAK2 MUTATED    10   0   0   0
  PAK2 WILD-TYPE 249   3  22  21
D1296V10, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            0             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"
D1296V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK2 MUTATED                                  0     0
  PAK2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK2 MUTATED                           1     9
  PAK2 WILD-TYPE                        18   167
D1296V12, multiclass
                                  clus
vv                                 PAK2 MUTATED PAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       9            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(1297) Variable = SGOL2 MUTATION ANALYSIS
D1297V1, survival
                 sevent
clus2               0   1
  SGOL2 MUTATED    11   1
  SGOL2 WILD-TYPE 266  77
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             12             343 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              1              77 
$`SGOL2 MUTATED`
TCGA-AD-6895 TCGA-AA-3710 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 
       25.08        26.99        34.98        58.39        12.76        21.14 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6675 TCGA-D5-5541 TCGA-G4-6304 TCGA-G4-6307 
        2.01        23.05        13.05        55.92        53.62        55.04 

$`SGOL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 
       85.45        15.62        51.32        21.99        82.95       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       65.85        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           2.01            0.00 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          58.39          148.01 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
         26.035          21.990 
[1] "2.0 - 58.4 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3.2"
D1297V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGOL2 MUTATED         1        0        0         4         2         0
  SGOL2 WILD-TYPE      63        1       26       104         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGOL2 MUTATED           0          0          3          0        1         0
  SGOL2 WILD-TYPE        18          6         41         33       34        12
                 vv
clus              STAGE IVB
  SGOL2 MUTATED           1
  SGOL2 WILD-TYPE         0
D1297V3, multiclass
            clus
vv           SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              12
  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     1   0   9   2
  SGOL2 WILD-TYPE   8  67 240  39
D1297V4, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             9             240
  T4             2              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
  SGOL2 MUTATED     7   4   1
  SGOL2 WILD-TYPE 213  77  65
D1297V5, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  N0             7             213
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1297V6, binary
                 cls
clus                0   1
  SGOL2 MUTATED    10   2
  SGOL2 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     10    2
  SGOL2 WILD-TYPE  275   46
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D1297V7, binary
                 cls
clus                0   1
  SGOL2 MUTATED     6   6
  SGOL2 WILD-TYPE 164 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      6    6
  SGOL2 WILD-TYPE  164  191
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  FEMALE             6             164
  MALE               6             191
[1] 2 2
[1] FALSE
D1297V8, binary
                 cls
clus                0   1
  SGOL2 MUTATED    12   0
  SGOL2 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     12    0
  SGOL2 WILD-TYPE  288    8
     clus
vv    SGOL2 MUTATED SGOL2 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1297V9, binary
                 cls
clus                0   1
  SGOL2 MUTATED    10   2
  SGOL2 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     10    2
  SGOL2 WILD-TYPE  304   46
                               clus
vv                              SGOL2 MUTATED SGOL2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SGOL2 MUTATED     9   0   0   3
  SGOL2 WILD-TYPE 250   3  22  18
D1297V10, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             3              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"
D1297V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGOL2 MUTATED                                  0     1
  SGOL2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SGOL2 MUTATED                           1     8
  SGOL2 WILD-TYPE                        18   168
D1297V12, multiclass
                                  clus
vv                                 SGOL2 MUTATED SGOL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = HECW2 MUTATION ANALYSIS
D1298V1, survival
                 sevent
clus2               0   1
  HECW2 MUTATED    19   7
  HECW2 WILD-TYPE 258  71
  HECW2 MUTATED HECW2 WILD-TYPE 
             26             329 
  HECW2 MUTATED HECW2 WILD-TYPE 
              7              71 
$`HECW2 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3986 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-2672 
       13.02         0.92        19.07        25.08       100.01        46.65 
TCGA-A6-5656 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3854 TCGA-AA-3977 TCGA-AA-A00N 
       32.91        29.19        63.98        36.03        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
       34.98        39.98        12.16        83.24        27.09        58.39 
TCGA-AZ-5403 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6674 TCGA-D5-6922 TCGA-D5-6924 
       62.79        12.76        21.14        12.95        10.13        14.30 
TCGA-G4-6307 TCGA-G4-6626 
       55.04        46.75 

$`HECW2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       15.52        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       33.34        32.75        36.53        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.39        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        85.48        61.91        36.00        13.78 

  HECW2 MUTATED HECW2 WILD-TYPE 
           0.92            0.00 
  HECW2 MUTATED HECW2 WILD-TYPE 
         100.01          148.01 
  HECW2 MUTATED HECW2 WILD-TYPE 
          28.14           21.99 
[1] "0.9 - 100.0 (28.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1298V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HECW2 MUTATED         7        0        3         6         3         0
  HECW2 WILD-TYPE      57        1       23       102         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HECW2 MUTATED           3          1          3          1        0         0
  HECW2 WILD-TYPE        15          5         41         32       35        12
                 vv
clus              STAGE IVB
  HECW2 MUTATED           0
  HECW2 WILD-TYPE         1
D1298V3, multiclass
            clus
vv           HECW2 MUTATED HECW2 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  HECW2 MUTATED     1   7  17   3
  HECW2 WILD-TYPE   8  60 232  38
D1298V4, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  T1             1               8
  T2             7              60
  T3            17             232
  T4             3              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
  HECW2 MUTATED    20   5   3
  HECW2 WILD-TYPE 200  76  63
D1298V5, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  N0            20             200
  N1             5              76
  N2             3              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"
D1298V6, binary
                 cls
clus                0   1
  HECW2 MUTATED    24   0
  HECW2 WILD-TYPE 261  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     24    0
  HECW2 WILD-TYPE  261   48
   clus
vv  HECW2 MUTATED HECW2 WILD-TYPE
  0            24             261
  1             0              48
[1] 2 2
[1] FALSE
D1298V7, binary
                 cls
clus                0   1
  HECW2 MUTATED     9  19
  HECW2 WILD-TYPE 161 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED      9   19
  HECW2 WILD-TYPE  161  178
        clus
vv       HECW2 MUTATED HECW2 WILD-TYPE
  FEMALE             9             161
  MALE              19             178
[1] 2 2
[1] FALSE
D1298V8, binary
                 cls
clus                0   1
  HECW2 MUTATED    24   0
  HECW2 WILD-TYPE 276   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     24    0
  HECW2 WILD-TYPE  276    8
     clus
vv    HECW2 MUTATED HECW2 WILD-TYPE
  NO             24             276
  YES             0               8
[1] 2 2
[1] FALSE
D1298V9, binary
                 cls
clus                0   1
  HECW2 MUTATED    23   5
  HECW2 WILD-TYPE 291  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     23    5
  HECW2 WILD-TYPE  291   43
                               clus
vv                              HECW2 MUTATED HECW2 WILD-TYPE
  COLON ADENOCARCINOMA                     23             291
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HECW2 MUTATED    19   0   0   3
  HECW2 WILD-TYPE 240   3  22  18
D1298V10, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             0              22
  RX             3              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"
D1298V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HECW2 MUTATED                                  0     2
  HECW2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HECW2 MUTATED                           1    15
  HECW2 WILD-TYPE                        18   161
D1298V12, multiclass
                                  clus
vv                                 HECW2 MUTATED HECW2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       15             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(1299) Variable = BTNL3 MUTATION ANALYSIS
D1299V1, survival
                 sevent
clus2               0   1
  BTNL3 MUTATED     7   0
  BTNL3 WILD-TYPE 270  78
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              7             348 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              0              78 
$`BTNL3 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6781 TCGA-CA-6717 TCGA-CM-4743 
       35.80        26.17        22.06        19.66        12.76        23.05 
TCGA-CM-5861 
       15.02 

$`BTNL3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  BTNL3 MUTATED BTNL3 WILD-TYPE 
          12.76            0.00 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
          35.80          148.01 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
          22.06           22.06 
[1] "12.8 - 35.8 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D1299V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTNL3 MUTATED         0        0        0         6         0         0
  BTNL3 WILD-TYPE      64        1       26       102         8         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  BTNL3 MUTATED           0
  BTNL3 WILD-TYPE         1
D1299V3, multiclass
            clus
vv           BTNL3 MUTATED BTNL3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  BTNL3 MUTATED     0   0   6   1
  BTNL3 WILD-TYPE   9  67 243  40
D1299V4, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  BTNL3 MUTATED     6   1   0
  BTNL3 WILD-TYPE 214  80  66
D1299V5, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1299V6, binary
                 cls
clus                0   1
  BTNL3 MUTATED     6   0
  BTNL3 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      6    0
  BTNL3 WILD-TYPE  279   48
   clus
vv  BTNL3 MUTATED BTNL3 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1299V7, binary
                 cls
clus                0   1
  BTNL3 MUTATED     4   3
  BTNL3 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      4    3
  BTNL3 WILD-TYPE  166  194
        clus
vv       BTNL3 MUTATED BTNL3 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1299V8, binary
                 cls
clus                0   1
  BTNL3 MUTATED     7   0
  BTNL3 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      7    0
  BTNL3 WILD-TYPE  293    8
     clus
vv    BTNL3 MUTATED BTNL3 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1299V9, binary
                 cls
clus                0   1
  BTNL3 MUTATED     5   2
  BTNL3 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      5    2
  BTNL3 WILD-TYPE  309   46
                               clus
vv                              BTNL3 MUTATED BTNL3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BTNL3 MUTATED     6   0   0   1
  BTNL3 WILD-TYPE 253   3  22  20
D1299V10, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1299V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTNL3 MUTATED                                  0     1
  BTNL3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTNL3 MUTATED                           0     6
  BTNL3 WILD-TYPE                        19   170
D1299V12, multiclass
                                  clus
vv                                 BTNL3 MUTATED BTNL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ATF2 MUTATION ANALYSIS
D1300V1, survival
                sevent
clus2              0   1
  ATF2 MUTATED     3   3
  ATF2 WILD-TYPE 274  75
  ATF2 MUTATED ATF2 WILD-TYPE 
             6            349 
  ATF2 MUTATED ATF2 WILD-TYPE 
             3             75 
$`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 

$`ATF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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        54.61        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ATF2 MUTATED ATF2 WILD-TYPE 
          1.02           0.00 
  ATF2 MUTATED ATF2 WILD-TYPE 
         44.32         148.01 
  ATF2 MUTATED ATF2 WILD-TYPE 
        13.105         22.090 
[1] "1.0 - 44.3 (13.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.6"
D1300V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATF2 MUTATED         0        0        1         3         0         0
  ATF2 WILD-TYPE      64        1       25       105         8         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        18          5         44         33       34        12
                vv
clus             STAGE IVB
  ATF2 MUTATED           0
  ATF2 WILD-TYPE         1
D1300V3, multiclass
            clus
vv           ATF2 MUTATED ATF2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  ATF2 MUTATED     0   0   5   1
  ATF2 WILD-TYPE   9  67 244  40
D1300V4, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            1             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
  ATF2 MUTATED     4   1   1
  ATF2 WILD-TYPE 216  80  65
D1300V5, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1300V6, binary
                cls
clus               0   1
  ATF2 MUTATED     5   1
  ATF2 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      5    1
  ATF2 WILD-TYPE  280   47
   clus
vv  ATF2 MUTATED ATF2 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D1300V7, binary
                cls
clus               0   1
  ATF2 MUTATED     1   5
  ATF2 WILD-TYPE 169 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      1    5
  ATF2 WILD-TYPE  169  192
        clus
vv       ATF2 MUTATED ATF2 WILD-TYPE
  FEMALE            1            169
  MALE              5            192
[1] 2 2
[1] FALSE
D1300V8, binary
                cls
clus               0   1
  ATF2 MUTATED     4   0
  ATF2 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      4    0
  ATF2 WILD-TYPE  296    8
     clus
vv    ATF2 MUTATED ATF2 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1300V9, binary
                cls
clus               0   1
  ATF2 MUTATED     5   1
  ATF2 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      5    1
  ATF2 WILD-TYPE  309   47
                               clus
vv                              ATF2 MUTATED ATF2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ATF2 MUTATED     2   0   1   2
  ATF2 WILD-TYPE 257   3  21  19
D1300V10, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            1             21
  RX            2             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"
D1300V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATF2 MUTATED                                  0     2
  ATF2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATF2 MUTATED                           0     2
  ATF2 WILD-TYPE                        19   174
D1300V12, multiclass
                                  clus
vv                                 ATF2 MUTATED ATF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(1301) Variable = STK38L MUTATION ANALYSIS
D1301V1, survival
                  sevent
clus2                0   1
  STK38L MUTATED     6   1
  STK38L WILD-TYPE 271  77
  STK38L MUTATED STK38L WILD-TYPE 
               7              348 
  STK38L MUTATED STK38L WILD-TYPE 
               1               77 
$`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 
       13.78 

$`STK38L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  STK38L MUTATED STK38L WILD-TYPE 
            4.01             0.00 
  STK38L MUTATED STK38L WILD-TYPE 
           34.98           148.01 
  STK38L MUTATED STK38L WILD-TYPE 
          17.820           22.075 
[1] "4.0 - 35.0 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1301V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK38L MUTATED         0        1        0         0         2         0
  STK38L WILD-TYPE      64        0       26       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK38L MUTATED           0          0          2          0        0
  STK38L WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  STK38L MUTATED           0         0
  STK38L WILD-TYPE        12         1
D1301V3, multiclass
            clus
vv           STK38L MUTATED STK38L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                0               26
  STAGE IIA               0              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  STK38L MUTATED     0   0   4   2
  STK38L WILD-TYPE   9  67 245  39
D1301V4, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              2               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
  STK38L MUTATED     5   2   0
  STK38L WILD-TYPE 215  79  66
D1301V5, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  N0              5              215
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1301V6, binary
                  cls
clus                 0   1
  STK38L MUTATED     5   0
  STK38L WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      5    0
  STK38L WILD-TYPE  280   48
   clus
vv  STK38L MUTATED STK38L WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1301V7, binary
                  cls
clus                 0   1
  STK38L MUTATED     3   4
  STK38L WILD-TYPE 167 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      3    4
  STK38L WILD-TYPE  167  193
        clus
vv       STK38L MUTATED STK38L WILD-TYPE
  FEMALE              3              167
  MALE                4              193
[1] 2 2
[1] FALSE
D1301V8, binary
                  cls
clus                 0   1
  STK38L MUTATED     6   0
  STK38L WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      6    0
  STK38L WILD-TYPE  294    8
     clus
vv    STK38L MUTATED STK38L WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1301V9, binary
                  cls
clus                 0   1
  STK38L MUTATED     6   1
  STK38L WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      6    1
  STK38L WILD-TYPE  308   47
                               clus
vv                              STK38L MUTATED STK38L WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  STK38L MUTATED     6   0   0   0
  STK38L WILD-TYPE 253   3  22  21
D1301V10, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1301V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK38L MUTATED                                  0     0
  STK38L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STK38L MUTATED                           2     3
  STK38L WILD-TYPE                        17   173
D1301V12, multiclass
                                  clus
vv                                 STK38L MUTATED STK38L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         3              173
[1] 4 2
[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 = B4GALT6 MUTATION ANALYSIS
D1302V1, survival
                   sevent
clus2                 0   1
  B4GALT6 MUTATED     8   2
  B4GALT6 WILD-TYPE 269  76
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               345 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                2                76 
$`B4GALT6 MUTATED`
TCGA-A6-6649 TCGA-AD-6895 TCGA-A6-2676 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 
       24.16        25.08        42.90        25.02        18.05        34.98 
TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CM-6162 
       35.01        58.39         3.19        12.00 

$`B4GALT6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
             3.19              0.00 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            58.39            148.01 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            25.05             21.99 
[1] "3.2 - 58.4 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1302V2, continuous
                   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      64        1       26       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALT6 MUTATED           1          0          4          0        1
  B4GALT6 WILD-TYPE        17          6         40         33       34
                   vv
clus                STAGE IVA STAGE IVB
  B4GALT6 MUTATED           0         0
  B4GALT6 WILD-TYPE        12         1
D1302V3, multiclass
            clus
vv           B4GALT6 MUTATED B4GALT6 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  B4GALT6 MUTATED     0   1   5   4
  B4GALT6 WILD-TYPE   9  66 244  37
D1302V4, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               4                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
  B4GALT6 MUTATED     4   4   2
  B4GALT6 WILD-TYPE 216  77  64
D1302V5, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  N0               4               216
  N1               4                77
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1302V6, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     8   1
  B4GALT6 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      8    1
  B4GALT6 WILD-TYPE  277   47
   clus
vv  B4GALT6 MUTATED B4GALT6 WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D1302V7, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     3   7
  B4GALT6 WILD-TYPE 167 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      3    7
  B4GALT6 WILD-TYPE  167  190
        clus
vv       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  FEMALE               3               167
  MALE                 7               190
[1] 2 2
[1] FALSE
D1302V8, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     9   1
  B4GALT6 WILD-TYPE 291   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      9    1
  B4GALT6 WILD-TYPE  291    7
     clus
vv    B4GALT6 MUTATED B4GALT6 WILD-TYPE
  NO                9               291
  YES               1                 7
[1] 2 2
[1] FALSE
D1302V9, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     7   3
  B4GALT6 WILD-TYPE 307  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      7    3
  B4GALT6 WILD-TYPE  307   45
                               clus
vv                              B4GALT6 MUTATED B4GALT6 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  B4GALT6 MUTATED     7   0   0   0
  B4GALT6 WILD-TYPE 252   3  22  21
D1302V10, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D1302V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B4GALT6 MUTATED                                  0     0
  B4GALT6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  B4GALT6 MUTATED                           0     6
  B4GALT6 WILD-TYPE                        19   170
D1302V12, multiclass
                                  clus
vv                                 B4GALT6 MUTATED B4GALT6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = MFSD4 MUTATION ANALYSIS
D1303V1, survival
                 sevent
clus2               0   1
  MFSD4 MUTATED     5   1
  MFSD4 WILD-TYPE 272  77
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             349 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              1              77 
$`MFSD4 MUTATED`
TCGA-AA-3520 TCGA-AA-A00U TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 
       24.03        17.03        83.24        58.39        12.20        12.76 

$`MFSD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02         0.99        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MFSD4 MUTATED MFSD4 WILD-TYPE 
           12.2             0.0 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
          83.24          148.01 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
          20.53           22.06 
[1] "12.2 - 83.2 (20.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1303V2, continuous
                 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      64        1       25       104         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  MFSD4 MUTATED           0
  MFSD4 WILD-TYPE         1
D1303V3, multiclass
            clus
vv           MFSD4 MUTATED MFSD4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MFSD4 MUTATED     0   0   6   0
  MFSD4 WILD-TYPE   9  67 243  41
D1303V4, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             0              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
  MFSD4 MUTATED     5   1   0
  MFSD4 WILD-TYPE 215  80  66
D1303V5, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1303V6, binary
                 cls
clus                0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      6    0
  MFSD4 WILD-TYPE  279   48
   clus
vv  MFSD4 MUTATED MFSD4 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1303V7, binary
                 cls
clus                0   1
  MFSD4 MUTATED     1   5
  MFSD4 WILD-TYPE 169 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      1    5
  MFSD4 WILD-TYPE  169  192
        clus
vv       MFSD4 MUTATED MFSD4 WILD-TYPE
  FEMALE             1             169
  MALE               5             192
[1] 2 2
[1] FALSE
D1303V8, binary
                 cls
clus                0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      6    0
  MFSD4 WILD-TYPE  294    8
     clus
vv    MFSD4 MUTATED MFSD4 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1303V9, binary
                 cls
clus                0   1
  MFSD4 MUTATED     5   1
  MFSD4 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      5    1
  MFSD4 WILD-TYPE  309   47
                               clus
vv                              MFSD4 MUTATED MFSD4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFSD4 MUTATED     4   0   0   2
  MFSD4 WILD-TYPE 255   3  22  19
D1303V10, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             2              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"
D1303V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFSD4 MUTATED                                  0     3
  MFSD4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFSD4 MUTATED                           0     1
  MFSD4 WILD-TYPE                        19   175
D1303V12, multiclass
                                  clus
vv                                 MFSD4 MUTATED MFSD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        1             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(1304) Variable = LRRC6 MUTATION ANALYSIS
D1304V1, survival
                 sevent
clus2               0   1
  LRRC6 MUTATED     2   1
  LRRC6 WILD-TYPE 275  77
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              3             352 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              1              77 
$`LRRC6 MUTATED`
TCGA-A6-6142 TCGA-AZ-6607 TCGA-F4-6808 
       25.08         3.19        33.67 

$`LRRC6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6626 
       61.91        36.00        13.78        46.75 

  LRRC6 MUTATED LRRC6 WILD-TYPE 
           3.19            0.00 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
          33.67          148.01 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
         25.080          22.045 
[1] "3.2 - 33.7 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D1304V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC6 MUTATED         1        0        0         0         0         0
  LRRC6 WILD-TYPE      63        1       26       108         8         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        18          6         44         33       34        11
                 vv
clus              STAGE IVB
  LRRC6 MUTATED           0
  LRRC6 WILD-TYPE         1
D1304V3, multiclass
            clus
vv           LRRC6 MUTATED LRRC6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  LRRC6 MUTATED     1   0   1   1
  LRRC6 WILD-TYPE   8  67 248  40
D1304V4, multiclass
    clus
vv   LRRC6 MUTATED LRRC6 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             1             248
  T4             1              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
  LRRC6 MUTATED     1   1   1
  LRRC6 WILD-TYPE 219  80  65
D1304V5, multiclass
    clus
vv   LRRC6 MUTATED LRRC6 WILD-TYPE
  N0             1             219
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1304V6, binary
                 cls
clus                0   1
  LRRC6 MUTATED     1   2
  LRRC6 WILD-TYPE 284  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      1    2
  LRRC6 WILD-TYPE  284   46
   clus
vv  LRRC6 MUTATED LRRC6 WILD-TYPE
  0             1             284
  1             2              46
[1] 2 2
[1] FALSE
D1304V7, binary
                 cls
clus                0   1
  LRRC6 MUTATED     2   1
  LRRC6 WILD-TYPE 168 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      2    1
  LRRC6 WILD-TYPE  168  196
        clus
vv       LRRC6 MUTATED LRRC6 WILD-TYPE
  FEMALE             2             168
  MALE               1             196
[1] 2 2
[1] FALSE
D1304V8, binary
                 cls
clus                0   1
  LRRC6 MUTATED     3   0
  LRRC6 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      3    0
  LRRC6 WILD-TYPE  297    8
     clus
vv    LRRC6 MUTATED LRRC6 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1304V9, binary
                 cls
clus                0   1
  LRRC6 MUTATED     3   0
  LRRC6 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      3    0
  LRRC6 WILD-TYPE  311   48
                               clus
vv                              LRRC6 MUTATED LRRC6 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LRRC6 MUTATED     1   0   0   0
  LRRC6 WILD-TYPE 258   3  22  21
D1304V10, multiclass
[1] "Remove cluster labels:" "LRRC6 MUTATED"         
clus
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              1             304 
     TCGA-A6-2677      TCGA-AA-3496      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-3527 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AD-6895      TCGA-AZ-4681      TCGA-CK-5912      TCGA-G4-6310 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-2676      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-3502      TCGA-AA-3510 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3526      TCGA-AA-3529      TCGA-AA-3532 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3544 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3553      TCGA-AA-3555 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3561      TCGA-AA-3655      TCGA-AA-3660 
"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-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3815      TCGA-AA-3818 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      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-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3955 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3975      TCGA-AA-3984      TCGA-AA-3989      TCGA-AA-3994 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00N 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00W      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-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4682 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
D1304V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC6 MUTATED                                  0     0
  LRRC6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRRC6 MUTATED                           0     3
  LRRC6 WILD-TYPE                        19   173
D1304V12, multiclass
                                  clus
vv                                 LRRC6 MUTATED LRRC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = MPP7 MUTATION ANALYSIS
D1305V1, survival
                sevent
clus2              0   1
  MPP7 MUTATED     3   2
  MPP7 WILD-TYPE 274  76
  MPP7 MUTATED MPP7 WILD-TYPE 
             5            350 
  MPP7 MUTATED MPP7 WILD-TYPE 
             2             76 
$`MPP7 MUTATED`
TCGA-AA-3525 TCGA-AZ-6608 TCGA-CM-5348 TCGA-D5-6535 TCGA-DM-A28F 
        8.05         1.94        22.98        15.12        35.97 

$`MPP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MPP7 MUTATED MPP7 WILD-TYPE 
          1.94           0.00 
  MPP7 MUTATED MPP7 WILD-TYPE 
         35.97         148.01 
  MPP7 MUTATED MPP7 WILD-TYPE 
        15.120         22.075 
[1] "1.9 - 36.0 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D1305V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MPP7 MUTATED         0        0        0         0         0         0
  MPP7 WILD-TYPE      64        1       26       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MPP7 MUTATED           0          1          4          0        0         0
  MPP7 WILD-TYPE        18          5         40         33       35        12
                vv
clus             STAGE IVB
  MPP7 MUTATED           0
  MPP7 WILD-TYPE         1
D1305V3, multiclass
            clus
vv           MPP7 MUTATED MPP7 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MPP7 MUTATED     0   1   4   0
  MPP7 WILD-TYPE   9  66 245  41
D1305V4, multiclass
    clus
vv   MPP7 MUTATED MPP7 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            0             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
  MPP7 MUTATED     0   5   0
  MPP7 WILD-TYPE 220  76  66
D1305V5, multiclass
    clus
vv   MPP7 MUTATED MPP7 WILD-TYPE
  N0            0            220
  N1            5             76
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1305V6, binary
                cls
clus               0   1
  MPP7 MUTATED     4   0
  MPP7 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      4    0
  MPP7 WILD-TYPE  281   48
   clus
vv  MPP7 MUTATED MPP7 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1305V7, binary
                cls
clus               0   1
  MPP7 MUTATED     2   3
  MPP7 WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      2    3
  MPP7 WILD-TYPE  168  194
        clus
vv       MPP7 MUTATED MPP7 WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D1305V8, binary
                cls
clus               0   1
  MPP7 MUTATED     4   0
  MPP7 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      4    0
  MPP7 WILD-TYPE  296    8
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1305V9, binary
                cls
clus               0   1
  MPP7 MUTATED     5   0
  MPP7 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      5    0
  MPP7 WILD-TYPE  309   48
                               clus
vv                              MPP7 MUTATED MPP7 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MPP7 MUTATED     2   0   0   1
  MPP7 WILD-TYPE 257   3  22  20
D1305V10, multiclass
    clus
vv   MPP7 MUTATED MPP7 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            0             22
  RX            1             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"
D1305V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPP7 MUTATED                                  0     0
  MPP7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MPP7 MUTATED                           0     4
  MPP7 WILD-TYPE                        19   172
D1305V12, multiclass
                                  clus
vv                                 MPP7 MUTATED MPP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = IKBKE MUTATION ANALYSIS
D1306V1, survival
                 sevent
clus2               0   1
  IKBKE MUTATED     3   3
  IKBKE WILD-TYPE 274  75
  IKBKE MUTATED IKBKE WILD-TYPE 
              6             349 
  IKBKE MUTATED IKBKE WILD-TYPE 
              3              75 
$`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 

$`IKBKE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  IKBKE MUTATED IKBKE WILD-TYPE 
           3.02            0.00 
  IKBKE MUTATED IKBKE WILD-TYPE 
         140.38          148.01 
  IKBKE MUTATED IKBKE WILD-TYPE 
          42.21           22.03 
[1] "3.0 - 140.4 (42.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1306V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKBKE MUTATED         0        0        2         3         0         0
  IKBKE WILD-TYPE      64        1       24       105         8         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        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  IKBKE MUTATED           0
  IKBKE WILD-TYPE         1
D1306V3, multiclass
            clus
vv           IKBKE MUTATED IKBKE WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  IKBKE MUTATED     0   0   7   0
  IKBKE WILD-TYPE   9  67 242  41
D1306V4, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             0              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
  IKBKE MUTATED     5   1   1
  IKBKE WILD-TYPE 215  80  65
D1306V5, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1306V6, binary
                 cls
clus                0   1
  IKBKE MUTATED     4   1
  IKBKE WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      4    1
  IKBKE WILD-TYPE  281   47
   clus
vv  IKBKE MUTATED IKBKE WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1306V7, binary
                 cls
clus                0   1
  IKBKE MUTATED     5   2
  IKBKE WILD-TYPE 165 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      5    2
  IKBKE WILD-TYPE  165  195
        clus
vv       IKBKE MUTATED IKBKE WILD-TYPE
  FEMALE             5             165
  MALE               2             195
[1] 2 2
[1] FALSE
D1306V8, binary
                 cls
clus                0   1
  IKBKE MUTATED     4   1
  IKBKE WILD-TYPE 296   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      4    1
  IKBKE WILD-TYPE  296    7
     clus
vv    IKBKE MUTATED IKBKE WILD-TYPE
  NO              4             296
  YES             1               7
[1] 2 2
[1] FALSE
D1306V9, binary
                 cls
clus                0   1
  IKBKE MUTATED     6   1
  IKBKE WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      6    1
  IKBKE WILD-TYPE  308   47
                               clus
vv                              IKBKE MUTATED IKBKE WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IKBKE MUTATED     5   0   0   0
  IKBKE WILD-TYPE 254   3  22  21
D1306V10, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1306V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IKBKE MUTATED                                  0     0
  IKBKE WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IKBKE MUTATED                           0     4
  IKBKE WILD-TYPE                        19   172
D1306V12, multiclass
                                  clus
vv                                 IKBKE MUTATED IKBKE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = MRPS22 MUTATION ANALYSIS
D1307V1, survival
                  sevent
clus2                0   1
  MRPS22 MUTATED     8   2
  MRPS22 WILD-TYPE 269  76
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              345 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
               2               76 
$`MRPS22 MUTATED`
TCGA-AZ-6608 TCGA-A6-5661 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6603 
        1.94        33.53        25.02        34.98        21.44        29.56 
TCGA-CM-4743 TCGA-D5-6541 TCGA-DM-A1HB TCGA-G4-6317 
       23.05        15.58       135.65        36.00 

$`MRPS22 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  MRPS22 MUTATED MRPS22 WILD-TYPE 
            1.94             0.00 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
          135.65           148.01 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
           27.29            21.99 
[1] "1.9 - 135.7 (27.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1307V2, continuous
                  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      64        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS22 MUTATED           0          1          1          1        0
  MRPS22 WILD-TYPE        18          5         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  MRPS22 MUTATED           0         0
  MRPS22 WILD-TYPE        12         1
D1307V3, multiclass
            clus
vv           MRPS22 MUTATED MRPS22 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  MRPS22 MUTATED     0   3   6   1
  MRPS22 WILD-TYPE   9  64 243  40
D1307V4, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              6              243
  T4              1               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
  MRPS22 MUTATED     6   3   1
  MRPS22 WILD-TYPE 214  78  65
D1307V5, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  N0              6              214
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1307V6, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     6   0
  MRPS22 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      6    0
  MRPS22 WILD-TYPE  279   48
   clus
vv  MRPS22 MUTATED MRPS22 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1307V7, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     5   5
  MRPS22 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      5    5
  MRPS22 WILD-TYPE  165  192
        clus
vv       MRPS22 MUTATED MRPS22 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D1307V8, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     9   0
  MRPS22 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      9    0
  MRPS22 WILD-TYPE  291    8
     clus
vv    MRPS22 MUTATED MRPS22 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1307V9, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     9   0
  MRPS22 WILD-TYPE 305  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      9    0
  MRPS22 WILD-TYPE  305   48
                               clus
vv                              MRPS22 MUTATED MRPS22 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MRPS22 MUTATED     6   0   0   0
  MRPS22 WILD-TYPE 253   3  22  21
D1307V10, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1307V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS22 MUTATED                                  0     0
  MRPS22 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPS22 MUTATED                           1     7
  MRPS22 WILD-TYPE                        18   169
D1307V12, multiclass
                                  clus
vv                                 MRPS22 MUTATED MRPS22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = HEATR4 MUTATION ANALYSIS
D1308V1, survival
                  sevent
clus2                0   1
  HEATR4 MUTATED    10   4
  HEATR4 WILD-TYPE 267  74
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              14              341 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
               4               74 
$`HEATR4 MUTATED`
TCGA-AA-3672 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3819 
        0.92        10.88        26.17        33.53         3.02        25.02 
TCGA-AA-A00A TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6920 TCGA-DM-A0XF 
       38.04        35.01        12.76        10.06        12.39        38.20 
TCGA-G4-6299 TCGA-G4-6304 
       74.56        53.62 

$`HEATR4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        10.06        35.05        33.04         0.99         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  HEATR4 MUTATED HEATR4 WILD-TYPE 
            0.92             0.00 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
           74.56           148.01 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
          25.595           22.030 
[1] "0.9 - 74.6 (25.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1308V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEATR4 MUTATED         0        0        1         7         1         0
  HEATR4 WILD-TYPE      64        1       25       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEATR4 MUTATED           2          0          0          2        0
  HEATR4 WILD-TYPE        16          6         44         31       35
                  vv
clus               STAGE IVA STAGE IVB
  HEATR4 MUTATED           0         0
  HEATR4 WILD-TYPE        12         1
D1308V3, multiclass
            clus
vv           HEATR4 MUTATED HEATR4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  HEATR4 MUTATED     0   0  12   2
  HEATR4 WILD-TYPE   9  67 237  39
D1308V4, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             12              237
  T4              2               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
  HEATR4 MUTATED     9   1   4
  HEATR4 WILD-TYPE 211  80  62
D1308V5, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  N0              9              211
  N1              1               80
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1308V6, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    13   0
  HEATR4 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     13    0
  HEATR4 WILD-TYPE  272   48
   clus
vv  HEATR4 MUTATED HEATR4 WILD-TYPE
  0             13              272
  1              0               48
[1] 2 2
[1] FALSE
D1308V7, binary
                  cls
clus                 0   1
  HEATR4 MUTATED     8   6
  HEATR4 WILD-TYPE 162 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED      8    6
  HEATR4 WILD-TYPE  162  191
        clus
vv       HEATR4 MUTATED HEATR4 WILD-TYPE
  FEMALE              8              162
  MALE                6              191
[1] 2 2
[1] FALSE
D1308V8, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    12   1
  HEATR4 WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     12    1
  HEATR4 WILD-TYPE  288    7
     clus
vv    HEATR4 MUTATED HEATR4 WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D1308V9, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    11   2
  HEATR4 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     11    2
  HEATR4 WILD-TYPE  303   46
                               clus
vv                              HEATR4 MUTATED HEATR4 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HEATR4 MUTATED    10   0   0   2
  HEATR4 WILD-TYPE 249   3  22  19
D1308V10, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D1308V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEATR4 MUTATED                                  0     2
  HEATR4 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HEATR4 MUTATED                           1     6
  HEATR4 WILD-TYPE                        18   170
D1308V12, multiclass
                                  clus
vv                                 HEATR4 MUTATED HEATR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = PSMD11 MUTATION ANALYSIS
D1309V1, survival
                  sevent
clus2                0   1
  PSMD11 MUTATED     6   2
  PSMD11 WILD-TYPE 271  76
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              347 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               2               76 
$`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        12.16        33.01        15.02 
TCGA-CM-6162 TCGA-DM-A1D8 
       12.00        12.59 

$`PSMD11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6163 
       15.02         5.03        15.02        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PSMD11 MUTATED PSMD11 WILD-TYPE 
            4.01             0.00 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           35.01           148.01 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
          13.805           22.090 
[1] "4.0 - 35.0 (13.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1309V2, continuous
                  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      62        1       26       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PSMD11 MUTATED           1          0          1          0        0
  PSMD11 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  PSMD11 MUTATED           1         0
  PSMD11 WILD-TYPE        11         1
D1309V3, multiclass
            clus
vv           PSMD11 MUTATED PSMD11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               0              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  PSMD11 MUTATED     0   2   4   2
  PSMD11 WILD-TYPE   9  65 245  39
D1309V4, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              2               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
  PSMD11 MUTATED     4   3   1
  PSMD11 WILD-TYPE 216  78  65
D1309V5, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  N0              4              216
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1309V6, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     5   1
  PSMD11 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      5    1
  PSMD11 WILD-TYPE  280   47
   clus
vv  PSMD11 MUTATED PSMD11 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D1309V7, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     5   3
  PSMD11 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      5    3
  PSMD11 WILD-TYPE  165  194
        clus
vv       PSMD11 MUTATED PSMD11 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1309V8, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     5   1
  PSMD11 WILD-TYPE 295   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      5    1
  PSMD11 WILD-TYPE  295    7
     clus
vv    PSMD11 MUTATED PSMD11 WILD-TYPE
  NO               5              295
  YES              1                7
[1] 2 2
[1] FALSE
D1309V9, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     4   4
  PSMD11 WILD-TYPE 310  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      4    4
  PSMD11 WILD-TYPE  310   44
                               clus
vv                              PSMD11 MUTATED PSMD11 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PSMD11 MUTATED     7   0   0   0
  PSMD11 WILD-TYPE 252   3  22  21
D1309V10, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1309V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMD11 MUTATED                                  0     0
  PSMD11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PSMD11 MUTATED                           1     4
  PSMD11 WILD-TYPE                        18   172
D1309V12, multiclass
                                  clus
vv                                 PSMD11 MUTATED PSMD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = KRTAP12-3 MUTATION ANALYSIS
D1310V1, survival
                     sevent
clus2                   0   1
  KRTAP12-3 MUTATED     2   1
  KRTAP12-3 WILD-TYPE 275  77
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 352 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  1                  77 
$`KRTAP12-3 MUTATED`
TCGA-G4-6586 TCGA-AZ-6599 TCGA-D5-6931 
       35.80         6.77        12.00 

$`KRTAP12-3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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              22.075 
[1] "6.8 - 35.8 (12.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D1310V2, continuous
                     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      63        1       26       107         8         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        18          6         44         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  KRTAP12-3 MUTATED           0         0
  KRTAP12-3 WILD-TYPE        12         1
D1310V3, multiclass
            clus
vv           KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  26
  STAGE IIA                  1                 107
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 0                  44
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  KRTAP12-3 MUTATED     0   1   1   1
  KRTAP12-3 WILD-TYPE   9  66 248  40
D1310V4, multiclass
    clus
vv   KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 1                 248
  T4                 1                  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
  KRTAP12-3 MUTATED     2   0   1
  KRTAP12-3 WILD-TYPE 218  81  65
D1310V5, multiclass
    clus
vv   KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  N0                 2                 218
  N1                 0                  81
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1310V6, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     2   0
  KRTAP12-3 WILD-TYPE 283  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      2    0
  KRTAP12-3 WILD-TYPE  283   48
   clus
vv  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  0                 2                 283
  1                 0                  48
[1] 2 2
[1] FALSE
D1310V7, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     1   2
  KRTAP12-3 WILD-TYPE 169 195
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      1    2
  KRTAP12-3 WILD-TYPE  169  195
        clus
vv       KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  FEMALE                 1                 169
  MALE                   2                 195
[1] 2 2
[1] FALSE
D1310V8, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     3   0
  KRTAP12-3 WILD-TYPE 297   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      3    0
  KRTAP12-3 WILD-TYPE  297    8
     clus
vv    KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  NO                  3                 297
  YES                 0                   8
[1] 2 2
[1] FALSE
D1310V9, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     3   0
  KRTAP12-3 WILD-TYPE 311  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      3    0
  KRTAP12-3 WILD-TYPE  311   48
                               clus
vv                              KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  COLON ADENOCARCINOMA                          3                 311
  COLON MUCINOUS ADENOCARCINOMA                 0                  48
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  KRTAP12-3 MUTATED     2   0   0   0
  KRTAP12-3 WILD-TYPE 257   3  22  21
D1310V10, multiclass
[1] "Remove cluster labels:" "KRTAP12-3 MUTATED"     
clus
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  2                 303 
         TCGA-A6-2677          TCGA-AA-3496          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-3527          TCGA-AA-3530 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3543          TCGA-AA-3552 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3554          TCGA-AA-3556          TCGA-AA-3560 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3562          TCGA-AA-3662          TCGA-AA-3672 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3697 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3713          TCGA-AA-3715          TCGA-AA-3814 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3860          TCGA-AA-3867 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3870          TCGA-AA-3939          TCGA-AA-3950 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3972          TCGA-AA-3976 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3979          TCGA-AA-3986          TCGA-AA-A00L 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A024          TCGA-AD-6548 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6895          TCGA-AZ-4681 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-5912          TCGA-G4-6310          TCGA-G4-6321 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6628 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         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-A6-2678          TCGA-A6-2683 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5657          TCGA-A6-5659 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-5661          TCGA-A6-5665          TCGA-A6-6781 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3489          TCGA-AA-3492          TCGA-AA-3502 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3510          TCGA-AA-3511          TCGA-AA-3514 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3517          TCGA-AA-3518          TCGA-AA-3519 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3526          TCGA-AA-3529          TCGA-AA-3532 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3534          TCGA-AA-3538          TCGA-AA-3542 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3544          TCGA-AA-3548          TCGA-AA-3549 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3555          TCGA-AA-3558 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3655          TCGA-AA-3660 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3663          TCGA-AA-3664          TCGA-AA-3666 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3667          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-3693 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3695          TCGA-AA-3696          TCGA-AA-3710 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3811          TCGA-AA-3812 
"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-3845 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3846          TCGA-AA-3848          TCGA-AA-3850 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3851          TCGA-AA-3852          TCGA-AA-3854 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3855          TCGA-AA-3856          TCGA-AA-3858 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3861          TCGA-AA-3864          TCGA-AA-3866 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3872          TCGA-AA-3875 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3877          TCGA-AA-3930          TCGA-AA-3941 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3947          TCGA-AA-3949          TCGA-AA-3955 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3956          TCGA-AA-3968          TCGA-AA-3971 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3973          TCGA-AA-3975          TCGA-AA-3984 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3989          TCGA-AA-3994          TCGA-AA-A004 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"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-A010          TCGA-AA-A017          TCGA-AA-A01D 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01F          TCGA-AA-A01G          TCGA-AA-A01I 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01K          TCGA-AA-A01P          TCGA-AA-A01Q 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01R          TCGA-AA-A01S          TCGA-AA-A01T 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01V          TCGA-AA-A01X          TCGA-AA-A01Z 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A022          TCGA-AA-A029          TCGA-AA-A02F 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A02H          TCGA-AA-A02J          TCGA-AA-A02K 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A02O          TCGA-AA-A02W          TCGA-AA-A02Y 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A03F          TCGA-AA-A03J          TCGA-AD-5900 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AD-6889          TCGA-AD-6965          TCGA-AU-3779 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          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-5913          TCGA-CK-5914 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6930 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-F4-6459 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6460          TCGA-F4-6569          TCGA-F4-6570 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6703          TCGA-F4-6704          TCGA-F4-6805 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6806          TCGA-F4-6807          TCGA-F4-6808 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6809          TCGA-F4-6854          TCGA-F4-6855 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6856          TCGA-G4-6293          TCGA-G4-6299 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6315 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6323          TCGA-G4-6626 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
D1310V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP12-3 MUTATED                                  0     0
  KRTAP12-3 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP12-3 MUTATED                           0     3
  KRTAP12-3 WILD-TYPE                        19   173
D1310V12, multiclass
                                  clus
vv                                 KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            3                 173
[1] 4 2
[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 = FLNB MUTATION ANALYSIS
D1311V1, survival
                sevent
clus2              0   1
  FLNB MUTATED    21   6
  FLNB WILD-TYPE 256  72
  FLNB MUTATED FLNB WILD-TYPE 
            27            328 
  FLNB MUTATED FLNB WILD-TYPE 
             6             72 
$`FLNB MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6138 TCGA-A6-6653 
       13.02        19.04        26.17        33.53        22.52        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 
       20.12        19.66         3.02         6.97        53.00        31.00 
TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R 
       38.04        18.05         4.01        34.98         1.02        35.01 
TCGA-AA-A01T TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5916 
       33.04        83.24        27.09        21.44        12.76        21.14 
TCGA-CM-4746 TCGA-D5-6920 TCGA-DM-A1D4 
       37.02        12.39        92.75 

$`FLNB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       21.76        24.69        23.87        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       13.94        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         7.53        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FLNB MUTATED FLNB WILD-TYPE 
          1.02           0.00 
  FLNB MUTATED FLNB WILD-TYPE 
         92.75         148.01 
  FLNB MUTATED FLNB WILD-TYPE 
        22.520         22.045 
[1] "1.0 - 92.8 (22.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1311V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLNB MUTATED         6        0        5         9         2         0
  FLNB WILD-TYPE      58        1       21        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLNB MUTATED           3          0          1          1        1         0
  FLNB WILD-TYPE        15          6         43         32       34        12
                vv
clus             STAGE IVB
  FLNB MUTATED           0
  FLNB WILD-TYPE         1
D1311V3, multiclass
            clus
vv           FLNB MUTATED FLNB WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA             9             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  FLNB MUTATED     2   4  17   5
  FLNB WILD-TYPE   7  63 232  36
D1311V4, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  T1            2              7
  T2            4             63
  T3           17            232
  T4            5             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
  FLNB MUTATED    23   3   2
  FLNB WILD-TYPE 197  78  64
D1311V5, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  N0           23            197
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1311V6, binary
                cls
clus               0   1
  FLNB MUTATED    24   1
  FLNB WILD-TYPE 261  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     24    1
  FLNB WILD-TYPE  261   47
   clus
vv  FLNB MUTATED FLNB WILD-TYPE
  0           24            261
  1            1             47
[1] 2 2
[1] FALSE
D1311V7, binary
                cls
clus               0   1
  FLNB MUTATED    12  16
  FLNB WILD-TYPE 158 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     12   16
  FLNB WILD-TYPE  158  181
        clus
vv       FLNB MUTATED FLNB WILD-TYPE
  FEMALE           12            158
  MALE             16            181
[1] 2 2
[1] FALSE
D1311V8, binary
                cls
clus               0   1
  FLNB MUTATED    21   2
  FLNB WILD-TYPE 279   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     21    2
  FLNB WILD-TYPE  279    6
     clus
vv    FLNB MUTATED FLNB WILD-TYPE
  NO            21            279
  YES            2              6
[1] 2 2
[1] FALSE
D1311V9, binary
                cls
clus               0   1
  FLNB MUTATED    20   8
  FLNB WILD-TYPE 294  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     20    8
  FLNB WILD-TYPE  294   40
                               clus
vv                              FLNB MUTATED FLNB WILD-TYPE
  COLON ADENOCARCINOMA                    20            294
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FLNB MUTATED    20   0   1   2
  FLNB WILD-TYPE 239   3  21  19
D1311V10, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  R0           20            239
  R1            0              3
  R2            1             21
  RX            2             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"
D1311V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLNB MUTATED                                  0     2
  FLNB WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLNB MUTATED                           2    10
  FLNB WILD-TYPE                        17   166
D1311V12, multiclass
                                  clus
vv                                 FLNB MUTATED FLNB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      10            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(1312) Variable = PALLD MUTATION ANALYSIS
D1312V1, survival
                 sevent
clus2               0   1
  PALLD MUTATED     7   2
  PALLD WILD-TYPE 270  76
  PALLD MUTATED PALLD WILD-TYPE 
              9             346 
  PALLD MUTATED PALLD WILD-TYPE 
              2              76 
$`PALLD MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3660 TCGA-AA-3680 TCGA-AA-3966 TCGA-AU-6004 
      100.01        26.17        78.08        11.01         2.01        27.09 
TCGA-CM-4747 TCGA-D5-6533 TCGA-DM-A1HB 
       25.02        25.48       135.65 

$`PALLD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PALLD MUTATED PALLD WILD-TYPE 
           2.01            0.00 
  PALLD MUTATED PALLD WILD-TYPE 
         135.65          148.01 
  PALLD MUTATED PALLD WILD-TYPE 
          26.17           21.99 
[1] "2.0 - 135.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1312V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PALLD MUTATED         1        0        2         2         0         0
  PALLD WILD-TYPE      63        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PALLD MUTATED           0          0          1          0        1         1
  PALLD WILD-TYPE        18          6         43         33       34        11
                 vv
clus              STAGE IVB
  PALLD MUTATED           0
  PALLD WILD-TYPE         1
D1312V3, multiclass
            clus
vv           PALLD MUTATED PALLD WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  PALLD MUTATED     0   1   5   3
  PALLD WILD-TYPE   9  66 244  38
D1312V4, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             3              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
  PALLD MUTATED     6   2   1
  PALLD WILD-TYPE 214  79  65
D1312V5, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1312V6, binary
                 cls
clus                0   1
  PALLD MUTATED     7   2
  PALLD WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      7    2
  PALLD WILD-TYPE  278   46
   clus
vv  PALLD MUTATED PALLD WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D1312V7, binary
                 cls
clus                0   1
  PALLD MUTATED     6   3
  PALLD WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      6    3
  PALLD WILD-TYPE  164  194
        clus
vv       PALLD MUTATED PALLD WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D1312V8, binary
                 cls
clus                0   1
  PALLD MUTATED     6   0
  PALLD WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      6    0
  PALLD WILD-TYPE  294    8
     clus
vv    PALLD MUTATED PALLD WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1312V9, binary
                 cls
clus                0   1
  PALLD MUTATED     7   1
  PALLD WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      7    1
  PALLD WILD-TYPE  307   47
                               clus
vv                              PALLD MUTATED PALLD WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PALLD MUTATED     5   0   1   0
  PALLD WILD-TYPE 254   3  21  21
D1312V10, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             0              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"
D1312V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PALLD MUTATED                                  0     0
  PALLD WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PALLD MUTATED                           0     6
  PALLD WILD-TYPE                        19   170
D1312V12, multiclass
                                  clus
vv                                 PALLD MUTATED PALLD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = GATA1 MUTATION ANALYSIS
D1313V1, survival
                 sevent
clus2               0   1
  GATA1 MUTATED    12   3
  GATA1 WILD-TYPE 265  75
  GATA1 MUTATED GATA1 WILD-TYPE 
             15             340 
  GATA1 MUTATED GATA1 WILD-TYPE 
              3              75 
$`GATA1 MUTATED`
TCGA-AA-3950 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-3966 
       24.00         3.02        78.08         6.97        33.01         2.01 
TCGA-AA-A01R TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6196 TCGA-CK-4952 TCGA-CK-5914 
       35.01        12.16        33.01         0.20        15.62        21.99 
TCGA-CM-6164 TCGA-D5-6537 TCGA-G4-6303 
       29.03         4.80        65.85 

$`GATA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        61.02        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
       26.47        14.50        27.09        16.31         0.95        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GATA1 MUTATED GATA1 WILD-TYPE 
            0.2             0.0 
  GATA1 MUTATED GATA1 WILD-TYPE 
          78.08          148.01 
  GATA1 MUTATED GATA1 WILD-TYPE 
         21.990          22.075 
[1] "0.2 - 78.1 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1313V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GATA1 MUTATED         1        0        3         4         1         0
  GATA1 WILD-TYPE      63        1       23       104         7         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        17          6         42         31       34        11
                 vv
clus              STAGE IVB
  GATA1 MUTATED           0
  GATA1 WILD-TYPE         1
D1313V3, multiclass
            clus
vv           GATA1 MUTATED GATA1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  GATA1 MUTATED     0   1  13   2
  GATA1 WILD-TYPE   9  66 236  39
D1313V4, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            13             236
  T4             2              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
  GATA1 MUTATED     9   4   3
  GATA1 WILD-TYPE 211  77  63
D1313V5, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  N0             9             211
  N1             4              77
  N2             3              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"
D1313V6, binary
                 cls
clus                0   1
  GATA1 MUTATED    10   2
  GATA1 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     10    2
  GATA1 WILD-TYPE  275   46
   clus
vv  GATA1 MUTATED GATA1 WILD-TYPE
  0            10             275
  1             2              46
[1] 2 2
[1] FALSE
D1313V7, binary
                 cls
clus                0   1
  GATA1 MUTATED    10   6
  GATA1 WILD-TYPE 160 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     10    6
  GATA1 WILD-TYPE  160  191
        clus
vv       GATA1 MUTATED GATA1 WILD-TYPE
  FEMALE            10             160
  MALE               6             191
[1] 2 2
[1] FALSE
D1313V8, binary
                 cls
clus                0   1
  GATA1 MUTATED    10   1
  GATA1 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     10    1
  GATA1 WILD-TYPE  290    7
     clus
vv    GATA1 MUTATED GATA1 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1313V9, binary
                 cls
clus                0   1
  GATA1 MUTATED     9   7
  GATA1 WILD-TYPE 305  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED      9    7
  GATA1 WILD-TYPE  305   41
                               clus
vv                              GATA1 MUTATED GATA1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GATA1 MUTATED    13   0   0   2
  GATA1 WILD-TYPE 246   3  22  19
D1313V10, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             2              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"
D1313V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GATA1 MUTATED                                  0     0
  GATA1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GATA1 MUTATED                           1     7
  GATA1 WILD-TYPE                        18   169
D1313V12, multiclass
                                  clus
vv                                 GATA1 MUTATED GATA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = TRIP12 MUTATION ANALYSIS
D1314V1, survival
                  sevent
clus2                0   1
  TRIP12 MUTATED    21   6
  TRIP12 WILD-TYPE 256  72
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              27              328 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               6               72 
$`TRIP12 MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3808 TCGA-A6-5661 
       24.00        25.08        35.80        26.17        33.34        33.53 
TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-3877 
        8.38        23.87        19.66         3.02         0.00        31.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 
        2.01        25.02         4.01        34.98        35.01        83.24 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6538 TCGA-DM-A0XD 
       14.50        27.09        58.39        15.62        17.13        24.43 
TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-F4-6703 
       12.59       135.65        47.87 

$`TRIP12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5662 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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       24.39        20.12        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        27.42        26.47        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TRIP12 MUTATED TRIP12 WILD-TYPE 
               0                0 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
          135.65           148.01 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
           25.02            21.99 
[1] "0.0 - 135.7 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1314V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIP12 MUTATED         2        0        1        14         2         0
  TRIP12 WILD-TYPE      62        1       25        94         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP12 MUTATED           1          0          4          2        0
  TRIP12 WILD-TYPE        17          6         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIP12 MUTATED           0         0
  TRIP12 WILD-TYPE        12         1
D1314V3, multiclass
            clus
vv           TRIP12 MUTATED TRIP12 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA              14               94
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  TRIP12 MUTATED     1   2  21   4
  TRIP12 WILD-TYPE   8  65 228  37
D1314V4, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  T1              1                8
  T2              2               65
  T3             21              228
  T4              4               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
  TRIP12 MUTATED    20   5   3
  TRIP12 WILD-TYPE 200  76  63
D1314V5, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  N0             20              200
  N1              5               76
  N2              3               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"
D1314V6, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    25   0
  TRIP12 WILD-TYPE 260  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     25    0
  TRIP12 WILD-TYPE  260   48
   clus
vv  TRIP12 MUTATED TRIP12 WILD-TYPE
  0             25              260
  1              0               48
[1] 2 2
[1] FALSE
D1314V7, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    16  12
  TRIP12 WILD-TYPE 154 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     16   12
  TRIP12 WILD-TYPE  154  185
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  FEMALE             16              154
  MALE               12              185
[1] 2 2
[1] FALSE
D1314V8, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    18   1
  TRIP12 WILD-TYPE 282   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     18    1
  TRIP12 WILD-TYPE  282    7
     clus
vv    TRIP12 MUTATED TRIP12 WILD-TYPE
  NO              18              282
  YES              1                7
[1] 2 2
[1] FALSE
D1314V9, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    20   7
  TRIP12 WILD-TYPE 294  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     20    7
  TRIP12 WILD-TYPE  294   41
                               clus
vv                              TRIP12 MUTATED TRIP12 WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIP12 MUTATED    20   0   0   1
  TRIP12 WILD-TYPE 239   3  22  20
D1314V10, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  R0             20              239
  R1              0                3
  R2              0               22
  RX              1               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"
D1314V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP12 MUTATED                                  0     1
  TRIP12 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIP12 MUTATED                           2    15
  TRIP12 WILD-TYPE                        17   161
D1314V12, multiclass
                                  clus
vv                                 TRIP12 MUTATED TRIP12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        15              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(1315) Variable = ZFP91 MUTATION ANALYSIS
D1315V1, survival
                 sevent
clus2               0   1
  ZFP91 MUTATED     5   2
  ZFP91 WILD-TYPE 272  76
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              7             348 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              2              76 
$`ZFP91 MUTATED`
TCGA-AA-3860 TCGA-AA-A00L TCGA-A6-5661 TCGA-AA-A01R TCGA-CM-6162 TCGA-DM-A28G 
       31.07        38.04        33.53        35.01        12.00        60.79 
TCGA-G4-6303 
       65.85 

$`ZFP91 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        24.00        19.07        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K 
      139.17        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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZFP91 MUTATED ZFP91 WILD-TYPE 
             12               0 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
          65.85          148.01 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
          35.01           21.99 
[1] "12.0 - 65.8 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1315V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP91 MUTATED         0        0        0         3         0         0
  ZFP91 WILD-TYPE      64        1       26       105         8         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        17          6         42         33       34        12
                 vv
clus              STAGE IVB
  ZFP91 MUTATED           0
  ZFP91 WILD-TYPE         1
D1315V3, multiclass
            clus
vv           ZFP91 MUTATED ZFP91 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ZFP91 MUTATED     0   0   7   0
  ZFP91 WILD-TYPE   9  67 242  41
D1315V4, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             0              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
  ZFP91 MUTATED     3   3   1
  ZFP91 WILD-TYPE 217  78  65
D1315V5, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  N0             3             217
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1315V6, binary
                 cls
clus                0   1
  ZFP91 MUTATED     6   1
  ZFP91 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      6    1
  ZFP91 WILD-TYPE  279   47
   clus
vv  ZFP91 MUTATED ZFP91 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1315V7, binary
                 cls
clus                0   1
  ZFP91 MUTATED     4   3
  ZFP91 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      4    3
  ZFP91 WILD-TYPE  166  194
        clus
vv       ZFP91 MUTATED ZFP91 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1315V8, binary
                 cls
clus                0   1
  ZFP91 MUTATED     5   1
  ZFP91 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      5    1
  ZFP91 WILD-TYPE  295    7
     clus
vv    ZFP91 MUTATED ZFP91 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D1315V9, binary
                 cls
clus                0   1
  ZFP91 MUTATED     5   2
  ZFP91 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      5    2
  ZFP91 WILD-TYPE  309   46
                               clus
vv                              ZFP91 MUTATED ZFP91 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFP91 MUTATED     6   0   0   0
  ZFP91 WILD-TYPE 253   3  22  21
D1315V10, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1315V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP91 MUTATED                                  0     0
  ZFP91 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZFP91 MUTATED                           1     3
  ZFP91 WILD-TYPE                        18   173
D1315V12, multiclass
                                  clus
vv                                 ZFP91 MUTATED ZFP91 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = OR9Q2 MUTATION ANALYSIS
D1316V1, survival
                 sevent
clus2               0   1
  OR9Q2 MUTATED     8   5
  OR9Q2 WILD-TYPE 269  73
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             13             342 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
              5              73 
$`OR9Q2 MUTATED`
TCGA-AA-3715 TCGA-G4-6310 TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-A010 TCGA-AY-6197 
       19.04        63.62        35.80        63.98        34.98        21.44 
TCGA-AZ-6606 TCGA-CM-5862 TCGA-CM-6680 TCGA-D5-6540 TCGA-DM-A1DB TCGA-DM-A28H 
       11.74         5.03        12.03        16.14        44.32       117.07 
TCGA-G4-6303 
       65.85 

$`OR9Q2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6588 
      100.01         1.94        49.08         5.88        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        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-6717 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17        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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.045 
[1] "5.0 - 117.1 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1316V2, continuous
                 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      63        1       24       104         7         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        18          6         42         32       33        11
                 vv
clus              STAGE IVB
  OR9Q2 MUTATED           0
  OR9Q2 WILD-TYPE         1
D1316V3, multiclass
            clus
vv           OR9Q2 MUTATED OR9Q2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              1              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
  OR9Q2 MUTATED     0   1  11   2
  OR9Q2 WILD-TYPE   9  66 238  39
D1316V4, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             2              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
  OR9Q2 MUTATED     8   3   3
  OR9Q2 WILD-TYPE 212  78  63
D1316V5, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             3              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"
D1316V6, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    10   3
  OR9Q2 WILD-TYPE 275  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     10    3
  OR9Q2 WILD-TYPE  275   45
   clus
vv  OR9Q2 MUTATED OR9Q2 WILD-TYPE
  0            10             275
  1             3              45
[1] 2 2
[1] FALSE
D1316V7, binary
                 cls
clus                0   1
  OR9Q2 MUTATED     5   9
  OR9Q2 WILD-TYPE 165 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED      5    9
  OR9Q2 WILD-TYPE  165  188
        clus
vv       OR9Q2 MUTATED OR9Q2 WILD-TYPE
  FEMALE             5             165
  MALE               9             188
[1] 2 2
[1] FALSE
D1316V8, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    10   1
  OR9Q2 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     10    1
  OR9Q2 WILD-TYPE  290    7
     clus
vv    OR9Q2 MUTATED OR9Q2 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1316V9, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    13   1
  OR9Q2 WILD-TYPE 301  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     13    1
  OR9Q2 WILD-TYPE  301   47
                               clus
vv                              OR9Q2 MUTATED OR9Q2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR9Q2 MUTATED    11   0   0   0
  OR9Q2 WILD-TYPE 248   3  22  21
D1316V10, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D1316V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR9Q2 MUTATED                                  0     0
  OR9Q2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR9Q2 MUTATED                           0    10
  OR9Q2 WILD-TYPE                        19   166
D1316V12, multiclass
                                  clus
vv                                 OR9Q2 MUTATED OR9Q2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1317) Variable = HIST1H2BC MUTATION ANALYSIS
D1317V1, survival
                     sevent
clus2                   0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 273  78
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 351 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  0                  78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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               21.99 
[1] "22.1 - 74.6 (49.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1317V2, continuous
                     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      64        1       25       107         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H2BC MUTATED           0          0          0          1        0
  HIST1H2BC WILD-TYPE        18          6         44         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  HIST1H2BC MUTATED           0         0
  HIST1H2BC WILD-TYPE        12         1
D1317V3, multiclass
            clus
vv           HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  STAGE I                    0                  64
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  1                 107
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 0                  44
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  HIST1H2BC MUTATED     0   0   3   1
  HIST1H2BC WILD-TYPE   9  67 246  40
D1317V4, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  T1                 0                   9
  T2                 0                  67
  T3                 3                 246
  T4                 1                  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
  HIST1H2BC MUTATED     3   0   1
  HIST1H2BC WILD-TYPE 217  81  65
D1317V5, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  N0                 3                 217
  N1                 0                  81
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1317V6, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 281  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  281   48
   clus
vv  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  0                 4                 281
  1                 0                  48
[1] 2 2
[1] FALSE
D1317V7, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     2   2
  HIST1H2BC WILD-TYPE 168 195
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      2    2
  HIST1H2BC WILD-TYPE  168  195
        clus
vv       HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  FEMALE                 2                 168
  MALE                   2                 195
[1] 2 2
[1] FALSE
D1317V8, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 296   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  296    8
     clus
vv    HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  NO                  4                 296
  YES                 0                   8
[1] 2 2
[1] FALSE
D1317V9, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 310  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  310   48
                               clus
vv                              HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  COLON ADENOCARCINOMA                          4                 310
  COLON MUCINOUS ADENOCARCINOMA                 0                  48
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  HIST1H2BC MUTATED     4   0   0   0
  HIST1H2BC WILD-TYPE 255   3  22  21
D1317V10, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  R0                 4                 255
  R1                 0                   3
  R2                 0                  22
  RX                 0                  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"
D1317V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H2BC MUTATED                                  0     0
  HIST1H2BC WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BC MUTATED                           0     2
  HIST1H2BC WILD-TYPE                        19   174
D1317V12, multiclass
[1] "Remove cluster labels:" "HIST1H2BC MUTATED"     
clus
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  2                 204 
         TCGA-A6-2677          TCGA-A6-4105          TCGA-A6-6649 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6548          TCGA-AD-6888          TCGA-AD-6895 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6964          TCGA-AZ-4681          TCGA-AZ-6601 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6608          TCGA-CK-5912          TCGA-DM-A285 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6321          TCGA-G4-6586 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6628 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2678          TCGA-A6-2683 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5656          TCGA-A6-5657 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5660          TCGA-A6-5661 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5662          TCGA-A6-5664          TCGA-A6-5666 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6137          TCGA-A6-6138          TCGA-A6-6141 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6142          TCGA-A6-6648          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-6889          TCGA-AD-6890 
"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-6965          TCGA-AU-3779          TCGA-AU-6004 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4323          TCGA-AZ-4616 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"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-CA-5254          TCGA-CA-5255 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-5796          TCGA-CA-5797          TCGA-CA-6715 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-6716          TCGA-CA-6717          TCGA-CA-6718 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-6719          TCGA-CK-4947          TCGA-CK-4948 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-4950          TCGA-CK-4952          TCGA-CK-5913 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6928          TCGA-D5-6929 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6930          TCGA-D5-6931          TCGA-D5-6932 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-7000          TCGA-DM-A0X9          TCGA-DM-A0XD 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A0XF          TCGA-DM-A1D0          TCGA-DM-A1D4 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1D6          TCGA-DM-A1D7          TCGA-DM-A1D8 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1D9          TCGA-DM-A1DA          TCGA-DM-A1DB 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1HA          TCGA-DM-A1HB          TCGA-DM-A282 
"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-G4-6315 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6323          TCGA-G4-6626 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 

Clustering(1318) Variable = CLK4 MUTATION ANALYSIS
D1318V1, survival
                sevent
clus2              0   1
  CLK4 MUTATED     6   3
  CLK4 WILD-TYPE 271  75
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            346 
  CLK4 MUTATED CLK4 WILD-TYPE 
             3             75 
$`CLK4 MUTATED`
TCGA-A6-5662 TCGA-AA-3518 TCGA-AA-3555 TCGA-AY-6196 TCGA-CA-6718 TCGA-D5-6540 
       23.61         1.02        29.95         0.20        10.06        16.14 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 
       12.59       140.38        31.96 

$`CLK4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
       38.20       130.65        92.75        49.91        13.32         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-F4-6569 
       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CLK4 MUTATED CLK4 WILD-TYPE 
           0.2            0.0 
  CLK4 MUTATED CLK4 WILD-TYPE 
        140.38         148.01 
  CLK4 MUTATED CLK4 WILD-TYPE 
        16.140         22.075 
[1] "0.2 - 140.4 (16.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1318V2, continuous
                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      63        1       26       104         8         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        18          6         43         32       35        11
                vv
clus             STAGE IVB
  CLK4 MUTATED           0
  CLK4 WILD-TYPE         1
D1318V3, multiclass
            clus
vv           CLK4 MUTATED CLK4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  CLK4 MUTATED     0   1   8   0
  CLK4 WILD-TYPE   9  66 241  41
D1318V4, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            0             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
  CLK4 MUTATED     5   2   2
  CLK4 WILD-TYPE 215  79  64
D1318V5, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  N0            5            215
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1318V6, binary
                cls
clus               0   1
  CLK4 MUTATED     6   1
  CLK4 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      6    1
  CLK4 WILD-TYPE  279   47
   clus
vv  CLK4 MUTATED CLK4 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D1318V7, binary
                cls
clus               0   1
  CLK4 MUTATED     5   4
  CLK4 WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      5    4
  CLK4 WILD-TYPE  165  193
        clus
vv       CLK4 MUTATED CLK4 WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D1318V8, binary
                cls
clus               0   1
  CLK4 MUTATED     5   0
  CLK4 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      5    0
  CLK4 WILD-TYPE  295    8
     clus
vv    CLK4 MUTATED CLK4 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1318V9, binary
                cls
clus               0   1
  CLK4 MUTATED     6   3
  CLK4 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      6    3
  CLK4 WILD-TYPE  308   45
                               clus
vv                              CLK4 MUTATED CLK4 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CLK4 MUTATED     5   0   0   1
  CLK4 WILD-TYPE 254   3  22  20
D1318V10, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1318V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLK4 MUTATED                                  0     1
  CLK4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CLK4 MUTATED                           0     6
  CLK4 WILD-TYPE                        19   170
D1318V12, multiclass
                                  clus
vv                                 CLK4 MUTATED CLK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = LPGAT1 MUTATION ANALYSIS
D1319V1, survival
                  sevent
clus2                0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 274  78
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               3              352 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               0               78 
$`LPGAT1 MUTATED`
TCGA-G4-6628 TCGA-D5-5540 TCGA-D5-6533 
       79.69        56.09        25.48 

$`LPGAT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       19.59        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
           25.48             0.00 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
           79.69           148.01 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
           56.09            22.01 
[1] "25.5 - 79.7 (56.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1319V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPGAT1 MUTATED         1        0        0         1         0         0
  LPGAT1 WILD-TYPE      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LPGAT1 MUTATED           0          0          0          0        0
  LPGAT1 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  LPGAT1 MUTATED           0         0
  LPGAT1 WILD-TYPE        12         1
D1319V3, multiclass
[1] "Remove cluster labels:" "LPGAT1 MUTATED"        
clus
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               2              355 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527       TCGA-AA-3530 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-DM-A285       TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-A6-2671       TCGA-A6-2672 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3667       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3712       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3845 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3858       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3980 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-3982       TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6899       TCGA-AD-6965       TCGA-AU-3779 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-CA-5254 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D9 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" "LPGAT1 WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  LPGAT1 MUTATED     0   1   1   1
  LPGAT1 WILD-TYPE   9  66 248  40
D1319V4, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              1              248
  T4              1               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
  LPGAT1 MUTATED     3   0   0
  LPGAT1 WILD-TYPE 217  81  66
D1319V5, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  N0              3              217
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1319V6, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    0
  LPGAT1 WILD-TYPE  282   48
   clus
vv  LPGAT1 MUTATED LPGAT1 WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D1319V7, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     1   2
  LPGAT1 WILD-TYPE 169 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      1    2
  LPGAT1 WILD-TYPE  169  195
        clus
vv       LPGAT1 MUTATED LPGAT1 WILD-TYPE
  FEMALE              1              169
  MALE                2              195
[1] 2 2
[1] FALSE
D1319V8, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    0
  LPGAT1 WILD-TYPE  297    8
     clus
vv    LPGAT1 MUTATED LPGAT1 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1319V9, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    0
  LPGAT1 WILD-TYPE  311   48
                               clus
vv                              LPGAT1 MUTATED LPGAT1 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LPGAT1 MUTATED     3   0   0   0
  LPGAT1 WILD-TYPE 256   3  22  21
D1319V10, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1319V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPGAT1 MUTATED                                  0     0
  LPGAT1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LPGAT1 MUTATED                           0     3
  LPGAT1 WILD-TYPE                        19   173
D1319V12, multiclass
                                  clus
vv                                 LPGAT1 MUTATED LPGAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = C1ORF85 MUTATION ANALYSIS
D1320V1, survival
                   sevent
clus2                 0   1
  C1ORF85 MUTATED     7   0
  C1ORF85 WILD-TYPE 270  78
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                7               348 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                0                78 
$`C1ORF85 MUTATED`
TCGA-G4-6588 TCGA-G4-6628 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5860 
       26.17        79.69        12.16        58.39        12.76        32.02 
TCGA-DM-A282 
      139.17 

$`C1ORF85 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        35.80        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
            12.16              0.00 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
           139.17            148.01 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
            32.02             22.01 
[1] "12.2 - 139.2 (32.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1320V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF85 MUTATED         2        0        0         5         0         0
  C1ORF85 WILD-TYPE      62        1       26       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF85 MUTATED           0          0          0          0        0
  C1ORF85 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF85 MUTATED           0         0
  C1ORF85 WILD-TYPE        12         1
D1320V3, multiclass
            clus
vv           C1ORF85 MUTATED C1ORF85 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C1ORF85 MUTATED     0   2   5   0
  C1ORF85 WILD-TYPE   9  65 244  41
D1320V4, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               0                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
  C1ORF85 MUTATED     7   0   0
  C1ORF85 WILD-TYPE 213  81  66
D1320V5, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  N0               7               213
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1320V6, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     6   0
  C1ORF85 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      6    0
  C1ORF85 WILD-TYPE  279   48
   clus
vv  C1ORF85 MUTATED C1ORF85 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1320V7, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     2   5
  C1ORF85 WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      2    5
  C1ORF85 WILD-TYPE  168  192
        clus
vv       C1ORF85 MUTATED C1ORF85 WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D1320V8, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     6   0
  C1ORF85 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      6    0
  C1ORF85 WILD-TYPE  294    8
     clus
vv    C1ORF85 MUTATED C1ORF85 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1320V9, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     5   2
  C1ORF85 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      5    2
  C1ORF85 WILD-TYPE  309   46
                               clus
vv                              C1ORF85 MUTATED C1ORF85 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C1ORF85 MUTATED     5   0   0   1
  C1ORF85 WILD-TYPE 254   3  22  20
D1320V10, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               1                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"
D1320V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF85 MUTATED                                  0     1
  C1ORF85 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF85 MUTATED                           0     6
  C1ORF85 WILD-TYPE                        19   170
D1320V12, multiclass
                                  clus
vv                                 C1ORF85 MUTATED C1ORF85 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = UGT2A1 MUTATION ANALYSIS
D1321V1, survival
                  sevent
clus2                0   1
  UGT2A1 MUTATED     7   2
  UGT2A1 WILD-TYPE 270  76
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               9              346 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               2               76 
$`UGT2A1 MUTATED`
TCGA-AA-3952 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01R 
        2.01         1.02        53.00        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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           22.045 
[1] "1.0 - 133.2 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1321V2, continuous
                  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      63        1       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT2A1 MUTATED           2          0          0          1        0
  UGT2A1 WILD-TYPE        16          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT2A1 MUTATED           0         0
  UGT2A1 WILD-TYPE        12         1
D1321V3, multiclass
            clus
vv           UGT2A1 MUTATED UGT2A1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  UGT2A1 MUTATED     0   2   6   2
  UGT2A1 WILD-TYPE   9  65 243  39
D1321V4, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              6              243
  T4              2               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
  UGT2A1 MUTATED     7   1   2
  UGT2A1 WILD-TYPE 213  80  64
D1321V5, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1321V6, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     9   0
  UGT2A1 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      9    0
  UGT2A1 WILD-TYPE  276   48
   clus
vv  UGT2A1 MUTATED UGT2A1 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1321V7, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     5   5
  UGT2A1 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      5    5
  UGT2A1 WILD-TYPE  165  192
        clus
vv       UGT2A1 MUTATED UGT2A1 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D1321V8, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     7   1
  UGT2A1 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      7    1
  UGT2A1 WILD-TYPE  293    7
     clus
vv    UGT2A1 MUTATED UGT2A1 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D1321V9, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     7   3
  UGT2A1 WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      7    3
  UGT2A1 WILD-TYPE  307   45
                               clus
vv                              UGT2A1 MUTATED UGT2A1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UGT2A1 MUTATED     8   0   0   1
  UGT2A1 WILD-TYPE 251   3  22  20
D1321V10, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              1               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"
D1321V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT2A1 MUTATED                                  0     1
  UGT2A1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT2A1 MUTATED                           0     2
  UGT2A1 WILD-TYPE                        19   174
D1321V12, multiclass
                                  clus
vv                                 UGT2A1 MUTATED UGT2A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1322) Variable = TMEM229B MUTATION ANALYSIS
D1322V1, survival
                    sevent
clus2                  0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 273  78
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                351 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 0                 78 
$`TMEM229B MUTATED`
TCGA-AD-6895 TCGA-AD-6890 TCGA-CM-4746 TCGA-CM-5344 
       25.08        24.53        37.02        22.03 

$`TMEM229B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TMEM229B MUTATED TMEM229B WILD-TYPE 
             22.03               0.00 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
             37.02             148.01 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
            24.805             21.990 
[1] "22.0 - 37.0 (24.8)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1322V2, continuous
                    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      63        1       26       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM229B MUTATED           0          0          2          0        0
  TMEM229B WILD-TYPE        18          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  TMEM229B MUTATED           0         0
  TMEM229B WILD-TYPE        12         1
D1322V3, multiclass
            clus
vv           TMEM229B MUTATED TMEM229B WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 0                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  TMEM229B MUTATED     1   1   2   0
  TMEM229B WILD-TYPE   8  66 247  41
D1322V4, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  T1                1                  8
  T2                1                 66
  T3                2                247
  T4                0                 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
  TMEM229B MUTATED     2   2   0
  TMEM229B WILD-TYPE 218  79  66
D1322V5, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  N0                2                218
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1322V6, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     3   0
  TMEM229B WILD-TYPE 282  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      3    0
  TMEM229B WILD-TYPE  282   48
   clus
vv  TMEM229B MUTATED TMEM229B WILD-TYPE
  0                3                282
  1                0                 48
[1] 2 2
[1] FALSE
D1322V7, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     1   3
  TMEM229B WILD-TYPE 169 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      1    3
  TMEM229B WILD-TYPE  169  194
        clus
vv       TMEM229B MUTATED TMEM229B WILD-TYPE
  FEMALE                1                169
  MALE                  3                194
[1] 2 2
[1] FALSE
D1322V8, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 296   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      4    0
  TMEM229B WILD-TYPE  296    8
     clus
vv    TMEM229B MUTATED TMEM229B WILD-TYPE
  NO                 4                296
  YES                0                  8
[1] 2 2
[1] FALSE
D1322V9, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 310  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      4    0
  TMEM229B WILD-TYPE  310   48
                               clus
vv                              TMEM229B MUTATED TMEM229B WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TMEM229B MUTATED     3   0   0   0
  TMEM229B WILD-TYPE 256   3  22  21
D1322V10, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1322V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM229B MUTATED                                  0     0
  TMEM229B WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMEM229B MUTATED                           1     3
  TMEM229B WILD-TYPE                        18   173
D1322V12, multiclass
                                  clus
vv                                 TMEM229B MUTATED TMEM229B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           3                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1323) Variable = FSHR MUTATION ANALYSIS
D1323V1, survival
                sevent
clus2              0   1
  FSHR MUTATED    11   3
  FSHR WILD-TYPE 266  75
  FSHR MUTATED FSHR WILD-TYPE 
            14            341 
  FSHR MUTATED FSHR WILD-TYPE 
             3             75 
$`FSHR MUTATED`
TCGA-A6-6649 TCGA-AA-3662 TCGA-A6-5657 TCGA-A6-5666 TCGA-AA-3710 TCGA-AA-A00J 
       24.16         6.05        31.63        32.71        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 
       14.04        11.01 

$`FSHR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09        16.31        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  FSHR MUTATED FSHR WILD-TYPE 
          0.95           0.00 
  FSHR MUTATED FSHR WILD-TYPE 
         34.98         148.01 
  FSHR MUTATED FSHR WILD-TYPE 
        16.045         22.090 
[1] "0.9 - 35.0 (16.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1323V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FSHR MUTATED         2        0        0         4         2         1
  FSHR WILD-TYPE      62        1       26       104         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FSHR MUTATED           0          0          4          0        2         0
  FSHR WILD-TYPE        18          6         40         33       33        12
                vv
clus             STAGE IVB
  FSHR MUTATED           0
  FSHR WILD-TYPE         1
D1323V3, multiclass
            clus
vv           FSHR MUTATED FSHR WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  FSHR MUTATED     1   1   7   6
  FSHR WILD-TYPE   8  66 242  35
D1323V4, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  T1            1              8
  T2            1             66
  T3            7            242
  T4            6             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
  FSHR MUTATED     9   4   2
  FSHR WILD-TYPE 211  77  64
D1323V5, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  N0            9            211
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1323V6, binary
                cls
clus               0   1
  FSHR MUTATED    12   2
  FSHR WILD-TYPE 273  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     12    2
  FSHR WILD-TYPE  273   46
   clus
vv  FSHR MUTATED FSHR WILD-TYPE
  0           12            273
  1            2             46
[1] 2 2
[1] FALSE
D1323V7, binary
                cls
clus               0   1
  FSHR MUTATED     8   7
  FSHR WILD-TYPE 162 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED      8    7
  FSHR WILD-TYPE  162  190
        clus
vv       FSHR MUTATED FSHR WILD-TYPE
  FEMALE            8            162
  MALE              7            190
[1] 2 2
[1] FALSE
D1323V8, binary
                cls
clus               0   1
  FSHR MUTATED    13   0
  FSHR WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     13    0
  FSHR WILD-TYPE  287    8
     clus
vv    FSHR MUTATED FSHR WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D1323V9, binary
                cls
clus               0   1
  FSHR MUTATED    11   3
  FSHR WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     11    3
  FSHR WILD-TYPE  303   45
                               clus
vv                              FSHR MUTATED FSHR WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FSHR MUTATED    10   0   1   1
  FSHR WILD-TYPE 249   3  21  20
D1323V10, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            1             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"
D1323V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FSHR MUTATED                                  0     1
  FSHR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FSHR MUTATED                           1     7
  FSHR WILD-TYPE                        18   169
D1323V12, multiclass
                                  clus
vv                                 FSHR MUTATED FSHR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = VEPH1 MUTATION ANALYSIS
D1324V1, survival
                 sevent
clus2               0   1
  VEPH1 MUTATED    12   4
  VEPH1 WILD-TYPE 265  74
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             16             339 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              4              74 
$`VEPH1 MUTATED`
TCGA-AA-3554 TCGA-AA-3715 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3815 
       17.95        19.04        24.39        20.12        29.95        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 
       25.48        11.64        81.37        85.48 

$`VEPH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F 
       44.32       131.51       135.65       139.17       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  VEPH1 MUTATED VEPH1 WILD-TYPE 
              0               0 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
          85.48          148.01 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
         21.585          22.060 
[1] "0.0 - 85.5 (21.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1324V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VEPH1 MUTATED         2        0        1        11         1         0
  VEPH1 WILD-TYPE      62        1       25        97         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VEPH1 MUTATED           0          0          1          0        0         0
  VEPH1 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  VEPH1 MUTATED           0
  VEPH1 WILD-TYPE         1
D1324V3, multiclass
            clus
vv           VEPH1 MUTATED VEPH1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             11              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  VEPH1 MUTATED     0   2  13   2
  VEPH1 WILD-TYPE   9  65 236  39
D1324V4, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            13             236
  T4             2              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
  VEPH1 MUTATED    16   1   0
  VEPH1 WILD-TYPE 204  80  66
D1324V5, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  N0            16             204
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1324V6, binary
                 cls
clus                0   1
  VEPH1 MUTATED    15   0
  VEPH1 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     15    0
  VEPH1 WILD-TYPE  270   48
   clus
vv  VEPH1 MUTATED VEPH1 WILD-TYPE
  0            15             270
  1             0              48
[1] 2 2
[1] FALSE
D1324V7, binary
                 cls
clus                0   1
  VEPH1 MUTATED     7  10
  VEPH1 WILD-TYPE 163 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED      7   10
  VEPH1 WILD-TYPE  163  187
        clus
vv       VEPH1 MUTATED VEPH1 WILD-TYPE
  FEMALE             7             163
  MALE              10             187
[1] 2 2
[1] FALSE
D1324V8, binary
                 cls
clus                0   1
  VEPH1 MUTATED    14   0
  VEPH1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     14    0
  VEPH1 WILD-TYPE  286    8
     clus
vv    VEPH1 MUTATED VEPH1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1324V9, binary
                 cls
clus                0   1
  VEPH1 MUTATED    13   4
  VEPH1 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     13    4
  VEPH1 WILD-TYPE  301   44
                               clus
vv                              VEPH1 MUTATED VEPH1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VEPH1 MUTATED    11   0   0   3
  VEPH1 WILD-TYPE 248   3  22  18
D1324V10, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             3              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"
D1324V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VEPH1 MUTATED                                  0     2
  VEPH1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VEPH1 MUTATED                           1     8
  VEPH1 WILD-TYPE                        18   168
D1324V12, multiclass
                                  clus
vv                                 VEPH1 MUTATED VEPH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = IFITM5 MUTATION ANALYSIS
D1325V1, survival
                  sevent
clus2                0   1
  IFITM5 MUTATED     2   1
  IFITM5 WILD-TYPE 275  77
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               3              352 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               1               77 
$`IFITM5 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-D5-6922 
       24.39         3.02        10.13 

$`IFITM5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  IFITM5 MUTATED IFITM5 WILD-TYPE 
            3.02             0.00 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
           24.39           148.01 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
          10.130           22.075 
[1] "3.0 - 24.4 (10.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.1"
D1325V2, continuous
                  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      63        1       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM5 MUTATED           0          1          0          0        0
  IFITM5 WILD-TYPE        18          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  IFITM5 MUTATED           0         0
  IFITM5 WILD-TYPE        12         1
D1325V3, multiclass
            clus
vv           IFITM5 MUTATED IFITM5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  IFITM5 MUTATED     0   1   2   0
  IFITM5 WILD-TYPE   9  66 247  41
D1325V4, multiclass
    clus
vv   IFITM5 MUTATED IFITM5 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              2              247
  T4              0               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
  IFITM5 MUTATED     2   1   0
  IFITM5 WILD-TYPE 218  80  66
D1325V5, multiclass
    clus
vv   IFITM5 MUTATED IFITM5 WILD-TYPE
  N0              2              218
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1325V6, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   0
  IFITM5 WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    0
  IFITM5 WILD-TYPE  282   48
   clus
vv  IFITM5 MUTATED IFITM5 WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D1325V7, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     1   2
  IFITM5 WILD-TYPE 169 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      1    2
  IFITM5 WILD-TYPE  169  195
        clus
vv       IFITM5 MUTATED IFITM5 WILD-TYPE
  FEMALE              1              169
  MALE                2              195
[1] 2 2
[1] FALSE
D1325V8, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   0
  IFITM5 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    0
  IFITM5 WILD-TYPE  297    8
     clus
vv    IFITM5 MUTATED IFITM5 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1325V9, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   0
  IFITM5 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    0
  IFITM5 WILD-TYPE  311   48
                               clus
vv                              IFITM5 MUTATED IFITM5 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IFITM5 MUTATED     2   0   0   0
  IFITM5 WILD-TYPE 257   3  22  21
D1325V10, multiclass
[1] "Remove cluster labels:" "IFITM5 MUTATED"        
clus
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               2              303 
      TCGA-A6-2677       TCGA-AA-3496       TCGA-AA-3520       TCGA-AA-3521 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-2676       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-3502       TCGA-AA-3510       TCGA-AA-3511 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518       TCGA-AA-3519 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532       TCGA-AA-3534 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544       TCGA-AA-3548 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555       TCGA-AA-3558 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660       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-3673 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693       TCGA-AA-3695 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3811 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3842       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-3861 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       TCGA-AA-3872 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3941 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N       TCGA-AA-A00O 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"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-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6889 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682       TCGA-CA-5254 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
D1325V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFITM5 MUTATED                                  0     0
  IFITM5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFITM5 MUTATED                           0     2
  IFITM5 WILD-TYPE                        19   174
D1325V12, multiclass
[1] "Remove cluster labels:" "IFITM5 MUTATED"        
clus
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 

Clustering(1326) Variable = SBSN MUTATION ANALYSIS
D1326V1, survival
                sevent
clus2              0   1
  SBSN MUTATED     8   2
  SBSN WILD-TYPE 269  76
  SBSN MUTATED SBSN WILD-TYPE 
            10            345 
  SBSN MUTATED SBSN WILD-TYPE 
             2             76 
$`SBSN MUTATED`
TCGA-AA-3554 TCGA-AD-6895 TCGA-AA-3655 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E 
       17.95        25.08        61.02        25.02        38.04        30.02 
TCGA-AD-5900 TCGA-AZ-6600 TCGA-CM-6171 TCGA-DM-A28F 
       12.16        12.10        14.04        35.97 

$`SBSN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        27.02        27.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SBSN MUTATED SBSN WILD-TYPE 
          12.1            0.0 
  SBSN MUTATED SBSN WILD-TYPE 
         61.02         148.01 
  SBSN MUTATED SBSN WILD-TYPE 
         25.05          22.03 
[1] "12.1 - 61.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1326V2, continuous
                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      62        1       25       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBSN MUTATED           0          0          2          0        1         0
  SBSN WILD-TYPE        18          6         42         33       34        12
                vv
clus             STAGE IVB
  SBSN MUTATED           0
  SBSN WILD-TYPE         1
D1326V3, multiclass
            clus
vv           SBSN MUTATED SBSN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  SBSN MUTATED     0   3   6   1
  SBSN WILD-TYPE   9  64 243  40
D1326V4, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  T1            0              9
  T2            3             64
  T3            6            243
  T4            1             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
  SBSN MUTATED     7   3   0
  SBSN WILD-TYPE 213  78  66
D1326V5, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  N0            7            213
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1326V6, binary
                cls
clus               0   1
  SBSN MUTATED     7   1
  SBSN WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      7    1
  SBSN WILD-TYPE  278   47
   clus
vv  SBSN MUTATED SBSN WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D1326V7, binary
                cls
clus               0   1
  SBSN MUTATED     2   8
  SBSN WILD-TYPE 168 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      2    8
  SBSN WILD-TYPE  168  189
        clus
vv       SBSN MUTATED SBSN WILD-TYPE
  FEMALE            2            168
  MALE              8            189
[1] 2 2
[1] FALSE
D1326V8, binary
                cls
clus               0   1
  SBSN MUTATED     9   0
  SBSN WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      9    0
  SBSN WILD-TYPE  291    8
     clus
vv    SBSN MUTATED SBSN WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1326V9, binary
                cls
clus               0   1
  SBSN MUTATED     9   1
  SBSN WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      9    1
  SBSN WILD-TYPE  305   47
                               clus
vv                              SBSN MUTATED SBSN WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SBSN MUTATED     7   0   0   0
  SBSN WILD-TYPE 252   3  22  21
D1326V10, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            0             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"
D1326V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBSN MUTATED                                  0     0
  SBSN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBSN MUTATED                           1     4
  SBSN WILD-TYPE                        18   172
D1326V12, multiclass
                                  clus
vv                                 SBSN MUTATED SBSN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = RUSC2 MUTATION ANALYSIS
D1327V1, survival
                 sevent
clus2               0   1
  RUSC2 MUTATED    10   1
  RUSC2 WILD-TYPE 267  77
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             11             344 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              1              77 
$`RUSC2 MUTATED`
TCGA-AA-3715 TCGA-A6-6648 TCGA-AA-3819 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A010 
       19.04        25.18        25.02        53.00        18.05        34.98 
TCGA-AD-5900 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6674 TCGA-DM-A1HB 
       12.16        85.45        37.02        12.95       135.65 

$`RUSC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RUSC2 MUTATED RUSC2 WILD-TYPE 
          12.16            0.00 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
         135.65          148.01 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          25.18           22.01 
[1] "12.2 - 135.7 (25.2)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.4"
D1327V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUSC2 MUTATED         2        0        2         2         2         0
  RUSC2 WILD-TYPE      62        1       24       106         6         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        18          6         41         33       35        11
                 vv
clus              STAGE IVB
  RUSC2 MUTATED           0
  RUSC2 WILD-TYPE         1
D1327V3, multiclass
            clus
vv           RUSC2 MUTATED RUSC2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  RUSC2 MUTATED     0   2   7   3
  RUSC2 WILD-TYPE   9  65 242  38
D1327V4, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             3              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
  RUSC2 MUTATED     9   3   0
  RUSC2 WILD-TYPE 211  78  66
D1327V5, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  N0             9             211
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1327V6, binary
                 cls
clus                0   1
  RUSC2 MUTATED     9   1
  RUSC2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      9    1
  RUSC2 WILD-TYPE  276   47
   clus
vv  RUSC2 MUTATED RUSC2 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1327V7, binary
                 cls
clus                0   1
  RUSC2 MUTATED     4   8
  RUSC2 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      4    8
  RUSC2 WILD-TYPE  166  189
        clus
vv       RUSC2 MUTATED RUSC2 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D1327V8, binary
                 cls
clus                0   1
  RUSC2 MUTATED    10   0
  RUSC2 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     10    0
  RUSC2 WILD-TYPE  290    8
     clus
vv    RUSC2 MUTATED RUSC2 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1327V9, binary
                 cls
clus                0   1
  RUSC2 MUTATED     8   3
  RUSC2 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      8    3
  RUSC2 WILD-TYPE  306   45
                               clus
vv                              RUSC2 MUTATED RUSC2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUSC2 MUTATED     8   1   0   1
  RUSC2 WILD-TYPE 251   2  22  20
D1327V10, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  R0             8             251
  R1             1               2
  R2             0              22
  RX             1              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"
D1327V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUSC2 MUTATED                                  0     0
  RUSC2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUSC2 MUTATED                           2     5
  RUSC2 WILD-TYPE                        17   171
D1327V12, multiclass
                                  clus
vv                                 RUSC2 MUTATED RUSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = CLVS1 MUTATION ANALYSIS
D1328V1, survival
                 sevent
clus2               0   1
  CLVS1 MUTATED     8   2
  CLVS1 WILD-TYPE 269  76
  CLVS1 MUTATED CLVS1 WILD-TYPE 
             10             345 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
              2              76 
$`CLVS1 MUTATED`
TCGA-AA-3516 TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A01Z TCGA-CA-6717 
       13.02        32.71        63.98        53.00        37.02        12.76 
TCGA-CM-6168 TCGA-CM-6676 TCGA-D5-6532 TCGA-DM-A1D8 
       12.99        11.08        18.25        12.59 

$`CLVS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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-A029 
       35.01         1.02        33.04         1.02        26.01        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CLVS1 MUTATED CLVS1 WILD-TYPE 
          11.08            0.00 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
          63.98          148.01 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
         15.635          22.090 
[1] "11.1 - 64.0 (15.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1328V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLVS1 MUTATED         1        0        3         3         0         1
  CLVS1 WILD-TYPE      63        1       23       105         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLVS1 MUTATED           1          0          0          0        0         0
  CLVS1 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  CLVS1 MUTATED           0
  CLVS1 WILD-TYPE         1
D1328V3, multiclass
            clus
vv           CLVS1 MUTATED CLVS1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CLVS1 MUTATED     0   1   8   1
  CLVS1 WILD-TYPE   9  66 241  40
D1328V4, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             1              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
  CLVS1 MUTATED     8   1   1
  CLVS1 WILD-TYPE 212  80  65
D1328V5, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1328V6, binary
                 cls
clus                0   1
  CLVS1 MUTATED     9   0
  CLVS1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      9    0
  CLVS1 WILD-TYPE  276   48
   clus
vv  CLVS1 MUTATED CLVS1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1328V7, binary
                 cls
clus                0   1
  CLVS1 MUTATED     3   7
  CLVS1 WILD-TYPE 167 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      3    7
  CLVS1 WILD-TYPE  167  190
        clus
vv       CLVS1 MUTATED CLVS1 WILD-TYPE
  FEMALE             3             167
  MALE               7             190
[1] 2 2
[1] FALSE
D1328V8, binary
                 cls
clus                0   1
  CLVS1 MUTATED     9   0
  CLVS1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      9    0
  CLVS1 WILD-TYPE  291    8
     clus
vv    CLVS1 MUTATED CLVS1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1328V9, binary
                 cls
clus                0   1
  CLVS1 MUTATED     8   2
  CLVS1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      8    2
  CLVS1 WILD-TYPE  306   46
                               clus
vv                              CLVS1 MUTATED CLVS1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLVS1 MUTATED     6   0   0   1
  CLVS1 WILD-TYPE 253   3  22  20
D1328V10, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1328V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLVS1 MUTATED                                  0     1
  CLVS1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLVS1 MUTATED                           1     4
  CLVS1 WILD-TYPE                        18   172
D1328V12, multiclass
                                  clus
vv                                 CLVS1 MUTATED CLVS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = FOXA2 MUTATION ANALYSIS
D1329V1, survival
                 sevent
clus2               0   1
  FOXA2 MUTATED     5   0
  FOXA2 WILD-TYPE 272  78
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              5             350 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              0              78 
$`FOXA2 MUTATED`
TCGA-AA-3844 TCGA-AA-3660 TCGA-AA-3663 TCGA-D5-5539 TCGA-DM-A282 
       14.93        78.08         6.97        19.59       139.17 

$`FOXA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FOXA2 MUTATED FOXA2 WILD-TYPE 
           6.97            0.00 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
         139.17          148.01 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
         19.590          22.075 
[1] "7.0 - 139.2 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9400000"
D1329V2, continuous
                 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      64        1       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXA2 MUTATED           0          1          0          1        0         0
  FOXA2 WILD-TYPE        18          5         44         32       35        12
                 vv
clus              STAGE IVB
  FOXA2 MUTATED           0
  FOXA2 WILD-TYPE         1
D1329V3, multiclass
            clus
vv           FOXA2 MUTATED FOXA2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  FOXA2 MUTATED     0   0   5   1
  FOXA2 WILD-TYPE   9  67 244  40
D1329V4, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             1              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
  FOXA2 MUTATED     4   1   1
  FOXA2 WILD-TYPE 216  80  65
D1329V5, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1329V6, binary
                 cls
clus                0   1
  FOXA2 MUTATED     5   0
  FOXA2 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      5    0
  FOXA2 WILD-TYPE  280   48
   clus
vv  FOXA2 MUTATED FOXA2 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1329V7, binary
                 cls
clus                0   1
  FOXA2 MUTATED     4   2
  FOXA2 WILD-TYPE 166 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      4    2
  FOXA2 WILD-TYPE  166  195
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  FEMALE             4             166
  MALE               2             195
[1] 2 2
[1] FALSE
D1329V8, binary
                 cls
clus                0   1
  FOXA2 MUTATED     3   1
  FOXA2 WILD-TYPE 297   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      3    1
  FOXA2 WILD-TYPE  297    7
     clus
vv    FOXA2 MUTATED FOXA2 WILD-TYPE
  NO              3             297
  YES             1               7
[1] 2 2
[1] FALSE
D1329V9, binary
                 cls
clus                0   1
  FOXA2 MUTATED     5   1
  FOXA2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      5    1
  FOXA2 WILD-TYPE  309   47
                               clus
vv                              FOXA2 MUTATED FOXA2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXA2 MUTATED     4   0   0   1
  FOXA2 WILD-TYPE 255   3  22  20
D1329V10, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1329V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXA2 MUTATED                                  0     0
  FOXA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXA2 MUTATED                           0     3
  FOXA2 WILD-TYPE                        19   173
D1329V12, multiclass
                                  clus
vv                                 FOXA2 MUTATED FOXA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1330) Variable = FAM70A MUTATION ANALYSIS
D1330V1, survival
                  sevent
clus2                0   1
  FAM70A MUTATED     4   3
  FAM70A WILD-TYPE 273  75
  FAM70A MUTATED FAM70A WILD-TYPE 
               7              348 
  FAM70A MUTATED FAM70A WILD-TYPE 
               3               75 
$`FAM70A MUTATED`
TCGA-AA-3660 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6537 
       78.08         4.01        83.24        58.39        12.76         4.80 
TCGA-G4-6317 
       36.00 

$`FAM70A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        61.91        13.78        46.75 

  FAM70A MUTATED FAM70A WILD-TYPE 
            4.01             0.00 
  FAM70A MUTATED FAM70A WILD-TYPE 
           83.24           148.01 
  FAM70A MUTATED FAM70A WILD-TYPE 
          36.000           22.045 
[1] "4.0 - 83.2 (36.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1330V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM70A MUTATED         0        0        1         3         1         0
  FAM70A WILD-TYPE      64        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM70A MUTATED           0          0          1          1        0
  FAM70A WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM70A MUTATED           0         0
  FAM70A WILD-TYPE        12         1
D1330V3, multiclass
            clus
vv           FAM70A MUTATED FAM70A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  FAM70A MUTATED     0   0   6   1
  FAM70A WILD-TYPE   9  67 243  40
D1330V4, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              1               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
  FAM70A MUTATED     5   1   1
  FAM70A WILD-TYPE 215  80  65
D1330V5, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  N0              5              215
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1330V6, binary
                  cls
clus                 0   1
  FAM70A MUTATED     5   0
  FAM70A WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      5    0
  FAM70A WILD-TYPE  280   48
   clus
vv  FAM70A MUTATED FAM70A WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1330V7, binary
                  cls
clus                 0   1
  FAM70A MUTATED     2   5
  FAM70A WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      2    5
  FAM70A WILD-TYPE  168  192
        clus
vv       FAM70A MUTATED FAM70A WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1330V8, binary
                  cls
clus                 0   1
  FAM70A MUTATED     6   0
  FAM70A WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      6    0
  FAM70A WILD-TYPE  294    8
     clus
vv    FAM70A MUTATED FAM70A WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1330V9, binary
                  cls
clus                 0   1
  FAM70A MUTATED     5   2
  FAM70A WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      5    2
  FAM70A WILD-TYPE  309   46
                               clus
vv                              FAM70A MUTATED FAM70A WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM70A MUTATED     6   0   0   1
  FAM70A WILD-TYPE 253   3  22  20
D1330V10, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1330V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM70A MUTATED                                  0     2
  FAM70A WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM70A MUTATED                           0     3
  FAM70A WILD-TYPE                        19   173
D1330V12, multiclass
                                  clus
vv                                 FAM70A MUTATED FAM70A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = MAOB MUTATION ANALYSIS
D1331V1, survival
                sevent
clus2              0   1
  MAOB MUTATED     6   0
  MAOB WILD-TYPE 271  78
  MAOB MUTATED MAOB WILD-TYPE 
             6            349 
  MAOB MUTATED MAOB WILD-TYPE 
             0             78 
$`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 

$`MAOB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MAOB MUTATED MAOB WILD-TYPE 
         11.01           0.00 
  MAOB MUTATED MAOB WILD-TYPE 
         24.00         148.01 
  MAOB MUTATED MAOB WILD-TYPE 
         18.23          22.09 
[1] "11.0 - 24.0 (18.2)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1331V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAOB MUTATED         0        0        0         5         0         0
  MAOB WILD-TYPE      64        1       26       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAOB MUTATED           0          0          0          0        0         1
  MAOB WILD-TYPE        18          6         44         33       35        11
                vv
clus             STAGE IVB
  MAOB MUTATED           0
  MAOB WILD-TYPE         1
D1331V3, multiclass
            clus
vv           MAOB MUTATED MAOB WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  MAOB MUTATED     0   0   5   1
  MAOB WILD-TYPE   9  67 244  40
D1331V4, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            1             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
  MAOB MUTATED     5   1   0
  MAOB WILD-TYPE 215  80  66
D1331V5, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  N0            5            215
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1331V6, binary
                cls
clus               0   1
  MAOB MUTATED     4   1
  MAOB WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      4    1
  MAOB WILD-TYPE  281   47
   clus
vv  MAOB MUTATED MAOB WILD-TYPE
  0            4            281
  1            1             47
[1] 2 2
[1] FALSE
D1331V7, binary
                cls
clus               0   1
  MAOB MUTATED     4   2
  MAOB WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      4    2
  MAOB WILD-TYPE  166  195
        clus
vv       MAOB MUTATED MAOB WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D1331V8, binary
                cls
clus               0   1
  MAOB MUTATED     6   0
  MAOB WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      6    0
  MAOB WILD-TYPE  294    8
     clus
vv    MAOB MUTATED MAOB WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1331V9, binary
                cls
clus               0   1
  MAOB MUTATED     5   1
  MAOB WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      5    1
  MAOB WILD-TYPE  309   47
                               clus
vv                              MAOB MUTATED MAOB WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAOB MUTATED     6   0   0   0
  MAOB WILD-TYPE 253   3  22  21
D1331V10, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D1331V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAOB MUTATED                                  0     0
  MAOB WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAOB MUTATED                           0     5
  MAOB WILD-TYPE                        19   171
D1331V12, multiclass
                                  clus
vv                                 MAOB MUTATED MAOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = CCDC6 MUTATION ANALYSIS
D1332V1, survival
                 sevent
clus2               0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 266  78
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             344 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              0              78 
$`CCDC6 MUTATED`
TCGA-G4-6586 TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3947 TCGA-AY-6386 
       35.80        22.52        63.98         1.02        33.01        17.82 
TCGA-CM-4743 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6538 TCGA-G4-6304 
       23.05        12.99        12.95        17.13        53.62 

$`CCDC6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01         6.97        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  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          22.045 
[1] "1.0 - 64.0 (22.5)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "2.5e+07"
D1332V2, continuous
                 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      62        1       25       104         6         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  CCDC6 MUTATED           0
  CCDC6 WILD-TYPE         1
D1332V3, multiclass
            clus
vv           CCDC6 MUTATED CCDC6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CCDC6 MUTATED     0   2   7   2
  CCDC6 WILD-TYPE   9  65 242  39
D1332V4, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             2              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
  CCDC6 MUTATED     9   1   1
  CCDC6 WILD-TYPE 211  80  65
D1332V5, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1332V6, binary
                 cls
clus                0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     11    0
  CCDC6 WILD-TYPE  274   48
   clus
vv  CCDC6 MUTATED CCDC6 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1332V7, binary
                 cls
clus                0   1
  CCDC6 MUTATED     7   4
  CCDC6 WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED      7    4
  CCDC6 WILD-TYPE  163  193
        clus
vv       CCDC6 MUTATED CCDC6 WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D1332V8, binary
                 cls
clus                0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     11    0
  CCDC6 WILD-TYPE  289    8
     clus
vv    CCDC6 MUTATED CCDC6 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1332V9, binary
                 cls
clus                0   1
  CCDC6 MUTATED    10   1
  CCDC6 WILD-TYPE 304  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     10    1
  CCDC6 WILD-TYPE  304   47
                               clus
vv                              CCDC6 MUTATED CCDC6 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCDC6 MUTATED    10   0   0   0
  CCDC6 WILD-TYPE 249   3  22  21
D1332V10, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D1332V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC6 MUTATED                                  0     0
  CCDC6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCDC6 MUTATED                           2     6
  CCDC6 WILD-TYPE                        17   170
D1332V12, multiclass
                                  clus
vv                                 CCDC6 MUTATED CCDC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        6             170
[1] 4 2
[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 = WNK4 MUTATION ANALYSIS
D1333V1, survival
                sevent
clus2              0   1
  WNK4 MUTATED    10   1
  WNK4 WILD-TYPE 267  77
  WNK4 MUTATED WNK4 WILD-TYPE 
            11            344 
  WNK4 MUTATED WNK4 WILD-TYPE 
             1             77 
$`WNK4 MUTATED`
TCGA-AA-3950 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 
       24.00        24.39         3.02         6.97        53.00        31.00 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-6747 TCGA-D5-6928 TCGA-D5-6930 
       27.09        58.39        82.95        11.64        13.35 

$`WNK4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  WNK4 MUTATED WNK4 WILD-TYPE 
          3.02           0.00 
  WNK4 MUTATED WNK4 WILD-TYPE 
         82.95         148.01 
  WNK4 MUTATED WNK4 WILD-TYPE 
         24.39          22.01 
[1] "3.0 - 83.0 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.7"
D1333V2, continuous
                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      61        1       23       103         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  WNK4 MUTATED           0
  WNK4 WILD-TYPE         1
D1333V3, multiclass
            clus
vv           WNK4 MUTATED WNK4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  WNK4 MUTATED     1   2   8   0
  WNK4 WILD-TYPE   8  65 241  41
D1333V4, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            8            241
  T4            0             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
  WNK4 MUTATED    11   0   0
  WNK4 WILD-TYPE 209  81  66
D1333V5, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  N0           11            209
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1333V6, binary
                cls
clus               0   1
  WNK4 MUTATED    10   0
  WNK4 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     10    0
  WNK4 WILD-TYPE  275   48
   clus
vv  WNK4 MUTATED WNK4 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1333V7, binary
                cls
clus               0   1
  WNK4 MUTATED     5   6
  WNK4 WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      5    6
  WNK4 WILD-TYPE  165  191
        clus
vv       WNK4 MUTATED WNK4 WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D1333V8, binary
                cls
clus               0   1
  WNK4 MUTATED    10   0
  WNK4 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     10    0
  WNK4 WILD-TYPE  290    8
     clus
vv    WNK4 MUTATED WNK4 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1333V9, binary
                cls
clus               0   1
  WNK4 MUTATED     7   4
  WNK4 WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      7    4
  WNK4 WILD-TYPE  307   44
                               clus
vv                              WNK4 MUTATED WNK4 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNK4 MUTATED     9   0   0   1
  WNK4 WILD-TYPE 250   3  22  20
D1333V10, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            1             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"
D1333V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK4 MUTATED                                  0     0
  WNK4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK4 MUTATED                           0     6
  WNK4 WILD-TYPE                        19   170
D1333V12, multiclass
                                  clus
vv                                 WNK4 MUTATED WNK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = METT5D1 MUTATION ANALYSIS
D1334V1, survival
                   sevent
clus2                 0   1
  METT5D1 MUTATED     6   0
  METT5D1 WILD-TYPE 271  78
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                6               349 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                0                78 
$`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 

$`METT5D1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       44.32       131.51        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  METT5D1 MUTATED METT5D1 WILD-TYPE 
             2.01              0.00 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
           139.17            148.01 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
            59.62             22.03 
[1] "2.0 - 139.2 (59.6)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.7e+07"
D1334V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METT5D1 MUTATED         0        0        0         3         0         0
  METT5D1 WILD-TYPE      64        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METT5D1 MUTATED           0          0          1          1        0
  METT5D1 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  METT5D1 MUTATED           0         0
  METT5D1 WILD-TYPE        12         1
D1334V3, multiclass
            clus
vv           METT5D1 MUTATED METT5D1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  METT5D1 MUTATED     0   1   5   0
  METT5D1 WILD-TYPE   9  66 244  41
D1334V4, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               0                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
  METT5D1 MUTATED     4   1   1
  METT5D1 WILD-TYPE 216  80  65
D1334V5, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1334V6, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     5   0
  METT5D1 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      5    0
  METT5D1 WILD-TYPE  280   48
   clus
vv  METT5D1 MUTATED METT5D1 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1334V7, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     2   4
  METT5D1 WILD-TYPE 168 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      2    4
  METT5D1 WILD-TYPE  168  193
        clus
vv       METT5D1 MUTATED METT5D1 WILD-TYPE
  FEMALE               2               168
  MALE                 4               193
[1] 2 2
[1] FALSE
D1334V8, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     3   0
  METT5D1 WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      3    0
  METT5D1 WILD-TYPE  297    8
     clus
vv    METT5D1 MUTATED METT5D1 WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D1334V9, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     4   1
  METT5D1 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      4    1
  METT5D1 WILD-TYPE  310   47
                               clus
vv                              METT5D1 MUTATED METT5D1 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  METT5D1 MUTATED     3   0   0   0
  METT5D1 WILD-TYPE 256   3  22  21
D1334V10, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D1334V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METT5D1 MUTATED                                  0     0
  METT5D1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  METT5D1 MUTATED                           0     5
  METT5D1 WILD-TYPE                        19   171
D1334V12, multiclass
                                  clus
vv                                 METT5D1 MUTATED METT5D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = SCYL2 MUTATION ANALYSIS
D1335V1, survival
                 sevent
clus2               0   1
  SCYL2 MUTATED    12   3
  SCYL2 WILD-TYPE 265  75
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             15             340 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
              3              75 
$`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        12.16 
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 
       13.41        12.00        60.79 

$`SCYL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       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-5864 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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SCYL2 MUTATED SCYL2 WILD-TYPE 
           6.97            0.00 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
          60.79          148.01 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
          15.02           22.39 
[1] "7.0 - 60.8 (15.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D1335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCYL2 MUTATED         2        0        1         7         0         0
  SCYL2 WILD-TYPE      62        1       25       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCYL2 MUTATED           0          0          2          1        2         0
  SCYL2 WILD-TYPE        18          6         42         32       33        12
                 vv
clus              STAGE IVB
  SCYL2 MUTATED           0
  SCYL2 WILD-TYPE         1
D1335V3, multiclass
            clus
vv           SCYL2 MUTATED SCYL2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  SCYL2 MUTATED     0   3  10   3
  SCYL2 WILD-TYPE   9  64 239  38
D1335V4, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             3              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
  SCYL2 MUTATED    11   3   2
  SCYL2 WILD-TYPE 209  78  64
D1335V5, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  N0            11             209
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1335V6, binary
                 cls
clus                0   1
  SCYL2 MUTATED    11   2
  SCYL2 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     11    2
  SCYL2 WILD-TYPE  274   46
   clus
vv  SCYL2 MUTATED SCYL2 WILD-TYPE
  0            11             274
  1             2              46
[1] 2 2
[1] FALSE
D1335V7, binary
                 cls
clus                0   1
  SCYL2 MUTATED     5  11
  SCYL2 WILD-TYPE 165 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED      5   11
  SCYL2 WILD-TYPE  165  186
        clus
vv       SCYL2 MUTATED SCYL2 WILD-TYPE
  FEMALE             5             165
  MALE              11             186
[1] 2 2
[1] FALSE
D1335V8, binary
                 cls
clus                0   1
  SCYL2 MUTATED    13   1
  SCYL2 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     13    1
  SCYL2 WILD-TYPE  287    7
     clus
vv    SCYL2 MUTATED SCYL2 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D1335V9, binary
                 cls
clus                0   1
  SCYL2 MUTATED    14   2
  SCYL2 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     14    2
  SCYL2 WILD-TYPE  300   46
                               clus
vv                              SCYL2 MUTATED SCYL2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCYL2 MUTATED    12   0   1   1
  SCYL2 WILD-TYPE 247   3  21  20
D1335V10, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             1              21
  RX             1              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"
D1335V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCYL2 MUTATED                                  0     1
  SCYL2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCYL2 MUTATED                           1    10
  SCYL2 WILD-TYPE                        18   166
D1335V12, multiclass
                                  clus
vv                                 SCYL2 MUTATED SCYL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(1336) Variable = RBM15B MUTATION ANALYSIS
D1336V1, survival
                  sevent
clus2                0   1
  RBM15B MUTATED     6   2
  RBM15B WILD-TYPE 271  76
  RBM15B MUTATED RBM15B WILD-TYPE 
               8              347 
  RBM15B MUTATED RBM15B WILD-TYPE 
               2               76 
$`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        12.16 
TCGA-CA-6718 TCGA-CM-6678 
       10.06        11.01 

$`RBM15B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RBM15B MUTATED RBM15B WILD-TYPE 
            3.02             0.00 
  RBM15B MUTATED RBM15B WILD-TYPE 
           53.00           148.01 
  RBM15B MUTATED RBM15B WILD-TYPE 
          15.105           22.090 
[1] "3.0 - 53.0 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1336V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM15B MUTATED         2        0        2         3         0         0
  RBM15B WILD-TYPE      62        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM15B MUTATED           0          0          0          0        0
  RBM15B WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  RBM15B MUTATED           1         0
  RBM15B WILD-TYPE        11         1
D1336V3, multiclass
            clus
vv           RBM15B MUTATED RBM15B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  RBM15B MUTATED     0   2   5   1
  RBM15B WILD-TYPE   9  65 244  40
D1336V4, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              1               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
  RBM15B MUTATED     7   1   0
  RBM15B WILD-TYPE 213  80  66
D1336V5, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  N0              7              213
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1336V6, binary
                  cls
clus                 0   1
  RBM15B MUTATED     6   1
  RBM15B WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      6    1
  RBM15B WILD-TYPE  279   47
   clus
vv  RBM15B MUTATED RBM15B WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D1336V7, binary
                  cls
clus                 0   1
  RBM15B MUTATED     3   5
  RBM15B WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      3    5
  RBM15B WILD-TYPE  167  192
        clus
vv       RBM15B MUTATED RBM15B WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D1336V8, binary
                  cls
clus                 0   1
  RBM15B MUTATED     7   0
  RBM15B WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      7    0
  RBM15B WILD-TYPE  293    8
     clus
vv    RBM15B MUTATED RBM15B WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1336V9, binary
                  cls
clus                 0   1
  RBM15B MUTATED     7   1
  RBM15B WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      7    1
  RBM15B WILD-TYPE  307   47
                               clus
vv                              RBM15B MUTATED RBM15B WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RBM15B MUTATED     6   0   0   1
  RBM15B WILD-TYPE 253   3  22  20
D1336V10, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1336V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM15B MUTATED                                  0     1
  RBM15B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RBM15B MUTATED                           1     3
  RBM15B WILD-TYPE                        18   173
D1336V12, multiclass
                                  clus
vv                                 RBM15B MUTATED RBM15B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = DHX36 MUTATION ANALYSIS
D1337V1, survival
                 sevent
clus2               0   1
  DHX36 MUTATED     8   4
  DHX36 WILD-TYPE 269  74
  DHX36 MUTATED DHX36 WILD-TYPE 
             12             343 
  DHX36 MUTATED DHX36 WILD-TYPE 
              4              74 
$`DHX36 MUTATED`
TCGA-AA-3516 TCGA-AD-6964 TCGA-G4-6625 TCGA-G4-6628 TCGA-AA-3663 TCGA-AZ-4315 
       13.02        10.88        91.79        79.69         6.97        58.39 
TCGA-AZ-6598 TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A0XF TCGA-G4-6307 
       49.41        12.95        16.14        11.64        38.20        55.04 

$`DHX36 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       26.17        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DHX36 MUTATED DHX36 WILD-TYPE 
           6.97            0.00 
  DHX36 MUTATED DHX36 WILD-TYPE 
          91.79          148.01 
  DHX36 MUTATED DHX36 WILD-TYPE 
          27.17           22.06 
[1] "7.0 - 91.8 (27.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1337V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHX36 MUTATED         2        0        2         4         0         0
  DHX36 WILD-TYPE      62        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHX36 MUTATED           1          0          1          1        0         0
  DHX36 WILD-TYPE        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  DHX36 MUTATED           0
  DHX36 WILD-TYPE         1
D1337V3, multiclass
            clus
vv           DHX36 MUTATED DHX36 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  DHX36 MUTATED     0   2   9   1
  DHX36 WILD-TYPE   9  65 240  40
D1337V4, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             1              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
  DHX36 MUTATED     8   1   3
  DHX36 WILD-TYPE 212  80  63
D1337V5, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             3              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"
D1337V6, binary
                 cls
clus                0   1
  DHX36 MUTATED    10   0
  DHX36 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     10    0
  DHX36 WILD-TYPE  275   48
   clus
vv  DHX36 MUTATED DHX36 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1337V7, binary
                 cls
clus                0   1
  DHX36 MUTATED     5   7
  DHX36 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      5    7
  DHX36 WILD-TYPE  165  190
        clus
vv       DHX36 MUTATED DHX36 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D1337V8, binary
                 cls
clus                0   1
  DHX36 MUTATED    11   0
  DHX36 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     11    0
  DHX36 WILD-TYPE  289    8
     clus
vv    DHX36 MUTATED DHX36 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1337V9, binary
                 cls
clus                0   1
  DHX36 MUTATED     8   3
  DHX36 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      8    3
  DHX36 WILD-TYPE  306   45
                               clus
vv                              DHX36 MUTATED DHX36 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHX36 MUTATED     8   0   0   0
  DHX36 WILD-TYPE 251   3  22  21
D1337V10, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1337V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHX36 MUTATED                                  0     0
  DHX36 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHX36 MUTATED                           0    10
  DHX36 WILD-TYPE                        19   166
D1337V12, multiclass
                                  clus
vv                                 DHX36 MUTATED DHX36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1338) Variable = GFRAL MUTATION ANALYSIS
D1338V1, survival
                 sevent
clus2               0   1
  GFRAL MUTATED     3   1
  GFRAL WILD-TYPE 274  77
  GFRAL MUTATED GFRAL WILD-TYPE 
              4             351 
  GFRAL MUTATED GFRAL WILD-TYPE 
              1              77 
$`GFRAL MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AZ-6600 TCGA-D5-6541 
       63.98         6.97        12.10        15.58 

$`GFRAL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GFRAL MUTATED GFRAL WILD-TYPE 
           6.97            0.00 
  GFRAL MUTATED GFRAL WILD-TYPE 
          63.98          148.01 
  GFRAL MUTATED GFRAL WILD-TYPE 
          13.84           22.09 
[1] "7.0 - 64.0 (13.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1338V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GFRAL MUTATED         0        0        2         1         0         0
  GFRAL WILD-TYPE      64        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GFRAL MUTATED           0          0          0          0        1         0
  GFRAL WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  GFRAL MUTATED           0
  GFRAL WILD-TYPE         1
D1338V3, multiclass
            clus
vv           GFRAL MUTATED GFRAL WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GFRAL MUTATED     0   0   3   1
  GFRAL WILD-TYPE   9  67 246  40
D1338V4, multiclass
    clus
vv   GFRAL MUTATED GFRAL WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             1              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
  GFRAL MUTATED     3   1   0
  GFRAL WILD-TYPE 217  80  66
D1338V5, multiclass
    clus
vv   GFRAL MUTATED GFRAL WILD-TYPE
  N0             3             217
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1338V6, binary
                 cls
clus                0   1
  GFRAL MUTATED     3   1
  GFRAL WILD-TYPE 282  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      3    1
  GFRAL WILD-TYPE  282   47
   clus
vv  GFRAL MUTATED GFRAL WILD-TYPE
  0             3             282
  1             1              47
[1] 2 2
[1] FALSE
D1338V7, binary
                 cls
clus                0   1
  GFRAL MUTATED     0   4
  GFRAL WILD-TYPE 170 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      0    4
  GFRAL WILD-TYPE  170  193
        clus
vv       GFRAL MUTATED GFRAL WILD-TYPE
  FEMALE             0             170
  MALE               4             193
[1] 2 2
[1] FALSE
D1338V8, binary
                 cls
clus                0   1
  GFRAL MUTATED     4   0
  GFRAL WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      4    0
  GFRAL WILD-TYPE  296    8
     clus
vv    GFRAL MUTATED GFRAL WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1338V9, binary
                 cls
clus                0   1
  GFRAL MUTATED     4   0
  GFRAL WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      4    0
  GFRAL WILD-TYPE  310   48
                               clus
vv                              GFRAL MUTATED GFRAL WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GFRAL MUTATED     3   0   0   0
  GFRAL WILD-TYPE 256   3  22  21
D1338V10, multiclass
    clus
vv   GFRAL MUTATED GFRAL WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1338V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFRAL MUTATED                                  0     0
  GFRAL WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GFRAL MUTATED                           1     1
  GFRAL WILD-TYPE                        18   175
D1338V12, multiclass
[1] "Remove cluster labels:" "GFRAL MUTATED"         
clus
  GFRAL MUTATED GFRAL WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6898      TCGA-D5-6920 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 

Clustering(1339) Variable = TAB3 MUTATION ANALYSIS
D1339V1, survival
                sevent
clus2              0   1
  TAB3 MUTATED     6   3
  TAB3 WILD-TYPE 271  75
  TAB3 MUTATED TAB3 WILD-TYPE 
             9            346 
  TAB3 MUTATED TAB3 WILD-TYPE 
             3             75 
$`TAB3 MUTATED`
TCGA-G4-6628 TCGA-A6-5662 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-5403 
       79.69        23.61         2.01         4.01        35.01        62.79 
TCGA-CA-6718 TCGA-CM-5348 TCGA-F4-6807 
       10.06        22.98        43.04 

$`TAB3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TAB3 MUTATED TAB3 WILD-TYPE 
          2.01           0.00 
  TAB3 MUTATED TAB3 WILD-TYPE 
         79.69         148.01 
  TAB3 MUTATED TAB3 WILD-TYPE 
         23.61          22.01 
[1] "2.0 - 79.7 (23.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1339V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAB3 MUTATED         1        0        1         2         1         0
  TAB3 WILD-TYPE      63        1       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAB3 MUTATED           2          0          1          1        0         1
  TAB3 WILD-TYPE        16          6         43         32       35        11
                vv
clus             STAGE IVB
  TAB3 MUTATED           0
  TAB3 WILD-TYPE         1
D1339V3, multiclass
            clus
vv           TAB3 MUTATED TAB3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  TAB3 MUTATED     0   1   8   1
  TAB3 WILD-TYPE   9  66 241  40
D1339V4, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            1             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
  TAB3 MUTATED     5   1   4
  TAB3 WILD-TYPE 215  80  62
D1339V5, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  N0            5            215
  N1            1             80
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1339V6, binary
                cls
clus               0   1
  TAB3 MUTATED     8   1
  TAB3 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      8    1
  TAB3 WILD-TYPE  277   47
   clus
vv  TAB3 MUTATED TAB3 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D1339V7, binary
                cls
clus               0   1
  TAB3 MUTATED     2   8
  TAB3 WILD-TYPE 168 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      2    8
  TAB3 WILD-TYPE  168  189
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  FEMALE            2            168
  MALE              8            189
[1] 2 2
[1] FALSE
D1339V8, binary
                cls
clus               0   1
  TAB3 MUTATED     6   1
  TAB3 WILD-TYPE 294   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      6    1
  TAB3 WILD-TYPE  294    7
     clus
vv    TAB3 MUTATED TAB3 WILD-TYPE
  NO             6            294
  YES            1              7
[1] 2 2
[1] FALSE
D1339V9, binary
                cls
clus               0   1
  TAB3 MUTATED     7   3
  TAB3 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      7    3
  TAB3 WILD-TYPE  307   45
                               clus
vv                              TAB3 MUTATED TAB3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAB3 MUTATED     6   0   0   1
  TAB3 WILD-TYPE 253   3  22  20
D1339V10, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D1339V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAB3 MUTATED                                  0     1
  TAB3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAB3 MUTATED                           0     5
  TAB3 WILD-TYPE                        19   171
D1339V12, multiclass
                                  clus
vv                                 TAB3 MUTATED TAB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = NXPH1 MUTATION ANALYSIS
D1340V1, survival
                 sevent
clus2               0   1
  NXPH1 MUTATED     7   1
  NXPH1 WILD-TYPE 270  77
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              8             347 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              1              77 
$`NXPH1 MUTATED`
TCGA-A6-6649 TCGA-G4-6628 TCGA-A6-6141 TCGA-AA-3861 TCGA-AA-A00N TCGA-AA-A010 
       24.16        79.69         8.38        30.05         4.01        34.98 
TCGA-D5-6541 TCGA-G4-6309 
       15.58        85.48 

$`NXPH1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  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          22.030 
[1] "4.0 - 85.5 (27.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D1340V2, continuous
                 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      63        1       26       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NXPH1 MUTATED           0          0          2          0        0         0
  NXPH1 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  NXPH1 MUTATED           0
  NXPH1 WILD-TYPE         1
D1340V3, multiclass
            clus
vv           NXPH1 MUTATED NXPH1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  NXPH1 MUTATED     0   1   5   2
  NXPH1 WILD-TYPE   9  66 244  39
D1340V4, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             2              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
  NXPH1 MUTATED     6   2   0
  NXPH1 WILD-TYPE 214  79  66
D1340V5, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1340V6, binary
                 cls
clus                0   1
  NXPH1 MUTATED     8   0
  NXPH1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      8    0
  NXPH1 WILD-TYPE  277   48
   clus
vv  NXPH1 MUTATED NXPH1 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1340V7, binary
                 cls
clus                0   1
  NXPH1 MUTATED     2   6
  NXPH1 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      2    6
  NXPH1 WILD-TYPE  168  191
        clus
vv       NXPH1 MUTATED NXPH1 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D1340V8, binary
                 cls
clus                0   1
  NXPH1 MUTATED     7   0
  NXPH1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      7    0
  NXPH1 WILD-TYPE  293    8
     clus
vv    NXPH1 MUTATED NXPH1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1340V9, binary
                 cls
clus                0   1
  NXPH1 MUTATED     7   1
  NXPH1 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      7    1
  NXPH1 WILD-TYPE  307   47
                               clus
vv                              NXPH1 MUTATED NXPH1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NXPH1 MUTATED     6   0   0   0
  NXPH1 WILD-TYPE 253   3  22  21
D1340V10, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1340V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NXPH1 MUTATED                                  0     0
  NXPH1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NXPH1 MUTATED                           2     3
  NXPH1 WILD-TYPE                        17   173
D1340V12, multiclass
                                  clus
vv                                 NXPH1 MUTATED NXPH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        3             173
[1] 4 2
[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 = KCNN4 MUTATION ANALYSIS
D1341V1, survival
                 sevent
clus2               0   1
  KCNN4 MUTATED     6   1
  KCNN4 WILD-TYPE 271  77
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              7             348 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       37.02        25.02        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-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  KCNN4 MUTATED KCNN4 WILD-TYPE 
          13.02            0.00 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
          88.21          148.01 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
          32.02           21.99 
[1] "13.0 - 88.2 (32.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D1341V2, continuous
                 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      63        1       26       106         7         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        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  KCNN4 MUTATED           0
  KCNN4 WILD-TYPE         1
D1341V3, multiclass
            clus
vv           KCNN4 MUTATED KCNN4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  KCNN4 MUTATED     1   0   5   1
  KCNN4 WILD-TYPE   8  67 244  40
D1341V4, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             5             244
  T4             1              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
  KCNN4 MUTATED     5   2   0
  KCNN4 WILD-TYPE 215  79  66
D1341V5, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1341V6, binary
                 cls
clus                0   1
  KCNN4 MUTATED     6   0
  KCNN4 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      6    0
  KCNN4 WILD-TYPE  279   48
   clus
vv  KCNN4 MUTATED KCNN4 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1341V7, binary
                 cls
clus                0   1
  KCNN4 MUTATED     4   3
  KCNN4 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      4    3
  KCNN4 WILD-TYPE  166  194
        clus
vv       KCNN4 MUTATED KCNN4 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1341V8, binary
                 cls
clus                0   1
  KCNN4 MUTATED     7   0
  KCNN4 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      7    0
  KCNN4 WILD-TYPE  293    8
     clus
vv    KCNN4 MUTATED KCNN4 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1341V9, binary
                 cls
clus                0   1
  KCNN4 MUTATED     6   1
  KCNN4 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      6    1
  KCNN4 WILD-TYPE  308   47
                               clus
vv                              KCNN4 MUTATED KCNN4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNN4 MUTATED     4   1   0   0
  KCNN4 WILD-TYPE 255   2  22  21
D1341V10, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  R0             4             255
  R1             1               2
  R2             0              22
  RX             0              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"
D1341V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNN4 MUTATED                                  0     0
  KCNN4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNN4 MUTATED                           2     5
  KCNN4 WILD-TYPE                        17   171
D1341V12, multiclass
                                  clus
vv                                 KCNN4 MUTATED KCNN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = SLC9A9 MUTATION ANALYSIS
D1342V1, survival
                  sevent
clus2                0   1
  SLC9A9 MUTATED    14   4
  SLC9A9 WILD-TYPE 263  74
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              18              337 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
               4               74 
$`SLC9A9 MUTATED`
TCGA-AA-3543 TCGA-G4-6310 TCGA-A6-2676 TCGA-A6-6654 TCGA-AA-3555 TCGA-AA-3949 
        0.99        63.62        42.90        23.87        29.95        26.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-CA-5796 
       25.02         4.01        34.98         1.02        35.01        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6535 
       12.76        10.06        29.03        14.04        54.61        15.12 

$`SLC9A9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6780 
       25.08        25.18        21.76        24.69        24.39        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
            0.99             0.00 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
           63.62           148.01 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
          24.445           22.030 
[1] "1.0 - 63.6 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1342V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC9A9 MUTATED         3        0        1         6         3         0
  SLC9A9 WILD-TYPE      61        1       25       102         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A9 MUTATED           2          0          5          0        0
  SLC9A9 WILD-TYPE        16          6         39         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC9A9 MUTATED           0         0
  SLC9A9 WILD-TYPE        12         1
D1342V3, multiclass
            clus
vv           SLC9A9 MUTATED SLC9A9 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              5               39
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SLC9A9 MUTATED     0   4  14   3
  SLC9A9 WILD-TYPE   9  63 235  38
D1342V4, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             14              235
  T4              3               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
  SLC9A9 MUTATED    14   5   2
  SLC9A9 WILD-TYPE 206  76  64
D1342V5, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  N0             14              206
  N1              5               76
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1342V6, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    18   0
  SLC9A9 WILD-TYPE 267  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     18    0
  SLC9A9 WILD-TYPE  267   48
   clus
vv  SLC9A9 MUTATED SLC9A9 WILD-TYPE
  0             18              267
  1              0               48
[1] 2 2
[1] FALSE
D1342V7, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    12   9
  SLC9A9 WILD-TYPE 158 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     12    9
  SLC9A9 WILD-TYPE  158  188
        clus
vv       SLC9A9 MUTATED SLC9A9 WILD-TYPE
  FEMALE             12              158
  MALE                9              188
[1] 2 2
[1] FALSE
D1342V8, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    14   2
  SLC9A9 WILD-TYPE 286   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     14    2
  SLC9A9 WILD-TYPE  286    6
     clus
vv    SLC9A9 MUTATED SLC9A9 WILD-TYPE
  NO              14              286
  YES              2                6
[1] 2 2
[1] FALSE
D1342V9, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    14   7
  SLC9A9 WILD-TYPE 300  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     14    7
  SLC9A9 WILD-TYPE  300   41
                               clus
vv                              SLC9A9 MUTATED SLC9A9 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC9A9 MUTATED    15   0   0   4
  SLC9A9 WILD-TYPE 244   3  22  17
D1342V10, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              4               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"
D1342V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A9 MUTATED                                  0     3
  SLC9A9 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC9A9 MUTATED                           0     8
  SLC9A9 WILD-TYPE                        19   168
D1342V12, multiclass
                                  clus
vv                                 SLC9A9 MUTATED SLC9A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = ATP6V0A4 MUTATION ANALYSIS
D1343V1, survival
                    sevent
clus2                  0   1
  ATP6V0A4 MUTATED     6   3
  ATP6V0A4 WILD-TYPE 271  75
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 9                346 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 3                 75 
$`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 
       10.06        85.45        10.26 

$`ATP6V0A4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       12.20        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
              4.01               0.00 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
             85.45             148.01 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
             19.04              22.09 
[1] "4.0 - 85.5 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1343V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP6V0A4 MUTATED         2        0        1         4         3         0
  ATP6V0A4 WILD-TYPE      62        1       25       104         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V0A4 MUTATED           0          0          1          0        0
  ATP6V0A4 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  ATP6V0A4 MUTATED           0         0
  ATP6V0A4 WILD-TYPE        12         1
D1343V3, multiclass
            clus
vv           ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  ATP6V0A4 MUTATED     0   2   6   3
  ATP6V0A4 WILD-TYPE   9  65 243  38
D1343V4, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                6                243
  T4                3                 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
  ATP6V0A4 MUTATED    10   1   0
  ATP6V0A4 WILD-TYPE 210  80  66
D1343V5, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  N0               10                210
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1343V6, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     9   0
  ATP6V0A4 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      9    0
  ATP6V0A4 WILD-TYPE  276   48
   clus
vv  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D1343V7, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     6   5
  ATP6V0A4 WILD-TYPE 164 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      6    5
  ATP6V0A4 WILD-TYPE  164  192
        clus
vv       ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  FEMALE                6                164
  MALE                  5                192
[1] 2 2
[1] FALSE
D1343V8, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     7   0
  ATP6V0A4 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      7    0
  ATP6V0A4 WILD-TYPE  293    8
     clus
vv    ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1343V9, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     7   4
  ATP6V0A4 WILD-TYPE 307  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      7    4
  ATP6V0A4 WILD-TYPE  307   44
                               clus
vv                              ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  COLON ADENOCARCINOMA                         7                307
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ATP6V0A4 MUTATED     7   1   0   3
  ATP6V0A4 WILD-TYPE 252   2  22  18
D1343V10, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  R0                7                252
  R1                1                  2
  R2                0                 22
  RX                3                 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"
D1343V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V0A4 MUTATED                                  0     2
  ATP6V0A4 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ATP6V0A4 MUTATED                           1     4
  ATP6V0A4 WILD-TYPE                        18   172
D1343V12, multiclass
                                  clus
vv                                 ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                172
[1] 4 2
[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 = ATG10 MUTATION ANALYSIS
D1344V1, survival
                 sevent
clus2               0   1
  ATG10 MUTATED     4   0
  ATG10 WILD-TYPE 273  78
  ATG10 MUTATED ATG10 WILD-TYPE 
              4             351 
  ATG10 MUTATED ATG10 WILD-TYPE 
              0              78 
$`ATG10 MUTATED`
TCGA-AA-3950 TCGA-AA-A010 TCGA-CM-5861 TCGA-D5-6927 
       24.00        34.98        15.02         9.44 

$`ATG10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ATG10 MUTATED ATG10 WILD-TYPE 
           9.44            0.00 
  ATG10 MUTATED ATG10 WILD-TYPE 
          34.98          148.01 
  ATG10 MUTATED ATG10 WILD-TYPE 
          19.51           22.06 
[1] "9.4 - 35.0 (19.5)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1344V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG10 MUTATED         0        0        0         3         1         0
  ATG10 WILD-TYPE      64        1       26       105         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  ATG10 MUTATED           0
  ATG10 WILD-TYPE         1
D1344V3, multiclass
            clus
vv           ATG10 MUTATED ATG10 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ATG10 MUTATED     0   0   3   1
  ATG10 WILD-TYPE   9  67 246  40
D1344V4, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             1              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
  ATG10 MUTATED     4   0   0
  ATG10 WILD-TYPE 216  81  66
D1344V5, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1344V6, binary
                 cls
clus                0   1
  ATG10 MUTATED     4   0
  ATG10 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      4    0
  ATG10 WILD-TYPE  281   48
   clus
vv  ATG10 MUTATED ATG10 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1344V7, binary
                 cls
clus                0   1
  ATG10 MUTATED     3   1
  ATG10 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      3    1
  ATG10 WILD-TYPE  167  196
        clus
vv       ATG10 MUTATED ATG10 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D1344V8, binary
                 cls
clus                0   1
  ATG10 MUTATED     4   0
  ATG10 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      4    0
  ATG10 WILD-TYPE  296    8
     clus
vv    ATG10 MUTATED ATG10 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1344V9, binary
                 cls
clus                0   1
  ATG10 MUTATED     3   1
  ATG10 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      3    1
  ATG10 WILD-TYPE  311   47
                               clus
vv                              ATG10 MUTATED ATG10 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATG10 MUTATED     4   0   0   0
  ATG10 WILD-TYPE 255   3  22  21
D1344V10, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1344V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG10 MUTATED                                  0     0
  ATG10 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATG10 MUTATED                           0     2
  ATG10 WILD-TYPE                        19   174
D1344V12, multiclass
[1] "Remove cluster labels:" "ATG10 MUTATED"         
clus
  ATG10 MUTATED ATG10 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5913      TCGA-CK-5914 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 

Clustering(1345) Variable = MORC2 MUTATION ANALYSIS
D1345V1, survival
                 sevent
clus2               0   1
  MORC2 MUTATED     8   3
  MORC2 WILD-TYPE 269  75
  MORC2 MUTATED MORC2 WILD-TYPE 
             11             344 
  MORC2 MUTATED MORC2 WILD-TYPE 
              3              75 
$`MORC2 MUTATED`
TCGA-AZ-6601 TCGA-A6-6137 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3811 TCGA-AA-A00R 
      100.01        27.09        63.98        12.99        10.06         0.99 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6532 TCGA-D5-6927 
        0.20        58.39        49.41        18.25         9.44 

$`MORC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MORC2 MUTATED MORC2 WILD-TYPE 
            0.2             0.0 
  MORC2 MUTATED MORC2 WILD-TYPE 
         100.01          148.01 
  MORC2 MUTATED MORC2 WILD-TYPE 
         18.250          22.075 
[1] "0.2 - 100.0 (18.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1345V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MORC2 MUTATED         1        0        3         3         1         0
  MORC2 WILD-TYPE      63        1       23       105         7         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        17          6         43         31       35        12
                 vv
clus              STAGE IVB
  MORC2 MUTATED           0
  MORC2 WILD-TYPE         1
D1345V3, multiclass
            clus
vv           MORC2 MUTATED MORC2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  MORC2 MUTATED     0   1  10   1
  MORC2 WILD-TYPE   9  66 239  40
D1345V4, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             1              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
  MORC2 MUTATED     8   1   3
  MORC2 WILD-TYPE 212  80  63
D1345V5, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             3              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"
D1345V6, binary
                 cls
clus                0   1
  MORC2 MUTATED     9   0
  MORC2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      9    0
  MORC2 WILD-TYPE  276   48
   clus
vv  MORC2 MUTATED MORC2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1345V7, binary
                 cls
clus                0   1
  MORC2 MUTATED     4   8
  MORC2 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      4    8
  MORC2 WILD-TYPE  166  189
        clus
vv       MORC2 MUTATED MORC2 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D1345V8, binary
                 cls
clus                0   1
  MORC2 MUTATED     9   0
  MORC2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      9    0
  MORC2 WILD-TYPE  291    8
     clus
vv    MORC2 MUTATED MORC2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1345V9, binary
                 cls
clus                0   1
  MORC2 MUTATED    11   1
  MORC2 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED     11    1
  MORC2 WILD-TYPE  303   47
                               clus
vv                              MORC2 MUTATED MORC2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MORC2 MUTATED     8   0   0   1
  MORC2 WILD-TYPE 251   3  22  20
D1345V10, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1345V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MORC2 MUTATED                                  0     0
  MORC2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MORC2 MUTATED                           0     8
  MORC2 WILD-TYPE                        19   168
D1345V12, multiclass
                                  clus
vv                                 MORC2 MUTATED MORC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = GRIN2B MUTATION ANALYSIS
D1346V1, survival
                  sevent
clus2                0   1
  GRIN2B MUTATED    16   9
  GRIN2B WILD-TYPE 261  69
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              25              330 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
               9               69 
$`GRIN2B MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3511 
       10.88       100.01        35.80        33.53         3.02         6.97 
TCGA-AA-3660 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       78.08        15.95        25.02         4.01        34.98         1.02 
TCGA-AD-6901 TCGA-AU-3779 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 
       22.42        14.50        49.41        12.76        10.06        85.45 
TCGA-CK-4952 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6931 TCGA-DM-A1D4 
       15.62        16.14        12.39        10.13        12.00        92.75 
TCGA-DM-A28G 
       60.79 

$`GRIN2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3514 
       19.66        20.28         7.04        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58         7.53        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        13.41        13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GRIN2B MUTATED GRIN2B WILD-TYPE 
            1.02             0.00 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
          100.01           148.01 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
           15.95            22.09 
[1] "1.0 - 100.0 (15.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1346V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRIN2B MUTATED         1        0        7         9         2         0
  GRIN2B WILD-TYPE      63        1       19        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRIN2B MUTATED           0          1          1          2        0
  GRIN2B WILD-TYPE        18          5         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GRIN2B MUTATED           0         0
  GRIN2B WILD-TYPE        12         1
D1346V3, multiclass
            clus
vv           GRIN2B MUTATED GRIN2B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                7               19
  STAGE IIA               9               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  GRIN2B MUTATED     0   2  17   7
  GRIN2B WILD-TYPE   9  65 232  34
D1346V4, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  T1              0                9
  T2              2               65
  T3             17              232
  T4              7               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
  GRIN2B MUTATED    21   2   3
  GRIN2B WILD-TYPE 199  79  63
D1346V5, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  N0             21              199
  N1              2               79
  N2              3               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"
D1346V6, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    22   0
  GRIN2B WILD-TYPE 263  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     22    0
  GRIN2B WILD-TYPE  263   48
   clus
vv  GRIN2B MUTATED GRIN2B WILD-TYPE
  0             22              263
  1              0               48
[1] 2 2
[1] FALSE
D1346V7, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    13  13
  GRIN2B WILD-TYPE 157 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     13   13
  GRIN2B WILD-TYPE  157  184
        clus
vv       GRIN2B MUTATED GRIN2B WILD-TYPE
  FEMALE             13              157
  MALE               13              184
[1] 2 2
[1] FALSE
D1346V8, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    20   0
  GRIN2B WILD-TYPE 280   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     20    0
  GRIN2B WILD-TYPE  280    8
     clus
vv    GRIN2B MUTATED GRIN2B WILD-TYPE
  NO              20              280
  YES              0                8
[1] 2 2
[1] FALSE
D1346V9, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    21   5
  GRIN2B WILD-TYPE 293  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     21    5
  GRIN2B WILD-TYPE  293   43
                               clus
vv                              GRIN2B MUTATED GRIN2B WILD-TYPE
  COLON ADENOCARCINOMA                      21              293
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GRIN2B MUTATED    15   1   0   3
  GRIN2B WILD-TYPE 244   2  22  18
D1346V10, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  R0             15              244
  R1              1                2
  R2              0               22
  RX              3               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"
D1346V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRIN2B MUTATED                                  0     2
  GRIN2B WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GRIN2B MUTATED                           2    13
  GRIN2B WILD-TYPE                        17   163
D1346V12, multiclass
                                  clus
vv                                 GRIN2B MUTATED GRIN2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        13              163
[1] 4 2
[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 = FSCB MUTATION ANALYSIS
D1347V1, survival
                sevent
clus2              0   1
  FSCB MUTATED    14   6
  FSCB WILD-TYPE 263  72
  FSCB MUTATED FSCB WILD-TYPE 
            20            335 
  FSCB MUTATED FSCB WILD-TYPE 
             6             72 
$`FSCB MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-AZ-6601 TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 
       19.04        10.88       100.01        33.53        29.95         6.97 
TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-4616 
       21.99        25.02         4.01        34.98        33.01         5.13 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6166 TCGA-D5-6932 
       12.20        12.76        13.02         5.03        21.99        11.38 
TCGA-DM-A1HB TCGA-G4-6299 
      135.65        74.56 

$`FSCB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41        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-6718 
       12.69        12.36        12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-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-6167 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-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        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  FSCB MUTATED FSCB WILD-TYPE 
          4.01           0.00 
  FSCB MUTATED FSCB WILD-TYPE 
        135.65         148.01 
  FSCB MUTATED FSCB WILD-TYPE 
        20.515         22.090 
[1] "4.0 - 135.7 (20.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1347V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FSCB MUTATED         2        0        3         6         2         0
  FSCB WILD-TYPE      62        1       23       102         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FSCB MUTATED           0          0          1          1        1         2
  FSCB WILD-TYPE        18          6         43         32       34        10
                vv
clus             STAGE IVB
  FSCB MUTATED           0
  FSCB WILD-TYPE         1
D1347V3, multiclass
            clus
vv           FSCB MUTATED FSCB WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             2             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
  FSCB MUTATED     0   3  14   3
  FSCB WILD-TYPE   9  64 235  38
D1347V4, multiclass
    clus
vv   FSCB MUTATED FSCB WILD-TYPE
  T1            0              9
  T2            3             64
  T3           14            235
  T4            3             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
  FSCB MUTATED    14   3   3
  FSCB WILD-TYPE 206  78  63
D1347V5, multiclass
    clus
vv   FSCB MUTATED FSCB WILD-TYPE
  N0           14            206
  N1            3             78
  N2            3             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"
D1347V6, binary
                cls
clus               0   1
  FSCB MUTATED    15   3
  FSCB WILD-TYPE 270  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSCB MUTATED     15    3
  FSCB WILD-TYPE  270   45
   clus
vv  FSCB MUTATED FSCB WILD-TYPE
  0           15            270
  1            3             45
[1] 2 2
[1] FALSE
D1347V7, binary
                cls
clus               0   1
  FSCB MUTATED     7  13
  FSCB WILD-TYPE 163 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSCB MUTATED      7   13
  FSCB WILD-TYPE  163  184
        clus
vv       FSCB MUTATED FSCB WILD-TYPE
  FEMALE            7            163
  MALE             13            184
[1] 2 2
[1] FALSE
D1347V8, binary
                cls
clus               0   1
  FSCB MUTATED    18   0
  FSCB WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSCB MUTATED     18    0
  FSCB WILD-TYPE  282    8
     clus
vv    FSCB MUTATED FSCB WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D1347V9, binary
                cls
clus               0   1
  FSCB MUTATED    16   3
  FSCB WILD-TYPE 298  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSCB MUTATED     16    3
  FSCB WILD-TYPE  298   45
                               clus
vv                              FSCB MUTATED FSCB WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FSCB MUTATED    13   0   0   2
  FSCB WILD-TYPE 246   3  22  19
D1347V10, multiclass
    clus
vv   FSCB MUTATED FSCB WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            2             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"
D1347V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FSCB MUTATED                                  0     2
  FSCB WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FSCB MUTATED                           3     8
  FSCB WILD-TYPE                        16   168
D1347V12, multiclass
                                  clus
vv                                 FSCB MUTATED FSCB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                       8            168
[1] 4 2
[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 = DLGAP5 MUTATION ANALYSIS
D1348V1, survival
                  sevent
clus2                0   1
  DLGAP5 MUTATED     5   3
  DLGAP5 WILD-TYPE 272  75
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               8              347 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               3               75 
$`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        21.99        13.02 
TCGA-D5-6537 TCGA-G4-6315 
        4.80        61.91 

$`DLGAP5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
             4.8              0.0 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
           61.91           148.01 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
          20.515           22.090 
[1] "4.8 - 61.9 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1348V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLGAP5 MUTATED         0        0        1         3         0         0
  DLGAP5 WILD-TYPE      64        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP5 MUTATED           0          0          2          0        1
  DLGAP5 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  DLGAP5 MUTATED           0         0
  DLGAP5 WILD-TYPE        12         1
D1348V3, multiclass
            clus
vv           DLGAP5 MUTATED DLGAP5 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  DLGAP5 MUTATED     0   1   7   0
  DLGAP5 WILD-TYPE   9  66 242  41
D1348V4, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              0               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
  DLGAP5 MUTATED     4   4   0
  DLGAP5 WILD-TYPE 216  77  66
D1348V5, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  N0              4              216
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1348V6, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     4   1
  DLGAP5 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      4    1
  DLGAP5 WILD-TYPE  281   47
   clus
vv  DLGAP5 MUTATED DLGAP5 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1348V7, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     1   7
  DLGAP5 WILD-TYPE 169 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      1    7
  DLGAP5 WILD-TYPE  169  190
        clus
vv       DLGAP5 MUTATED DLGAP5 WILD-TYPE
  FEMALE              1              169
  MALE                7              190
[1] 2 2
[1] FALSE
D1348V8, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     7   0
  DLGAP5 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      7    0
  DLGAP5 WILD-TYPE  293    8
     clus
vv    DLGAP5 MUTATED DLGAP5 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1348V9, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     7   1
  DLGAP5 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      7    1
  DLGAP5 WILD-TYPE  307   47
                               clus
vv                              DLGAP5 MUTATED DLGAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DLGAP5 MUTATED     5   0   0   2
  DLGAP5 WILD-TYPE 254   3  22  19
D1348V10, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D1348V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLGAP5 MUTATED                                  0     1
  DLGAP5 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DLGAP5 MUTATED                           1     5
  DLGAP5 WILD-TYPE                        18   171
D1348V12, multiclass
                                  clus
vv                                 DLGAP5 MUTATED DLGAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = ACCN5 MUTATION ANALYSIS
D1349V1, survival
                 sevent
clus2               0   1
  ACCN5 MUTATED     9   3
  ACCN5 WILD-TYPE 268  75
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             12             343 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
              3              75 
$`ACCN5 MUTATED`
TCGA-AD-6888 TCGA-DM-A285 TCGA-AA-3510 TCGA-AA-3681 TCGA-AA-A00N TCGA-AA-A010 
       15.52         5.88        63.98         5.98         4.01        34.98 
TCGA-AU-3779 TCGA-CM-6162 TCGA-D5-6532 TCGA-D5-6536 TCGA-DM-A1HB TCGA-G4-6306 
       14.50        12.00        18.25        17.85       135.65        44.68 

$`ACCN5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3685 
       14.01        50.04        47.01        15.02        11.01        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ACCN5 MUTATED ACCN5 WILD-TYPE 
           4.01            0.00 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
         135.65          148.01 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
         16.685          22.090 
[1] "4.0 - 135.7 (16.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1349V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACCN5 MUTATED         0        0        1         4         2         0
  ACCN5 WILD-TYPE      64        1       25       104         6         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        17          6         41         33       34        12
                 vv
clus              STAGE IVB
  ACCN5 MUTATED           0
  ACCN5 WILD-TYPE         1
D1349V3, multiclass
            clus
vv           ACCN5 MUTATED ACCN5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ACCN5 MUTATED     0   1  10   2
  ACCN5 WILD-TYPE   9  66 239  39
D1349V4, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             2              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
  ACCN5 MUTATED     8   4   1
  ACCN5 WILD-TYPE 212  77  65
D1349V5, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1349V6, binary
                 cls
clus                0   1
  ACCN5 MUTATED    12   1
  ACCN5 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED     12    1
  ACCN5 WILD-TYPE  273   47
   clus
vv  ACCN5 MUTATED ACCN5 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D1349V7, binary
                 cls
clus                0   1
  ACCN5 MUTATED     6   7
  ACCN5 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED      6    7
  ACCN5 WILD-TYPE  164  190
        clus
vv       ACCN5 MUTATED ACCN5 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1349V8, binary
                 cls
clus                0   1
  ACCN5 MUTATED     9   0
  ACCN5 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED      9    0
  ACCN5 WILD-TYPE  291    8
     clus
vv    ACCN5 MUTATED ACCN5 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1349V9, binary
                 cls
clus                0   1
  ACCN5 MUTATED     9   3
  ACCN5 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED      9    3
  ACCN5 WILD-TYPE  305   45
                               clus
vv                              ACCN5 MUTATED ACCN5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACCN5 MUTATED    11   0   0   0
  ACCN5 WILD-TYPE 248   3  22  21
D1349V10, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D1349V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACCN5 MUTATED                                  0     0
  ACCN5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACCN5 MUTATED                           0     8
  ACCN5 WILD-TYPE                        19   168
D1349V12, multiclass
                                  clus
vv                                 ACCN5 MUTATED ACCN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = DLGAP3 MUTATION ANALYSIS
D1350V1, survival
                  sevent
clus2                0   1
  DLGAP3 MUTATED    12   3
  DLGAP3 WILD-TYPE 265  75
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              15              340 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               3               75 
$`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 
       83.24        49.41        12.76        10.06        15.62        51.32 
TCGA-CM-5861 TCGA-D5-6529 TCGA-D5-6928 
       15.02        20.19        11.64 

$`DLGAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        85.45        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
            1.02             0.00 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           83.24           148.01 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           20.19            22.09 
[1] "1.0 - 83.2 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1350V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLGAP3 MUTATED         0        0        4        10         1         0
  DLGAP3 WILD-TYPE      64        1       22        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP3 MUTATED           0          0          0          1        0
  DLGAP3 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  DLGAP3 MUTATED           0         0
  DLGAP3 WILD-TYPE        12         1
D1350V3, multiclass
            clus
vv           DLGAP3 MUTATED DLGAP3 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA              10               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  DLGAP3 MUTATED     0   0  14   2
  DLGAP3 WILD-TYPE   9  67 235  39
D1350V4, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  T1              0                9
  T2              0               67
  T3             14              235
  T4              2               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
  DLGAP3 MUTATED    15   0   1
  DLGAP3 WILD-TYPE 205  81  65
D1350V5, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  N0             15              205
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1350V6, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    14   0
  DLGAP3 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     14    0
  DLGAP3 WILD-TYPE  271   48
   clus
vv  DLGAP3 MUTATED DLGAP3 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D1350V7, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     9   7
  DLGAP3 WILD-TYPE 161 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      9    7
  DLGAP3 WILD-TYPE  161  190
        clus
vv       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  FEMALE              9              161
  MALE                7              190
[1] 2 2
[1] FALSE
D1350V8, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    13   0
  DLGAP3 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     13    0
  DLGAP3 WILD-TYPE  287    8
     clus
vv    DLGAP3 MUTATED DLGAP3 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1350V9, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    13   3
  DLGAP3 WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     13    3
  DLGAP3 WILD-TYPE  301   45
                               clus
vv                              DLGAP3 MUTATED DLGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DLGAP3 MUTATED    11   0   0   4
  DLGAP3 WILD-TYPE 248   3  22  17
D1350V10, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              4               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"
D1350V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLGAP3 MUTATED                                  0     3
  DLGAP3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DLGAP3 MUTATED                           0     7
  DLGAP3 WILD-TYPE                        19   169
D1350V12, multiclass
                                  clus
vv                                 DLGAP3 MUTATED DLGAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = HSPBAP1 MUTATION ANALYSIS
D1351V1, survival
                   sevent
clus2                 0   1
  HSPBAP1 MUTATED     3   4
  HSPBAP1 WILD-TYPE 274  74
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                7               348 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                4                74 
$`HSPBAP1 MUTATED`
TCGA-A6-6142 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-5913 TCGA-DM-A1HB 
       25.08         4.01        83.24        49.41        51.32       135.65 
TCGA-F4-6459 
        8.61 

$`HSPBAP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
             4.01              0.00 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
           135.65            148.01 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
            49.41             22.01 
[1] "4.0 - 135.7 (49.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1351V2, continuous
                   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      64        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPBAP1 MUTATED           0          0          2          0        0
  HSPBAP1 WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  HSPBAP1 MUTATED           1         0
  HSPBAP1 WILD-TYPE        11         1
D1351V3, multiclass
            clus
vv           HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  HSPBAP1 MUTATED     0   0   6   1
  HSPBAP1 WILD-TYPE   9  67 243  40
D1351V4, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               6               243
  T4               1                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
  HSPBAP1 MUTATED     4   2   1
  HSPBAP1 WILD-TYPE 216  79  65
D1351V5, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  N0               4               216
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1351V6, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     4   1
  HSPBAP1 WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      4    1
  HSPBAP1 WILD-TYPE  281   47
   clus
vv  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D1351V7, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     4   3
  HSPBAP1 WILD-TYPE 166 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      4    3
  HSPBAP1 WILD-TYPE  166  194
        clus
vv       HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  FEMALE               4               166
  MALE                 3               194
[1] 2 2
[1] FALSE
D1351V8, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     5   0
  HSPBAP1 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      5    0
  HSPBAP1 WILD-TYPE  295    8
     clus
vv    HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1351V9, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     5   1
  HSPBAP1 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      5    1
  HSPBAP1 WILD-TYPE  309   47
                               clus
vv                              HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HSPBAP1 MUTATED     3   0   0   1
  HSPBAP1 WILD-TYPE 256   3  22  20
D1351V10, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               1                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"
D1351V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPBAP1 MUTATED                                  0     1
  HSPBAP1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HSPBAP1 MUTATED                           0     5
  HSPBAP1 WILD-TYPE                        19   171
D1351V12, multiclass
                                  clus
vv                                 HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = COLEC12 MUTATION ANALYSIS
D1352V1, survival
                   sevent
clus2                 0   1
  COLEC12 MUTATED    15   2
  COLEC12 WILD-TYPE 262  76
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               17               338 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
                2                76 
$`COLEC12 MUTATED`
TCGA-AD-6888 TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3831 
       15.52        32.75        33.53         6.97        26.99        17.98 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 
       26.01        25.02        34.98        27.09        58.39        12.76 
TCGA-CK-4952 TCGA-CM-5862 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 
       15.62         5.03        11.64       135.65        35.31 

$`COLEC12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  COLEC12 MUTATED COLEC12 WILD-TYPE 
             5.03              0.00 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
           135.65            148.01 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
            26.01             22.01 
[1] "5.0 - 135.7 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1352V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COLEC12 MUTATED         2        0        1         6         2         0
  COLEC12 WILD-TYPE      62        1       25       102         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COLEC12 MUTATED           0          0          3          1        0
  COLEC12 WILD-TYPE        18          6         41         32       35
                   vv
clus                STAGE IVA STAGE IVB
  COLEC12 MUTATED           1         0
  COLEC12 WILD-TYPE        11         1
D1352V3, multiclass
            clus
vv           COLEC12 MUTATED COLEC12 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                6               102
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                1                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
  COLEC12 MUTATED     0   3  11   3
  COLEC12 WILD-TYPE   9  64 238  38
D1352V4, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              11               238
  T4               3                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
  COLEC12 MUTATED    12   4   1
  COLEC12 WILD-TYPE 208  77  65
D1352V5, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  N0              12               208
  N1               4                77
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1352V6, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    15   1
  COLEC12 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     15    1
  COLEC12 WILD-TYPE  270   47
   clus
vv  COLEC12 MUTATED COLEC12 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D1352V7, binary
                   cls
clus                  0   1
  COLEC12 MUTATED     7  10
  COLEC12 WILD-TYPE 163 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED      7   10
  COLEC12 WILD-TYPE  163  187
        clus
vv       COLEC12 MUTATED COLEC12 WILD-TYPE
  FEMALE               7               163
  MALE                10               187
[1] 2 2
[1] FALSE
D1352V8, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    14   0
  COLEC12 WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     14    0
  COLEC12 WILD-TYPE  286    8
     clus
vv    COLEC12 MUTATED COLEC12 WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D1352V9, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    10   6
  COLEC12 WILD-TYPE 304  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     10    6
  COLEC12 WILD-TYPE  304   42
                               clus
vv                              COLEC12 MUTATED COLEC12 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  COLEC12 MUTATED    13   0   0   2
  COLEC12 WILD-TYPE 246   3  22  19
D1352V10, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               2                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"
D1352V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COLEC12 MUTATED                                  0     1
  COLEC12 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COLEC12 MUTATED                           1     9
  COLEC12 WILD-TYPE                        18   167
D1352V12, multiclass
                                  clus
vv                                 COLEC12 MUTATED COLEC12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          9               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(1353) Variable = KIFC2 MUTATION ANALYSIS
D1353V1, survival
                 sevent
clus2               0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 271  78
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             349 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              0              78 
$`KIFC2 MUTATED`
TCGA-AA-3697 TCGA-A6-5665 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6386 TCGA-DM-A1HB 
       85.05        22.06        14.50        27.09        17.82       135.65 

$`KIFC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       26.47        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.030 
[1] "14.5 - 135.7 (24.6)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1353V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIFC2 MUTATED         1        0        1         2         0         0
  KIFC2 WILD-TYPE      63        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIFC2 MUTATED           0          0          2          0        0         0
  KIFC2 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  KIFC2 MUTATED           0
  KIFC2 WILD-TYPE         1
D1353V3, multiclass
            clus
vv           KIFC2 MUTATED KIFC2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  KIFC2 MUTATED     0   1   5   0
  KIFC2 WILD-TYPE   9  66 244  41
D1353V4, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             0              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
  KIFC2 MUTATED     4   2   0
  KIFC2 WILD-TYPE 216  79  66
D1353V5, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1353V6, binary
                 cls
clus                0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      6    0
  KIFC2 WILD-TYPE  279   48
   clus
vv  KIFC2 MUTATED KIFC2 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1353V7, binary
                 cls
clus                0   1
  KIFC2 MUTATED     4   2
  KIFC2 WILD-TYPE 166 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      4    2
  KIFC2 WILD-TYPE  166  195
        clus
vv       KIFC2 MUTATED KIFC2 WILD-TYPE
  FEMALE             4             166
  MALE               2             195
[1] 2 2
[1] FALSE
D1353V8, binary
                 cls
clus                0   1
  KIFC2 MUTATED     4   0
  KIFC2 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      4    0
  KIFC2 WILD-TYPE  296    8
     clus
vv    KIFC2 MUTATED KIFC2 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1353V9, binary
                 cls
clus                0   1
  KIFC2 MUTATED     5   0
  KIFC2 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      5    0
  KIFC2 WILD-TYPE  309   48
                               clus
vv                              KIFC2 MUTATED KIFC2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KIFC2 MUTATED     5   0   0   0
  KIFC2 WILD-TYPE 254   3  22  21
D1353V10, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1353V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIFC2 MUTATED                                  0     0
  KIFC2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIFC2 MUTATED                           1     4
  KIFC2 WILD-TYPE                        18   172
D1353V12, multiclass
                                  clus
vv                                 KIFC2 MUTATED KIFC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = PPYR1 MUTATION ANALYSIS
D1354V1, survival
                 sevent
clus2               0   1
  PPYR1 MUTATED     3   1
  PPYR1 WILD-TYPE 274  77
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              4             351 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              1              77 
$`PPYR1 MUTATED`
TCGA-G4-6586 TCGA-AU-6004 TCGA-CM-6674 TCGA-G4-6626 
       35.80        27.09        12.95        46.75 

$`PPYR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  PPYR1 MUTATED PPYR1 WILD-TYPE 
          12.95            0.00 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
          46.75          148.01 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
         31.445          22.030 
[1] "12.9 - 46.8 (31.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1354V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPYR1 MUTATED         1        0        0         4         0         0
  PPYR1 WILD-TYPE      63        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPYR1 MUTATED           0          0          0          0        0         0
  PPYR1 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  PPYR1 MUTATED           0
  PPYR1 WILD-TYPE         1
D1354V3, multiclass
            clus
vv           PPYR1 MUTATED PPYR1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PPYR1 MUTATED     0   1   4   0
  PPYR1 WILD-TYPE   9  66 245  41
D1354V4, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             0              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
  PPYR1 MUTATED     5   0   0
  PPYR1 WILD-TYPE 215  81  66
D1354V5, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1354V6, binary
                 cls
clus                0   1
  PPYR1 MUTATED     5   0
  PPYR1 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      5    0
  PPYR1 WILD-TYPE  280   48
   clus
vv  PPYR1 MUTATED PPYR1 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1354V7, binary
                 cls
clus                0   1
  PPYR1 MUTATED     3   2
  PPYR1 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      3    2
  PPYR1 WILD-TYPE  167  195
        clus
vv       PPYR1 MUTATED PPYR1 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1354V8, binary
                 cls
clus                0   1
  PPYR1 MUTATED     3   0
  PPYR1 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      3    0
  PPYR1 WILD-TYPE  297    8
     clus
vv    PPYR1 MUTATED PPYR1 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1354V9, binary
                 cls
clus                0   1
  PPYR1 MUTATED     5   0
  PPYR1 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      5    0
  PPYR1 WILD-TYPE  309   48
                               clus
vv                              PPYR1 MUTATED PPYR1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPYR1 MUTATED     5   0   0   0
  PPYR1 WILD-TYPE 254   3  22  21
D1354V10, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1354V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPYR1 MUTATED                                  0     0
  PPYR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PPYR1 MUTATED                           0     4
  PPYR1 WILD-TYPE                        19   172
D1354V12, multiclass
                                  clus
vv                                 PPYR1 MUTATED PPYR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = CASP10 MUTATION ANALYSIS
D1355V1, survival
                  sevent
clus2                0   1
  CASP10 MUTATED     6   0
  CASP10 WILD-TYPE 271  78
  CASP10 MUTATED CASP10 WILD-TYPE 
               6              349 
  CASP10 MUTATED CASP10 WILD-TYPE 
               0               78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
        3.02        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.030 
[1] "12.8 - 133.2 (33.3)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "9300000"
D1355V2, continuous
                  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      64        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP10 MUTATED           2          0          1          0        0
  CASP10 WILD-TYPE        16          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CASP10 MUTATED           0         0
  CASP10 WILD-TYPE        12         1
D1355V3, multiclass
            clus
vv           CASP10 MUTATED CASP10 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CASP10 MUTATED     0   0   6   1
  CASP10 WILD-TYPE   9  67 243  40
D1355V4, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              1               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
  CASP10 MUTATED     4   2   1
  CASP10 WILD-TYPE 216  79  65
D1355V5, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  N0              4              216
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1355V6, binary
                  cls
clus                 0   1
  CASP10 MUTATED     7   0
  CASP10 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      7    0
  CASP10 WILD-TYPE  278   48
   clus
vv  CASP10 MUTATED CASP10 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1355V7, binary
                  cls
clus                 0   1
  CASP10 MUTATED     3   4
  CASP10 WILD-TYPE 167 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      3    4
  CASP10 WILD-TYPE  167  193
        clus
vv       CASP10 MUTATED CASP10 WILD-TYPE
  FEMALE              3              167
  MALE                4              193
[1] 2 2
[1] FALSE
D1355V8, binary
                  cls
clus                 0   1
  CASP10 MUTATED     6   0
  CASP10 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      6    0
  CASP10 WILD-TYPE  294    8
     clus
vv    CASP10 MUTATED CASP10 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1355V9, binary
                  cls
clus                 0   1
  CASP10 MUTATED     6   1
  CASP10 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      6    1
  CASP10 WILD-TYPE  308   47
                               clus
vv                              CASP10 MUTATED CASP10 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CASP10 MUTATED     6   0   0   1
  CASP10 WILD-TYPE 253   3  22  20
D1355V10, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1355V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP10 MUTATED                                  0     1
  CASP10 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CASP10 MUTATED                           1     2
  CASP10 WILD-TYPE                        18   174
D1355V12, multiclass
                                  clus
vv                                 CASP10 MUTATED CASP10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(1356) Variable = STAU1 MUTATION ANALYSIS
D1356V1, survival
                 sevent
clus2               0   1
  STAU1 MUTATED     3   3
  STAU1 WILD-TYPE 274  75
  STAU1 MUTATED STAU1 WILD-TYPE 
              6             349 
  STAU1 MUTATED STAU1 WILD-TYPE 
              3              75 
$`STAU1 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-AY-6386 TCGA-AZ-6603 TCGA-D5-5538 TCGA-D5-6536 
       19.04       100.01        17.82        29.56        54.61        17.85 

$`STAU1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6605 
       62.79        88.21        49.41         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  STAU1 MUTATED STAU1 WILD-TYPE 
          17.82            0.00 
  STAU1 MUTATED STAU1 WILD-TYPE 
         100.01          148.01 
  STAU1 MUTATED STAU1 WILD-TYPE 
          24.30           22.06 
[1] "17.8 - 100.0 (24.3)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.6"
D1356V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAU1 MUTATED         0        0        1         1         0         0
  STAU1 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAU1 MUTATED           1          0          2          0        1         0
  STAU1 WILD-TYPE        17          6         42         33       34        12
                 vv
clus              STAGE IVB
  STAU1 MUTATED           0
  STAU1 WILD-TYPE         1
D1356V3, multiclass
            clus
vv           STAU1 MUTATED STAU1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  STAU1 MUTATED     0   1   6   0
  STAU1 WILD-TYPE   9  66 243  41
D1356V4, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             0              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
  STAU1 MUTATED     3   3   1
  STAU1 WILD-TYPE 217  78  65
D1356V5, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  N0             3             217
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1356V6, binary
                 cls
clus                0   1
  STAU1 MUTATED     5   1
  STAU1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      5    1
  STAU1 WILD-TYPE  280   47
   clus
vv  STAU1 MUTATED STAU1 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D1356V7, binary
                 cls
clus                0   1
  STAU1 MUTATED     3   4
  STAU1 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      3    4
  STAU1 WILD-TYPE  167  193
        clus
vv       STAU1 MUTATED STAU1 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1356V8, binary
                 cls
clus                0   1
  STAU1 MUTATED     5   1
  STAU1 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      5    1
  STAU1 WILD-TYPE  295    7
     clus
vv    STAU1 MUTATED STAU1 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D1356V9, binary
                 cls
clus                0   1
  STAU1 MUTATED     7   0
  STAU1 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      7    0
  STAU1 WILD-TYPE  307   48
                               clus
vv                              STAU1 MUTATED STAU1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAU1 MUTATED     4   0   1   0
  STAU1 WILD-TYPE 255   3  21  21
D1356V10, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D1356V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAU1 MUTATED                                  0     0
  STAU1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAU1 MUTATED                           1     4
  STAU1 WILD-TYPE                        18   172
D1356V12, multiclass
                                  clus
vv                                 STAU1 MUTATED STAU1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = EFNB3 MUTATION ANALYSIS
D1357V1, survival
                 sevent
clus2               0   1
  EFNB3 MUTATED     6   2
  EFNB3 WILD-TYPE 271  76
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              8             347 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              2              76 
$`EFNB3 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3851 TCGA-AA-A02O TCGA-AZ-4315 TCGA-AZ-6598 
       19.04        24.00        33.07         0.92        58.39        49.41 
TCGA-CM-5861 TCGA-DM-A1D8 
       15.02        12.59 

$`EFNB3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  EFNB3 MUTATED EFNB3 WILD-TYPE 
           0.92            0.00 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
          58.39          148.01 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
          21.52           22.06 
[1] "0.9 - 58.4 (21.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1357V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFNB3 MUTATED         0        0        2         4         0         0
  EFNB3 WILD-TYPE      64        1       24       104         8         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  EFNB3 MUTATED           0
  EFNB3 WILD-TYPE         1
D1357V3, multiclass
            clus
vv           EFNB3 MUTATED EFNB3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  EFNB3 MUTATED     0   0   8   0
  EFNB3 WILD-TYPE   9  67 241  41
D1357V4, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             8             241
  T4             0              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
  EFNB3 MUTATED     7   1   0
  EFNB3 WILD-TYPE 213  80  66
D1357V5, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1357V6, binary
                 cls
clus                0   1
  EFNB3 MUTATED     5   1
  EFNB3 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      5    1
  EFNB3 WILD-TYPE  280   47
   clus
vv  EFNB3 MUTATED EFNB3 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D1357V7, binary
                 cls
clus                0   1
  EFNB3 MUTATED     4   4
  EFNB3 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      4    4
  EFNB3 WILD-TYPE  166  193
        clus
vv       EFNB3 MUTATED EFNB3 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D1357V8, binary
                 cls
clus                0   1
  EFNB3 MUTATED     5   1
  EFNB3 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      5    1
  EFNB3 WILD-TYPE  295    7
     clus
vv    EFNB3 MUTATED EFNB3 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D1357V9, binary
                 cls
clus                0   1
  EFNB3 MUTATED     7   1
  EFNB3 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      7    1
  EFNB3 WILD-TYPE  307   47
                               clus
vv                              EFNB3 MUTATED EFNB3 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EFNB3 MUTATED     5   0   1   0
  EFNB3 WILD-TYPE 254   3  21  21
D1357V10, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             0              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"
D1357V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFNB3 MUTATED                                  0     0
  EFNB3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFNB3 MUTATED                           0     4
  EFNB3 WILD-TYPE                        19   172
D1357V12, multiclass
                                  clus
vv                                 EFNB3 MUTATED EFNB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = ICAM5 MUTATION ANALYSIS
D1358V1, survival
                 sevent
clus2               0   1
  ICAM5 MUTATED     7   2
  ICAM5 WILD-TYPE 270  76
  ICAM5 MUTATED ICAM5 WILD-TYPE 
              9             346 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
              2              76 
$`ICAM5 MUTATED`
TCGA-AA-3713 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3492 
       19.04        63.62        22.09        26.17        22.06         3.02 
TCGA-AZ-6600 TCGA-CM-4746 TCGA-D5-6540 
       12.10        37.02        16.14 

$`ICAM5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6586 TCGA-G4-6625 
      100.01         1.94        49.08         5.88        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ICAM5 MUTATED ICAM5 WILD-TYPE 
           3.02            0.00 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
          63.62          148.01 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
          22.06           22.06 
[1] "3.0 - 63.6 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1358V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ICAM5 MUTATED         2        0        1         3         0         0
  ICAM5 WILD-TYPE      62        1       25       105         8         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        17          6         43         33       33        12
                 vv
clus              STAGE IVB
  ICAM5 MUTATED           0
  ICAM5 WILD-TYPE         1
D1358V3, multiclass
            clus
vv           ICAM5 MUTATED ICAM5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  ICAM5 MUTATED     0   3   6   1
  ICAM5 WILD-TYPE   9  64 243  40
D1358V4, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             6             243
  T4             1              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
  ICAM5 MUTATED     7   3   0
  ICAM5 WILD-TYPE 213  78  66
D1358V5, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1358V6, binary
                 cls
clus                0   1
  ICAM5 MUTATED     7   2
  ICAM5 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      7    2
  ICAM5 WILD-TYPE  278   46
   clus
vv  ICAM5 MUTATED ICAM5 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D1358V7, binary
                 cls
clus                0   1
  ICAM5 MUTATED     5   5
  ICAM5 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      5    5
  ICAM5 WILD-TYPE  165  192
        clus
vv       ICAM5 MUTATED ICAM5 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1358V8, binary
                 cls
clus                0   1
  ICAM5 MUTATED     7   2
  ICAM5 WILD-TYPE 293   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      7    2
  ICAM5 WILD-TYPE  293    6
     clus
vv    ICAM5 MUTATED ICAM5 WILD-TYPE
  NO              7             293
  YES             2               6
[1] 2 2
[1] FALSE
D1358V9, binary
                 cls
clus                0   1
  ICAM5 MUTATED     9   1
  ICAM5 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      9    1
  ICAM5 WILD-TYPE  305   47
                               clus
vv                              ICAM5 MUTATED ICAM5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ICAM5 MUTATED     8   0   1   0
  ICAM5 WILD-TYPE 251   3  21  21
D1358V10, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             0              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"
D1358V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ICAM5 MUTATED                                  0     0
  ICAM5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ICAM5 MUTATED                           2     5
  ICAM5 WILD-TYPE                        17   171
D1358V12, multiclass
                                  clus
vv                                 ICAM5 MUTATED ICAM5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = ZP2 MUTATION ANALYSIS
D1359V1, survival
               sevent
clus2             0   1
  ZP2 MUTATED    12   0
  ZP2 WILD-TYPE 265  78
  ZP2 MUTATED ZP2 WILD-TYPE 
           12           343 
  ZP2 MUTATED ZP2 WILD-TYPE 
            0            78 
$`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 

$`ZP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZP2 MUTATED ZP2 WILD-TYPE 
        11.64          0.00 
  ZP2 MUTATED ZP2 WILD-TYPE 
       148.01        140.38 
  ZP2 MUTATED ZP2 WILD-TYPE 
        29.85         21.99 
[1] "11.6 - 148.0 (29.9)" "0.0 - 140.4 (22.0)" 
[1] "hr="     "2.6e+07"
D1359V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZP2 MUTATED         2        0        1         2         2         1
  ZP2 WILD-TYPE      62        1       25       106         6         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        17          6         44         32       35        12
               vv
clus            STAGE IVB
  ZP2 MUTATED           0
  ZP2 WILD-TYPE         1
D1359V3, multiclass
            clus
vv           ZP2 MUTATED ZP2 WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            2           106
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  ZP2 MUTATED     0   4   5   3
  ZP2 WILD-TYPE   9  63 244  38
D1359V4, multiclass
    clus
vv   ZP2 MUTATED ZP2 WILD-TYPE
  T1           0             9
  T2           4            63
  T3           5           244
  T4           3            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
  ZP2 MUTATED    10   1   1
  ZP2 WILD-TYPE 210  80  65
D1359V5, multiclass
    clus
vv   ZP2 MUTATED ZP2 WILD-TYPE
  N0          10           210
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1359V6, binary
               cls
clus              0   1
  ZP2 MUTATED    11   0
  ZP2 WILD-TYPE 274  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED     11    0
  ZP2 WILD-TYPE  274   48
   clus
vv  ZP2 MUTATED ZP2 WILD-TYPE
  0          11           274
  1           0            48
[1] 2 2
[1] FALSE
D1359V7, binary
               cls
clus              0   1
  ZP2 MUTATED     6   6
  ZP2 WILD-TYPE 164 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED      6    6
  ZP2 WILD-TYPE  164  191
        clus
vv       ZP2 MUTATED ZP2 WILD-TYPE
  FEMALE           6           164
  MALE             6           191
[1] 2 2
[1] FALSE
D1359V8, binary
               cls
clus              0   1
  ZP2 MUTATED    12   0
  ZP2 WILD-TYPE 288   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED     12    0
  ZP2 WILD-TYPE  288    8
     clus
vv    ZP2 MUTATED ZP2 WILD-TYPE
  NO           12           288
  YES           0             8
[1] 2 2
[1] FALSE
D1359V9, binary
               cls
clus              0   1
  ZP2 MUTATED    10   2
  ZP2 WILD-TYPE 304  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED     10    2
  ZP2 WILD-TYPE  304   46
                               clus
vv                              ZP2 MUTATED ZP2 WILD-TYPE
  COLON ADENOCARCINOMA                   10           304
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ZP2 MUTATED     9   0   0   0
  ZP2 WILD-TYPE 250   3  22  21
D1359V10, multiclass
    clus
vv   ZP2 MUTATED ZP2 WILD-TYPE
  R0           9           250
  R1           0             3
  R2           0            22
  RX           0            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"
D1359V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZP2 MUTATED                                  0     0
  ZP2 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZP2 MUTATED                           1     7
  ZP2 WILD-TYPE                        18   169
D1359V12, multiclass
                                  clus
vv                                 ZP2 MUTATED ZP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      7           169
[1] 4 2
[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 = RXRA MUTATION ANALYSIS
D1360V1, survival
                sevent
clus2              0   1
  RXRA MUTATED     6   2
  RXRA WILD-TYPE 271  76
  RXRA MUTATED RXRA WILD-TYPE 
             8            347 
  RXRA MUTATED RXRA WILD-TYPE 
             2             76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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         21.990 
[1] "3.0 - 135.7 (30.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1360V2, continuous
                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      63        1       24       105         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  RXRA MUTATED           0
  RXRA WILD-TYPE         1
D1360V3, multiclass
            clus
vv           RXRA MUTATED RXRA WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RXRA MUTATED     0   2   6   0
  RXRA WILD-TYPE   9  65 243  41
D1360V4, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            0             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
  RXRA MUTATED     7   1   0
  RXRA WILD-TYPE 213  80  66
D1360V5, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  N0            7            213
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1360V6, binary
                cls
clus               0   1
  RXRA MUTATED     6   0
  RXRA WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      6    0
  RXRA WILD-TYPE  279   48
   clus
vv  RXRA MUTATED RXRA WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1360V7, binary
                cls
clus               0   1
  RXRA MUTATED     2   6
  RXRA WILD-TYPE 168 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      2    6
  RXRA WILD-TYPE  168  191
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  FEMALE            2            168
  MALE              6            191
[1] 2 2
[1] FALSE
D1360V8, binary
                cls
clus               0   1
  RXRA MUTATED     7   0
  RXRA WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      7    0
  RXRA WILD-TYPE  293    8
     clus
vv    RXRA MUTATED RXRA WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1360V9, binary
                cls
clus               0   1
  RXRA MUTATED     5   2
  RXRA WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      5    2
  RXRA WILD-TYPE  309   46
                               clus
vv                              RXRA MUTATED RXRA WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RXRA MUTATED     5   0   0   0
  RXRA WILD-TYPE 254   3  22  21
D1360V10, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1360V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RXRA MUTATED                                  0     0
  RXRA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RXRA MUTATED                           0     6
  RXRA WILD-TYPE                        19   170
D1360V12, multiclass
                                  clus
vv                                 RXRA MUTATED RXRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = CCT5 MUTATION ANALYSIS
D1361V1, survival
                sevent
clus2              0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 270  78
  CCT5 MUTATED CCT5 WILD-TYPE 
             7            348 
  CCT5 MUTATED CCT5 WILD-TYPE 
             0             78 
$`CCT5 MUTATED`
TCGA-G4-6321 TCGA-A6-5661 TCGA-AA-3544 TCGA-AA-3949 TCGA-AA-A010 TCGA-CM-5861 
       22.09        33.53        14.01        26.01        34.98        15.02 
TCGA-D5-6928 
       11.64 

$`CCT5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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         22.045 
[1] "11.6 - 35.0 (22.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1361V2, continuous
                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      63        1       26       105         7         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        16          6         43         33       35        12
                vv
clus             STAGE IVB
  CCT5 MUTATED           0
  CCT5 WILD-TYPE         1
D1361V3, multiclass
            clus
vv           CCT5 MUTATED CCT5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CCT5 MUTATED     0   2   5   1
  CCT5 WILD-TYPE   9  65 244  40
D1361V4, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            1             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
  CCT5 MUTATED     5   2   1
  CCT5 WILD-TYPE 215  79  65
D1361V5, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  N0            5            215
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1361V6, binary
                cls
clus               0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      7    0
  CCT5 WILD-TYPE  278   48
   clus
vv  CCT5 MUTATED CCT5 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1361V7, binary
                cls
clus               0   1
  CCT5 MUTATED     5   3
  CCT5 WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      5    3
  CCT5 WILD-TYPE  165  194
        clus
vv       CCT5 MUTATED CCT5 WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D1361V8, binary
                cls
clus               0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      7    0
  CCT5 WILD-TYPE  293    8
     clus
vv    CCT5 MUTATED CCT5 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1361V9, binary
                cls
clus               0   1
  CCT5 MUTATED     6   2
  CCT5 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      6    2
  CCT5 WILD-TYPE  308   46
                               clus
vv                              CCT5 MUTATED CCT5 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCT5 MUTATED     8   0   0   0
  CCT5 WILD-TYPE 251   3  22  21
D1361V10, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            0             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"
D1361V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCT5 MUTATED                                  0     0
  CCT5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCT5 MUTATED                           1     3
  CCT5 WILD-TYPE                        18   173
D1361V12, multiclass
                                  clus
vv                                 CCT5 MUTATED CCT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = DOCK8 MUTATION ANALYSIS
D1362V1, survival
                 sevent
clus2               0   1
  DOCK8 MUTATED    15   4
  DOCK8 WILD-TYPE 262  74
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             19             336 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              4              74 
$`DOCK8 MUTATED`
TCGA-AA-3979 TCGA-G4-6628 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3842 
       24.00        79.69        78.08         6.97        33.04        37.02 
TCGA-AA-A010 TCGA-AD-6890 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-6598 
       34.98        24.53        27.09         0.20        21.44        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-5537 TCGA-F4-6570 
       12.76        10.06        14.99        14.04        45.40         6.18 
TCGA-G4-6309 
       85.48 

$`DOCK8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        38.99         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       26.47        14.50        16.31         0.95        33.01        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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  DOCK8 MUTATED DOCK8 WILD-TYPE 
            0.2             0.0 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          85.48          148.01 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          24.53           22.01 
[1] "0.2 - 85.5 (24.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1362V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK8 MUTATED         3        0        3         8         1         0
  DOCK8 WILD-TYPE      61        1       23       100         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK8 MUTATED           0          1          1          2        0         0
  DOCK8 WILD-TYPE        18          5         43         31       35        12
                 vv
clus              STAGE IVB
  DOCK8 MUTATED           0
  DOCK8 WILD-TYPE         1
D1362V3, multiclass
            clus
vv           DOCK8 MUTATED DOCK8 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  DOCK8 MUTATED     1   4  14   1
  DOCK8 WILD-TYPE   8  63 235  40
D1362V4, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            14             235
  T4             1              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
  DOCK8 MUTATED    15   2   3
  DOCK8 WILD-TYPE 205  79  63
D1362V5, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  N0            15             205
  N1             2              79
  N2             3              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"
D1362V6, binary
                 cls
clus                0   1
  DOCK8 MUTATED    15   0
  DOCK8 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     15    0
  DOCK8 WILD-TYPE  270   48
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0            15             270
  1             0              48
[1] 2 2
[1] FALSE
D1362V7, binary
                 cls
clus                0   1
  DOCK8 MUTATED    10  10
  DOCK8 WILD-TYPE 160 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     10   10
  DOCK8 WILD-TYPE  160  187
        clus
vv       DOCK8 MUTATED DOCK8 WILD-TYPE
  FEMALE            10             160
  MALE              10             187
[1] 2 2
[1] FALSE
D1362V8, binary
                 cls
clus                0   1
  DOCK8 MUTATED    17   0
  DOCK8 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     17    0
  DOCK8 WILD-TYPE  283    8
     clus
vv    DOCK8 MUTATED DOCK8 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D1362V9, binary
                 cls
clus                0   1
  DOCK8 MUTATED    18   2
  DOCK8 WILD-TYPE 296  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     18    2
  DOCK8 WILD-TYPE  296   46
                               clus
vv                              DOCK8 MUTATED DOCK8 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK8 MUTATED    15   0   0   3
  DOCK8 WILD-TYPE 244   3  22  18
D1362V10, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             0              22
  RX             3              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"
D1362V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK8 MUTATED                                  0     2
  DOCK8 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK8 MUTATED                           2     9
  DOCK8 WILD-TYPE                        17   167
D1362V12, multiclass
                                  clus
vv                                 DOCK8 MUTATED DOCK8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(1363) Variable = ZNF512 MUTATION ANALYSIS
D1363V1, survival
                  sevent
clus2                0   1
  ZNF512 MUTATED     2   1
  ZNF512 WILD-TYPE 275  77
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              352 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               1               77 
$`ZNF512 MUTATED`
TCGA-AD-6963 TCGA-AZ-6600 TCGA-G4-6315 
       27.42        12.10        61.91 

$`ZNF512 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  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           22.045 
[1] "12.1 - 61.9 (27.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1363V2, continuous
                  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      64        1       26       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF512 MUTATED           0          0          0          0        2
  ZNF512 WILD-TYPE        18          6         44         33       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF512 MUTATED           0         0
  ZNF512 WILD-TYPE        12         1
D1363V3, multiclass
[1] "Remove cluster labels:" "ZNF512 MUTATED"        
clus
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               2              355 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3516       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-3527       TCGA-AA-3530 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A285       TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-3810       TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5660       TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5665       TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6141       TCGA-A6-6142       TCGA-A6-6648       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-3502       TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3517       TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3526 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3542       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3561 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3663       TCGA-AA-3664 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3673       TCGA-AA-3678 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3811       TCGA-AA-3812 
"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-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3861       TCGA-AA-3864 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3866       TCGA-AA-3869       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-3941       TCGA-AA-3947 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984       TCGA-AA-3989 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"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-A010       TCGA-AA-A017 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       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-6889       TCGA-AD-6899       TCGA-AD-6965 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       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-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-CA-5254 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"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-D5-6534       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-D5-6540       TCGA-D5-6541 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6307       TCGA-G4-6309 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  ZNF512 MUTATED     0   0   2   1
  ZNF512 WILD-TYPE   9  67 247  40
D1363V4, multiclass
    clus
vv   ZNF512 MUTATED ZNF512 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              2              247
  T4              1               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
  ZNF512 MUTATED     1   2   0
  ZNF512 WILD-TYPE 219  79  66
D1363V5, multiclass
    clus
vv   ZNF512 MUTATED ZNF512 WILD-TYPE
  N0              1              219
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1363V6, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     0   2
  ZNF512 WILD-TYPE 285  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      0    2
  ZNF512 WILD-TYPE  285   46
   clus
vv  ZNF512 MUTATED ZNF512 WILD-TYPE
  0              0              285
  1              2               46
[1] 2 2
[1] FALSE
D1363V7, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     0   3
  ZNF512 WILD-TYPE 170 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      0    3
  ZNF512 WILD-TYPE  170  194
        clus
vv       ZNF512 MUTATED ZNF512 WILD-TYPE
  FEMALE              0              170
  MALE                3              194
[1] 2 2
[1] FALSE
D1363V8, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     3   0
  ZNF512 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      3    0
  ZNF512 WILD-TYPE  297    8
     clus
vv    ZNF512 MUTATED ZNF512 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1363V9, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     3   0
  ZNF512 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      3    0
  ZNF512 WILD-TYPE  311   48
                               clus
vv                              ZNF512 MUTATED ZNF512 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF512 MUTATED     1   0   0   0
  ZNF512 WILD-TYPE 258   3  22  21
D1363V10, multiclass
[1] "Remove cluster labels:" "ZNF512 MUTATED"        
clus
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               1              304 
      TCGA-A6-2677       TCGA-AA-3496       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-3527 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2676       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-3502       TCGA-AA-3510 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       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-3544 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660 
"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-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-3693 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       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-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3984       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-A00N 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00W       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-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
D1363V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF512 MUTATED                                  0     0
  ZNF512 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF512 MUTATED                           1     2
  ZNF512 WILD-TYPE                        18   174
D1363V12, multiclass
                                  clus
vv                                 ZNF512 MUTATED ZNF512 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(1364) Variable = TBCA MUTATION ANALYSIS
D1364V1, survival
                sevent
clus2              0   1
  TBCA MUTATED     4   0
  TBCA WILD-TYPE 273  78
  TBCA MUTATED TBCA WILD-TYPE 
             4            351 
  TBCA MUTATED TBCA WILD-TYPE 
             0             78 
$`TBCA MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-AY-6196 TCGA-CM-5349 
       33.01        34.98         0.20        30.08 

$`TBCA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TBCA MUTATED TBCA WILD-TYPE 
           0.2            0.0 
  TBCA MUTATED TBCA WILD-TYPE 
         34.98         148.01 
  TBCA MUTATED TBCA WILD-TYPE 
        31.545         22.030 
[1] "0.2 - 35.0 (31.5)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1364V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBCA MUTATED         0        0        0         1         2         0
  TBCA WILD-TYPE      64        1       26       107         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBCA MUTATED           0          0          0          1        0         0
  TBCA WILD-TYPE        18          6         44         32       35        12
                vv
clus             STAGE IVB
  TBCA MUTATED           0
  TBCA WILD-TYPE         1
D1364V3, multiclass
            clus
vv           TBCA MUTATED TBCA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TBCA MUTATED     0   0   2   2
  TBCA WILD-TYPE   9  67 247  39
D1364V4, multiclass
    clus
vv   TBCA MUTATED TBCA WILD-TYPE
  T1            0              9
  T2            0             67
  T3            2            247
  T4            2             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
  TBCA MUTATED     3   0   1
  TBCA WILD-TYPE 217  81  65
D1364V5, multiclass
    clus
vv   TBCA MUTATED TBCA WILD-TYPE
  N0            3            217
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1364V6, binary
                cls
clus               0   1
  TBCA MUTATED     3   0
  TBCA WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCA MUTATED      3    0
  TBCA WILD-TYPE  282   48
   clus
vv  TBCA MUTATED TBCA WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1364V7, binary
                cls
clus               0   1
  TBCA MUTATED     3   1
  TBCA WILD-TYPE 167 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCA MUTATED      3    1
  TBCA WILD-TYPE  167  196
        clus
vv       TBCA MUTATED TBCA WILD-TYPE
  FEMALE            3            167
  MALE              1            196
[1] 2 2
[1] FALSE
D1364V8, binary
                cls
clus               0   1
  TBCA MUTATED     3   0
  TBCA WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCA MUTATED      3    0
  TBCA WILD-TYPE  297    8
     clus
vv    TBCA MUTATED TBCA WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1364V9, binary
                cls
clus               0   1
  TBCA MUTATED     2   2
  TBCA WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCA MUTATED      2    2
  TBCA WILD-TYPE  312   46
                               clus
vv                              TBCA MUTATED TBCA WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TBCA MUTATED     4   0   0   0
  TBCA WILD-TYPE 255   3  22  21
D1364V10, multiclass
    clus
vv   TBCA MUTATED TBCA WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D1364V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBCA MUTATED                                  0     0
  TBCA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TBCA MUTATED                           0     2
  TBCA WILD-TYPE                        19   174
D1364V12, multiclass
[1] "Remove cluster labels:" "TBCA MUTATED"          
clus
  TBCA MUTATED TBCA WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6651     TCGA-A6-6652 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 

Clustering(1365) Variable = EPHA2 MUTATION ANALYSIS
D1365V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED     8   3
  EPHA2 WILD-TYPE 269  75
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             344 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              3              75 
$`EPHA2 MUTATED`
TCGA-AA-3715 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00A 
       19.04        33.53        19.66         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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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          22.075 
[1] "1.0 - 49.4 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1365V2, continuous
                 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      62        1       24       103         8         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        18          6         44         31       35        12
                 vv
clus              STAGE IVB
  EPHA2 MUTATED           0
  EPHA2 WILD-TYPE         1
D1365V3, multiclass
            clus
vv           EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  EPHA2 MUTATED     0   2   8   1
  EPHA2 WILD-TYPE   9  65 241  40
D1365V4, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             1              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
  EPHA2 MUTATED     9   1   1
  EPHA2 WILD-TYPE 211  80  65
D1365V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1365V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9   0
  EPHA2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9    0
  EPHA2 WILD-TYPE  276   48
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1365V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     5   6
  EPHA2 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      5    6
  EPHA2 WILD-TYPE  165  191
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1365V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9   0
  EPHA2 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9    0
  EPHA2 WILD-TYPE  291    8
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1365V9, binary
                 cls
clus                0   1
  EPHA2 MUTATED     8   3
  EPHA2 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      8    3
  EPHA2 WILD-TYPE  306   45
                               clus
vv                              EPHA2 MUTATED EPHA2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA2 MUTATED     8   0   0   0
  EPHA2 WILD-TYPE 251   3  22  21
D1365V10, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1365V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA2 MUTATED                                  0     0
  EPHA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED                           2     5
  EPHA2 WILD-TYPE                        17   171
D1365V12, multiclass
                                  clus
vv                                 EPHA2 MUTATED EPHA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = OR6K2 MUTATION ANALYSIS
D1366V1, survival
                 sevent
clus2               0   1
  OR6K2 MUTATED    11   3
  OR6K2 WILD-TYPE 266  75
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             14             341 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
              3              75 
$`OR6K2 MUTATED`
TCGA-AA-3554 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3809 TCGA-AA-3663 TCGA-AA-3989 
       17.95        35.80        26.17        32.75         6.97         7.96 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-D5-6920 
        4.01        12.16        21.44        58.39        10.06        12.39 
TCGA-DM-A0X9 TCGA-F4-6856 
      119.70        35.31 

$`OR6K2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 
       13.05        34.06        25.02        27.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        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         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR6K2 MUTATED OR6K2 WILD-TYPE 
           4.01            0.00 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
         119.70          148.01 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
         19.695          22.090 
[1] "4.0 - 119.7 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1366V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR6K2 MUTATED         2        0        1         8         2         0
  OR6K2 WILD-TYPE      62        1       25       100         6         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  OR6K2 MUTATED           0
  OR6K2 WILD-TYPE         1
D1366V3, multiclass
            clus
vv           OR6K2 MUTATED OR6K2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  OR6K2 MUTATED     0   2  10   2
  OR6K2 WILD-TYPE   9  65 239  39
D1366V4, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             2              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
  OR6K2 MUTATED    13   0   1
  OR6K2 WILD-TYPE 207  81  65
D1366V5, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  N0            13             207
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1366V6, binary
                 cls
clus                0   1
  OR6K2 MUTATED    11   1
  OR6K2 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     11    1
  OR6K2 WILD-TYPE  274   47
   clus
vv  OR6K2 MUTATED OR6K2 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D1366V7, binary
                 cls
clus                0   1
  OR6K2 MUTATED     6   8
  OR6K2 WILD-TYPE 164 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED      6    8
  OR6K2 WILD-TYPE  164  189
        clus
vv       OR6K2 MUTATED OR6K2 WILD-TYPE
  FEMALE             6             164
  MALE               8             189
[1] 2 2
[1] FALSE
D1366V8, binary
                 cls
clus                0   1
  OR6K2 MUTATED    12   0
  OR6K2 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     12    0
  OR6K2 WILD-TYPE  288    8
     clus
vv    OR6K2 MUTATED OR6K2 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1366V9, binary
                 cls
clus                0   1
  OR6K2 MUTATED    10   4
  OR6K2 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     10    4
  OR6K2 WILD-TYPE  304   44
                               clus
vv                              OR6K2 MUTATED OR6K2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR6K2 MUTATED    11   0   1   1
  OR6K2 WILD-TYPE 248   3  21  20
D1366V10, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             1              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"
D1366V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6K2 MUTATED                                  0     1
  OR6K2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6K2 MUTATED                           0     9
  OR6K2 WILD-TYPE                        19   167
D1366V12, multiclass
                                  clus
vv                                 OR6K2 MUTATED OR6K2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(1367) Variable = CTR9 MUTATION ANALYSIS
D1367V1, survival
                sevent
clus2              0   1
  CTR9 MUTATED    13   4
  CTR9 WILD-TYPE 264  74
  CTR9 MUTATED CTR9 WILD-TYPE 
            17            338 
  CTR9 MUTATED CTR9 WILD-TYPE 
             4             74 
$`CTR9 MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6137 TCGA-AA-3663 TCGA-AA-3864 
      100.01        79.69        22.06        27.09         6.97        53.00 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-5254 
        2.01        16.08         4.01        34.98        58.39        12.69 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-6168 TCGA-DM-A1D4 
       12.76        10.06        14.30        12.99        92.75 

$`CTR9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       23.61        22.09        32.71        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       20.98        34.03        21.99        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.36        12.39        12.59        12.59        12.20 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CTR9 MUTATED CTR9 WILD-TYPE 
          2.01           0.00 
  CTR9 MUTATED CTR9 WILD-TYPE 
        100.01         148.01 
  CTR9 MUTATED CTR9 WILD-TYPE 
         16.08          22.09 
[1] "2.0 - 100.0 (16.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1367V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTR9 MUTATED         1        0        3         9         2         0
  CTR9 WILD-TYPE      63        1       23        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTR9 MUTATED           1          0          1          0        0         0
  CTR9 WILD-TYPE        17          6         43         33       35        12
                vv
clus             STAGE IVB
  CTR9 MUTATED           0
  CTR9 WILD-TYPE         1
D1367V3, multiclass
            clus
vv           CTR9 MUTATED CTR9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             9             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CTR9 MUTATED     0   1  14   2
  CTR9 WILD-TYPE   9  66 235  39
D1367V4, multiclass
    clus
vv   CTR9 MUTATED CTR9 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           14            235
  T4            2             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
  CTR9 MUTATED    15   2   0
  CTR9 WILD-TYPE 205  79  66
D1367V5, multiclass
    clus
vv   CTR9 MUTATED CTR9 WILD-TYPE
  N0           15            205
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1367V6, binary
                cls
clus               0   1
  CTR9 MUTATED    17   0
  CTR9 WILD-TYPE 268  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTR9 MUTATED     17    0
  CTR9 WILD-TYPE  268   48
   clus
vv  CTR9 MUTATED CTR9 WILD-TYPE
  0           17            268
  1            0             48
[1] 2 2
[1] FALSE
D1367V7, binary
                cls
clus               0   1
  CTR9 MUTATED     5  12
  CTR9 WILD-TYPE 165 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTR9 MUTATED      5   12
  CTR9 WILD-TYPE  165  185
        clus
vv       CTR9 MUTATED CTR9 WILD-TYPE
  FEMALE            5            165
  MALE             12            185
[1] 2 2
[1] FALSE
D1367V8, binary
                cls
clus               0   1
  CTR9 MUTATED    14   0
  CTR9 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTR9 MUTATED     14    0
  CTR9 WILD-TYPE  286    8
     clus
vv    CTR9 MUTATED CTR9 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1367V9, binary
                cls
clus               0   1
  CTR9 MUTATED    14   3
  CTR9 WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTR9 MUTATED     14    3
  CTR9 WILD-TYPE  300   45
                               clus
vv                              CTR9 MUTATED CTR9 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTR9 MUTATED     9   0   0   4
  CTR9 WILD-TYPE 250   3  22  17
D1367V10, multiclass
    clus
vv   CTR9 MUTATED CTR9 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            4             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"
D1367V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTR9 MUTATED                                  0     4
  CTR9 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTR9 MUTATED                           1     6
  CTR9 WILD-TYPE                        18   170
D1367V12, multiclass
                                  clus
vv                                 CTR9 MUTATED CTR9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = RWDD4A MUTATION ANALYSIS
D1368V1, survival
                  sevent
clus2                0   1
  RWDD4A MUTATED     5   0
  RWDD4A WILD-TYPE 272  78
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               5              350 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               0               78 
$`RWDD4A MUTATED`
TCGA-AA-3520 TCGA-AA-3510 TCGA-AD-6963 TCGA-CM-6678 TCGA-DM-A282 
       24.03        63.98        27.42        11.01       139.17 

$`RWDD4A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RWDD4A MUTATED RWDD4A WILD-TYPE 
           11.01             0.00 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
          139.17           148.01 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
           27.42            22.01 
[1] "11.0 - 139.2 (27.4)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "9400000"
D1368V2, continuous
                  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      64        1       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RWDD4A MUTATED           0          0          0          0        0
  RWDD4A WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  RWDD4A MUTATED           1         0
  RWDD4A WILD-TYPE        11         1
D1368V3, multiclass
            clus
vv           RWDD4A MUTATED RWDD4A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  RWDD4A MUTATED     0   0   4   1
  RWDD4A WILD-TYPE   9  67 245  40
D1368V4, multiclass
    clus
vv   RWDD4A MUTATED RWDD4A WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              1               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
  RWDD4A MUTATED     4   1   0
  RWDD4A WILD-TYPE 216  80  66
D1368V5, multiclass
    clus
vv   RWDD4A MUTATED RWDD4A WILD-TYPE
  N0              4              216
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1368V6, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     3   1
  RWDD4A WILD-TYPE 282  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      3    1
  RWDD4A WILD-TYPE  282   47
   clus
vv  RWDD4A MUTATED RWDD4A WILD-TYPE
  0              3              282
  1              1               47
[1] 2 2
[1] FALSE
D1368V7, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     3   2
  RWDD4A WILD-TYPE 167 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      3    2
  RWDD4A WILD-TYPE  167  195
        clus
vv       RWDD4A MUTATED RWDD4A WILD-TYPE
  FEMALE              3              167
  MALE                2              195
[1] 2 2
[1] FALSE
D1368V8, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     4   0
  RWDD4A WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      4    0
  RWDD4A WILD-TYPE  296    8
     clus
vv    RWDD4A MUTATED RWDD4A WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1368V9, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     5   0
  RWDD4A WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      5    0
  RWDD4A WILD-TYPE  309   48
                               clus
vv                              RWDD4A MUTATED RWDD4A WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RWDD4A MUTATED     3   0   0   0
  RWDD4A WILD-TYPE 256   3  22  21
D1368V10, multiclass
    clus
vv   RWDD4A MUTATED RWDD4A WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1368V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RWDD4A MUTATED                                  0     0
  RWDD4A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RWDD4A MUTATED                           0     3
  RWDD4A WILD-TYPE                        19   173
D1368V12, multiclass
                                  clus
vv                                 RWDD4A MUTATED RWDD4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = STK40 MUTATION ANALYSIS
D1369V1, survival
                 sevent
clus2               0   1
  STK40 MUTATED     7   0
  STK40 WILD-TYPE 270  78
  STK40 MUTATED STK40 WILD-TYPE 
              7             348 
  STK40 MUTATED STK40 WILD-TYPE 
              0              78 
$`STK40 MUTATED`
TCGA-AA-3525 TCGA-G4-6321 TCGA-AA-3864 TCGA-AA-3949 TCGA-CK-4947 TCGA-D5-6533 
        8.05        22.09        53.00        26.01        17.56        25.48 
TCGA-F4-6569 
       35.74 

$`STK40 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6570 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  STK40 MUTATED STK40 WILD-TYPE 
           8.05            0.00 
  STK40 MUTATED STK40 WILD-TYPE 
          53.00          148.01 
  STK40 MUTATED STK40 WILD-TYPE 
          25.48           22.01 
[1] "8.1 - 53.0 (25.5)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1369V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK40 MUTATED         1        0        1         0         0         0
  STK40 WILD-TYPE      63        1       25       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK40 MUTATED           1          0          3          0        0         0
  STK40 WILD-TYPE        17          6         41         33       35        12
                 vv
clus              STAGE IVB
  STK40 MUTATED           0
  STK40 WILD-TYPE         1
D1369V3, multiclass
            clus
vv           STK40 MUTATED STK40 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              0             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  STK40 MUTATED     0   2   3   2
  STK40 WILD-TYPE   9  65 246  39
D1369V4, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             2              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
  STK40 MUTATED     3   4   0
  STK40 WILD-TYPE 217  77  66
D1369V5, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  N0             3             217
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1369V6, binary
                 cls
clus                0   1
  STK40 MUTATED     6   0
  STK40 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      6    0
  STK40 WILD-TYPE  279   48
   clus
vv  STK40 MUTATED STK40 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1369V7, binary
                 cls
clus                0   1
  STK40 MUTATED     4   3
  STK40 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      4    3
  STK40 WILD-TYPE  166  194
        clus
vv       STK40 MUTATED STK40 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1369V8, binary
                 cls
clus                0   1
  STK40 MUTATED     7   0
  STK40 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      7    0
  STK40 WILD-TYPE  293    8
     clus
vv    STK40 MUTATED STK40 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1369V9, binary
                 cls
clus                0   1
  STK40 MUTATED     6   1
  STK40 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      6    1
  STK40 WILD-TYPE  308   47
                               clus
vv                              STK40 MUTATED STK40 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK40 MUTATED     6   0   0   1
  STK40 WILD-TYPE 253   3  22  20
D1369V10, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1369V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK40 MUTATED                                  0     0
  STK40 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK40 MUTATED                           0     4
  STK40 WILD-TYPE                        19   172
D1369V12, multiclass
                                  clus
vv                                 STK40 MUTATED STK40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SLC44A1 MUTATION ANALYSIS
D1370V1, survival
                   sevent
clus2                 0   1
  SLC44A1 MUTATED     7   1
  SLC44A1 WILD-TYPE 270  77
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                8               347 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                1                77 
$`SLC44A1 MUTATED`
TCGA-AA-3844 TCGA-AD-6964 TCGA-AA-3821 TCGA-AY-6386 TCGA-CA-6717 TCGA-CM-4743 
       14.93        10.88         1.02        17.82        12.76        23.05 
TCGA-D5-6535 TCGA-G4-6323 
       15.12        13.78 

$`SLC44A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
             1.02              0.00 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
            23.05            148.01 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
           14.355            22.360 
[1] "1.0 - 23.1 (14.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1"  
D1370V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC44A1 MUTATED         1        1        0         3         0         0
  SLC44A1 WILD-TYPE      63        0       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A1 MUTATED           0          0          2          1        0
  SLC44A1 WILD-TYPE        18          6         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC44A1 MUTATED           0         0
  SLC44A1 WILD-TYPE        12         1
D1370V3, multiclass
            clus
vv           SLC44A1 MUTATED SLC44A1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 1                 0
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC44A1 MUTATED     0   1   6   1
  SLC44A1 WILD-TYPE   9  66 243  40
D1370V4, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               6               243
  T4               1                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
  SLC44A1 MUTATED     5   2   2
  SLC44A1 WILD-TYPE 215  79  64
D1370V5, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  N0               5               215
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1370V6, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     6   0
  SLC44A1 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      6    0
  SLC44A1 WILD-TYPE  279   48
   clus
vv  SLC44A1 MUTATED SLC44A1 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1370V7, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     5   4
  SLC44A1 WILD-TYPE 165 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      5    4
  SLC44A1 WILD-TYPE  165  193
        clus
vv       SLC44A1 MUTATED SLC44A1 WILD-TYPE
  FEMALE               5               165
  MALE                 4               193
[1] 2 2
[1] FALSE
D1370V8, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     7   1
  SLC44A1 WILD-TYPE 293   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      7    1
  SLC44A1 WILD-TYPE  293    7
     clus
vv    SLC44A1 MUTATED SLC44A1 WILD-TYPE
  NO                7               293
  YES               1                 7
[1] 2 2
[1] FALSE
D1370V9, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     7   2
  SLC44A1 WILD-TYPE 307  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      7    2
  SLC44A1 WILD-TYPE  307   46
                               clus
vv                              SLC44A1 MUTATED SLC44A1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC44A1 MUTATED     6   0   0   2
  SLC44A1 WILD-TYPE 253   3  22  19
D1370V10, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               2                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"
D1370V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC44A1 MUTATED                                  0     1
  SLC44A1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC44A1 MUTATED                           2     3
  SLC44A1 WILD-TYPE                        17   173
D1370V12, multiclass
                                  clus
vv                                 SLC44A1 MUTATED SLC44A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          3               173
[1] 4 2
[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 = LPIN2 MUTATION ANALYSIS
D1371V1, survival
                 sevent
clus2               0   1
  LPIN2 MUTATED     7   1
  LPIN2 WILD-TYPE 270  77
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              8             347 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              1              77 
$`LPIN2 MUTATED`
TCGA-G4-6586 TCGA-AA-A010 TCGA-AA-A02J TCGA-AZ-4315 TCGA-CK-4948 TCGA-D5-6922 
       35.80        34.98         5.03        58.39       148.01        10.13 
TCGA-F4-6703 TCGA-F4-6856 
       47.87        35.31 

$`LPIN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LPIN2 MUTATED LPIN2 WILD-TYPE 
           5.03            0.00 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
         148.01          140.38 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
         35.555          21.990 
[1] "5.0 - 148.0 (35.6)" "0.0 - 140.4 (22.0)"
[1] "hr=" "2.5"
D1371V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPIN2 MUTATED         1        0        0         4         1         0
  LPIN2 WILD-TYPE      63        1       26       104         7         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        17          5         44         33       34        12
                 vv
clus              STAGE IVB
  LPIN2 MUTATED           0
  LPIN2 WILD-TYPE         1
D1371V3, multiclass
            clus
vv           LPIN2 MUTATED LPIN2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  LPIN2 MUTATED     0   1   7   1
  LPIN2 WILD-TYPE   9  66 242  40
D1371V4, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             1              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
  LPIN2 MUTATED     7   2   0
  LPIN2 WILD-TYPE 213  79  66
D1371V5, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1371V6, binary
                 cls
clus                0   1
  LPIN2 MUTATED     8   1
  LPIN2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      8    1
  LPIN2 WILD-TYPE  277   47
   clus
vv  LPIN2 MUTATED LPIN2 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1371V7, binary
                 cls
clus                0   1
  LPIN2 MUTATED     5   4
  LPIN2 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      5    4
  LPIN2 WILD-TYPE  165  193
        clus
vv       LPIN2 MUTATED LPIN2 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1371V8, binary
                 cls
clus                0   1
  LPIN2 MUTATED     7   0
  LPIN2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      7    0
  LPIN2 WILD-TYPE  293    8
     clus
vv    LPIN2 MUTATED LPIN2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1371V9, binary
                 cls
clus                0   1
  LPIN2 MUTATED     8   1
  LPIN2 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      8    1
  LPIN2 WILD-TYPE  306   47
                               clus
vv                              LPIN2 MUTATED LPIN2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LPIN2 MUTATED     8   0   1   0
  LPIN2 WILD-TYPE 251   3  21  21
D1371V10, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             0              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"
D1371V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPIN2 MUTATED                                  0     0
  LPIN2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LPIN2 MUTATED                           0     6
  LPIN2 WILD-TYPE                        19   170
D1371V12, multiclass
                                  clus
vv                                 LPIN2 MUTATED LPIN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = BLM MUTATION ANALYSIS
D1372V1, survival
               sevent
clus2             0   1
  BLM MUTATED    14   2
  BLM WILD-TYPE 263  76
  BLM MUTATED BLM WILD-TYPE 
           16           339 
  BLM MUTATED BLM WILD-TYPE 
            2            76 
$`BLM MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3977 
       25.08        79.69        46.65        22.06         1.02        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CA-6718 
       18.05         4.01        34.98        33.01        58.39        10.06 
TCGA-CM-4744 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6534 
       20.02        14.04        11.01        43.27 

$`BLM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       35.80        26.17        91.79        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  BLM MUTATED BLM WILD-TYPE 
         1.02          0.00 
  BLM MUTATED BLM WILD-TYPE 
        79.69        148.01 
  BLM MUTATED BLM WILD-TYPE 
        23.54         22.03 
[1] "1.0 - 79.7 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1372V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BLM MUTATED         3        0        0         6         2         0
  BLM WILD-TYPE      61        1       26       102         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BLM MUTATED           0          0          3          0        0         2
  BLM WILD-TYPE        18          6         41         33       35        10
               vv
clus            STAGE IVB
  BLM MUTATED           0
  BLM WILD-TYPE         1
D1372V3, multiclass
            clus
vv           BLM MUTATED BLM WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            6           102
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           3            41
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            2            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
  BLM MUTATED     0   4   9   4
  BLM WILD-TYPE   9  63 240  37
D1372V4, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  T1           0             9
  T2           4            63
  T3           9           240
  T4           4            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
  BLM MUTATED    12   5   0
  BLM WILD-TYPE 208  76  66
D1372V5, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  N0          12           208
  N1           5            76
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1372V6, binary
               cls
clus              0   1
  BLM MUTATED    14   2
  BLM WILD-TYPE 271  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     14    2
  BLM WILD-TYPE  271   46
   clus
vv  BLM MUTATED BLM WILD-TYPE
  0          14           271
  1           2            46
[1] 2 2
[1] FALSE
D1372V7, binary
               cls
clus              0   1
  BLM MUTATED     9   8
  BLM WILD-TYPE 161 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      9    8
  BLM WILD-TYPE  161  189
        clus
vv       BLM MUTATED BLM WILD-TYPE
  FEMALE           9           161
  MALE             8           189
[1] 2 2
[1] FALSE
D1372V8, binary
               cls
clus              0   1
  BLM MUTATED    14   0
  BLM WILD-TYPE 286   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     14    0
  BLM WILD-TYPE  286    8
     clus
vv    BLM MUTATED BLM WILD-TYPE
  NO           14           286
  YES           0             8
[1] 2 2
[1] FALSE
D1372V9, binary
               cls
clus              0   1
  BLM MUTATED    14   3
  BLM WILD-TYPE 300  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     14    3
  BLM WILD-TYPE  300   45
                               clus
vv                              BLM MUTATED BLM WILD-TYPE
  COLON ADENOCARCINOMA                   14           300
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  BLM MUTATED    15   0   0   1
  BLM WILD-TYPE 244   3  22  20
D1372V10, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  R0          15           244
  R1           0             3
  R2           0            22
  RX           1            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"
D1372V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BLM MUTATED                                  0     1
  BLM WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  BLM MUTATED                           1     9
  BLM WILD-TYPE                        18   167
D1372V12, multiclass
                                  clus
vv                                 BLM MUTATED BLM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      9           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(1373) Variable = C4ORF29 MUTATION ANALYSIS
D1373V1, survival
                   sevent
clus2                 0   1
  C4ORF29 MUTATED     4   1
  C4ORF29 WILD-TYPE 273  77
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                5               350 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                1                77 
$`C4ORF29 MUTATED`
TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3811 
       79.69        22.06        19.66        63.98        10.06 

$`C4ORF29 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
            10.06              0.00 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
            79.69            148.01 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
            22.06             22.06 
[1] "10.1 - 79.7 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1373V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C4ORF29 MUTATED         1        0        1         1         0         0
  C4ORF29 WILD-TYPE      63        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF29 MUTATED           1          0          0          1        0
  C4ORF29 WILD-TYPE        17          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  C4ORF29 MUTATED           0         0
  C4ORF29 WILD-TYPE        12         1
D1373V3, multiclass
            clus
vv           C4ORF29 MUTATED C4ORF29 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  C4ORF29 MUTATED     0   1   3   1
  C4ORF29 WILD-TYPE   9  66 246  40
D1373V4, multiclass
    clus
vv   C4ORF29 MUTATED C4ORF29 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               1                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
  C4ORF29 MUTATED     3   1   1
  C4ORF29 WILD-TYPE 217  80  65
D1373V5, multiclass
    clus
vv   C4ORF29 MUTATED C4ORF29 WILD-TYPE
  N0               3               217
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1373V6, binary
                   cls
clus                  0   1
  C4ORF29 MUTATED     4   0
  C4ORF29 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF29 MUTATED      4    0
  C4ORF29 WILD-TYPE  281   48
   clus
vv  C4ORF29 MUTATED C4ORF29 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1373V7, binary
                   cls
clus                  0   1
  C4ORF29 MUTATED     2   3
  C4ORF29 WILD-TYPE 168 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF29 MUTATED      2    3
  C4ORF29 WILD-TYPE  168  194
        clus
vv       C4ORF29 MUTATED C4ORF29 WILD-TYPE
  FEMALE               2               168
  MALE                 3               194
[1] 2 2
[1] FALSE
D1373V8, binary
                   cls
clus                  0   1
  C4ORF29 MUTATED     5   0
  C4ORF29 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF29 MUTATED      5    0
  C4ORF29 WILD-TYPE  295    8
     clus
vv    C4ORF29 MUTATED C4ORF29 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1373V9, binary
                   cls
clus                  0   1
  C4ORF29 MUTATED     4   1
  C4ORF29 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF29 MUTATED      4    1
  C4ORF29 WILD-TYPE  310   47
                               clus
vv                              C4ORF29 MUTATED C4ORF29 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C4ORF29 MUTATED     5   0   0   0
  C4ORF29 WILD-TYPE 254   3  22  21
D1373V10, multiclass
    clus
vv   C4ORF29 MUTATED C4ORF29 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1373V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C4ORF29 MUTATED                                  0     0
  C4ORF29 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C4ORF29 MUTATED                           0     3
  C4ORF29 WILD-TYPE                        19   173
D1373V12, multiclass
                                  clus
vv                                 C4ORF29 MUTATED C4ORF29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = GPR161 MUTATION ANALYSIS
D1374V1, survival
                  sevent
clus2                0   1
  GPR161 MUTATED     6   2
  GPR161 WILD-TYPE 271  76
  GPR161 MUTATED GPR161 WILD-TYPE 
               8              347 
  GPR161 MUTATED GPR161 WILD-TYPE 
               2               76 
$`GPR161 MUTATED`
TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6718 
        0.92        26.99        34.98        35.01        12.76        10.06 
TCGA-D5-6930 TCGA-F4-6570 
       13.35         6.18 

$`GPR161 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPR161 MUTATED GPR161 WILD-TYPE 
            0.92             0.00 
  GPR161 MUTATED GPR161 WILD-TYPE 
           35.01           148.01 
  GPR161 MUTATED GPR161 WILD-TYPE 
          13.055           22.090 
[1] "0.9 - 35.0 (13.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1374V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR161 MUTATED         0        0        1         5         1         0
  GPR161 WILD-TYPE      64        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR161 MUTATED           2          0          0          0        0
  GPR161 WILD-TYPE        16          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR161 MUTATED           0         0
  GPR161 WILD-TYPE        12         1
D1374V3, multiclass
            clus
vv           GPR161 MUTATED GPR161 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  GPR161 MUTATED     0   0   7   2
  GPR161 WILD-TYPE   9  67 242  39
D1374V4, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              7              242
  T4              2               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
  GPR161 MUTATED     7   1   1
  GPR161 WILD-TYPE 213  80  65
D1374V5, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1374V6, binary
                  cls
clus                 0   1
  GPR161 MUTATED     9   0
  GPR161 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      9    0
  GPR161 WILD-TYPE  276   48
   clus
vv  GPR161 MUTATED GPR161 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1374V7, binary
                  cls
clus                 0   1
  GPR161 MUTATED     5   4
  GPR161 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      5    4
  GPR161 WILD-TYPE  165  193
        clus
vv       GPR161 MUTATED GPR161 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1374V8, binary
                  cls
clus                 0   1
  GPR161 MUTATED     7   1
  GPR161 WILD-TYPE 293   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      7    1
  GPR161 WILD-TYPE  293    7
     clus
vv    GPR161 MUTATED GPR161 WILD-TYPE
  NO               7              293
  YES              1                7
[1] 2 2
[1] FALSE
D1374V9, binary
                  cls
clus                 0   1
  GPR161 MUTATED     6   3
  GPR161 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      6    3
  GPR161 WILD-TYPE  308   45
                               clus
vv                              GPR161 MUTATED GPR161 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR161 MUTATED     7   0   0   2
  GPR161 WILD-TYPE 252   3  22  19
D1374V10, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D1374V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR161 MUTATED                                  0     2
  GPR161 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR161 MUTATED                           0     2
  GPR161 WILD-TYPE                        19   174
D1374V12, multiclass
                                  clus
vv                                 GPR161 MUTATED GPR161 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1375) Variable = HAUS1 MUTATION ANALYSIS
D1375V1, survival
                 sevent
clus2               0   1
  HAUS1 MUTATED     4   2
  HAUS1 WILD-TYPE 273  76
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             349 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              2              76 
$`HAUS1 MUTATED`
TCGA-AA-3715 TCGA-A6-6141 TCGA-AA-A01Q TCGA-AZ-4323 TCGA-CM-6161 TCGA-G4-6307 
       19.04         8.38         1.02         1.41        15.02        55.04 

$`HAUS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.09 
[1] "1.0 - 55.0 (11.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1375V2, continuous
                 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      63        1       24       107         8         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  HAUS1 MUTATED           0
  HAUS1 WILD-TYPE         1
D1375V3, multiclass
            clus
vv           HAUS1 MUTATED HAUS1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HAUS1 MUTATED     0   1   4   1
  HAUS1 WILD-TYPE   9  66 245  40
D1375V4, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             1              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
  HAUS1 MUTATED     4   1   1
  HAUS1 WILD-TYPE 216  80  65
D1375V5, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1375V6, binary
                 cls
clus                0   1
  HAUS1 MUTATED     5   1
  HAUS1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      5    1
  HAUS1 WILD-TYPE  280   47
   clus
vv  HAUS1 MUTATED HAUS1 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D1375V7, binary
                 cls
clus                0   1
  HAUS1 MUTATED     3   3
  HAUS1 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      3    3
  HAUS1 WILD-TYPE  167  194
        clus
vv       HAUS1 MUTATED HAUS1 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1375V8, binary
                 cls
clus                0   1
  HAUS1 MUTATED     5   0
  HAUS1 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      5    0
  HAUS1 WILD-TYPE  295    8
     clus
vv    HAUS1 MUTATED HAUS1 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1375V9, binary
                 cls
clus                0   1
  HAUS1 MUTATED     6   0
  HAUS1 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      6    0
  HAUS1 WILD-TYPE  308   48
                               clus
vv                              HAUS1 MUTATED HAUS1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HAUS1 MUTATED     4   0   0   0
  HAUS1 WILD-TYPE 255   3  22  21
D1375V10, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1375V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAUS1 MUTATED                                  0     0
  HAUS1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HAUS1 MUTATED                           1     3
  HAUS1 WILD-TYPE                        18   173
D1375V12, multiclass
                                  clus
vv                                 HAUS1 MUTATED HAUS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = BTBD3 MUTATION ANALYSIS
D1376V1, survival
                 sevent
clus2               0   1
  BTBD3 MUTATED    10   2
  BTBD3 WILD-TYPE 267  76
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             12             343 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
              2              76 
$`BTBD3 MUTATED`
TCGA-AA-3662 TCGA-G4-6321 TCGA-A6-5661 TCGA-A6-6137 TCGA-AA-3663 TCGA-AA-A00N 
        6.05        22.09        33.53        27.09         6.97         4.01 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-6162 TCGA-D5-6541 TCGA-G4-6315 
       27.09        58.39        49.41        12.00        15.58        61.91 

$`BTBD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.03 
[1] "4.0 - 61.9 (24.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1376V2, continuous
                 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      63        1       23       105         7         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        17          6         42         33       33        12
                 vv
clus              STAGE IVB
  BTBD3 MUTATED           0
  BTBD3 WILD-TYPE         1
D1376V3, multiclass
            clus
vv           BTBD3 MUTATED BTBD3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  BTBD3 MUTATED     0   2   8   3
  BTBD3 WILD-TYPE   9  65 241  38
D1376V4, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             3              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
  BTBD3 MUTATED     8   4   1
  BTBD3 WILD-TYPE 212  77  65
D1376V5, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1376V6, binary
                 cls
clus                0   1
  BTBD3 MUTATED     9   2
  BTBD3 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED      9    2
  BTBD3 WILD-TYPE  276   46
   clus
vv  BTBD3 MUTATED BTBD3 WILD-TYPE
  0             9             276
  1             2              46
[1] 2 2
[1] FALSE
D1376V7, binary
                 cls
clus                0   1
  BTBD3 MUTATED     7   6
  BTBD3 WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED      7    6
  BTBD3 WILD-TYPE  163  191
        clus
vv       BTBD3 MUTATED BTBD3 WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D1376V8, binary
                 cls
clus                0   1
  BTBD3 MUTATED    10   0
  BTBD3 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED     10    0
  BTBD3 WILD-TYPE  290    8
     clus
vv    BTBD3 MUTATED BTBD3 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1376V9, binary
                 cls
clus                0   1
  BTBD3 MUTATED    11   2
  BTBD3 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED     11    2
  BTBD3 WILD-TYPE  303   46
                               clus
vv                              BTBD3 MUTATED BTBD3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BTBD3 MUTATED    10   0   1   0
  BTBD3 WILD-TYPE 249   3  21  21
D1376V10, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             1              21
  RX             0              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"
D1376V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTBD3 MUTATED                                  0     0
  BTBD3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTBD3 MUTATED                           1     8
  BTBD3 WILD-TYPE                        18   168
D1376V12, multiclass
                                  clus
vv                                 BTBD3 MUTATED BTBD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = KLKB1 MUTATION ANALYSIS
D1377V1, survival
                 sevent
clus2               0   1
  KLKB1 MUTATED    11   2
  KLKB1 WILD-TYPE 266  76
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             13             342 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
              2              76 
$`KLKB1 MUTATED`
TCGA-AA-3525 TCGA-AA-3950 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 
        8.05        24.00        26.17        42.90        33.53        22.06 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6715 TCGA-CM-4743 TCGA-CM-6171 
       18.05         4.01        12.16        12.59        23.05        14.04 
TCGA-D5-6927 
        9.44 

$`KLKB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  KLKB1 MUTATED KLKB1 WILD-TYPE 
           4.01            0.00 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
          42.90          148.01 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
          18.05           22.09 
[1] "4.0 - 42.9 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1377V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLKB1 MUTATED         2        0        0         6         2         0
  KLKB1 WILD-TYPE      62        1       26       102         6         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        18          6         41         33       35        12
                 vv
clus              STAGE IVB
  KLKB1 MUTATED           0
  KLKB1 WILD-TYPE         1
D1377V3, multiclass
            clus
vv           KLKB1 MUTATED KLKB1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  KLKB1 MUTATED     0   2   8   3
  KLKB1 WILD-TYPE   9  65 241  38
D1377V4, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             3              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
  KLKB1 MUTATED    10   3   0
  KLKB1 WILD-TYPE 210  78  66
D1377V5, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  N0            10             210
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1377V6, binary
                 cls
clus                0   1
  KLKB1 MUTATED    12   0
  KLKB1 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED     12    0
  KLKB1 WILD-TYPE  273   48
   clus
vv  KLKB1 MUTATED KLKB1 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D1377V7, binary
                 cls
clus                0   1
  KLKB1 MUTATED     6   7
  KLKB1 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED      6    7
  KLKB1 WILD-TYPE  164  190
        clus
vv       KLKB1 MUTATED KLKB1 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1377V8, binary
                 cls
clus                0   1
  KLKB1 MUTATED    12   0
  KLKB1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED     12    0
  KLKB1 WILD-TYPE  288    8
     clus
vv    KLKB1 MUTATED KLKB1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1377V9, binary
                 cls
clus                0   1
  KLKB1 MUTATED     9   4
  KLKB1 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED      9    4
  KLKB1 WILD-TYPE  305   44
                               clus
vv                              KLKB1 MUTATED KLKB1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLKB1 MUTATED    12   0   0   1
  KLKB1 WILD-TYPE 247   3  22  20
D1377V10, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D1377V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLKB1 MUTATED                                  0     1
  KLKB1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLKB1 MUTATED                           1     7
  KLKB1 WILD-TYPE                        18   169
D1377V12, multiclass
                                  clus
vv                                 KLKB1 MUTATED KLKB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = SENP8 MUTATION ANALYSIS
D1378V1, survival
                 sevent
clus2               0   1
  SENP8 MUTATED     3   0
  SENP8 WILD-TYPE 274  78
  SENP8 MUTATED SENP8 WILD-TYPE 
              3             352 
  SENP8 MUTATED SENP8 WILD-TYPE 
              0              78 
$`SENP8 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-CM-6674 
       20.12        19.66        12.95 

$`SENP8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SENP8 MUTATED SENP8 WILD-TYPE 
          12.95            0.00 
  SENP8 MUTATED SENP8 WILD-TYPE 
          20.12          148.01 
  SENP8 MUTATED SENP8 WILD-TYPE 
          19.66           22.09 
[1] "12.9 - 20.1 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1378V2, continuous
                 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      64        1       26       106         7         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  SENP8 MUTATED           0
  SENP8 WILD-TYPE         1
D1378V3, multiclass
            clus
vv           SENP8 MUTATED SENP8 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  SENP8 MUTATED     0   0   2   2
  SENP8 WILD-TYPE   9  67 247  39
D1378V4, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             2             247
  T4             2              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
  SENP8 MUTATED     3   1   0
  SENP8 WILD-TYPE 217  80  66
D1378V5, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1378V6, binary
                 cls
clus                0   1
  SENP8 MUTATED     1   0
  SENP8 WILD-TYPE 284  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      1    0
  SENP8 WILD-TYPE  284   48
   clus
vv  SENP8 MUTATED SENP8 WILD-TYPE
  0             1             284
  1             0              48
[1] 2 2
[1] FALSE
D1378V7, binary
                 cls
clus                0   1
  SENP8 MUTATED     1   3
  SENP8 WILD-TYPE 169 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      1    3
  SENP8 WILD-TYPE  169  194
        clus
vv       SENP8 MUTATED SENP8 WILD-TYPE
  FEMALE             1             169
  MALE               3             194
[1] 2 2
[1] FALSE
D1378V8, binary
                 cls
clus                0   1
  SENP8 MUTATED     3   0
  SENP8 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      3    0
  SENP8 WILD-TYPE  297    8
     clus
vv    SENP8 MUTATED SENP8 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1378V9, binary
                 cls
clus                0   1
  SENP8 MUTATED     2   2
  SENP8 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      2    2
  SENP8 WILD-TYPE  312   46
                               clus
vv                              SENP8 MUTATED SENP8 WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SENP8 MUTATED     2   0   0   1
  SENP8 WILD-TYPE 257   3  22  20
D1378V10, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             1              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"
D1378V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SENP8 MUTATED                                  0     0
  SENP8 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SENP8 MUTATED                           0     4
  SENP8 WILD-TYPE                        19   172
D1378V12, multiclass
                                  clus
vv                                 SENP8 MUTATED SENP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = DPP8 MUTATION ANALYSIS
D1379V1, survival
                sevent
clus2              0   1
  DPP8 MUTATED    10   2
  DPP8 WILD-TYPE 267  76
  DPP8 MUTATED DPP8 WILD-TYPE 
            12            343 
  DPP8 MUTATED DPP8 WILD-TYPE 
             2             76 
$`DPP8 MUTATED`
TCGA-AA-3715 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A010 
       19.04        63.98        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        12.16        49.41        12.00        53.62 

$`DPP8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  DPP8 MUTATED DPP8 WILD-TYPE 
          1.02           0.00 
  DPP8 MUTATED DPP8 WILD-TYPE 
         63.98         148.01 
  DPP8 MUTATED DPP8 WILD-TYPE 
        30.495         21.990 
[1] "1.0 - 64.0 (30.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1379V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPP8 MUTATED         2        0        4         1         2         0
  DPP8 WILD-TYPE      62        1       22       107         6         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        17          6         42         33       35        12
                vv
clus             STAGE IVB
  DPP8 MUTATED           0
  DPP8 WILD-TYPE         1
D1379V3, multiclass
            clus
vv           DPP8 MUTATED DPP8 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             1            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  DPP8 MUTATED     0   3   8   2
  DPP8 WILD-TYPE   9  64 241  39
D1379V4, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            8            241
  T4            2             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
  DPP8 MUTATED    10   3   0
  DPP8 WILD-TYPE 210  78  66
D1379V5, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  N0           10            210
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1379V6, binary
                cls
clus               0   1
  DPP8 MUTATED    10   0
  DPP8 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     10    0
  DPP8 WILD-TYPE  275   48
   clus
vv  DPP8 MUTATED DPP8 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1379V7, binary
                cls
clus               0   1
  DPP8 MUTATED     8   5
  DPP8 WILD-TYPE 162 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED      8    5
  DPP8 WILD-TYPE  162  192
        clus
vv       DPP8 MUTATED DPP8 WILD-TYPE
  FEMALE            8            162
  MALE              5            192
[1] 2 2
[1] FALSE
D1379V8, binary
                cls
clus               0   1
  DPP8 MUTATED    11   0
  DPP8 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     11    0
  DPP8 WILD-TYPE  289    8
     clus
vv    DPP8 MUTATED DPP8 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1379V9, binary
                cls
clus               0   1
  DPP8 MUTATED    10   3
  DPP8 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     10    3
  DPP8 WILD-TYPE  304   45
                               clus
vv                              DPP8 MUTATED DPP8 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DPP8 MUTATED    11   0   0   0
  DPP8 WILD-TYPE 248   3  22  21
D1379V10, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            0             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"
D1379V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPP8 MUTATED                                  0     0
  DPP8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DPP8 MUTATED                           0     4
  DPP8 WILD-TYPE                        19   172
D1379V12, multiclass
                                  clus
vv                                 DPP8 MUTATED DPP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = SLC22A10 MUTATION ANALYSIS
D1380V1, survival
                    sevent
clus2                  0   1
  SLC22A10 MUTATED    14   1
  SLC22A10 WILD-TYPE 263  77
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                15                340 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                 1                 77 
$`SLC22A10 MUTATED`
TCGA-AA-3950 TCGA-A6-6653 TCGA-AA-3812 TCGA-AA-3877 TCGA-AA-A010 TCGA-AD-6889 
       24.00        24.39        35.05        31.00        34.98        83.24 
TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-5348 
       27.09         0.20        12.76        85.45        20.02        22.98 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        12.00        16.04 

$`SLC22A10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3815 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        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-4682 TCGA-AZ-5403 TCGA-AZ-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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-6163 TCGA-CM-6164 
        5.03        15.02        15.02        17.03        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
               0.2                0.0 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
             85.45             148.01 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
             24.00              22.01 
[1] "0.2 - 85.5 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3.5"
D1380V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A10 MUTATED         5        0        0         5         1         0
  SLC22A10 WILD-TYPE      59        1       26       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A10 MUTATED           0          0          3          1        0
  SLC22A10 WILD-TYPE        18          6         41         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC22A10 MUTATED           0         0
  SLC22A10 WILD-TYPE        12         1
D1380V3, multiclass
            clus
vv           SLC22A10 MUTATED SLC22A10 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SLC22A10 MUTATED     1   4   9   1
  SLC22A10 WILD-TYPE   8  63 240  40
D1380V4, multiclass
    clus
vv   SLC22A10 MUTATED SLC22A10 WILD-TYPE
  T1                1                  8
  T2                4                 63
  T3                9                240
  T4                1                 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
  SLC22A10 MUTATED    11   3   1
  SLC22A10 WILD-TYPE 209  78  65
D1380V5, multiclass
    clus
vv   SLC22A10 MUTATED SLC22A10 WILD-TYPE
  N0               11                209
  N1                3                 78
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1380V6, binary
                    cls
clus                   0   1
  SLC22A10 MUTATED    14   0
  SLC22A10 WILD-TYPE 271  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A10 MUTATED     14    0
  SLC22A10 WILD-TYPE  271   48
   clus
vv  SLC22A10 MUTATED SLC22A10 WILD-TYPE
  0               14                271
  1                0                 48
[1] 2 2
[1] FALSE
D1380V7, binary
                    cls
clus                   0   1
  SLC22A10 MUTATED     8   7
  SLC22A10 WILD-TYPE 162 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A10 MUTATED      8    7
  SLC22A10 WILD-TYPE  162  190
        clus
vv       SLC22A10 MUTATED SLC22A10 WILD-TYPE
  FEMALE                8                162
  MALE                  7                190
[1] 2 2
[1] FALSE
D1380V8, binary
                    cls
clus                   0   1
  SLC22A10 MUTATED    13   0
  SLC22A10 WILD-TYPE 287   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A10 MUTATED     13    0
  SLC22A10 WILD-TYPE  287    8
     clus
vv    SLC22A10 MUTATED SLC22A10 WILD-TYPE
  NO                13                287
  YES                0                  8
[1] 2 2
[1] FALSE
D1380V9, binary
                    cls
clus                   0   1
  SLC22A10 MUTATED     9   6
  SLC22A10 WILD-TYPE 305  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A10 MUTATED      9    6
  SLC22A10 WILD-TYPE  305   42
                               clus
vv                              SLC22A10 MUTATED SLC22A10 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                6                 42
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC22A10 MUTATED    12   1   0   1
  SLC22A10 WILD-TYPE 247   2  22  20
D1380V10, multiclass
    clus
vv   SLC22A10 MUTATED SLC22A10 WILD-TYPE
  R0               12                247
  R1                1                  2
  R2                0                 22
  RX                1                 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"
D1380V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A10 MUTATED                                  0     2
  SLC22A10 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC22A10 MUTATED                           1     8
  SLC22A10 WILD-TYPE                        18   168
D1380V12, multiclass
                                  clus
vv                                 SLC22A10 MUTATED SLC22A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           8                168
[1] 4 2
[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 = FANCD2 MUTATION ANALYSIS
D1381V1, survival
                  sevent
clus2                0   1
  FANCD2 MUTATED     8   5
  FANCD2 WILD-TYPE 269  73
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              13              342 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               5               73 
$`FANCD2 MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-G4-6588 TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3947 
       19.04        10.88        26.17         6.97         0.00        33.01 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A02F TCGA-AZ-6600 TCGA-CK-4950 TCGA-D5-6532 
       18.05         4.01        39.98        12.10        85.45        18.25 
TCGA-G4-6299 
       74.56 

$`FANCD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  FANCD2 MUTATED FANCD2 WILD-TYPE 
               0                0 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           85.45           148.01 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           18.25            22.09 
[1] "0.0 - 85.5 (18.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1381V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FANCD2 MUTATED         0        0        2         4         3         0
  FANCD2 WILD-TYPE      64        1       24       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FANCD2 MUTATED           0          0          2          1        2
  FANCD2 WILD-TYPE        18          6         42         32       33
                  vv
clus               STAGE IVA STAGE IVB
  FANCD2 MUTATED           0         0
  FANCD2 WILD-TYPE        12         1
D1381V3, multiclass
            clus
vv           FANCD2 MUTATED FANCD2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                2               33
  STAGE IVA               0               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
  FANCD2 MUTATED     0   0   9   6
  FANCD2 WILD-TYPE   9  67 240  35
D1381V4, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              9              240
  T4              6               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
  FANCD2 MUTATED     9   4   2
  FANCD2 WILD-TYPE 211  77  64
D1381V5, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  N0              9              211
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1381V6, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    11   2
  FANCD2 WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     11    2
  FANCD2 WILD-TYPE  274   46
   clus
vv  FANCD2 MUTATED FANCD2 WILD-TYPE
  0             11              274
  1              2               46
[1] 2 2
[1] FALSE
D1381V7, binary
                  cls
clus                 0   1
  FANCD2 MUTATED     7   8
  FANCD2 WILD-TYPE 163 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      7    8
  FANCD2 WILD-TYPE  163  189
        clus
vv       FANCD2 MUTATED FANCD2 WILD-TYPE
  FEMALE              7              163
  MALE                8              189
[1] 2 2
[1] FALSE
D1381V8, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    11   0
  FANCD2 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     11    0
  FANCD2 WILD-TYPE  289    8
     clus
vv    FANCD2 MUTATED FANCD2 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1381V9, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    11   4
  FANCD2 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     11    4
  FANCD2 WILD-TYPE  303   44
                               clus
vv                              FANCD2 MUTATED FANCD2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FANCD2 MUTATED    10   1   1   1
  FANCD2 WILD-TYPE 249   2  21  20
D1381V10, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  R0             10              249
  R1              1                2
  R2              1               21
  RX              1               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"
D1381V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FANCD2 MUTATED                                  0     0
  FANCD2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FANCD2 MUTATED                           2     5
  FANCD2 WILD-TYPE                        17   171
D1381V12, multiclass
                                  clus
vv                                 FANCD2 MUTATED FANCD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         5              171
[1] 4 2
[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 = CDS2 MUTATION ANALYSIS
D1382V1, survival
                sevent
clus2              0   1
  CDS2 MUTATED     7   1
  CDS2 WILD-TYPE 270  77
  CDS2 MUTATED CDS2 WILD-TYPE 
             8            347 
  CDS2 MUTATED CDS2 WILD-TYPE 
             1             77 
$`CDS2 MUTATED`
TCGA-AA-3525 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-A010 
        8.05        79.69         3.02        29.95        26.99        34.98 
TCGA-CM-5861 TCGA-CM-5868 
       15.02        17.03 

$`CDS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CDS2 MUTATED CDS2 WILD-TYPE 
          3.02           0.00 
  CDS2 MUTATED CDS2 WILD-TYPE 
         79.69         148.01 
  CDS2 MUTATED CDS2 WILD-TYPE 
         22.01          22.06 
[1] "3.0 - 79.7 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1382V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDS2 MUTATED         1        0        1         3         2         0
  CDS2 WILD-TYPE      63        1       25       105         6         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        18          6         43         33       35        11
                vv
clus             STAGE IVB
  CDS2 MUTATED           0
  CDS2 WILD-TYPE         1
D1382V3, multiclass
            clus
vv           CDS2 MUTATED CDS2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  CDS2 MUTATED     0   1   5   3
  CDS2 WILD-TYPE   9  66 244  38
D1382V4, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            3             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
  CDS2 MUTATED     7   2   0
  CDS2 WILD-TYPE 213  79  66
D1382V5, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  N0            7            213
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1382V6, binary
                cls
clus               0   1
  CDS2 MUTATED     7   1
  CDS2 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      7    1
  CDS2 WILD-TYPE  278   47
   clus
vv  CDS2 MUTATED CDS2 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D1382V7, binary
                cls
clus               0   1
  CDS2 MUTATED     7   2
  CDS2 WILD-TYPE 163 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      7    2
  CDS2 WILD-TYPE  163  195
        clus
vv       CDS2 MUTATED CDS2 WILD-TYPE
  FEMALE            7            163
  MALE              2            195
[1] 2 2
[1] FALSE
D1382V8, binary
                cls
clus               0   1
  CDS2 MUTATED     8   0
  CDS2 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      8    0
  CDS2 WILD-TYPE  292    8
     clus
vv    CDS2 MUTATED CDS2 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1382V9, binary
                cls
clus               0   1
  CDS2 MUTATED     8   1
  CDS2 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      8    1
  CDS2 WILD-TYPE  306   47
                               clus
vv                              CDS2 MUTATED CDS2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDS2 MUTATED     8   0   0   1
  CDS2 WILD-TYPE 251   3  22  20
D1382V10, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D1382V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDS2 MUTATED                                  0     0
  CDS2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDS2 MUTATED                           0     4
  CDS2 WILD-TYPE                        19   172
D1382V12, multiclass
                                  clus
vv                                 CDS2 MUTATED CDS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = CCDC66 MUTATION ANALYSIS
D1383V1, survival
                  sevent
clus2                0   1
  CCDC66 MUTATED     5   4
  CCDC66 WILD-TYPE 272  74
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               9              346 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               74 
$`CCDC66 MUTATED`
TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3877 TCGA-AA-A02K TCGA-CA-6717 TCGA-CA-6718 
       10.88        22.06        31.00        14.01        12.76        10.06 
TCGA-CK-5913 TCGA-D5-6540 TCGA-F4-6570 
       51.32        16.14         6.18 

$`CCDC66 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CCDC66 MUTATED CCDC66 WILD-TYPE 
            6.18             0.00 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
           51.32           148.01 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
          14.010           22.225 
[1] "6.2 - 51.3 (14.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2.8"
D1383V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC66 MUTATED         2        0        0         5         0         0
  CCDC66 WILD-TYPE      62        1       26       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC66 MUTATED           0          0          0          0        1
  CCDC66 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC66 MUTATED           0         0
  CCDC66 WILD-TYPE        12         1
D1383V3, multiclass
            clus
vv           CCDC66 MUTATED CCDC66 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CCDC66 MUTATED     1   1   5   2
  CCDC66 WILD-TYPE   8  66 244  39
D1383V4, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              5              244
  T4              2               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
  CCDC66 MUTATED     7   0   2
  CCDC66 WILD-TYPE 213  81  64
D1383V5, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1383V6, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     6   1
  CCDC66 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      6    1
  CCDC66 WILD-TYPE  279   47
   clus
vv  CCDC66 MUTATED CCDC66 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D1383V7, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     4   5
  CCDC66 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      4    5
  CCDC66 WILD-TYPE  166  192
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D1383V8, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     9   0
  CCDC66 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      9    0
  CCDC66 WILD-TYPE  291    8
     clus
vv    CCDC66 MUTATED CCDC66 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1383V9, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     6   3
  CCDC66 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      6    3
  CCDC66 WILD-TYPE  308   45
                               clus
vv                              CCDC66 MUTATED CCDC66 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC66 MUTATED     4   0   1   3
  CCDC66 WILD-TYPE 255   3  21  18
D1383V10, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              1               21
  RX              3               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"
D1383V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC66 MUTATED                                  0     2
  CCDC66 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC66 MUTATED                           0     5
  CCDC66 WILD-TYPE                        19   171
D1383V12, multiclass
                                  clus
vv                                 CCDC66 MUTATED CCDC66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = TTC13 MUTATION ANALYSIS
D1384V1, survival
                 sevent
clus2               0   1
  TTC13 MUTATED     6   3
  TTC13 WILD-TYPE 271  75
  TTC13 MUTATED TTC13 WILD-TYPE 
              9             346 
  TTC13 MUTATED TTC13 WILD-TYPE 
              3              75 
$`TTC13 MUTATED`
TCGA-G4-6628 TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-6599 
       79.69        29.95        10.06         4.01        35.01         6.77 
TCGA-CA-5255 TCGA-CK-5913 TCGA-CM-4744 
       12.36        51.32        20.02 

$`TTC13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TTC13 MUTATED TTC13 WILD-TYPE 
           4.01            0.00 
  TTC13 MUTATED TTC13 WILD-TYPE 
          79.69          148.01 
  TTC13 MUTATED TTC13 WILD-TYPE 
         20.020          22.075 
[1] "4.0 - 79.7 (20.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1384V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTC13 MUTATED         3        0        0         3         1         0
  TTC13 WILD-TYPE      61        1       26       105         7         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        16          6         44         33       35        12
                 vv
clus              STAGE IVB
  TTC13 MUTATED           0
  TTC13 WILD-TYPE         1
D1384V3, multiclass
            clus
vv           TTC13 MUTATED TTC13 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  TTC13 MUTATED     0   3   5   1
  TTC13 WILD-TYPE   9  64 244  40
D1384V4, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             5             244
  T4             1              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
  TTC13 MUTATED     7   0   2
  TTC13 WILD-TYPE 213  81  64
D1384V5, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1384V6, binary
                 cls
clus                0   1
  TTC13 MUTATED     7   0
  TTC13 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      7    0
  TTC13 WILD-TYPE  278   48
   clus
vv  TTC13 MUTATED TTC13 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1384V7, binary
                 cls
clus                0   1
  TTC13 MUTATED     3   6
  TTC13 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      3    6
  TTC13 WILD-TYPE  167  191
        clus
vv       TTC13 MUTATED TTC13 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1384V8, binary
                 cls
clus                0   1
  TTC13 MUTATED     6   2
  TTC13 WILD-TYPE 294   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      6    2
  TTC13 WILD-TYPE  294    6
     clus
vv    TTC13 MUTATED TTC13 WILD-TYPE
  NO              6             294
  YES             2               6
[1] 2 2
[1] FALSE
D1384V9, binary
                 cls
clus                0   1
  TTC13 MUTATED     6   3
  TTC13 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      6    3
  TTC13 WILD-TYPE  308   45
                               clus
vv                              TTC13 MUTATED TTC13 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TTC13 MUTATED     6   0   0   2
  TTC13 WILD-TYPE 253   3  22  19
D1384V10, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1384V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTC13 MUTATED                                  0     1
  TTC13 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTC13 MUTATED                           0     4
  TTC13 WILD-TYPE                        19   172
D1384V12, multiclass
                                  clus
vv                                 TTC13 MUTATED TTC13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = GLT8D1 MUTATION ANALYSIS
D1385V1, survival
                  sevent
clus2                0   1
  GLT8D1 MUTATED     7   0
  GLT8D1 WILD-TYPE 270  78
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               7              348 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               0               78 
$`GLT8D1 MUTATED`
TCGA-AD-6895 TCGA-A6-6780 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CK-4952 
       25.08        20.12        34.98        12.16        58.39        15.62 
TCGA-D5-6930 
       13.35 

$`GLT8D1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           12.16             0.00 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           58.39           148.01 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
          20.120           22.075 
[1] "12.2 - 58.4 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D1385V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLT8D1 MUTATED         1        0        0         4         1         0
  GLT8D1 WILD-TYPE      63        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT8D1 MUTATED           0          0          1          1        0
  GLT8D1 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  GLT8D1 MUTATED           0         0
  GLT8D1 WILD-TYPE        12         1
D1385V3, multiclass
            clus
vv           GLT8D1 MUTATED GLT8D1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  GLT8D1 MUTATED     0   1   5   2
  GLT8D1 WILD-TYPE   9  66 244  39
D1385V4, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              2               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
  GLT8D1 MUTATED     6   1   1
  GLT8D1 WILD-TYPE 214  80  65
D1385V5, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1385V6, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     6   0
  GLT8D1 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      6    0
  GLT8D1 WILD-TYPE  279   48
   clus
vv  GLT8D1 MUTATED GLT8D1 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1385V7, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     3   5
  GLT8D1 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      3    5
  GLT8D1 WILD-TYPE  167  192
        clus
vv       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D1385V8, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     6   0
  GLT8D1 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      6    0
  GLT8D1 WILD-TYPE  294    8
     clus
vv    GLT8D1 MUTATED GLT8D1 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1385V9, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     4   4
  GLT8D1 WILD-TYPE 310  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      4    4
  GLT8D1 WILD-TYPE  310   44
                               clus
vv                              GLT8D1 MUTATED GLT8D1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GLT8D1 MUTATED     6   0   0   1
  GLT8D1 WILD-TYPE 253   3  22  20
D1385V10, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1385V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLT8D1 MUTATED                                  0     0
  GLT8D1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GLT8D1 MUTATED                           0     6
  GLT8D1 WILD-TYPE                        19   170
D1385V12, multiclass
                                  clus
vv                                 GLT8D1 MUTATED GLT8D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = UBC MUTATION ANALYSIS
D1386V1, survival
               sevent
clus2             0   1
  UBC MUTATED     4   0
  UBC WILD-TYPE 273  78
  UBC MUTATED UBC WILD-TYPE 
            4           351 
  UBC MUTATED UBC WILD-TYPE 
            0            78 
$`UBC MUTATED`
TCGA-A6-6652 TCGA-CM-5349 TCGA-CM-6162 TCGA-G4-6315 
       24.69        30.08        12.00        61.91 

$`UBC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6653 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  UBC MUTATED UBC WILD-TYPE 
           12             0 
  UBC MUTATED UBC WILD-TYPE 
        61.91        148.01 
  UBC MUTATED UBC WILD-TYPE 
       27.385        22.030 
[1] "12.0 - 61.9 (27.4)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1386V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBC MUTATED         0        0        0         1         0         0
  UBC WILD-TYPE      64        1       26       107         8         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        18          6         43         33       34        11
               vv
clus            STAGE IVB
  UBC MUTATED           0
  UBC WILD-TYPE         1
D1386V3, multiclass
            clus
vv           UBC MUTATED UBC WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            1           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            1            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
  UBC MUTATED     0   0   4   0
  UBC WILD-TYPE   9  67 245  41
D1386V4, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  T1           0             9
  T2           0            67
  T3           4           245
  T4           0            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
  UBC MUTATED     2   2   0
  UBC WILD-TYPE 218  79  66
D1386V5, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  N0           2           218
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1386V6, binary
               cls
clus              0   1
  UBC MUTATED     2   2
  UBC WILD-TYPE 283  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      2    2
  UBC WILD-TYPE  283   46
   clus
vv  UBC MUTATED UBC WILD-TYPE
  0           2           283
  1           2            46
[1] 2 2
[1] FALSE
D1386V7, binary
               cls
clus              0   1
  UBC MUTATED     2   2
  UBC WILD-TYPE 168 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      2    2
  UBC WILD-TYPE  168  195
        clus
vv       UBC MUTATED UBC WILD-TYPE
  FEMALE           2           168
  MALE             2           195
[1] 2 2
[1] FALSE
D1386V8, binary
               cls
clus              0   1
  UBC MUTATED     4   0
  UBC WILD-TYPE 296   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      4    0
  UBC WILD-TYPE  296    8
     clus
vv    UBC MUTATED UBC WILD-TYPE
  NO            4           296
  YES           0             8
[1] 2 2
[1] FALSE
D1386V9, binary
               cls
clus              0   1
  UBC MUTATED     3   1
  UBC WILD-TYPE 311  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      3    1
  UBC WILD-TYPE  311   47
                               clus
vv                              UBC MUTATED UBC WILD-TYPE
  COLON ADENOCARCINOMA                    3           311
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  UBC MUTATED     3   0   0   0
  UBC WILD-TYPE 256   3  22  21
D1386V10, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  R0           3           256
  R1           0             3
  R2           0            22
  RX           0            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"
D1386V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBC MUTATED                                  0     0
  UBC WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  UBC MUTATED                           1     3
  UBC WILD-TYPE                        18   173
D1386V12, multiclass
                                  clus
vv                                 UBC MUTATED UBC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      3           173
[1] 4 2
[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 = ZNF594 MUTATION ANALYSIS
D1387V1, survival
                  sevent
clus2                0   1
  ZNF594 MUTATED    10   3
  ZNF594 WILD-TYPE 267  75
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              13              342 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
               3               75 
$`ZNF594 MUTATED`
TCGA-AA-3950 TCGA-A6-6141 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 
       24.00         8.38        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         7.53         6.18 
TCGA-G4-6309 
       85.48 

$`ZNF594 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  ZNF594 MUTATED ZNF594 WILD-TYPE 
            6.18             0.00 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
           85.48           148.01 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
           13.02            22.09 
[1] "6.2 - 85.5 (13.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1387V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF594 MUTATED         2        0        1         9         0         0
  ZNF594 WILD-TYPE      62        1       25        99         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF594 MUTATED           0          0          1          0        0
  ZNF594 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF594 MUTATED           0         0
  ZNF594 WILD-TYPE        12         1
D1387V3, multiclass
            clus
vv           ZNF594 MUTATED ZNF594 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               9               99
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF594 MUTATED     0   3  11   0
  ZNF594 WILD-TYPE   9  64 238  41
D1387V4, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             11              238
  T4              0               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
  ZNF594 MUTATED    13   1   0
  ZNF594 WILD-TYPE 207  80  66
D1387V5, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  N0             13              207
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1387V6, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    12   0
  ZNF594 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     12    0
  ZNF594 WILD-TYPE  273   48
   clus
vv  ZNF594 MUTATED ZNF594 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1387V7, binary
                  cls
clus                 0   1
  ZNF594 MUTATED     7   7
  ZNF594 WILD-TYPE 163 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED      7    7
  ZNF594 WILD-TYPE  163  190
        clus
vv       ZNF594 MUTATED ZNF594 WILD-TYPE
  FEMALE              7              163
  MALE                7              190
[1] 2 2
[1] FALSE
D1387V8, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    13   0
  ZNF594 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     13    0
  ZNF594 WILD-TYPE  287    8
     clus
vv    ZNF594 MUTATED ZNF594 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1387V9, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    12   2
  ZNF594 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     12    2
  ZNF594 WILD-TYPE  302   46
                               clus
vv                              ZNF594 MUTATED ZNF594 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF594 MUTATED     9   0   0   2
  ZNF594 WILD-TYPE 250   3  22  19
D1387V10, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              2               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"
D1387V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF594 MUTATED                                  0     2
  ZNF594 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF594 MUTATED                           3     6
  ZNF594 WILD-TYPE                        16   170
D1387V12, multiclass
                                  clus
vv                                 ZNF594 MUTATED ZNF594 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         6              170
[1] 4 2
[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 = BTF3L4 MUTATION ANALYSIS
D1388V1, survival
                  sevent
clus2                0   1
  BTF3L4 MUTATED     2   3
  BTF3L4 WILD-TYPE 275  75
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              350 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               3               75 
$`BTF3L4 MUTATED`
TCGA-AD-6964 TCGA-AZ-6608 TCGA-CK-5916 TCGA-CM-4743 TCGA-D5-6539 
       10.88         1.94        21.14        23.05        12.49 

$`BTF3L4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
            1.94             0.00 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
           23.05           148.01 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
           12.49            22.09 
[1] "1.9 - 23.1 (12.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "5.3"
D1388V2, continuous
                  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      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTF3L4 MUTATED           0          1          0          0        0
  BTF3L4 WILD-TYPE        18          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  BTF3L4 MUTATED           0         0
  BTF3L4 WILD-TYPE        12         1
D1388V3, multiclass
            clus
vv           BTF3L4 MUTATED BTF3L4 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  BTF3L4 MUTATED     1   1   2   1
  BTF3L4 WILD-TYPE   8  66 247  40
D1388V4, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              2              247
  T4              1               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
  BTF3L4 MUTATED     3   1   1
  BTF3L4 WILD-TYPE 217  80  65
D1388V5, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  N0              3              217
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1388V6, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     4   0
  BTF3L4 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      4    0
  BTF3L4 WILD-TYPE  281   48
   clus
vv  BTF3L4 MUTATED BTF3L4 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1388V7, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     3   2
  BTF3L4 WILD-TYPE 167 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      3    2
  BTF3L4 WILD-TYPE  167  195
        clus
vv       BTF3L4 MUTATED BTF3L4 WILD-TYPE
  FEMALE              3              167
  MALE                2              195
[1] 2 2
[1] FALSE
D1388V8, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     5   0
  BTF3L4 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      5    0
  BTF3L4 WILD-TYPE  295    8
     clus
vv    BTF3L4 MUTATED BTF3L4 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1388V9, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     5   0
  BTF3L4 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      5    0
  BTF3L4 WILD-TYPE  309   48
                               clus
vv                              BTF3L4 MUTATED BTF3L4 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BTF3L4 MUTATED     2   0   0   1
  BTF3L4 WILD-TYPE 257   3  22  20
D1388V10, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              1               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"
D1388V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTF3L4 MUTATED                                  0     0
  BTF3L4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BTF3L4 MUTATED                           0     5
  BTF3L4 WILD-TYPE                        19   171
D1388V12, multiclass
                                  clus
vv                                 BTF3L4 MUTATED BTF3L4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = C14ORF105 MUTATION ANALYSIS
D1389V1, survival
                     sevent
clus2                   0   1
  C14ORF105 MUTATED     3   0
  C14ORF105 WILD-TYPE 274  78
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 352 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  0                  78 
$`C14ORF105 MUTATED`
TCGA-AA-3977 TCGA-AA-A010 TCGA-D5-6928 
       25.02        34.98        11.64 

$`C14ORF105 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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              22.045 
[1] "11.6 - 35.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1389V2, continuous
                     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      64        1       26       107         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF105 MUTATED           0          0          0          0        0
  C14ORF105 WILD-TYPE        18          6         44         33       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF105 MUTATED           0         0
  C14ORF105 WILD-TYPE        12         1
D1389V3, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  2                 355 
         TCGA-A6-2677          TCGA-A6-4105          TCGA-A6-6649 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3516          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-3527          TCGA-AA-3530 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3543          TCGA-AA-3552 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3554          TCGA-AA-3556          TCGA-AA-3560 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3562          TCGA-AA-3662          TCGA-AA-3672 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3697 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3713          TCGA-AA-3715          TCGA-AA-3814 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3860          TCGA-AA-3867 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3870          TCGA-AA-3939          TCGA-AA-3950 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3972          TCGA-AA-3976 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3979          TCGA-AA-3986          TCGA-AA-A00L 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A024          TCGA-AD-6548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6895          TCGA-AZ-4681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6601          TCGA-AZ-6608          TCGA-CK-5912 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A285          TCGA-G4-6310          TCGA-G4-6321 
"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-G4-6628          TCGA-A6-2671          TCGA-A6-2672 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2674          TCGA-A6-2676          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-A6-5656 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5657          TCGA-A6-5659          TCGA-A6-5660 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5661          TCGA-A6-5662          TCGA-A6-5664 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5665          TCGA-A6-5666          TCGA-A6-6137 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6138          TCGA-A6-6141          TCGA-A6-6142 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6648          TCGA-A6-6651          TCGA-A6-6652 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6653          TCGA-A6-6654          TCGA-A6-6780 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6781          TCGA-A6-6782          TCGA-AA-3489 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3492          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-3526 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3532          TCGA-AA-3534 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3538          TCGA-AA-3542          TCGA-AA-3544 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3553 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3558          TCGA-AA-3561 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3655          TCGA-AA-3660          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-3673          TCGA-AA-3678          TCGA-AA-3679 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3680          TCGA-AA-3681          TCGA-AA-3684 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3685          TCGA-AA-3693          TCGA-AA-3695 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3710          TCGA-AA-3712 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3815 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3818          TCGA-AA-3819          TCGA-AA-3821 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3831          TCGA-AA-3833          TCGA-AA-3837 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3842          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-3861 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3869 
"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-3941          TCGA-AA-3947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3949          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-3973          TCGA-AA-3975          TCGA-AA-3980 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3982          TCGA-AA-3984          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-A00N 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00O          TCGA-AA-A00Q          TCGA-AA-A00R 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00U          TCGA-AA-A00W          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-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-6889          TCGA-AD-6899 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6965          TCGA-AU-3779          TCGA-AU-6004 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4323          TCGA-AZ-4616 
"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-6605          TCGA-AZ-6606          TCGA-AZ-6607 
"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-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-D5-6534 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6535          TCGA-D5-6536          TCGA-D5-6537 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6538          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-A1D9          TCGA-DM-A1DA 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1DB          TCGA-DM-A1HA          TCGA-DM-A1HB 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A282          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-G4-6307          TCGA-G4-6309 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6323 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6626 
"C14ORF105 WILD-TYPE" 
                     vv
clus                   T1  T2  T3  T4
  C14ORF105 MUTATED     0   1   1   1
  C14ORF105 WILD-TYPE   9  66 248  40
D1389V4, multiclass
    clus
vv   C14ORF105 MUTATED C14ORF105 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 1                 248
  T4                 1                  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
  C14ORF105 MUTATED     3   0   0
  C14ORF105 WILD-TYPE 217  81  66
D1389V5, multiclass
    clus
vv   C14ORF105 MUTATED C14ORF105 WILD-TYPE
  N0                 3                 217
  N1                 0                  81
  N2                 0                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1389V6, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     2   0
  C14ORF105 WILD-TYPE 283  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      2    0
  C14ORF105 WILD-TYPE  283   48
   clus
vv  C14ORF105 MUTATED C14ORF105 WILD-TYPE
  0                 2                 283
  1                 0                  48
[1] 2 2
[1] FALSE
D1389V7, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     1   2
  C14ORF105 WILD-TYPE 169 195
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      1    2
  C14ORF105 WILD-TYPE  169  195
        clus
vv       C14ORF105 MUTATED C14ORF105 WILD-TYPE
  FEMALE                 1                 169
  MALE                   2                 195
[1] 2 2
[1] FALSE
D1389V8, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     3   0
  C14ORF105 WILD-TYPE 297   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      3    0
  C14ORF105 WILD-TYPE  297    8
     clus
vv    C14ORF105 MUTATED C14ORF105 WILD-TYPE
  NO                  3                 297
  YES                 0                   8
[1] 2 2
[1] FALSE
D1389V9, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     2   1
  C14ORF105 WILD-TYPE 312  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      2    1
  C14ORF105 WILD-TYPE  312   47
                               clus
vv                              C14ORF105 MUTATED C14ORF105 WILD-TYPE
  COLON ADENOCARCINOMA                          2                 312
  COLON MUCINOUS ADENOCARCINOMA                 1                  47
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF105 MUTATED     2   0   0   0
  C14ORF105 WILD-TYPE 257   3  22  21
D1389V10, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  2                 303 
         TCGA-A6-2677          TCGA-AA-3496          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-3527          TCGA-AA-3530 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3543          TCGA-AA-3552 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3554          TCGA-AA-3556          TCGA-AA-3560 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3562          TCGA-AA-3662          TCGA-AA-3672 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3697 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3713          TCGA-AA-3715          TCGA-AA-3814 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3860          TCGA-AA-3867 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3870          TCGA-AA-3939          TCGA-AA-3950 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3972          TCGA-AA-3976 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3979          TCGA-AA-3986          TCGA-AA-A00L 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A024          TCGA-AD-6548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6895          TCGA-AZ-4681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5912          TCGA-G4-6310          TCGA-G4-6321 
"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-G4-6628          TCGA-A6-2671          TCGA-A6-2672 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2674          TCGA-A6-2676          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-3502          TCGA-AA-3510          TCGA-AA-3511 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3514          TCGA-AA-3517          TCGA-AA-3518 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3519          TCGA-AA-3526          TCGA-AA-3529 
"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-3544          TCGA-AA-3548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3549          TCGA-AA-3553          TCGA-AA-3555 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3558          TCGA-AA-3561          TCGA-AA-3655 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3663          TCGA-AA-3664 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3666          TCGA-AA-3667          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-3693          TCGA-AA-3695          TCGA-AA-3696 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3710          TCGA-AA-3712          TCGA-AA-3811 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3812          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-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-3861          TCGA-AA-3864 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3866          TCGA-AA-3869          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-3941          TCGA-AA-3947          TCGA-AA-3949 
"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-3973          TCGA-AA-3975 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3989          TCGA-AA-3994 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A004          TCGA-AA-A00A          TCGA-AA-A00D 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00E          TCGA-AA-A00F          TCGA-AA-A00J 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00K          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-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-A029          TCGA-AA-A02F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02H          TCGA-AA-A02J          TCGA-AA-A02K 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02O          TCGA-AA-A02W          TCGA-AA-A02Y 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A03F          TCGA-AA-A03J          TCGA-AD-5900 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6889          TCGA-AD-6965          TCGA-AU-3779 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          TCGA-AZ-4682 
"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-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-G4-6315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6323          TCGA-G4-6626 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
D1389V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF105 MUTATED                                  0     0
  C14ORF105 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF105 MUTATED                           0     1
  C14ORF105 WILD-TYPE                        19   175
D1389V12, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  1                 205 
         TCGA-A6-2677          TCGA-A6-4105          TCGA-A6-6649 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6548          TCGA-AD-6888          TCGA-AD-6895 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6964          TCGA-AZ-4681          TCGA-AZ-6601 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6608          TCGA-CK-5912          TCGA-DM-A285 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6321          TCGA-G4-6586 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6628 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2678          TCGA-A6-2683 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5656          TCGA-A6-5657 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5660          TCGA-A6-5661 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5662          TCGA-A6-5664          TCGA-A6-5665 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5666          TCGA-A6-6137          TCGA-A6-6138 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6141          TCGA-A6-6142          TCGA-A6-6648 
"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-6889 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6890          TCGA-AD-6899          TCGA-AD-6901 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6963          TCGA-AD-6965          TCGA-AU-3779 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          TCGA-AZ-4323 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4616          TCGA-AZ-4682          TCGA-AZ-5403 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-5407          TCGA-AZ-6598          TCGA-AZ-6599 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6600          TCGA-AZ-6603          TCGA-AZ-6605 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6606          TCGA-AZ-6607          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-5913          TCGA-CK-5914          TCGA-CK-5915 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5916          TCGA-CK-6746          TCGA-CK-6747 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6748          TCGA-CK-6751          TCGA-CM-4743 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4744          TCGA-CM-4746          TCGA-CM-4747 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4752          TCGA-CM-5341          TCGA-CM-5344 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5348          TCGA-CM-5349          TCGA-CM-5860 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5861          TCGA-CM-5862          TCGA-CM-5863 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5864          TCGA-CM-5868          TCGA-CM-6161 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6162          TCGA-CM-6163          TCGA-CM-6164 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6165          TCGA-CM-6166          TCGA-CM-6167 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6168          TCGA-CM-6169          TCGA-CM-6170 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6171          TCGA-CM-6172          TCGA-CM-6674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6675          TCGA-CM-6676          TCGA-CM-6677 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6678          TCGA-CM-6679          TCGA-CM-6680 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5537          TCGA-D5-5538          TCGA-D5-5539 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5540          TCGA-D5-5541          TCGA-D5-6529 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6532          TCGA-D5-6533          TCGA-D5-6534 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6535          TCGA-D5-6536          TCGA-D5-6537 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6538          TCGA-D5-6539          TCGA-D5-6540 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6541          TCGA-D5-6898          TCGA-D5-6920 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6922          TCGA-D5-6923          TCGA-D5-6924 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6926          TCGA-D5-6927          TCGA-D5-6929 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6930          TCGA-D5-6931          TCGA-D5-6932 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-7000          TCGA-DM-A0X9          TCGA-DM-A0XD 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A0XF          TCGA-DM-A1D0          TCGA-DM-A1D4 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D6          TCGA-DM-A1D7          TCGA-DM-A1D8 
"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-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-G4-6315          TCGA-G4-6317          TCGA-G4-6323 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6626 
"C14ORF105 WILD-TYPE" 

Clustering(1390) Variable = UBA3 MUTATION ANALYSIS
D1390V1, survival
                sevent
clus2              0   1
  UBA3 MUTATED     4   1
  UBA3 WILD-TYPE 273  77
  UBA3 MUTATED UBA3 WILD-TYPE 
             5            350 
  UBA3 MUTATED UBA3 WILD-TYPE 
             1             77 
$`UBA3 MUTATED`
TCGA-A6-3809 TCGA-AA-3489 TCGA-AA-3510 TCGA-AZ-5407 TCGA-CM-5349 
       32.75         7.04        63.98        88.21        30.08 

$`UBA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3492 
       24.39        23.87        20.12        19.66        20.28         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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  UBA3 MUTATED UBA3 WILD-TYPE 
          7.04           0.00 
  UBA3 MUTATED UBA3 WILD-TYPE 
         88.21         148.01 
  UBA3 MUTATED UBA3 WILD-TYPE 
         32.75          22.01 
[1] "7.0 - 88.2 (32.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1390V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBA3 MUTATED         1        0        2         2         1         0
  UBA3 WILD-TYPE      63        1       24       106         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  UBA3 MUTATED           0
  UBA3 WILD-TYPE         1
D1390V3, multiclass
            clus
vv           UBA3 MUTATED UBA3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  UBA3 MUTATED     1   0   4   1
  UBA3 WILD-TYPE   8  67 245  40
D1390V4, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  T1            1              8
  T2            0             67
  T3            4            245
  T4            1             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
  UBA3 MUTATED     6   0   0
  UBA3 WILD-TYPE 214  81  66
D1390V5, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1390V6, binary
                cls
clus               0   1
  UBA3 MUTATED     6   0
  UBA3 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      6    0
  UBA3 WILD-TYPE  279   48
   clus
vv  UBA3 MUTATED UBA3 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1390V7, binary
                cls
clus               0   1
  UBA3 MUTATED     4   2
  UBA3 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      4    2
  UBA3 WILD-TYPE  166  195
        clus
vv       UBA3 MUTATED UBA3 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D1390V8, binary
                cls
clus               0   1
  UBA3 MUTATED     5   0
  UBA3 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      5    0
  UBA3 WILD-TYPE  295    8
     clus
vv    UBA3 MUTATED UBA3 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1390V9, binary
                cls
clus               0   1
  UBA3 MUTATED     5   1
  UBA3 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      5    1
  UBA3 WILD-TYPE  309   47
                               clus
vv                              UBA3 MUTATED UBA3 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UBA3 MUTATED     5   0   0   0
  UBA3 WILD-TYPE 254   3  22  21
D1390V10, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1390V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBA3 MUTATED                                  0     0
  UBA3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBA3 MUTATED                           0     3
  UBA3 WILD-TYPE                        19   173
D1390V12, multiclass
                                  clus
vv                                 UBA3 MUTATED UBA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = UBE3C MUTATION ANALYSIS
D1391V1, survival
                 sevent
clus2               0   1
  UBE3C MUTATED    14   4
  UBE3C WILD-TYPE 263  74
  UBE3C MUTATED UBE3C WILD-TYPE 
             18             337 
  UBE3C MUTATED UBE3C WILD-TYPE 
              4              74 
$`UBE3C MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3819 TCGA-AA-3977 
       19.04        35.80        31.63        23.61        25.02        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 
        4.01        34.98        31.00        12.16        27.09        58.39 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5864 TCGA-DM-A1D9 TCGA-F4-6808 
       62.79        12.10        12.76        15.02       140.38        33.67 

$`UBE3C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       36.53        32.91        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  UBE3C MUTATED UBE3C WILD-TYPE 
           4.01            0.00 
  UBE3C MUTATED UBE3C WILD-TYPE 
         140.38          148.01 
  UBE3C MUTATED UBE3C WILD-TYPE 
         26.055          21.990 
[1] "4.0 - 140.4 (26.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1391V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBE3C MUTATED         5        0        2         5         2         0
  UBE3C WILD-TYPE      59        1       24       103         6         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        18          6         43         33       34        11
                 vv
clus              STAGE IVB
  UBE3C MUTATED           0
  UBE3C WILD-TYPE         1
D1391V3, multiclass
            clus
vv           UBE3C MUTATED UBE3C WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  UBE3C MUTATED     1   5   9   3
  UBE3C WILD-TYPE   8  62 240  38
D1391V4, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  T1             1               8
  T2             5              62
  T3             9             240
  T4             3              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
  UBE3C MUTATED    15   2   1
  UBE3C WILD-TYPE 205  79  65
D1391V5, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  N0            15             205
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1391V6, binary
                 cls
clus                0   1
  UBE3C MUTATED    13   2
  UBE3C WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     13    2
  UBE3C WILD-TYPE  272   46
   clus
vv  UBE3C MUTATED UBE3C WILD-TYPE
  0            13             272
  1             2              46
[1] 2 2
[1] FALSE
D1391V7, binary
                 cls
clus                0   1
  UBE3C MUTATED     6  12
  UBE3C WILD-TYPE 164 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED      6   12
  UBE3C WILD-TYPE  164  185
        clus
vv       UBE3C MUTATED UBE3C WILD-TYPE
  FEMALE             6             164
  MALE              12             185
[1] 2 2
[1] FALSE
D1391V8, binary
                 cls
clus                0   1
  UBE3C MUTATED    15   0
  UBE3C WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     15    0
  UBE3C WILD-TYPE  285    8
     clus
vv    UBE3C MUTATED UBE3C WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D1391V9, binary
                 cls
clus                0   1
  UBE3C MUTATED    15   3
  UBE3C WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     15    3
  UBE3C WILD-TYPE  299   45
                               clus
vv                              UBE3C MUTATED UBE3C WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UBE3C MUTATED    12   0   0   1
  UBE3C WILD-TYPE 247   3  22  20
D1391V10, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D1391V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBE3C MUTATED                                  0     1
  UBE3C WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UBE3C MUTATED                           2     9
  UBE3C WILD-TYPE                        17   167
D1391V12, multiclass
                                  clus
vv                                 UBE3C MUTATED UBE3C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(1392) Variable = ZCWPW2 MUTATION ANALYSIS
D1392V1, survival
                  sevent
clus2                0   1
  ZCWPW2 MUTATED     9   2
  ZCWPW2 WILD-TYPE 268  76
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              11              344 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
               2               76 
$`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 
       83.24        58.39        11.01        11.01        13.78 

$`ZCWPW2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.90        42.28        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-6679 
       14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6626 
       36.00        46.75 

  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
            2.01             0.00 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
           83.24           148.01 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
           19.66            22.09 
[1] "2.0 - 83.2 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1392V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZCWPW2 MUTATED         0        1        1         4         1         0
  ZCWPW2 WILD-TYPE      64        0       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCWPW2 MUTATED           0          0          1          1        1
  ZCWPW2 WILD-TYPE        18          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  ZCWPW2 MUTATED           1         0
  ZCWPW2 WILD-TYPE        11         1
D1392V3, multiclass
            clus
vv           ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  ZCWPW2 MUTATED     0   0   6   4
  ZCWPW2 WILD-TYPE   9  67 243  37
D1392V4, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              4               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
  ZCWPW2 MUTATED     8   3   0
  ZCWPW2 WILD-TYPE 212  78  66
D1392V5, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  N0              8              212
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1392V6, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED     7   2
  ZCWPW2 WILD-TYPE 278  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED      7    2
  ZCWPW2 WILD-TYPE  278   46
   clus
vv  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  0              7              278
  1              2               46
[1] 2 2
[1] FALSE
D1392V7, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED     6   5
  ZCWPW2 WILD-TYPE 164 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED      6    5
  ZCWPW2 WILD-TYPE  164  192
        clus
vv       ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  FEMALE              6              164
  MALE                5              192
[1] 2 2
[1] FALSE
D1392V8, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED    10   0
  ZCWPW2 WILD-TYPE 290   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED     10    0
  ZCWPW2 WILD-TYPE  290    8
     clus
vv    ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  NO              10              290
  YES              0                8
[1] 2 2
[1] FALSE
D1392V9, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED     9   2
  ZCWPW2 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED      9    2
  ZCWPW2 WILD-TYPE  305   46
                               clus
vv                              ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZCWPW2 MUTATED    10   0   0   0
  ZCWPW2 WILD-TYPE 249   3  22  21
D1392V10, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              0               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"
D1392V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZCWPW2 MUTATED                                  0     1
  ZCWPW2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZCWPW2 MUTATED                           1     6
  ZCWPW2 WILD-TYPE                        18   170
D1392V12, multiclass
                                  clus
vv                                 ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = ZNF711 MUTATION ANALYSIS
D1393V1, survival
                  sevent
clus2                0   1
  ZNF711 MUTATED     7   2
  ZNF711 WILD-TYPE 270  76
  ZNF711 MUTATED ZNF711 WILD-TYPE 
               9              346 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
               2               76 
$`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 
       12.49        11.64         6.18 

$`ZNF711 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6652 TCGA-A6-6653 
       27.09         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF711 MUTATED ZNF711 WILD-TYPE 
            1.02             0.00 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
           55.92           148.01 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
           12.49            22.09 
[1] "1.0 - 55.9 (12.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1393V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF711 MUTATED         2        0        2         2         0         0
  ZNF711 WILD-TYPE      62        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF711 MUTATED           0          0          2          0        1
  ZNF711 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF711 MUTATED           0         0
  ZNF711 WILD-TYPE        12         1
D1393V3, multiclass
            clus
vv           ZNF711 MUTATED ZNF711 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF711 MUTATED     0   2   7   1
  ZNF711 WILD-TYPE   9  65 242  40
D1393V4, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              1               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
  ZNF711 MUTATED     7   2   1
  ZNF711 WILD-TYPE 213  79  65
D1393V5, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1393V6, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     8   1
  ZNF711 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      8    1
  ZNF711 WILD-TYPE  277   47
   clus
vv  ZNF711 MUTATED ZNF711 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1393V7, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     6   4
  ZNF711 WILD-TYPE 164 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      6    4
  ZNF711 WILD-TYPE  164  193
        clus
vv       ZNF711 MUTATED ZNF711 WILD-TYPE
  FEMALE              6              164
  MALE                4              193
[1] 2 2
[1] FALSE
D1393V8, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     7   0
  ZNF711 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      7    0
  ZNF711 WILD-TYPE  293    8
     clus
vv    ZNF711 MUTATED ZNF711 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1393V9, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     9   1
  ZNF711 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      9    1
  ZNF711 WILD-TYPE  305   47
                               clus
vv                              ZNF711 MUTATED ZNF711 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF711 MUTATED     7   0   1   0
  ZNF711 WILD-TYPE 252   3  21  21
D1393V10, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              1               21
  RX              0               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"
D1393V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF711 MUTATED                                  0     0
  ZNF711 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF711 MUTATED                           0     7
  ZNF711 WILD-TYPE                        19   169
D1393V12, multiclass
                                  clus
vv                                 ZNF711 MUTATED ZNF711 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = PRSS48 MUTATION ANALYSIS
D1394V1, survival
                  sevent
clus2                0   1
  PRSS48 MUTATED     4   2
  PRSS48 WILD-TYPE 273  76
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               6              349 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               2               76 
$`PRSS48 MUTATED`
TCGA-AD-6889 TCGA-CM-5348 TCGA-D5-6536 TCGA-D5-6541 TCGA-F4-6570 TCGA-G4-6323 
       83.24        22.98        17.85        15.58         6.18        13.78 

$`PRSS48 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6626 
       46.75 

  PRSS48 MUTATED PRSS48 WILD-TYPE 
            6.18             0.00 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
           83.24           148.01 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
          16.715           22.090 
[1] "6.2 - 83.2 (16.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1394V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRSS48 MUTATED         0        1        0         5         0         0
  PRSS48 WILD-TYPE      64        0       26       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS48 MUTATED           0          0          1          0        0
  PRSS48 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  PRSS48 MUTATED           0         0
  PRSS48 WILD-TYPE        12         1
D1394V3, multiclass
            clus
vv           PRSS48 MUTATED PRSS48 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  PRSS48 MUTATED     0   0   6   0
  PRSS48 WILD-TYPE   9  67 243  41
D1394V4, multiclass
    clus
vv   PRSS48 MUTATED PRSS48 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              0               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
  PRSS48 MUTATED     6   1   0
  PRSS48 WILD-TYPE 214  80  66
D1394V5, multiclass
    clus
vv   PRSS48 MUTATED PRSS48 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1394V6, binary
                  cls
clus                 0   1
  PRSS48 MUTATED     6   0
  PRSS48 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS48 MUTATED      6    0
  PRSS48 WILD-TYPE  279   48
   clus
vv  PRSS48 MUTATED PRSS48 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1394V7, binary
                  cls
clus                 0   1
  PRSS48 MUTATED     2   5
  PRSS48 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS48 MUTATED      2    5
  PRSS48 WILD-TYPE  168  192
        clus
vv       PRSS48 MUTATED PRSS48 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1394V8, binary
                  cls
clus                 0   1
  PRSS48 MUTATED     6   0
  PRSS48 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS48 MUTATED      6    0
  PRSS48 WILD-TYPE  294    8
     clus
vv    PRSS48 MUTATED PRSS48 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1394V9, binary
                  cls
clus                 0   1
  PRSS48 MUTATED     7   0
  PRSS48 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS48 MUTATED      7    0
  PRSS48 WILD-TYPE  307   48
                               clus
vv                              PRSS48 MUTATED PRSS48 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRSS48 MUTATED     7   0   0   0
  PRSS48 WILD-TYPE 252   3  22  21
D1394V10, multiclass
    clus
vv   PRSS48 MUTATED PRSS48 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1394V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRSS48 MUTATED                                  0     1
  PRSS48 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRSS48 MUTATED                           1     4
  PRSS48 WILD-TYPE                        18   172
D1394V12, multiclass
                                  clus
vv                                 PRSS48 MUTATED PRSS48 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = MMP7 MUTATION ANALYSIS
D1395V1, survival
                sevent
clus2              0   1
  MMP7 MUTATED     6   2
  MMP7 WILD-TYPE 271  76
  MMP7 MUTATED MMP7 WILD-TYPE 
             8            347 
  MMP7 MUTATED MMP7 WILD-TYPE 
             2             76 
$`MMP7 MUTATED`
TCGA-AA-3950 TCGA-G4-6588 TCGA-A6-6141 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A01X 
       24.00        26.17         8.38        10.06         4.01        26.01 
TCGA-AY-5543 TCGA-AZ-4315 
       33.01        58.39 

$`MMP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MMP7 MUTATED MMP7 WILD-TYPE 
          4.01           0.00 
  MMP7 MUTATED MMP7 WILD-TYPE 
         58.39         148.01 
  MMP7 MUTATED MMP7 WILD-TYPE 
        25.005         22.030 
[1] "4.0 - 58.4 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1395V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP7 MUTATED         0        0        0         4         1         0
  MMP7 WILD-TYPE      64        1       26       104         7         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        16          6         44         33       35        11
                vv
clus             STAGE IVB
  MMP7 MUTATED           0
  MMP7 WILD-TYPE         1
D1395V3, multiclass
            clus
vv           MMP7 MUTATED MMP7 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  MMP7 MUTATED     0   1   6   1
  MMP7 WILD-TYPE   9  66 243  40
D1395V4, multiclass
    clus
vv   MMP7 MUTATED MMP7 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            1             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
  MMP7 MUTATED     5   2   1
  MMP7 WILD-TYPE 215  79  65
D1395V5, multiclass
    clus
vv   MMP7 MUTATED MMP7 WILD-TYPE
  N0            5            215
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1395V6, binary
                cls
clus               0   1
  MMP7 MUTATED     7   1
  MMP7 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      7    1
  MMP7 WILD-TYPE  278   47
   clus
vv  MMP7 MUTATED MMP7 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D1395V7, binary
                cls
clus               0   1
  MMP7 MUTATED     5   3
  MMP7 WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      5    3
  MMP7 WILD-TYPE  165  194
        clus
vv       MMP7 MUTATED MMP7 WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D1395V8, binary
                cls
clus               0   1
  MMP7 MUTATED     7   0
  MMP7 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      7    0
  MMP7 WILD-TYPE  293    8
     clus
vv    MMP7 MUTATED MMP7 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1395V9, binary
                cls
clus               0   1
  MMP7 MUTATED     6   2
  MMP7 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      6    2
  MMP7 WILD-TYPE  308   46
                               clus
vv                              MMP7 MUTATED MMP7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MMP7 MUTATED     6   0   0   1
  MMP7 WILD-TYPE 253   3  22  20
D1395V10, multiclass
    clus
vv   MMP7 MUTATED MMP7 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D1395V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP7 MUTATED                                  0     0
  MMP7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MMP7 MUTATED                           2     2
  MMP7 WILD-TYPE                        17   174
D1395V12, multiclass
                                  clus
vv                                 MMP7 MUTATED MMP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       2            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(1396) Variable = FAM120C MUTATION ANALYSIS
D1396V1, survival
                   sevent
clus2                 0   1
  FAM120C MUTATED     4   3
  FAM120C WILD-TYPE 273  75
  FAM120C MUTATED FAM120C WILD-TYPE 
                7               348 
  FAM120C MUTATED FAM120C WILD-TYPE 
                3                75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79        88.21        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6569 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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            22.045 
[1] "6.8 - 53.0 (29.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1396V2, continuous
                   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      62        1       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM120C MUTATED           0          0          2          0        0
  FAM120C WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM120C MUTATED           0         0
  FAM120C WILD-TYPE        12         1
D1396V3, multiclass
            clus
vv           FAM120C MUTATED FAM120C WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM120C MUTATED     0   2   5   1
  FAM120C WILD-TYPE   9  65 244  40
D1396V4, multiclass
    clus
vv   FAM120C MUTATED FAM120C WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               1                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
  FAM120C MUTATED     6   2   0
  FAM120C WILD-TYPE 214  79  66
D1396V5, multiclass
    clus
vv   FAM120C MUTATED FAM120C WILD-TYPE
  N0               6               214
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1396V6, binary
                   cls
clus                  0   1
  FAM120C MUTATED     6   0
  FAM120C WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      6    0
  FAM120C WILD-TYPE  279   48
   clus
vv  FAM120C MUTATED FAM120C WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1396V7, binary
                   cls
clus                  0   1
  FAM120C MUTATED     6   2
  FAM120C WILD-TYPE 164 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      6    2
  FAM120C WILD-TYPE  164  195
        clus
vv       FAM120C MUTATED FAM120C WILD-TYPE
  FEMALE               6               164
  MALE                 2               195
[1] 2 2
[1] FALSE
D1396V8, binary
                   cls
clus                  0   1
  FAM120C MUTATED     7   0
  FAM120C WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      7    0
  FAM120C WILD-TYPE  293    8
     clus
vv    FAM120C MUTATED FAM120C WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1396V9, binary
                   cls
clus                  0   1
  FAM120C MUTATED     8   0
  FAM120C WILD-TYPE 306  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      8    0
  FAM120C WILD-TYPE  306   48
                               clus
vv                              FAM120C MUTATED FAM120C WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM120C MUTATED     5   0   0   1
  FAM120C WILD-TYPE 254   3  22  20
D1396V10, multiclass
    clus
vv   FAM120C MUTATED FAM120C WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               1                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"
D1396V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM120C MUTATED                                  0     0
  FAM120C WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM120C MUTATED                           0     6
  FAM120C WILD-TYPE                        19   170
D1396V12, multiclass
                                  clus
vv                                 FAM120C MUTATED FAM120C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = TMSB15B MUTATION ANALYSIS
D1397V1, survival
                   sevent
clus2                 0   1
  TMSB15B MUTATED     1   2
  TMSB15B WILD-TYPE 276  76
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                3               352 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                2                76 
$`TMSB15B MUTATED`
TCGA-DM-A285 TCGA-D5-6540 TCGA-F4-6459 
        5.88        16.14         8.61 

$`TMSB15B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TMSB15B MUTATED TMSB15B WILD-TYPE 
             5.88              0.00 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
            16.14            148.01 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
             8.61             22.09 
[1] "5.9 - 16.1 (8.6)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "6.8"
D1397V2, continuous
                   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      63        1       26       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMSB15B MUTATED           0          0          1          0        1
  TMSB15B WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  TMSB15B MUTATED           0         0
  TMSB15B WILD-TYPE        12         1
D1397V3, multiclass
            clus
vv           TMSB15B MUTATED TMSB15B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                0               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  TMSB15B MUTATED     0   1   2   0
  TMSB15B WILD-TYPE   9  66 247  41
D1397V4, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               2               247
  T4               0                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
  TMSB15B MUTATED     1   0   2
  TMSB15B WILD-TYPE 219  81  64
D1397V5, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  N0               1               219
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1397V6, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     2   1
  TMSB15B WILD-TYPE 283  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      2    1
  TMSB15B WILD-TYPE  283   47
   clus
vv  TMSB15B MUTATED TMSB15B WILD-TYPE
  0               2               283
  1               1                47
[1] 2 2
[1] FALSE
D1397V7, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     2   1
  TMSB15B WILD-TYPE 168 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      2    1
  TMSB15B WILD-TYPE  168  196
        clus
vv       TMSB15B MUTATED TMSB15B WILD-TYPE
  FEMALE               2               168
  MALE                 1               196
[1] 2 2
[1] FALSE
D1397V8, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     2   0
  TMSB15B WILD-TYPE 298   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      2    0
  TMSB15B WILD-TYPE  298    8
     clus
vv    TMSB15B MUTATED TMSB15B WILD-TYPE
  NO                2               298
  YES               0                 8
[1] 2 2
[1] FALSE
D1397V9, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     1   2
  TMSB15B WILD-TYPE 313  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      1    2
  TMSB15B WILD-TYPE  313   46
                               clus
vv                              TMSB15B MUTATED TMSB15B WILD-TYPE
  COLON ADENOCARCINOMA                        1               313
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMSB15B MUTATED     2   0   0   0
  TMSB15B WILD-TYPE 257   3  22  21
D1397V10, multiclass
[1] "Remove cluster labels:" "TMSB15B MUTATED"       
clus
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        TCGA-AA-3520        TCGA-AA-3521 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3527 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3662        TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AD-6895        TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3502        TCGA-AA-3510 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3561        TCGA-AA-3655        TCGA-AA-3660 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3815        TCGA-AA-3818 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3845        TCGA-AA-3846 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3955 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3973 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3975        TCGA-AA-3984        TCGA-AA-3989        TCGA-AA-3994 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00N 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00W        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A022        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4682 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6460 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6315 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
D1397V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMSB15B MUTATED                                  0     0
  TMSB15B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMSB15B MUTATED                           0     3
  TMSB15B WILD-TYPE                        19   173
D1397V12, multiclass
                                  clus
vv                                 TMSB15B MUTATED TMSB15B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = UHRF1BP1L MUTATION ANALYSIS
D1398V1, survival
                     sevent
clus2                   0   1
  UHRF1BP1L MUTATED    11   8
  UHRF1BP1L WILD-TYPE 266  70
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 19                 336 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                  8                  70 
$`UHRF1BP1L MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6628 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3845 
       19.04        24.00        79.69        29.19        22.06         0.00 
TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6901 
       53.00         2.01        25.02         4.01        83.24        22.42 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6677 TCGA-F4-6460 
       49.41         6.77        15.02        15.02        11.08        31.96 
TCGA-G4-6317 
       36.00 

$`UHRF1BP1L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79        88.21        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        61.91        13.78        46.75 

  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                  0                   0 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
              83.24              148.01 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
              22.42               22.01 
[1] "0.0 - 83.2 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1398V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UHRF1BP1L MUTATED         3        0        3         8         1         0
  UHRF1BP1L WILD-TYPE      61        1       23       100         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UHRF1BP1L MUTATED           0          0          1          2        0
  UHRF1BP1L WILD-TYPE        18          6         43         31       35
                     vv
clus                  STAGE IVA STAGE IVB
  UHRF1BP1L MUTATED           0         0
  UHRF1BP1L WILD-TYPE        12         1
D1398V3, multiclass
            clus
vv           UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  STAGE I                    3                  61
  STAGE IA                   0                   1
  STAGE II                   3                  23
  STAGE IIA                  8                 100
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 1                  43
  STAGE IIIC                 2                  31
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  UHRF1BP1L MUTATED     0   4  15   1
  UHRF1BP1L WILD-TYPE   9  63 234  40
D1398V4, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  T1                 0                   9
  T2                 4                  63
  T3                15                 234
  T4                 1                  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
  UHRF1BP1L MUTATED    17   1   2
  UHRF1BP1L WILD-TYPE 203  80  64
D1398V5, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  N0                17                 203
  N1                 1                  80
  N2                 2                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1398V6, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    15   0
  UHRF1BP1L WILD-TYPE 270  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     15    0
  UHRF1BP1L WILD-TYPE  270   48
   clus
vv  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  0                15                 270
  1                 0                  48
[1] 2 2
[1] FALSE
D1398V7, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    11   9
  UHRF1BP1L WILD-TYPE 159 188
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     11    9
  UHRF1BP1L WILD-TYPE  159  188
        clus
vv       UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  FEMALE                11                 159
  MALE                   9                 188
[1] 2 2
[1] FALSE
D1398V8, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    16   0
  UHRF1BP1L WILD-TYPE 284   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     16    0
  UHRF1BP1L WILD-TYPE  284    8
     clus
vv    UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  NO                 16                 284
  YES                 0                   8
[1] 2 2
[1] FALSE
D1398V9, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    17   3
  UHRF1BP1L WILD-TYPE 297  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     17    3
  UHRF1BP1L WILD-TYPE  297   45
                               clus
vv                              UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  COLON ADENOCARCINOMA                         17                 297
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  UHRF1BP1L MUTATED    14   0   0   0
  UHRF1BP1L WILD-TYPE 245   3  22  21
D1398V10, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  R0                14                 245
  R1                 0                   3
  R2                 0                  22
  RX                 0                  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"
D1398V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UHRF1BP1L MUTATED                                  0     1
  UHRF1BP1L WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  UHRF1BP1L MUTATED                           1    10
  UHRF1BP1L WILD-TYPE                        18   166
D1398V12, multiclass
                                  clus
vv                                 UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                   9
  BLACK OR AFRICAN AMERICAN                        1                  18
  WHITE                                           10                 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(1399) Variable = PLEKHH2 MUTATION ANALYSIS
D1399V1, survival
                   sevent
clus2                 0   1
  PLEKHH2 MUTATED    13   5
  PLEKHH2 WILD-TYPE 264  73
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               18               337 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
                5                73 
$`PLEKHH2 MUTATED`
TCGA-AA-3525 TCGA-AA-3950 TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3663 TCGA-AA-3977 
        8.05        24.00        42.90         8.38         6.97        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        83.24        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        13.35 

$`PLEKHH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01         0.20         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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
             4.01              0.00 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
            83.24            148.01 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
            19.63             22.09 
[1] "4.0 - 83.2 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1399V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHH2 MUTATED         0        0        1        10         3         0
  PLEKHH2 WILD-TYPE      64        1       25        98         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHH2 MUTATED           1          0          2          0        1
  PLEKHH2 WILD-TYPE        17          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHH2 MUTATED           0         0
  PLEKHH2 WILD-TYPE        12         1
D1399V3, multiclass
            clus
vv           PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA               10                98
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  PLEKHH2 MUTATED     0   1  14   4
  PLEKHH2 WILD-TYPE   9  66 235  37
D1399V4, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              14               235
  T4               4                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
  PLEKHH2 MUTATED    15   2   2
  PLEKHH2 WILD-TYPE 205  79  64
D1399V5, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  N0              15               205
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1399V6, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    16   1
  PLEKHH2 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     16    1
  PLEKHH2 WILD-TYPE  269   47
   clus
vv  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  0              16               269
  1               1                47
[1] 2 2
[1] FALSE
D1399V7, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED     5  14
  PLEKHH2 WILD-TYPE 165 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED      5   14
  PLEKHH2 WILD-TYPE  165  183
        clus
vv       PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  FEMALE               5               165
  MALE                14               183
[1] 2 2
[1] FALSE
D1399V8, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    16   1
  PLEKHH2 WILD-TYPE 284   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     16    1
  PLEKHH2 WILD-TYPE  284    7
     clus
vv    PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  NO               16               284
  YES               1                 7
[1] 2 2
[1] FALSE
D1399V9, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    14   5
  PLEKHH2 WILD-TYPE 300  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     14    5
  PLEKHH2 WILD-TYPE  300   43
                               clus
vv                              PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  COLON ADENOCARCINOMA                       14               300
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHH2 MUTATED    14   0   1   2
  PLEKHH2 WILD-TYPE 245   3  21  19
D1399V10, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  R0              14               245
  R1               0                 3
  R2               1                21
  RX               2                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"
D1399V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHH2 MUTATED                                  0     3
  PLEKHH2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHH2 MUTATED                           2     5
  PLEKHH2 WILD-TYPE                        17   171
D1399V12, multiclass
                                  clus
vv                                 PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          5               171
[1] 4 2
[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 = VPRBP MUTATION ANALYSIS
D1400V1, survival
                 sevent
clus2               0   1
  VPRBP MUTATED     9   2
  VPRBP WILD-TYPE 268  76
  VPRBP MUTATED VPRBP WILD-TYPE 
             11             344 
  VPRBP MUTATED VPRBP WILD-TYPE 
              2              76 
$`VPRBP MUTATED`
TCGA-AA-3844 TCGA-AD-6895 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-A010 TCGA-AY-6386 
       14.93        25.08        33.53        24.39        34.98        17.82 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5868 TCGA-CM-6171 TCGA-G4-6309 
       10.06        21.14        17.03        14.04        85.48 

$`VPRBP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  VPRBP MUTATED VPRBP WILD-TYPE 
          10.06            0.00 
  VPRBP MUTATED VPRBP WILD-TYPE 
          85.48          148.01 
  VPRBP MUTATED VPRBP WILD-TYPE 
         21.140          22.075 
[1] "10.1 - 85.5 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1400V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPRBP MUTATED         3        0        0         3         1         0
  VPRBP WILD-TYPE      61        1       26       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VPRBP MUTATED           0          0          3          1        0         1
  VPRBP WILD-TYPE        18          6         41         32       35        11
                 vv
clus              STAGE IVB
  VPRBP MUTATED           0
  VPRBP WILD-TYPE         1
D1400V3, multiclass
            clus
vv           VPRBP MUTATED VPRBP WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  VPRBP MUTATED     1   2   7   2
  VPRBP WILD-TYPE   8  65 242  39
D1400V4, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             2              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
  VPRBP MUTATED     7   4   1
  VPRBP WILD-TYPE 213  77  65
D1400V5, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  N0             7             213
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1400V6, binary
                 cls
clus                0   1
  VPRBP MUTATED    11   1
  VPRBP WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED     11    1
  VPRBP WILD-TYPE  274   47
   clus
vv  VPRBP MUTATED VPRBP WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D1400V7, binary
                 cls
clus                0   1
  VPRBP MUTATED     9   3
  VPRBP WILD-TYPE 161 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      9    3
  VPRBP WILD-TYPE  161  194
        clus
vv       VPRBP MUTATED VPRBP WILD-TYPE
  FEMALE             9             161
  MALE               3             194
[1] 2 2
[1] FALSE
D1400V8, binary
                 cls
clus                0   1
  VPRBP MUTATED    10   1
  VPRBP WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED     10    1
  VPRBP WILD-TYPE  290    7
     clus
vv    VPRBP MUTATED VPRBP WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1400V9, binary
                 cls
clus                0   1
  VPRBP MUTATED    12   0
  VPRBP WILD-TYPE 302  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED     12    0
  VPRBP WILD-TYPE  302   48
                               clus
vv                              VPRBP MUTATED VPRBP WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VPRBP MUTATED     9   0   0   2
  VPRBP WILD-TYPE 250   3  22  19
D1400V10, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D1400V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPRBP MUTATED                                  0     1
  VPRBP WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VPRBP MUTATED                           3     5
  VPRBP WILD-TYPE                        16   171
D1400V12, multiclass
                                  clus
vv                                 VPRBP MUTATED VPRBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        5             171
[1] 4 2
[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 = ZP3 MUTATION ANALYSIS
D1401V1, survival
               sevent
clus2             0   1
  ZP3 MUTATED     4   1
  ZP3 WILD-TYPE 273  77
  ZP3 MUTATED ZP3 WILD-TYPE 
            5           350 
  ZP3 MUTATED ZP3 WILD-TYPE 
            1            77 
$`ZP3 MUTATED`
TCGA-AA-3819 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6603 TCGA-CM-6169 
       25.02        34.98        21.44        29.56        13.02 

$`ZP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6605 
       62.79        88.21        49.41         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ZP3 MUTATED ZP3 WILD-TYPE 
        13.02          0.00 
  ZP3 MUTATED ZP3 WILD-TYPE 
        34.98        148.01 
  ZP3 MUTATED ZP3 WILD-TYPE 
       25.020        22.045 
[1] "13.0 - 35.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1401V2, continuous
               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      64        1       26       105         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZP3 MUTATED           0          0          0          0        0         0
  ZP3 WILD-TYPE        18          6         44         33       35        12
               vv
clus            STAGE IVB
  ZP3 MUTATED           0
  ZP3 WILD-TYPE         1
D1401V3, multiclass
            clus
vv           ZP3 MUTATED ZP3 WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            3           105
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  ZP3 MUTATED     0   1   3   2
  ZP3 WILD-TYPE   9  66 246  39
D1401V4, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  T1           0             9
  T2           1            66
  T3           3           246
  T4           2            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
  ZP3 MUTATED     5   1   0
  ZP3 WILD-TYPE 215  80  66
D1401V5, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  N0           5           215
  N1           1            80
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1401V6, binary
               cls
clus              0   1
  ZP3 MUTATED     3   0
  ZP3 WILD-TYPE 282  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      3    0
  ZP3 WILD-TYPE  282   48
   clus
vv  ZP3 MUTATED ZP3 WILD-TYPE
  0           3           282
  1           0            48
[1] 2 2
[1] FALSE
D1401V7, binary
               cls
clus              0   1
  ZP3 MUTATED     4   2
  ZP3 WILD-TYPE 166 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      4    2
  ZP3 WILD-TYPE  166  195
        clus
vv       ZP3 MUTATED ZP3 WILD-TYPE
  FEMALE           4           166
  MALE             2           195
[1] 2 2
[1] FALSE
D1401V8, binary
               cls
clus              0   1
  ZP3 MUTATED     5   0
  ZP3 WILD-TYPE 295   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      5    0
  ZP3 WILD-TYPE  295    8
     clus
vv    ZP3 MUTATED ZP3 WILD-TYPE
  NO            5           295
  YES           0             8
[1] 2 2
[1] FALSE
D1401V9, binary
               cls
clus              0   1
  ZP3 MUTATED     6   0
  ZP3 WILD-TYPE 308  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      6    0
  ZP3 WILD-TYPE  308   48
                               clus
vv                              ZP3 MUTATED ZP3 WILD-TYPE
  COLON ADENOCARCINOMA                    6           308
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ZP3 MUTATED     4   0   0   1
  ZP3 WILD-TYPE 255   3  22  20
D1401V10, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  R0           4           255
  R1           0             3
  R2           0            22
  RX           1            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"
D1401V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZP3 MUTATED                                  0     0
  ZP3 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZP3 MUTATED                           1     3
  ZP3 WILD-TYPE                        18   173
D1401V12, multiclass
                                  clus
vv                                 ZP3 MUTATED ZP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      3           173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1402) Variable = OR11H12 MUTATION ANALYSIS
D1402V1, survival
                   sevent
clus2                 0   1
  OR11H12 MUTATED     3   0
  OR11H12 WILD-TYPE 274  78
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                3               352 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                0                78 
$`OR11H12 MUTATED`
TCGA-G4-6628 TCGA-AU-3779 TCGA-D5-6535 
       79.69        14.50        15.12 

$`OR11H12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  OR11H12 MUTATED OR11H12 WILD-TYPE 
             14.5               0.0 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
            79.69            148.01 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
           15.120            22.075 
[1] "14.5 - 79.7 (15.1)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1402V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR11H12 MUTATED         1        0        0         1         0         0
  OR11H12 WILD-TYPE      63        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR11H12 MUTATED           0          0          1          0        0
  OR11H12 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  OR11H12 MUTATED           0         0
  OR11H12 WILD-TYPE        12         1
D1402V3, multiclass
            clus
vv           OR11H12 MUTATED OR11H12 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  OR11H12 MUTATED     0   1   2   0
  OR11H12 WILD-TYPE   9  66 247  41
D1402V4, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               2               247
  T4               0                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
  OR11H12 MUTATED     2   1   0
  OR11H12 WILD-TYPE 218  80  66
D1402V5, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  N0               2               218
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1402V6, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     2   0
  OR11H12 WILD-TYPE 283  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      2    0
  OR11H12 WILD-TYPE  283   48
   clus
vv  OR11H12 MUTATED OR11H12 WILD-TYPE
  0               2               283
  1               0                48
[1] 2 2
[1] FALSE
D1402V7, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     2   1
  OR11H12 WILD-TYPE 168 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      2    1
  OR11H12 WILD-TYPE  168  196
        clus
vv       OR11H12 MUTATED OR11H12 WILD-TYPE
  FEMALE               2               168
  MALE                 1               196
[1] 2 2
[1] FALSE
D1402V8, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     3   0
  OR11H12 WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      3    0
  OR11H12 WILD-TYPE  297    8
     clus
vv    OR11H12 MUTATED OR11H12 WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D1402V9, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     3   0
  OR11H12 WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      3    0
  OR11H12 WILD-TYPE  311   48
                               clus
vv                              OR11H12 MUTATED OR11H12 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  OR11H12 MUTATED     2   0   0   1
  OR11H12 WILD-TYPE 257   3  22  20
D1402V10, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  R0               2               257
  R1               0                 3
  R2               0                22
  RX               1                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"
D1402V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR11H12 MUTATED                                  0     0
  OR11H12 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  OR11H12 MUTATED                           0     3
  OR11H12 WILD-TYPE                        19   173
D1402V12, multiclass
                                  clus
vv                                 OR11H12 MUTATED OR11H12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = MMAA MUTATION ANALYSIS
D1403V1, survival
                sevent
clus2              0   1
  MMAA MUTATED     7   2
  MMAA WILD-TYPE 270  76
  MMAA MUTATED MMAA WILD-TYPE 
             9            346 
  MMAA MUTATED MMAA WILD-TYPE 
             2             76 
$`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 
       12.76        29.06        30.08 

$`MMAA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        19.66         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MMAA MUTATED MMAA WILD-TYPE 
          3.19           0.00 
  MMAA MUTATED MMAA WILD-TYPE 
         58.39         148.01 
  MMAA MUTATED MMAA WILD-TYPE 
         12.76          22.09 
[1] "3.2 - 58.4 (12.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1403V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMAA MUTATED         0        0        1         4         2         0
  MMAA WILD-TYPE      64        1       25       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMAA MUTATED           0          1          0          0        1         0
  MMAA WILD-TYPE        18          5         44         33       34        12
                vv
clus             STAGE IVB
  MMAA MUTATED           0
  MMAA WILD-TYPE         1
D1403V3, multiclass
            clus
vv           MMAA MUTATED MMAA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  MMAA MUTATED     0   1   5   3
  MMAA WILD-TYPE   9  66 244  38
D1403V4, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            3             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
  MMAA MUTATED     7   1   1
  MMAA WILD-TYPE 213  80  65
D1403V5, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  N0            7            213
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1403V6, binary
                cls
clus               0   1
  MMAA MUTATED     7   1
  MMAA WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      7    1
  MMAA WILD-TYPE  278   47
   clus
vv  MMAA MUTATED MMAA WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D1403V7, binary
                cls
clus               0   1
  MMAA MUTATED     2   7
  MMAA WILD-TYPE 168 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      2    7
  MMAA WILD-TYPE  168  190
        clus
vv       MMAA MUTATED MMAA WILD-TYPE
  FEMALE            2            168
  MALE              7            190
[1] 2 2
[1] FALSE
D1403V8, binary
                cls
clus               0   1
  MMAA MUTATED     8   0
  MMAA WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      8    0
  MMAA WILD-TYPE  292    8
     clus
vv    MMAA MUTATED MMAA WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1403V9, binary
                cls
clus               0   1
  MMAA MUTATED     7   2
  MMAA WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      7    2
  MMAA WILD-TYPE  307   46
                               clus
vv                              MMAA MUTATED MMAA WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MMAA MUTATED     5   0   0   1
  MMAA WILD-TYPE 254   3  22  20
D1403V10, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1403V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMAA MUTATED                                  0     1
  MMAA WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MMAA MUTATED                           1     5
  MMAA WILD-TYPE                        18   171
D1403V12, multiclass
                                  clus
vv                                 MMAA MUTATED MMAA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = CALCOCO2 MUTATION ANALYSIS
D1404V1, survival
                    sevent
clus2                  0   1
  CALCOCO2 MUTATED     5   1
  CALCOCO2 WILD-TYPE 272  77
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 6                349 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 1                 77 
$`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 

$`CALCOCO2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
             12.76               0.00 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
             61.91             148.01 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
             25.53              22.06 
[1] "12.8 - 61.9 (25.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1404V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CALCOCO2 MUTATED         0        0        0         2         1         0
  CALCOCO2 WILD-TYPE      64        1       26       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CALCOCO2 MUTATED           0          0          1          0        3
  CALCOCO2 WILD-TYPE        18          6         43         33       32
                    vv
clus                 STAGE IVA STAGE IVB
  CALCOCO2 MUTATED           0         0
  CALCOCO2 WILD-TYPE        12         1
D1404V3, multiclass
            clus
vv           CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 2                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  3                 32
  STAGE IVA                 0                 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
  CALCOCO2 MUTATED     0   0   5   2
  CALCOCO2 WILD-TYPE   9  67 244  39
D1404V4, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                5                244
  T4                2                 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
  CALCOCO2 MUTATED     4   2   1
  CALCOCO2 WILD-TYPE 216  79  65
D1404V5, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  N0                4                216
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1404V6, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     3   3
  CALCOCO2 WILD-TYPE 282  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      3    3
  CALCOCO2 WILD-TYPE  282   45
   clus
vv  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  0                3                282
  1                3                 45
[1] 2 2
[1] FALSE
D1404V7, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     2   5
  CALCOCO2 WILD-TYPE 168 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      2    5
  CALCOCO2 WILD-TYPE  168  192
        clus
vv       CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  FEMALE                2                168
  MALE                  5                192
[1] 2 2
[1] FALSE
D1404V8, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     4   2
  CALCOCO2 WILD-TYPE 296   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      4    2
  CALCOCO2 WILD-TYPE  296    6
     clus
vv    CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  NO                 4                296
  YES                2                  6
[1] 2 2
[1] FALSE
D1404V9, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     4   3
  CALCOCO2 WILD-TYPE 310  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      4    3
  CALCOCO2 WILD-TYPE  310   45
                               clus
vv                              CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CALCOCO2 MUTATED     3   0   2   2
  CALCOCO2 WILD-TYPE 256   3  20  19
D1404V10, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                2                 20
  RX                2                 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"
D1404V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CALCOCO2 MUTATED                                  0     1
  CALCOCO2 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CALCOCO2 MUTATED                           0     3
  CALCOCO2 WILD-TYPE                        19   173
D1404V12, multiclass
                                  clus
vv                                 CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[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 = ZNF385B MUTATION ANALYSIS
D1405V1, survival
                   sevent
clus2                 0   1
  ZNF385B MUTATED     4   3
  ZNF385B WILD-TYPE 273  75
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               348 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                3                75 
$`ZNF385B MUTATED`
TCGA-AA-3952 TCGA-G4-6321 TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4315 TCGA-D5-6529 
        2.01        22.09         5.79        21.44        58.39        20.19 
TCGA-DM-A28G 
       60.79 

$`ZNF385B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF385B MUTATED ZNF385B WILD-TYPE 
             2.01              0.00 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            60.79            148.01 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
           21.440            22.075 
[1] "2.0 - 60.8 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1405V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF385B MUTATED         0        0        0         4         0         0
  ZNF385B WILD-TYPE      64        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF385B MUTATED           1          0          0          2        0
  ZNF385B WILD-TYPE        17          6         44         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF385B MUTATED           0         0
  ZNF385B WILD-TYPE        12         1
D1405V3, multiclass
            clus
vv           ZNF385B MUTATED ZNF385B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                0                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
  ZNF385B MUTATED     0   1   5   1
  ZNF385B WILD-TYPE   9  66 244  40
D1405V4, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               1                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
  ZNF385B MUTATED     4   1   2
  ZNF385B WILD-TYPE 216  80  64
D1405V5, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  N0               4               216
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1405V6, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     4   0
  ZNF385B WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      4    0
  ZNF385B WILD-TYPE  281   48
   clus
vv  ZNF385B MUTATED ZNF385B WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1405V7, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     1   6
  ZNF385B WILD-TYPE 169 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      1    6
  ZNF385B WILD-TYPE  169  191
        clus
vv       ZNF385B MUTATED ZNF385B WILD-TYPE
  FEMALE               1               169
  MALE                 6               191
[1] 2 2
[1] FALSE
D1405V8, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     5   0
  ZNF385B WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      5    0
  ZNF385B WILD-TYPE  295    8
     clus
vv    ZNF385B MUTATED ZNF385B WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1405V9, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     6   1
  ZNF385B WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      6    1
  ZNF385B WILD-TYPE  308   47
                               clus
vv                              ZNF385B MUTATED ZNF385B WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF385B MUTATED     5   0   0   0
  ZNF385B WILD-TYPE 254   3  22  21
D1405V10, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1405V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF385B MUTATED                                  0     0
  ZNF385B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF385B MUTATED                           0     6
  ZNF385B WILD-TYPE                        19   170
D1405V12, multiclass
                                  clus
vv                                 ZNF385B MUTATED ZNF385B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = SUPT3H MUTATION ANALYSIS
D1406V1, survival
                  sevent
clus2                0   1
  SUPT3H MUTATED     6   2
  SUPT3H WILD-TYPE 271  76
  SUPT3H MUTATED SUPT3H WILD-TYPE 
               8              347 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
               2               76 
$`SUPT3H MUTATED`
TCGA-AA-3516 TCGA-AA-3950 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-6599 TCGA-CA-6719 
       13.02        24.00        63.98        34.98         6.77        14.30 
TCGA-CM-6674 TCGA-F4-6854 
       12.95         0.53 

$`SUPT3H WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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            22.09 
[1] "0.5 - 64.0 (13.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1406V2, continuous
                  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      63        1       25       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUPT3H MUTATED           2          0          0          0        0
  SUPT3H WILD-TYPE        16          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SUPT3H MUTATED           0         0
  SUPT3H WILD-TYPE        12         1
D1406V3, multiclass
            clus
vv           SUPT3H MUTATED SUPT3H WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SUPT3H MUTATED     0   1   8   2
  SUPT3H WILD-TYPE   9  66 241  39
D1406V4, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  T1              0                9
  T2              1               66
  T3              8              241
  T4              2               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
  SUPT3H MUTATED     9   0   2
  SUPT3H WILD-TYPE 211  81  64
D1406V5, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  N0              9              211
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1406V6, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     9   0
  SUPT3H WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      9    0
  SUPT3H WILD-TYPE  276   48
   clus
vv  SUPT3H MUTATED SUPT3H WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1406V7, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     6   5
  SUPT3H WILD-TYPE 164 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      6    5
  SUPT3H WILD-TYPE  164  192
        clus
vv       SUPT3H MUTATED SUPT3H WILD-TYPE
  FEMALE              6              164
  MALE                5              192
[1] 2 2
[1] FALSE
D1406V8, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     8   0
  SUPT3H WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      8    0
  SUPT3H WILD-TYPE  292    8
     clus
vv    SUPT3H MUTATED SUPT3H WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1406V9, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     9   2
  SUPT3H WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      9    2
  SUPT3H WILD-TYPE  305   46
                               clus
vv                              SUPT3H MUTATED SUPT3H WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SUPT3H MUTATED     7   0   0   2
  SUPT3H WILD-TYPE 252   3  22  19
D1406V10, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D1406V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUPT3H MUTATED                                  0     1
  SUPT3H WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SUPT3H MUTATED                           0     4
  SUPT3H WILD-TYPE                        19   172
D1406V12, multiclass
                                  clus
vv                                 SUPT3H MUTATED SUPT3H WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = FMO5 MUTATION ANALYSIS
D1407V1, survival
                sevent
clus2              0   1
  FMO5 MUTATED     6   4
  FMO5 WILD-TYPE 271  74
  FMO5 MUTATED FMO5 WILD-TYPE 
            10            345 
  FMO5 MUTATED FMO5 WILD-TYPE 
             4             74 
$`FMO5 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-A029 TCGA-AU-3779 TCGA-AZ-6603 TCGA-CA-6718 
        8.38        19.66        51.98        14.50        29.56        10.06 
TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-5861 TCGA-G4-6303 
       21.14        30.08        15.02        65.85 

$`FMO5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5864 
       22.03        22.98        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 
       74.56        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FMO5 MUTATED FMO5 WILD-TYPE 
          8.38           0.00 
  FMO5 MUTATED FMO5 WILD-TYPE 
         65.85         148.01 
  FMO5 MUTATED FMO5 WILD-TYPE 
         20.40          22.09 
[1] "8.4 - 65.8 (20.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1407V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FMO5 MUTATED         1        0        1         5         0         0
  FMO5 WILD-TYPE      63        1       25       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMO5 MUTATED           0          0          0          1        1         0
  FMO5 WILD-TYPE        18          6         44         32       34        12
                vv
clus             STAGE IVB
  FMO5 MUTATED           0
  FMO5 WILD-TYPE         1
D1407V3, multiclass
            clus
vv           FMO5 MUTATED FMO5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  FMO5 MUTATED     1   1   7   1
  FMO5 WILD-TYPE   8  66 242  40
D1407V4, multiclass
    clus
vv   FMO5 MUTATED FMO5 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            7            242
  T4            1             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
  FMO5 MUTATED     7   3   0
  FMO5 WILD-TYPE 213  78  66
D1407V5, multiclass
    clus
vv   FMO5 MUTATED FMO5 WILD-TYPE
  N0            7            213
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1407V6, binary
                cls
clus               0   1
  FMO5 MUTATED     7   1
  FMO5 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED      7    1
  FMO5 WILD-TYPE  278   47
   clus
vv  FMO5 MUTATED FMO5 WILD-TYPE
  0            7            278
  1            1             47
[1] 2 2
[1] FALSE
D1407V7, binary
                cls
clus               0   1
  FMO5 MUTATED     6   4
  FMO5 WILD-TYPE 164 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED      6    4
  FMO5 WILD-TYPE  164  193
        clus
vv       FMO5 MUTATED FMO5 WILD-TYPE
  FEMALE            6            164
  MALE              4            193
[1] 2 2
[1] FALSE
D1407V8, binary
                cls
clus               0   1
  FMO5 MUTATED    10   0
  FMO5 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED     10    0
  FMO5 WILD-TYPE  290    8
     clus
vv    FMO5 MUTATED FMO5 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1407V9, binary
                cls
clus               0   1
  FMO5 MUTATED     9   1
  FMO5 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED      9    1
  FMO5 WILD-TYPE  305   47
                               clus
vv                              FMO5 MUTATED FMO5 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FMO5 MUTATED     6   0   0   2
  FMO5 WILD-TYPE 253   3  22  19
D1407V10, multiclass
    clus
vv   FMO5 MUTATED FMO5 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            2             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"
D1407V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FMO5 MUTATED                                  0     1
  FMO5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FMO5 MUTATED                           1     7
  FMO5 WILD-TYPE                        18   169
D1407V12, multiclass
                                  clus
vv                                 FMO5 MUTATED FMO5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1408) Variable = CHRM3 MUTATION ANALYSIS
D1408V1, survival
                 sevent
clus2               0   1
  CHRM3 MUTATED     7   6
  CHRM3 WILD-TYPE 270  72
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             13             342 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
              6              72 
$`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 
       65.85 

$`CHRM3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-F4-6703 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        43.04        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.045 
[1] "4.0 - 88.2 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1408V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRM3 MUTATED         2        0        1         5         1         0
  CHRM3 WILD-TYPE      62        1       25       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHRM3 MUTATED           1          0          0          1        1         0
  CHRM3 WILD-TYPE        17          6         44         32       34        12
                 vv
clus              STAGE IVB
  CHRM3 MUTATED           0
  CHRM3 WILD-TYPE         1
D1408V3, multiclass
            clus
vv           CHRM3 MUTATED CHRM3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  CHRM3 MUTATED     1   1   9   2
  CHRM3 WILD-TYPE   8  66 240  39
D1408V4, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             9             240
  T4             2              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
  CHRM3 MUTATED    10   1   2
  CHRM3 WILD-TYPE 210  80  64
D1408V5, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1408V6, binary
                 cls
clus                0   1
  CHRM3 MUTATED    11   1
  CHRM3 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED     11    1
  CHRM3 WILD-TYPE  274   47
   clus
vv  CHRM3 MUTATED CHRM3 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D1408V7, binary
                 cls
clus                0   1
  CHRM3 MUTATED     5   8
  CHRM3 WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED      5    8
  CHRM3 WILD-TYPE  165  189
        clus
vv       CHRM3 MUTATED CHRM3 WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D1408V8, binary
                 cls
clus                0   1
  CHRM3 MUTATED    10   1
  CHRM3 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED     10    1
  CHRM3 WILD-TYPE  290    7
     clus
vv    CHRM3 MUTATED CHRM3 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1408V9, binary
                 cls
clus                0   1
  CHRM3 MUTATED     9   4
  CHRM3 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED      9    4
  CHRM3 WILD-TYPE  305   44
                               clus
vv                              CHRM3 MUTATED CHRM3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHRM3 MUTATED     8   0   0   2
  CHRM3 WILD-TYPE 251   3  22  19
D1408V10, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D1408V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRM3 MUTATED                                  0     2
  CHRM3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRM3 MUTATED                           0     8
  CHRM3 WILD-TYPE                        19   168
D1408V12, multiclass
                                  clus
vv                                 CHRM3 MUTATED CHRM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = SYT2 MUTATION ANALYSIS
D1409V1, survival
                sevent
clus2              0   1
  SYT2 MUTATED     5   3
  SYT2 WILD-TYPE 272  75
  SYT2 MUTATED SYT2 WILD-TYPE 
             8            347 
  SYT2 MUTATED SYT2 WILD-TYPE 
             3             75 
$`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 
       16.14        98.24 

$`SYT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SYT2 MUTATED SYT2 WILD-TYPE 
          1.02           0.00 
  SYT2 MUTATED SYT2 WILD-TYPE 
         98.24         148.01 
  SYT2 MUTATED SYT2 WILD-TYPE 
         14.58          22.09 
[1] "1.0 - 98.2 (14.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1409V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT2 MUTATED         1        0        2         2         2         0
  SYT2 WILD-TYPE      63        1       24       106         6         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        18          6         44         33       34        12
                vv
clus             STAGE IVB
  SYT2 MUTATED           0
  SYT2 WILD-TYPE         1
D1409V3, multiclass
            clus
vv           SYT2 MUTATED SYT2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  SYT2 MUTATED     0   1   4   3
  SYT2 WILD-TYPE   9  66 245  38
D1409V4, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            3             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
  SYT2 MUTATED     7   0   1
  SYT2 WILD-TYPE 213  81  65
D1409V5, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  N0            7            213
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1409V6, binary
                cls
clus               0   1
  SYT2 MUTATED     6   1
  SYT2 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      6    1
  SYT2 WILD-TYPE  279   47
   clus
vv  SYT2 MUTATED SYT2 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D1409V7, binary
                cls
clus               0   1
  SYT2 MUTATED     3   5
  SYT2 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      3    5
  SYT2 WILD-TYPE  167  192
        clus
vv       SYT2 MUTATED SYT2 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D1409V8, binary
                cls
clus               0   1
  SYT2 MUTATED     5   0
  SYT2 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      5    0
  SYT2 WILD-TYPE  295    8
     clus
vv    SYT2 MUTATED SYT2 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1409V9, binary
                cls
clus               0   1
  SYT2 MUTATED     5   3
  SYT2 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      5    3
  SYT2 WILD-TYPE  309   45
                               clus
vv                              SYT2 MUTATED SYT2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SYT2 MUTATED     5   0   0   0
  SYT2 WILD-TYPE 254   3  22  21
D1409V10, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1409V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYT2 MUTATED                                  0     0
  SYT2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SYT2 MUTATED                           1     4
  SYT2 WILD-TYPE                        18   172
D1409V12, multiclass
                                  clus
vv                                 SYT2 MUTATED SYT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = NCL MUTATION ANALYSIS
D1410V1, survival
               sevent
clus2             0   1
  NCL MUTATED     5   5
  NCL WILD-TYPE 272  73
  NCL MUTATED NCL WILD-TYPE 
           10           345 
  NCL MUTATED NCL WILD-TYPE 
            5            73 
$`NCL MUTATED`
TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6608 TCGA-AA-3845 TCGA-AA-A00N TCGA-AD-6889 
       85.05        10.88         1.94         0.00         4.01        83.24 
TCGA-AU-3779 TCGA-CM-5341 TCGA-CM-6674 TCGA-DM-A28H 
       14.50        29.06        12.95       117.07 

$`NCL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NCL MUTATED NCL WILD-TYPE 
            0             0 
  NCL MUTATED NCL WILD-TYPE 
       117.07        148.01 
  NCL MUTATED NCL WILD-TYPE 
       13.725        22.090 
[1] "0.0 - 117.1 (13.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1410V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCL MUTATED         0        0        1         4         1         0
  NCL WILD-TYPE      64        1       25       104         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCL MUTATED           0          2          0          1        0         0
  NCL WILD-TYPE        18          4         44         32       35        12
               vv
clus            STAGE IVB
  NCL MUTATED           0
  NCL WILD-TYPE         1
D1410V3, multiclass
            clus
vv           NCL MUTATED NCL WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           2             4
  STAGE IIIB           0            44
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  NCL MUTATED     0   2   6   2
  NCL WILD-TYPE   9  65 243  39
D1410V4, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  T1           0             9
  T2           2            65
  T3           6           243
  T4           2            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
  NCL MUTATED     6   2   2
  NCL WILD-TYPE 214  79  64
D1410V5, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  N0           6           214
  N1           2            79
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1410V6, binary
               cls
clus              0   1
  NCL MUTATED     9   0
  NCL WILD-TYPE 276  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      9    0
  NCL WILD-TYPE  276   48
   clus
vv  NCL MUTATED NCL WILD-TYPE
  0           9           276
  1           0            48
[1] 2 2
[1] FALSE
D1410V7, binary
               cls
clus              0   1
  NCL MUTATED     4   6
  NCL WILD-TYPE 166 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      4    6
  NCL WILD-TYPE  166  191
        clus
vv       NCL MUTATED NCL WILD-TYPE
  FEMALE           4           166
  MALE             6           191
[1] 2 2
[1] FALSE
D1410V8, binary
               cls
clus              0   1
  NCL MUTATED     7   0
  NCL WILD-TYPE 293   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      7    0
  NCL WILD-TYPE  293    8
     clus
vv    NCL MUTATED NCL WILD-TYPE
  NO            7           293
  YES           0             8
[1] 2 2
[1] FALSE
D1410V9, binary
               cls
clus              0   1
  NCL MUTATED     9   1
  NCL WILD-TYPE 305  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      9    1
  NCL WILD-TYPE  305   47
                               clus
vv                              NCL MUTATED NCL WILD-TYPE
  COLON ADENOCARCINOMA                    9           305
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NCL MUTATED     7   0   0   0
  NCL WILD-TYPE 252   3  22  21
D1410V10, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  R0           7           252
  R1           0             3
  R2           0            22
  RX           0            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"
D1410V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCL MUTATED                                  0     1
  NCL WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NCL MUTATED                           0     6
  NCL WILD-TYPE                        19   170
D1410V12, multiclass
                                  clus
vv                                 NCL MUTATED NCL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      6           170
[1] 4 2
[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 = ZNF462 MUTATION ANALYSIS
D1411V1, survival
                  sevent
clus2                0   1
  ZNF462 MUTATED    16   7
  ZNF462 WILD-TYPE 261  71
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              23              332 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
               7               71 
$`ZNF462 MUTATED`
TCGA-AA-3516 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3811 
       13.02        26.17        22.06        24.39        20.12        10.06 
TCGA-AA-3877 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6890 
       31.00        38.04        34.98        38.07        12.16        24.53 
TCGA-AD-6901 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CM-4743 
       22.42        27.09        58.39        49.41         3.19        23.05 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A28F 
       17.03        12.00        14.04        13.35        35.97 

$`ZNF462 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.08        25.18        21.76        24.69        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        83.24         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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-6163 TCGA-CM-6164 
        5.03        15.02        15.02        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ZNF462 MUTATED ZNF462 WILD-TYPE 
            3.19             0.00 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
           58.39           148.01 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
           23.05            21.99 
[1] "3.2 - 58.4 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1411V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF462 MUTATED         5        0        2         8         1         0
  ZNF462 WILD-TYPE      59        1       24       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF462 MUTATED           3          0          2          0        2
  ZNF462 WILD-TYPE        15          6         42         33       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF462 MUTATED           1         0
  ZNF462 WILD-TYPE        11         1
D1411V3, multiclass
            clus
vv           ZNF462 MUTATED ZNF462 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               15
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               1               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
  ZNF462 MUTATED     2   4  15   5
  ZNF462 WILD-TYPE   7  63 234  36
D1411V4, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  T1              2                7
  T2              4               63
  T3             15              234
  T4              5               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
  ZNF462 MUTATED    18   5   3
  ZNF462 WILD-TYPE 202  76  63
D1411V5, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  N0             18              202
  N1              5               76
  N2              3               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"
D1411V6, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    18   3
  ZNF462 WILD-TYPE 267  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     18    3
  ZNF462 WILD-TYPE  267   45
   clus
vv  ZNF462 MUTATED ZNF462 WILD-TYPE
  0             18              267
  1              3               45
[1] 2 2
[1] FALSE
D1411V7, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    15  11
  ZNF462 WILD-TYPE 155 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     15   11
  ZNF462 WILD-TYPE  155  186
        clus
vv       ZNF462 MUTATED ZNF462 WILD-TYPE
  FEMALE             15              155
  MALE               11              186
[1] 2 2
[1] FALSE
D1411V8, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    21   0
  ZNF462 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     21    0
  ZNF462 WILD-TYPE  279    8
     clus
vv    ZNF462 MUTATED ZNF462 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D1411V9, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    20   6
  ZNF462 WILD-TYPE 294  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     20    6
  ZNF462 WILD-TYPE  294   42
                               clus
vv                              ZNF462 MUTATED ZNF462 WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF462 MUTATED    17   0   1   0
  ZNF462 WILD-TYPE 242   3  21  21
D1411V10, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  R0             17              242
  R1              0                3
  R2              1               21
  RX              0               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"
D1411V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF462 MUTATED                                  0     0
  ZNF462 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF462 MUTATED                           0    17
  ZNF462 WILD-TYPE                        19   159
D1411V12, multiclass
                                  clus
vv                                 ZNF462 MUTATED ZNF462 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        17              159
[1] 4 2
[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 = SIX5 MUTATION ANALYSIS
D1412V1, survival
                sevent
clus2              0   1
  SIX5 MUTATED     4   1
  SIX5 WILD-TYPE 273  77
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            350 
  SIX5 MUTATED SIX5 WILD-TYPE 
             1             77 
$`SIX5 MUTATED`
TCGA-G4-6586 TCGA-AA-3947 TCGA-AA-3966 TCGA-AD-5900 TCGA-F4-6570 
       35.80        33.01         2.01        12.16         6.18 

$`SIX5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SIX5 MUTATED SIX5 WILD-TYPE 
          2.01           0.00 
  SIX5 MUTATED SIX5 WILD-TYPE 
         35.80         148.01 
  SIX5 MUTATED SIX5 WILD-TYPE 
        12.160         22.075 
[1] "2.0 - 35.8 (12.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1412V2, continuous
                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      63        1       26       105         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  SIX5 MUTATED           0
  SIX5 WILD-TYPE         1
D1412V3, multiclass
            clus
vv           SIX5 MUTATED SIX5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  SIX5 MUTATED     0   1   3   1
  SIX5 WILD-TYPE   9  66 246  40
D1412V4, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            1             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
  SIX5 MUTATED     5   0   0
  SIX5 WILD-TYPE 215  81  66
D1412V5, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  N0            5            215
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1412V6, binary
                cls
clus               0   1
  SIX5 MUTATED     4   0
  SIX5 WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      4    0
  SIX5 WILD-TYPE  281   48
   clus
vv  SIX5 MUTATED SIX5 WILD-TYPE
  0            4            281
  1            0             48
[1] 2 2
[1] FALSE
D1412V7, binary
                cls
clus               0   1
  SIX5 MUTATED     4   1
  SIX5 WILD-TYPE 166 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      4    1
  SIX5 WILD-TYPE  166  196
        clus
vv       SIX5 MUTATED SIX5 WILD-TYPE
  FEMALE            4            166
  MALE              1            196
[1] 2 2
[1] FALSE
D1412V8, binary
                cls
clus               0   1
  SIX5 MUTATED     4   0
  SIX5 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      4    0
  SIX5 WILD-TYPE  296    8
     clus
vv    SIX5 MUTATED SIX5 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1412V9, binary
                cls
clus               0   1
  SIX5 MUTATED     2   3
  SIX5 WILD-TYPE 312  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      2    3
  SIX5 WILD-TYPE  312   45
                               clus
vv                              SIX5 MUTATED SIX5 WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SIX5 MUTATED     4   0   0   0
  SIX5 WILD-TYPE 255   3  22  21
D1412V10, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D1412V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIX5 MUTATED                                  0     0
  SIX5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SIX5 MUTATED                           0     3
  SIX5 WILD-TYPE                        19   173
D1412V12, multiclass
                                  clus
vv                                 SIX5 MUTATED SIX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = C9ORF125 MUTATION ANALYSIS
D1413V1, survival
                    sevent
clus2                  0   1
  C9ORF125 MUTATED     9   3
  C9ORF125 WILD-TYPE 268  75
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                343 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                 3                 75 
$`C9ORF125 MUTATED`
TCGA-AA-3516 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3710 
       13.02        25.08        26.17        22.06         3.02        26.99 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6930 TCGA-DM-A1HB 
       38.04        30.02        58.39        49.41        13.35       135.65 

$`C9ORF125 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        19.00        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
              3.02               0.00 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
            135.65             148.01 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
             26.58              21.99 
[1] "3.0 - 135.7 (26.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1413V2, continuous
                    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      64        1       24       101         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF125 MUTATED           1          0          2          0        0
  C9ORF125 WILD-TYPE        17          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF125 MUTATED           0         0
  C9ORF125 WILD-TYPE        12         1
D1413V3, multiclass
            clus
vv           C9ORF125 MUTATED C9ORF125 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 7                101
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C9ORF125 MUTATED     0   0  12   0
  C9ORF125 WILD-TYPE   9  67 237  41
D1413V4, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3               12                237
  T4                0                 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
  C9ORF125 MUTATED     9   2   1
  C9ORF125 WILD-TYPE 211  79  65
D1413V5, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  N0                9                211
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1413V6, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED    11   0
  C9ORF125 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED     11    0
  C9ORF125 WILD-TYPE  274   48
   clus
vv  C9ORF125 MUTATED C9ORF125 WILD-TYPE
  0               11                274
  1                0                 48
[1] 2 2
[1] FALSE
D1413V7, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED     6   6
  C9ORF125 WILD-TYPE 164 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED      6    6
  C9ORF125 WILD-TYPE  164  191
        clus
vv       C9ORF125 MUTATED C9ORF125 WILD-TYPE
  FEMALE                6                164
  MALE                  6                191
[1] 2 2
[1] FALSE
D1413V8, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED    11   0
  C9ORF125 WILD-TYPE 289   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED     11    0
  C9ORF125 WILD-TYPE  289    8
     clus
vv    C9ORF125 MUTATED C9ORF125 WILD-TYPE
  NO                11                289
  YES                0                  8
[1] 2 2
[1] FALSE
D1413V9, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED     9   2
  C9ORF125 WILD-TYPE 305  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED      9    2
  C9ORF125 WILD-TYPE  305   46
                               clus
vv                              C9ORF125 MUTATED C9ORF125 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF125 MUTATED     9   0   0   0
  C9ORF125 WILD-TYPE 250   3  22  21
D1413V10, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1413V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF125 MUTATED                                  0     0
  C9ORF125 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF125 MUTATED                           0     7
  C9ORF125 WILD-TYPE                        19   169
D1413V12, multiclass
                                  clus
vv                                 C9ORF125 MUTATED C9ORF125 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           7                169
[1] 4 2
[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 = AMBRA1 MUTATION ANALYSIS
D1414V1, survival
                  sevent
clus2                0   1
  AMBRA1 MUTATED    14   4
  AMBRA1 WILD-TYPE 263  74
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              18              337 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
               4               74 
$`AMBRA1 MUTATED`
TCGA-AZ-6601 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3864 TCGA-AA-A01I TCGA-AA-A01Q 
      100.01         3.02         1.02        53.00        31.00         1.02 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-6748 TCGA-CM-5861 TCGA-CM-6171 
       27.09        58.39         6.77         2.01        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        10.13       135.65        81.37        55.04 

$`AMBRA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       32.02        12.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
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-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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      131.51       139.17       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
            1.02             0.00 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
          135.65           148.01 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
          16.435           22.090 
[1] "1.0 - 135.7 (16.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1414V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMBRA1 MUTATED         4        0        4         6         0         0
  AMBRA1 WILD-TYPE      60        1       22       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMBRA1 MUTATED           0          1          2          0        1
  AMBRA1 WILD-TYPE        18          5         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  AMBRA1 MUTATED           0         0
  AMBRA1 WILD-TYPE        12         1
D1414V3, multiclass
            clus
vv           AMBRA1 MUTATED AMBRA1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  AMBRA1 MUTATED     0   4  14   0
  AMBRA1 WILD-TYPE   9  63 235  41
D1414V4, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             14              235
  T4              0               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
  AMBRA1 MUTATED    14   4   0
  AMBRA1 WILD-TYPE 206  77  66
D1414V5, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  N0             14              206
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1414V6, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    16   1
  AMBRA1 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     16    1
  AMBRA1 WILD-TYPE  269   47
   clus
vv  AMBRA1 MUTATED AMBRA1 WILD-TYPE
  0             16              269
  1              1               47
[1] 2 2
[1] FALSE
D1414V7, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED     8  10
  AMBRA1 WILD-TYPE 162 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED      8   10
  AMBRA1 WILD-TYPE  162  187
        clus
vv       AMBRA1 MUTATED AMBRA1 WILD-TYPE
  FEMALE              8              162
  MALE               10              187
[1] 2 2
[1] FALSE
D1414V8, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    13   0
  AMBRA1 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     13    0
  AMBRA1 WILD-TYPE  287    8
     clus
vv    AMBRA1 MUTATED AMBRA1 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1414V9, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    16   1
  AMBRA1 WILD-TYPE 298  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     16    1
  AMBRA1 WILD-TYPE  298   47
                               clus
vv                              AMBRA1 MUTATED AMBRA1 WILD-TYPE
  COLON ADENOCARCINOMA                      16              298
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AMBRA1 MUTATED    13   0   0   1
  AMBRA1 WILD-TYPE 246   3  22  20
D1414V10, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              1               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"
D1414V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMBRA1 MUTATED                                  0     0
  AMBRA1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AMBRA1 MUTATED                           0    13
  AMBRA1 WILD-TYPE                        19   163
D1414V12, multiclass
                                  clus
vv                                 AMBRA1 MUTATED AMBRA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        13              163
[1] 4 2
[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 = ANAPC16 MUTATION ANALYSIS
D1415V1, survival
                   sevent
clus2                 0   1
  ANAPC16 MUTATED     2   1
  ANAPC16 WILD-TYPE 275  77
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                3               352 
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                1                77 
$`ANAPC16 MUTATED`
TCGA-AA-A00K TCGA-AY-5543 TCGA-AZ-6605 
       18.05        33.01         5.23 

$`ANAPC16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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            22.075 
[1] "5.2 - 33.0 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1415V2, continuous
                   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      64        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC16 MUTATED           0          0          1          0        0
  ANAPC16 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ANAPC16 MUTATED           1         0
  ANAPC16 WILD-TYPE        11         1
D1415V3, multiclass
            clus
vv           ANAPC16 MUTATED ANAPC16 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  ANAPC16 MUTATED     0   0   2   1
  ANAPC16 WILD-TYPE   9  67 247  40
D1415V4, multiclass
    clus
vv   ANAPC16 MUTATED ANAPC16 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               2               247
  T4               1                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
  ANAPC16 MUTATED     1   2   0
  ANAPC16 WILD-TYPE 219  79  66
D1415V5, multiclass
    clus
vv   ANAPC16 MUTATED ANAPC16 WILD-TYPE
  N0               1               219
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1415V6, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     2   1
  ANAPC16 WILD-TYPE 283  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      2    1
  ANAPC16 WILD-TYPE  283   47
   clus
vv  ANAPC16 MUTATED ANAPC16 WILD-TYPE
  0               2               283
  1               1                47
[1] 2 2
[1] FALSE
D1415V7, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     1   2
  ANAPC16 WILD-TYPE 169 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      1    2
  ANAPC16 WILD-TYPE  169  195
        clus
vv       ANAPC16 MUTATED ANAPC16 WILD-TYPE
  FEMALE               1               169
  MALE                 2               195
[1] 2 2
[1] FALSE
D1415V8, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     2   0
  ANAPC16 WILD-TYPE 298   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      2    0
  ANAPC16 WILD-TYPE  298    8
     clus
vv    ANAPC16 MUTATED ANAPC16 WILD-TYPE
  NO                2               298
  YES               0                 8
[1] 2 2
[1] FALSE
D1415V9, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     3   0
  ANAPC16 WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      3    0
  ANAPC16 WILD-TYPE  311   48
                               clus
vv                              ANAPC16 MUTATED ANAPC16 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANAPC16 MUTATED     2   0   0   0
  ANAPC16 WILD-TYPE 257   3  22  21
D1415V10, multiclass
[1] "Remove cluster labels:" "ANAPC16 MUTATED"       
clus
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        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-3527 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3662        TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6895        TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-2676        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-3502        TCGA-AA-3510 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3561        TCGA-AA-3655        TCGA-AA-3660 
"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-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3815        TCGA-AA-3818 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3842        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-3861        TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3955 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3973 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3975        TCGA-AA-3984        TCGA-AA-3989        TCGA-AA-3994 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00N        TCGA-AA-A00O 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"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-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6889 
"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-4682        TCGA-CA-5254        TCGA-CA-5255 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5913 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6315 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
D1415V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANAPC16 MUTATED                                  0     0
  ANAPC16 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANAPC16 MUTATED                           1     1
  ANAPC16 WILD-TYPE                        18   175
D1415V12, multiclass
[1] "Remove cluster labels:" "ANAPC16 MUTATED"       
clus
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6606        TCGA-AZ-6607        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-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 

Clustering(1416) Variable = SETX MUTATION ANALYSIS
D1416V1, survival
                sevent
clus2              0   1
  SETX MUTATED    17   7
  SETX WILD-TYPE 260  71
  SETX MUTATED SETX WILD-TYPE 
            24            331 
  SETX MUTATED SETX WILD-TYPE 
             7             71 
$`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 
       83.24        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 

$`SETX WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        19.66         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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        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        21.99        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SETX MUTATED SETX WILD-TYPE 
          0.53           0.00 
  SETX MUTATED SETX WILD-TYPE 
         83.24         148.01 
  SETX MUTATED SETX WILD-TYPE 
        19.035         22.520 
[1] "0.5 - 83.2 (19.0)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.6"
D1416V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETX MUTATED         2        0        4        11         4         0
  SETX WILD-TYPE      62        1       22        97         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETX MUTATED           0          0          3          1        0         0
  SETX WILD-TYPE        18          6         41         32       35        12
                vv
clus             STAGE IVB
  SETX MUTATED           0
  SETX WILD-TYPE         1
D1416V3, multiclass
            clus
vv           SETX MUTATED SETX WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            11             97
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  SETX MUTATED     1   2  18   5
  SETX WILD-TYPE   8  65 231  36
D1416V4, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  T1            1              8
  T2            2             65
  T3           18            231
  T4            5             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
  SETX MUTATED    22   3   1
  SETX WILD-TYPE 198  78  65
D1416V5, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  N0           22            198
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1416V6, binary
                cls
clus               0   1
  SETX MUTATED    21   0
  SETX WILD-TYPE 264  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     21    0
  SETX WILD-TYPE  264   48
   clus
vv  SETX MUTATED SETX WILD-TYPE
  0           21            264
  1            0             48
[1] 2 2
[1] FALSE
D1416V7, binary
                cls
clus               0   1
  SETX MUTATED    13  13
  SETX WILD-TYPE 157 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     13   13
  SETX WILD-TYPE  157  184
        clus
vv       SETX MUTATED SETX WILD-TYPE
  FEMALE           13            157
  MALE             13            184
[1] 2 2
[1] FALSE
D1416V8, binary
                cls
clus               0   1
  SETX MUTATED    21   0
  SETX WILD-TYPE 279   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     21    0
  SETX WILD-TYPE  279    8
     clus
vv    SETX MUTATED SETX WILD-TYPE
  NO            21            279
  YES            0              8
[1] 2 2
[1] FALSE
D1416V9, binary
                cls
clus               0   1
  SETX MUTATED    21   5
  SETX WILD-TYPE 293  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     21    5
  SETX WILD-TYPE  293   43
                               clus
vv                              SETX MUTATED SETX WILD-TYPE
  COLON ADENOCARCINOMA                    21            293
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SETX MUTATED    18   0   0   4
  SETX WILD-TYPE 241   3  22  17
D1416V10, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  R0           18            241
  R1            0              3
  R2            0             22
  RX            4             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"
D1416V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETX MUTATED                                  0     3
  SETX WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SETX MUTATED                           0    12
  SETX WILD-TYPE                        19   164
D1416V12, multiclass
                                  clus
vv                                 SETX MUTATED SETX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      12            164
[1] 4 2
[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 = PEBP4 MUTATION ANALYSIS
D1417V1, survival
                 sevent
clus2               0   1
  PEBP4 MUTATED     4   2
  PEBP4 WILD-TYPE 273  76
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              6             349 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              2              76 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.09 
[1] "6.8 - 44.7 (12.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1417V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PEBP4 MUTATED         2        0        1         2         1         0
  PEBP4 WILD-TYPE      62        1       25       106         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  PEBP4 MUTATED           0
  PEBP4 WILD-TYPE         1
D1417V3, multiclass
            clus
vv           PEBP4 MUTATED PEBP4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PEBP4 MUTATED     0   3   3   1
  PEBP4 WILD-TYPE   9  64 246  40
D1417V4, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             3             246
  T4             1              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
  PEBP4 MUTATED     7   0   0
  PEBP4 WILD-TYPE 213  81  66
D1417V5, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1417V6, binary
                 cls
clus                0   1
  PEBP4 MUTATED     5   0
  PEBP4 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      5    0
  PEBP4 WILD-TYPE  280   48
   clus
vv  PEBP4 MUTATED PEBP4 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1417V7, binary
                 cls
clus                0   1
  PEBP4 MUTATED     1   6
  PEBP4 WILD-TYPE 169 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      1    6
  PEBP4 WILD-TYPE  169  191
        clus
vv       PEBP4 MUTATED PEBP4 WILD-TYPE
  FEMALE             1             169
  MALE               6             191
[1] 2 2
[1] FALSE
D1417V8, binary
                 cls
clus                0   1
  PEBP4 MUTATED     5   0
  PEBP4 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      5    0
  PEBP4 WILD-TYPE  295    8
     clus
vv    PEBP4 MUTATED PEBP4 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1417V9, binary
                 cls
clus                0   1
  PEBP4 MUTATED     6   1
  PEBP4 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      6    1
  PEBP4 WILD-TYPE  308   47
                               clus
vv                              PEBP4 MUTATED PEBP4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PEBP4 MUTATED     4   0   0   1
  PEBP4 WILD-TYPE 255   3  22  20
D1417V10, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1417V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PEBP4 MUTATED                                  0     0
  PEBP4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PEBP4 MUTATED                           0     6
  PEBP4 WILD-TYPE                        19   170
D1417V12, multiclass
                                  clus
vv                                 PEBP4 MUTATED PEBP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1418) Variable = LEPROTL1 MUTATION ANALYSIS
D1418V1, survival
                    sevent
clus2                  0   1
  LEPROTL1 MUTATED     4   1
  LEPROTL1 WILD-TYPE 273  77
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 5                350 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 1                 77 
$`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        13.35 

$`LEPROTL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
             12.95               0.00 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
             53.00             148.01 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
            18.050             22.075 
[1] "12.9 - 53.0 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1418V2, continuous
                    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      64        1       25       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEPROTL1 MUTATED           1          0          1          0        0
  LEPROTL1 WILD-TYPE        17          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  LEPROTL1 MUTATED           0         0
  LEPROTL1 WILD-TYPE        12         1
D1418V3, multiclass
            clus
vv           LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  LEPROTL1 MUTATED     0   0   4   1
  LEPROTL1 WILD-TYPE   9  67 245  40
D1418V4, multiclass
    clus
vv   LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                4                245
  T4                1                 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
  LEPROTL1 MUTATED     3   2   0
  LEPROTL1 WILD-TYPE 217  79  66
D1418V5, multiclass
    clus
vv   LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  N0                3                217
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1418V6, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     5   0
  LEPROTL1 WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      5    0
  LEPROTL1 WILD-TYPE  280   48
   clus
vv  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  0                5                280
  1                0                 48
[1] 2 2
[1] FALSE
D1418V7, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     1   4
  LEPROTL1 WILD-TYPE 169 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      1    4
  LEPROTL1 WILD-TYPE  169  193
        clus
vv       LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  FEMALE                1                169
  MALE                  4                193
[1] 2 2
[1] FALSE
D1418V8, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     5   0
  LEPROTL1 WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      5    0
  LEPROTL1 WILD-TYPE  295    8
     clus
vv    LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D1418V9, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     3   2
  LEPROTL1 WILD-TYPE 311  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      3    2
  LEPROTL1 WILD-TYPE  311   46
                               clus
vv                              LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  COLON ADENOCARCINOMA                         3                311
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  LEPROTL1 MUTATED     5   0   0   0
  LEPROTL1 WILD-TYPE 254   3  22  21
D1418V10, multiclass
    clus
vv   LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1418V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEPROTL1 MUTATED                                  0     0
  LEPROTL1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  LEPROTL1 MUTATED                           0     2
  LEPROTL1 WILD-TYPE                        19   174
D1418V12, multiclass
[1] "Remove cluster labels:" "LEPROTL1 MUTATED"      
clus
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6675 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 

Clustering(1419) Variable = MAP7 MUTATION ANALYSIS
D1419V1, survival
                sevent
clus2              0   1
  MAP7 MUTATED     8   2
  MAP7 WILD-TYPE 269  76
  MAP7 MUTATED MAP7 WILD-TYPE 
            10            345 
  MAP7 MUTATED MAP7 WILD-TYPE 
             2             76 
$`MAP7 MUTATED`
TCGA-AA-3543 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A010 
        0.99        24.39        29.95        26.01         2.01        34.98 
TCGA-AA-A01Q TCGA-AD-6889 TCGA-CA-6718 TCGA-D5-6540 
        1.02        83.24        10.06        16.14 

$`MAP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        33.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MAP7 MUTATED MAP7 WILD-TYPE 
          0.99           0.00 
  MAP7 MUTATED MAP7 WILD-TYPE 
         83.24         148.01 
  MAP7 MUTATED MAP7 WILD-TYPE 
        20.265         22.060 
[1] "1.0 - 83.2 (20.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1419V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP7 MUTATED         3        0        1         5         1         0
  MAP7 WILD-TYPE      61        1       25       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP7 MUTATED           0          0          1          0        0         0
  MAP7 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  MAP7 MUTATED           0
  MAP7 WILD-TYPE         1
D1419V3, multiclass
            clus
vv           MAP7 MUTATED MAP7 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  MAP7 MUTATED     0   3   7   1
  MAP7 WILD-TYPE   9  64 242  40
D1419V4, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            7            242
  T4            1             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
  MAP7 MUTATED    10   1   0
  MAP7 WILD-TYPE 210  80  66
D1419V5, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1419V6, binary
                cls
clus               0   1
  MAP7 MUTATED    11   0
  MAP7 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED     11    0
  MAP7 WILD-TYPE  274   48
   clus
vv  MAP7 MUTATED MAP7 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D1419V7, binary
                cls
clus               0   1
  MAP7 MUTATED     6   5
  MAP7 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      6    5
  MAP7 WILD-TYPE  164  192
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D1419V8, binary
                cls
clus               0   1
  MAP7 MUTATED     8   0
  MAP7 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      8    0
  MAP7 WILD-TYPE  292    8
     clus
vv    MAP7 MUTATED MAP7 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1419V9, binary
                cls
clus               0   1
  MAP7 MUTATED     6   5
  MAP7 WILD-TYPE 308  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      6    5
  MAP7 WILD-TYPE  308   43
                               clus
vv                              MAP7 MUTATED MAP7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAP7 MUTATED     8   0   0   1
  MAP7 WILD-TYPE 251   3  22  20
D1419V10, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D1419V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP7 MUTATED                                  0     2
  MAP7 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAP7 MUTATED                           0     2
  MAP7 WILD-TYPE                        19   174
D1419V12, multiclass
                                  clus
vv                                 MAP7 MUTATED MAP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       2            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(1420) Variable = MCF2L2 MUTATION ANALYSIS
D1420V1, survival
                  sevent
clus2                0   1
  MCF2L2 MUTATED    13   4
  MCF2L2 WILD-TYPE 264  74
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              17              338 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
               4               74 
$`MCF2L2 MUTATED`
TCGA-AA-3952 TCGA-AD-6964 TCGA-G4-6588 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A00N 
        2.01        10.88        26.17        63.98        25.02         4.01 
TCGA-AA-A01R TCGA-AA-A02Y TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6164 
       35.01        39.98        27.09        12.76        10.06        29.03 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6929 TCGA-G4-6309 
       15.12        17.85        16.14        13.41        85.48 

$`MCF2L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       25.48        43.27         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 
        7.53        12.39        10.13        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        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
            2.01             0.00 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
           85.48           148.01 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
          17.850           22.075 
[1] "2.0 - 85.5 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1420V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCF2L2 MUTATED         3        0        1         6         2         0
  MCF2L2 WILD-TYPE      61        1       25       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCF2L2 MUTATED           1          0          2          1        1
  MCF2L2 WILD-TYPE        17          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  MCF2L2 MUTATED           0         0
  MCF2L2 WILD-TYPE        12         1
D1420V3, multiclass
            clus
vv           MCF2L2 MUTATED MCF2L2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               6              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  MCF2L2 MUTATED     0   4  12   3
  MCF2L2 WILD-TYPE   9  63 237  38
D1420V4, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             12              237
  T4              3               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
  MCF2L2 MUTATED    13   3   3
  MCF2L2 WILD-TYPE 207  78  63
D1420V5, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  N0             13              207
  N1              3               78
  N2              3               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"
D1420V6, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    14   1
  MCF2L2 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     14    1
  MCF2L2 WILD-TYPE  271   47
   clus
vv  MCF2L2 MUTATED MCF2L2 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D1420V7, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED     8  11
  MCF2L2 WILD-TYPE 162 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED      8   11
  MCF2L2 WILD-TYPE  162  186
        clus
vv       MCF2L2 MUTATED MCF2L2 WILD-TYPE
  FEMALE              8              162
  MALE               11              186
[1] 2 2
[1] FALSE
D1420V8, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    13   1
  MCF2L2 WILD-TYPE 287   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     13    1
  MCF2L2 WILD-TYPE  287    7
     clus
vv    MCF2L2 MUTATED MCF2L2 WILD-TYPE
  NO              13              287
  YES              1                7
[1] 2 2
[1] FALSE
D1420V9, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    15   4
  MCF2L2 WILD-TYPE 299  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     15    4
  MCF2L2 WILD-TYPE  299   44
                               clus
vv                              MCF2L2 MUTATED MCF2L2 WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MCF2L2 MUTATED    13   0   0   4
  MCF2L2 WILD-TYPE 246   3  22  17
D1420V10, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              4               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"
D1420V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCF2L2 MUTATED                                  0     2
  MCF2L2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MCF2L2 MUTATED                           1     9
  MCF2L2 WILD-TYPE                        18   167
D1420V12, multiclass
                                  clus
vv                                 MCF2L2 MUTATED MCF2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(1421) Variable = ANKRD26 MUTATION ANALYSIS
D1421V1, survival
                   sevent
clus2                 0   1
  ANKRD26 MUTATED    15   3
  ANKRD26 WILD-TYPE 262  75
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               18               337 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
                3                75 
$`ANKRD26 MUTATED`
TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5659 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3977 
       26.17        32.75        30.44         6.97        26.99        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-6748 
        4.01        34.98        83.24        58.39        12.76         2.01 
TCGA-CM-4744 TCGA-CM-5860 TCGA-CM-6162 TCGA-D5-5539 TCGA-DM-A1D4 TCGA-DM-A28K 
       20.02        32.02        12.00        19.59        92.75        98.24 

$`ANKRD26 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
             2.01              0.00 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
            98.24            148.01 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
            26.58             21.99 
[1] "2.0 - 98.2 (26.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1421V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD26 MUTATED         3        0        1         8         3         0
  ANKRD26 WILD-TYPE      61        1       25       100         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD26 MUTATED           0          1          1          0        1
  ANKRD26 WILD-TYPE        18          5         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD26 MUTATED           0         0
  ANKRD26 WILD-TYPE        12         1
D1421V3, multiclass
            clus
vv           ANKRD26 MUTATED ANKRD26 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                8               100
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               1                 5
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  ANKRD26 MUTATED     0   4  12   3
  ANKRD26 WILD-TYPE   9  63 237  38
D1421V4, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3              12               237
  T4               3                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
  ANKRD26 MUTATED    16   3   0
  ANKRD26 WILD-TYPE 204  78  66
D1421V5, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  N0              16               204
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1421V6, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    16   1
  ANKRD26 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     16    1
  ANKRD26 WILD-TYPE  269   47
   clus
vv  ANKRD26 MUTATED ANKRD26 WILD-TYPE
  0              16               269
  1               1                47
[1] 2 2
[1] FALSE
D1421V7, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED     6  13
  ANKRD26 WILD-TYPE 164 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED      6   13
  ANKRD26 WILD-TYPE  164  184
        clus
vv       ANKRD26 MUTATED ANKRD26 WILD-TYPE
  FEMALE               6               164
  MALE                13               184
[1] 2 2
[1] FALSE
D1421V8, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    15   0
  ANKRD26 WILD-TYPE 285   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     15    0
  ANKRD26 WILD-TYPE  285    8
     clus
vv    ANKRD26 MUTATED ANKRD26 WILD-TYPE
  NO               15               285
  YES               0                 8
[1] 2 2
[1] FALSE
D1421V9, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    12   7
  ANKRD26 WILD-TYPE 302  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     12    7
  ANKRD26 WILD-TYPE  302   41
                               clus
vv                              ANKRD26 MUTATED ANKRD26 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD26 MUTATED    13   0   0   3
  ANKRD26 WILD-TYPE 246   3  22  18
D1421V10, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               0                22
  RX               3                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"
D1421V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD26 MUTATED                                  0     2
  ANKRD26 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD26 MUTATED                           0    12
  ANKRD26 WILD-TYPE                        19   164
D1421V12, multiclass
                                  clus
vv                                 ANKRD26 MUTATED ANKRD26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                         12               164
[1] 4 2
[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 = DNAJC18 MUTATION ANALYSIS
D1422V1, survival
                   sevent
clus2                 0   1
  DNAJC18 MUTATED     6   1
  DNAJC18 WILD-TYPE 271  77
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                7               348 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                1                77 
$`DNAJC18 MUTATED`
TCGA-G4-6628 TCGA-A6-5662 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CK-5913 TCGA-CM-5860 
       79.69        23.61         4.01        58.39        51.32        32.02 
TCGA-D5-5540 
       56.09 

$`DNAJC18 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-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 
       54.61        19.59        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
             4.01              0.00 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
            79.69            148.01 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
            51.32             21.99 
[1] "4.0 - 79.7 (51.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1422V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC18 MUTATED         1        0        0         4         1         0
  DNAJC18 WILD-TYPE      63        1       26       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC18 MUTATED           0          0          0          0        0
  DNAJC18 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC18 MUTATED           1         0
  DNAJC18 WILD-TYPE        11         1
D1422V3, multiclass
            clus
vv           DNAJC18 MUTATED DNAJC18 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  DNAJC18 MUTATED     0   1   5   1
  DNAJC18 WILD-TYPE   9  66 244  40
D1422V4, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               1                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
  DNAJC18 MUTATED     6   0   1
  DNAJC18 WILD-TYPE 214  81  65
D1422V5, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  N0               6               214
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1422V6, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     5   1
  DNAJC18 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      5    1
  DNAJC18 WILD-TYPE  280   47
   clus
vv  DNAJC18 MUTATED DNAJC18 WILD-TYPE
  0               5               280
  1               1                47
[1] 2 2
[1] FALSE
D1422V7, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     1   6
  DNAJC18 WILD-TYPE 169 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      1    6
  DNAJC18 WILD-TYPE  169  191
        clus
vv       DNAJC18 MUTATED DNAJC18 WILD-TYPE
  FEMALE               1               169
  MALE                 6               191
[1] 2 2
[1] FALSE
D1422V8, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     6   0
  DNAJC18 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      6    0
  DNAJC18 WILD-TYPE  294    8
     clus
vv    DNAJC18 MUTATED DNAJC18 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1422V9, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     6   1
  DNAJC18 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      6    1
  DNAJC18 WILD-TYPE  308   47
                               clus
vv                              DNAJC18 MUTATED DNAJC18 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DNAJC18 MUTATED     5   0   0   1
  DNAJC18 WILD-TYPE 254   3  22  20
D1422V10, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               1                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"
D1422V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC18 MUTATED                                  0     0
  DNAJC18 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJC18 MUTATED                           0     6
  DNAJC18 WILD-TYPE                        19   170
D1422V12, multiclass
                                  clus
vv                                 DNAJC18 MUTATED DNAJC18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = ESRP2 MUTATION ANALYSIS
D1423V1, survival
                 sevent
clus2               0   1
  ESRP2 MUTATED     6   3
  ESRP2 WILD-TYPE 271  75
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              9             346 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              3              75 
$`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 
       22.03        17.85       140.38 

$`ESRP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ESRP2 MUTATED ESRP2 WILD-TYPE 
           1.02            0.00 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
         140.38          148.01 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
         22.360          22.025 
[1] "1.0 - 140.4 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1423V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESRP2 MUTATED         0        0        1         4         1         0
  ESRP2 WILD-TYPE      64        1       25       104         7         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        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  ESRP2 MUTATED           0
  ESRP2 WILD-TYPE         1
D1423V3, multiclass
            clus
vv           ESRP2 MUTATED ESRP2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  ESRP2 MUTATED     0   0   8   1
  ESRP2 WILD-TYPE   9  67 241  40
D1423V4, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             8             241
  T4             1              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
  ESRP2 MUTATED     8   1   0
  ESRP2 WILD-TYPE 212  80  66
D1423V5, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1423V6, binary
                 cls
clus                0   1
  ESRP2 MUTATED     7   1
  ESRP2 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      7    1
  ESRP2 WILD-TYPE  278   47
   clus
vv  ESRP2 MUTATED ESRP2 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D1423V7, binary
                 cls
clus                0   1
  ESRP2 MUTATED     5   4
  ESRP2 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      5    4
  ESRP2 WILD-TYPE  165  193
        clus
vv       ESRP2 MUTATED ESRP2 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1423V8, binary
                 cls
clus                0   1
  ESRP2 MUTATED     7   0
  ESRP2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      7    0
  ESRP2 WILD-TYPE  293    8
     clus
vv    ESRP2 MUTATED ESRP2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1423V9, binary
                 cls
clus                0   1
  ESRP2 MUTATED     9   0
  ESRP2 WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      9    0
  ESRP2 WILD-TYPE  305   48
                               clus
vv                              ESRP2 MUTATED ESRP2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESRP2 MUTATED     6   0   0   1
  ESRP2 WILD-TYPE 253   3  22  20
D1423V10, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1423V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESRP2 MUTATED                                  0     1
  ESRP2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESRP2 MUTATED                           0     5
  ESRP2 WILD-TYPE                        19   171
D1423V12, multiclass
                                  clus
vv                                 ESRP2 MUTATED ESRP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = NLRP13 MUTATION ANALYSIS
D1424V1, survival
                  sevent
clus2                0   1
  NLRP13 MUTATED    21   3
  NLRP13 WILD-TYPE 256  75
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              24              331 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
               3               75 
$`NLRP13 MUTATED`
TCGA-AA-3525 TCGA-AA-3860 TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-5666 TCGA-A6-6137 
        8.05        31.07        24.00        35.80        32.71        27.09 
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6890 
       19.66        63.98        31.00        34.98        31.00        24.53 
TCGA-AD-6899 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5344 
        5.79         0.20        58.39        62.79        12.76        22.03 
TCGA-CM-5861 TCGA-D5-6541 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6299 TCGA-G4-6309 
       15.02        15.58        13.35        44.32        74.56        85.48 

$`NLRP13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       22.06        22.52         8.38        25.08        25.18        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6901 
       39.98        18.05        40.96        12.16        83.24        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-4682 
       33.01        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  NLRP13 MUTATED NLRP13 WILD-TYPE 
             0.2              0.0 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
           85.48           148.01 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
          29.045           21.990 
[1] "0.2 - 85.5 (29.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1424V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRP13 MUTATED         1        0        2         9         1         1
  NLRP13 WILD-TYPE      63        1       24        99         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLRP13 MUTATED           1          0          5          5        1
  NLRP13 WILD-TYPE        17          6         39         28       34
                  vv
clus               STAGE IVA STAGE IVB
  NLRP13 MUTATED           0         0
  NLRP13 WILD-TYPE        12         1
D1424V3, multiclass
            clus
vv           NLRP13 MUTATED NLRP13 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               9               99
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              5               39
  STAGE IIIC              5               28
  STAGE IV                1               34
  STAGE IVA               0               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
  NLRP13 MUTATED     2   0  21   4
  NLRP13 WILD-TYPE   7  67 228  37
D1424V4, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  T1              2                7
  T2              0               67
  T3             21              228
  T4              4               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
  NLRP13 MUTATED    15   6   6
  NLRP13 WILD-TYPE 205  75  60
D1424V5, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  N0             15              205
  N1              6               75
  N2              6               60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1424V6, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    21   1
  NLRP13 WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     21    1
  NLRP13 WILD-TYPE  264   47
   clus
vv  NLRP13 MUTATED NLRP13 WILD-TYPE
  0             21              264
  1              1               47
[1] 2 2
[1] FALSE
D1424V7, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    11  16
  NLRP13 WILD-TYPE 159 181
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     11   16
  NLRP13 WILD-TYPE  159  181
        clus
vv       NLRP13 MUTATED NLRP13 WILD-TYPE
  FEMALE             11              159
  MALE               16              181
[1] 2 2
[1] FALSE
D1424V8, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    22   0
  NLRP13 WILD-TYPE 278   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     22    0
  NLRP13 WILD-TYPE  278    8
     clus
vv    NLRP13 MUTATED NLRP13 WILD-TYPE
  NO              22              278
  YES              0                8
[1] 2 2
[1] FALSE
D1424V9, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    20   7
  NLRP13 WILD-TYPE 294  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     20    7
  NLRP13 WILD-TYPE  294   41
                               clus
vv                              NLRP13 MUTATED NLRP13 WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NLRP13 MUTATED    19   0   1   1
  NLRP13 WILD-TYPE 240   3  21  20
D1424V10, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  R0             19              240
  R1              0                3
  R2              1               21
  RX              1               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"
D1424V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP13 MUTATED                                  0     1
  NLRP13 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NLRP13 MUTATED                           1    15
  NLRP13 WILD-TYPE                        18   161
D1424V12, multiclass
                                  clus
vv                                 NLRP13 MUTATED NLRP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        15              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(1425) Variable = LRRN1 MUTATION ANALYSIS
D1425V1, survival
                 sevent
clus2               0   1
  LRRN1 MUTATED    10   6
  LRRN1 WILD-TYPE 267  72
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             16             339 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
              6              72 
$`LRRN1 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3715 TCGA-AZ-6601 TCGA-A6-6141 TCGA-A6-6653 
       13.02        19.04        19.04       100.01         8.38        24.39 
TCGA-AA-3526 TCGA-AA-A01Q TCGA-AD-5900 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       19.07         1.02        12.16        12.76        10.06        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5861 TCGA-F4-6570 
       51.32        21.14        15.02         6.18 

$`LRRN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02         9.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       85.45        21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LRRN1 MUTATED LRRN1 WILD-TYPE 
           1.02            0.00 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
         100.01          148.01 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
          15.32           22.52 
[1] "1.0 - 100.0 (15.3)" "0.0 - 148.0 (22.5)"
[1] "hr=" "2.1"
D1425V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRN1 MUTATED         4        0        3         6         1         0
  LRRN1 WILD-TYPE      60        1       23       102         7         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        17          6         44         32       34        12
                 vv
clus              STAGE IVB
  LRRN1 MUTATED           0
  LRRN1 WILD-TYPE         1
D1425V3, multiclass
            clus
vv           LRRN1 MUTATED LRRN1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  LRRN1 MUTATED     1   3  11   2
  LRRN1 WILD-TYPE   8  64 238  39
D1425V4, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            11             238
  T4             2              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
  LRRN1 MUTATED    15   0   2
  LRRN1 WILD-TYPE 205  81  64
D1425V5, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  N0            15             205
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1425V6, binary
                 cls
clus                0   1
  LRRN1 MUTATED    13   1
  LRRN1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     13    1
  LRRN1 WILD-TYPE  272   47
   clus
vv  LRRN1 MUTATED LRRN1 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D1425V7, binary
                 cls
clus                0   1
  LRRN1 MUTATED     8   9
  LRRN1 WILD-TYPE 162 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED      8    9
  LRRN1 WILD-TYPE  162  188
        clus
vv       LRRN1 MUTATED LRRN1 WILD-TYPE
  FEMALE             8             162
  MALE               9             188
[1] 2 2
[1] FALSE
D1425V8, binary
                 cls
clus                0   1
  LRRN1 MUTATED    13   1
  LRRN1 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     13    1
  LRRN1 WILD-TYPE  287    7
     clus
vv    LRRN1 MUTATED LRRN1 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D1425V9, binary
                 cls
clus                0   1
  LRRN1 MUTATED    13   4
  LRRN1 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     13    4
  LRRN1 WILD-TYPE  301   44
                               clus
vv                              LRRN1 MUTATED LRRN1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LRRN1 MUTATED     6   0   1   6
  LRRN1 WILD-TYPE 253   3  21  15
D1425V10, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             1              21
  RX             6              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"
D1425V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRN1 MUTATED                                  0     2
  LRRN1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRRN1 MUTATED                           1     9
  LRRN1 WILD-TYPE                        18   167
D1425V12, multiclass
                                  clus
vv                                 LRRN1 MUTATED LRRN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(1426) Variable = VIM MUTATION ANALYSIS
D1426V1, survival
               sevent
clus2             0   1
  VIM MUTATED     5   2
  VIM WILD-TYPE 272  76
  VIM MUTATED VIM WILD-TYPE 
            7           348 
  VIM MUTATED VIM WILD-TYPE 
            2            76 
$`VIM MUTATED`
TCGA-AA-3713 TCGA-AA-3510 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A02K TCGA-CK-4950 
       19.04        63.98        18.05         0.99        14.01        85.45 
TCGA-D5-5537 
       45.40 

$`VIM WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  VIM MUTATED VIM WILD-TYPE 
         0.99          0.00 
  VIM MUTATED VIM WILD-TYPE 
        85.45        148.01 
  VIM MUTATED VIM WILD-TYPE 
       19.040        22.075 
[1] "1.0 - 85.5 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1426V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VIM MUTATED         1        0        1         2         0         0
  VIM WILD-TYPE      63        1       25       106         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VIM MUTATED           0          0          1          0        2         0
  VIM WILD-TYPE        18          6         43         33       33        12
               vv
clus            STAGE IVB
  VIM MUTATED           0
  VIM WILD-TYPE         1
D1426V3, multiclass
            clus
vv           VIM MUTATED VIM WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            2           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             2            33
  STAGE IVA            0            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
  VIM MUTATED     0   1   5   1
  VIM WILD-TYPE   9  66 244  40
D1426V4, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  T1           0             9
  T2           1            66
  T3           5           244
  T4           1            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
  VIM MUTATED     4   1   2
  VIM WILD-TYPE 216  80  64
D1426V5, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  N0           4           216
  N1           1            80
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1426V6, binary
               cls
clus              0   1
  VIM MUTATED     4   2
  VIM WILD-TYPE 281  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      4    2
  VIM WILD-TYPE  281   46
   clus
vv  VIM MUTATED VIM WILD-TYPE
  0           4           281
  1           2            46
[1] 2 2
[1] FALSE
D1426V7, binary
               cls
clus              0   1
  VIM MUTATED     2   5
  VIM WILD-TYPE 168 192
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      2    5
  VIM WILD-TYPE  168  192
        clus
vv       VIM MUTATED VIM WILD-TYPE
  FEMALE           2           168
  MALE             5           192
[1] 2 2
[1] FALSE
D1426V8, binary
               cls
clus              0   1
  VIM MUTATED     4   1
  VIM WILD-TYPE 296   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      4    1
  VIM WILD-TYPE  296    7
     clus
vv    VIM MUTATED VIM WILD-TYPE
  NO            4           296
  YES           1             7
[1] 2 2
[1] FALSE
D1426V9, binary
               cls
clus              0   1
  VIM MUTATED     6   1
  VIM WILD-TYPE 308  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      6    1
  VIM WILD-TYPE  308   47
                               clus
vv                              VIM MUTATED VIM WILD-TYPE
  COLON ADENOCARCINOMA                    6           308
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  VIM MUTATED     3   1   2   1
  VIM WILD-TYPE 256   2  20  20
D1426V10, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  R0           3           256
  R1           1             2
  R2           2            20
  RX           1            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"
D1426V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VIM MUTATED                                  0     0
  VIM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  VIM MUTATED                           1     1
  VIM WILD-TYPE                        18   175
D1426V12, multiclass
[1] "Remove cluster labels:" "VIM MUTATED"           
clus
  VIM MUTATED VIM WILD-TYPE 
            2           204 
   TCGA-A6-2677    TCGA-A6-4105    TCGA-A6-6649    TCGA-AD-6548    TCGA-AD-6888 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AD-6895    TCGA-AD-6964    TCGA-AZ-4681    TCGA-AZ-6601    TCGA-AZ-6608 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CK-5912    TCGA-DM-A285    TCGA-G4-6310    TCGA-G4-6321    TCGA-G4-6586 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-G4-6588    TCGA-G4-6625    TCGA-G4-6628    TCGA-A6-2671    TCGA-A6-2672 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-3808    TCGA-A6-3809    TCGA-A6-3810    TCGA-A6-5656    TCGA-A6-5657 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-5659    TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-5665    TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-6142    TCGA-A6-6648    TCGA-A6-6651    TCGA-A6-6652    TCGA-A6-6653 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-6654    TCGA-A6-6780    TCGA-A6-6781    TCGA-A6-6782    TCGA-AD-5900 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AD-6889    TCGA-AD-6890    TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AD-6965    TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AY-5543    TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AZ-4323    TCGA-AZ-4616    TCGA-AZ-4682    TCGA-AZ-5403    TCGA-AZ-5407 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AZ-6598    TCGA-AZ-6599    TCGA-AZ-6600    TCGA-AZ-6603    TCGA-AZ-6605 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AZ-6606    TCGA-AZ-6607    TCGA-CA-5254    TCGA-CA-5255    TCGA-CA-5796 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CA-5797    TCGA-CA-6715    TCGA-CA-6716    TCGA-CA-6717    TCGA-CA-6718 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CA-6719    TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4952    TCGA-CK-5913 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CK-5914    TCGA-CK-5915    TCGA-CK-5916    TCGA-CK-6746    TCGA-CK-6747 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CK-6748    TCGA-CK-6751    TCGA-CM-4743    TCGA-CM-4744    TCGA-CM-4746 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-4747    TCGA-CM-4752    TCGA-CM-5341    TCGA-CM-5344    TCGA-CM-5348 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-5349    TCGA-CM-5860    TCGA-CM-5861    TCGA-CM-5862    TCGA-CM-5863 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-5864    TCGA-CM-5868    TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6164    TCGA-CM-6165    TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6169    TCGA-CM-6170    TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6675    TCGA-CM-6676    TCGA-CM-6677    TCGA-CM-6678    TCGA-CM-6679 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6680    TCGA-D5-5538    TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6529    TCGA-D5-6532    TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6536    TCGA-D5-6537    TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6541    TCGA-D5-6898    TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6924    TCGA-D5-6926    TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6930    TCGA-D5-6931    TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A0XD    TCGA-DM-A0XF    TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A1D7    TCGA-DM-A1D8    TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A1HA    TCGA-DM-A1HB    TCGA-DM-A282    TCGA-DM-A28C    TCGA-DM-A28E 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A28F    TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-F4-6460    TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-F4-6805    TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-F4-6854    TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-G4-6303    TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6323    TCGA-G4-6626 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 

Clustering(1427) Variable = WDR45L MUTATION ANALYSIS
D1427V1, survival
                  sevent
clus2                0   1
  WDR45L MUTATED     4   2
  WDR45L WILD-TYPE 273  76
  WDR45L MUTATED WDR45L WILD-TYPE 
               6              349 
  WDR45L MUTATED WDR45L WILD-TYPE 
               2               76 
$`WDR45L MUTATED`
TCGA-AD-6895 TCGA-AA-3660 TCGA-CA-6718 TCGA-D5-6532 TCGA-D5-6930 TCGA-G4-6626 
       25.08        78.08        10.06        18.25        13.35        46.75 

$`WDR45L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  WDR45L MUTATED WDR45L WILD-TYPE 
           10.06             0.00 
  WDR45L MUTATED WDR45L WILD-TYPE 
           78.08           148.01 
  WDR45L MUTATED WDR45L WILD-TYPE 
          21.665           22.060 
[1] "10.1 - 78.1 (21.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1427V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR45L MUTATED         0        0        2         4         0         0
  WDR45L WILD-TYPE      64        1       24       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR45L MUTATED           0          0          1          0        0
  WDR45L WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  WDR45L MUTATED           0         0
  WDR45L WILD-TYPE        12         1
D1427V3, multiclass
            clus
vv           WDR45L MUTATED WDR45L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  WDR45L MUTATED     0   0   6   1
  WDR45L WILD-TYPE   9  67 243  40
D1427V4, multiclass
    clus
vv   WDR45L MUTATED WDR45L WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              1               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
  WDR45L MUTATED     6   1   0
  WDR45L WILD-TYPE 214  80  66
D1427V5, multiclass
    clus
vv   WDR45L MUTATED WDR45L WILD-TYPE
  N0              6              214
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1427V6, binary
                  cls
clus                 0   1
  WDR45L MUTATED     7   0
  WDR45L WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  WDR45L MUTATED      7    0
  WDR45L WILD-TYPE  278   48
   clus
vv  WDR45L MUTATED WDR45L WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1427V7, binary
                  cls
clus                 0   1
  WDR45L MUTATED     2   5
  WDR45L WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  WDR45L MUTATED      2    5
  WDR45L WILD-TYPE  168  192
        clus
vv       WDR45L MUTATED WDR45L WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1427V8, binary
                  cls
clus                 0   1
  WDR45L MUTATED     6   0
  WDR45L WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  WDR45L MUTATED      6    0
  WDR45L WILD-TYPE  294    8
     clus
vv    WDR45L MUTATED WDR45L WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1427V9, binary
                  cls
clus                 0   1
  WDR45L MUTATED     6   1
  WDR45L WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  WDR45L MUTATED      6    1
  WDR45L WILD-TYPE  308   47
                               clus
vv                              WDR45L MUTATED WDR45L WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  WDR45L MUTATED     6   0   0   1
  WDR45L WILD-TYPE 253   3  22  20
D1427V10, multiclass
    clus
vv   WDR45L MUTATED WDR45L WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1427V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR45L MUTATED                                  0     1
  WDR45L WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  WDR45L MUTATED                           0     4
  WDR45L WILD-TYPE                        19   172
D1427V12, multiclass
                                  clus
vv                                 WDR45L MUTATED WDR45L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = PISD MUTATION ANALYSIS
D1428V1, survival
                sevent
clus2              0   1
  PISD MUTATED     2   1
  PISD WILD-TYPE 275  77
  PISD MUTATED PISD WILD-TYPE 
             3            352 
  PISD MUTATED PISD WILD-TYPE 
             1             77 
$`PISD MUTATED`
TCGA-G4-6321 TCGA-AZ-5403 TCGA-G4-6307 
       22.09        62.79        55.04 

$`PISD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        88.21        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PISD MUTATED PISD WILD-TYPE 
         22.09           0.00 
  PISD MUTATED PISD WILD-TYPE 
         62.79         148.01 
  PISD MUTATED PISD WILD-TYPE 
         55.04          22.01 
[1] "22.1 - 62.8 (55.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1428V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PISD MUTATED         0        0        1         0         0         0
  PISD WILD-TYPE      64        1       25       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PISD MUTATED           1          0          1          0        0         0
  PISD WILD-TYPE        17          6         43         33       35        12
                vv
clus             STAGE IVB
  PISD MUTATED           0
  PISD WILD-TYPE         1
D1428V3, multiclass
            clus
vv           PISD MUTATED PISD WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PISD MUTATED     0   1   2   0
  PISD WILD-TYPE   9  66 247  41
D1428V4, multiclass
    clus
vv   PISD MUTATED PISD WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            0             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
  PISD MUTATED     1   2   0
  PISD WILD-TYPE 219  79  66
D1428V5, multiclass
    clus
vv   PISD MUTATED PISD WILD-TYPE
  N0            1            219
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1428V6, binary
                cls
clus               0   1
  PISD MUTATED     1   0
  PISD WILD-TYPE 284  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      1    0
  PISD WILD-TYPE  284   48
   clus
vv  PISD MUTATED PISD WILD-TYPE
  0            1            284
  1            0             48
[1] 2 2
[1] FALSE
D1428V7, binary
                cls
clus               0   1
  PISD MUTATED     2   1
  PISD WILD-TYPE 168 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      2    1
  PISD WILD-TYPE  168  196
        clus
vv       PISD MUTATED PISD WILD-TYPE
  FEMALE            2            168
  MALE              1            196
[1] 2 2
[1] FALSE
D1428V8, binary
                cls
clus               0   1
  PISD MUTATED     3   0
  PISD WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      3    0
  PISD WILD-TYPE  297    8
     clus
vv    PISD MUTATED PISD WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1428V9, binary
                cls
clus               0   1
  PISD MUTATED     3   0
  PISD WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      3    0
  PISD WILD-TYPE  311   48
                               clus
vv                              PISD MUTATED PISD WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PISD MUTATED     2   0   0   0
  PISD WILD-TYPE 257   3  22  21
D1428V10, multiclass
[1] "Remove cluster labels:" "PISD MUTATED"          
clus
  PISD MUTATED PISD WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     TCGA-AA-3520     TCGA-AA-3521 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3527 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6628 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657     TCGA-A6-5659 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781     TCGA-AA-3489 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3492     TCGA-AA-3502     TCGA-AA-3510     TCGA-AA-3511 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518     TCGA-AA-3519 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532     TCGA-AA-3534 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544     TCGA-AA-3548 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555     TCGA-AA-3558 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3663 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3673 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693     TCGA-AA-3695 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3811 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3861 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3941 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955     TCGA-AA-3956 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973     TCGA-AA-3975 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N     TCGA-AA-A00O 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6889 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4682     TCGA-CA-5254 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6309     TCGA-G4-6315 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"PISD WILD-TYPE" "PISD WILD-TYPE" "PISD WILD-TYPE" 
D1428V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PISD MUTATED                                  0     0
  PISD WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PISD MUTATED                           0     3
  PISD WILD-TYPE                        19   173
D1428V12, multiclass
                                  clus
vv                                 PISD MUTATED PISD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = ST18 MUTATION ANALYSIS
D1429V1, survival
                sevent
clus2              0   1
  ST18 MUTATED    18   4
  ST18 WILD-TYPE 259  74
  ST18 MUTATED ST18 WILD-TYPE 
            22            333 
  ST18 MUTATED ST18 WILD-TYPE 
             4             74 
$`ST18 MUTATED`
TCGA-AD-6895 TCGA-G4-6321 TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A00R 
       25.08        22.09        35.80        63.98         4.01         0.99 
TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6716 
       34.98        27.09         0.20        21.44        12.10        12.20 
TCGA-CA-6718 TCGA-CK-4952 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6932 
       10.06        15.62        12.49        16.14        15.58        11.38 
TCGA-DM-A1HB TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6307 
      135.65        13.25       133.18        55.04 

$`ST18 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6588 
      100.01         1.94        49.08         5.88        63.62        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05        18.05        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
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-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        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        12.36        12.39        12.59        12.59 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       12.76        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6920 
       15.12        17.85         4.80        17.13         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        33.67         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       74.56        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ST18 MUTATED ST18 WILD-TYPE 
           0.2            0.0 
  ST18 MUTATED ST18 WILD-TYPE 
        135.65         148.01 
  ST18 MUTATED ST18 WILD-TYPE 
         15.88          22.36 
[1] "0.2 - 135.7 (15.9)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.3"
D1429V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST18 MUTATED         3        0        1         7         2         0
  ST18 WILD-TYPE      61        1       25       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ST18 MUTATED           2          0          3          2        1         1
  ST18 WILD-TYPE        16          6         41         31       34        11
                vv
clus             STAGE IVB
  ST18 MUTATED           0
  ST18 WILD-TYPE         1
D1429V3, multiclass
            clus
vv           ST18 MUTATED ST18 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             1             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
  ST18 MUTATED     0   4  15   4
  ST18 WILD-TYPE   9  63 234  37
D1429V4, multiclass
    clus
vv   ST18 MUTATED ST18 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           15            234
  T4            4             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
  ST18 MUTATED    14   7   2
  ST18 WILD-TYPE 206  74  64
D1429V5, multiclass
    clus
vv   ST18 MUTATED ST18 WILD-TYPE
  N0           14            206
  N1            7             74
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1429V6, binary
                cls
clus               0   1
  ST18 MUTATED    18   2
  ST18 WILD-TYPE 267  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     18    2
  ST18 WILD-TYPE  267   46
   clus
vv  ST18 MUTATED ST18 WILD-TYPE
  0           18            267
  1            2             46
[1] 2 2
[1] FALSE
D1429V7, binary
                cls
clus               0   1
  ST18 MUTATED    11  12
  ST18 WILD-TYPE 159 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     11   12
  ST18 WILD-TYPE  159  185
        clus
vv       ST18 MUTATED ST18 WILD-TYPE
  FEMALE           11            159
  MALE             12            185
[1] 2 2
[1] FALSE
D1429V8, binary
                cls
clus               0   1
  ST18 MUTATED    16   0
  ST18 WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     16    0
  ST18 WILD-TYPE  284    8
     clus
vv    ST18 MUTATED ST18 WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D1429V9, binary
                cls
clus               0   1
  ST18 MUTATED    18   4
  ST18 WILD-TYPE 296  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     18    4
  ST18 WILD-TYPE  296   44
                               clus
vv                              ST18 MUTATED ST18 WILD-TYPE
  COLON ADENOCARCINOMA                    18            296
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ST18 MUTATED    18   0   0   3
  ST18 WILD-TYPE 241   3  22  18
D1429V10, multiclass
    clus
vv   ST18 MUTATED ST18 WILD-TYPE
  R0           18            241
  R1            0              3
  R2            0             22
  RX            3             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"
D1429V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST18 MUTATED                                  0     2
  ST18 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ST18 MUTATED                           1    15
  ST18 WILD-TYPE                        18   161
D1429V12, multiclass
                                  clus
vv                                 ST18 MUTATED ST18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      15            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(1430) Variable = MAGOHB MUTATION ANALYSIS
D1430V1, survival
                  sevent
clus2                0   1
  MAGOHB MUTATED     2   1
  MAGOHB WILD-TYPE 275  77
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              352 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               1               77 
$`MAGOHB MUTATED`
TCGA-AY-6196 TCGA-AZ-6605 TCGA-F4-6569 
        0.20         5.23        35.74 

$`MAGOHB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MAGOHB MUTATED MAGOHB WILD-TYPE 
             0.2              0.0 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
           35.74           148.01 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
           5.230           22.075 
[1] "0.2 - 35.7 (5.2)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "3.4"
D1430V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGOHB MUTATED         1        0        0         0         0         0
  MAGOHB WILD-TYPE      63        1       26       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGOHB MUTATED           0          0          1          1        0
  MAGOHB WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  MAGOHB MUTATED           0         0
  MAGOHB WILD-TYPE        12         1
D1430V3, multiclass
            clus
vv           MAGOHB MUTATED MAGOHB WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  MAGOHB MUTATED     0   1   1   1
  MAGOHB WILD-TYPE   9  66 248  40
D1430V4, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  T1              0                9
  T2              1               66
  T3              1              248
  T4              1               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
  MAGOHB MUTATED     1   1   1
  MAGOHB WILD-TYPE 219  80  65
D1430V5, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  N0              1              219
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1430V6, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     2   0
  MAGOHB WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      2    0
  MAGOHB WILD-TYPE  283   48
   clus
vv  MAGOHB MUTATED MAGOHB WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D1430V7, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     0   3
  MAGOHB WILD-TYPE 170 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      0    3
  MAGOHB WILD-TYPE  170  194
        clus
vv       MAGOHB MUTATED MAGOHB WILD-TYPE
  FEMALE              0              170
  MALE                3              194
[1] 2 2
[1] FALSE
D1430V8, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     2   0
  MAGOHB WILD-TYPE 298   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      2    0
  MAGOHB WILD-TYPE  298    8
     clus
vv    MAGOHB MUTATED MAGOHB WILD-TYPE
  NO               2              298
  YES              0                8
[1] 2 2
[1] FALSE
D1430V9, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     2   1
  MAGOHB WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      2    1
  MAGOHB WILD-TYPE  312   47
                               clus
vv                              MAGOHB MUTATED MAGOHB WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGOHB MUTATED     2   0   0   0
  MAGOHB WILD-TYPE 257   3  22  21
D1430V10, multiclass
[1] "Remove cluster labels:" "MAGOHB MUTATED"        
clus
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               2              303 
      TCGA-A6-2677       TCGA-AA-3496       TCGA-AA-3520       TCGA-AA-3521 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6197 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682       TCGA-CA-5254 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
D1430V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGOHB MUTATED                                  0     0
  MAGOHB WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGOHB MUTATED                           0     3
  MAGOHB WILD-TYPE                        19   173
D1430V12, multiclass
                                  clus
vv                                 MAGOHB MUTATED MAGOHB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = DEFB129 MUTATION ANALYSIS
D1431V1, survival
                   sevent
clus2                 0   1
  DEFB129 MUTATED     4   1
  DEFB129 WILD-TYPE 273  77
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               350 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                1                77 
$`DEFB129 MUTATED`
TCGA-AA-3516 TCGA-G4-6628 TCGA-AA-3710 TCGA-AA-3968 TCGA-D5-6536 
       13.02        79.69        26.99        21.99        17.85 

$`DEFB129 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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            22.075 
[1] "13.0 - 79.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1431V2, continuous
                   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      62        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEFB129 MUTATED           1          0          0          0        0
  DEFB129 WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  DEFB129 MUTATED           0         0
  DEFB129 WILD-TYPE        12         1
D1431V3, multiclass
            clus
vv           DEFB129 MUTATED DEFB129 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  DEFB129 MUTATED     0   2   3   0
  DEFB129 WILD-TYPE   9  65 246  41
D1431V4, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               3               246
  T4               0                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
  DEFB129 MUTATED     4   0   1
  DEFB129 WILD-TYPE 216  81  65
D1431V5, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  N0               4               216
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1431V6, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     5   0
  DEFB129 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      5    0
  DEFB129 WILD-TYPE  280   48
   clus
vv  DEFB129 MUTATED DEFB129 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1431V7, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     3   2
  DEFB129 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      3    2
  DEFB129 WILD-TYPE  167  195
        clus
vv       DEFB129 MUTATED DEFB129 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1431V8, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     5   0
  DEFB129 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      5    0
  DEFB129 WILD-TYPE  295    8
     clus
vv    DEFB129 MUTATED DEFB129 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1431V9, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     4   1
  DEFB129 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      4    1
  DEFB129 WILD-TYPE  310   47
                               clus
vv                              DEFB129 MUTATED DEFB129 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DEFB129 MUTATED     4   0   0   0
  DEFB129 WILD-TYPE 255   3  22  21
D1431V10, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1431V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEFB129 MUTATED                                  0     0
  DEFB129 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DEFB129 MUTATED                           0     2
  DEFB129 WILD-TYPE                        19   174
D1431V12, multiclass
[1] "Remove cluster labels:" "DEFB129 MUTATED"       
clus
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6625        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-2676        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-A6-5656 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660        TCGA-A6-5661 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665        TCGA-A6-5666 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141        TCGA-A6-6142 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6651        TCGA-A6-6652        TCGA-A6-6653 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781        TCGA-A6-6782 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6899 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965        TCGA-AU-3779 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"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-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 

Clustering(1432) Variable = OR8K3 MUTATION ANALYSIS
D1432V1, survival
                 sevent
clus2               0   1
  OR8K3 MUTATED     9   1
  OR8K3 WILD-TYPE 268  77
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             10             345 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
              1              77 
$`OR8K3 MUTATED`
TCGA-G4-6625 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3821 TCGA-AA-A010 TCGA-AU-3779 
       91.79         8.38        20.12         1.02        34.98        14.50 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-DM-A1HB 
       12.76        10.06       148.01       135.65 

$`OR8K3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.09 
[1] "1.0 - 148.0 (17.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "3.2"
D1432V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8K3 MUTATED         1        0        0         6         1         0
  OR8K3 WILD-TYPE      63        1       26       102         7         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  OR8K3 MUTATED           0
  OR8K3 WILD-TYPE         1
D1432V3, multiclass
            clus
vv           OR8K3 MUTATED OR8K3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  OR8K3 MUTATED     0   1   8   1
  OR8K3 WILD-TYPE   9  66 241  40
D1432V4, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             1              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
  OR8K3 MUTATED     8   2   0
  OR8K3 WILD-TYPE 212  79  66
D1432V5, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1432V6, binary
                 cls
clus                0   1
  OR8K3 MUTATED     9   0
  OR8K3 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      9    0
  OR8K3 WILD-TYPE  276   48
   clus
vv  OR8K3 MUTATED OR8K3 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1432V7, binary
                 cls
clus                0   1
  OR8K3 MUTATED     5   5
  OR8K3 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      5    5
  OR8K3 WILD-TYPE  165  192
        clus
vv       OR8K3 MUTATED OR8K3 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1432V8, binary
                 cls
clus                0   1
  OR8K3 MUTATED     9   0
  OR8K3 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      9    0
  OR8K3 WILD-TYPE  291    8
     clus
vv    OR8K3 MUTATED OR8K3 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1432V9, binary
                 cls
clus                0   1
  OR8K3 MUTATED     6   3
  OR8K3 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      6    3
  OR8K3 WILD-TYPE  308   45
                               clus
vv                              OR8K3 MUTATED OR8K3 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR8K3 MUTATED     5   0   0   2
  OR8K3 WILD-TYPE 254   3  22  19
D1432V10, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D1432V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8K3 MUTATED                                  0     2
  OR8K3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR8K3 MUTATED                           1     5
  OR8K3 WILD-TYPE                        18   171
D1432V12, multiclass
                                  clus
vv                                 OR8K3 MUTATED OR8K3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = G2E3 MUTATION ANALYSIS
D1433V1, survival
                sevent
clus2              0   1
  G2E3 MUTATED    10   2
  G2E3 WILD-TYPE 267  76
  G2E3 MUTATED G2E3 WILD-TYPE 
            12            343 
  G2E3 MUTATED G2E3 WILD-TYPE 
             2             76 
$`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 

$`G2E3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-6677 
       13.02        15.02        11.01        12.95        13.05        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  G2E3 MUTATED G2E3 WILD-TYPE 
          4.01           0.00 
  G2E3 MUTATED G2E3 WILD-TYPE 
         63.98         148.01 
  G2E3 MUTATED G2E3 WILD-TYPE 
         13.40          22.09 
[1] "4.0 - 64.0 (13.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1433V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  G2E3 MUTATED         2        0        2         4         2         0
  G2E3 WILD-TYPE      62        1       24       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  G2E3 MUTATED           0          0          1          0        0         1
  G2E3 WILD-TYPE        18          6         43         33       35        11
                vv
clus             STAGE IVB
  G2E3 MUTATED           0
  G2E3 WILD-TYPE         1
D1433V3, multiclass
            clus
vv           G2E3 MUTATED G2E3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  G2E3 MUTATED     0   2   7   3
  G2E3 WILD-TYPE   9  65 242  38
D1433V4, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            7            242
  T4            3             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
  G2E3 MUTATED    10   2   0
  G2E3 WILD-TYPE 210  79  66
D1433V5, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  N0           10            210
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1433V6, binary
                cls
clus               0   1
  G2E3 MUTATED    11   1
  G2E3 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED     11    1
  G2E3 WILD-TYPE  274   47
   clus
vv  G2E3 MUTATED G2E3 WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D1433V7, binary
                cls
clus               0   1
  G2E3 MUTATED     4   8
  G2E3 WILD-TYPE 166 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      4    8
  G2E3 WILD-TYPE  166  189
        clus
vv       G2E3 MUTATED G2E3 WILD-TYPE
  FEMALE            4            166
  MALE              8            189
[1] 2 2
[1] FALSE
D1433V8, binary
                cls
clus               0   1
  G2E3 MUTATED    10   0
  G2E3 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED     10    0
  G2E3 WILD-TYPE  290    8
     clus
vv    G2E3 MUTATED G2E3 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1433V9, binary
                cls
clus               0   1
  G2E3 MUTATED     8   4
  G2E3 WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      8    4
  G2E3 WILD-TYPE  306   44
                               clus
vv                              G2E3 MUTATED G2E3 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  G2E3 MUTATED    10   0   0   1
  G2E3 WILD-TYPE 249   3  22  20
D1433V10, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D1433V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G2E3 MUTATED                                  0     1
  G2E3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  G2E3 MUTATED                           0     8
  G2E3 WILD-TYPE                        19   168
D1433V12, multiclass
                                  clus
vv                                 G2E3 MUTATED G2E3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1434) Variable = GRK5 MUTATION ANALYSIS
D1434V1, survival
                sevent
clus2              0   1
  GRK5 MUTATED     8   3
  GRK5 WILD-TYPE 269  75
  GRK5 MUTATED GRK5 WILD-TYPE 
            11            344 
  GRK5 MUTATED GRK5 WILD-TYPE 
             3             75 
$`GRK5 MUTATED`
TCGA-AA-3692 TCGA-AA-3950 TCGA-A6-6651 TCGA-AA-3848 TCGA-AA-3994 TCGA-AU-6004 
       36.00        24.00        21.76        10.06        27.02        27.09 
TCGA-CA-5254 TCGA-CM-5344 TCGA-CM-5862 TCGA-D5-6930 TCGA-G4-6293 
       12.69        22.03         5.03        13.35       133.18 

$`GRK5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GRK5 MUTATED GRK5 WILD-TYPE 
          5.03           0.00 
  GRK5 MUTATED GRK5 WILD-TYPE 
        133.18         148.01 
  GRK5 MUTATED GRK5 WILD-TYPE 
        22.030         22.075 
[1] "5.0 - 133.2 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1434V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRK5 MUTATED         1        0        0         3         0         0
  GRK5 WILD-TYPE      63        1       26       105         8         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        17          6         41         32       34        11
                vv
clus             STAGE IVB
  GRK5 MUTATED           0
  GRK5 WILD-TYPE         1
D1434V3, multiclass
            clus
vv           GRK5 MUTATED GRK5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  GRK5 MUTATED     0   1  10   0
  GRK5 WILD-TYPE   9  66 239  41
D1434V4, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           10            239
  T4            0             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
  GRK5 MUTATED     4   5   2
  GRK5 WILD-TYPE 216  76  64
D1434V5, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  N0            4            216
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1434V6, binary
                cls
clus               0   1
  GRK5 MUTATED     8   2
  GRK5 WILD-TYPE 277  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      8    2
  GRK5 WILD-TYPE  277   46
   clus
vv  GRK5 MUTATED GRK5 WILD-TYPE
  0            8            277
  1            2             46
[1] 2 2
[1] FALSE
D1434V7, binary
                cls
clus               0   1
  GRK5 MUTATED     8   3
  GRK5 WILD-TYPE 162 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      8    3
  GRK5 WILD-TYPE  162  194
        clus
vv       GRK5 MUTATED GRK5 WILD-TYPE
  FEMALE            8            162
  MALE              3            194
[1] 2 2
[1] FALSE
D1434V8, binary
                cls
clus               0   1
  GRK5 MUTATED     9   1
  GRK5 WILD-TYPE 291   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      9    1
  GRK5 WILD-TYPE  291    7
     clus
vv    GRK5 MUTATED GRK5 WILD-TYPE
  NO             9            291
  YES            1              7
[1] 2 2
[1] FALSE
D1434V9, binary
                cls
clus               0   1
  GRK5 MUTATED     7   4
  GRK5 WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      7    4
  GRK5 WILD-TYPE  307   44
                               clus
vv                              GRK5 MUTATED GRK5 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GRK5 MUTATED     8   0   1   1
  GRK5 WILD-TYPE 251   3  21  20
D1434V10, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            1             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"
D1434V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRK5 MUTATED                                  0     1
  GRK5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRK5 MUTATED                           0     6
  GRK5 WILD-TYPE                        19   170
D1434V12, multiclass
                                  clus
vv                                 GRK5 MUTATED GRK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = GLDN MUTATION ANALYSIS
D1435V1, survival
                sevent
clus2              0   1
  GLDN MUTATED     4   2
  GLDN WILD-TYPE 273  76
  GLDN MUTATED GLDN WILD-TYPE 
             6            349 
  GLDN MUTATED GLDN WILD-TYPE 
             2             76 
$`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 

$`GLDN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GLDN MUTATED GLDN WILD-TYPE 
           4.8            0.0 
  GLDN MUTATED GLDN WILD-TYPE 
         44.68         148.01 
  GLDN MUTATED GLDN WILD-TYPE 
         17.54          22.06 
[1] "4.8 - 44.7 (17.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1435V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLDN MUTATED         1        0        0         3         0         0
  GLDN WILD-TYPE      63        1       26       105         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  GLDN MUTATED           0
  GLDN WILD-TYPE         1
D1435V3, multiclass
            clus
vv           GLDN MUTATED GLDN WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GLDN MUTATED     0   3   4   0
  GLDN WILD-TYPE   9  64 245  41
D1435V4, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  T1            0              9
  T2            3             64
  T3            4            245
  T4            0             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
  GLDN MUTATED     6   1   0
  GLDN WILD-TYPE 214  80  66
D1435V5, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  N0            6            214
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1435V6, binary
                cls
clus               0   1
  GLDN MUTATED     5   0
  GLDN WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      5    0
  GLDN WILD-TYPE  280   48
   clus
vv  GLDN MUTATED GLDN WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1435V7, binary
                cls
clus               0   1
  GLDN MUTATED     1   6
  GLDN WILD-TYPE 169 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      1    6
  GLDN WILD-TYPE  169  191
        clus
vv       GLDN MUTATED GLDN WILD-TYPE
  FEMALE            1            169
  MALE              6            191
[1] 2 2
[1] FALSE
D1435V8, binary
                cls
clus               0   1
  GLDN MUTATED     6   0
  GLDN WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      6    0
  GLDN WILD-TYPE  294    8
     clus
vv    GLDN MUTATED GLDN WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1435V9, binary
                cls
clus               0   1
  GLDN MUTATED     6   1
  GLDN WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      6    1
  GLDN WILD-TYPE  308   47
                               clus
vv                              GLDN MUTATED GLDN WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GLDN MUTATED     5   0   0   1
  GLDN WILD-TYPE 254   3  22  20
D1435V10, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1435V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLDN MUTATED                                  0     1
  GLDN WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLDN MUTATED                           0     4
  GLDN WILD-TYPE                        19   172
D1435V12, multiclass
                                  clus
vv                                 GLDN MUTATED GLDN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = LAMA3 MUTATION ANALYSIS
D1436V1, survival
                 sevent
clus2               0   1
  LAMA3 MUTATED    25   7
  LAMA3 WILD-TYPE 252  71
  LAMA3 MUTATED LAMA3 WILD-TYPE 
             32             323 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              7              71 
$`LAMA3 MUTATED`
TCGA-AA-3662 TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 
        6.05         0.92       100.01        26.17        79.69        43.76 
TCGA-A6-3807 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3529 TCGA-AA-3663 TCGA-AA-3685 
       34.65        29.19        22.06         0.00         6.97        37.05 
TCGA-AA-3821 TCGA-AA-3861 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
        1.02        30.05        34.03        25.02        18.05         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-4746 
       34.98        58.39        49.41        12.10        12.76        37.02 
TCGA-CM-5349 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A0X9 TCGA-F4-6570 
       30.08        14.04        15.12        16.14       119.70         6.18 
TCGA-F4-6806 TCGA-G4-6323 
       41.42        13.78 

$`LAMA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       13.02        17.95        23.01        19.99        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 
       46.65        43.76        42.90        42.28        16.57        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        88.21         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6703 TCGA-F4-6704 
       98.24         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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        46.75 

  LAMA3 MUTATED LAMA3 WILD-TYPE 
              0               0 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
         119.70          148.01 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
         25.595          21.990 
[1] "0.0 - 119.7 (25.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1436V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAMA3 MUTATED         6        1        5        10         2         0
  LAMA3 WILD-TYPE      58        0       21        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAMA3 MUTATED           1          0          2          3        3         0
  LAMA3 WILD-TYPE        17          6         42         30       32        12
                 vv
clus              STAGE IVB
  LAMA3 MUTATED           0
  LAMA3 WILD-TYPE         1
D1436V3, multiclass
            clus
vv           LAMA3 MUTATED LAMA3 WILD-TYPE
  STAGE I                6              58
  STAGE IA               1               0
  STAGE II               5              21
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             3              30
  STAGE IV               3              32
  STAGE IVA              0              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
  LAMA3 MUTATED     0   7  20   6
  LAMA3 WILD-TYPE   9  60 229  35
D1436V4, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  T1             0               9
  T2             7              60
  T3            20             229
  T4             6              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
  LAMA3 MUTATED    25   4   5
  LAMA3 WILD-TYPE 195  77  61
D1436V5, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  N0            25             195
  N1             4              77
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1436V6, binary
                 cls
clus                0   1
  LAMA3 MUTATED    27   3
  LAMA3 WILD-TYPE 258  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED     27    3
  LAMA3 WILD-TYPE  258   45
   clus
vv  LAMA3 MUTATED LAMA3 WILD-TYPE
  0            27             258
  1             3              45
[1] 2 2
[1] FALSE
D1436V7, binary
                 cls
clus                0   1
  LAMA3 MUTATED    17  17
  LAMA3 WILD-TYPE 153 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED     17   17
  LAMA3 WILD-TYPE  153  180
        clus
vv       LAMA3 MUTATED LAMA3 WILD-TYPE
  FEMALE            17             153
  MALE              17             180
[1] 2 2
[1] FALSE
D1436V8, binary
                 cls
clus                0   1
  LAMA3 MUTATED    29   0
  LAMA3 WILD-TYPE 271   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED     29    0
  LAMA3 WILD-TYPE  271    8
     clus
vv    LAMA3 MUTATED LAMA3 WILD-TYPE
  NO             29             271
  YES             0               8
[1] 2 2
[1] FALSE
D1436V9, binary
                 cls
clus                0   1
  LAMA3 MUTATED    29   5
  LAMA3 WILD-TYPE 285  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED     29    5
  LAMA3 WILD-TYPE  285   43
                               clus
vv                              LAMA3 MUTATED LAMA3 WILD-TYPE
  COLON ADENOCARCINOMA                     29             285
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LAMA3 MUTATED    25   0   1   2
  LAMA3 WILD-TYPE 234   3  21  19
D1436V10, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  R0            25             234
  R1             0               3
  R2             1              21
  RX             2              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"
D1436V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAMA3 MUTATED                                  0     1
  LAMA3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAMA3 MUTATED                           4    15
  LAMA3 WILD-TYPE                        15   161
D1436V12, multiclass
                                  clus
vv                                 LAMA3 MUTATED LAMA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       15             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(1437) Variable = GNG12 MUTATION ANALYSIS
D1437V1, survival
                 sevent
clus2               0   1
  GNG12 MUTATED     6   2
  GNG12 WILD-TYPE 271  76
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             347 
  GNG12 MUTATED GNG12 WILD-TYPE 
              2              76 
$`GNG12 MUTATED`
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AD-6889 
       35.80        79.69        22.06        19.66         6.97        83.24 
TCGA-AZ-6598 TCGA-DM-A1HB 
       49.41       135.65 

$`GNG12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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          21.990 
[1] "7.0 - 135.7 (42.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1437V2, continuous
                 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      63        1       24       105         8         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  GNG12 MUTATED           0
  GNG12 WILD-TYPE         1
D1437V3, multiclass
            clus
vv           GNG12 MUTATED GNG12 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  GNG12 MUTATED     0   1   6   1
  GNG12 WILD-TYPE   9  66 243  40
D1437V4, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             1              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
  GNG12 MUTATED     6   2   0
  GNG12 WILD-TYPE 214  79  66
D1437V5, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1437V6, binary
                 cls
clus                0   1
  GNG12 MUTATED     6   0
  GNG12 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      6    0
  GNG12 WILD-TYPE  279   48
   clus
vv  GNG12 MUTATED GNG12 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1437V7, binary
                 cls
clus                0   1
  GNG12 MUTATED     3   5
  GNG12 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      3    5
  GNG12 WILD-TYPE  167  192
        clus
vv       GNG12 MUTATED GNG12 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D1437V8, binary
                 cls
clus                0   1
  GNG12 MUTATED     7   0
  GNG12 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      7    0
  GNG12 WILD-TYPE  293    8
     clus
vv    GNG12 MUTATED GNG12 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1437V9, binary
                 cls
clus                0   1
  GNG12 MUTATED     6   1
  GNG12 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      6    1
  GNG12 WILD-TYPE  308   47
                               clus
vv                              GNG12 MUTATED GNG12 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GNG12 MUTATED     6   0   0   0
  GNG12 WILD-TYPE 253   3  22  21
D1437V10, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1437V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNG12 MUTATED                                  0     1
  GNG12 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNG12 MUTATED                           0     6
  GNG12 WILD-TYPE                        19   170
D1437V12, multiclass
                                  clus
vv                                 GNG12 MUTATED GNG12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = GUCY1A3 MUTATION ANALYSIS
D1438V1, survival
                   sevent
clus2                 0   1
  GUCY1A3 MUTATED    16   6
  GUCY1A3 WILD-TYPE 261  72
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               22               333 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
                6                72 
$`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        83.24        12.76        15.02 
TCGA-D5-6533 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-G4-6315 
       25.48       119.70         7.50        61.91 

$`GUCY1A3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 
       61.02        78.08        54.02        14.01        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        15.02        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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-F4-6459 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
             2.01              0.00 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
           119.70            148.01 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
            25.25             22.03 
[1] "2.0 - 119.7 (25.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1438V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GUCY1A3 MUTATED         0        0        2         7         3         1
  GUCY1A3 WILD-TYPE      64        1       24       101         5         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GUCY1A3 MUTATED           3          0          1          2        1
  GUCY1A3 WILD-TYPE        15          6         43         31       34
                   vv
clus                STAGE IVA STAGE IVB
  GUCY1A3 MUTATED           0         0
  GUCY1A3 WILD-TYPE        12         1
D1438V3, multiclass
            clus
vv           GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                7               101
  STAGE IIB                3                 5
  STAGE IIC                1                 0
  STAGE III                3                15
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  GUCY1A3 MUTATED     0   1  16   5
  GUCY1A3 WILD-TYPE   9  66 233  36
D1438V4, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              16               233
  T4               5                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
  GUCY1A3 MUTATED    15   3   4
  GUCY1A3 WILD-TYPE 205  78  62
D1438V5, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  N0              15               205
  N1               3                78
  N2               4                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1438V6, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    19   1
  GUCY1A3 WILD-TYPE 266  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     19    1
  GUCY1A3 WILD-TYPE  266   47
   clus
vv  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  0              19               266
  1               1                47
[1] 2 2
[1] FALSE
D1438V7, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    11  11
  GUCY1A3 WILD-TYPE 159 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     11   11
  GUCY1A3 WILD-TYPE  159  186
        clus
vv       GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  FEMALE              11               159
  MALE                11               186
[1] 2 2
[1] FALSE
D1438V8, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    17   1
  GUCY1A3 WILD-TYPE 283   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     17    1
  GUCY1A3 WILD-TYPE  283    7
     clus
vv    GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  NO               17               283
  YES               1                 7
[1] 2 2
[1] FALSE
D1438V9, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    17   5
  GUCY1A3 WILD-TYPE 297  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     17    5
  GUCY1A3 WILD-TYPE  297   43
                               clus
vv                              GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GUCY1A3 MUTATED    15   0   0   1
  GUCY1A3 WILD-TYPE 244   3  22  20
D1438V10, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  R0              15               244
  R1               0                 3
  R2               0                22
  RX               1                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"
D1438V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GUCY1A3 MUTATED                                  0     2
  GUCY1A3 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GUCY1A3 MUTATED                           2     7
  GUCY1A3 WILD-TYPE                        17   169
D1438V12, multiclass
                                  clus
vv                                 GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          7               169
[1] 4 2
[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 = CALB2 MUTATION ANALYSIS
D1439V1, survival
                 sevent
clus2               0   1
  CALB2 MUTATED     3   1
  CALB2 WILD-TYPE 274  77
  CALB2 MUTATED CALB2 WILD-TYPE 
              4             351 
  CALB2 MUTATED CALB2 WILD-TYPE 
              1              77 
$`CALB2 MUTATED`
TCGA-G4-6628 TCGA-AA-3966 TCGA-AD-5900 TCGA-AZ-6606 
       79.69         2.01        12.16        11.74 

$`CALB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CALB2 MUTATED CALB2 WILD-TYPE 
           2.01            0.00 
  CALB2 MUTATED CALB2 WILD-TYPE 
          79.69          148.01 
  CALB2 MUTATED CALB2 WILD-TYPE 
          11.95           22.09 
[1] "2.0 - 79.7 (11.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1439V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CALB2 MUTATED         2        0        0         1         0         0
  CALB2 WILD-TYPE      62        1       26       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CALB2 MUTATED           0          0          0          0        1         0
  CALB2 WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  CALB2 MUTATED           0
  CALB2 WILD-TYPE         1
D1439V3, multiclass
            clus
vv           CALB2 MUTATED CALB2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  CALB2 MUTATED     0   2   1   1
  CALB2 WILD-TYPE   9  65 248  40
D1439V4, multiclass
    clus
vv   CALB2 MUTATED CALB2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             1             248
  T4             1              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
  CALB2 MUTATED     3   0   1
  CALB2 WILD-TYPE 217  81  65
D1439V5, multiclass
    clus
vv   CALB2 MUTATED CALB2 WILD-TYPE
  N0             3             217
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1439V6, binary
                 cls
clus                0   1
  CALB2 MUTATED     2   1
  CALB2 WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALB2 MUTATED      2    1
  CALB2 WILD-TYPE  283   47
   clus
vv  CALB2 MUTATED CALB2 WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D1439V7, binary
                 cls
clus                0   1
  CALB2 MUTATED     1   3
  CALB2 WILD-TYPE 169 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALB2 MUTATED      1    3
  CALB2 WILD-TYPE  169  194
        clus
vv       CALB2 MUTATED CALB2 WILD-TYPE
  FEMALE             1             169
  MALE               3             194
[1] 2 2
[1] FALSE
D1439V8, binary
                 cls
clus                0   1
  CALB2 MUTATED     3   0
  CALB2 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALB2 MUTATED      3    0
  CALB2 WILD-TYPE  297    8
     clus
vv    CALB2 MUTATED CALB2 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1439V9, binary
                 cls
clus                0   1
  CALB2 MUTATED     2   2
  CALB2 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALB2 MUTATED      2    2
  CALB2 WILD-TYPE  312   46
                               clus
vv                              CALB2 MUTATED CALB2 WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CALB2 MUTATED     2   0   0   0
  CALB2 WILD-TYPE 257   3  22  21
D1439V10, multiclass
[1] "Remove cluster labels:" "CALB2 MUTATED"         
clus
  CALB2 MUTATED CALB2 WILD-TYPE 
              2             303 
     TCGA-A6-2677      TCGA-AA-3496      TCGA-AA-3520      TCGA-AA-3521 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3527 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AD-6895      TCGA-AZ-4681      TCGA-CK-5912      TCGA-G4-6310 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657      TCGA-A6-5659 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781      TCGA-AA-3489 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3492      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3526      TCGA-AA-3529      TCGA-AA-3532      TCGA-AA-3534 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3544      TCGA-AA-3548 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3549      TCGA-AA-3553      TCGA-AA-3555      TCGA-AA-3558 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3561      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3663 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3673 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693      TCGA-AA-3695 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3811 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3812      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3941 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3955      TCGA-AA-3956 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973      TCGA-AA-3975 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00N      TCGA-AA-A00O 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-6889      TCGA-AD-6965 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5913 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6315 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
D1439V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CALB2 MUTATED                                  0     0
  CALB2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CALB2 MUTATED                           0     3
  CALB2 WILD-TYPE                        19   173
D1439V12, multiclass
                                  clus
vv                                 CALB2 MUTATED CALB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = LRRN3 MUTATION ANALYSIS
D1440V1, survival
                 sevent
clus2               0   1
  LRRN3 MUTATED    16   4
  LRRN3 WILD-TYPE 261  74
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             20             335 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
              4              74 
$`LRRN3 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-G4-6628 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5666 
        0.92        19.04        79.69        34.65        32.75        32.71 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3941 TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A01P 
        3.02        63.98        24.00        30.02         0.99        38.07 
TCGA-AA-A01R TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-6165 TCGA-CM-6676 TCGA-D5-6930 
       35.01        58.39        23.05        16.04        11.08        13.35 
TCGA-F4-6570 TCGA-G4-6293 
        6.18       133.18 

$`LRRN3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       42.28        16.57        33.34        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6166 
       17.03        15.02        12.00        14.04        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-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LRRN3 MUTATED LRRN3 WILD-TYPE 
           0.92            0.00 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
         133.18          148.01 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
          27.01           21.99 
[1] "0.9 - 133.2 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1440V2, continuous
                 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      61        1       23       102         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRN3 MUTATED           4          0          0          1        1         1
  LRRN3 WILD-TYPE        14          6         44         32       34        11
                 vv
clus              STAGE IVB
  LRRN3 MUTATED           0
  LRRN3 WILD-TYPE         1
D1440V3, multiclass
            clus
vv           LRRN3 MUTATED LRRN3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              4              14
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  LRRN3 MUTATED     0   3  14   4
  LRRN3 WILD-TYPE   9  64 235  37
D1440V4, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            14             235
  T4             4              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
  LRRN3 MUTATED    14   4   3
  LRRN3 WILD-TYPE 206  77  63
D1440V5, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  N0            14             206
  N1             4              77
  N2             3              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"
D1440V6, binary
                 cls
clus                0   1
  LRRN3 MUTATED    19   2
  LRRN3 WILD-TYPE 266  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     19    2
  LRRN3 WILD-TYPE  266   46
   clus
vv  LRRN3 MUTATED LRRN3 WILD-TYPE
  0            19             266
  1             2              46
[1] 2 2
[1] FALSE
D1440V7, binary
                 cls
clus                0   1
  LRRN3 MUTATED     9  12
  LRRN3 WILD-TYPE 161 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED      9   12
  LRRN3 WILD-TYPE  161  185
        clus
vv       LRRN3 MUTATED LRRN3 WILD-TYPE
  FEMALE             9             161
  MALE              12             185
[1] 2 2
[1] FALSE
D1440V8, binary
                 cls
clus                0   1
  LRRN3 MUTATED    18   1
  LRRN3 WILD-TYPE 282   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     18    1
  LRRN3 WILD-TYPE  282    7
     clus
vv    LRRN3 MUTATED LRRN3 WILD-TYPE
  NO             18             282
  YES             1               7
[1] 2 2
[1] FALSE
D1440V9, binary
                 cls
clus                0   1
  LRRN3 MUTATED    18   3
  LRRN3 WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     18    3
  LRRN3 WILD-TYPE  296   45
                               clus
vv                              LRRN3 MUTATED LRRN3 WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LRRN3 MUTATED    19   0   1   0
  LRRN3 WILD-TYPE 240   3  21  21
D1440V10, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             1              21
  RX             0              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"
D1440V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRN3 MUTATED                                  0     0
  LRRN3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRRN3 MUTATED                           0    11
  LRRN3 WILD-TYPE                        19   165
D1440V12, multiclass
                                  clus
vv                                 LRRN3 MUTATED LRRN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       11             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(1441) Variable = DEK MUTATION ANALYSIS
D1441V1, survival
               sevent
clus2             0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 273  76
  DEK MUTATED DEK WILD-TYPE 
            6           349 
  DEK MUTATED DEK WILD-TYPE 
            2            76 
$`DEK MUTATED`
TCGA-G4-6586 TCGA-A6-5660 TCGA-AA-A00N TCGA-AY-6197 TCGA-CA-6717 TCGA-G4-6626 
       35.80        29.19         4.01        21.44        12.76        46.75 

$`DEK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  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        22.060 
[1] "4.0 - 46.8 (25.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1441V2, continuous
               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      64        1       26       104         7         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        18          6         44         32       35        12
               vv
clus            STAGE IVB
  DEK MUTATED           0
  DEK WILD-TYPE         1
D1441V3, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  DEK MUTATED     0   0   5   1
  DEK WILD-TYPE   9  67 244  40
D1441V4, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  T1           0             9
  T2           0            67
  T3           5           244
  T4           1            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
  DEK MUTATED     5   0   1
  DEK WILD-TYPE 215  81  65
D1441V5, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  N0           5           215
  N1           0            81
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1441V6, binary
               cls
clus              0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    0
  DEK WILD-TYPE  280   48
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           5           280
  1           0            48
[1] 2 2
[1] FALSE
D1441V7, binary
               cls
clus              0   1
  DEK MUTATED     1   5
  DEK WILD-TYPE 169 192
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      1    5
  DEK WILD-TYPE  169  192
        clus
vv       DEK MUTATED DEK WILD-TYPE
  FEMALE           1           169
  MALE             5           192
[1] 2 2
[1] FALSE
D1441V8, binary
               cls
clus              0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 295   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    0
  DEK WILD-TYPE  295    8
     clus
vv    DEK MUTATED DEK WILD-TYPE
  NO            5           295
  YES           0             8
[1] 2 2
[1] FALSE
D1441V9, binary
               cls
clus              0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 310  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    2
  DEK WILD-TYPE  310   46
                               clus
vv                              DEK MUTATED DEK WILD-TYPE
  COLON ADENOCARCINOMA                    4           310
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  DEK MUTATED     4   0   0   1
  DEK WILD-TYPE 255   3  22  20
D1441V10, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  R0           4           255
  R1           0             3
  R2           0            22
  RX           1            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"
D1441V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEK MUTATED                                  0     1
  DEK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DEK MUTATED                           1     3
  DEK WILD-TYPE                        18   173
D1441V12, multiclass
                                  clus
vv                                 DEK MUTATED DEK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      3           173
[1] 4 2
[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 = PCDH9 MUTATION ANALYSIS
D1442V1, survival
                 sevent
clus2               0   1
  PCDH9 MUTATED    32   6
  PCDH9 WILD-TYPE 245  72
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             38             317 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
              6              72 
$`PCDH9 MUTATED`
TCGA-AA-3715 TCGA-AA-3939 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-6141 
       19.04        12.99        25.08       100.01        35.80         8.38 
TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3555 TCGA-AA-3679 TCGA-AA-3815 
       63.98        29.00        12.99        29.95        15.02        33.04 
TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3977 
        0.99        17.98        37.02        34.03         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01K TCGA-AU-6004 TCGA-AY-6197 
        4.01        17.03        34.98        31.00        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6717 
       58.39        62.79        49.41        12.69        12.59        12.76 
TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6538 
       23.05        13.02        22.03        21.99        14.04        17.13 
TCGA-D5-6898 TCGA-G4-6293 
        7.53       133.18 

$`PCDH9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        26.17        91.79        79.69 
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-A6-5656 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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 
        1.02         9.07        19.07         0.00        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 
       26.99        10.06        35.05        25.02         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A017 
       18.05        27.02        42.02         0.99        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.36        12.39        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PCDH9 MUTATED PCDH9 WILD-TYPE 
           0.99            0.00 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
         133.18          148.01 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
          22.01           22.09 
[1] "1.0 - 133.2 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1442V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH9 MUTATED         4        0        5        16         2         0
  PCDH9 WILD-TYPE      60        1       21        92         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDH9 MUTATED           1          1          5          2        1         0
  PCDH9 WILD-TYPE        17          5         39         31       34        12
                 vv
clus              STAGE IVB
  PCDH9 MUTATED           0
  PCDH9 WILD-TYPE         1
D1442V3, multiclass
            clus
vv           PCDH9 MUTATED PCDH9 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             16              92
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             5              39
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  PCDH9 MUTATED     0   6  30   2
  PCDH9 WILD-TYPE   9  61 219  39
D1442V4, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  T1             0               9
  T2             6              61
  T3            30             219
  T4             2              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
  PCDH9 MUTATED    28   6   4
  PCDH9 WILD-TYPE 192  75  62
D1442V5, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  N0            28             192
  N1             6              75
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1442V6, binary
                 cls
clus                0   1
  PCDH9 MUTATED    33   1
  PCDH9 WILD-TYPE 252  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     33    1
  PCDH9 WILD-TYPE  252   47
   clus
vv  PCDH9 MUTATED PCDH9 WILD-TYPE
  0            33             252
  1             1              47
[1] 2 2
[1] FALSE
D1442V7, binary
                 cls
clus                0   1
  PCDH9 MUTATED    17  21
  PCDH9 WILD-TYPE 153 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     17   21
  PCDH9 WILD-TYPE  153  176
        clus
vv       PCDH9 MUTATED PCDH9 WILD-TYPE
  FEMALE            17             153
  MALE              21             176
[1] 2 2
[1] FALSE
D1442V8, binary
                 cls
clus                0   1
  PCDH9 MUTATED    34   0
  PCDH9 WILD-TYPE 266   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     34    0
  PCDH9 WILD-TYPE  266    8
     clus
vv    PCDH9 MUTATED PCDH9 WILD-TYPE
  NO             34             266
  YES             0               8
[1] 2 2
[1] FALSE
D1442V9, binary
                 cls
clus                0   1
  PCDH9 MUTATED    34   4
  PCDH9 WILD-TYPE 280  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     34    4
  PCDH9 WILD-TYPE  280   44
                               clus
vv                              PCDH9 MUTATED PCDH9 WILD-TYPE
  COLON ADENOCARCINOMA                     34             280
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCDH9 MUTATED    28   0   1   3
  PCDH9 WILD-TYPE 231   3  21  18
D1442V10, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  R0            28             231
  R1             0               3
  R2             1              21
  RX             3              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"
D1442V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH9 MUTATED                                  0     3
  PCDH9 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCDH9 MUTATED                           2    15
  PCDH9 WILD-TYPE                        17   161
D1442V12, multiclass
                                  clus
vv                                 PCDH9 MUTATED PCDH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       15             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(1443) Variable = LIX1 MUTATION ANALYSIS
D1443V1, survival
                sevent
clus2              0   1
  LIX1 MUTATED     6   2
  LIX1 WILD-TYPE 271  76
  LIX1 MUTATED LIX1 WILD-TYPE 
             8            347 
  LIX1 MUTATED LIX1 WILD-TYPE 
             2             76 
$`LIX1 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-AA-3555 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6600 
       19.04       100.01        29.95        25.02        34.98        12.10 
TCGA-CM-4744 TCGA-D5-6928 
       20.02        11.64 

$`LIX1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LIX1 MUTATED LIX1 WILD-TYPE 
         11.64           0.00 
  LIX1 MUTATED LIX1 WILD-TYPE 
        100.01         148.01 
  LIX1 MUTATED LIX1 WILD-TYPE 
         22.52          22.06 
[1] "11.6 - 100.0 (22.5)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1"  
D1443V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIX1 MUTATED         1        0        1         2         1         0
  LIX1 WILD-TYPE      63        1       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIX1 MUTATED           1          0          0          0        2         0
  LIX1 WILD-TYPE        17          6         44         33       33        12
                vv
clus             STAGE IVB
  LIX1 MUTATED           0
  LIX1 WILD-TYPE         1
D1443V3, multiclass
            clus
vv           LIX1 MUTATED LIX1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  LIX1 MUTATED     0   2   5   2
  LIX1 WILD-TYPE   9  65 244  39
D1443V4, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            2             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
  LIX1 MUTATED     7   1   1
  LIX1 WILD-TYPE 213  80  65
D1443V5, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1443V6, binary
                cls
clus               0   1
  LIX1 MUTATED     6   2
  LIX1 WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      6    2
  LIX1 WILD-TYPE  279   46
   clus
vv  LIX1 MUTATED LIX1 WILD-TYPE
  0            6            279
  1            2             46
[1] 2 2
[1] FALSE
D1443V7, binary
                cls
clus               0   1
  LIX1 MUTATED     2   7
  LIX1 WILD-TYPE 168 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      2    7
  LIX1 WILD-TYPE  168  190
        clus
vv       LIX1 MUTATED LIX1 WILD-TYPE
  FEMALE            2            168
  MALE              7            190
[1] 2 2
[1] FALSE
D1443V8, binary
                cls
clus               0   1
  LIX1 MUTATED     7   1
  LIX1 WILD-TYPE 293   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      7    1
  LIX1 WILD-TYPE  293    7
     clus
vv    LIX1 MUTATED LIX1 WILD-TYPE
  NO             7            293
  YES            1              7
[1] 2 2
[1] FALSE
D1443V9, binary
                cls
clus               0   1
  LIX1 MUTATED     7   2
  LIX1 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      7    2
  LIX1 WILD-TYPE  307   46
                               clus
vv                              LIX1 MUTATED LIX1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LIX1 MUTATED     5   0   1   0
  LIX1 WILD-TYPE 254   3  21  21
D1443V10, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            1             21
  RX            0             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"
D1443V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIX1 MUTATED                                  0     0
  LIX1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIX1 MUTATED                           1     3
  LIX1 WILD-TYPE                        18   173
D1443V12, multiclass
                                  clus
vv                                 LIX1 MUTATED LIX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = C3ORF63 MUTATION ANALYSIS
D1444V1, survival
                   sevent
clus2                 0   1
  C3ORF63 MUTATED    16   4
  C3ORF63 WILD-TYPE 261  74
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
               20               335 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
                4                74 
$`C3ORF63 MUTATED`
TCGA-AD-6895 TCGA-CK-5912 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3555 
       25.08        49.08        26.17        32.75        33.53        29.95 
TCGA-AA-3845 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.00         4.01        34.98        58.39        49.41        12.76 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-6169 TCGA-D5-5540 TCGA-D5-6532 TCGA-G4-6307 
       23.05        22.98        13.02        56.09        18.25        55.04 
TCGA-G4-6309 TCGA-G4-6315 
       85.48        61.91 

$`C3ORF63 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        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-D5-5541 
       10.06        12.03        45.40        54.61        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       53.62        44.68        36.00        13.78        46.75 

  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
                0                 0 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
            85.48            148.01 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
            31.35             21.99 
[1] "0.0 - 85.5 (31.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1444V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C3ORF63 MUTATED         1        0        1        11         3         0
  C3ORF63 WILD-TYPE      63        1       25        97         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF63 MUTATED           0          0          4          0        1
  C3ORF63 WILD-TYPE        18          6         40         33       34
                   vv
clus                STAGE IVA STAGE IVB
  C3ORF63 MUTATED           0         0
  C3ORF63 WILD-TYPE        12         1
D1444V3, multiclass
            clus
vv           C3ORF63 MUTATED C3ORF63 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA               11                97
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  C3ORF63 MUTATED     0   1  17   3
  C3ORF63 WILD-TYPE   9  66 232  38
D1444V4, multiclass
    clus
vv   C3ORF63 MUTATED C3ORF63 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              17               232
  T4               3                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
  C3ORF63 MUTATED    16   5   0
  C3ORF63 WILD-TYPE 204  76  66
D1444V5, multiclass
    clus
vv   C3ORF63 MUTATED C3ORF63 WILD-TYPE
  N0              16               204
  N1               5                76
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1444V6, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    18   1
  C3ORF63 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     18    1
  C3ORF63 WILD-TYPE  267   47
   clus
vv  C3ORF63 MUTATED C3ORF63 WILD-TYPE
  0              18               267
  1               1                47
[1] 2 2
[1] FALSE
D1444V7, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    10  11
  C3ORF63 WILD-TYPE 160 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     10   11
  C3ORF63 WILD-TYPE  160  186
        clus
vv       C3ORF63 MUTATED C3ORF63 WILD-TYPE
  FEMALE              10               160
  MALE                11               186
[1] 2 2
[1] FALSE
D1444V8, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    18   0
  C3ORF63 WILD-TYPE 282   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     18    0
  C3ORF63 WILD-TYPE  282    8
     clus
vv    C3ORF63 MUTATED C3ORF63 WILD-TYPE
  NO               18               282
  YES               0                 8
[1] 2 2
[1] FALSE
D1444V9, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    17   4
  C3ORF63 WILD-TYPE 297  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     17    4
  C3ORF63 WILD-TYPE  297   44
                               clus
vv                              C3ORF63 MUTATED C3ORF63 WILD-TYPE
  COLON ADENOCARCINOMA                       17               297
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C3ORF63 MUTATED    18   0   0   2
  C3ORF63 WILD-TYPE 241   3  22  19
D1444V10, multiclass
    clus
vv   C3ORF63 MUTATED C3ORF63 WILD-TYPE
  R0              18               241
  R1               0                 3
  R2               0                22
  RX               2                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"
D1444V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3ORF63 MUTATED                                  0     1
  C3ORF63 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C3ORF63 MUTATED                           3    12
  C3ORF63 WILD-TYPE                        16   164
D1444V12, multiclass
                                  clus
vv                                 C3ORF63 MUTATED C3ORF63 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      3                16
  WHITE                                         12               164
[1] 4 2
[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 = FAM199X MUTATION ANALYSIS
D1445V1, survival
                   sevent
clus2                 0   1
  FAM199X MUTATED     6   4
  FAM199X WILD-TYPE 271  74
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               345 
  FAM199X MUTATED FAM199X WILD-TYPE 
                4                74 
$`FAM199X MUTATED`
TCGA-DM-A285 TCGA-AA-3866 TCGA-AA-3877 TCGA-AZ-6599 TCGA-CM-6162 TCGA-CM-6169 
        5.88        17.03        31.00         6.77        12.00        13.02 
TCGA-D5-6928 TCGA-DM-A1DA TCGA-F4-6459 TCGA-G4-6307 
       11.64         7.50         8.61        55.04 

$`FAM199X WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       31.07        30.05        53.00        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 
       74.56        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FAM199X MUTATED FAM199X WILD-TYPE 
             5.88              0.00 
  FAM199X MUTATED FAM199X WILD-TYPE 
            55.04            148.01 
  FAM199X MUTATED FAM199X WILD-TYPE 
            11.82             22.36 
[1] "5.9 - 55.0 (11.8)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.8"
D1445V2, continuous
                   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      61        1       26       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM199X MUTATED           0          0          3          1        1
  FAM199X WILD-TYPE        18          6         41         32       34
                   vv
clus                STAGE IVA STAGE IVB
  FAM199X MUTATED           0         0
  FAM199X WILD-TYPE        12         1
D1445V3, multiclass
            clus
vv           FAM199X MUTATED FAM199X WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  FAM199X MUTATED     1   2   7   0
  FAM199X WILD-TYPE   8  65 242  41
D1445V4, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               7               242
  T4               0                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
  FAM199X MUTATED     5   2   3
  FAM199X WILD-TYPE 215  79  63
D1445V5, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  N0               5               215
  N1               2                79
  N2               3                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"
D1445V6, binary
                   cls
clus                  0   1
  FAM199X MUTATED     8   1
  FAM199X WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      8    1
  FAM199X WILD-TYPE  277   47
   clus
vv  FAM199X MUTATED FAM199X WILD-TYPE
  0               8               277
  1               1                47
[1] 2 2
[1] FALSE
D1445V7, binary
                   cls
clus                  0   1
  FAM199X MUTATED     7   3
  FAM199X WILD-TYPE 163 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      7    3
  FAM199X WILD-TYPE  163  194
        clus
vv       FAM199X MUTATED FAM199X WILD-TYPE
  FEMALE               7               163
  MALE                 3               194
[1] 2 2
[1] FALSE
D1445V8, binary
                   cls
clus                  0   1
  FAM199X MUTATED     8   0
  FAM199X WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      8    0
  FAM199X WILD-TYPE  292    8
     clus
vv    FAM199X MUTATED FAM199X WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1445V9, binary
                   cls
clus                  0   1
  FAM199X MUTATED     6   4
  FAM199X WILD-TYPE 308  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      6    4
  FAM199X WILD-TYPE  308   44
                               clus
vv                              FAM199X MUTATED FAM199X WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM199X MUTATED     7   0   0   0
  FAM199X WILD-TYPE 252   3  22  21
D1445V10, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D1445V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM199X MUTATED                                  0     0
  FAM199X WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM199X MUTATED                           1     7
  FAM199X WILD-TYPE                        18   169
D1445V12, multiclass
                                  clus
vv                                 FAM199X MUTATED FAM199X WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          7               169
[1] 4 2
[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 = SKIV2L MUTATION ANALYSIS
D1446V1, survival
                  sevent
clus2                0   1
  SKIV2L MUTATED     8   4
  SKIV2L WILD-TYPE 269  74
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              12              343 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
               4               74 
$`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 

$`SKIV2L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        20.12        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SKIV2L MUTATED SKIV2L WILD-TYPE 
            1.02             0.00 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
          133.18           148.01 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
           23.34            22.06 
[1] "1.0 - 133.2 (23.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1446V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKIV2L MUTATED         1        0        2         1         1         0
  SKIV2L WILD-TYPE      63        1       24       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SKIV2L MUTATED           1          0          2          2        2
  SKIV2L WILD-TYPE        17          6         42         31       33
                  vv
clus               STAGE IVA STAGE IVB
  SKIV2L MUTATED           0         0
  SKIV2L WILD-TYPE        12         1
D1446V3, multiclass
            clus
vv           SKIV2L MUTATED SKIV2L WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                2               33
  STAGE IVA               0               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
  SKIV2L MUTATED     0   1   8   3
  SKIV2L WILD-TYPE   9  66 241  38
D1446V4, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  T1              0                9
  T2              1               66
  T3              8              241
  T4              3               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
  SKIV2L MUTATED     5   6   1
  SKIV2L WILD-TYPE 215  75  65
D1446V5, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  N0              5              215
  N1              6               75
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1446V6, binary
                  cls
clus                 0   1
  SKIV2L MUTATED     9   2
  SKIV2L WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED      9    2
  SKIV2L WILD-TYPE  276   46
   clus
vv  SKIV2L MUTATED SKIV2L WILD-TYPE
  0              9              276
  1              2               46
[1] 2 2
[1] FALSE
D1446V7, binary
                  cls
clus                 0   1
  SKIV2L MUTATED     8   4
  SKIV2L WILD-TYPE 162 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED      8    4
  SKIV2L WILD-TYPE  162  193
        clus
vv       SKIV2L MUTATED SKIV2L WILD-TYPE
  FEMALE              8              162
  MALE                4              193
[1] 2 2
[1] FALSE
D1446V8, binary
                  cls
clus                 0   1
  SKIV2L MUTATED    11   0
  SKIV2L WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED     11    0
  SKIV2L WILD-TYPE  289    8
     clus
vv    SKIV2L MUTATED SKIV2L WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1446V9, binary
                  cls
clus                 0   1
  SKIV2L MUTATED    10   2
  SKIV2L WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED     10    2
  SKIV2L WILD-TYPE  304   46
                               clus
vv                              SKIV2L MUTATED SKIV2L WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SKIV2L MUTATED    10   0   0   0
  SKIV2L WILD-TYPE 249   3  22  21
D1446V10, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              0               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"
D1446V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKIV2L MUTATED                                  0     0
  SKIV2L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SKIV2L MUTATED                           3     4
  SKIV2L WILD-TYPE                        16   172
D1446V12, multiclass
                                  clus
vv                                 SKIV2L MUTATED SKIV2L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         4              172
[1] 4 2
[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 = TAPBP MUTATION ANALYSIS
D1447V1, survival
                 sevent
clus2               0   1
  TAPBP MUTATED     2   1
  TAPBP WILD-TYPE 275  77
  TAPBP MUTATED TAPBP WILD-TYPE 
              3             352 
  TAPBP MUTATED TAPBP WILD-TYPE 
              1              77 
$`TAPBP MUTATED`
TCGA-AA-3833 TCGA-AA-A00J TCGA-CM-5862 
       15.95        18.05         5.03 

$`TAPBP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TAPBP MUTATED TAPBP WILD-TYPE 
           5.03            0.00 
  TAPBP MUTATED TAPBP WILD-TYPE 
          18.05          148.01 
  TAPBP MUTATED TAPBP WILD-TYPE 
          15.95           22.09 
[1] "5.0 - 18.1 (15.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1447V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAPBP MUTATED         0        0        0         1         0         0
  TAPBP WILD-TYPE      64        1       26       107         8         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        18          6         43         33       35        11
                 vv
clus              STAGE IVB
  TAPBP MUTATED           0
  TAPBP WILD-TYPE         1
D1447V3, multiclass
            clus
vv           TAPBP MUTATED TAPBP WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  TAPBP MUTATED     0   0   2   1
  TAPBP WILD-TYPE   9  67 247  40
D1447V4, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  T1             0               9
  T2             0              67
  T3             2             247
  T4             1              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
  TAPBP MUTATED     1   2   0
  TAPBP WILD-TYPE 219  79  66
D1447V5, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  N0             1             219
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1447V6, binary
                 cls
clus                0   1
  TAPBP MUTATED     2   1
  TAPBP WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      2    1
  TAPBP WILD-TYPE  283   47
   clus
vv  TAPBP MUTATED TAPBP WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D1447V7, binary
                 cls
clus                0   1
  TAPBP MUTATED     1   2
  TAPBP WILD-TYPE 169 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      1    2
  TAPBP WILD-TYPE  169  195
        clus
vv       TAPBP MUTATED TAPBP WILD-TYPE
  FEMALE             1             169
  MALE               2             195
[1] 2 2
[1] FALSE
D1447V8, binary
                 cls
clus                0   1
  TAPBP MUTATED     3   0
  TAPBP WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      3    0
  TAPBP WILD-TYPE  297    8
     clus
vv    TAPBP MUTATED TAPBP WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1447V9, binary
                 cls
clus                0   1
  TAPBP MUTATED     2   1
  TAPBP WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      2    1
  TAPBP WILD-TYPE  312   47
                               clus
vv                              TAPBP MUTATED TAPBP WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAPBP MUTATED     3   0   0   0
  TAPBP WILD-TYPE 256   3  22  21
D1447V10, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1447V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAPBP MUTATED                                  0     0
  TAPBP WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAPBP MUTATED                           0     1
  TAPBP WILD-TYPE                        19   175
D1447V12, multiclass
[1] "Remove cluster labels:" "TAPBP MUTATED"         
clus
  TAPBP MUTATED TAPBP WILD-TYPE 
              1             205 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6607      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-5913      TCGA-CK-5914 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6626 
"TAPBP WILD-TYPE" 

Clustering(1448) Variable = CDHR3 MUTATION ANALYSIS
D1448V1, survival
                 sevent
clus2               0   1
  CDHR3 MUTATED    12   1
  CDHR3 WILD-TYPE 265  77
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             13             342 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
              1              77 
$`CDHR3 MUTATED`
TCGA-AD-6964 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AD-5900 
       10.88        33.53        22.06         8.38        63.98        12.16 
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        13.35 
TCGA-DM-A1HB 
      135.65 

$`CDHR3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CDHR3 MUTATED CDHR3 WILD-TYPE 
           8.38            0.00 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
         135.65          148.01 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
          13.35           22.09 
[1] "8.4 - 135.7 (13.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3.2"
D1448V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDHR3 MUTATED         1        0        1         9         0         0
  CDHR3 WILD-TYPE      63        1       25        99         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  CDHR3 MUTATED           0
  CDHR3 WILD-TYPE         1
D1448V3, multiclass
            clus
vv           CDHR3 MUTATED CDHR3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              9              99
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CDHR3 MUTATED     0   1  11   1
  CDHR3 WILD-TYPE   9  66 238  40
D1448V4, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             1              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
  CDHR3 MUTATED    11   1   1
  CDHR3 WILD-TYPE 209  80  65
D1448V5, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  N0            11             209
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1448V6, binary
                 cls
clus                0   1
  CDHR3 MUTATED    11   0
  CDHR3 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     11    0
  CDHR3 WILD-TYPE  274   48
   clus
vv  CDHR3 MUTATED CDHR3 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1448V7, binary
                 cls
clus                0   1
  CDHR3 MUTATED     2  11
  CDHR3 WILD-TYPE 168 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED      2   11
  CDHR3 WILD-TYPE  168  186
        clus
vv       CDHR3 MUTATED CDHR3 WILD-TYPE
  FEMALE             2             168
  MALE              11             186
[1] 2 2
[1] FALSE
D1448V8, binary
                 cls
clus                0   1
  CDHR3 MUTATED    12   0
  CDHR3 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     12    0
  CDHR3 WILD-TYPE  288    8
     clus
vv    CDHR3 MUTATED CDHR3 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1448V9, binary
                 cls
clus                0   1
  CDHR3 MUTATED     9   3
  CDHR3 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED      9    3
  CDHR3 WILD-TYPE  305   45
                               clus
vv                              CDHR3 MUTATED CDHR3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDHR3 MUTATED     9   0   0   1
  CDHR3 WILD-TYPE 250   3  22  20
D1448V10, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D1448V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDHR3 MUTATED                                  0     1
  CDHR3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDHR3 MUTATED                           2     9
  CDHR3 WILD-TYPE                        17   167
D1448V12, multiclass
                                  clus
vv                                 CDHR3 MUTATED CDHR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(1449) Variable = TJP1 MUTATION ANALYSIS
D1449V1, survival
                sevent
clus2              0   1
  TJP1 MUTATED    12   6
  TJP1 WILD-TYPE 265  72
  TJP1 MUTATED TJP1 WILD-TYPE 
            18            337 
  TJP1 MUTATED TJP1 WILD-TYPE 
             6             72 
$`TJP1 MUTATED`
TCGA-AA-3715 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3660 
       19.04        25.08        26.17        32.71         3.02        78.08 
TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AY-6196 TCGA-AZ-5403 
        6.97        53.00        25.02         4.01         0.20        62.79 
TCGA-CA-6718 TCGA-D5-5539 TCGA-D5-6538 TCGA-D5-6928 TCGA-DM-A1D6 TCGA-DM-A1HB 
       10.06        19.59        17.13        11.64        49.91       135.65 

$`TJP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TJP1 MUTATED TJP1 WILD-TYPE 
           0.2            0.0 
  TJP1 MUTATED TJP1 WILD-TYPE 
        135.65         148.01 
  TJP1 MUTATED TJP1 WILD-TYPE 
        22.305         22.060 
[1] "0.2 - 135.7 (22.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1449V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TJP1 MUTATED         0        0        6         4         1         1
  TJP1 WILD-TYPE      64        1       20       104         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TJP1 MUTATED           0          1          3          1        0         0
  TJP1 WILD-TYPE        18          5         41         32       35        12
                vv
clus             STAGE IVB
  TJP1 MUTATED           0
  TJP1 WILD-TYPE         1
D1449V3, multiclass
            clus
vv           TJP1 MUTATED TJP1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              6             20
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TJP1 MUTATED     0   1  15   2
  TJP1 WILD-TYPE   9  66 234  39
D1449V4, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           15            234
  T4            2             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
  TJP1 MUTATED    13   3   2
  TJP1 WILD-TYPE 207  78  64
D1449V5, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  N0           13            207
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1449V6, binary
                cls
clus               0   1
  TJP1 MUTATED    15   0
  TJP1 WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     15    0
  TJP1 WILD-TYPE  270   48
   clus
vv  TJP1 MUTATED TJP1 WILD-TYPE
  0           15            270
  1            0             48
[1] 2 2
[1] FALSE
D1449V7, binary
                cls
clus               0   1
  TJP1 MUTATED     4  14
  TJP1 WILD-TYPE 166 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED      4   14
  TJP1 WILD-TYPE  166  183
        clus
vv       TJP1 MUTATED TJP1 WILD-TYPE
  FEMALE            4            166
  MALE             14            183
[1] 2 2
[1] FALSE
D1449V8, binary
                cls
clus               0   1
  TJP1 MUTATED    14   0
  TJP1 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     14    0
  TJP1 WILD-TYPE  286    8
     clus
vv    TJP1 MUTATED TJP1 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1449V9, binary
                cls
clus               0   1
  TJP1 MUTATED    12   5
  TJP1 WILD-TYPE 302  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     12    5
  TJP1 WILD-TYPE  302   43
                               clus
vv                              TJP1 MUTATED TJP1 WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TJP1 MUTATED    12   0   0   1
  TJP1 WILD-TYPE 247   3  22  20
D1449V10, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            1             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"
D1449V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TJP1 MUTATED                                  0     1
  TJP1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TJP1 MUTATED                           0    10
  TJP1 WILD-TYPE                        19   166
D1449V12, multiclass
                                  clus
vv                                 TJP1 MUTATED TJP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(1450) Variable = DPPA2 MUTATION ANALYSIS
D1450V1, survival
                 sevent
clus2               0   1
  DPPA2 MUTATED     4   3
  DPPA2 WILD-TYPE 273  75
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              7             348 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              3              75 
$`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 
       15.02 

$`DPPA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DPPA2 MUTATED DPPA2 WILD-TYPE 
           6.97            0.00 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
          21.14          148.01 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
          14.53           22.39 
[1] "7.0 - 21.1 (14.5)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "3.4"
D1450V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPPA2 MUTATED         2        0        1         3         0         0
  DPPA2 WILD-TYPE      62        1       25       105         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  DPPA2 MUTATED           0
  DPPA2 WILD-TYPE         1
D1450V3, multiclass
            clus
vv           DPPA2 MUTATED DPPA2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DPPA2 MUTATED     1   1   4   1
  DPPA2 WILD-TYPE   8  66 245  40
D1450V4, multiclass
    clus
vv   DPPA2 MUTATED DPPA2 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             4             245
  T4             1              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
  DPPA2 MUTATED     6   1   0
  DPPA2 WILD-TYPE 214  80  66
D1450V5, multiclass
    clus
vv   DPPA2 MUTATED DPPA2 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1450V6, binary
                 cls
clus                0   1
  DPPA2 MUTATED     7   0
  DPPA2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      7    0
  DPPA2 WILD-TYPE  278   48
   clus
vv  DPPA2 MUTATED DPPA2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1450V7, binary
                 cls
clus                0   1
  DPPA2 MUTATED     2   5
  DPPA2 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      2    5
  DPPA2 WILD-TYPE  168  192
        clus
vv       DPPA2 MUTATED DPPA2 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1450V8, binary
                 cls
clus                0   1
  DPPA2 MUTATED     7   0
  DPPA2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      7    0
  DPPA2 WILD-TYPE  293    8
     clus
vv    DPPA2 MUTATED DPPA2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1450V9, binary
                 cls
clus                0   1
  DPPA2 MUTATED     5   2
  DPPA2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      5    2
  DPPA2 WILD-TYPE  309   46
                               clus
vv                              DPPA2 MUTATED DPPA2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DPPA2 MUTATED     3   0   0   3
  DPPA2 WILD-TYPE 256   3  22  18
D1450V10, multiclass
    clus
vv   DPPA2 MUTATED DPPA2 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             3              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"
D1450V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPPA2 MUTATED                                  0     2
  DPPA2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPPA2 MUTATED                           0     3
  DPPA2 WILD-TYPE                        19   173
D1450V12, multiclass
                                  clus
vv                                 DPPA2 MUTATED DPPA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = HIST1H4L MUTATION ANALYSIS
D1451V1, survival
                    sevent
clus2                  0   1
  HIST1H4L MUTATED     3   3
  HIST1H4L WILD-TYPE 274  75
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 6                349 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 3                 75 
$`HIST1H4L MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-A6-6142 TCGA-CK-5916 TCGA-CM-6170 TCGA-DM-A1D6 
       19.04        35.80        25.08        21.14        15.02        49.91 

$`HIST1H4L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
             15.02               0.00 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
             49.91             148.01 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
             23.11              22.06 
[1] "15.0 - 49.9 (23.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1451V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H4L MUTATED         2        0        1         2         0         0
  HIST1H4L WILD-TYPE      62        1       25       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H4L MUTATED           0          0          0          0        0
  HIST1H4L WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H4L MUTATED           1         0
  HIST1H4L WILD-TYPE        11         1
D1451V3, multiclass
            clus
vv           HIST1H4L MUTATED HIST1H4L WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  HIST1H4L MUTATED     1   1   4   0
  HIST1H4L WILD-TYPE   8  66 245  41
D1451V4, multiclass
    clus
vv   HIST1H4L MUTATED HIST1H4L WILD-TYPE
  T1                1                  8
  T2                1                 66
  T3                4                245
  T4                0                 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
  HIST1H4L MUTATED     5   1   0
  HIST1H4L WILD-TYPE 215  80  66
D1451V5, multiclass
    clus
vv   HIST1H4L MUTATED HIST1H4L WILD-TYPE
  N0                5                215
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1451V6, binary
                    cls
clus                   0   1
  HIST1H4L MUTATED     5   1
  HIST1H4L WILD-TYPE 280  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4L MUTATED      5    1
  HIST1H4L WILD-TYPE  280   47
   clus
vv  HIST1H4L MUTATED HIST1H4L WILD-TYPE
  0                5                280
  1                1                 47
[1] 2 2
[1] FALSE
D1451V7, binary
                    cls
clus                   0   1
  HIST1H4L MUTATED     4   2
  HIST1H4L WILD-TYPE 166 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4L MUTATED      4    2
  HIST1H4L WILD-TYPE  166  195
        clus
vv       HIST1H4L MUTATED HIST1H4L WILD-TYPE
  FEMALE                4                166
  MALE                  2                195
[1] 2 2
[1] FALSE
D1451V8, binary
                    cls
clus                   0   1
  HIST1H4L MUTATED     5   0
  HIST1H4L WILD-TYPE 295   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4L MUTATED      5    0
  HIST1H4L WILD-TYPE  295    8
     clus
vv    HIST1H4L MUTATED HIST1H4L WILD-TYPE
  NO                 5                295
  YES                0                  8
[1] 2 2
[1] FALSE
D1451V9, binary
                    cls
clus                   0   1
  HIST1H4L MUTATED     5   1
  HIST1H4L WILD-TYPE 309  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4L MUTATED      5    1
  HIST1H4L WILD-TYPE  309   47
                               clus
vv                              HIST1H4L MUTATED HIST1H4L WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H4L MUTATED     3   0   0   1
  HIST1H4L WILD-TYPE 256   3  22  20
D1451V10, multiclass
    clus
vv   HIST1H4L MUTATED HIST1H4L WILD-TYPE
  R0                3                256
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1451V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H4L MUTATED                                  0     0
  HIST1H4L WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H4L MUTATED                           0     5
  HIST1H4L WILD-TYPE                        19   171
D1451V12, multiclass
                                  clus
vv                                 HIST1H4L MUTATED HIST1H4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = AFF3 MUTATION ANALYSIS
D1452V1, survival
                sevent
clus2              0   1
  AFF3 MUTATED    17   5
  AFF3 WILD-TYPE 260  73
  AFF3 MUTATED AFF3 WILD-TYPE 
            22            333 
  AFF3 MUTATED AFF3 WILD-TYPE 
             5             73 
$`AFF3 MUTATED`
TCGA-AZ-6601 TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 
      100.01        23.61        63.98         1.02         0.00        53.00 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A02O 
       25.02        18.05         4.01        34.98        38.07         0.92 
TCGA-AA-A02Y TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6168 
       39.98        12.16        58.39        12.76        30.08        12.99 
TCGA-D5-6930 TCGA-DM-A1DB TCGA-DM-A28H TCGA-G4-6309 
       13.35        44.32       117.07        85.48 

$`AFF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A03F 
       39.98         2.01         5.03        14.01        41.00        18.05 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50       131.51       135.65       139.17        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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  AFF3 MUTATED AFF3 WILD-TYPE 
             0              0 
  AFF3 MUTATED AFF3 WILD-TYPE 
        117.07         148.01 
  AFF3 MUTATED AFF3 WILD-TYPE 
         27.55          21.99 
[1] "0.0 - 117.1 (27.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1452V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AFF3 MUTATED         3        0        4         7         2         0
  AFF3 WILD-TYPE      61        1       22       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFF3 MUTATED           1          0          2          1        0         1
  AFF3 WILD-TYPE        17          6         42         32       35        11
                vv
clus             STAGE IVB
  AFF3 MUTATED           0
  AFF3 WILD-TYPE         1
D1452V3, multiclass
            clus
vv           AFF3 MUTATED AFF3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  AFF3 MUTATED     0   4  15   3
  AFF3 WILD-TYPE   9  63 234  38
D1452V4, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           15            234
  T4            3             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
  AFF3 MUTATED    17   3   2
  AFF3 WILD-TYPE 203  78  64
D1452V5, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  N0           17            203
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1452V6, binary
                cls
clus               0   1
  AFF3 MUTATED    19   1
  AFF3 WILD-TYPE 266  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     19    1
  AFF3 WILD-TYPE  266   47
   clus
vv  AFF3 MUTATED AFF3 WILD-TYPE
  0           19            266
  1            1             47
[1] 2 2
[1] FALSE
D1452V7, binary
                cls
clus               0   1
  AFF3 MUTATED     7  15
  AFF3 WILD-TYPE 163 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED      7   15
  AFF3 WILD-TYPE  163  182
        clus
vv       AFF3 MUTATED AFF3 WILD-TYPE
  FEMALE            7            163
  MALE             15            182
[1] 2 2
[1] FALSE
D1452V8, binary
                cls
clus               0   1
  AFF3 MUTATED    17   0
  AFF3 WILD-TYPE 283   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     17    0
  AFF3 WILD-TYPE  283    8
     clus
vv    AFF3 MUTATED AFF3 WILD-TYPE
  NO            17            283
  YES            0              8
[1] 2 2
[1] FALSE
D1452V9, binary
                cls
clus               0   1
  AFF3 MUTATED    16   6
  AFF3 WILD-TYPE 298  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     16    6
  AFF3 WILD-TYPE  298   42
                               clus
vv                              AFF3 MUTATED AFF3 WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AFF3 MUTATED    16   0   0   1
  AFF3 WILD-TYPE 243   3  22  20
D1452V10, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            1             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"
D1452V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AFF3 MUTATED                                  0     1
  AFF3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AFF3 MUTATED                           2     8
  AFF3 WILD-TYPE                        17   168
D1452V12, multiclass
                                  clus
vv                                 AFF3 MUTATED AFF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       8            168
[1] 4 2
[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 = TRAF3IP3 MUTATION ANALYSIS
D1453V1, survival
                    sevent
clus2                  0   1
  TRAF3IP3 MUTATED     8   3
  TRAF3IP3 WILD-TYPE 269  75
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                11                344 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                 3                 75 
$`TRAF3IP3 MUTATED`
TCGA-AA-3525 TCGA-AA-3672 TCGA-A6-2676 TCGA-AA-3811 TCGA-CA-6717 TCGA-CA-6718 
        8.05         0.92        42.90        10.06        12.76        10.06 
TCGA-CM-5860 TCGA-CM-5864 TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1HB 
       32.02        15.02        25.48        13.35       135.65 

$`TRAF3IP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
              0.92               0.00 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
            135.65             148.01 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
             13.35              22.09 
[1] "0.9 - 135.7 (13.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1453V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAF3IP3 MUTATED         1        0        0         5         1         0
  TRAF3IP3 WILD-TYPE      63        1       26       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAF3IP3 MUTATED           2          0          2          0        0
  TRAF3IP3 WILD-TYPE        16          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  TRAF3IP3 MUTATED           0         0
  TRAF3IP3 WILD-TYPE        12         1
D1453V3, multiclass
            clus
vv           TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 2                 16
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  TRAF3IP3 MUTATED     0   1   9   2
  TRAF3IP3 WILD-TYPE   9  66 240  39
D1453V4, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                9                240
  T4                2                 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
  TRAF3IP3 MUTATED     8   3   1
  TRAF3IP3 WILD-TYPE 212  78  65
D1453V5, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  N0                8                212
  N1                3                 78
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1453V6, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED    12   0
  TRAF3IP3 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED     12    0
  TRAF3IP3 WILD-TYPE  273   48
   clus
vv  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  0               12                273
  1                0                 48
[1] 2 2
[1] FALSE
D1453V7, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED     5   7
  TRAF3IP3 WILD-TYPE 165 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED      5    7
  TRAF3IP3 WILD-TYPE  165  190
        clus
vv       TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  FEMALE                5                165
  MALE                  7                190
[1] 2 2
[1] FALSE
D1453V8, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED    10   0
  TRAF3IP3 WILD-TYPE 290   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED     10    0
  TRAF3IP3 WILD-TYPE  290    8
     clus
vv    TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  NO                10                290
  YES                0                  8
[1] 2 2
[1] FALSE
D1453V9, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED     9   2
  TRAF3IP3 WILD-TYPE 305  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED      9    2
  TRAF3IP3 WILD-TYPE  305   46
                               clus
vv                              TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TRAF3IP3 MUTATED     9   0   0   2
  TRAF3IP3 WILD-TYPE 250   3  22  19
D1453V10, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1453V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAF3IP3 MUTATED                                  0     2
  TRAF3IP3 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TRAF3IP3 MUTATED                           0     6
  TRAF3IP3 WILD-TYPE                        19   170
D1453V12, multiclass
                                  clus
vv                                 TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = CDH24 MUTATION ANALYSIS
D1454V1, survival
                 sevent
clus2               0   1
  CDH24 MUTATED    10   2
  CDH24 WILD-TYPE 267  76
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             343 
  CDH24 MUTATED CDH24 WILD-TYPE 
              2              76 
$`CDH24 MUTATED`
TCGA-A6-4105 TCGA-AA-3672 TCGA-AA-3713 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 
       14.53         0.92        19.04        22.06        19.66         3.02 
TCGA-AA-3710 TCGA-AA-3966 TCGA-AA-A00U TCGA-AA-A010 TCGA-AY-6386 TCGA-CK-6747 
       26.99         2.01        17.03        34.98        17.82        82.95 

$`CDH24 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       27.02        42.02         0.99        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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           22.36 
[1] "0.9 - 83.0 (18.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1"  
D1454V2, continuous
                 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      64        1       25       103         7         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        17          6         42         32       34        12
                 vv
clus              STAGE IVB
  CDH24 MUTATED           0
  CDH24 WILD-TYPE         1
D1454V3, multiclass
            clus
vv           CDH24 MUTATED CDH24 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  CDH24 MUTATED     0   0  10   2
  CDH24 WILD-TYPE   9  67 239  39
D1454V4, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            10             239
  T4             2              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
  CDH24 MUTATED     8   4   0
  CDH24 WILD-TYPE 212  77  66
D1454V5, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1454V6, binary
                 cls
clus                0   1
  CDH24 MUTATED     9   1
  CDH24 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      9    1
  CDH24 WILD-TYPE  276   47
   clus
vv  CDH24 MUTATED CDH24 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1454V7, binary
                 cls
clus                0   1
  CDH24 MUTATED     8   4
  CDH24 WILD-TYPE 162 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      8    4
  CDH24 WILD-TYPE  162  193
        clus
vv       CDH24 MUTATED CDH24 WILD-TYPE
  FEMALE             8             162
  MALE               4             193
[1] 2 2
[1] FALSE
D1454V8, binary
                 cls
clus                0   1
  CDH24 MUTATED    10   1
  CDH24 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     10    1
  CDH24 WILD-TYPE  290    7
     clus
vv    CDH24 MUTATED CDH24 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1454V9, binary
                 cls
clus                0   1
  CDH24 MUTATED    10   2
  CDH24 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     10    2
  CDH24 WILD-TYPE  304   46
                               clus
vv                              CDH24 MUTATED CDH24 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH24 MUTATED     8   0   1   1
  CDH24 WILD-TYPE 251   3  21  20
D1454V10, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             1              21
  RX             1              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"
D1454V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH24 MUTATED                                  0     0
  CDH24 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH24 MUTATED                           1     4
  CDH24 WILD-TYPE                        18   172
D1454V12, multiclass
                                  clus
vv                                 CDH24 MUTATED CDH24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = TYW3 MUTATION ANALYSIS
D1455V1, survival
                sevent
clus2              0   1
  TYW3 MUTATED     3   2
  TYW3 WILD-TYPE 274  76
  TYW3 MUTATED TYW3 WILD-TYPE 
             5            350 
  TYW3 MUTATED TYW3 WILD-TYPE 
             2             76 
$`TYW3 MUTATED`
TCGA-AD-6964 TCGA-AZ-6600 TCGA-CM-6170 TCGA-D5-6536 TCGA-F4-6805 
       10.88        12.10        15.02        17.85        34.42 

$`TYW3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TYW3 MUTATED TYW3 WILD-TYPE 
         10.88           0.00 
  TYW3 MUTATED TYW3 WILD-TYPE 
         34.42         148.01 
  TYW3 MUTATED TYW3 WILD-TYPE 
         15.02          22.09 
[1] "10.9 - 34.4 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1455V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TYW3 MUTATED         1        0        0         2         0         0
  TYW3 WILD-TYPE      63        1       26       106         8         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        17          6         44         33       34        12
                vv
clus             STAGE IVB
  TYW3 MUTATED           0
  TYW3 WILD-TYPE         1
D1455V3, multiclass
            clus
vv           TYW3 MUTATED TYW3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  TYW3 MUTATED     0   1   3   2
  TYW3 WILD-TYPE   9  66 246  39
D1455V4, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            2             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
  TYW3 MUTATED     3   1   2
  TYW3 WILD-TYPE 217  80  64
D1455V5, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  N0            3            217
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1455V6, binary
                cls
clus               0   1
  TYW3 MUTATED     4   1
  TYW3 WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      4    1
  TYW3 WILD-TYPE  281   47
   clus
vv  TYW3 MUTATED TYW3 WILD-TYPE
  0            4            281
  1            1             47
[1] 2 2
[1] FALSE
D1455V7, binary
                cls
clus               0   1
  TYW3 MUTATED     2   4
  TYW3 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      2    4
  TYW3 WILD-TYPE  168  193
        clus
vv       TYW3 MUTATED TYW3 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1455V8, binary
                cls
clus               0   1
  TYW3 MUTATED     5   0
  TYW3 WILD-TYPE 295   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      5    0
  TYW3 WILD-TYPE  295    8
     clus
vv    TYW3 MUTATED TYW3 WILD-TYPE
  NO             5            295
  YES            0              8
[1] 2 2
[1] FALSE
D1455V9, binary
                cls
clus               0   1
  TYW3 MUTATED     6   0
  TYW3 WILD-TYPE 308  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      6    0
  TYW3 WILD-TYPE  308   48
                               clus
vv                              TYW3 MUTATED TYW3 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TYW3 MUTATED     4   0   0   0
  TYW3 WILD-TYPE 255   3  22  21
D1455V10, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D1455V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TYW3 MUTATED                                  0     0
  TYW3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TYW3 MUTATED                           1     4
  TYW3 WILD-TYPE                        18   172
D1455V12, multiclass
                                  clus
vv                                 TYW3 MUTATED TYW3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = ZNF197 MUTATION ANALYSIS
D1456V1, survival
                  sevent
clus2                0   1
  ZNF197 MUTATED     7   2
  ZNF197 WILD-TYPE 270  76
  ZNF197 MUTATED ZNF197 WILD-TYPE 
               9              346 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
               2               76 
$`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 
       23.05        16.14        24.43 

$`ZNF197 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF197 MUTATED ZNF197 WILD-TYPE 
            3.02             0.00 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
           63.98           148.01 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
          23.050           22.045 
[1] "3.0 - 64.0 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1456V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF197 MUTATED         1        0        3         3         1         0
  ZNF197 WILD-TYPE      63        1       23       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF197 MUTATED           0          0          0          0        0
  ZNF197 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF197 MUTATED           0         0
  ZNF197 WILD-TYPE        12         1
D1456V3, multiclass
            clus
vv           ZNF197 MUTATED ZNF197 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF197 MUTATED     0   2   6   1
  ZNF197 WILD-TYPE   9  65 243  40
D1456V4, multiclass
    clus
vv   ZNF197 MUTATED ZNF197 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              6              243
  T4              1               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
  ZNF197 MUTATED     9   0   0
  ZNF197 WILD-TYPE 211  81  66
D1456V5, multiclass
    clus
vv   ZNF197 MUTATED ZNF197 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1456V6, binary
                  cls
clus                 0   1
  ZNF197 MUTATED     8   0
  ZNF197 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED      8    0
  ZNF197 WILD-TYPE  277   48
   clus
vv  ZNF197 MUTATED ZNF197 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1456V7, binary
                  cls
clus                 0   1
  ZNF197 MUTATED     2   7
  ZNF197 WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED      2    7
  ZNF197 WILD-TYPE  168  190
        clus
vv       ZNF197 MUTATED ZNF197 WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D1456V8, binary
                  cls
clus                 0   1
  ZNF197 MUTATED     8   0
  ZNF197 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED      8    0
  ZNF197 WILD-TYPE  292    8
     clus
vv    ZNF197 MUTATED ZNF197 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1456V9, binary
                  cls
clus                 0   1
  ZNF197 MUTATED     8   1
  ZNF197 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED      8    1
  ZNF197 WILD-TYPE  306   47
                               clus
vv                              ZNF197 MUTATED ZNF197 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF197 MUTATED     6   0   0   0
  ZNF197 WILD-TYPE 253   3  22  21
D1456V10, multiclass
    clus
vv   ZNF197 MUTATED ZNF197 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1456V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF197 MUTATED                                  0     0
  ZNF197 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF197 MUTATED                           1     3
  ZNF197 WILD-TYPE                        18   173
D1456V12, multiclass
                                  clus
vv                                 ZNF197 MUTATED ZNF197 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = ESCO1 MUTATION ANALYSIS
D1457V1, survival
                 sevent
clus2               0   1
  ESCO1 MUTATED     9   3
  ESCO1 WILD-TYPE 268  75
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             12             343 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              3              75 
$`ESCO1 MUTATED`
TCGA-AA-3697 TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3947 
       85.05        32.75         8.38        63.98        29.95        33.01 
TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       25.02        83.24        58.39        49.41        12.76        21.14 

$`ESCO1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6142 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ESCO1 MUTATED ESCO1 WILD-TYPE 
           8.38            0.00 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
          85.05          148.01 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
          32.88           21.99 
[1] "8.4 - 85.0 (32.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1457V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESCO1 MUTATED         1        0        3         6         2         0
  ESCO1 WILD-TYPE      63        1       23       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESCO1 MUTATED           0          0          0          0        0         0
  ESCO1 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  ESCO1 MUTATED           0
  ESCO1 WILD-TYPE         1
D1457V3, multiclass
            clus
vv           ESCO1 MUTATED ESCO1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ESCO1 MUTATED     1   1   9   2
  ESCO1 WILD-TYPE   8  66 240  39
D1457V4, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             9             240
  T4             2              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
  ESCO1 MUTATED    13   0   0
  ESCO1 WILD-TYPE 207  81  66
D1457V5, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  N0            13             207
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1457V6, binary
                 cls
clus                0   1
  ESCO1 MUTATED    11   0
  ESCO1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED     11    0
  ESCO1 WILD-TYPE  274   48
   clus
vv  ESCO1 MUTATED ESCO1 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1457V7, binary
                 cls
clus                0   1
  ESCO1 MUTATED     6   7
  ESCO1 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      6    7
  ESCO1 WILD-TYPE  164  190
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1457V8, binary
                 cls
clus                0   1
  ESCO1 MUTATED    12   0
  ESCO1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED     12    0
  ESCO1 WILD-TYPE  288    8
     clus
vv    ESCO1 MUTATED ESCO1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1457V9, binary
                 cls
clus                0   1
  ESCO1 MUTATED     9   4
  ESCO1 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      9    4
  ESCO1 WILD-TYPE  305   44
                               clus
vv                              ESCO1 MUTATED ESCO1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESCO1 MUTATED     8   0   0   2
  ESCO1 WILD-TYPE 251   3  22  19
D1457V10, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D1457V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESCO1 MUTATED                                  0     2
  ESCO1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESCO1 MUTATED                           1     4
  ESCO1 WILD-TYPE                        18   172
D1457V12, multiclass
                                  clus
vv                                 ESCO1 MUTATED ESCO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[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 = NT5C3L MUTATION ANALYSIS
D1458V1, survival
                  sevent
clus2                0   1
  NT5C3L MUTATED     5   0
  NT5C3L WILD-TYPE 272  78
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               5              350 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               0               78 
$`NT5C3L MUTATED`
TCGA-A6-6780 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A01R TCGA-CM-6169 
       20.12        26.01        25.02        35.01        13.02 

$`NT5C3L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NT5C3L MUTATED NT5C3L WILD-TYPE 
           13.02             0.00 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
           35.01           148.01 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
          25.020           22.045 
[1] "13.0 - 35.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1458V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NT5C3L MUTATED         0        0        0         2         0         0
  NT5C3L WILD-TYPE      64        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5C3L MUTATED           1          0          1          0        0
  NT5C3L WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  NT5C3L MUTATED           0         0
  NT5C3L WILD-TYPE        12         1
D1458V3, multiclass
            clus
vv           NT5C3L MUTATED NT5C3L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  NT5C3L MUTATED     0   1   4   0
  NT5C3L WILD-TYPE   9  66 245  41
D1458V4, multiclass
    clus
vv   NT5C3L MUTATED NT5C3L WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              0               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
  NT5C3L MUTATED     3   1   1
  NT5C3L WILD-TYPE 217  80  65
D1458V5, multiclass
    clus
vv   NT5C3L MUTATED NT5C3L WILD-TYPE
  N0              3              217
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1458V6, binary
                  cls
clus                 0   1
  NT5C3L MUTATED     3   0
  NT5C3L WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5C3L MUTATED      3    0
  NT5C3L WILD-TYPE  282   48
   clus
vv  NT5C3L MUTATED NT5C3L WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D1458V7, binary
                  cls
clus                 0   1
  NT5C3L MUTATED     1   4
  NT5C3L WILD-TYPE 169 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5C3L MUTATED      1    4
  NT5C3L WILD-TYPE  169  193
        clus
vv       NT5C3L MUTATED NT5C3L WILD-TYPE
  FEMALE              1              169
  MALE                4              193
[1] 2 2
[1] FALSE
D1458V8, binary
                  cls
clus                 0   1
  NT5C3L MUTATED     4   1
  NT5C3L WILD-TYPE 296   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5C3L MUTATED      4    1
  NT5C3L WILD-TYPE  296    7
     clus
vv    NT5C3L MUTATED NT5C3L WILD-TYPE
  NO               4              296
  YES              1                7
[1] 2 2
[1] FALSE
D1458V9, binary
                  cls
clus                 0   1
  NT5C3L MUTATED     2   3
  NT5C3L WILD-TYPE 312  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5C3L MUTATED      2    3
  NT5C3L WILD-TYPE  312   45
                               clus
vv                              NT5C3L MUTATED NT5C3L WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NT5C3L MUTATED     3   0   0   0
  NT5C3L WILD-TYPE 256   3  22  21
D1458V10, multiclass
    clus
vv   NT5C3L MUTATED NT5C3L WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1458V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NT5C3L MUTATED                                  0     0
  NT5C3L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NT5C3L MUTATED                           1     1
  NT5C3L WILD-TYPE                        18   175
D1458V12, multiclass
[1] "Remove cluster labels:" "NT5C3L MUTATED"        
clus
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6781       TCGA-A6-6782 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 

Clustering(1459) Variable = KIAA1919 MUTATION ANALYSIS
D1459V1, survival
                    sevent
clus2                  0   1
  KIAA1919 MUTATED     6   3
  KIAA1919 WILD-TYPE 271  75
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                346 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 3                 75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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-6748 
       85.45        15.62        51.32        21.99        21.14         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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             22.075 
[1] "6.2 - 83.0 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1459V2, continuous
                    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      63        1       26       102         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1919 MUTATED           0          0          0          0        0
  KIAA1919 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1919 MUTATED           0         0
  KIAA1919 WILD-TYPE        12         1
D1459V3, multiclass
            clus
vv           KIAA1919 MUTATED KIAA1919 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 6                102
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA1919 MUTATED     0   1   6   2
  KIAA1919 WILD-TYPE   9  66 243  39
D1459V4, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                6                243
  T4                2                 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
  KIAA1919 MUTATED     9   0   0
  KIAA1919 WILD-TYPE 211  81  66
D1459V5, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  N0                9                211
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1459V6, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     8   0
  KIAA1919 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      8    0
  KIAA1919 WILD-TYPE  277   48
   clus
vv  KIAA1919 MUTATED KIAA1919 WILD-TYPE
  0                8                277
  1                0                 48
[1] 2 2
[1] FALSE
D1459V7, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     5   4
  KIAA1919 WILD-TYPE 165 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      5    4
  KIAA1919 WILD-TYPE  165  193
        clus
vv       KIAA1919 MUTATED KIAA1919 WILD-TYPE
  FEMALE                5                165
  MALE                  4                193
[1] 2 2
[1] FALSE
D1459V8, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     9   0
  KIAA1919 WILD-TYPE 291   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      9    0
  KIAA1919 WILD-TYPE  291    8
     clus
vv    KIAA1919 MUTATED KIAA1919 WILD-TYPE
  NO                 9                291
  YES                0                  8
[1] 2 2
[1] FALSE
D1459V9, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     8   1
  KIAA1919 WILD-TYPE 306  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      8    1
  KIAA1919 WILD-TYPE  306   47
                               clus
vv                              KIAA1919 MUTATED KIAA1919 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1919 MUTATED     6   0   0   3
  KIAA1919 WILD-TYPE 253   3  22  18
D1459V10, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D1459V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1919 MUTATED                                  0     2
  KIAA1919 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1919 MUTATED                           0     6
  KIAA1919 WILD-TYPE                        19   170
D1459V12, multiclass
                                  clus
vv                                 KIAA1919 MUTATED KIAA1919 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = EPB41L4B MUTATION ANALYSIS
D1460V1, survival
                    sevent
clus2                  0   1
  EPB41L4B MUTATED     6   3
  EPB41L4B WILD-TYPE 271  75
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 9                346 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 3                 75 
$`EPB41L4B MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-6599 
       63.98         6.97        33.04         4.01        35.01         6.77 
TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6537 
       51.32        15.02         4.80 

$`EPB41L4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
              4.01               0.00 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
             63.98             148.01 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
            15.020             22.075 
[1] "4.0 - 64.0 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1460V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPB41L4B MUTATED         2        0        3         4         1         0
  EPB41L4B WILD-TYPE      62        1       23       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB41L4B MUTATED           1          0          1          0        0
  EPB41L4B WILD-TYPE        17          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  EPB41L4B MUTATED           0         0
  EPB41L4B WILD-TYPE        12         1
D1460V3, multiclass
            clus
vv           EPB41L4B MUTATED EPB41L4B WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                 4                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  EPB41L4B MUTATED     0   2   8   2
  EPB41L4B WILD-TYPE   9  65 241  39
D1460V4, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                8                241
  T4                2                 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
  EPB41L4B MUTATED    10   1   1
  EPB41L4B WILD-TYPE 210  80  65
D1460V5, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  N0               10                210
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1460V6, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED     8   0
  EPB41L4B WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      8    0
  EPB41L4B WILD-TYPE  277   48
   clus
vv  EPB41L4B MUTATED EPB41L4B WILD-TYPE
  0                8                277
  1                0                 48
[1] 2 2
[1] FALSE
D1460V7, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED     5   7
  EPB41L4B WILD-TYPE 165 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      5    7
  EPB41L4B WILD-TYPE  165  190
        clus
vv       EPB41L4B MUTATED EPB41L4B WILD-TYPE
  FEMALE                5                165
  MALE                  7                190
[1] 2 2
[1] FALSE
D1460V8, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED     7   1
  EPB41L4B WILD-TYPE 293   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      7    1
  EPB41L4B WILD-TYPE  293    7
     clus
vv    EPB41L4B MUTATED EPB41L4B WILD-TYPE
  NO                 7                293
  YES                1                  7
[1] 2 2
[1] FALSE
D1460V9, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED    10   2
  EPB41L4B WILD-TYPE 304  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED     10    2
  EPB41L4B WILD-TYPE  304   46
                               clus
vv                              EPB41L4B MUTATED EPB41L4B WILD-TYPE
  COLON ADENOCARCINOMA                        10                304
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  EPB41L4B MUTATED     9   0   0   2
  EPB41L4B WILD-TYPE 250   3  22  19
D1460V10, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1460V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPB41L4B MUTATED                                  0     0
  EPB41L4B WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  EPB41L4B MUTATED                           0     5
  EPB41L4B WILD-TYPE                        19   171
D1460V12, multiclass
                                  clus
vv                                 EPB41L4B MUTATED EPB41L4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = SRL MUTATION ANALYSIS
D1461V1, survival
               sevent
clus2             0   1
  SRL MUTATED     8   4
  SRL WILD-TYPE 269  74
  SRL MUTATED SRL WILD-TYPE 
           12           343 
  SRL MUTATED SRL WILD-TYPE 
            4            74 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-A1HA TCGA-DM-A282 
       13.32        12.59       140.38         7.50       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.09 
[1] "4.0 - 135.7 (16.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1461V2, continuous
               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      62        1       25       102         7         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        18          6         42         33       35        12
               vv
clus            STAGE IVB
  SRL MUTATED           0
  SRL WILD-TYPE         1
D1461V3, multiclass
            clus
vv           SRL MUTATED SRL WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            6           102
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  SRL MUTATED     0   2   9   1
  SRL WILD-TYPE   9  65 240  40
D1461V4, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  T1           0             9
  T2           2            65
  T3           9           240
  T4           1            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
  SRL MUTATED    10   2   0
  SRL WILD-TYPE 210  79  66
D1461V5, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  N0          10           210
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1461V6, binary
               cls
clus              0   1
  SRL MUTATED     9   0
  SRL WILD-TYPE 276  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      9    0
  SRL WILD-TYPE  276   48
   clus
vv  SRL MUTATED SRL WILD-TYPE
  0           9           276
  1           0            48
[1] 2 2
[1] FALSE
D1461V7, binary
               cls
clus              0   1
  SRL MUTATED     0  12
  SRL WILD-TYPE 170 185
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      0   12
  SRL WILD-TYPE  170  185
        clus
vv       SRL MUTATED SRL WILD-TYPE
  FEMALE           0           170
  MALE            12           185
[1] 2 2
[1] FALSE
D1461V8, binary
               cls
clus              0   1
  SRL MUTATED     8   0
  SRL WILD-TYPE 292   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      8    0
  SRL WILD-TYPE  292    8
     clus
vv    SRL MUTATED SRL WILD-TYPE
  NO            8           292
  YES           0             8
[1] 2 2
[1] FALSE
D1461V9, binary
               cls
clus              0   1
  SRL MUTATED     8   3
  SRL WILD-TYPE 306  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      8    3
  SRL WILD-TYPE  306   45
                               clus
vv                              SRL MUTATED SRL WILD-TYPE
  COLON ADENOCARCINOMA                    8           306
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SRL MUTATED     6   0   0   1
  SRL WILD-TYPE 253   3  22  20
D1461V10, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  R0           6           253
  R1           0             3
  R2           0            22
  RX           1            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"
D1461V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRL MUTATED                                  0     1
  SRL WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SRL MUTATED                           2     7
  SRL WILD-TYPE                        17   169
D1461V12, multiclass
                                  clus
vv                                 SRL MUTATED SRL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                      7           169
[1] 4 2
[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 = SKIV2L2 MUTATION ANALYSIS
D1462V1, survival
                   sevent
clus2                 0   1
  SKIV2L2 MUTATED     3   8
  SKIV2L2 WILD-TYPE 274  70
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               11               344 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
                8                70 
$`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 
       55.92        24.43        35.97        31.96         6.18 

$`SKIV2L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       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 
       54.61        19.59        56.09        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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            22.075 
[1] "3.0 - 55.9 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "4.7"
D1462V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKIV2L2 MUTATED         2        0        1         2         1         0
  SKIV2L2 WILD-TYPE      62        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SKIV2L2 MUTATED           0          0          4          0        0
  SKIV2L2 WILD-TYPE        18          6         40         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SKIV2L2 MUTATED           1         0
  SKIV2L2 WILD-TYPE        11         1
D1462V3, multiclass
            clus
vv           SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               4                40
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  SKIV2L2 MUTATED     1   1   7   2
  SKIV2L2 WILD-TYPE   8  66 242  39
D1462V4, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               7               242
  T4               2                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
  SKIV2L2 MUTATED     6   5   0
  SKIV2L2 WILD-TYPE 214  76  66
D1462V5, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  N0               6               214
  N1               5                76
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1462V6, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED    10   1
  SKIV2L2 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED     10    1
  SKIV2L2 WILD-TYPE  275   47
   clus
vv  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  0              10               275
  1               1                47
[1] 2 2
[1] FALSE
D1462V7, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED     5   6
  SKIV2L2 WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED      5    6
  SKIV2L2 WILD-TYPE  165  191
        clus
vv       SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D1462V8, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED     7   0
  SKIV2L2 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED      7    0
  SKIV2L2 WILD-TYPE  293    8
     clus
vv    SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1462V9, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED     9   2
  SKIV2L2 WILD-TYPE 305  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED      9    2
  SKIV2L2 WILD-TYPE  305   46
                               clus
vv                              SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SKIV2L2 MUTATED     8   0   0   1
  SKIV2L2 WILD-TYPE 251   3  22  20
D1462V10, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               1                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"
D1462V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKIV2L2 MUTATED                                  0     0
  SKIV2L2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SKIV2L2 MUTATED                           0     8
  SKIV2L2 WILD-TYPE                        19   168
D1462V12, multiclass
                                  clus
vv                                 SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          8               168
[1] 4 2
[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 = KBTBD4 MUTATION ANALYSIS
D1463V1, survival
                  sevent
clus2                0   1
  KBTBD4 MUTATED     3   4
  KBTBD4 WILD-TYPE 274  74
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               7              348 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               4               74 
$`KBTBD4 MUTATED`
TCGA-G4-6628 TCGA-AA-3811 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CK-5916 TCGA-F4-6570 
       79.69        10.06        49.41        51.32        21.14         6.18 
TCGA-G4-6293 
      133.18 

$`KBTBD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        85.45        15.62        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
            6.18             0.00 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
          133.18           148.01 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
          49.410           22.045 
[1] "6.2 - 133.2 (49.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1463V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KBTBD4 MUTATED         2        0        1         2         0         0
  KBTBD4 WILD-TYPE      62        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KBTBD4 MUTATED           2          0          0          0        0
  KBTBD4 WILD-TYPE        16          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  KBTBD4 MUTATED           0         0
  KBTBD4 WILD-TYPE        12         1
D1463V3, multiclass
            clus
vv           KBTBD4 MUTATED KBTBD4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  KBTBD4 MUTATED     1   1   5   0
  KBTBD4 WILD-TYPE   8  66 244  41
D1463V4, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              5              244
  T4              0               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
  KBTBD4 MUTATED     5   1   1
  KBTBD4 WILD-TYPE 215  80  65
D1463V5, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1463V6, binary
                  cls
clus                 0   1
  KBTBD4 MUTATED     5   0
  KBTBD4 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      5    0
  KBTBD4 WILD-TYPE  280   48
   clus
vv  KBTBD4 MUTATED KBTBD4 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1463V7, binary
                  cls
clus                 0   1
  KBTBD4 MUTATED     6   1
  KBTBD4 WILD-TYPE 164 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      6    1
  KBTBD4 WILD-TYPE  164  196
        clus
vv       KBTBD4 MUTATED KBTBD4 WILD-TYPE
  FEMALE              6              164
  MALE                1              196
[1] 2 2
[1] FALSE
D1463V8, binary
                  cls
clus                 0   1
  KBTBD4 MUTATED     7   0
  KBTBD4 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      7    0
  KBTBD4 WILD-TYPE  293    8
     clus
vv    KBTBD4 MUTATED KBTBD4 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1463V9, binary
                  cls
clus                 0   1
  KBTBD4 MUTATED     7   0
  KBTBD4 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      7    0
  KBTBD4 WILD-TYPE  307   48
                               clus
vv                              KBTBD4 MUTATED KBTBD4 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KBTBD4 MUTATED     4   0   0   2
  KBTBD4 WILD-TYPE 255   3  22  19
D1463V10, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              2               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"
D1463V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KBTBD4 MUTATED                                  0     0
  KBTBD4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KBTBD4 MUTATED                           0     6
  KBTBD4 WILD-TYPE                        19   170
D1463V12, multiclass
                                  clus
vv                                 KBTBD4 MUTATED KBTBD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = OLFML1 MUTATION ANALYSIS
D1464V1, survival
                  sevent
clus2                0   1
  OLFML1 MUTATED     9   1
  OLFML1 WILD-TYPE 268  77
  OLFML1 MUTATED OLFML1 WILD-TYPE 
              10              345 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
               1               77 
$`OLFML1 MUTATED`
TCGA-AA-3715 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3966 
       19.04        63.98        26.99        53.00        18.05         2.01 
TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6161 TCGA-D5-6931 
       34.98        12.76        15.02        12.00 

$`OLFML1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  OLFML1 MUTATED OLFML1 WILD-TYPE 
            2.01             0.00 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
           63.98           148.01 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
          18.545           22.090 
[1] "2.0 - 64.0 (18.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1464V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OLFML1 MUTATED         2        0        3         4         1         0
  OLFML1 WILD-TYPE      62        1       23       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OLFML1 MUTATED           0          0          0          1        0
  OLFML1 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  OLFML1 MUTATED           0         0
  OLFML1 WILD-TYPE        12         1
D1464V3, multiclass
            clus
vv           OLFML1 MUTATED OLFML1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  OLFML1 MUTATED     1   1   7   2
  OLFML1 WILD-TYPE   8  66 242  39
D1464V4, multiclass
    clus
vv   OLFML1 MUTATED OLFML1 WILD-TYPE
  T1              1                8
  T2              1               66
  T3              7              242
  T4              2               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
  OLFML1 MUTATED    10   0   1
  OLFML1 WILD-TYPE 210  81  65
D1464V5, multiclass
    clus
vv   OLFML1 MUTATED OLFML1 WILD-TYPE
  N0             10              210
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1464V6, binary
                  cls
clus                 0   1
  OLFML1 MUTATED    11   0
  OLFML1 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML1 MUTATED     11    0
  OLFML1 WILD-TYPE  274   48
   clus
vv  OLFML1 MUTATED OLFML1 WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D1464V7, binary
                  cls
clus                 0   1
  OLFML1 MUTATED     6   5
  OLFML1 WILD-TYPE 164 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML1 MUTATED      6    5
  OLFML1 WILD-TYPE  164  192
        clus
vv       OLFML1 MUTATED OLFML1 WILD-TYPE
  FEMALE              6              164
  MALE                5              192
[1] 2 2
[1] FALSE
D1464V8, binary
                  cls
clus                 0   1
  OLFML1 MUTATED     9   0
  OLFML1 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML1 MUTATED      9    0
  OLFML1 WILD-TYPE  291    8
     clus
vv    OLFML1 MUTATED OLFML1 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1464V9, binary
                  cls
clus                 0   1
  OLFML1 MUTATED     9   2
  OLFML1 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML1 MUTATED      9    2
  OLFML1 WILD-TYPE  305   46
                               clus
vv                              OLFML1 MUTATED OLFML1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OLFML1 MUTATED     9   0   0   1
  OLFML1 WILD-TYPE 250   3  22  20
D1464V10, multiclass
    clus
vv   OLFML1 MUTATED OLFML1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D1464V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OLFML1 MUTATED                                  0     1
  OLFML1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OLFML1 MUTATED                           0     2
  OLFML1 WILD-TYPE                        19   174
D1464V12, multiclass
                                  clus
vv                                 OLFML1 MUTATED OLFML1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1465) Variable = C7ORF60 MUTATION ANALYSIS
D1465V1, survival
                   sevent
clus2                 0   1
  C7ORF60 MUTATED     5   1
  C7ORF60 WILD-TYPE 272  77
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               349 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44        17.82         1.41        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6626 
       46.75 

  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             22.09 
[1] "5.1 - 58.4 (18.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1465V2, continuous
                   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      63        0       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF60 MUTATED           0          0          2          0        1
  C7ORF60 WILD-TYPE        18          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF60 MUTATED           0         0
  C7ORF60 WILD-TYPE        12         1
D1465V3, multiclass
            clus
vv           C7ORF60 MUTATED C7ORF60 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 1                 0
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  C7ORF60 MUTATED     0   1   4   0
  C7ORF60 WILD-TYPE   9  66 245  41
D1465V4, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               0                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
  C7ORF60 MUTATED     3   2   1
  C7ORF60 WILD-TYPE 217  79  65
D1465V5, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  N0               3               217
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1465V6, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     3   1
  C7ORF60 WILD-TYPE 282  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      3    1
  C7ORF60 WILD-TYPE  282   47
   clus
vv  C7ORF60 MUTATED C7ORF60 WILD-TYPE
  0               3               282
  1               1                47
[1] 2 2
[1] FALSE
D1465V7, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     3   3
  C7ORF60 WILD-TYPE 167 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      3    3
  C7ORF60 WILD-TYPE  167  194
        clus
vv       C7ORF60 MUTATED C7ORF60 WILD-TYPE
  FEMALE               3               167
  MALE                 3               194
[1] 2 2
[1] FALSE
D1465V8, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     6   0
  C7ORF60 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      6    0
  C7ORF60 WILD-TYPE  294    8
     clus
vv    C7ORF60 MUTATED C7ORF60 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1465V9, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     6   0
  C7ORF60 WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      6    0
  C7ORF60 WILD-TYPE  308   48
                               clus
vv                              C7ORF60 MUTATED C7ORF60 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF60 MUTATED     3   0   0   0
  C7ORF60 WILD-TYPE 256   3  22  21
D1465V10, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D1465V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF60 MUTATED                                  0     0
  C7ORF60 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF60 MUTATED                           1     5
  C7ORF60 WILD-TYPE                        18   171
D1465V12, multiclass
                                  clus
vv                                 C7ORF60 MUTATED C7ORF60 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1466) Variable = IDE MUTATION ANALYSIS
D1466V1, survival
               sevent
clus2             0   1
  IDE MUTATED     8   1
  IDE WILD-TYPE 269  77
  IDE MUTATED IDE WILD-TYPE 
            9           346 
  IDE MUTATED IDE WILD-TYPE 
            1            77 
$`IDE MUTATED`
TCGA-AA-3496 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3492 TCGA-AA-3982 TCGA-AA-A010 
        1.02        85.05        14.93         3.02        27.02        34.98 
TCGA-AD-6890 TCGA-CM-5861 TCGA-D5-6932 
       24.53        15.02        11.38 

$`IDE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        19.04        19.04        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        83.24         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  IDE MUTATED IDE WILD-TYPE 
         1.02          0.00 
  IDE MUTATED IDE WILD-TYPE 
        85.05        148.01 
  IDE MUTATED IDE WILD-TYPE 
       15.020        22.075 
[1] "1.0 - 85.0 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1466V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDE MUTATED         0        0        3         3         1         0
  IDE WILD-TYPE      64        1       23       105         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDE MUTATED           0          0          1          1        0         0
  IDE WILD-TYPE        18          6         43         32       35        12
               vv
clus            STAGE IVB
  IDE MUTATED           0
  IDE WILD-TYPE         1
D1466V3, multiclass
            clus
vv           IDE MUTATED IDE WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            3           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            0            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
  IDE MUTATED     1   0   8   1
  IDE WILD-TYPE   8  67 241  40
D1466V4, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  T1           1             8
  T2           0            67
  T3           8           241
  T4           1            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
  IDE MUTATED     8   1   1
  IDE WILD-TYPE 212  80  65
D1466V5, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  N0           8           212
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1466V6, binary
               cls
clus              0   1
  IDE MUTATED     9   0
  IDE WILD-TYPE 276  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      9    0
  IDE WILD-TYPE  276   48
   clus
vv  IDE MUTATED IDE WILD-TYPE
  0           9           276
  1           0            48
[1] 2 2
[1] FALSE
D1466V7, binary
               cls
clus              0   1
  IDE MUTATED     6   4
  IDE WILD-TYPE 164 193
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      6    4
  IDE WILD-TYPE  164  193
        clus
vv       IDE MUTATED IDE WILD-TYPE
  FEMALE           6           164
  MALE             4           193
[1] 2 2
[1] FALSE
D1466V8, binary
               cls
clus              0   1
  IDE MUTATED     7   1
  IDE WILD-TYPE 293   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      7    1
  IDE WILD-TYPE  293    7
     clus
vv    IDE MUTATED IDE WILD-TYPE
  NO            7           293
  YES           1             7
[1] 2 2
[1] FALSE
D1466V9, binary
               cls
clus              0   1
  IDE MUTATED    10   0
  IDE WILD-TYPE 304  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED     10    0
  IDE WILD-TYPE  304   48
                               clus
vv                              IDE MUTATED IDE WILD-TYPE
  COLON ADENOCARCINOMA                   10           304
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  IDE MUTATED     8   0   0   0
  IDE WILD-TYPE 251   3  22  21
D1466V10, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  R0           8           251
  R1           0             3
  R2           0            22
  RX           0            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"
D1466V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDE MUTATED                                  0     0
  IDE WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IDE MUTATED                           0     3
  IDE WILD-TYPE                        19   173
D1466V12, multiclass
                                  clus
vv                                 IDE MUTATED IDE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      3           173
[1] 4 2
[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 = C1ORF124 MUTATION ANALYSIS
D1467V1, survival
                    sevent
clus2                  0   1
  C1ORF124 MUTATED     6   2
  C1ORF124 WILD-TYPE 271  76
  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
                 8                347 
  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
                 2                 76 
$`C1ORF124 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00N TCGA-CA-6718 TCGA-CM-5861 
        0.92        24.00        30.02         4.01        10.06        15.02 
TCGA-D5-6928 TCGA-G4-6307 
       11.64        55.04 

$`C1ORF124 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
              0.92               0.00 
  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
             55.04             148.01 
  C1ORF124 MUTATED C1ORF124 WILD-TYPE 
             13.33              22.09 
[1] "0.9 - 55.0 (13.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1467V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF124 MUTATED         0        0        0         5         1         0
  C1ORF124 WILD-TYPE      64        1       26       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF124 MUTATED           1          0          1          0        0
  C1ORF124 WILD-TYPE        17          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C1ORF124 MUTATED           0         0
  C1ORF124 WILD-TYPE        12         1
D1467V3, multiclass
            clus
vv           C1ORF124 MUTATED C1ORF124 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C1ORF124 MUTATED     0   0   7   1
  C1ORF124 WILD-TYPE   9  67 242  40
D1467V4, multiclass
    clus
vv   C1ORF124 MUTATED C1ORF124 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                7                242
  T4                1                 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
  C1ORF124 MUTATED     6   2   0
  C1ORF124 WILD-TYPE 214  79  66
D1467V5, multiclass
    clus
vv   C1ORF124 MUTATED C1ORF124 WILD-TYPE
  N0                6                214
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1467V6, binary
                    cls
clus                   0   1
  C1ORF124 MUTATED     8   0
  C1ORF124 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF124 MUTATED      8    0
  C1ORF124 WILD-TYPE  277   48
   clus
vv  C1ORF124 MUTATED C1ORF124 WILD-TYPE
  0                8                277
  1                0                 48
[1] 2 2
[1] FALSE
D1467V7, binary
                    cls
clus                   0   1
  C1ORF124 MUTATED     4   4
  C1ORF124 WILD-TYPE 166 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF124 MUTATED      4    4
  C1ORF124 WILD-TYPE  166  193
        clus
vv       C1ORF124 MUTATED C1ORF124 WILD-TYPE
  FEMALE                4                166
  MALE                  4                193
[1] 2 2
[1] FALSE
D1467V8, binary
                    cls
clus                   0   1
  C1ORF124 MUTATED     7   0
  C1ORF124 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF124 MUTATED      7    0
  C1ORF124 WILD-TYPE  293    8
     clus
vv    C1ORF124 MUTATED C1ORF124 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1467V9, binary
                    cls
clus                   0   1
  C1ORF124 MUTATED     5   3
  C1ORF124 WILD-TYPE 309  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF124 MUTATED      5    3
  C1ORF124 WILD-TYPE  309   45
                               clus
vv                              C1ORF124 MUTATED C1ORF124 WILD-TYPE
  COLON ADENOCARCINOMA                         5                309
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C1ORF124 MUTATED     7   0   0   1
  C1ORF124 WILD-TYPE 252   3  22  20
D1467V10, multiclass
    clus
vv   C1ORF124 MUTATED C1ORF124 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1467V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF124 MUTATED                                  0     1
  C1ORF124 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF124 MUTATED                           0     3
  C1ORF124 WILD-TYPE                        19   173
D1467V12, multiclass
                                  clus
vv                                 C1ORF124 MUTATED C1ORF124 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[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 = PIGK MUTATION ANALYSIS
D1468V1, survival
                sevent
clus2              0   1
  PIGK MUTATED     8   2
  PIGK WILD-TYPE 269  76
  PIGK MUTATED PIGK WILD-TYPE 
            10            345 
  PIGK MUTATED PIGK WILD-TYPE 
             2             76 
$`PIGK MUTATED`
TCGA-AA-3516 TCGA-AD-6888 TCGA-G4-6321 TCGA-A6-5660 TCGA-AA-3663 TCGA-AA-3864 
       13.02        15.52        22.09        29.19         6.97        53.00 
TCGA-AA-A00J TCGA-AY-5543 TCGA-CK-4947 TCGA-D5-6930 
       18.05        33.01        17.56        13.35 

$`PIGK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PIGK MUTATED PIGK WILD-TYPE 
          6.97           0.00 
  PIGK MUTATED PIGK WILD-TYPE 
         53.00         148.01 
  PIGK MUTATED PIGK WILD-TYPE 
        17.805         22.090 
[1] "7.0 - 53.0 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1468V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGK MUTATED         0        0        2         1         0         0
  PIGK WILD-TYPE      64        1       24       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGK MUTATED           2          0          3          1        0         1
  PIGK WILD-TYPE        16          6         41         32       35        11
                vv
clus             STAGE IVB
  PIGK MUTATED           0
  PIGK WILD-TYPE         1
D1468V3, multiclass
            clus
vv           PIGK MUTATED PIGK WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  PIGK MUTATED     0   1   7   2
  PIGK WILD-TYPE   9  66 242  39
D1468V4, multiclass
    clus
vv   PIGK MUTATED PIGK WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            2             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
  PIGK MUTATED     3   5   2
  PIGK WILD-TYPE 217  76  64
D1468V5, multiclass
    clus
vv   PIGK MUTATED PIGK WILD-TYPE
  N0            3            217
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1468V6, binary
                cls
clus               0   1
  PIGK MUTATED     8   1
  PIGK WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED      8    1
  PIGK WILD-TYPE  277   47
   clus
vv  PIGK MUTATED PIGK WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D1468V7, binary
                cls
clus               0   1
  PIGK MUTATED     4   6
  PIGK WILD-TYPE 166 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED      4    6
  PIGK WILD-TYPE  166  191
        clus
vv       PIGK MUTATED PIGK WILD-TYPE
  FEMALE            4            166
  MALE              6            191
[1] 2 2
[1] FALSE
D1468V8, binary
                cls
clus               0   1
  PIGK MUTATED    10   0
  PIGK WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED     10    0
  PIGK WILD-TYPE  290    8
     clus
vv    PIGK MUTATED PIGK WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1468V9, binary
                cls
clus               0   1
  PIGK MUTATED     7   3
  PIGK WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED      7    3
  PIGK WILD-TYPE  307   45
                               clus
vv                              PIGK MUTATED PIGK WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PIGK MUTATED     7   0   0   1
  PIGK WILD-TYPE 252   3  22  20
D1468V10, multiclass
    clus
vv   PIGK MUTATED PIGK WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D1468V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGK MUTATED                                  0     0
  PIGK WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGK MUTATED                           2     4
  PIGK WILD-TYPE                        17   172
D1468V12, multiclass
                                  clus
vv                                 PIGK MUTATED PIGK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       4            172
[1] 4 2
[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 = TRIB1 MUTATION ANALYSIS
D1469V1, survival
                 sevent
clus2               0   1
  TRIB1 MUTATED     5   2
  TRIB1 WILD-TYPE 272  76
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              7             348 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              2              76 
$`TRIB1 MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-A6-6781 TCGA-AY-6197 TCGA-CK-4950 TCGA-CK-4952 
       19.04        10.88        19.66        21.44        85.45        15.62 
TCGA-D5-6533 
       25.48 

$`TRIB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TRIB1 MUTATED TRIB1 WILD-TYPE 
          10.88            0.00 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
          85.45          148.01 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
          19.66           22.09 
[1] "10.9 - 85.5 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1469V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIB1 MUTATED         0        0        1         1         0         0
  TRIB1 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIB1 MUTATED           0          0          1          2        0         0
  TRIB1 WILD-TYPE        18          6         43         31       35        12
                 vv
clus              STAGE IVB
  TRIB1 MUTATED           0
  TRIB1 WILD-TYPE         1
D1469V3, multiclass
            clus
vv           TRIB1 MUTATED TRIB1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  TRIB1 MUTATED     0   0   3   4
  TRIB1 WILD-TYPE   9  67 246  37
D1469V4, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             4              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
  TRIB1 MUTATED     3   2   2
  TRIB1 WILD-TYPE 217  79  64
D1469V5, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  N0             3             217
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1469V6, binary
                 cls
clus                0   1
  TRIB1 MUTATED     4   0
  TRIB1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      4    0
  TRIB1 WILD-TYPE  281   48
   clus
vv  TRIB1 MUTATED TRIB1 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1469V7, binary
                 cls
clus                0   1
  TRIB1 MUTATED     3   4
  TRIB1 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      3    4
  TRIB1 WILD-TYPE  167  193
        clus
vv       TRIB1 MUTATED TRIB1 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1469V8, binary
                 cls
clus                0   1
  TRIB1 MUTATED     6   0
  TRIB1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      6    0
  TRIB1 WILD-TYPE  294    8
     clus
vv    TRIB1 MUTATED TRIB1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1469V9, binary
                 cls
clus                0   1
  TRIB1 MUTATED     4   3
  TRIB1 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      4    3
  TRIB1 WILD-TYPE  310   45
                               clus
vv                              TRIB1 MUTATED TRIB1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRIB1 MUTATED     4   1   0   1
  TRIB1 WILD-TYPE 255   2  22  20
D1469V10, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  R0             4             255
  R1             1               2
  R2             0              22
  RX             1              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"
D1469V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIB1 MUTATED                                  0     0
  TRIB1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRIB1 MUTATED                           1     5
  TRIB1 WILD-TYPE                        18   171
D1469V12, multiclass
                                  clus
vv                                 TRIB1 MUTATED TRIB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = MYST3 MUTATION ANALYSIS
D1470V1, survival
                 sevent
clus2               0   1
  MYST3 MUTATED    17   7
  MYST3 WILD-TYPE 260  71
  MYST3 MUTATED MYST3 WILD-TYPE 
             24             331 
  MYST3 MUTATED MYST3 WILD-TYPE 
              7              71 
$`MYST3 MUTATED`
TCGA-AA-3525 TCGA-G4-6625 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3710 
        8.05        91.79        33.53        22.06         6.97        26.99 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 
       26.01        25.02         7.96        38.04         4.01        34.98 
TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6607 
        1.02        83.24        58.39        22.36        49.41         3.19 
TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6171 TCGA-DM-A28E TCGA-G4-6303 TCGA-G4-6315 
       12.76        23.05        14.04       119.93        65.85        61.91 

$`MYST3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYST3 MUTATED MYST3 WILD-TYPE 
           1.02            0.00 
  MYST3 MUTATED MYST3 WILD-TYPE 
         119.93          148.01 
  MYST3 MUTATED MYST3 WILD-TYPE 
         25.515          21.990 
[1] "1.0 - 119.9 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1470V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYST3 MUTATED         1        0        3        10         2         0
  MYST3 WILD-TYPE      63        1       23        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYST3 MUTATED           0          0          2          0        4         1
  MYST3 WILD-TYPE        18          6         42         33       31        11
                 vv
clus              STAGE IVB
  MYST3 MUTATED           0
  MYST3 WILD-TYPE         1
D1470V3, multiclass
            clus
vv           MYST3 MUTATED MYST3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               4              31
  STAGE IVA              1              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
  MYST3 MUTATED     0   2  19   3
  MYST3 WILD-TYPE   9  65 230  38
D1470V4, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            19             230
  T4             3              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
  MYST3 MUTATED    18   4   2
  MYST3 WILD-TYPE 202  77  64
D1470V5, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  N0            18             202
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1470V6, binary
                 cls
clus                0   1
  MYST3 MUTATED    17   5
  MYST3 WILD-TYPE 268  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     17    5
  MYST3 WILD-TYPE  268   43
   clus
vv  MYST3 MUTATED MYST3 WILD-TYPE
  0            17             268
  1             5              43
[1] 2 2
[1] FALSE
D1470V7, binary
                 cls
clus                0   1
  MYST3 MUTATED    11  13
  MYST3 WILD-TYPE 159 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     11   13
  MYST3 WILD-TYPE  159  184
        clus
vv       MYST3 MUTATED MYST3 WILD-TYPE
  FEMALE            11             159
  MALE              13             184
[1] 2 2
[1] FALSE
D1470V8, binary
                 cls
clus                0   1
  MYST3 MUTATED    21   0
  MYST3 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     21    0
  MYST3 WILD-TYPE  279    8
     clus
vv    MYST3 MUTATED MYST3 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D1470V9, binary
                 cls
clus                0   1
  MYST3 MUTATED    21   3
  MYST3 WILD-TYPE 293  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     21    3
  MYST3 WILD-TYPE  293   45
                               clus
vv                              MYST3 MUTATED MYST3 WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYST3 MUTATED    18   0   1   1
  MYST3 WILD-TYPE 241   3  21  20
D1470V10, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  R0            18             241
  R1             0               3
  R2             1              21
  RX             1              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"
D1470V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYST3 MUTATED                                  0     2
  MYST3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYST3 MUTATED                           1    11
  MYST3 WILD-TYPE                        18   165
D1470V12, multiclass
                                  clus
vv                                 MYST3 MUTATED MYST3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(1471) Variable = KLF12 MUTATION ANALYSIS
D1471V1, survival
                 sevent
clus2               0   1
  KLF12 MUTATED     3   0
  KLF12 WILD-TYPE 274  78
  KLF12 MUTATED KLF12 WILD-TYPE 
              3             352 
  KLF12 MUTATED KLF12 WILD-TYPE 
              0              78 
$`KLF12 MUTATED`
TCGA-G4-6321 TCGA-AA-3949 TCGA-CA-5797 
       22.09        26.01        12.59 

$`KLF12 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  KLF12 MUTATED KLF12 WILD-TYPE 
          12.59            0.00 
  KLF12 MUTATED KLF12 WILD-TYPE 
          26.01          148.01 
  KLF12 MUTATED KLF12 WILD-TYPE 
         22.090          22.045 
[1] "12.6 - 26.0 (22.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1471V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF12 MUTATED         0        0        0         1         0         0
  KLF12 WILD-TYPE      64        1       26       107         8         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  KLF12 MUTATED           0
  KLF12 WILD-TYPE         1
D1471V3, multiclass
            clus
vv           KLF12 MUTATED KLF12 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  KLF12 MUTATED     0   1   2   0
  KLF12 WILD-TYPE   9  66 247  41
D1471V4, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             2             247
  T4             0              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
  KLF12 MUTATED     1   2   0
  KLF12 WILD-TYPE 219  79  66
D1471V5, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  N0             1             219
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1471V6, binary
                 cls
clus                0   1
  KLF12 MUTATED     2   0
  KLF12 WILD-TYPE 283  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      2    0
  KLF12 WILD-TYPE  283   48
   clus
vv  KLF12 MUTATED KLF12 WILD-TYPE
  0             2             283
  1             0              48
[1] 2 2
[1] FALSE
D1471V7, binary
                 cls
clus                0   1
  KLF12 MUTATED     2   1
  KLF12 WILD-TYPE 168 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      2    1
  KLF12 WILD-TYPE  168  196
        clus
vv       KLF12 MUTATED KLF12 WILD-TYPE
  FEMALE             2             168
  MALE               1             196
[1] 2 2
[1] FALSE
D1471V8, binary
                 cls
clus                0   1
  KLF12 MUTATED     3   0
  KLF12 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      3    0
  KLF12 WILD-TYPE  297    8
     clus
vv    KLF12 MUTATED KLF12 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1471V9, binary
                 cls
clus                0   1
  KLF12 MUTATED     2   1
  KLF12 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      2    1
  KLF12 WILD-TYPE  312   47
                               clus
vv                              KLF12 MUTATED KLF12 WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLF12 MUTATED     3   0   0   0
  KLF12 WILD-TYPE 256   3  22  21
D1471V10, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             0              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"
D1471V11, continuous
[1] "Remove cluster labels:" "KLF12 MUTATED"         
clus
  KLF12 MUTATED KLF12 WILD-TYPE 
              2             344 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AA-3496 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3527      TCGA-AA-3530 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552      TCGA-AA-3554 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3662 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3697 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814      TCGA-AA-3844 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870      TCGA-AA-3939 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972      TCGA-AA-3976 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L      TCGA-AA-A00Z 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6895 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6964      TCGA-AZ-6601      TCGA-AZ-6608      TCGA-DM-A285 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5656 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3502      TCGA-AA-3510 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3526      TCGA-AA-3529      TCGA-AA-3532 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3544 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3553      TCGA-AA-3555 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3663 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3673 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693      TCGA-AA-3695 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3811 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3812      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3941 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3966 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973      TCGA-AA-3975 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A010 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A029 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6806      TCGA-F4-6807 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF12 MUTATED                                  0     1
  KLF12 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLF12 MUTATED                           0     1
  KLF12 WILD-TYPE                        19   175
D1471V12, multiclass
[1] "Remove cluster labels:" "KLF12 MUTATED"         
clus
  KLF12 MUTATED KLF12 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5656 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-6715 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 

Clustering(1472) Variable = APLP1 MUTATION ANALYSIS
D1472V1, survival
                 sevent
clus2               0   1
  APLP1 MUTATED    11   5
  APLP1 WILD-TYPE 266  73
  APLP1 MUTATED APLP1 WILD-TYPE 
             16             339 
  APLP1 MUTATED APLP1 WILD-TYPE 
              5              73 
$`APLP1 MUTATED`
TCGA-A6-2677 TCGA-AA-3525 TCGA-A6-2672 TCGA-AA-3492 TCGA-AA-3542 TCGA-AA-3821 
       24.33         8.05        46.65         3.02        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        26.47        58.39 
TCGA-AZ-6606 TCGA-CK-5913 TCGA-F4-6459 TCGA-F4-6856 
       11.74        51.32         8.61        35.31 

$`APLP1 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        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-6717 
       12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  APLP1 MUTATED APLP1 WILD-TYPE 
           1.02            0.00 
  APLP1 MUTATED APLP1 WILD-TYPE 
          58.39          148.01 
  APLP1 MUTATED APLP1 WILD-TYPE 
         21.155          22.060 
[1] "1.0 - 58.4 (21.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1472V2, continuous
                 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      61        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APLP1 MUTATED           0          0          3          3        1         0
  APLP1 WILD-TYPE        18          6         41         30       34        12
                 vv
clus              STAGE IVB
  APLP1 MUTATED           0
  APLP1 WILD-TYPE         1
D1472V3, multiclass
            clus
vv           APLP1 MUTATED APLP1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             3              30
  STAGE IV               1              34
  STAGE IVA              0              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
  APLP1 MUTATED     1   3   9   3
  APLP1 WILD-TYPE   8  64 240  38
D1472V4, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  T1             1               8
  T2             3              64
  T3             9             240
  T4             3              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
  APLP1 MUTATED     9   2   5
  APLP1 WILD-TYPE 211  79  61
D1472V5, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  N0             9             211
  N1             2              79
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1472V6, binary
                 cls
clus                0   1
  APLP1 MUTATED    13   1
  APLP1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     13    1
  APLP1 WILD-TYPE  272   47
   clus
vv  APLP1 MUTATED APLP1 WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D1472V7, binary
                 cls
clus                0   1
  APLP1 MUTATED     7   9
  APLP1 WILD-TYPE 163 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED      7    9
  APLP1 WILD-TYPE  163  188
        clus
vv       APLP1 MUTATED APLP1 WILD-TYPE
  FEMALE             7             163
  MALE               9             188
[1] 2 2
[1] FALSE
D1472V8, binary
                 cls
clus                0   1
  APLP1 MUTATED    15   0
  APLP1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     15    0
  APLP1 WILD-TYPE  285    8
     clus
vv    APLP1 MUTATED APLP1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D1472V9, binary
                 cls
clus                0   1
  APLP1 MUTATED    12   4
  APLP1 WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     12    4
  APLP1 WILD-TYPE  302   44
                               clus
vv                              APLP1 MUTATED APLP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  APLP1 MUTATED    12   1   0   1
  APLP1 WILD-TYPE 247   2  22  20
D1472V10, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  R0            12             247
  R1             1               2
  R2             0              22
  RX             1              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"
D1472V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APLP1 MUTATED                                  0     0
  APLP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  APLP1 MUTATED                           0     8
  APLP1 WILD-TYPE                        19   168
D1472V12, multiclass
                                  clus
vv                                 APLP1 MUTATED APLP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = SPARCL1 MUTATION ANALYSIS
D1473V1, survival
                   sevent
clus2                 0   1
  SPARCL1 MUTATED    11   3
  SPARCL1 WILD-TYPE 266  75
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               14               341 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
                3                75 
$`SPARCL1 MUTATED`
TCGA-AA-3543 TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-3510 
        0.99        19.04        24.00        79.69        24.39        63.98 
TCGA-AA-3663 TCGA-AA-A00J TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        6.97        18.05        83.24        58.39        12.76        10.06 
TCGA-CM-4746 TCGA-DM-A0XD 
       37.02        24.43 

$`SPARCL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
             0.99              0.00 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
            83.24            148.01 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
           24.195            22.030 
[1] "1.0 - 83.2 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1473V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPARCL1 MUTATED         4        0        2         6         0         0
  SPARCL1 WILD-TYPE      60        1       24       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPARCL1 MUTATED           0          0          1          0        1
  SPARCL1 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SPARCL1 MUTATED           0         0
  SPARCL1 WILD-TYPE        12         1
D1473V3, multiclass
            clus
vv           SPARCL1 MUTATED SPARCL1 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                6               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SPARCL1 MUTATED     0   4   9   1
  SPARCL1 WILD-TYPE   9  63 240  40
D1473V4, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               9               240
  T4               1                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
  SPARCL1 MUTATED    13   1   0
  SPARCL1 WILD-TYPE 207  80  66
D1473V5, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  N0              13               207
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1473V6, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    13   1
  SPARCL1 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     13    1
  SPARCL1 WILD-TYPE  272   47
   clus
vv  SPARCL1 MUTATED SPARCL1 WILD-TYPE
  0              13               272
  1               1                47
[1] 2 2
[1] FALSE
D1473V7, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED     1  13
  SPARCL1 WILD-TYPE 169 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED      1   13
  SPARCL1 WILD-TYPE  169  184
        clus
vv       SPARCL1 MUTATED SPARCL1 WILD-TYPE
  FEMALE               1               169
  MALE                13               184
[1] 2 2
[1] FALSE
D1473V8, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    12   1
  SPARCL1 WILD-TYPE 288   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     12    1
  SPARCL1 WILD-TYPE  288    7
     clus
vv    SPARCL1 MUTATED SPARCL1 WILD-TYPE
  NO               12               288
  YES               1                 7
[1] 2 2
[1] FALSE
D1473V9, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    10   4
  SPARCL1 WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     10    4
  SPARCL1 WILD-TYPE  304   44
                               clus
vv                              SPARCL1 MUTATED SPARCL1 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SPARCL1 MUTATED     9   0   1   2
  SPARCL1 WILD-TYPE 250   3  21  19
D1473V10, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               2                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"
D1473V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPARCL1 MUTATED                                  0     3
  SPARCL1 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPARCL1 MUTATED                           1     4
  SPARCL1 WILD-TYPE                        18   172
D1473V12, multiclass
                                  clus
vv                                 SPARCL1 MUTATED SPARCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = UGT1A9 MUTATION ANALYSIS
D1474V1, survival
                  sevent
clus2                0   1
  UGT1A9 MUTATED     6   2
  UGT1A9 WILD-TYPE 271  76
  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
               8              347 
  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
               2               76 
$`UGT1A9 MUTATED`
TCGA-A6-2671 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01D 
       43.76        63.98        53.00        25.02        34.98        10.98 
TCGA-AZ-4315 TCGA-CA-6717 
       58.39        12.76 

$`UGT1A9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        79.69        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01F TCGA-AA-A01G 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
           10.98             0.00 
  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
           63.98           148.01 
  UGT1A9 MUTATED UGT1A9 WILD-TYPE 
           39.37            21.99 
[1] "11.0 - 64.0 (39.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1474V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGT1A9 MUTATED         0        0        2         3         1         0
  UGT1A9 WILD-TYPE      64        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A9 MUTATED           0          0          0          1        1
  UGT1A9 WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  UGT1A9 MUTATED           0         0
  UGT1A9 WILD-TYPE        12         1
D1474V3, multiclass
            clus
vv           UGT1A9 MUTATED UGT1A9 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  UGT1A9 MUTATED     0   1   7   1
  UGT1A9 WILD-TYPE   9  66 242  40
D1474V4, multiclass
    clus
vv   UGT1A9 MUTATED UGT1A9 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              1               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
  UGT1A9 MUTATED     7   0   2
  UGT1A9 WILD-TYPE 213  81  64
D1474V5, multiclass
    clus
vv   UGT1A9 MUTATED UGT1A9 WILD-TYPE
  N0              7              213
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1474V6, binary
                  cls
clus                 0   1
  UGT1A9 MUTATED     7   1
  UGT1A9 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A9 MUTATED      7    1
  UGT1A9 WILD-TYPE  278   47
   clus
vv  UGT1A9 MUTATED UGT1A9 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D1474V7, binary
                  cls
clus                 0   1
  UGT1A9 MUTATED     3   6
  UGT1A9 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A9 MUTATED      3    6
  UGT1A9 WILD-TYPE  167  191
        clus
vv       UGT1A9 MUTATED UGT1A9 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D1474V8, binary
                  cls
clus                 0   1
  UGT1A9 MUTATED     8   0
  UGT1A9 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A9 MUTATED      8    0
  UGT1A9 WILD-TYPE  292    8
     clus
vv    UGT1A9 MUTATED UGT1A9 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1474V9, binary
                  cls
clus                 0   1
  UGT1A9 MUTATED     7   2
  UGT1A9 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A9 MUTATED      7    2
  UGT1A9 WILD-TYPE  307   46
                               clus
vv                              UGT1A9 MUTATED UGT1A9 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UGT1A9 MUTATED     7   0   0   1
  UGT1A9 WILD-TYPE 252   3  22  20
D1474V10, multiclass
    clus
vv   UGT1A9 MUTATED UGT1A9 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1474V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT1A9 MUTATED                                  0     1
  UGT1A9 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT1A9 MUTATED                           0     2
  UGT1A9 WILD-TYPE                        19   174
D1474V12, multiclass
                                  clus
vv                                 UGT1A9 MUTATED UGT1A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1475) Variable = MBP MUTATION ANALYSIS
D1475V1, survival
               sevent
clus2             0   1
  MBP MUTATED     5   1
  MBP WILD-TYPE 272  77
  MBP MUTATED MBP WILD-TYPE 
            6           349 
  MBP MUTATED MBP WILD-TYPE 
            1            77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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        22.030 
[1] "12.9 - 49.4 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1475V2, continuous
               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      64        1       25       105         7         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        18          6         43         33       35        12
               vv
clus            STAGE IVB
  MBP MUTATED           0
  MBP WILD-TYPE         1
D1475V3, multiclass
            clus
vv           MBP MUTATED MBP WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            3           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  MBP MUTATED     0   0   5   1
  MBP WILD-TYPE   9  67 244  40
D1475V4, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  T1           0             9
  T2           0            67
  T3           5           244
  T4           1            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
  MBP MUTATED     5   1   0
  MBP WILD-TYPE 215  80  66
D1475V5, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  N0           5           215
  N1           1            80
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1475V6, binary
               cls
clus              0   1
  MBP MUTATED     5   0
  MBP WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      5    0
  MBP WILD-TYPE  280   48
   clus
vv  MBP MUTATED MBP WILD-TYPE
  0           5           280
  1           0            48
[1] 2 2
[1] FALSE
D1475V7, binary
               cls
clus              0   1
  MBP MUTATED     4   2
  MBP WILD-TYPE 166 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      4    2
  MBP WILD-TYPE  166  195
        clus
vv       MBP MUTATED MBP WILD-TYPE
  FEMALE           4           166
  MALE             2           195
[1] 2 2
[1] FALSE
D1475V8, binary
               cls
clus              0   1
  MBP MUTATED     6   0
  MBP WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      6    0
  MBP WILD-TYPE  294    8
     clus
vv    MBP MUTATED MBP WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D1475V9, binary
               cls
clus              0   1
  MBP MUTATED     6   0
  MBP WILD-TYPE 308  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      6    0
  MBP WILD-TYPE  308   48
                               clus
vv                              MBP MUTATED MBP WILD-TYPE
  COLON ADENOCARCINOMA                    6           308
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MBP MUTATED     5   0   0   0
  MBP WILD-TYPE 254   3  22  21
D1475V10, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  R0           5           254
  R1           0             3
  R2           0            22
  RX           0            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"
D1475V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBP MUTATED                                  0     0
  MBP WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MBP MUTATED                           0     4
  MBP WILD-TYPE                        19   172
D1475V12, multiclass
                                  clus
vv                                 MBP MUTATED MBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      4           172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1476) Variable = AAMP MUTATION ANALYSIS
D1476V1, survival
                sevent
clus2              0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 274  78
  AAMP MUTATED AAMP WILD-TYPE 
             3            352 
  AAMP MUTATED AAMP WILD-TYPE 
             0             78 
$`AAMP MUTATED`
TCGA-G4-6628 TCGA-A6-6781 TCGA-G4-6309 
       79.69        19.66        85.48 

$`AAMP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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         22.045 
[1] "19.7 - 85.5 (79.7)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1476V2, continuous
                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      63        1       26       108         8         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  AAMP MUTATED           0
  AAMP WILD-TYPE         1
D1476V3, multiclass
            clus
vv           AAMP MUTATED AAMP WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  AAMP MUTATED     0   1   1   1
  AAMP WILD-TYPE   9  66 248  40
D1476V4, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  T1            0              9
  T2            1             66
  T3            1            248
  T4            1             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
  AAMP MUTATED     1   2   0
  AAMP WILD-TYPE 219  79  66
D1476V5, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  N0            1            219
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1476V6, binary
                cls
clus               0   1
  AAMP MUTATED     2   0
  AAMP WILD-TYPE 283  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    0
  AAMP WILD-TYPE  283   48
   clus
vv  AAMP MUTATED AAMP WILD-TYPE
  0            2            283
  1            0             48
[1] 2 2
[1] FALSE
D1476V7, binary
                cls
clus               0   1
  AAMP MUTATED     1   2
  AAMP WILD-TYPE 169 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      1    2
  AAMP WILD-TYPE  169  195
        clus
vv       AAMP MUTATED AAMP WILD-TYPE
  FEMALE            1            169
  MALE              2            195
[1] 2 2
[1] FALSE
D1476V8, binary
                cls
clus               0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    0
  AAMP WILD-TYPE  297    8
     clus
vv    AAMP MUTATED AAMP WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1476V9, binary
                cls
clus               0   1
  AAMP MUTATED     2   1
  AAMP WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    1
  AAMP WILD-TYPE  312   47
                               clus
vv                              AAMP MUTATED AAMP WILD-TYPE
  COLON ADENOCARCINOMA                     2            312
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AAMP MUTATED     3   0   0   0
  AAMP WILD-TYPE 256   3  22  21
D1476V10, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1476V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AAMP MUTATED                                  0     0
  AAMP WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AAMP MUTATED                           1     2
  AAMP WILD-TYPE                        18   174
D1476V12, multiclass
                                  clus
vv                                 AAMP MUTATED AAMP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(1477) Variable = MGEA5 MUTATION ANALYSIS
D1477V1, survival
                 sevent
clus2               0   1
  MGEA5 MUTATED     4   3
  MGEA5 WILD-TYPE 273  75
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              7             348 
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              3              75 
$`MGEA5 MUTATED`
TCGA-AA-3715 TCGA-A6-5661 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-6165 
       19.04        33.53        58.39        12.10        12.76        16.04 
TCGA-DM-A1DB 
       44.32 

$`MGEA5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C 
      140.38         7.50       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.075 
[1] "12.1 - 58.4 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1477V2, continuous
                 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      64        1       25       103         8         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        18          6         44         33       33        12
                 vv
clus              STAGE IVB
  MGEA5 MUTATED           0
  MGEA5 WILD-TYPE         1
D1477V3, multiclass
            clus
vv           MGEA5 MUTATED MGEA5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  MGEA5 MUTATED     0   0   6   2
  MGEA5 WILD-TYPE   9  67 243  39
D1477V4, multiclass
    clus
vv   MGEA5 MUTATED MGEA5 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             2              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
  MGEA5 MUTATED     6   1   1
  MGEA5 WILD-TYPE 214  80  65
D1477V5, multiclass
    clus
vv   MGEA5 MUTATED MGEA5 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1477V6, binary
                 cls
clus                0   1
  MGEA5 MUTATED     6   2
  MGEA5 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      6    2
  MGEA5 WILD-TYPE  279   46
   clus
vv  MGEA5 MUTATED MGEA5 WILD-TYPE
  0             6             279
  1             2              46
[1] 2 2
[1] FALSE
D1477V7, binary
                 cls
clus                0   1
  MGEA5 MUTATED     2   6
  MGEA5 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      2    6
  MGEA5 WILD-TYPE  168  191
        clus
vv       MGEA5 MUTATED MGEA5 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D1477V8, binary
                 cls
clus                0   1
  MGEA5 MUTATED     6   0
  MGEA5 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      6    0
  MGEA5 WILD-TYPE  294    8
     clus
vv    MGEA5 MUTATED MGEA5 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1477V9, binary
                 cls
clus                0   1
  MGEA5 MUTATED     6   2
  MGEA5 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      6    2
  MGEA5 WILD-TYPE  308   46
                               clus
vv                              MGEA5 MUTATED MGEA5 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MGEA5 MUTATED     4   0   1   1
  MGEA5 WILD-TYPE 255   3  21  20
D1477V10, multiclass
    clus
vv   MGEA5 MUTATED MGEA5 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             1              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"
D1477V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGEA5 MUTATED                                  0     1
  MGEA5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MGEA5 MUTATED                           2     3
  MGEA5 WILD-TYPE                        17   173
D1477V12, multiclass
                                  clus
vv                                 MGEA5 MUTATED MGEA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        3             173
[1] 4 2
[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 = BEX5 MUTATION ANALYSIS
D1478V1, survival
                sevent
clus2              0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 272  76
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            348 
  BEX5 MUTATED BEX5 WILD-TYPE 
             2             76 
$`BEX5 MUTATED`
TCGA-AD-6964 TCGA-AA-3854 TCGA-AA-3966 TCGA-CM-5349 TCGA-D5-6541 TCGA-G4-6293 
       10.88        36.03         2.01        30.08        15.58       133.18 
TCGA-G4-6303 
       65.85 

$`BEX5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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         22.045 
[1] "2.0 - 133.2 (30.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1478V2, continuous
                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      63        1       26       105         8         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        17          6         44         33       34        12
                vv
clus             STAGE IVB
  BEX5 MUTATED           0
  BEX5 WILD-TYPE         1
D1478V3, multiclass
            clus
vv           BEX5 MUTATED BEX5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  BEX5 MUTATED     0   1   5   1
  BEX5 WILD-TYPE   9  66 244  40
D1478V4, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            5            244
  T4            1             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
  BEX5 MUTATED     4   2   1
  BEX5 WILD-TYPE 216  79  65
D1478V5, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  N0            4            216
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1478V6, binary
                cls
clus               0   1
  BEX5 MUTATED     5   1
  BEX5 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    1
  BEX5 WILD-TYPE  280   47
   clus
vv  BEX5 MUTATED BEX5 WILD-TYPE
  0            5            280
  1            1             47
[1] 2 2
[1] FALSE
D1478V7, binary
                cls
clus               0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 165 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    2
  BEX5 WILD-TYPE  165  195
        clus
vv       BEX5 MUTATED BEX5 WILD-TYPE
  FEMALE            5            165
  MALE              2            195
[1] 2 2
[1] FALSE
D1478V8, binary
                cls
clus               0   1
  BEX5 MUTATED     6   0
  BEX5 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      6    0
  BEX5 WILD-TYPE  294    8
     clus
vv    BEX5 MUTATED BEX5 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1478V9, binary
                cls
clus               0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    2
  BEX5 WILD-TYPE  309   46
                               clus
vv                              BEX5 MUTATED BEX5 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BEX5 MUTATED     5   0   0   0
  BEX5 WILD-TYPE 254   3  22  21
D1478V10, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1478V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BEX5 MUTATED                                  0     0
  BEX5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BEX5 MUTATED                           0     5
  BEX5 WILD-TYPE                        19   171
D1478V12, multiclass
                                  clus
vv                                 BEX5 MUTATED BEX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = HAUS3 MUTATION ANALYSIS
D1479V1, survival
                 sevent
clus2               0   1
  HAUS3 MUTATED     6   3
  HAUS3 WILD-TYPE 271  75
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              9             346 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              3              75 
$`HAUS3 MUTATED`
TCGA-CK-5912 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 TCGA-D5-6932 
       49.08        22.06        63.98         4.01        34.98        11.38 
TCGA-DM-A1D0 TCGA-DM-A1HB TCGA-F4-6570 
      130.65       135.65         6.18 

$`HAUS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        12.00        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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  HAUS3 MUTATED HAUS3 WILD-TYPE 
           4.01            0.00 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
         135.65          148.01 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
          34.98           22.01 
[1] "4.0 - 135.7 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1479V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAUS3 MUTATED         1        0        1         4         2         0
  HAUS3 WILD-TYPE      63        1       25       104         6         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  HAUS3 MUTATED           0
  HAUS3 WILD-TYPE         1
D1479V3, multiclass
            clus
vv           HAUS3 MUTATED HAUS3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  HAUS3 MUTATED     0   1   6   2
  HAUS3 WILD-TYPE   9  66 243  39
D1479V4, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             2              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
  HAUS3 MUTATED     8   1   0
  HAUS3 WILD-TYPE 212  80  66
D1479V5, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1479V6, binary
                 cls
clus                0   1
  HAUS3 MUTATED     8   0
  HAUS3 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      8    0
  HAUS3 WILD-TYPE  277   48
   clus
vv  HAUS3 MUTATED HAUS3 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1479V7, binary
                 cls
clus                0   1
  HAUS3 MUTATED     4   5
  HAUS3 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      4    5
  HAUS3 WILD-TYPE  166  192
        clus
vv       HAUS3 MUTATED HAUS3 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1479V8, binary
                 cls
clus                0   1
  HAUS3 MUTATED     6   0
  HAUS3 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      6    0
  HAUS3 WILD-TYPE  294    8
     clus
vv    HAUS3 MUTATED HAUS3 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1479V9, binary
                 cls
clus                0   1
  HAUS3 MUTATED     7   1
  HAUS3 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      7    1
  HAUS3 WILD-TYPE  307   47
                               clus
vv                              HAUS3 MUTATED HAUS3 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HAUS3 MUTATED     6   0   0   1
  HAUS3 WILD-TYPE 253   3  22  20
D1479V10, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1479V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAUS3 MUTATED                                  0     0
  HAUS3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HAUS3 MUTATED                           0     6
  HAUS3 WILD-TYPE                        19   170
D1479V12, multiclass
                                  clus
vv                                 HAUS3 MUTATED HAUS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = HYDIN MUTATION ANALYSIS
D1480V1, survival
                 sevent
clus2               0   1
  HYDIN MUTATED    58  18
  HYDIN WILD-TYPE 219  60
  HYDIN MUTATED HYDIN WILD-TYPE 
             76             279 
  HYDIN MUTATED HYDIN WILD-TYPE 
             18              60 
$`HYDIN MUTATED`
TCGA-AA-3524 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3972 TCGA-AD-6888 
       36.03         6.05        19.04        24.00        50.99        15.52 
TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-3809 
       25.08       100.01        35.80        26.17        79.69        32.75 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
       32.91        30.44        29.19        33.53        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3518 
       25.08        24.39        20.28         3.02        63.98         1.02 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3833 
       61.02         6.97         2.01        26.99        33.04        15.95 
TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
       17.03        36.03        30.05        53.00        31.00        33.01 
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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 
       83.24         5.79        26.47        27.09         0.20        58.39 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
       22.36        49.41        11.74         3.19        12.76        10.06 
TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 
       82.95        37.02        25.02        12.00        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6535 TCGA-D5-6538 
       13.05        12.03        45.40        54.61        15.12        17.13 
TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A282 
       15.58        14.30         9.44        11.38       140.38       139.17 
TCGA-DM-A28G TCGA-F4-6570 TCGA-F4-6855 TCGA-G4-6317 
       60.79         6.18        47.41        36.00 

$`HYDIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       29.98        12.99         2.01        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6964 TCGA-AZ-4681 
       38.04        21.99        39.06        21.37        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
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-A6-3810 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 
       34.65        33.34        36.53        31.63        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       32.71        27.09        22.52        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.12        19.66         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 
       24.00        29.95        20.98        13.94        78.08        54.02 
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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 
        1.02        17.98        38.99        37.02         0.00        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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       17.03        27.02        18.05         2.01        24.00        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-A03J TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       41.00        39.98        40.96        24.53        22.42        27.42 
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-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       23.05        20.02        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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.08        11.01        10.06        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        25.48        43.27        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04        11.64        13.41        13.35        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  HYDIN MUTATED HYDIN WILD-TYPE 
            0.2             0.0 
  HYDIN MUTATED HYDIN WILD-TYPE 
         140.38          148.01 
  HYDIN MUTATED HYDIN WILD-TYPE 
          25.02           21.99 
[1] "0.2 - 140.4 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1480V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HYDIN MUTATED        10        0       10        30         6         0
  HYDIN WILD-TYPE      54        1       16        78         2         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HYDIN MUTATED           3          0          7          5        4         3
  HYDIN WILD-TYPE        15          6         37         28       31         9
                 vv
clus              STAGE IVB
  HYDIN MUTATED           1
  HYDIN WILD-TYPE         0
D1480V3, multiclass
            clus
vv           HYDIN MUTATED HYDIN WILD-TYPE
  STAGE I               10              54
  STAGE IA               0               1
  STAGE II              10              16
  STAGE IIA             30              78
  STAGE IIB              6               2
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             7              37
  STAGE IIIC             5              28
  STAGE IV               4              31
  STAGE IVA              3               9
  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     1  10  56  13
  HYDIN WILD-TYPE   8  57 193  28
D1480V4, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  T1             1               8
  T2            10              57
  T3            56             193
  T4            13              28
[1] 4 2
[1] TRUE
[1] "dimension 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    57   9  14
  HYDIN WILD-TYPE 163  72  52
D1480V5, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  N0            57             163
  N1             9              72
  N2            14              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1480V6, binary
                 cls
clus                0   1
  HYDIN MUTATED    61   8
  HYDIN WILD-TYPE 224  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     61    8
  HYDIN WILD-TYPE  224   40
   clus
vv  HYDIN MUTATED HYDIN WILD-TYPE
  0            61             224
  1             8              40
[1] 2 2
[1] FALSE
D1480V7, binary
                 cls
clus                0   1
  HYDIN MUTATED    36  44
  HYDIN WILD-TYPE 134 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     36   44
  HYDIN WILD-TYPE  134  153
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  FEMALE            36             134
  MALE              44             153
[1] 2 2
[1] FALSE
D1480V8, binary
                 cls
clus                0   1
  HYDIN MUTATED    67   0
  HYDIN WILD-TYPE 233   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     67    0
  HYDIN WILD-TYPE  233    8
     clus
vv    HYDIN MUTATED HYDIN WILD-TYPE
  NO             67             233
  YES             0               8
[1] 2 2
[1] FALSE
D1480V9, binary
                 cls
clus                0   1
  HYDIN MUTATED    68  12
  HYDIN WILD-TYPE 246  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     68   12
  HYDIN WILD-TYPE  246   36
                               clus
vv                              HYDIN MUTATED HYDIN WILD-TYPE
  COLON ADENOCARCINOMA                     68             246
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HYDIN MUTATED    56   1   2   6
  HYDIN WILD-TYPE 203   2  20  15
D1480V10, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  R0            56             203
  R1             1               2
  R2             2              20
  RX             6              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"
D1480V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HYDIN MUTATED                                  0     3
  HYDIN WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HYDIN MUTATED                           5    44
  HYDIN WILD-TYPE                        14   132
D1480V12, multiclass
                                  clus
vv                                 HYDIN MUTATED HYDIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       44             132
[1] 4 2
[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 = NUDT16L1 MUTATION ANALYSIS
D1481V1, survival
                    sevent
clus2                  0   1
  NUDT16L1 MUTATED     3   0
  NUDT16L1 WILD-TYPE 274  78
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                352 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 0                 78 
$`NUDT16L1 MUTATED`
TCGA-AA-A01R TCGA-CK-6747 TCGA-CM-6674 
       35.01        82.95        12.95 

$`NUDT16L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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             22.045 
[1] "12.9 - 83.0 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1481V2, continuous
                    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      64        1       26       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDT16L1 MUTATED           1          0          0          0        0
  NUDT16L1 WILD-TYPE        17          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  NUDT16L1 MUTATED           0         0
  NUDT16L1 WILD-TYPE        12         1
D1481V3, multiclass
            clus
vv           NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 2                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  NUDT16L1 MUTATED     0   0   3   0
  NUDT16L1 WILD-TYPE   9  67 246  41
D1481V4, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                3                246
  T4                0                 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
  NUDT16L1 MUTATED     2   0   1
  NUDT16L1 WILD-TYPE 218  81  65
D1481V5, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  N0                2                218
  N1                0                 81
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1481V6, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   0
  NUDT16L1 WILD-TYPE 283  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    0
  NUDT16L1 WILD-TYPE  283   48
   clus
vv  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  0                2                283
  1                0                 48
[1] 2 2
[1] FALSE
D1481V7, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     1   2
  NUDT16L1 WILD-TYPE 169 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      1    2
  NUDT16L1 WILD-TYPE  169  195
        clus
vv       NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  FEMALE                1                169
  MALE                  2                195
[1] 2 2
[1] FALSE
D1481V8, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   1
  NUDT16L1 WILD-TYPE 298   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    1
  NUDT16L1 WILD-TYPE  298    7
     clus
vv    NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  NO                 2                298
  YES                1                  7
[1] 2 2
[1] FALSE
D1481V9, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   1
  NUDT16L1 WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    1
  NUDT16L1 WILD-TYPE  312   47
                               clus
vv                              NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  COLON ADENOCARCINOMA                         2                312
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  NUDT16L1 MUTATED     2   0   0   1
  NUDT16L1 WILD-TYPE 257   3  22  20
D1481V10, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  R0                2                257
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1481V11, continuous
[1] "Remove cluster labels:" "NUDT16L1 MUTATED"      
clus
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 2                344 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3516         TCGA-AA-3520 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3527         TCGA-AA-3530 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3662         TCGA-AA-3672 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3697 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3814 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3860         TCGA-AA-3867 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3939         TCGA-AA-3950 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3972         TCGA-AA-3976 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3986         TCGA-AA-A00L 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A024         TCGA-AD-6548 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AD-6964 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6608         TCGA-DM-A285 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-3502         TCGA-AA-3510         TCGA-AA-3511 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3517         TCGA-AA-3518 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3526         TCGA-AA-3529 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3544         TCGA-AA-3548 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3553         TCGA-AA-3555 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3655         TCGA-AA-3660 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3663         TCGA-AA-3664         TCGA-AA-3666 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3667         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-3693 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3811         TCGA-AA-3812 
"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-3845 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3861         TCGA-AA-3864         TCGA-AA-3866 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3872         TCGA-AA-3875 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3941 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3955 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3973         TCGA-AA-3975 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3980         TCGA-AA-3982 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3989         TCGA-AA-3994 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00K         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-A010         TCGA-AA-A017 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01S         TCGA-AA-A01T 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A029         TCGA-AA-A02F 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02K 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A02O         TCGA-AA-A02W         TCGA-AA-A02Y 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A03F         TCGA-AA-A03J         TCGA-AD-5900 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6890         TCGA-AD-6899 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6901         TCGA-AD-6963         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-6603         TCGA-AZ-6605 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-6715 
"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-CM-4743         TCGA-CM-4744 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6675         TCGA-CM-6676 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-F4-6806 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6807         TCGA-F4-6808         TCGA-F4-6809 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6854         TCGA-F4-6855         TCGA-F4-6856 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6293         TCGA-G4-6299         TCGA-G4-6303 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6306         TCGA-G4-6307 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6309         TCGA-G4-6315         TCGA-G4-6317 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6626 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT16L1 MUTATED                                  0     0
  NUDT16L1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  NUDT16L1 MUTATED                           0     2
  NUDT16L1 WILD-TYPE                        19   174
D1481V12, multiclass
[1] "Remove cluster labels:" "NUDT16L1 MUTATED"      
clus
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         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-6603         TCGA-AZ-6605 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6748 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6675         TCGA-CM-6676 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 

Clustering(1482) Variable = AGBL5 MUTATION ANALYSIS
D1482V1, survival
                 sevent
clus2               0   1
  AGBL5 MUTATED    10   2
  AGBL5 WILD-TYPE 267  76
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             343 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
              2              76 
$`AGBL5 MUTATED`
TCGA-AD-6895 TCGA-AZ-6608 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-A00J 
       25.08         1.94        33.53        24.39        19.66        18.05 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AY-6197 TCGA-CM-4746 TCGA-DM-A1HB TCGA-G4-6309 
        4.01        12.16        21.44        37.02       135.65        85.48 

$`AGBL5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        21.76        24.69        23.87        20.12 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  AGBL5 MUTATED AGBL5 WILD-TYPE 
           1.94            0.00 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         135.65          148.01 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         22.915          22.060 
[1] "1.9 - 135.7 (22.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1482V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGBL5 MUTATED         3        0        0         2         1         0
  AGBL5 WILD-TYPE      61        1       26       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGBL5 MUTATED           0          1          4          1        0         0
  AGBL5 WILD-TYPE        18          5         40         32       35        12
                 vv
clus              STAGE IVB
  AGBL5 MUTATED           0
  AGBL5 WILD-TYPE         1
D1482V3, multiclass
            clus
vv           AGBL5 MUTATED AGBL5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  AGBL5 MUTATED     0   4   5   3
  AGBL5 WILD-TYPE   9  63 244  38
D1482V4, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  T1             0               9
  T2             4              63
  T3             5             244
  T4             3              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
  AGBL5 MUTATED     6   6   0
  AGBL5 WILD-TYPE 214  75  66
D1482V5, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  N0             6             214
  N1             6              75
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1482V6, binary
                 cls
clus                0   1
  AGBL5 MUTATED     9   0
  AGBL5 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      9    0
  AGBL5 WILD-TYPE  276   48
   clus
vv  AGBL5 MUTATED AGBL5 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1482V7, binary
                 cls
clus                0   1
  AGBL5 MUTATED     3   9
  AGBL5 WILD-TYPE 167 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      3    9
  AGBL5 WILD-TYPE  167  188
        clus
vv       AGBL5 MUTATED AGBL5 WILD-TYPE
  FEMALE             3             167
  MALE               9             188
[1] 2 2
[1] FALSE
D1482V8, binary
                 cls
clus                0   1
  AGBL5 MUTATED    10   0
  AGBL5 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED     10    0
  AGBL5 WILD-TYPE  290    8
     clus
vv    AGBL5 MUTATED AGBL5 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1482V9, binary
                 cls
clus                0   1
  AGBL5 MUTATED     7   4
  AGBL5 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      7    4
  AGBL5 WILD-TYPE  307   44
                               clus
vv                              AGBL5 MUTATED AGBL5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGBL5 MUTATED     9   0   0   0
  AGBL5 WILD-TYPE 250   3  22  21
D1482V10, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1482V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGBL5 MUTATED                                  0     0
  AGBL5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGBL5 MUTATED                           3     7
  AGBL5 WILD-TYPE                        16   169
D1482V12, multiclass
                                  clus
vv                                 AGBL5 MUTATED AGBL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        7             169
[1] 4 2
[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 = C14ORF104 MUTATION ANALYSIS
D1483V1, survival
                     sevent
clus2                   0   1
  C14ORF104 MUTATED     3   0
  C14ORF104 WILD-TYPE 274  78
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  3                 352 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  0                  78 
$`C14ORF104 MUTATED`
TCGA-AA-A010 TCGA-AD-6963 TCGA-D5-6930 
       34.98        27.42        13.35 

$`C14ORF104 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
              13.35                0.00 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
              34.98              148.01 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
             27.420              22.045 
[1] "13.3 - 35.0 (27.4)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1483V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF104 MUTATED         0        0        0         2         1         0
  C14ORF104 WILD-TYPE      64        1       26       106         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF104 MUTATED           0          0          0          0        0
  C14ORF104 WILD-TYPE        18          6         44         33       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF104 MUTATED           0         0
  C14ORF104 WILD-TYPE        12         1
D1483V3, multiclass
            clus
vv           C14ORF104 MUTATED C14ORF104 WILD-TYPE
  STAGE I                    0                  64
  STAGE IA                   0                   1
  STAGE II                   0                  26
  STAGE IIA                  2                 106
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 0                  44
  STAGE IIIC                 0                  33
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C14ORF104 MUTATED     0   0   3   1
  C14ORF104 WILD-TYPE   9  67 246  40
D1483V4, multiclass
    clus
vv   C14ORF104 MUTATED C14ORF104 WILD-TYPE
  T1                 0                   9
  T2                 0                  67
  T3                 3                 246
  T4                 1                  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
  C14ORF104 MUTATED     4   0   0
  C14ORF104 WILD-TYPE 216  81  66
D1483V5, multiclass
    clus
vv   C14ORF104 MUTATED C14ORF104 WILD-TYPE
  N0                 4                 216
  N1                 0                  81
  N2                 0                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1483V6, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     3   0
  C14ORF104 WILD-TYPE 282  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      3    0
  C14ORF104 WILD-TYPE  282   48
   clus
vv  C14ORF104 MUTATED C14ORF104 WILD-TYPE
  0                 3                 282
  1                 0                  48
[1] 2 2
[1] FALSE
D1483V7, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     2   2
  C14ORF104 WILD-TYPE 168 195
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      2    2
  C14ORF104 WILD-TYPE  168  195
        clus
vv       C14ORF104 MUTATED C14ORF104 WILD-TYPE
  FEMALE                 2                 168
  MALE                   2                 195
[1] 2 2
[1] FALSE
D1483V8, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     3   0
  C14ORF104 WILD-TYPE 297   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      3    0
  C14ORF104 WILD-TYPE  297    8
     clus
vv    C14ORF104 MUTATED C14ORF104 WILD-TYPE
  NO                  3                 297
  YES                 0                   8
[1] 2 2
[1] FALSE
D1483V9, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     3   1
  C14ORF104 WILD-TYPE 311  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      3    1
  C14ORF104 WILD-TYPE  311   47
                               clus
vv                              C14ORF104 MUTATED C14ORF104 WILD-TYPE
  COLON ADENOCARCINOMA                          3                 311
  COLON MUCINOUS ADENOCARCINOMA                 1                  47
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF104 MUTATED     3   0   0   0
  C14ORF104 WILD-TYPE 256   3  22  21
D1483V10, multiclass
    clus
vv   C14ORF104 MUTATED C14ORF104 WILD-TYPE
  R0                 3                 256
  R1                 0                   3
  R2                 0                  22
  RX                 0                  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"
D1483V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF104 MUTATED                                  0     0
  C14ORF104 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF104 MUTATED                           0     2
  C14ORF104 WILD-TYPE                        19   174
D1483V12, multiclass
[1] "Remove cluster labels:" "C14ORF104 MUTATED"     
clus
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  2                 204 
         TCGA-A6-2677          TCGA-A6-4105          TCGA-A6-6649 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6548          TCGA-AD-6888          TCGA-AD-6895 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6964          TCGA-AZ-4681          TCGA-AZ-6601 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-6608          TCGA-CK-5912          TCGA-DM-A285 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6321          TCGA-G4-6586 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6628 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2678          TCGA-A6-2683 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5656          TCGA-A6-5657 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5660          TCGA-A6-5661 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-5662          TCGA-A6-5664          TCGA-A6-5665 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-5666          TCGA-A6-6137          TCGA-A6-6138 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-6141          TCGA-A6-6142          TCGA-A6-6648 
"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-6889 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6890          TCGA-AD-6899          TCGA-AD-6901 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6965          TCGA-AU-3779          TCGA-AU-6004 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4323          TCGA-AZ-4616 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"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-CA-5254          TCGA-CA-5255 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CA-5796          TCGA-CA-5797          TCGA-CA-6715 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CA-6716          TCGA-CA-6717          TCGA-CA-6718 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CA-6719          TCGA-CK-4947          TCGA-CK-4948 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-4950          TCGA-CK-4952          TCGA-CK-5913 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6928          TCGA-D5-6929 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A0X9          TCGA-DM-A0XD          TCGA-DM-A0XF 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1D0          TCGA-DM-A1D4          TCGA-DM-A1D6 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1D7          TCGA-DM-A1D8          TCGA-DM-A1D9 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1DA          TCGA-DM-A1DB          TCGA-DM-A1HA 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1HB          TCGA-DM-A282          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-G4-6315 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6323          TCGA-G4-6626 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 

Clustering(1484) Variable = ZSCAN20 MUTATION ANALYSIS
D1484V1, survival
                   sevent
clus2                 0   1
  ZSCAN20 MUTATED     9   4
  ZSCAN20 WILD-TYPE 268  74
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               13               342 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
                4                74 
$`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        13.35 
TCGA-DM-A1D4 
       92.75 

$`ZSCAN20 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
       37.02         0.00        17.03         0.00        33.07        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
                0                 0 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
            92.75            148.01 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
           23.050            22.045 
[1] "0.0 - 92.8 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1484V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZSCAN20 MUTATED         1        0        0         8         0         0
  ZSCAN20 WILD-TYPE      63        1       26       100         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZSCAN20 MUTATED           0          0          0          1        0
  ZSCAN20 WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  ZSCAN20 MUTATED           2         0
  ZSCAN20 WILD-TYPE        10         1
D1484V3, multiclass
            clus
vv           ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                8               100
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                2                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
  ZSCAN20 MUTATED     0   2  11   0
  ZSCAN20 WILD-TYPE   9  65 238  41
D1484V4, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              11               238
  T4               0                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
  ZSCAN20 MUTATED    10   2   1
  ZSCAN20 WILD-TYPE 210  79  65
D1484V5, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  N0              10               210
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1484V6, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED     9   2
  ZSCAN20 WILD-TYPE 276  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED      9    2
  ZSCAN20 WILD-TYPE  276   46
   clus
vv  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  0               9               276
  1               2                46
[1] 2 2
[1] FALSE
D1484V7, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED     5   8
  ZSCAN20 WILD-TYPE 165 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED      5    8
  ZSCAN20 WILD-TYPE  165  189
        clus
vv       ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  FEMALE               5               165
  MALE                 8               189
[1] 2 2
[1] FALSE
D1484V8, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED    11   0
  ZSCAN20 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED     11    0
  ZSCAN20 WILD-TYPE  289    8
     clus
vv    ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D1484V9, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED    10   3
  ZSCAN20 WILD-TYPE 304  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED     10    3
  ZSCAN20 WILD-TYPE  304   45
                               clus
vv                              ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZSCAN20 MUTATED     8   0   0   1
  ZSCAN20 WILD-TYPE 251   3  22  20
D1484V10, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               1                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"
D1484V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZSCAN20 MUTATED                                  0     1
  ZSCAN20 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZSCAN20 MUTATED                           2     6
  ZSCAN20 WILD-TYPE                        17   170
D1484V12, multiclass
                                  clus
vv                                 ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = PLCB2 MUTATION ANALYSIS
D1485V1, survival
                 sevent
clus2               0   1
  PLCB2 MUTATED     6   3
  PLCB2 WILD-TYPE 271  75
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              9             346 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              3              75 
$`PLCB2 MUTATED`
TCGA-AA-3672 TCGA-AZ-6608 TCGA-AA-3949 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CK-5914 
        0.92         1.94        26.01        25.02        58.39        21.99 
TCGA-D5-6536 TCGA-DM-A1D6 TCGA-DM-A1DB 
       17.85        49.91        44.32 

$`PLCB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PLCB2 MUTATED PLCB2 WILD-TYPE 
           0.92            0.00 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
          58.39          148.01 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
         25.020          22.045 
[1] "0.9 - 58.4 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1485V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCB2 MUTATED         0        0        0         4         0         0
  PLCB2 WILD-TYPE      64        1       26       104         8         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        17          5         42         33       35        12
                 vv
clus              STAGE IVB
  PLCB2 MUTATED           0
  PLCB2 WILD-TYPE         1
D1485V3, multiclass
            clus
vv           PLCB2 MUTATED PLCB2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PLCB2 MUTATED     0   2   7   0
  PLCB2 WILD-TYPE   9  65 242  41
D1485V4, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             0              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
  PLCB2 MUTATED     5   4   0
  PLCB2 WILD-TYPE 215  77  66
D1485V5, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  N0             5             215
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1485V6, binary
                 cls
clus                0   1
  PLCB2 MUTATED     7   0
  PLCB2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      7    0
  PLCB2 WILD-TYPE  278   48
   clus
vv  PLCB2 MUTATED PLCB2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1485V7, binary
                 cls
clus                0   1
  PLCB2 MUTATED     3   6
  PLCB2 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      3    6
  PLCB2 WILD-TYPE  167  191
        clus
vv       PLCB2 MUTATED PLCB2 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1485V8, binary
                 cls
clus                0   1
  PLCB2 MUTATED     6   0
  PLCB2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      6    0
  PLCB2 WILD-TYPE  294    8
     clus
vv    PLCB2 MUTATED PLCB2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1485V9, binary
                 cls
clus                0   1
  PLCB2 MUTATED     7   2
  PLCB2 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      7    2
  PLCB2 WILD-TYPE  307   46
                               clus
vv                              PLCB2 MUTATED PLCB2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PLCB2 MUTATED     4   0   0   1
  PLCB2 WILD-TYPE 255   3  22  20
D1485V10, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1485V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCB2 MUTATED                                  0     0
  PLCB2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCB2 MUTATED                           0     6
  PLCB2 WILD-TYPE                        19   170
D1485V12, multiclass
                                  clus
vv                                 PLCB2 MUTATED PLCB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = SAFB MUTATION ANALYSIS
D1486V1, survival
                sevent
clus2              0   1
  SAFB MUTATED    12   1
  SAFB WILD-TYPE 265  77
  SAFB MUTATED SAFB WILD-TYPE 
            13            342 
  SAFB MUTATED SAFB WILD-TYPE 
             1             77 
$`SAFB MUTATED`
TCGA-AA-3950 TCGA-AZ-6608 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 
       24.00         1.94        33.53        22.06        19.66         6.97 
TCGA-AA-3833 TCGA-AA-3973 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6161 TCGA-D5-6930 
       15.95        13.05        12.76        23.05        15.02        13.35 
TCGA-G4-6293 
      133.18 

$`SAFB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        21.99        16.08        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SAFB MUTATED SAFB WILD-TYPE 
          1.94           0.00 
  SAFB MUTATED SAFB WILD-TYPE 
        133.18         148.01 
  SAFB MUTATED SAFB WILD-TYPE 
        15.950         22.225 
[1] "1.9 - 133.2 (15.9)" "0.0 - 148.0 (22.2)"
[1] "hr=" "2.6"
D1486V2, continuous
                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      63        1       25       100         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAFB MUTATED           1          1          0          1        1         0
  SAFB WILD-TYPE        17          5         44         32       34        12
                vv
clus             STAGE IVB
  SAFB MUTATED           0
  SAFB WILD-TYPE         1
D1486V3, multiclass
            clus
vv           SAFB MUTATED SAFB WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  SAFB MUTATED     0   2  10   2
  SAFB WILD-TYPE   9  65 239  39
D1486V4, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  T1            0              9
  T2            2             65
  T3           10            239
  T4            2             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
  SAFB MUTATED    10   4   0
  SAFB WILD-TYPE 210  77  66
D1486V5, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  N0           10            210
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1486V6, binary
                cls
clus               0   1
  SAFB MUTATED    12   1
  SAFB WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     12    1
  SAFB WILD-TYPE  273   47
   clus
vv  SAFB MUTATED SAFB WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D1486V7, binary
                cls
clus               0   1
  SAFB MUTATED     8   6
  SAFB WILD-TYPE 162 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      8    6
  SAFB WILD-TYPE  162  191
        clus
vv       SAFB MUTATED SAFB WILD-TYPE
  FEMALE            8            162
  MALE              6            191
[1] 2 2
[1] FALSE
D1486V8, binary
                cls
clus               0   1
  SAFB MUTATED    13   0
  SAFB WILD-TYPE 287   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     13    0
  SAFB WILD-TYPE  287    8
     clus
vv    SAFB MUTATED SAFB WILD-TYPE
  NO            13            287
  YES            0              8
[1] 2 2
[1] FALSE
D1486V9, binary
                cls
clus               0   1
  SAFB MUTATED    10   4
  SAFB WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     10    4
  SAFB WILD-TYPE  304   44
                               clus
vv                              SAFB MUTATED SAFB WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SAFB MUTATED    11   0   1   1
  SAFB WILD-TYPE 248   3  21  20
D1486V10, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  R0           11            248
  R1            0              3
  R2            1             21
  RX            1             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"
D1486V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAFB MUTATED                                  0     1
  SAFB WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SAFB MUTATED                           1     7
  SAFB WILD-TYPE                        18   169
D1486V12, multiclass
                                  clus
vv                                 SAFB MUTATED SAFB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = GSK3B MUTATION ANALYSIS
D1487V1, survival
                 sevent
clus2               0   1
  GSK3B MUTATED    10   3
  GSK3B WILD-TYPE 267  75
  GSK3B MUTATED GSK3B WILD-TYPE 
             13             342 
  GSK3B MUTATED GSK3B WILD-TYPE 
              3              75 
$`GSK3B MUTATED`
TCGA-AA-3715 TCGA-DM-A285 TCGA-G4-6586 TCGA-A6-3808 TCGA-AA-3663 TCGA-AA-3821 
       19.04         5.88        35.80        33.34         6.97         1.02 
TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CM-5868 
       34.98        33.01        58.39        11.74        12.76        17.03 
TCGA-D5-6920 
       12.39 

$`GSK3B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
      100.01         1.94        49.08        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GSK3B MUTATED GSK3B WILD-TYPE 
           1.02            0.00 
  GSK3B MUTATED GSK3B WILD-TYPE 
          58.39          148.01 
  GSK3B MUTATED GSK3B WILD-TYPE 
          17.03           22.09 
[1] "1.0 - 58.4 (17.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1487V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSK3B MUTATED         1        0        2         6         1         0
  GSK3B WILD-TYPE      63        1       24       102         7         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        18          6         44         33       33        10
                 vv
clus              STAGE IVB
  GSK3B MUTATED           0
  GSK3B WILD-TYPE         1
D1487V3, multiclass
            clus
vv           GSK3B MUTATED GSK3B WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              2              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
  GSK3B MUTATED     0   1  10   3
  GSK3B WILD-TYPE   9  66 239  38
D1487V4, multiclass
    clus
vv   GSK3B MUTATED GSK3B WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             3              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
  GSK3B MUTATED    10   2   2
  GSK3B WILD-TYPE 210  79  64
D1487V5, multiclass
    clus
vv   GSK3B MUTATED GSK3B WILD-TYPE
  N0            10             210
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1487V6, binary
                 cls
clus                0   1
  GSK3B MUTATED    10   4
  GSK3B WILD-TYPE 275  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED     10    4
  GSK3B WILD-TYPE  275   44
   clus
vv  GSK3B MUTATED GSK3B WILD-TYPE
  0            10             275
  1             4              44
[1] 2 2
[1] FALSE
D1487V7, binary
                 cls
clus                0   1
  GSK3B MUTATED     8   6
  GSK3B WILD-TYPE 162 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED      8    6
  GSK3B WILD-TYPE  162  191
        clus
vv       GSK3B MUTATED GSK3B WILD-TYPE
  FEMALE             8             162
  MALE               6             191
[1] 2 2
[1] FALSE
D1487V8, binary
                 cls
clus                0   1
  GSK3B MUTATED    12   0
  GSK3B WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED     12    0
  GSK3B WILD-TYPE  288    8
     clus
vv    GSK3B MUTATED GSK3B WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1487V9, binary
                 cls
clus                0   1
  GSK3B MUTATED    11   3
  GSK3B WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED     11    3
  GSK3B WILD-TYPE  303   45
                               clus
vv                              GSK3B MUTATED GSK3B WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GSK3B MUTATED    11   0   0   1
  GSK3B WILD-TYPE 248   3  22  20
D1487V10, multiclass
    clus
vv   GSK3B MUTATED GSK3B WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1487V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSK3B MUTATED                                  0     1
  GSK3B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GSK3B MUTATED                           1     7
  GSK3B WILD-TYPE                        18   169
D1487V12, multiclass
                                  clus
vv                                 GSK3B MUTATED GSK3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = DNAJB11 MUTATION ANALYSIS
D1488V1, survival
                   sevent
clus2                 0   1
  DNAJB11 MUTATED     8   1
  DNAJB11 WILD-TYPE 269  77
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                9               346 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                1                77 
$`DNAJB11 MUTATED`
TCGA-G4-6310 TCGA-AA-3821 TCGA-AA-A00R TCGA-AD-5900 TCGA-AD-6889 TCGA-CM-4743 
       63.62         1.02         0.99        12.16        83.24        23.05 
TCGA-D5-5540 TCGA-D5-6926 TCGA-G4-6306 
       56.09         9.04        44.68 

$`DNAJB11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02        17.03        14.99        34.98        15.02 
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         1.02        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-6890 
        0.92        41.00        39.98        18.05        40.96        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-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 
       54.61        19.59        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
             0.99              0.00 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
            83.24            148.01 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
           23.050            22.045 
[1] "1.0 - 83.2 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D1488V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJB11 MUTATED         3        0        0         3         0         0
  DNAJB11 WILD-TYPE      61        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJB11 MUTATED           0          0          2          0        0
  DNAJB11 WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  DNAJB11 MUTATED           0         0
  DNAJB11 WILD-TYPE        12         1
D1488V3, multiclass
            clus
vv           DNAJB11 MUTATED DNAJB11 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  DNAJB11 MUTATED     0   4   4   1
  DNAJB11 WILD-TYPE   9  63 245  40
D1488V4, multiclass
    clus
vv   DNAJB11 MUTATED DNAJB11 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               4               245
  T4               1                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
  DNAJB11 MUTATED     7   2   0
  DNAJB11 WILD-TYPE 213  79  66
D1488V5, multiclass
    clus
vv   DNAJB11 MUTATED DNAJB11 WILD-TYPE
  N0               7               213
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1488V6, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     8   0
  DNAJB11 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      8    0
  DNAJB11 WILD-TYPE  277   48
   clus
vv  DNAJB11 MUTATED DNAJB11 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D1488V7, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     2   7
  DNAJB11 WILD-TYPE 168 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      2    7
  DNAJB11 WILD-TYPE  168  190
        clus
vv       DNAJB11 MUTATED DNAJB11 WILD-TYPE
  FEMALE               2               168
  MALE                 7               190
[1] 2 2
[1] FALSE
D1488V8, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     6   2
  DNAJB11 WILD-TYPE 294   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      6    2
  DNAJB11 WILD-TYPE  294    6
     clus
vv    DNAJB11 MUTATED DNAJB11 WILD-TYPE
  NO                6               294
  YES               2                 6
[1] 2 2
[1] FALSE
D1488V9, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     7   2
  DNAJB11 WILD-TYPE 307  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      7    2
  DNAJB11 WILD-TYPE  307   46
                               clus
vv                              DNAJB11 MUTATED DNAJB11 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DNAJB11 MUTATED     9   0   0   0
  DNAJB11 WILD-TYPE 250   3  22  21
D1488V10, multiclass
    clus
vv   DNAJB11 MUTATED DNAJB11 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               0                22
  RX               0                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"
D1488V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJB11 MUTATED                                  0     1
  DNAJB11 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJB11 MUTATED                           0     6
  DNAJB11 WILD-TYPE                        19   170
D1488V12, multiclass
                                  clus
vv                                 DNAJB11 MUTATED DNAJB11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = SLC46A3 MUTATION ANALYSIS
D1489V1, survival
                   sevent
clus2                 0   1
  SLC46A3 MUTATED     7   1
  SLC46A3 WILD-TYPE 270  77
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                8               347 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                1                77 
$`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 
        6.77        12.76 

$`SLC46A3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
             6.77              0.00 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
            63.98            148.01 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
           23.375            22.060 
[1] "6.8 - 64.0 (23.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1489V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC46A3 MUTATED         4        0        1         1         1         0
  SLC46A3 WILD-TYPE      60        1       25       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC46A3 MUTATED           0          0          0          1        0
  SLC46A3 WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC46A3 MUTATED           0         0
  SLC46A3 WILD-TYPE        12         1
D1489V3, multiclass
            clus
vv           SLC46A3 MUTATED SLC46A3 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC46A3 MUTATED     1   3   2   2
  SLC46A3 WILD-TYPE   8  64 247  39
D1489V4, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  T1               1                 8
  T2               3                64
  T3               2               247
  T4               2                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
  SLC46A3 MUTATED     7   1   0
  SLC46A3 WILD-TYPE 213  80  66
D1489V5, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  N0               7               213
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1489V6, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     6   0
  SLC46A3 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      6    0
  SLC46A3 WILD-TYPE  279   48
   clus
vv  SLC46A3 MUTATED SLC46A3 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1489V7, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     3   5
  SLC46A3 WILD-TYPE 167 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      3    5
  SLC46A3 WILD-TYPE  167  192
        clus
vv       SLC46A3 MUTATED SLC46A3 WILD-TYPE
  FEMALE               3               167
  MALE                 5               192
[1] 2 2
[1] FALSE
D1489V8, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     7   0
  SLC46A3 WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      7    0
  SLC46A3 WILD-TYPE  293    8
     clus
vv    SLC46A3 MUTATED SLC46A3 WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1489V9, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     5   3
  SLC46A3 WILD-TYPE 309  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      5    3
  SLC46A3 WILD-TYPE  309   45
                               clus
vv                              SLC46A3 MUTATED SLC46A3 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC46A3 MUTATED     6   0   0   1
  SLC46A3 WILD-TYPE 253   3  22  20
D1489V10, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D1489V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC46A3 MUTATED                                  0     1
  SLC46A3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC46A3 MUTATED                           0     3
  SLC46A3 WILD-TYPE                        19   173
D1489V12, multiclass
                                  clus
vv                                 SLC46A3 MUTATED SLC46A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = C9ORF102 MUTATION ANALYSIS
D1490V1, survival
                    sevent
clus2                  0   1
  C9ORF102 MUTATED     7   0
  C9ORF102 WILD-TYPE 270  78
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 7                348 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 0                 78 
$`C9ORF102 MUTATED`
TCGA-AD-6895 TCGA-A6-3808 TCGA-A6-6780 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       25.08        33.34        20.12        25.02        34.98        12.16 
TCGA-CM-6167 
       14.99 

$`C9ORF102 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        34.65        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
             12.16               0.00 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
             34.98             148.01 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
            25.020             22.045 
[1] "12.2 - 35.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9200000"
D1490V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF102 MUTATED         1        0        0         3         1         0
  C9ORF102 WILD-TYPE      63        1       26       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF102 MUTATED           0          0          1          1        0
  C9ORF102 WILD-TYPE        18          6         43         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF102 MUTATED           0         0
  C9ORF102 WILD-TYPE        12         1
D1490V3, multiclass
            clus
vv           C9ORF102 MUTATED C9ORF102 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 3                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C9ORF102 MUTATED     0   2   5   1
  C9ORF102 WILD-TYPE   9  65 244  40
D1490V4, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                5                244
  T4                1                 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
  C9ORF102 MUTATED     6   1   1
  C9ORF102 WILD-TYPE 214  80  65
D1490V5, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  N0                6                214
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1490V6, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     5   0
  C9ORF102 WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      5    0
  C9ORF102 WILD-TYPE  280   48
   clus
vv  C9ORF102 MUTATED C9ORF102 WILD-TYPE
  0                5                280
  1                0                 48
[1] 2 2
[1] FALSE
D1490V7, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     3   5
  C9ORF102 WILD-TYPE 167 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      3    5
  C9ORF102 WILD-TYPE  167  192
        clus
vv       C9ORF102 MUTATED C9ORF102 WILD-TYPE
  FEMALE                3                167
  MALE                  5                192
[1] 2 2
[1] FALSE
D1490V8, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     7   0
  C9ORF102 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      7    0
  C9ORF102 WILD-TYPE  293    8
     clus
vv    C9ORF102 MUTATED C9ORF102 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1490V9, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     6   2
  C9ORF102 WILD-TYPE 308  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      6    2
  C9ORF102 WILD-TYPE  308   46
                               clus
vv                              C9ORF102 MUTATED C9ORF102 WILD-TYPE
  COLON ADENOCARCINOMA                         6                308
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF102 MUTATED     6   0   0   0
  C9ORF102 WILD-TYPE 253   3  22  21
D1490V10, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1490V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF102 MUTATED                                  0     0
  C9ORF102 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF102 MUTATED                           1     4
  C9ORF102 WILD-TYPE                        18   172
D1490V12, multiclass
                                  clus
vv                                 C9ORF102 MUTATED C9ORF102 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                172
[1] 4 2
[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 = NSF MUTATION ANALYSIS
D1491V1, survival
               sevent
clus2             0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 273  78
  NSF MUTATED NSF WILD-TYPE 
            4           351 
  NSF MUTATED NSF WILD-TYPE 
            0            78 
$`NSF MUTATED`
TCGA-AA-A01R TCGA-CA-5255 TCGA-CM-6676 TCGA-D5-6930 
       35.01        12.36        11.08        13.35 

$`NSF WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NSF MUTATED NSF WILD-TYPE 
        11.08          0.00 
  NSF MUTATED NSF WILD-TYPE 
        35.01        148.01 
  NSF MUTATED NSF WILD-TYPE 
       12.855        22.090 
[1] "11.1 - 35.0 (12.9)" "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1491V2, continuous
               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      63        1       26       106         8         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        17          6         44         33       35        12
               vv
clus            STAGE IVB
  NSF MUTATED           0
  NSF WILD-TYPE         1
D1491V3, multiclass
            clus
vv           NSF MUTATED NSF WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            2           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  NSF MUTATED     0   1   3   0
  NSF WILD-TYPE   9  66 246  41
D1491V4, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  T1           0             9
  T2           1            66
  T3           3           246
  T4           0            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
  NSF MUTATED     3   0   1
  NSF WILD-TYPE 217  81  65
D1491V5, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  N0           3           217
  N1           0            81
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1491V6, binary
               cls
clus              0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 281  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      4    0
  NSF WILD-TYPE  281   48
   clus
vv  NSF MUTATED NSF WILD-TYPE
  0           4           281
  1           0            48
[1] 2 2
[1] FALSE
D1491V7, binary
               cls
clus              0   1
  NSF MUTATED     0   4
  NSF WILD-TYPE 170 193
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      0    4
  NSF WILD-TYPE  170  193
        clus
vv       NSF MUTATED NSF WILD-TYPE
  FEMALE           0           170
  MALE             4           193
[1] 2 2
[1] FALSE
D1491V8, binary
               cls
clus              0   1
  NSF MUTATED     2   2
  NSF WILD-TYPE 298   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      2    2
  NSF WILD-TYPE  298    6
     clus
vv    NSF MUTATED NSF WILD-TYPE
  NO            2           298
  YES           2             6
[1] 2 2
[1] FALSE
D1491V9, binary
               cls
clus              0   1
  NSF MUTATED     2   2
  NSF WILD-TYPE 312  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      2    2
  NSF WILD-TYPE  312   46
                               clus
vv                              NSF MUTATED NSF WILD-TYPE
  COLON ADENOCARCINOMA                    2           312
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NSF MUTATED     3   0   0   1
  NSF WILD-TYPE 256   3  22  20
D1491V10, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  R0           3           256
  R1           0             3
  R2           0            22
  RX           1            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"
D1491V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSF MUTATED                                  0     1
  NSF WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NSF MUTATED                           0     2
  NSF WILD-TYPE                        19   174
D1491V12, multiclass
                                  clus
vv                                 NSF MUTATED NSF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      2           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(1492) Variable = MTIF2 MUTATION ANALYSIS
D1492V1, survival
                 sevent
clus2               0   1
  MTIF2 MUTATED     8   1
  MTIF2 WILD-TYPE 269  77
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              9             346 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              1              77 
$`MTIF2 MUTATED`
TCGA-G4-6628 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6719 
       79.69         2.01        34.98        35.01        12.76        14.30 
TCGA-CM-5861 TCGA-D5-5538 TCGA-D5-6927 
       15.02        54.61         9.44 

$`MTIF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        10.06        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MTIF2 MUTATED MTIF2 WILD-TYPE 
           2.01            0.00 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          79.69          148.01 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
         15.020          22.075 
[1] "2.0 - 79.7 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1492V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTIF2 MUTATED         1        0        0         5         1         0
  MTIF2 WILD-TYPE      63        1       26       103         7         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  MTIF2 MUTATED           0
  MTIF2 WILD-TYPE         1
D1492V3, multiclass
            clus
vv           MTIF2 MUTATED MTIF2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MTIF2 MUTATED     0   1   7   1
  MTIF2 WILD-TYPE   9  66 242  40
D1492V4, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             1              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
  MTIF2 MUTATED     7   1   1
  MTIF2 WILD-TYPE 213  80  65
D1492V5, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1492V6, binary
                 cls
clus                0   1
  MTIF2 MUTATED     9   0
  MTIF2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      9    0
  MTIF2 WILD-TYPE  276   48
   clus
vv  MTIF2 MUTATED MTIF2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1492V7, binary
                 cls
clus                0   1
  MTIF2 MUTATED     4   5
  MTIF2 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      4    5
  MTIF2 WILD-TYPE  166  192
        clus
vv       MTIF2 MUTATED MTIF2 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1492V8, binary
                 cls
clus                0   1
  MTIF2 MUTATED     7   1
  MTIF2 WILD-TYPE 293   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      7    1
  MTIF2 WILD-TYPE  293    7
     clus
vv    MTIF2 MUTATED MTIF2 WILD-TYPE
  NO              7             293
  YES             1               7
[1] 2 2
[1] FALSE
D1492V9, binary
                 cls
clus                0   1
  MTIF2 MUTATED     6   3
  MTIF2 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      6    3
  MTIF2 WILD-TYPE  308   45
                               clus
vv                              MTIF2 MUTATED MTIF2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MTIF2 MUTATED     6   0   0   2
  MTIF2 WILD-TYPE 253   3  22  19
D1492V10, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1492V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTIF2 MUTATED                                  0     2
  MTIF2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MTIF2 MUTATED                           0     4
  MTIF2 WILD-TYPE                        19   172
D1492V12, multiclass
                                  clus
vv                                 MTIF2 MUTATED MTIF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = MEGF8 MUTATION ANALYSIS
D1493V1, survival
                 sevent
clus2               0   1
  MEGF8 MUTATED    18   5
  MEGF8 WILD-TYPE 259  73
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             23             332 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
              5              73 
$`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        83.24 
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 
       14.04        16.14         9.44       119.70       135.65 

$`MEGF8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.12        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MEGF8 MUTATED MEGF8 WILD-TYPE 
              0               0 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
         135.65          148.01 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
          21.44           22.09 
[1] "0.0 - 135.7 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1493V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEGF8 MUTATED         6        0        4        10         2         0
  MEGF8 WILD-TYPE      58        1       22        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEGF8 MUTATED           0          0          1          1        0         0
  MEGF8 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  MEGF8 MUTATED           0
  MEGF8 WILD-TYPE         1
D1493V3, multiclass
            clus
vv           MEGF8 MUTATED MEGF8 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  MEGF8 MUTATED     2   4  14   4
  MEGF8 WILD-TYPE   7  63 235  37
D1493V4, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  T1             2               7
  T2             4              63
  T3            14             235
  T4             4              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
  MEGF8 MUTATED    22   2   0
  MEGF8 WILD-TYPE 198  79  66
D1493V5, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  N0            22             198
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1493V6, binary
                 cls
clus                0   1
  MEGF8 MUTATED    21   0
  MEGF8 WILD-TYPE 264  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     21    0
  MEGF8 WILD-TYPE  264   48
   clus
vv  MEGF8 MUTATED MEGF8 WILD-TYPE
  0            21             264
  1             0              48
[1] 2 2
[1] FALSE
D1493V7, binary
                 cls
clus                0   1
  MEGF8 MUTATED    16   8
  MEGF8 WILD-TYPE 154 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     16    8
  MEGF8 WILD-TYPE  154  189
        clus
vv       MEGF8 MUTATED MEGF8 WILD-TYPE
  FEMALE            16             154
  MALE               8             189
[1] 2 2
[1] FALSE
D1493V8, binary
                 cls
clus                0   1
  MEGF8 MUTATED    19   0
  MEGF8 WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     19    0
  MEGF8 WILD-TYPE  281    8
     clus
vv    MEGF8 MUTATED MEGF8 WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D1493V9, binary
                 cls
clus                0   1
  MEGF8 MUTATED    17   6
  MEGF8 WILD-TYPE 297  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     17    6
  MEGF8 WILD-TYPE  297   42
                               clus
vv                              MEGF8 MUTATED MEGF8 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MEGF8 MUTATED    19   0   0   2
  MEGF8 WILD-TYPE 240   3  22  19
D1493V10, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             0              22
  RX             2              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"
D1493V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEGF8 MUTATED                                  0     2
  MEGF8 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MEGF8 MUTATED                           1    12
  MEGF8 WILD-TYPE                        18   164
D1493V12, multiclass
                                  clus
vv                                 MEGF8 MUTATED MEGF8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       12             164
[1] 4 2
[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 = ARID2 MUTATION ANALYSIS
D1494V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    22   6
  ARID2 WILD-TYPE 255  72
  ARID2 MUTATED ARID2 WILD-TYPE 
             28             327 
  ARID2 MUTATED ARID2 WILD-TYPE 
              6              72 
$`ARID2 MUTATED`
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3867 TCGA-AD-6895 
        0.92        85.05        19.04        19.04        24.03        25.08 
TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5657 TCGA-A6-6137 TCGA-A6-6138 
       10.88        35.80        79.69        31.63        27.09        22.52 
TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       23.87        26.99         0.00        25.02         4.01        34.98 
TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-6168 
        1.02        58.39        10.06        21.99        22.98        12.99 
TCGA-CM-6171 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6570 
       14.04        11.64       135.65         6.18 

$`ARID2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.00        36.00        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 
       38.04        21.99        39.06        21.37        15.52       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 
       22.06        32.71         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ARID2 MUTATED ARID2 WILD-TYPE 
              0               0 
  ARID2 MUTATED ARID2 WILD-TYPE 
         135.65          148.01 
  ARID2 MUTATED ARID2 WILD-TYPE 
          22.75           22.03 
[1] "0.0 - 135.7 (22.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1494V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID2 MUTATED         4        0        4         8         2         0
  ARID2 WILD-TYPE      60        1       22       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARID2 MUTATED           1          0          7          0        3         0
  ARID2 WILD-TYPE        17          6         37         33       32        12
                 vv
clus              STAGE IVB
  ARID2 MUTATED           0
  ARID2 WILD-TYPE         1
D1494V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             7              37
  STAGE IIIC             0              33
  STAGE IV               3              32
  STAGE IVA              0              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
  ARID2 MUTATED     0   5  22   4
  ARID2 WILD-TYPE   9  62 227  37
D1494V4, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            22             227
  T4             4              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
  ARID2 MUTATED    20   8   3
  ARID2 WILD-TYPE 200  73  63
D1494V5, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            20             200
  N1             8              73
  N2             3              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"
D1494V6, binary
                 cls
clus                0   1
  ARID2 MUTATED    24   3
  ARID2 WILD-TYPE 261  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     24    3
  ARID2 WILD-TYPE  261   45
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            24             261
  1             3              45
[1] 2 2
[1] FALSE
D1494V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    12  19
  ARID2 WILD-TYPE 158 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     12   19
  ARID2 WILD-TYPE  158  178
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            12             158
  MALE              19             178
[1] 2 2
[1] FALSE
D1494V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    22   1
  ARID2 WILD-TYPE 278   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     22    1
  ARID2 WILD-TYPE  278    7
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             22             278
  YES             1               7
[1] 2 2
[1] FALSE
D1494V9, binary
                 cls
clus                0   1
  ARID2 MUTATED    28   2
  ARID2 WILD-TYPE 286  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     28    2
  ARID2 WILD-TYPE  286   46
                               clus
vv                              ARID2 MUTATED ARID2 WILD-TYPE
  COLON ADENOCARCINOMA                     28             286
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ARID2 MUTATED    19   0   3   3
  ARID2 WILD-TYPE 240   3  19  18
D1494V10, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             3              19
  RX             3              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"
D1494V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0     1
  ARID2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           2    15
  ARID2 WILD-TYPE                        17   161
D1494V12, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       15             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(1495) Variable = PCDHGA4 MUTATION ANALYSIS
D1495V1, survival
                   sevent
clus2                 0   1
  PCDHGA4 MUTATED    13   4
  PCDHGA4 WILD-TYPE 264  74
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               17               338 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
                4                74 
$`PCDHGA4 MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 
       19.04       100.01        26.17        30.44         8.38        19.66 
TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00N TCGA-AD-6899 
        3.02        26.99        53.00        33.01         4.01         5.79 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6171 TCGA-CM-6676 TCGA-G4-6309 
       58.39        12.76        14.04        11.08        85.48 

$`PCDHGA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
             3.02              0.00 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
           100.01            148.01 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
           19.660            22.075 
[1] "3.0 - 100.0 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1495V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGA4 MUTATED         3        0        4         5         2         0
  PCDHGA4 WILD-TYPE      61        1       22       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA4 MUTATED           0          0          1          2        1
  PCDHGA4 WILD-TYPE        18          6         43         31       34
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGA4 MUTATED           0         0
  PCDHGA4 WILD-TYPE        12         1
D1495V3, multiclass
            clus
vv           PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 4                22
  STAGE IIA                5               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  PCDHGA4 MUTATED     0   3  10   5
  PCDHGA4 WILD-TYPE   9  64 239  36
D1495V4, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              10               239
  T4               5                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
  PCDHGA4 MUTATED    15   2   1
  PCDHGA4 WILD-TYPE 205  79  65
D1495V5, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  N0              15               205
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1495V6, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    15   1
  PCDHGA4 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     15    1
  PCDHGA4 WILD-TYPE  270   47
   clus
vv  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D1495V7, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED     7  11
  PCDHGA4 WILD-TYPE 163 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED      7   11
  PCDHGA4 WILD-TYPE  163  186
        clus
vv       PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  FEMALE               7               163
  MALE                11               186
[1] 2 2
[1] FALSE
D1495V8, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    15   1
  PCDHGA4 WILD-TYPE 285   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     15    1
  PCDHGA4 WILD-TYPE  285    7
     clus
vv    PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  NO               15               285
  YES               1                 7
[1] 2 2
[1] FALSE
D1495V9, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    13   5
  PCDHGA4 WILD-TYPE 301  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     13    5
  PCDHGA4 WILD-TYPE  301   43
                               clus
vv                              PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PCDHGA4 MUTATED    13   0   1   1
  PCDHGA4 WILD-TYPE 246   3  21  20
D1495V10, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               1                21
  RX               1                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"
D1495V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA4 MUTATED                                  0     1
  PCDHGA4 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA4 MUTATED                           2     8
  PCDHGA4 WILD-TYPE                        17   168
D1495V12, multiclass
                                  clus
vv                                 PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          8               168
[1] 4 2
[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 = NRAP MUTATION ANALYSIS
D1496V1, survival
                sevent
clus2              0   1
  NRAP MUTATED    16   6
  NRAP WILD-TYPE 261  72
  NRAP MUTATED NRAP WILD-TYPE 
            22            333 
  NRAP MUTATED NRAP WILD-TYPE 
             6             72 
$`NRAP MUTATED`
TCGA-AD-6964 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 
       10.88        35.80        26.17         8.38        20.12        63.98 
TCGA-AA-3811 TCGA-AA-3854 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 
       10.06        36.03         4.01        83.24        14.50        27.09 
TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-5861 
       11.74        12.76        10.06        15.62        30.08        15.02 
TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A28E TCGA-F4-6703 
       12.00        13.35       119.93        47.87 

$`NRAP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 
       24.53         5.79        22.42        27.42        26.47        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        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 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28F 
       44.32       131.51       135.65       139.17        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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  NRAP MUTATED NRAP WILD-TYPE 
          4.01           0.00 
  NRAP MUTATED NRAP WILD-TYPE 
        119.93         148.01 
  NRAP MUTATED NRAP WILD-TYPE 
         15.32          22.09 
[1] "4.0 - 119.9 (15.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1496V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRAP MUTATED         2        0        1        14         1         0
  NRAP WILD-TYPE      62        1       25        94         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAP MUTATED           1          0          1          1        2         0
  NRAP WILD-TYPE        17          6         43         32       33        12
                vv
clus             STAGE IVB
  NRAP MUTATED           0
  NRAP WILD-TYPE         1
D1496V3, multiclass
            clus
vv           NRAP MUTATED NRAP WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA            14             94
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  NRAP MUTATED     0   2  17   5
  NRAP WILD-TYPE   9  65 232  36
D1496V4, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  T1            0              9
  T2            2             65
  T3           17            232
  T4            5             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
  NRAP MUTATED    18   1   5
  NRAP WILD-TYPE 202  80  61
D1496V5, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  N0           18            202
  N1            1             80
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1496V6, binary
                cls
clus               0   1
  NRAP MUTATED    20   2
  NRAP WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     20    2
  NRAP WILD-TYPE  265   46
   clus
vv  NRAP MUTATED NRAP WILD-TYPE
  0           20            265
  1            2             46
[1] 2 2
[1] FALSE
D1496V7, binary
                cls
clus               0   1
  NRAP MUTATED    13  11
  NRAP WILD-TYPE 157 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     13   11
  NRAP WILD-TYPE  157  186
        clus
vv       NRAP MUTATED NRAP WILD-TYPE
  FEMALE           13            157
  MALE             11            186
[1] 2 2
[1] FALSE
D1496V8, binary
                cls
clus               0   1
  NRAP MUTATED    18   0
  NRAP WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     18    0
  NRAP WILD-TYPE  282    8
     clus
vv    NRAP MUTATED NRAP WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D1496V9, binary
                cls
clus               0   1
  NRAP MUTATED    16   8
  NRAP WILD-TYPE 298  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     16    8
  NRAP WILD-TYPE  298   40
                               clus
vv                              NRAP MUTATED NRAP WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NRAP MUTATED    15   0   1   3
  NRAP WILD-TYPE 244   3  21  18
D1496V10, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  R0           15            244
  R1            0              3
  R2            1             21
  RX            3             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"
D1496V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAP MUTATED                                  0     3
  NRAP WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAP MUTATED                           1    14
  NRAP WILD-TYPE                        18   162
D1496V12, multiclass
                                  clus
vv                                 NRAP MUTATED NRAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      14            162
[1] 4 2
[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 = DDX11 MUTATION ANALYSIS
D1497V1, survival
                 sevent
clus2               0   1
  DDX11 MUTATED     5   2
  DDX11 WILD-TYPE 272  76
  DDX11 MUTATED DDX11 WILD-TYPE 
              7             348 
  DDX11 MUTATED DDX11 WILD-TYPE 
              2              76 
$`DDX11 MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3655 TCGA-AZ-6599 
       19.04        35.80        26.17        22.06        61.02         6.77 
TCGA-CM-6674 
       12.95 

$`DDX11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DDX11 MUTATED DDX11 WILD-TYPE 
           6.77            0.00 
  DDX11 MUTATED DDX11 WILD-TYPE 
          61.02          148.01 
  DDX11 MUTATED DDX11 WILD-TYPE 
          22.06           22.06 
[1] "6.8 - 61.0 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1497V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX11 MUTATED         1        0        2         4         0         0
  DDX11 WILD-TYPE      63        1       24       104         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  DDX11 MUTATED           0
  DDX11 WILD-TYPE         1
D1497V3, multiclass
            clus
vv           DDX11 MUTATED DDX11 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DDX11 MUTATED     0   1   6   0
  DDX11 WILD-TYPE   9  66 243  41
D1497V4, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             0              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
  DDX11 MUTATED     7   0   0
  DDX11 WILD-TYPE 213  81  66
D1497V5, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  N0             7             213
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1497V6, binary
                 cls
clus                0   1
  DDX11 MUTATED     6   0
  DDX11 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      6    0
  DDX11 WILD-TYPE  279   48
   clus
vv  DDX11 MUTATED DDX11 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1497V7, binary
                 cls
clus                0   1
  DDX11 MUTATED     3   4
  DDX11 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      3    4
  DDX11 WILD-TYPE  167  193
        clus
vv       DDX11 MUTATED DDX11 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1497V8, binary
                 cls
clus                0   1
  DDX11 MUTATED     7   0
  DDX11 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      7    0
  DDX11 WILD-TYPE  293    8
     clus
vv    DDX11 MUTATED DDX11 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1497V9, binary
                 cls
clus                0   1
  DDX11 MUTATED     7   0
  DDX11 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      7    0
  DDX11 WILD-TYPE  307   48
                               clus
vv                              DDX11 MUTATED DDX11 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX11 MUTATED     6   0   0   0
  DDX11 WILD-TYPE 253   3  22  21
D1497V10, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1497V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX11 MUTATED                                  0     0
  DDX11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX11 MUTATED                           0     5
  DDX11 WILD-TYPE                        19   171
D1497V12, multiclass
                                  clus
vv                                 DDX11 MUTATED DDX11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = KIF5B MUTATION ANALYSIS
D1498V1, survival
                 sevent
clus2               0   1
  KIF5B MUTATED     9   4
  KIF5B WILD-TYPE 268  74
  KIF5B MUTATED KIF5B WILD-TYPE 
             13             342 
  KIF5B MUTATED KIF5B WILD-TYPE 
              4              74 
$`KIF5B MUTATED`
TCGA-G4-6310 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       63.62        19.66         6.97        53.00        25.02         4.01 
TCGA-AD-6889 TCGA-CA-6718 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6537 
       83.24        10.06        15.02        14.04        12.95         4.80 
TCGA-G4-6317 
       36.00 

$`KIF5B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        61.91        13.78        46.75 

  KIF5B MUTATED KIF5B WILD-TYPE 
           4.01            0.00 
  KIF5B MUTATED KIF5B WILD-TYPE 
          83.24          148.01 
  KIF5B MUTATED KIF5B WILD-TYPE 
          15.02           22.09 
[1] "4.0 - 83.2 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1498V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF5B MUTATED         2        0        3         3         1         0
  KIF5B WILD-TYPE      62        1       23       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF5B MUTATED           0          0          2          2        0         0
  KIF5B WILD-TYPE        18          6         42         31       35        12
                 vv
clus              STAGE IVB
  KIF5B MUTATED           0
  KIF5B WILD-TYPE         1
D1498V3, multiclass
            clus
vv           KIF5B MUTATED KIF5B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  KIF5B MUTATED     0   3   8   3
  KIF5B WILD-TYPE   9  64 241  38
D1498V4, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  T1             0               9
  T2             3              64
  T3             8             241
  T4             3              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
  KIF5B MUTATED    10   3   1
  KIF5B WILD-TYPE 210  78  65
D1498V5, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  N0            10             210
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1498V6, binary
                 cls
clus                0   1
  KIF5B MUTATED    10   0
  KIF5B WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     10    0
  KIF5B WILD-TYPE  275   48
   clus
vv  KIF5B MUTATED KIF5B WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1498V7, binary
                 cls
clus                0   1
  KIF5B MUTATED     4  10
  KIF5B WILD-TYPE 166 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED      4   10
  KIF5B WILD-TYPE  166  187
        clus
vv       KIF5B MUTATED KIF5B WILD-TYPE
  FEMALE             4             166
  MALE              10             187
[1] 2 2
[1] FALSE
D1498V8, binary
                 cls
clus                0   1
  KIF5B MUTATED    11   1
  KIF5B WILD-TYPE 289   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     11    1
  KIF5B WILD-TYPE  289    7
     clus
vv    KIF5B MUTATED KIF5B WILD-TYPE
  NO             11             289
  YES             1               7
[1] 2 2
[1] FALSE
D1498V9, binary
                 cls
clus                0   1
  KIF5B MUTATED    12   2
  KIF5B WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     12    2
  KIF5B WILD-TYPE  302   46
                               clus
vv                              KIF5B MUTATED KIF5B WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KIF5B MUTATED    12   0   0   1
  KIF5B WILD-TYPE 247   3  22  20
D1498V10, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D1498V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF5B MUTATED                                  0     2
  KIF5B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF5B MUTATED                           0     7
  KIF5B WILD-TYPE                        19   169
D1498V12, multiclass
                                  clus
vv                                 KIF5B MUTATED KIF5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = ZNF418 MUTATION ANALYSIS
D1499V1, survival
                  sevent
clus2                0   1
  ZNF418 MUTATED    11   2
  ZNF418 WILD-TYPE 266  76
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              13              342 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
               2               76 
$`ZNF418 MUTATED`
TCGA-AA-3715 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-3977 TCGA-AZ-4315 
       19.04        24.39        63.98         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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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           22.075 
[1] "2.0 - 83.0 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1499V2, continuous
                  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      63        1       23       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF418 MUTATED           0          0          1          1        0
  ZNF418 WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF418 MUTATED           1         1
  ZNF418 WILD-TYPE        11         0
D1499V3, multiclass
            clus
vv           ZNF418 MUTATED ZNF418 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               11
  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   9  65 239  39
D1499V4, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              2               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
  ZNF418 MUTATED    10   2   2
  ZNF418 WILD-TYPE 210  79  64
D1499V5, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  N0             10              210
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1499V6, binary
                  cls
clus                 0   1
  ZNF418 MUTATED     8   2
  ZNF418 WILD-TYPE 277  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED      8    2
  ZNF418 WILD-TYPE  277   46
   clus
vv  ZNF418 MUTATED ZNF418 WILD-TYPE
  0              8              277
  1              2               46
[1] 2 2
[1] FALSE
D1499V7, binary
                  cls
clus                 0   1
  ZNF418 MUTATED     6   8
  ZNF418 WILD-TYPE 164 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED      6    8
  ZNF418 WILD-TYPE  164  189
        clus
vv       ZNF418 MUTATED ZNF418 WILD-TYPE
  FEMALE              6              164
  MALE                8              189
[1] 2 2
[1] FALSE
D1499V8, binary
                  cls
clus                 0   1
  ZNF418 MUTATED    12   0
  ZNF418 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED     12    0
  ZNF418 WILD-TYPE  288    8
     clus
vv    ZNF418 MUTATED ZNF418 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1499V9, binary
                  cls
clus                 0   1
  ZNF418 MUTATED    12   2
  ZNF418 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED     12    2
  ZNF418 WILD-TYPE  302   46
                               clus
vv                              ZNF418 MUTATED ZNF418 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF418 MUTATED     7   0   0   3
  ZNF418 WILD-TYPE 252   3  22  18
D1499V10, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              3               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"
D1499V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF418 MUTATED                                  0     1
  ZNF418 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF418 MUTATED                           1     7
  ZNF418 WILD-TYPE                        18   169
D1499V12, multiclass
                                  clus
vv                                 ZNF418 MUTATED ZNF418 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = TRPC1 MUTATION ANALYSIS
D1500V1, survival
                 sevent
clus2               0   1
  TRPC1 MUTATED     6   5
  TRPC1 WILD-TYPE 271  73
  TRPC1 MUTATED TRPC1 WILD-TYPE 
             11             344 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
              5              73 
$`TRPC1 MUTATED`
TCGA-AD-6895 TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00A TCGA-AA-A010 TCGA-AZ-6607 
       25.08         6.97        31.00        38.04        34.98         3.19 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-5538 TCGA-DM-A1D7 TCGA-F4-6570 
       12.76        10.06        54.61        13.32         6.18 

$`TRPC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TRPC1 MUTATED TRPC1 WILD-TYPE 
           3.19            0.00 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
          54.61          148.01 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
         13.320          22.075 
[1] "3.2 - 54.6 (13.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1500V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPC1 MUTATED         1        0        1         6         2         0
  TRPC1 WILD-TYPE      63        1       25       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPC1 MUTATED           0          0          2          0        1         0
  TRPC1 WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  TRPC1 MUTATED           0
  TRPC1 WILD-TYPE         1
D1500V3, multiclass
            clus
vv           TRPC1 MUTATED TRPC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TRPC1 MUTATED     1   0   8   4
  TRPC1 WILD-TYPE   8  67 241  37
D1500V4, multiclass
    clus
vv   TRPC1 MUTATED TRPC1 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             8             241
  T4             4              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
  TRPC1 MUTATED    10   2   1
  TRPC1 WILD-TYPE 210  79  65
D1500V5, multiclass
    clus
vv   TRPC1 MUTATED TRPC1 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1500V6, binary
                 cls
clus                0   1
  TRPC1 MUTATED    11   1
  TRPC1 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC1 MUTATED     11    1
  TRPC1 WILD-TYPE  274   47
   clus
vv  TRPC1 MUTATED TRPC1 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D1500V7, binary
                 cls
clus                0   1
  TRPC1 MUTATED     6   7
  TRPC1 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC1 MUTATED      6    7
  TRPC1 WILD-TYPE  164  190
        clus
vv       TRPC1 MUTATED TRPC1 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1500V8, binary
                 cls
clus                0   1
  TRPC1 MUTATED    10   0
  TRPC1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC1 MUTATED     10    0
  TRPC1 WILD-TYPE  290    8
     clus
vv    TRPC1 MUTATED TRPC1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1500V9, binary
                 cls
clus                0   1
  TRPC1 MUTATED    10   2
  TRPC1 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC1 MUTATED     10    2
  TRPC1 WILD-TYPE  304   46
                               clus
vv                              TRPC1 MUTATED TRPC1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRPC1 MUTATED     8   0   0   3
  TRPC1 WILD-TYPE 251   3  22  18
D1500V10, multiclass
    clus
vv   TRPC1 MUTATED TRPC1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             3              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"
D1500V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPC1 MUTATED                                  0     2
  TRPC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPC1 MUTATED                           0     6
  TRPC1 WILD-TYPE                        19   170
D1500V12, multiclass
                                  clus
vv                                 TRPC1 MUTATED TRPC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ZNF124 MUTATION ANALYSIS
D1501V1, survival
                  sevent
clus2                0   1
  ZNF124 MUTATED     6   2
  ZNF124 WILD-TYPE 271  76
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              347 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               2               76 
$`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        83.24        27.09        58.39 
TCGA-CA-6717 TCGA-CM-4743 
       12.76        23.05 

$`ZNF124 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF124 MUTATED ZNF124 WILD-TYPE 
            4.01             0.00 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           83.24           148.01 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           25.07            21.99 
[1] "4.0 - 83.2 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1501V2, continuous
                  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      63        1       26       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF124 MUTATED           0          0          0          0        0
  ZNF124 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF124 MUTATED           0         0
  ZNF124 WILD-TYPE        12         1
D1501V3, multiclass
            clus
vv           ZNF124 MUTATED ZNF124 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF124 MUTATED     0   1   5   2
  ZNF124 WILD-TYPE   9  66 244  39
D1501V4, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              2               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
  ZNF124 MUTATED     8   0   0
  ZNF124 WILD-TYPE 212  81  66
D1501V5, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1501V6, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     8   0
  ZNF124 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      8    0
  ZNF124 WILD-TYPE  277   48
   clus
vv  ZNF124 MUTATED ZNF124 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1501V7, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     3   5
  ZNF124 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      3    5
  ZNF124 WILD-TYPE  167  192
        clus
vv       ZNF124 MUTATED ZNF124 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D1501V8, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     6   0
  ZNF124 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      6    0
  ZNF124 WILD-TYPE  294    8
     clus
vv    ZNF124 MUTATED ZNF124 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1501V9, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     5   3
  ZNF124 WILD-TYPE 309  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      5    3
  ZNF124 WILD-TYPE  309   45
                               clus
vv                              ZNF124 MUTATED ZNF124 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF124 MUTATED     7   0   0   1
  ZNF124 WILD-TYPE 252   3  22  20
D1501V10, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1501V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF124 MUTATED                                  0     2
  ZNF124 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF124 MUTATED                           0     5
  ZNF124 WILD-TYPE                        19   171
D1501V12, multiclass
                                  clus
vv                                 ZNF124 MUTATED ZNF124 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = KLC3 MUTATION ANALYSIS
D1502V1, survival
                sevent
clus2              0   1
  KLC3 MUTATED     6   0
  KLC3 WILD-TYPE 271  78
  KLC3 MUTATED KLC3 WILD-TYPE 
             6            349 
  KLC3 MUTATED KLC3 WILD-TYPE 
             0             78 
$`KLC3 MUTATED`
TCGA-G4-6588 TCGA-CA-6717 TCGA-CM-4752 TCGA-D5-6533 TCGA-D5-6928 TCGA-D5-6930 
       26.17        12.76        13.02        25.48        11.64        13.35 

$`KLC3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KLC3 MUTATED KLC3 WILD-TYPE 
         11.64           0.00 
  KLC3 MUTATED KLC3 WILD-TYPE 
         26.17         148.01 
  KLC3 MUTATED KLC3 WILD-TYPE 
        13.185         22.090 
[1] "11.6 - 26.2 (13.2)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1502V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLC3 MUTATED         0        0        0         5         0         0
  KLC3 WILD-TYPE      64        1       26       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLC3 MUTATED           0          0          0          0        0         0
  KLC3 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  KLC3 MUTATED           0
  KLC3 WILD-TYPE         1
D1502V3, multiclass
            clus
vv           KLC3 MUTATED KLC3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  KLC3 MUTATED     0   0   5   1
  KLC3 WILD-TYPE   9  67 244  40
D1502V4, multiclass
    clus
vv   KLC3 MUTATED KLC3 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            1             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
  KLC3 MUTATED     6   0   0
  KLC3 WILD-TYPE 214  81  66
D1502V5, multiclass
    clus
vv   KLC3 MUTATED KLC3 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1502V6, binary
                cls
clus               0   1
  KLC3 MUTATED     6   0
  KLC3 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC3 MUTATED      6    0
  KLC3 WILD-TYPE  279   48
   clus
vv  KLC3 MUTATED KLC3 WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1502V7, binary
                cls
clus               0   1
  KLC3 MUTATED     2   4
  KLC3 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC3 MUTATED      2    4
  KLC3 WILD-TYPE  168  193
        clus
vv       KLC3 MUTATED KLC3 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1502V8, binary
                cls
clus               0   1
  KLC3 MUTATED     6   0
  KLC3 WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC3 MUTATED      6    0
  KLC3 WILD-TYPE  294    8
     clus
vv    KLC3 MUTATED KLC3 WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1502V9, binary
                cls
clus               0   1
  KLC3 MUTATED     3   3
  KLC3 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC3 MUTATED      3    3
  KLC3 WILD-TYPE  311   45
                               clus
vv                              KLC3 MUTATED KLC3 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLC3 MUTATED     5   0   0   1
  KLC3 WILD-TYPE 254   3  22  20
D1502V10, multiclass
    clus
vv   KLC3 MUTATED KLC3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1502V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLC3 MUTATED                                  0     1
  KLC3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLC3 MUTATED                           1     4
  KLC3 WILD-TYPE                        18   172
D1502V12, multiclass
                                  clus
vv                                 KLC3 MUTATED KLC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       4            172
[1] 4 2
[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 = KIAA0528 MUTATION ANALYSIS
D1503V1, survival
                    sevent
clus2                  0   1
  KIAA0528 MUTATED    11   3
  KIAA0528 WILD-TYPE 266  75
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                14                341 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                 3                 75 
$`KIAA0528 MUTATED`
TCGA-AA-3543 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3956 
        0.99        10.88       100.01        63.98         6.97        34.03 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A02K TCGA-AU-6004 TCGA-AZ-4315 TCGA-CM-5861 
       25.02        34.98        14.01        27.09        58.39        15.02 
TCGA-CM-6165 TCGA-CM-6166 
       16.04        21.99 

$`KIAA0528 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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             22.060 
[1] "1.0 - 100.0 (23.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1503V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0528 MUTATED         3        0        3         4         2         0
  KIAA0528 WILD-TYPE      61        1       23       104         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0528 MUTATED           0          0          0          0        1
  KIAA0528 WILD-TYPE        18          6         44         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0528 MUTATED           0         0
  KIAA0528 WILD-TYPE        12         1
D1503V3, multiclass
            clus
vv           KIAA0528 MUTATED KIAA0528 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                 4                104
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  KIAA0528 MUTATED     0   4   7   4
  KIAA0528 WILD-TYPE   9  63 242  37
D1503V4, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  T1                0                  9
  T2                4                 63
  T3                7                242
  T4                4                 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
  KIAA0528 MUTATED    13   0   2
  KIAA0528 WILD-TYPE 207  81  64
D1503V5, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  N0               13                207
  N1                0                 81
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1503V6, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    11   1
  KIAA0528 WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     11    1
  KIAA0528 WILD-TYPE  274   47
   clus
vv  KIAA0528 MUTATED KIAA0528 WILD-TYPE
  0               11                274
  1                1                 47
[1] 2 2
[1] FALSE
D1503V7, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED     5  10
  KIAA0528 WILD-TYPE 165 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED      5   10
  KIAA0528 WILD-TYPE  165  187
        clus
vv       KIAA0528 MUTATED KIAA0528 WILD-TYPE
  FEMALE                5                165
  MALE                 10                187
[1] 2 2
[1] FALSE
D1503V8, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    13   0
  KIAA0528 WILD-TYPE 287   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     13    0
  KIAA0528 WILD-TYPE  287    8
     clus
vv    KIAA0528 MUTATED KIAA0528 WILD-TYPE
  NO                13                287
  YES                0                  8
[1] 2 2
[1] FALSE
D1503V9, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    14   1
  KIAA0528 WILD-TYPE 300  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     14    1
  KIAA0528 WILD-TYPE  300   47
                               clus
vv                              KIAA0528 MUTATED KIAA0528 WILD-TYPE
  COLON ADENOCARCINOMA                        14                300
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0528 MUTATED    10   0   1   1
  KIAA0528 WILD-TYPE 249   3  21  20
D1503V10, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  R0               10                249
  R1                0                  3
  R2                1                 21
  RX                1                 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"
D1503V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0528 MUTATED                                  0     0
  KIAA0528 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0528 MUTATED                           0     8
  KIAA0528 WILD-TYPE                        19   168
D1503V12, multiclass
                                  clus
vv                                 KIAA0528 MUTATED KIAA0528 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           8                168
[1] 4 2
[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 = RNF219 MUTATION ANALYSIS
D1504V1, survival
                  sevent
clus2                0   1
  RNF219 MUTATED    12   2
  RNF219 WILD-TYPE 265  76
  RNF219 MUTATED RNF219 WILD-TYPE 
              14              341 
  RNF219 MUTATED RNF219 WILD-TYPE 
               2               76 
$`RNF219 MUTATED`
TCGA-A6-5660 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-6598 TCGA-CA-6717 
       29.19         1.02        14.50         0.20        49.41        12.76 
TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-6540 TCGA-D5-6923 TCGA-D5-6928 
       10.06        15.02        19.59        16.14        12.43        11.64 
TCGA-G4-6309 TCGA-G4-6323 
       85.48        13.78 

$`RNF219 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       12.39        10.13        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        46.75 

  RNF219 MUTATED RNF219 WILD-TYPE 
             0.2              0.0 
  RNF219 MUTATED RNF219 WILD-TYPE 
           85.48           148.01 
  RNF219 MUTATED RNF219 WILD-TYPE 
           14.14            22.42 
[1] "0.2 - 85.5 (14.1)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D1504V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF219 MUTATED         2        1        2         5         0         0
  RNF219 WILD-TYPE      62        0       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF219 MUTATED           0          1          1          2        0
  RNF219 WILD-TYPE        18          5         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF219 MUTATED           0         0
  RNF219 WILD-TYPE        12         1
D1504V3, multiclass
            clus
vv           RNF219 MUTATED RNF219 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  RNF219 MUTATED     0   2  11   0
  RNF219 WILD-TYPE   9  65 238  41
D1504V4, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             11              238
  T4              0               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
  RNF219 MUTATED    10   2   2
  RNF219 WILD-TYPE 210  79  64
D1504V5, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  N0             10              210
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1504V6, binary
                  cls
clus                 0   1
  RNF219 MUTATED    11   0
  RNF219 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED     11    0
  RNF219 WILD-TYPE  274   48
   clus
vv  RNF219 MUTATED RNF219 WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D1504V7, binary
                  cls
clus                 0   1
  RNF219 MUTATED     5   9
  RNF219 WILD-TYPE 165 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED      5    9
  RNF219 WILD-TYPE  165  188
        clus
vv       RNF219 MUTATED RNF219 WILD-TYPE
  FEMALE              5              165
  MALE                9              188
[1] 2 2
[1] FALSE
D1504V8, binary
                  cls
clus                 0   1
  RNF219 MUTATED    12   0
  RNF219 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED     12    0
  RNF219 WILD-TYPE  288    8
     clus
vv    RNF219 MUTATED RNF219 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1504V9, binary
                  cls
clus                 0   1
  RNF219 MUTATED     9   5
  RNF219 WILD-TYPE 305  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED      9    5
  RNF219 WILD-TYPE  305   43
                               clus
vv                              RNF219 MUTATED RNF219 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF219 MUTATED    10   0   0   2
  RNF219 WILD-TYPE 249   3  22  19
D1504V10, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D1504V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF219 MUTATED                                  0     2
  RNF219 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF219 MUTATED                           3     8
  RNF219 WILD-TYPE                        16   168
D1504V12, multiclass
                                  clus
vv                                 RNF219 MUTATED RNF219 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         8              168
[1] 4 2
[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 = MED12L MUTATION ANALYSIS
D1505V1, survival
                  sevent
clus2                0   1
  MED12L MUTATED    24   3
  MED12L WILD-TYPE 253  75
  MED12L MUTATED MED12L WILD-TYPE 
              27              328 
  MED12L MUTATED MED12L WILD-TYPE 
               3               75 
$`MED12L MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3713 TCGA-AA-3950 
       14.53         1.02        34.03         0.99        19.04        24.00 
TCGA-AA-3986 TCGA-AD-6895 TCGA-AZ-4681 TCGA-G4-6586 TCGA-A6-5659 TCGA-AA-3510 
       19.07        25.08       106.75        35.80        30.44        63.98 
TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       29.95        26.01        25.02         4.01        34.98         1.02 
TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 
       12.16        33.01        58.39        49.41        12.76        51.32 
TCGA-D5-6920 TCGA-D5-6928 TCGA-F4-6807 
       12.39        11.64        43.04 

$`MED12L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        24.16        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
        8.05        19.07        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        24.00        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MED12L MUTATED MED12L WILD-TYPE 
            0.99             0.00 
  MED12L MUTATED MED12L WILD-TYPE 
          106.75           148.01 
  MED12L MUTATED MED12L WILD-TYPE 
           25.08            21.99 
[1] "1.0 - 106.8 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1505V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED12L MUTATED         4        0        4        12         2         0
  MED12L WILD-TYPE      60        1       22        96         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MED12L MUTATED           0          0          2          1        1
  MED12L WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  MED12L MUTATED           1         0
  MED12L WILD-TYPE        11         1
D1505V3, multiclass
            clus
vv           MED12L MUTATED MED12L WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA              12               96
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  MED12L MUTATED     0   5  21   2
  MED12L WILD-TYPE   9  62 228  39
D1505V4, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  T1              0                9
  T2              5               62
  T3             21              228
  T4              2               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
  MED12L MUTATED    24   3   1
  MED12L WILD-TYPE 196  78  65
D1505V5, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  N0             24              196
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1505V6, binary
                  cls
clus                 0   1
  MED12L MUTATED    22   2
  MED12L WILD-TYPE 263  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     22    2
  MED12L WILD-TYPE  263   46
   clus
vv  MED12L MUTATED MED12L WILD-TYPE
  0             22              263
  1              2               46
[1] 2 2
[1] FALSE
D1505V7, binary
                  cls
clus                 0   1
  MED12L MUTATED    15  13
  MED12L WILD-TYPE 155 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     15   13
  MED12L WILD-TYPE  155  184
        clus
vv       MED12L MUTATED MED12L WILD-TYPE
  FEMALE             15              155
  MALE               13              184
[1] 2 2
[1] FALSE
D1505V8, binary
                  cls
clus                 0   1
  MED12L MUTATED    23   1
  MED12L WILD-TYPE 277   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     23    1
  MED12L WILD-TYPE  277    7
     clus
vv    MED12L MUTATED MED12L WILD-TYPE
  NO              23              277
  YES              1                7
[1] 2 2
[1] FALSE
D1505V9, binary
                  cls
clus                 0   1
  MED12L MUTATED    20   8
  MED12L WILD-TYPE 294  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     20    8
  MED12L WILD-TYPE  294   40
                               clus
vv                              MED12L MUTATED MED12L WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MED12L MUTATED    22   0   1   2
  MED12L WILD-TYPE 237   3  21  19
D1505V10, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  R0             22              237
  R1              0                3
  R2              1               21
  RX              2               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"
D1505V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED12L MUTATED                                  0     1
  MED12L WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MED12L MUTATED                           1    12
  MED12L WILD-TYPE                        18   164
D1505V12, multiclass
                                  clus
vv                                 MED12L MUTATED MED12L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = PIWIL1 MUTATION ANALYSIS
D1506V1, survival
                  sevent
clus2                0   1
  PIWIL1 MUTATED    19   2
  PIWIL1 WILD-TYPE 258  76
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
              21              334 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
               2               76 
$`PIWIL1 MUTATED`
TCGA-AD-6548 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       21.37        30.44        33.53         8.38        21.76        24.39 
TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6890 TCGA-AZ-6600 
        3.02         1.02        25.02        34.98        24.53        12.10 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-4746 TCGA-D5-5539 
       12.39        12.20        12.76        17.56        37.02        19.59 
TCGA-D5-6532 TCGA-D5-6927 TCGA-D5-6930 
       18.25         9.44        13.35 

$`PIWIL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 
       32.75        36.53        32.91        31.63        29.19        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-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       25.18        24.69        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
       12.69        12.36        12.59        12.59        10.06        14.30 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         2.01       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        14.04        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-D5-6533 
       45.40        54.61        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
            1.02             0.00 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
           37.02           148.01 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
           18.25            22.39 
[1] "1.0 - 37.0 (18.2)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D1506V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIWIL1 MUTATED         5        0        2         8         1         0
  PIWIL1 WILD-TYPE      59        1       24       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIWIL1 MUTATED           0          1          2          0        1
  PIWIL1 WILD-TYPE        18          5         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PIWIL1 MUTATED           0         0
  PIWIL1 WILD-TYPE        12         1
D1506V3, multiclass
            clus
vv           PIWIL1 MUTATED PIWIL1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  PIWIL1 MUTATED     1   6  11   4
  PIWIL1 WILD-TYPE   8  61 238  37
D1506V4, multiclass
    clus
vv   PIWIL1 MUTATED PIWIL1 WILD-TYPE
  T1              1                8
  T2              6               61
  T3             11              238
  T4              4               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
  PIWIL1 MUTATED    18   4   0
  PIWIL1 WILD-TYPE 202  77  66
D1506V5, multiclass
    clus
vv   PIWIL1 MUTATED PIWIL1 WILD-TYPE
  N0             18              202
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1506V6, binary
                  cls
clus                 0   1
  PIWIL1 MUTATED    18   1
  PIWIL1 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL1 MUTATED     18    1
  PIWIL1 WILD-TYPE  267   47
   clus
vv  PIWIL1 MUTATED PIWIL1 WILD-TYPE
  0             18              267
  1              1               47
[1] 2 2
[1] FALSE
D1506V7, binary
                  cls
clus                 0   1
  PIWIL1 MUTATED     9  13
  PIWIL1 WILD-TYPE 161 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL1 MUTATED      9   13
  PIWIL1 WILD-TYPE  161  184
        clus
vv       PIWIL1 MUTATED PIWIL1 WILD-TYPE
  FEMALE              9              161
  MALE               13              184
[1] 2 2
[1] FALSE
D1506V8, binary
                  cls
clus                 0   1
  PIWIL1 MUTATED    21   0
  PIWIL1 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL1 MUTATED     21    0
  PIWIL1 WILD-TYPE  279    8
     clus
vv    PIWIL1 MUTATED PIWIL1 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D1506V9, binary
                  cls
clus                 0   1
  PIWIL1 MUTATED    17   5
  PIWIL1 WILD-TYPE 297  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL1 MUTATED     17    5
  PIWIL1 WILD-TYPE  297   43
                               clus
vv                              PIWIL1 MUTATED PIWIL1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIWIL1 MUTATED    13   0   0   3
  PIWIL1 WILD-TYPE 246   3  22  18
D1506V10, multiclass
    clus
vv   PIWIL1 MUTATED PIWIL1 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              3               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"
D1506V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIWIL1 MUTATED                                  0     3
  PIWIL1 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIWIL1 MUTATED                           4    10
  PIWIL1 WILD-TYPE                        15   166
D1506V12, multiclass
                                  clus
vv                                 PIWIL1 MUTATED PIWIL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                        10              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(1507) Variable = ZNF546 MUTATION ANALYSIS
D1507V1, survival
                  sevent
clus2                0   1
  ZNF546 MUTATED    11   3
  ZNF546 WILD-TYPE 266  75
  ZNF546 MUTATED ZNF546 WILD-TYPE 
              14              341 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
               3               75 
$`ZNF546 MUTATED`
TCGA-G4-6310 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3977 
       63.62        32.75        32.71         3.02        63.98        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 
        4.01        34.98        21.44        17.82        58.39        12.76 
TCGA-CM-6678 TCGA-F4-6570 
       11.01         6.18 

$`ZNF546 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        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-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20         1.41         5.13        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF546 MUTATED ZNF546 WILD-TYPE 
            3.02             0.00 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
           63.98           148.01 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
           23.23            22.06 
[1] "3.0 - 64.0 (23.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1507V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF546 MUTATED         0        0        2         5         3         1
  ZNF546 WILD-TYPE      64        1       24       103         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF546 MUTATED           0          0          2          0        0
  ZNF546 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF546 MUTATED           1         0
  ZNF546 WILD-TYPE        11         1
D1507V3, multiclass
            clus
vv           ZNF546 MUTATED ZNF546 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF546 MUTATED     0   1   9   5
  ZNF546 WILD-TYPE   9  66 240  36
D1507V4, multiclass
    clus
vv   ZNF546 MUTATED ZNF546 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              9              240
  T4              5               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
  ZNF546 MUTATED    12   3   0
  ZNF546 WILD-TYPE 208  78  66
D1507V5, multiclass
    clus
vv   ZNF546 MUTATED ZNF546 WILD-TYPE
  N0             12              208
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1507V6, binary
                  cls
clus                 0   1
  ZNF546 MUTATED    12   1
  ZNF546 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF546 MUTATED     12    1
  ZNF546 WILD-TYPE  273   47
   clus
vv  ZNF546 MUTATED ZNF546 WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D1507V7, binary
                  cls
clus                 0   1
  ZNF546 MUTATED     7   8
  ZNF546 WILD-TYPE 163 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF546 MUTATED      7    8
  ZNF546 WILD-TYPE  163  189
        clus
vv       ZNF546 MUTATED ZNF546 WILD-TYPE
  FEMALE              7              163
  MALE                8              189
[1] 2 2
[1] FALSE
D1507V8, binary
                  cls
clus                 0   1
  ZNF546 MUTATED    12   1
  ZNF546 WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF546 MUTATED     12    1
  ZNF546 WILD-TYPE  288    7
     clus
vv    ZNF546 MUTATED ZNF546 WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D1507V9, binary
                  cls
clus                 0   1
  ZNF546 MUTATED    12   3
  ZNF546 WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF546 MUTATED     12    3
  ZNF546 WILD-TYPE  302   45
                               clus
vv                              ZNF546 MUTATED ZNF546 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF546 MUTATED    12   0   0   1
  ZNF546 WILD-TYPE 247   3  22  20
D1507V10, multiclass
    clus
vv   ZNF546 MUTATED ZNF546 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              1               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"
D1507V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF546 MUTATED                                  0     1
  ZNF546 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF546 MUTATED                           1     7
  ZNF546 WILD-TYPE                        18   169
D1507V12, multiclass
                                  clus
vv                                 ZNF546 MUTATED ZNF546 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         7              169
[1] 4 2
[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 = ZNF643 MUTATION ANALYSIS
D1508V1, survival
                  sevent
clus2                0   1
  ZNF643 MUTATED     6   2
  ZNF643 WILD-TYPE 271  76
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               8              347 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               2               76 
$`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 
       35.74        46.75 

$`ZNF643 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6570 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        43.04        33.67        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 
       55.04        85.48        61.91        36.00        13.78 

  ZNF643 MUTATED ZNF643 WILD-TYPE 
            4.01             0.00 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
           85.05           148.01 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
           35.36            22.03 
[1] "4.0 - 85.0 (35.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1508V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF643 MUTATED         1        0        1         3         2         0
  ZNF643 WILD-TYPE      63        1       25       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF643 MUTATED           0          0          2          0        0
  ZNF643 WILD-TYPE        18          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF643 MUTATED           0         0
  ZNF643 WILD-TYPE        12         1
D1508V3, multiclass
            clus
vv           ZNF643 MUTATED ZNF643 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF643 MUTATED     0   1   5   3
  ZNF643 WILD-TYPE   9  66 244  38
D1508V4, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              3               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
  ZNF643 MUTATED     7   2   0
  ZNF643 WILD-TYPE 213  79  66
D1508V5, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1508V6, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     8   0
  ZNF643 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      8    0
  ZNF643 WILD-TYPE  277   48
   clus
vv  ZNF643 MUTATED ZNF643 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1508V7, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     4   5
  ZNF643 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      4    5
  ZNF643 WILD-TYPE  166  192
        clus
vv       ZNF643 MUTATED ZNF643 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D1508V8, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     7   0
  ZNF643 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      7    0
  ZNF643 WILD-TYPE  293    8
     clus
vv    ZNF643 MUTATED ZNF643 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1508V9, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     8   1
  ZNF643 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      8    1
  ZNF643 WILD-TYPE  306   47
                               clus
vv                              ZNF643 MUTATED ZNF643 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF643 MUTATED     7   0   0   2
  ZNF643 WILD-TYPE 252   3  22  19
D1508V10, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              2               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"
D1508V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF643 MUTATED                                  0     0
  ZNF643 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF643 MUTATED                           0     5
  ZNF643 WILD-TYPE                        19   171
D1508V12, multiclass
                                  clus
vv                                 ZNF643 MUTATED ZNF643 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = ANK3 MUTATION ANALYSIS
D1509V1, survival
                sevent
clus2              0   1
  ANK3 MUTATED    35  10
  ANK3 WILD-TYPE 242  68
  ANK3 MUTATED ANK3 WILD-TYPE 
            45            310 
  ANK3 MUTATED ANK3 WILD-TYPE 
            10             68 
$`ANK3 MUTATED`
TCGA-A6-2677 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 
       24.33         1.02        13.02        17.95         0.92        19.04 
TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5661 
       19.04        24.00       100.01        35.80        79.69        33.53 
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3663 
       22.06         8.38         3.02        35.01        63.98         6.97 
TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 
       10.06        25.02        18.05         4.01        17.03        34.98 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 
       38.07         1.02        35.01        12.16        83.24        14.50 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-6168 
       27.09        58.39        49.41        12.76        82.95        12.99 
TCGA-CM-6171 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6703 
       14.04        16.14        12.39        11.64       135.65        47.87 
TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6309 
       33.67        53.62        85.48 

$`ANK3 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       14.53        24.16        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 
       19.99         6.05        19.00        36.00        85.05        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3511 
       23.87        20.12        19.66        20.28         7.04         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
        0.99        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        31.00         1.02        33.04         1.02        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-6890 
        0.92        41.00        39.98        18.05        40.96        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        27.42        26.47        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ANK3 MUTATED ANK3 WILD-TYPE 
          0.92           0.00 
  ANK3 MUTATED ANK3 WILD-TYPE 
        135.65         148.01 
  ANK3 MUTATED ANK3 WILD-TYPE 
         22.06          22.06 
[1] "0.9 - 135.7 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1509V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANK3 MUTATED         7        0        8        17         3         0
  ANK3 WILD-TYPE      57        1       18        91         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ANK3 MUTATED           6          0          4          1        1         0
  ANK3 WILD-TYPE        12          6         40         32       34        12
                vv
clus             STAGE IVB
  ANK3 MUTATED           0
  ANK3 WILD-TYPE         1
D1509V3, multiclass
            clus
vv           ANK3 MUTATED ANK3 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              8             18
  STAGE IIA            17             91
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             6             12
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  ANK3 MUTATED     1   7  36   4
  ANK3 WILD-TYPE   8  60 213  37
D1509V4, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  T1            1              8
  T2            7             60
  T3           36            213
  T4            4             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
  ANK3 MUTATED    37   6   5
  ANK3 WILD-TYPE 183  75  61
D1509V5, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  N0           37            183
  N1            6             75
  N2            5             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1509V6, binary
                cls
clus               0   1
  ANK3 MUTATED    43   1
  ANK3 WILD-TYPE 242  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     43    1
  ANK3 WILD-TYPE  242   47
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0           43            242
  1            1             47
[1] 2 2
[1] FALSE
D1509V7, binary
                cls
clus               0   1
  ANK3 MUTATED    26  22
  ANK3 WILD-TYPE 144 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     26   22
  ANK3 WILD-TYPE  144  175
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE           26            144
  MALE             22            175
[1] 2 2
[1] FALSE
D1509V8, binary
                cls
clus               0   1
  ANK3 MUTATED    38   2
  ANK3 WILD-TYPE 262   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     38    2
  ANK3 WILD-TYPE  262    6
     clus
vv    ANK3 MUTATED ANK3 WILD-TYPE
  NO            38            262
  YES            2              6
[1] 2 2
[1] FALSE
D1509V9, binary
                cls
clus               0   1
  ANK3 MUTATED    38   9
  ANK3 WILD-TYPE 276  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     38    9
  ANK3 WILD-TYPE  276   39
                               clus
vv                              ANK3 MUTATED ANK3 WILD-TYPE
  COLON ADENOCARCINOMA                    38            276
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ANK3 MUTATED    39   0   1   2
  ANK3 WILD-TYPE 220   3  21  19
D1509V10, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  R0           39            220
  R1            0              3
  R2            1             21
  RX            2             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"
D1509V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANK3 MUTATED                                  0     2
  ANK3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ANK3 MUTATED                           4    19
  ANK3 WILD-TYPE                        15   157
D1509V12, multiclass
                                  clus
vv                                 ANK3 MUTATED ANK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      19            157
[1] 4 2
[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 = KRT25 MUTATION ANALYSIS
D1510V1, survival
                 sevent
clus2               0   1
  KRT25 MUTATED     8   2
  KRT25 WILD-TYPE 269  76
  KRT25 MUTATED KRT25 WILD-TYPE 
             10             345 
  KRT25 MUTATED KRT25 WILD-TYPE 
              2              76 
$`KRT25 MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3715 TCGA-A6-6781 TCGA-AA-3833 TCGA-AA-A01Q 
       14.53         6.05        19.04        19.66        15.95         1.02 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5860 TCGA-F4-6856 
       12.76       148.01        32.02        35.31 

$`KRT25 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02         1.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        12.20 
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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KRT25 MUTATED KRT25 WILD-TYPE 
           1.02            0.00 
  KRT25 MUTATED KRT25 WILD-TYPE 
         148.01          140.38 
  KRT25 MUTATED KRT25 WILD-TYPE 
         17.495          22.090 
[1] "1.0 - 148.0 (17.5)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D1510V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT25 MUTATED         1        0        2         4         0         0
  KRT25 WILD-TYPE      63        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT25 MUTATED           1          0          0          1        1         0
  KRT25 WILD-TYPE        17          6         44         32       34        12
                 vv
clus              STAGE IVB
  KRT25 MUTATED           0
  KRT25 WILD-TYPE         1
D1510V3, multiclass
            clus
vv           KRT25 MUTATED KRT25 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  KRT25 MUTATED     0   1   7   2
  KRT25 WILD-TYPE   9  66 242  39
D1510V4, multiclass
    clus
vv   KRT25 MUTATED KRT25 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             2              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
  KRT25 MUTATED     7   2   1
  KRT25 WILD-TYPE 213  79  65
D1510V5, multiclass
    clus
vv   KRT25 MUTATED KRT25 WILD-TYPE
  N0             7             213
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1510V6, binary
                 cls
clus                0   1
  KRT25 MUTATED     8   1
  KRT25 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      8    1
  KRT25 WILD-TYPE  277   47
   clus
vv  KRT25 MUTATED KRT25 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1510V7, binary
                 cls
clus                0   1
  KRT25 MUTATED     4   6
  KRT25 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      4    6
  KRT25 WILD-TYPE  166  191
        clus
vv       KRT25 MUTATED KRT25 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1510V8, binary
                 cls
clus                0   1
  KRT25 MUTATED     9   0
  KRT25 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      9    0
  KRT25 WILD-TYPE  291    8
     clus
vv    KRT25 MUTATED KRT25 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1510V9, binary
                 cls
clus                0   1
  KRT25 MUTATED     7   3
  KRT25 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      7    3
  KRT25 WILD-TYPE  307   45
                               clus
vv                              KRT25 MUTATED KRT25 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KRT25 MUTATED     7   0   1   1
  KRT25 WILD-TYPE 252   3  21  20
D1510V10, multiclass
    clus
vv   KRT25 MUTATED KRT25 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             1              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"
D1510V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT25 MUTATED                                  0     1
  KRT25 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT25 MUTATED                           0     5
  KRT25 WILD-TYPE                        19   171
D1510V12, multiclass
                                  clus
vv                                 KRT25 MUTATED KRT25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = ACTA1 MUTATION ANALYSIS
D1511V1, survival
                 sevent
clus2               0   1
  ACTA1 MUTATED     7   5
  ACTA1 WILD-TYPE 270  73
  ACTA1 MUTATED ACTA1 WILD-TYPE 
             12             343 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
              5              73 
$`ACTA1 MUTATED`
TCGA-AA-3715 TCGA-AD-6964 TCGA-G4-6586 TCGA-A6-5665 TCGA-AA-3833 TCGA-AA-A01R 
       19.04        10.88        35.80        22.06        15.95        35.01 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6928 TCGA-DM-A0XD TCGA-F4-6460 TCGA-F4-6704 
       49.41        12.76        11.64        24.43        31.96         1.55 

$`ACTA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02         1.02        17.98        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        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-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ACTA1 MUTATED ACTA1 WILD-TYPE 
           1.55            0.00 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
          49.41          148.01 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
          20.55           22.09 
[1] "1.6 - 49.4 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D1511V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTA1 MUTATED         0        0        2         6         0         0
  ACTA1 WILD-TYPE      64        1       24       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTA1 MUTATED           1          0          1          1        0         0
  ACTA1 WILD-TYPE        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  ACTA1 MUTATED           0
  ACTA1 WILD-TYPE         1
D1511V3, multiclass
            clus
vv           ACTA1 MUTATED ACTA1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ACTA1 MUTATED     0   0  11   1
  ACTA1 WILD-TYPE   9  67 238  40
D1511V4, multiclass
    clus
vv   ACTA1 MUTATED ACTA1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            11             238
  T4             1              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
  ACTA1 MUTATED     8   1   3
  ACTA1 WILD-TYPE 212  80  63
D1511V5, multiclass
    clus
vv   ACTA1 MUTATED ACTA1 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             3              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"
D1511V6, binary
                 cls
clus                0   1
  ACTA1 MUTATED     9   0
  ACTA1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED      9    0
  ACTA1 WILD-TYPE  276   48
   clus
vv  ACTA1 MUTATED ACTA1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1511V7, binary
                 cls
clus                0   1
  ACTA1 MUTATED     5   7
  ACTA1 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED      5    7
  ACTA1 WILD-TYPE  165  190
        clus
vv       ACTA1 MUTATED ACTA1 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D1511V8, binary
                 cls
clus                0   1
  ACTA1 MUTATED     9   1
  ACTA1 WILD-TYPE 291   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED      9    1
  ACTA1 WILD-TYPE  291    7
     clus
vv    ACTA1 MUTATED ACTA1 WILD-TYPE
  NO              9             291
  YES             1               7
[1] 2 2
[1] FALSE
D1511V9, binary
                 cls
clus                0   1
  ACTA1 MUTATED     8   4
  ACTA1 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED      8    4
  ACTA1 WILD-TYPE  306   44
                               clus
vv                              ACTA1 MUTATED ACTA1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACTA1 MUTATED     8   0   0   1
  ACTA1 WILD-TYPE 251   3  22  20
D1511V10, multiclass
    clus
vv   ACTA1 MUTATED ACTA1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1511V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTA1 MUTATED                                  1     1
  ACTA1 WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACTA1 MUTATED                           0     7
  ACTA1 WILD-TYPE                        19   169
D1511V12, multiclass
                                  clus
vv                                 ACTA1 MUTATED ACTA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = RNF10 MUTATION ANALYSIS
D1512V1, survival
                 sevent
clus2               0   1
  RNF10 MUTATED    12   1
  RNF10 WILD-TYPE 265  77
  RNF10 MUTATED RNF10 WILD-TYPE 
             13             342 
  RNF10 MUTATED RNF10 WILD-TYPE 
              1              77 
$`RNF10 MUTATED`
TCGA-AA-3554 TCGA-AA-3950 TCGA-G4-6321 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3864 
       17.95        24.00        22.09        63.98        33.04        53.00 
TCGA-AA-A00U TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5348 TCGA-DM-A0XD 
       17.03        58.39        12.76        20.02        22.98        24.43 
TCGA-DM-A1D9 
      140.38 

$`RNF10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       18.05         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        23.05        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RNF10 MUTATED RNF10 WILD-TYPE 
          12.76            0.00 
  RNF10 MUTATED RNF10 WILD-TYPE 
         140.38          148.01 
  RNF10 MUTATED RNF10 WILD-TYPE 
          24.00           21.99 
[1] "12.8 - 140.4 (24.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3.9"
D1512V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF10 MUTATED         1        0        2         7         0         0
  RNF10 WILD-TYPE      63        1       24       101         8         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        17          6         42         33       35        12
                 vv
clus              STAGE IVB
  RNF10 MUTATED           0
  RNF10 WILD-TYPE         1
D1512V3, multiclass
            clus
vv           RNF10 MUTATED RNF10 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RNF10 MUTATED     0   2  11   0
  RNF10 WILD-TYPE   9  65 238  41
D1512V4, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            11             238
  T4             0              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
  RNF10 MUTATED    10   3   0
  RNF10 WILD-TYPE 210  78  66
D1512V5, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  N0            10             210
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1512V6, binary
                 cls
clus                0   1
  RNF10 MUTATED    12   0
  RNF10 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     12    0
  RNF10 WILD-TYPE  273   48
   clus
vv  RNF10 MUTATED RNF10 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D1512V7, binary
                 cls
clus                0   1
  RNF10 MUTATED     5   8
  RNF10 WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED      5    8
  RNF10 WILD-TYPE  165  189
        clus
vv       RNF10 MUTATED RNF10 WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D1512V8, binary
                 cls
clus                0   1
  RNF10 MUTATED    11   0
  RNF10 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     11    0
  RNF10 WILD-TYPE  289    8
     clus
vv    RNF10 MUTATED RNF10 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1512V9, binary
                 cls
clus                0   1
  RNF10 MUTATED    11   2
  RNF10 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     11    2
  RNF10 WILD-TYPE  303   46
                               clus
vv                              RNF10 MUTATED RNF10 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF10 MUTATED    10   0   0   1
  RNF10 WILD-TYPE 249   3  22  20
D1512V10, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             1              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"
D1512V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF10 MUTATED                                  0     1
  RNF10 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF10 MUTATED                           0     6
  RNF10 WILD-TYPE                        19   170
D1512V12, multiclass
                                  clus
vv                                 RNF10 MUTATED RNF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ZNF577 MUTATION ANALYSIS
D1513V1, survival
                  sevent
clus2                0   1
  ZNF577 MUTATED    10   2
  ZNF577 WILD-TYPE 267  76
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              12              343 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
               2               76 
$`ZNF577 MUTATED`
TCGA-A6-6649 TCGA-G4-6628 TCGA-A6-2678 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 
       24.16        79.69        42.28        29.95         4.01        34.98 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-6171 TCGA-D5-6931 
       12.76        10.06        22.98        15.02        14.04        12.00 

$`ZNF577 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.90        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZNF577 MUTATED ZNF577 WILD-TYPE 
            4.01             0.00 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
           79.69           148.01 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
           19.00            22.06 
[1] "4.0 - 79.7 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1513V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF577 MUTATED         3        0        0         3         2         0
  ZNF577 WILD-TYPE      61        1       26       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF577 MUTATED           0          0          3          1        0
  ZNF577 WILD-TYPE        18          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF577 MUTATED           0         0
  ZNF577 WILD-TYPE        12         1
D1513V3, multiclass
            clus
vv           ZNF577 MUTATED ZNF577 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF577 MUTATED     0   3   6   3
  ZNF577 WILD-TYPE   9  64 243  38
D1513V4, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              6              243
  T4              3               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
  ZNF577 MUTATED     8   3   1
  ZNF577 WILD-TYPE 212  78  65
D1513V5, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  N0              8              212
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1513V6, binary
                  cls
clus                 0   1
  ZNF577 MUTATED    12   0
  ZNF577 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED     12    0
  ZNF577 WILD-TYPE  273   48
   clus
vv  ZNF577 MUTATED ZNF577 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1513V7, binary
                  cls
clus                 0   1
  ZNF577 MUTATED     4   8
  ZNF577 WILD-TYPE 166 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED      4    8
  ZNF577 WILD-TYPE  166  189
        clus
vv       ZNF577 MUTATED ZNF577 WILD-TYPE
  FEMALE              4              166
  MALE                8              189
[1] 2 2
[1] FALSE
D1513V8, binary
                  cls
clus                 0   1
  ZNF577 MUTATED    11   0
  ZNF577 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED     11    0
  ZNF577 WILD-TYPE  289    8
     clus
vv    ZNF577 MUTATED ZNF577 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1513V9, binary
                  cls
clus                 0   1
  ZNF577 MUTATED     9   3
  ZNF577 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED      9    3
  ZNF577 WILD-TYPE  305   45
                               clus
vv                              ZNF577 MUTATED ZNF577 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF577 MUTATED     9   0   0   2
  ZNF577 WILD-TYPE 250   3  22  19
D1513V10, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              2               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"
D1513V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF577 MUTATED                                  0     2
  ZNF577 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF577 MUTATED                           0     7
  ZNF577 WILD-TYPE                        19   169
D1513V12, multiclass
                                  clus
vv                                 ZNF577 MUTATED ZNF577 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = SRGAP3 MUTATION ANALYSIS
D1514V1, survival
                  sevent
clus2                0   1
  SRGAP3 MUTATED    13   3
  SRGAP3 WILD-TYPE 264  75
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              16              339 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
               3               75 
$`SRGAP3 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6895 TCGA-DM-A285 TCGA-G4-6310 
        6.05        19.04        24.00        25.08         5.88        63.62 
TCGA-A6-6653 TCGA-AA-3666 TCGA-AA-3815 TCGA-AA-A029 TCGA-AD-5900 TCGA-CA-6717 
       24.39         2.01        33.04        51.98        12.16        12.76 
TCGA-CM-6674 TCGA-D5-6535 TCGA-D5-6927 TCGA-D5-6930 
       12.95        15.12         9.44        13.35 

$`SRGAP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       37.02        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
            2.01             0.00 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
           63.62           148.01 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
          14.235           22.090 
[1] "2.0 - 63.6 (14.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1514V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SRGAP3 MUTATED         2        0        2         6         1         0
  SRGAP3 WILD-TYPE      62        1       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRGAP3 MUTATED           1          0          3          0        2
  SRGAP3 WILD-TYPE        17          6         41         33       33
                  vv
clus               STAGE IVA STAGE IVB
  SRGAP3 MUTATED           0         0
  SRGAP3 WILD-TYPE        12         1
D1514V3, multiclass
            clus
vv           SRGAP3 MUTATED SRGAP3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                2               33
  STAGE IVA               0               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
  SRGAP3 MUTATED     0   2  13   2
  SRGAP3 WILD-TYPE   9  65 236  39
D1514V4, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             13              236
  T4              2               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
  SRGAP3 MUTATED    11   4   2
  SRGAP3 WILD-TYPE 209  77  64
D1514V5, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  N0             11              209
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1514V6, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    12   2
  SRGAP3 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     12    2
  SRGAP3 WILD-TYPE  273   46
   clus
vv  SRGAP3 MUTATED SRGAP3 WILD-TYPE
  0             12              273
  1              2               46
[1] 2 2
[1] FALSE
D1514V7, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED     6  11
  SRGAP3 WILD-TYPE 164 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED      6   11
  SRGAP3 WILD-TYPE  164  186
        clus
vv       SRGAP3 MUTATED SRGAP3 WILD-TYPE
  FEMALE              6              164
  MALE               11              186
[1] 2 2
[1] FALSE
D1514V8, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    13   1
  SRGAP3 WILD-TYPE 287   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     13    1
  SRGAP3 WILD-TYPE  287    7
     clus
vv    SRGAP3 MUTATED SRGAP3 WILD-TYPE
  NO              13              287
  YES              1                7
[1] 2 2
[1] FALSE
D1514V9, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    12   5
  SRGAP3 WILD-TYPE 302  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     12    5
  SRGAP3 WILD-TYPE  302   43
                               clus
vv                              SRGAP3 MUTATED SRGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SRGAP3 MUTATED    11   0   1   3
  SRGAP3 WILD-TYPE 248   3  21  18
D1514V10, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              1               21
  RX              3               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"
D1514V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRGAP3 MUTATED                                  0     1
  SRGAP3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SRGAP3 MUTATED                           0    10
  SRGAP3 WILD-TYPE                        19   166
D1514V12, multiclass
                                  clus
vv                                 SRGAP3 MUTATED SRGAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(1515) Variable = ZMYND8 MUTATION ANALYSIS
D1515V1, survival
                  sevent
clus2                0   1
  ZMYND8 MUTATED    18   7
  ZMYND8 WILD-TYPE 259  71
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              25              330 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               7               71 
$`ZMYND8 MUTATED`
TCGA-AA-3662 TCGA-AD-6895 TCGA-G4-6586 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3542 
        6.05        25.08        35.80        20.12        63.98        12.99 
TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P 
       78.08        33.04        25.02         4.01        34.98        38.07 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CK-4952 TCGA-CK-6751 
       58.39        88.21        49.41        12.10        15.62       124.27 
TCGA-CM-4744 TCGA-CM-6675 TCGA-D5-5538 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1HB 
       20.02        13.05        54.61        24.43        13.32       135.65 
TCGA-G4-6309 
       85.48 

$`ZMYND8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        22.36        62.79         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        2.01        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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        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-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
            4.01             0.00 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
          135.65           148.01 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           33.04            21.99 
[1] "4.0 - 135.7 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1515V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZMYND8 MUTATED         3        0        3         6         2         0
  ZMYND8 WILD-TYPE      61        1       23       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYND8 MUTATED           1          0          4          2        2
  ZMYND8 WILD-TYPE        17          6         40         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ZMYND8 MUTATED           0         1
  ZMYND8 WILD-TYPE        12         0
D1515V3, multiclass
            clus
vv           ZMYND8 MUTATED ZMYND8 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               6              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              4               40
  STAGE IIIC              2               31
  STAGE IV                2               33
  STAGE IVA               0               12
  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   3  16   5
  ZMYND8 WILD-TYPE   8  64 233  36
D1515V4, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             16              233
  T4              5               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
  ZMYND8 MUTATED    15   6   4
  ZMYND8 WILD-TYPE 205  75  62
D1515V5, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  N0             15              205
  N1              6               75
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1515V6, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    18   3
  ZMYND8 WILD-TYPE 267  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     18    3
  ZMYND8 WILD-TYPE  267   45
   clus
vv  ZMYND8 MUTATED ZMYND8 WILD-TYPE
  0             18              267
  1              3               45
[1] 2 2
[1] FALSE
D1515V7, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    12  13
  ZMYND8 WILD-TYPE 158 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     12   13
  ZMYND8 WILD-TYPE  158  184
        clus
vv       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  FEMALE             12              158
  MALE               13              184
[1] 2 2
[1] FALSE
D1515V8, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    20   0
  ZMYND8 WILD-TYPE 280   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     20    0
  ZMYND8 WILD-TYPE  280    8
     clus
vv    ZMYND8 MUTATED ZMYND8 WILD-TYPE
  NO              20              280
  YES              0                8
[1] 2 2
[1] FALSE
D1515V9, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    19   4
  ZMYND8 WILD-TYPE 295  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     19    4
  ZMYND8 WILD-TYPE  295   44
                               clus
vv                              ZMYND8 MUTATED ZMYND8 WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZMYND8 MUTATED    14   0   1   2
  ZMYND8 WILD-TYPE 245   3  21  19
D1515V10, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              1               21
  RX              2               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"
D1515V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMYND8 MUTATED                                  0     0
  ZMYND8 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZMYND8 MUTATED                           3    13
  ZMYND8 WILD-TYPE                        16   163
D1515V12, multiclass
                                  clus
vv                                 ZMYND8 MUTATED ZMYND8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        13              163
[1] 4 2
[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 = KIAA0319 MUTATION ANALYSIS
D1516V1, survival
                    sevent
clus2                  0   1
  KIAA0319 MUTATED    12   2
  KIAA0319 WILD-TYPE 265  76
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                14                341 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                 2                 76 
$`KIAA0319 MUTATED`
TCGA-AA-3715 TCGA-A6-3807 TCGA-A6-6780 TCGA-AA-3941 TCGA-AA-A00J TCGA-AA-A01F 
       19.04        34.65        20.12        24.00        18.05        32.02 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6535 
       83.24        21.44        58.39        12.76        51.32        15.12 
TCGA-DM-A1HB TCGA-G4-6304 
      135.65        53.62 

$`KIAA0319 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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-A01G 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
             12.76               0.00 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
            135.65             148.01 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
             28.01              22.03 
[1] "12.8 - 135.7 (28.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.3"
D1516V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0319 MUTATED         0        0        1         7         1         0
  KIAA0319 WILD-TYPE      64        1       25       101         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0319 MUTATED           0          0          4          1        0
  KIAA0319 WILD-TYPE        18          6         40         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0319 MUTATED           1         0
  KIAA0319 WILD-TYPE        11         1
D1516V3, multiclass
            clus
vv           KIAA0319 MUTATED KIAA0319 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 7                101
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                4                 40
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 1                 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
  KIAA0319 MUTATED     0   0  12   3
  KIAA0319 WILD-TYPE   9  67 237  38
D1516V4, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3               12                237
  T4                3                 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
  KIAA0319 MUTATED     9   5   1
  KIAA0319 WILD-TYPE 211  76  65
D1516V5, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  N0                9                211
  N1                5                 76
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1516V6, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    10   1
  KIAA0319 WILD-TYPE 275  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     10    1
  KIAA0319 WILD-TYPE  275   47
   clus
vv  KIAA0319 MUTATED KIAA0319 WILD-TYPE
  0               10                275
  1                1                 47
[1] 2 2
[1] FALSE
D1516V7, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED     6   9
  KIAA0319 WILD-TYPE 164 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED      6    9
  KIAA0319 WILD-TYPE  164  188
        clus
vv       KIAA0319 MUTATED KIAA0319 WILD-TYPE
  FEMALE                6                164
  MALE                  9                188
[1] 2 2
[1] FALSE
D1516V8, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    13   0
  KIAA0319 WILD-TYPE 287   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     13    0
  KIAA0319 WILD-TYPE  287    8
     clus
vv    KIAA0319 MUTATED KIAA0319 WILD-TYPE
  NO                13                287
  YES                0                  8
[1] 2 2
[1] FALSE
D1516V9, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    11   3
  KIAA0319 WILD-TYPE 303  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     11    3
  KIAA0319 WILD-TYPE  303   45
                               clus
vv                              KIAA0319 MUTATED KIAA0319 WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0319 MUTATED    10   0   0   3
  KIAA0319 WILD-TYPE 249   3  22  18
D1516V10, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  R0               10                249
  R1                0                  3
  R2                0                 22
  RX                3                 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"
D1516V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0319 MUTATED                                  0     2
  KIAA0319 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0319 MUTATED                           0     8
  KIAA0319 WILD-TYPE                        19   168
D1516V12, multiclass
                                  clus
vv                                 KIAA0319 MUTATED KIAA0319 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           8                168
[1] 4 2
[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 = PUS7 MUTATION ANALYSIS
D1517V1, survival
                sevent
clus2              0   1
  PUS7 MUTATED    11   2
  PUS7 WILD-TYPE 266  76
  PUS7 MUTATED PUS7 WILD-TYPE 
            13            342 
  PUS7 MUTATED PUS7 WILD-TYPE 
             2             76 
$`PUS7 MUTATED`
TCGA-G4-6588 TCGA-A6-3809 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-3977 TCGA-AA-A00E 
       26.17        32.75        33.04        32.05        25.02        30.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6928 
        0.99        34.98        83.24        12.76        10.06        11.64 
TCGA-D5-6930 
       13.35 

$`PUS7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PUS7 MUTATED PUS7 WILD-TYPE 
          0.99           0.00 
  PUS7 MUTATED PUS7 WILD-TYPE 
         83.24         148.01 
  PUS7 MUTATED PUS7 WILD-TYPE 
         26.17          22.01 
[1] "1.0 - 83.2 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1517V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PUS7 MUTATED         2        0        0         8         2         0
  PUS7 WILD-TYPE      62        1       26       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PUS7 MUTATED           0          0          0          0        0         0
  PUS7 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  PUS7 MUTATED           0
  PUS7 WILD-TYPE         1
D1517V3, multiclass
            clus
vv           PUS7 MUTATED PUS7 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PUS7 MUTATED     0   3   8   2
  PUS7 WILD-TYPE   9  64 241  39
D1517V4, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            8            241
  T4            2             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
  PUS7 MUTATED    13   0   0
  PUS7 WILD-TYPE 207  81  66
D1517V5, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  N0           13            207
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1517V6, binary
                cls
clus               0   1
  PUS7 MUTATED    12   0
  PUS7 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED     12    0
  PUS7 WILD-TYPE  273   48
   clus
vv  PUS7 MUTATED PUS7 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D1517V7, binary
                cls
clus               0   1
  PUS7 MUTATED     5   8
  PUS7 WILD-TYPE 165 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED      5    8
  PUS7 WILD-TYPE  165  189
        clus
vv       PUS7 MUTATED PUS7 WILD-TYPE
  FEMALE            5            165
  MALE              8            189
[1] 2 2
[1] FALSE
D1517V8, binary
                cls
clus               0   1
  PUS7 MUTATED    12   0
  PUS7 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED     12    0
  PUS7 WILD-TYPE  288    8
     clus
vv    PUS7 MUTATED PUS7 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1517V9, binary
                cls
clus               0   1
  PUS7 MUTATED     9   4
  PUS7 WILD-TYPE 305  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED      9    4
  PUS7 WILD-TYPE  305   44
                               clus
vv                              PUS7 MUTATED PUS7 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PUS7 MUTATED    10   0   0   2
  PUS7 WILD-TYPE 249   3  22  19
D1517V10, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            2             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"
D1517V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PUS7 MUTATED                                  0     3
  PUS7 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PUS7 MUTATED                           0     4
  PUS7 WILD-TYPE                        19   172
D1517V12, multiclass
                                  clus
vv                                 PUS7 MUTATED PUS7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = DCLRE1C MUTATION ANALYSIS
D1518V1, survival
                   sevent
clus2                 0   1
  DCLRE1C MUTATED     6   2
  DCLRE1C WILD-TYPE 271  76
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                8               347 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                2                76 
$`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 
       82.95        56.09 

$`DCLRE1C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        20.12        20.28         7.04        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
             3.02              0.00 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
            82.95            148.01 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
           27.535            22.030 
[1] "3.0 - 83.0 (27.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1518V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLRE1C MUTATED         0        0        3         4         1         0
  DCLRE1C WILD-TYPE      64        1       23       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1C MUTATED           0          0          0          1        0
  DCLRE1C WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  DCLRE1C MUTATED           0         0
  DCLRE1C WILD-TYPE        12         1
D1518V3, multiclass
            clus
vv           DCLRE1C MUTATED DCLRE1C WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  DCLRE1C MUTATED     0   0   6   3
  DCLRE1C WILD-TYPE   9  67 243  38
D1518V4, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               6               243
  T4               3                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
  DCLRE1C MUTATED     8   1   0
  DCLRE1C WILD-TYPE 212  80  66
D1518V5, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  N0               8               212
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1518V6, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     6   0
  DCLRE1C WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      6    0
  DCLRE1C WILD-TYPE  279   48
   clus
vv  DCLRE1C MUTATED DCLRE1C WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1518V7, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     6   3
  DCLRE1C WILD-TYPE 164 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      6    3
  DCLRE1C WILD-TYPE  164  194
        clus
vv       DCLRE1C MUTATED DCLRE1C WILD-TYPE
  FEMALE               6               164
  MALE                 3               194
[1] 2 2
[1] FALSE
D1518V8, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     8   0
  DCLRE1C WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      8    0
  DCLRE1C WILD-TYPE  292    8
     clus
vv    DCLRE1C MUTATED DCLRE1C WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1518V9, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     6   3
  DCLRE1C WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      6    3
  DCLRE1C WILD-TYPE  308   45
                               clus
vv                              DCLRE1C MUTATED DCLRE1C WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DCLRE1C MUTATED     6   0   0   2
  DCLRE1C WILD-TYPE 253   3  22  19
D1518V10, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               2                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"
D1518V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCLRE1C MUTATED                                  0     1
  DCLRE1C WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DCLRE1C MUTATED                           0     5
  DCLRE1C WILD-TYPE                        19   171
D1518V12, multiclass
                                  clus
vv                                 DCLRE1C MUTATED DCLRE1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = TEX2 MUTATION ANALYSIS
D1519V1, survival
                sevent
clus2              0   1
  TEX2 MUTATED     9   3
  TEX2 WILD-TYPE 268  75
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            343 
  TEX2 MUTATED TEX2 WILD-TYPE 
             3             75 
$`TEX2 MUTATED`
TCGA-AA-3522 TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 
       37.05       100.01        26.17        34.98        83.24        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-5861 
       58.39        12.76        10.06        85.45        20.02        15.02 

$`TEX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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         22.030 
[1] "10.1 - 100.0 (30.6)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.3"
D1519V2, continuous
                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      63        1       25       100         7         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  TEX2 MUTATED           0
  TEX2 WILD-TYPE         1
D1519V3, multiclass
            clus
vv           TEX2 MUTATED TEX2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TEX2 MUTATED     0   1  10   1
  TEX2 WILD-TYPE   9  66 239  40
D1519V4, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           10            239
  T4            1             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
  TEX2 MUTATED    11   1   0
  TEX2 WILD-TYPE 209  80  66
D1519V5, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  N0           11            209
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1519V6, binary
                cls
clus               0   1
  TEX2 MUTATED    11   0
  TEX2 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     11    0
  TEX2 WILD-TYPE  274   48
   clus
vv  TEX2 MUTATED TEX2 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D1519V7, binary
                cls
clus               0   1
  TEX2 MUTATED     4   8
  TEX2 WILD-TYPE 166 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      4    8
  TEX2 WILD-TYPE  166  189
        clus
vv       TEX2 MUTATED TEX2 WILD-TYPE
  FEMALE            4            166
  MALE              8            189
[1] 2 2
[1] FALSE
D1519V8, binary
                cls
clus               0   1
  TEX2 MUTATED    12   0
  TEX2 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     12    0
  TEX2 WILD-TYPE  288    8
     clus
vv    TEX2 MUTATED TEX2 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1519V9, binary
                cls
clus               0   1
  TEX2 MUTATED    10   2
  TEX2 WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     10    2
  TEX2 WILD-TYPE  304   46
                               clus
vv                              TEX2 MUTATED TEX2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TEX2 MUTATED     8   1   0   2
  TEX2 WILD-TYPE 251   2  22  19
D1519V10, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  R0            8            251
  R1            1              2
  R2            0             22
  RX            2             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"
D1519V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEX2 MUTATED                                  0     3
  TEX2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TEX2 MUTATED                           1     6
  TEX2 WILD-TYPE                        18   170
D1519V12, multiclass
                                  clus
vv                                 TEX2 MUTATED TEX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = BRD4 MUTATION ANALYSIS
D1520V1, survival
                sevent
clus2              0   1
  BRD4 MUTATED    17   2
  BRD4 WILD-TYPE 260  76
  BRD4 MUTATED BRD4 WILD-TYPE 
            19            336 
  BRD4 MUTATED BRD4 WILD-TYPE 
             2             76 
$`BRD4 MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3710 
       25.08        79.69        20.12        19.66        63.98        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3949 TCGA-AD-5900 TCGA-AD-6889 
       35.05        33.04        53.00        26.01        12.16        83.24 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6171 TCGA-D5-6539 TCGA-D5-6928 
       13.02        15.02         5.03        14.04        12.49        11.64 
TCGA-DM-A1D9 
      140.38 

$`BRD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-5863 TCGA-CM-5864 
       22.03        22.98        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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  BRD4 MUTATED BRD4 WILD-TYPE 
          5.03           0.00 
  BRD4 MUTATED BRD4 WILD-TYPE 
        140.38         148.01 
  BRD4 MUTATED BRD4 WILD-TYPE 
        25.080         22.045 
[1] "5.0 - 140.4 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.7"
D1520V2, continuous
                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      61        1       24        99         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD4 MUTATED           1          0          2          1        0         1
  BRD4 WILD-TYPE        17          6         42         32       35        11
                vv
clus             STAGE IVB
  BRD4 MUTATED           0
  BRD4 WILD-TYPE         1
D1520V3, multiclass
            clus
vv           BRD4 MUTATED BRD4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             9             99
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  BRD4 MUTATED     0   3  16   1
  BRD4 WILD-TYPE   9  64 233  40
D1520V4, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           16            233
  T4            1             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
  BRD4 MUTATED    15   4   1
  BRD4 WILD-TYPE 205  77  65
D1520V5, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  N0           15            205
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1520V6, binary
                cls
clus               0   1
  BRD4 MUTATED    16   1
  BRD4 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     16    1
  BRD4 WILD-TYPE  269   47
   clus
vv  BRD4 MUTATED BRD4 WILD-TYPE
  0           16            269
  1            1             47
[1] 2 2
[1] FALSE
D1520V7, binary
                cls
clus               0   1
  BRD4 MUTATED     8  12
  BRD4 WILD-TYPE 162 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED      8   12
  BRD4 WILD-TYPE  162  185
        clus
vv       BRD4 MUTATED BRD4 WILD-TYPE
  FEMALE            8            162
  MALE             12            185
[1] 2 2
[1] FALSE
D1520V8, binary
                cls
clus               0   1
  BRD4 MUTATED    18   0
  BRD4 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     18    0
  BRD4 WILD-TYPE  282    8
     clus
vv    BRD4 MUTATED BRD4 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D1520V9, binary
                cls
clus               0   1
  BRD4 MUTATED    15   5
  BRD4 WILD-TYPE 299  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     15    5
  BRD4 WILD-TYPE  299   43
                               clus
vv                              BRD4 MUTATED BRD4 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRD4 MUTATED    18   0   0   0
  BRD4 WILD-TYPE 241   3  22  21
D1520V10, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  R0           18            241
  R1            0              3
  R2            0             22
  RX            0             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"
D1520V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD4 MUTATED                                  0     1
  BRD4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD4 MUTATED                           1    11
  BRD4 WILD-TYPE                        18   165
D1520V12, multiclass
                                  clus
vv                                 BRD4 MUTATED BRD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(1521) Variable = ZMIZ1 MUTATION ANALYSIS
D1521V1, survival
                 sevent
clus2               0   1
  ZMIZ1 MUTATED     8   1
  ZMIZ1 WILD-TYPE 269  77
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              9             346 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              1              77 
$`ZMIZ1 MUTATED`
TCGA-G4-6586 TCGA-A6-2676 TCGA-AA-3663 TCGA-AA-3977 TCGA-AY-6386 TCGA-D5-6533 
       35.80        42.90         6.97        25.02        17.82        25.48 
TCGA-D5-6928 TCGA-DM-A1HB TCGA-G4-6317 
       11.64       135.65        36.00 

$`ZMIZ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
           6.97            0.00 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         135.65          148.01 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
          25.48           22.01 
[1] "7.0 - 135.7 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1521V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZMIZ1 MUTATED         0        0        1         2         1         0
  ZMIZ1 WILD-TYPE      64        1       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZMIZ1 MUTATED           0          0          2          1        0         0
  ZMIZ1 WILD-TYPE        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  ZMIZ1 MUTATED           0
  ZMIZ1 WILD-TYPE         1
D1521V3, multiclass
            clus
vv           ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ZMIZ1 MUTATED     0   1   6   2
  ZMIZ1 WILD-TYPE   9  66 243  39
D1521V4, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             2              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
  ZMIZ1 MUTATED     6   2   1
  ZMIZ1 WILD-TYPE 214  79  65
D1521V5, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1521V6, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     7   0
  ZMIZ1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      7    0
  ZMIZ1 WILD-TYPE  278   48
   clus
vv  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1521V7, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     5   4
  ZMIZ1 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      5    4
  ZMIZ1 WILD-TYPE  165  193
        clus
vv       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1521V8, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     8   0
  ZMIZ1 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      8    0
  ZMIZ1 WILD-TYPE  292    8
     clus
vv    ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1521V9, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     7   1
  ZMIZ1 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      7    1
  ZMIZ1 WILD-TYPE  307   47
                               clus
vv                              ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMIZ1 MUTATED     7   0   0   0
  ZMIZ1 WILD-TYPE 252   3  22  21
D1521V10, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1521V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMIZ1 MUTATED                                  0     0
  ZMIZ1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ1 MUTATED                           1     6
  ZMIZ1 WILD-TYPE                        18   170
D1521V12, multiclass
                                  clus
vv                                 ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = SLC44A4 MUTATION ANALYSIS
D1522V1, survival
                   sevent
clus2                 0   1
  SLC44A4 MUTATED     7   4
  SLC44A4 WILD-TYPE 270  74
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               11               344 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
                4                74 
$`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        83.24        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            10.06              0.00 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            83.24            148.01 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            21.14             22.09 
[1] "10.1 - 83.2 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1522V2, continuous
                   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      62        1       25       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A4 MUTATED           1          0          0          1        0
  SLC44A4 WILD-TYPE        17          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC44A4 MUTATED           0         0
  SLC44A4 WILD-TYPE        12         1
D1522V3, multiclass
            clus
vv           SLC44A4 MUTATED SLC44A4 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                6               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC44A4 MUTATED     1   1   8   2
  SLC44A4 WILD-TYPE   8  66 241  39
D1522V4, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               8               241
  T4               2                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
  SLC44A4 MUTATED    10   1   1
  SLC44A4 WILD-TYPE 210  80  65
D1522V5, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  N0              10               210
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1522V6, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    10   0
  SLC44A4 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     10    0
  SLC44A4 WILD-TYPE  275   48
   clus
vv  SLC44A4 MUTATED SLC44A4 WILD-TYPE
  0              10               275
  1               0                48
[1] 2 2
[1] FALSE
D1522V7, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED     8   4
  SLC44A4 WILD-TYPE 162 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED      8    4
  SLC44A4 WILD-TYPE  162  193
        clus
vv       SLC44A4 MUTATED SLC44A4 WILD-TYPE
  FEMALE               8               162
  MALE                 4               193
[1] 2 2
[1] FALSE
D1522V8, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    11   0
  SLC44A4 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     11    0
  SLC44A4 WILD-TYPE  289    8
     clus
vv    SLC44A4 MUTATED SLC44A4 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D1522V9, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    10   2
  SLC44A4 WILD-TYPE 304  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     10    2
  SLC44A4 WILD-TYPE  304   46
                               clus
vv                              SLC44A4 MUTATED SLC44A4 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC44A4 MUTATED    10   0   0   1
  SLC44A4 WILD-TYPE 249   3  22  20
D1522V10, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               1                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"
D1522V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC44A4 MUTATED                                  0     1
  SLC44A4 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC44A4 MUTATED                           1     7
  SLC44A4 WILD-TYPE                        18   169
D1522V12, multiclass
                                  clus
vv                                 SLC44A4 MUTATED SLC44A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          7               169
[1] 4 2
[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 = NCF2 MUTATION ANALYSIS
D1523V1, survival
                sevent
clus2              0   1
  NCF2 MUTATED     8   0
  NCF2 WILD-TYPE 269  78
  NCF2 MUTATED NCF2 WILD-TYPE 
             8            347 
  NCF2 MUTATED NCF2 WILD-TYPE 
             0             78 
$`NCF2 MUTATED`
TCGA-G4-6588 TCGA-AA-3660 TCGA-AA-3864 TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-4743 
       26.17        78.08        53.00        21.44        12.76        23.05 
TCGA-CM-5348 TCGA-CM-6163 
       22.98        14.04 

$`NCF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       124.27        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-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NCF2 MUTATED NCF2 WILD-TYPE 
         12.76           0.00 
  NCF2 MUTATED NCF2 WILD-TYPE 
         78.08         148.01 
  NCF2 MUTATED NCF2 WILD-TYPE 
        23.015         22.030 
[1] "12.8 - 78.1 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1523V2, continuous
                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      63        1       24       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCF2 MUTATED           0          0          1          0        0         0
  NCF2 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  NCF2 MUTATED           0
  NCF2 WILD-TYPE         1
D1523V3, multiclass
            clus
vv           NCF2 MUTATED NCF2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  NCF2 MUTATED     1   0   7   0
  NCF2 WILD-TYPE   8  67 242  41
D1523V4, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  T1            1              8
  T2            0             67
  T3            7            242
  T4            0             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
  NCF2 MUTATED     7   1   0
  NCF2 WILD-TYPE 213  80  66
D1523V5, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1523V6, binary
                cls
clus               0   1
  NCF2 MUTATED     7   0
  NCF2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      7    0
  NCF2 WILD-TYPE  278   48
   clus
vv  NCF2 MUTATED NCF2 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1523V7, binary
                cls
clus               0   1
  NCF2 MUTATED     2   6
  NCF2 WILD-TYPE 168 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      2    6
  NCF2 WILD-TYPE  168  191
        clus
vv       NCF2 MUTATED NCF2 WILD-TYPE
  FEMALE            2            168
  MALE              6            191
[1] 2 2
[1] FALSE
D1523V8, binary
                cls
clus               0   1
  NCF2 MUTATED     8   0
  NCF2 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      8    0
  NCF2 WILD-TYPE  292    8
     clus
vv    NCF2 MUTATED NCF2 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1523V9, binary
                cls
clus               0   1
  NCF2 MUTATED     7   1
  NCF2 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      7    1
  NCF2 WILD-TYPE  307   47
                               clus
vv                              NCF2 MUTATED NCF2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NCF2 MUTATED     7   0   0   1
  NCF2 WILD-TYPE 252   3  22  20
D1523V10, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D1523V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCF2 MUTATED                                  0     1
  NCF2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NCF2 MUTATED                           0     5
  NCF2 WILD-TYPE                        19   171
D1523V12, multiclass
                                  clus
vv                                 NCF2 MUTATED NCF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = MFRP MUTATION ANALYSIS
D1524V1, survival
                sevent
clus2              0   1
  MFRP MUTATED     8   3
  MFRP WILD-TYPE 269  75
  MFRP MUTATED MFRP WILD-TYPE 
            11            344 
  MFRP MUTATED MFRP WILD-TYPE 
             3             75 
$`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        83.24        27.09 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-6162 TCGA-F4-6856 
       12.76        51.32       124.27        12.00        35.31 

$`MFRP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        30.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95         2.01        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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MFRP MUTATED MFRP WILD-TYPE 
          7.04           0.00 
  MFRP MUTATED MFRP WILD-TYPE 
        124.27         148.01 
  MFRP MUTATED MFRP WILD-TYPE 
         22.06          22.06 
[1] "7.0 - 124.3 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1524V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFRP MUTATED         3        0        1         5         0         0
  MFRP WILD-TYPE      61        1       25       103         8         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        18          6         43         33       34        12
                vv
clus             STAGE IVB
  MFRP MUTATED           0
  MFRP WILD-TYPE         1
D1524V3, multiclass
            clus
vv           MFRP MUTATED MFRP WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  MFRP MUTATED     0   3   8   0
  MFRP WILD-TYPE   9  64 241  41
D1524V4, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  T1            0              9
  T2            3             64
  T3            8            241
  T4            0             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
  MFRP MUTATED     9   1   1
  MFRP WILD-TYPE 211  80  65
D1524V5, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  N0            9            211
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1524V6, binary
                cls
clus               0   1
  MFRP MUTATED     8   1
  MFRP WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      8    1
  MFRP WILD-TYPE  277   47
   clus
vv  MFRP MUTATED MFRP WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D1524V7, binary
                cls
clus               0   1
  MFRP MUTATED     6   5
  MFRP WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      6    5
  MFRP WILD-TYPE  164  192
        clus
vv       MFRP MUTATED MFRP WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D1524V8, binary
                cls
clus               0   1
  MFRP MUTATED    10   0
  MFRP WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED     10    0
  MFRP WILD-TYPE  290    8
     clus
vv    MFRP MUTATED MFRP WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1524V9, binary
                cls
clus               0   1
  MFRP MUTATED     7   4
  MFRP WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      7    4
  MFRP WILD-TYPE  307   44
                               clus
vv                              MFRP MUTATED MFRP WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MFRP MUTATED     7   0   1   3
  MFRP WILD-TYPE 252   3  21  18
D1524V10, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            3             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"
D1524V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFRP MUTATED                                  0     2
  MFRP WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MFRP MUTATED                           0     6
  MFRP WILD-TYPE                        19   170
D1524V12, multiclass
                                  clus
vv                                 MFRP MUTATED MFRP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = PKHD1 MUTATION ANALYSIS
D1525V1, survival
                 sevent
clus2               0   1
  PKHD1 MUTATED    35  20
  PKHD1 WILD-TYPE 242  58
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             55             300 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             20              58 
$`PKHD1 MUTATED`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3950 TCGA-AZ-6608 TCGA-G4-6321 
       24.33        13.02        85.05        24.00         1.94        22.09 
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3553 
       32.75        22.06         3.02        63.98        12.99        24.00 
TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3864 
        6.97        11.01        26.99        15.95         0.00        53.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A 
       33.01        26.01         2.01        25.02         7.96        38.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A029 TCGA-AZ-4315 TCGA-AZ-5403 
        4.01        34.98        35.01        51.98        58.39        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       49.41        12.10        12.69        12.76        10.06       148.01 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       21.14         2.01        22.03        30.08        32.02         5.03 
TCGA-CM-5864 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6540 
       15.02        54.61        56.09        18.25        43.27        16.14 
TCGA-D5-6923 TCGA-D5-6928 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A28F TCGA-F4-6570 
       12.43        11.64        12.59        44.32        35.97         6.18 
TCGA-G4-6626 
       46.75 

$`PKHD1 WILD-TYPE`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       14.53        24.16         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75       100.01        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       63.62        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       37.02        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
       17.82         1.41         5.13        22.36        88.21         6.77 
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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.99        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-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       55.92        20.19        25.48        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         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A1HA 
       92.75        49.91        13.32       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  PKHD1 MUTATED PKHD1 WILD-TYPE 
              0               0 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
         148.01          140.38 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
          22.09           21.99 
[1] "0.0 - 148.0 (22.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.9"
D1525V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKHD1 MUTATED         5        0        8        22         4         0
  PKHD1 WILD-TYPE      59        1       18        86         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKHD1 MUTATED           4          1          4          2        4         1
  PKHD1 WILD-TYPE        14          5         40         31       31        11
                 vv
clus              STAGE IVB
  PKHD1 MUTATED           0
  PKHD1 WILD-TYPE         1
D1525V3, multiclass
            clus
vv           PKHD1 MUTATED PKHD1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               8              18
  STAGE IIA             22              86
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              4              14
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               4              31
  STAGE IVA              1              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
  PKHD1 MUTATED     1   7  43   6
  PKHD1 WILD-TYPE   8  60 206  35
D1525V4, multiclass
    clus
vv   PKHD1 MUTATED PKHD1 WILD-TYPE
  T1             1               8
  T2             7              60
  T3            43             206
  T4             6              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
  PKHD1 MUTATED    40  11   6
  PKHD1 WILD-TYPE 180  70  60
D1525V5, multiclass
    clus
vv   PKHD1 MUTATED PKHD1 WILD-TYPE
  N0            40             180
  N1            11              70
  N2             6              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1525V6, binary
                 cls
clus                0   1
  PKHD1 MUTATED    47   5
  PKHD1 WILD-TYPE 238  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PKHD1 MUTATED     47    5
  PKHD1 WILD-TYPE  238   43
   clus
vv  PKHD1 MUTATED PKHD1 WILD-TYPE
  0            47             238
  1             5              43
[1] 2 2
[1] FALSE
D1525V7, binary
                 cls
clus                0   1
  PKHD1 MUTATED    30  27
  PKHD1 WILD-TYPE 140 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PKHD1 MUTATED     30   27
  PKHD1 WILD-TYPE  140  170
        clus
vv       PKHD1 MUTATED PKHD1 WILD-TYPE
  FEMALE            30             140
  MALE              27             170
[1] 2 2
[1] FALSE
D1525V8, binary
                 cls
clus                0   1
  PKHD1 MUTATED    48   1
  PKHD1 WILD-TYPE 252   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PKHD1 MUTATED     48    1
  PKHD1 WILD-TYPE  252    7
     clus
vv    PKHD1 MUTATED PKHD1 WILD-TYPE
  NO             48             252
  YES             1               7
[1] 2 2
[1] FALSE
D1525V9, binary
                 cls
clus                0   1
  PKHD1 MUTATED    44  13
  PKHD1 WILD-TYPE 270  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PKHD1 MUTATED     44   13
  PKHD1 WILD-TYPE  270   35
                               clus
vv                              PKHD1 MUTATED PKHD1 WILD-TYPE
  COLON ADENOCARCINOMA                     44             270
  COLON MUCINOUS ADENOCARCINOMA            13              35
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PKHD1 MUTATED    40   0   2   5
  PKHD1 WILD-TYPE 219   3  20  16
D1525V10, multiclass
    clus
vv   PKHD1 MUTATED PKHD1 WILD-TYPE
  R0            40             219
  R1             0               3
  R2             2              20
  RX             5              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"
D1525V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKHD1 MUTATED                                  0     3
  PKHD1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PKHD1 MUTATED                           1    28
  PKHD1 WILD-TYPE                        18   148
D1525V12, multiclass
                                  clus
vv                                 PKHD1 MUTATED PKHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       28             148
[1] 4 2
[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 = TAF4 MUTATION ANALYSIS
D1526V1, survival
                sevent
clus2              0   1
  TAF4 MUTATED     4   4
  TAF4 WILD-TYPE 273  74
  TAF4 MUTATED TAF4 WILD-TYPE 
             8            347 
  TAF4 MUTATED TAF4 WILD-TYPE 
             4             74 
$`TAF4 MUTATED`
TCGA-AA-3692 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3977 TCGA-AZ-4682 
       36.00         3.02        78.08        10.06        25.02        22.36 
TCGA-CM-6169 TCGA-G4-6309 
       13.02        85.48 

$`TAF4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  TAF4 MUTATED TAF4 WILD-TYPE 
          3.02           0.00 
  TAF4 MUTATED TAF4 WILD-TYPE 
         85.48         148.01 
  TAF4 MUTATED TAF4 WILD-TYPE 
         23.69          22.03 
[1] "3.0 - 85.5 (23.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1526V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF4 MUTATED         0        0        3         1         0         0
  TAF4 WILD-TYPE      64        1       23       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF4 MUTATED           1          0          1          0        1         1
  TAF4 WILD-TYPE        17          6         43         33       34        11
                vv
clus             STAGE IVB
  TAF4 MUTATED           0
  TAF4 WILD-TYPE         1
D1526V3, multiclass
            clus
vv           TAF4 MUTATED TAF4 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             1             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
  TAF4 MUTATED     0   1   7   1
  TAF4 WILD-TYPE   9  66 242  40
D1526V4, multiclass
    clus
vv   TAF4 MUTATED TAF4 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            1             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
  TAF4 MUTATED     6   1   2
  TAF4 WILD-TYPE 214  80  64
D1526V5, multiclass
    clus
vv   TAF4 MUTATED TAF4 WILD-TYPE
  N0            6            214
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1526V6, binary
                cls
clus               0   1
  TAF4 MUTATED     6   2
  TAF4 WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF4 MUTATED      6    2
  TAF4 WILD-TYPE  279   46
   clus
vv  TAF4 MUTATED TAF4 WILD-TYPE
  0            6            279
  1            2             46
[1] 2 2
[1] FALSE
D1526V7, binary
                cls
clus               0   1
  TAF4 MUTATED     6   3
  TAF4 WILD-TYPE 164 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF4 MUTATED      6    3
  TAF4 WILD-TYPE  164  194
        clus
vv       TAF4 MUTATED TAF4 WILD-TYPE
  FEMALE            6            164
  MALE              3            194
[1] 2 2
[1] FALSE
D1526V8, binary
                cls
clus               0   1
  TAF4 MUTATED     7   1
  TAF4 WILD-TYPE 293   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF4 MUTATED      7    1
  TAF4 WILD-TYPE  293    7
     clus
vv    TAF4 MUTATED TAF4 WILD-TYPE
  NO             7            293
  YES            1              7
[1] 2 2
[1] FALSE
D1526V9, binary
                cls
clus               0   1
  TAF4 MUTATED     8   1
  TAF4 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF4 MUTATED      8    1
  TAF4 WILD-TYPE  306   47
                               clus
vv                              TAF4 MUTATED TAF4 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAF4 MUTATED     7   0   1   0
  TAF4 WILD-TYPE 252   3  21  21
D1526V10, multiclass
    clus
vv   TAF4 MUTATED TAF4 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            0             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"
D1526V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF4 MUTATED                                  0     0
  TAF4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF4 MUTATED                           2     1
  TAF4 WILD-TYPE                        17   175
D1526V12, multiclass
                                  clus
vv                                 TAF4 MUTATED TAF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       1            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(1527) Variable = USP1 MUTATION ANALYSIS
D1527V1, survival
                sevent
clus2              0   1
  USP1 MUTATED     7   2
  USP1 WILD-TYPE 270  76
  USP1 MUTATED USP1 WILD-TYPE 
             9            346 
  USP1 MUTATED USP1 WILD-TYPE 
             2             76 
$`USP1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AY-6196 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6162 
       22.06        63.98         0.20        12.76        10.06        12.00 
TCGA-CM-6171 TCGA-D5-6927 TCGA-F4-6570 
       14.04         9.44         6.18 

$`USP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  USP1 MUTATED USP1 WILD-TYPE 
           0.2            0.0 
  USP1 MUTATED USP1 WILD-TYPE 
         63.98         148.01 
  USP1 MUTATED USP1 WILD-TYPE 
         12.00          22.39 
[1] "0.2 - 64.0 (12.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.5"
D1527V2, continuous
                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      63        1       25       103         8         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        18          6         43         32       35        12
                vv
clus             STAGE IVB
  USP1 MUTATED           0
  USP1 WILD-TYPE         1
D1527V3, multiclass
            clus
vv           USP1 MUTATED USP1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  USP1 MUTATED     0   1   8   0
  USP1 WILD-TYPE   9  66 241  41
D1527V4, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            0             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
  USP1 MUTATED     7   1   1
  USP1 WILD-TYPE 213  80  65
D1527V5, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1527V6, binary
                cls
clus               0   1
  USP1 MUTATED     8   0
  USP1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      8    0
  USP1 WILD-TYPE  277   48
   clus
vv  USP1 MUTATED USP1 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1527V7, binary
                cls
clus               0   1
  USP1 MUTATED     4   5
  USP1 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      4    5
  USP1 WILD-TYPE  166  192
        clus
vv       USP1 MUTATED USP1 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D1527V8, binary
                cls
clus               0   1
  USP1 MUTATED     8   0
  USP1 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      8    0
  USP1 WILD-TYPE  292    8
     clus
vv    USP1 MUTATED USP1 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1527V9, binary
                cls
clus               0   1
  USP1 MUTATED     6   3
  USP1 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      6    3
  USP1 WILD-TYPE  308   45
                               clus
vv                              USP1 MUTATED USP1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  USP1 MUTATED     7   0   0   2
  USP1 WILD-TYPE 252   3  22  19
D1527V10, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            2             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"
D1527V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP1 MUTATED                                  0     2
  USP1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USP1 MUTATED                           0     6
  USP1 WILD-TYPE                        19   170
D1527V12, multiclass
                                  clus
vv                                 USP1 MUTATED USP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1528) Variable = TRHDE MUTATION ANALYSIS
D1528V1, survival
                 sevent
clus2               0   1
  TRHDE MUTATED    21   6
  TRHDE WILD-TYPE 256  72
  TRHDE MUTATED TRHDE WILD-TYPE 
             27             328 
  TRHDE MUTATED TRHDE WILD-TYPE 
              6              72 
$`TRHDE MUTATED`
TCGA-AA-3672 TCGA-AA-3979 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6625 TCGA-G4-6628 
        0.92        24.00         1.94         5.88        91.79        79.69 
TCGA-A6-5661 TCGA-A6-6138 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3977 
       33.53        22.52         3.02         1.02         6.97        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-4315 TCGA-CA-5255 
       18.05         4.01        34.98         0.95        58.39        12.36 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-6678 TCGA-D5-6535 TCGA-DM-A1HB 
       12.76        10.06        30.08        11.01        15.12       135.65 
TCGA-F4-6569 TCGA-G4-6299 TCGA-G4-6323 
       35.74        74.56        13.78 

$`TRHDE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2671 
       49.08        63.62        22.09        35.80        26.17        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31        33.01         0.20        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-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-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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-F4-6570 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        43.04        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-G4-6317 TCGA-G4-6626 
       85.48        61.91        36.00        46.75 

  TRHDE MUTATED TRHDE WILD-TYPE 
           0.92            0.00 
  TRHDE MUTATED TRHDE WILD-TYPE 
         135.65          148.01 
  TRHDE MUTATED TRHDE WILD-TYPE 
          15.12           22.09 
[1] "0.9 - 135.7 (15.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1528V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRHDE MUTATED         4        1        2         9         2         0
  TRHDE WILD-TYPE      60        0       24        99         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRHDE MUTATED           1          1          3          1        1         1
  TRHDE WILD-TYPE        17          5         41         32       34        11
                 vv
clus              STAGE IVB
  TRHDE MUTATED           0
  TRHDE WILD-TYPE         1
D1528V3, multiclass
            clus
vv           TRHDE MUTATED TRHDE WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA              9              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  TRHDE MUTATED     1   5  16   4
  TRHDE WILD-TYPE   8  62 233  37
D1528V4, multiclass
    clus
vv   TRHDE MUTATED TRHDE WILD-TYPE
  T1             1               8
  T2             5              62
  T3            16             233
  T4             4              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
  TRHDE MUTATED    19   6   2
  TRHDE WILD-TYPE 201  75  64
D1528V5, multiclass
    clus
vv   TRHDE MUTATED TRHDE WILD-TYPE
  N0            19             201
  N1             6              75
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1528V6, binary
                 cls
clus                0   1
  TRHDE MUTATED    21   2
  TRHDE WILD-TYPE 264  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRHDE MUTATED     21    2
  TRHDE WILD-TYPE  264   46
   clus
vv  TRHDE MUTATED TRHDE WILD-TYPE
  0            21             264
  1             2              46
[1] 2 2
[1] FALSE
D1528V7, binary
                 cls
clus                0   1
  TRHDE MUTATED    12  15
  TRHDE WILD-TYPE 158 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRHDE MUTATED     12   15
  TRHDE WILD-TYPE  158  182
        clus
vv       TRHDE MUTATED TRHDE WILD-TYPE
  FEMALE            12             158
  MALE              15             182
[1] 2 2
[1] FALSE
D1528V8, binary
                 cls
clus                0   1
  TRHDE MUTATED    22   1
  TRHDE WILD-TYPE 278   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRHDE MUTATED     22    1
  TRHDE WILD-TYPE  278    7
     clus
vv    TRHDE MUTATED TRHDE WILD-TYPE
  NO             22             278
  YES             1               7
[1] 2 2
[1] FALSE
D1528V9, binary
                 cls
clus                0   1
  TRHDE MUTATED    21   4
  TRHDE WILD-TYPE 293  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRHDE MUTATED     21    4
  TRHDE WILD-TYPE  293   44
                               clus
vv                              TRHDE MUTATED TRHDE WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRHDE MUTATED    18   0   0   4
  TRHDE WILD-TYPE 241   3  22  17
D1528V10, multiclass
    clus
vv   TRHDE MUTATED TRHDE WILD-TYPE
  R0            18             241
  R1             0               3
  R2             0              22
  RX             4              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"
D1528V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRHDE MUTATED                                  0     3
  TRHDE WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRHDE MUTATED                           2    13
  TRHDE WILD-TYPE                        17   163
D1528V12, multiclass
                                  clus
vv                                 TRHDE MUTATED TRHDE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       13             163
[1] 4 2
[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 = STK3 MUTATION ANALYSIS
D1529V1, survival
                sevent
clus2              0   1
  STK3 MUTATED     6   3
  STK3 WILD-TYPE 271  75
  STK3 MUTATED STK3 WILD-TYPE 
             9            346 
  STK3 MUTATED STK3 WILD-TYPE 
             3             75 
$`STK3 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A01R 
        1.02        19.04        20.12        63.98        26.99        35.01 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6718 
       88.21        49.41        10.06 

$`STK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  STK3 MUTATED STK3 WILD-TYPE 
          1.02           0.00 
  STK3 MUTATED STK3 WILD-TYPE 
         88.21         148.01 
  STK3 MUTATED STK3 WILD-TYPE 
        26.990         22.045 
[1] "1.0 - 88.2 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1529V2, continuous
                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      63        1       22       105         8         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        17          6         44         33       35        12
                vv
clus             STAGE IVB
  STK3 MUTATED           0
  STK3 WILD-TYPE         1
D1529V3, multiclass
            clus
vv           STK3 MUTATED STK3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  STK3 MUTATED     1   0   8   0
  STK3 WILD-TYPE   8  67 241  41
D1529V4, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  T1            1              8
  T2            0             67
  T3            8            241
  T4            0             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
  STK3 MUTATED     8   0   1
  STK3 WILD-TYPE 212  81  65
D1529V5, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1529V6, binary
                cls
clus               0   1
  STK3 MUTATED     7   0
  STK3 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      7    0
  STK3 WILD-TYPE  278   48
   clus
vv  STK3 MUTATED STK3 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1529V7, binary
                cls
clus               0   1
  STK3 MUTATED     4   5
  STK3 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      4    5
  STK3 WILD-TYPE  166  192
        clus
vv       STK3 MUTATED STK3 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D1529V8, binary
                cls
clus               0   1
  STK3 MUTATED     7   1
  STK3 WILD-TYPE 293   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      7    1
  STK3 WILD-TYPE  293    7
     clus
vv    STK3 MUTATED STK3 WILD-TYPE
  NO             7            293
  YES            1              7
[1] 2 2
[1] FALSE
D1529V9, binary
                cls
clus               0   1
  STK3 MUTATED     7   2
  STK3 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      7    2
  STK3 WILD-TYPE  307   46
                               clus
vv                              STK3 MUTATED STK3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  STK3 MUTATED     5   0   0   1
  STK3 WILD-TYPE 254   3  22  20
D1529V10, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            1             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"
D1529V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK3 MUTATED                                  0     1
  STK3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STK3 MUTATED                           0     3
  STK3 WILD-TYPE                        19   173
D1529V12, multiclass
                                  clus
vv                                 STK3 MUTATED STK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = SEC14L1 MUTATION ANALYSIS
D1530V1, survival
                   sevent
clus2                 0   1
  SEC14L1 MUTATED     7   2
  SEC14L1 WILD-TYPE 270  76
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
                9               346 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
                2                76 
$`SEC14L1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A00N 
      100.01        26.17        33.53         6.97        33.04         4.01 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6928 
       25.48        15.12        11.64 

$`SEC14L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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-D5-6540 
       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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
             4.01              0.00 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
           100.01            148.01 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
           25.480            22.045 
[1] "4.0 - 100.0 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1530V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEC14L1 MUTATED         0        0        3         4         1         0
  SEC14L1 WILD-TYPE      64        1       23       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC14L1 MUTATED           0          0          1          0        0
  SEC14L1 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SEC14L1 MUTATED           0         0
  SEC14L1 WILD-TYPE        12         1
D1530V3, multiclass
            clus
vv           SEC14L1 MUTATED SEC14L1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SEC14L1 MUTATED     0   0   7   3
  SEC14L1 WILD-TYPE   9  67 242  38
D1530V4, multiclass
    clus
vv   SEC14L1 MUTATED SEC14L1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               7               242
  T4               3                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
  SEC14L1 MUTATED     9   1   0
  SEC14L1 WILD-TYPE 211  80  66
D1530V5, multiclass
    clus
vv   SEC14L1 MUTATED SEC14L1 WILD-TYPE
  N0               9               211
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1530V6, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED     9   0
  SEC14L1 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED      9    0
  SEC14L1 WILD-TYPE  276   48
   clus
vv  SEC14L1 MUTATED SEC14L1 WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D1530V7, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED     6   4
  SEC14L1 WILD-TYPE 164 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED      6    4
  SEC14L1 WILD-TYPE  164  193
        clus
vv       SEC14L1 MUTATED SEC14L1 WILD-TYPE
  FEMALE               6               164
  MALE                 4               193
[1] 2 2
[1] FALSE
D1530V8, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED     8   0
  SEC14L1 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED      8    0
  SEC14L1 WILD-TYPE  292    8
     clus
vv    SEC14L1 MUTATED SEC14L1 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1530V9, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED     8   2
  SEC14L1 WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED      8    2
  SEC14L1 WILD-TYPE  306   46
                               clus
vv                              SEC14L1 MUTATED SEC14L1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SEC14L1 MUTATED     8   0   0   1
  SEC14L1 WILD-TYPE 251   3  22  20
D1530V10, multiclass
    clus
vv   SEC14L1 MUTATED SEC14L1 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               1                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"
D1530V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC14L1 MUTATED                                  0     0
  SEC14L1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SEC14L1 MUTATED                           1     5
  SEC14L1 WILD-TYPE                        18   171
D1530V12, multiclass
                                  clus
vv                                 SEC14L1 MUTATED SEC14L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = IL18R1 MUTATION ANALYSIS
D1531V1, survival
                  sevent
clus2                0   1
  IL18R1 MUTATED    11   2
  IL18R1 WILD-TYPE 266  76
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              13              342 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
               2               76 
$`IL18R1 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3877 
       13.02         0.92         3.02        63.98        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 
       44.68 

$`IL18R1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        21.99        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01        23.05        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  IL18R1 MUTATED IL18R1 WILD-TYPE 
            0.92             0.00 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
          124.27           148.01 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
          31.000           22.045 
[1] "0.9 - 124.3 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1531V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL18R1 MUTATED         2        0        3         2         1         0
  IL18R1 WILD-TYPE      62        1       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL18R1 MUTATED           3          0          1          0        0
  IL18R1 WILD-TYPE        15          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  IL18R1 MUTATED           0         0
  IL18R1 WILD-TYPE        12         1
D1531V3, multiclass
            clus
vv           IL18R1 MUTATED IL18R1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               15
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  IL18R1 MUTATED     1   3   8   1
  IL18R1 WILD-TYPE   8  64 241  40
D1531V4, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  T1              1                8
  T2              3               64
  T3              8              241
  T4              1               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
  IL18R1 MUTATED     9   2   2
  IL18R1 WILD-TYPE 211  79  64
D1531V5, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  N0              9              211
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1531V6, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    12   0
  IL18R1 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     12    0
  IL18R1 WILD-TYPE  273   48
   clus
vv  IL18R1 MUTATED IL18R1 WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1531V7, binary
                  cls
clus                 0   1
  IL18R1 MUTATED     7   6
  IL18R1 WILD-TYPE 163 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED      7    6
  IL18R1 WILD-TYPE  163  191
        clus
vv       IL18R1 MUTATED IL18R1 WILD-TYPE
  FEMALE              7              163
  MALE                6              191
[1] 2 2
[1] FALSE
D1531V8, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    12   0
  IL18R1 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     12    0
  IL18R1 WILD-TYPE  288    8
     clus
vv    IL18R1 MUTATED IL18R1 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1531V9, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    10   3
  IL18R1 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     10    3
  IL18R1 WILD-TYPE  304   45
                               clus
vv                              IL18R1 MUTATED IL18R1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IL18R1 MUTATED    11   0   0   1
  IL18R1 WILD-TYPE 248   3  22  20
D1531V10, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              1               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"
D1531V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL18R1 MUTATED                                  0     0
  IL18R1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IL18R1 MUTATED                           0     3
  IL18R1 WILD-TYPE                        19   173
D1531V12, multiclass
                                  clus
vv                                 IL18R1 MUTATED IL18R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = TOX MUTATION ANALYSIS
D1532V1, survival
               sevent
clus2             0   1
  TOX MUTATED    12   3
  TOX WILD-TYPE 265  75
  TOX MUTATED TOX WILD-TYPE 
           15           340 
  TOX MUTATED TOX WILD-TYPE 
            3            75 
$`TOX MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3664 
       24.00       100.01        20.12        63.98         6.97        54.02 
TCGA-AA-3710 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 
       26.99        21.99        25.02        38.04        18.05        34.98 
TCGA-AZ-4315 TCGA-DM-A28F TCGA-G4-6626 
       58.39        35.97        46.75 

$`TOX WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        78.08         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03         2.01        16.08        13.05        34.06        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  TOX MUTATED TOX WILD-TYPE 
         6.97          0.00 
  TOX MUTATED TOX WILD-TYPE 
       100.01        148.01 
  TOX MUTATED TOX WILD-TYPE 
        34.98         21.99 
[1] "7.0 - 100.0 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1532V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOX MUTATED         1        0        4         6         1         0
  TOX WILD-TYPE      63        1       22       102         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOX MUTATED           0          0          2          0        0         0
  TOX WILD-TYPE        18          6         42         33       35        12
               vv
clus            STAGE IVB
  TOX MUTATED           0
  TOX WILD-TYPE         1
D1532V3, multiclass
            clus
vv           TOX MUTATED TOX WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             4            22
  STAGE IIA            6           102
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  TOX MUTATED     0   2  11   2
  TOX WILD-TYPE   9  65 238  39
D1532V4, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  T1           0             9
  T2           2            65
  T3          11           238
  T4           2            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
  TOX MUTATED    13   2   0
  TOX WILD-TYPE 207  79  66
D1532V5, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  N0          13           207
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1532V6, binary
               cls
clus              0   1
  TOX MUTATED    13   0
  TOX WILD-TYPE 272  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     13    0
  TOX WILD-TYPE  272   48
   clus
vv  TOX MUTATED TOX WILD-TYPE
  0          13           272
  1           0            48
[1] 2 2
[1] FALSE
D1532V7, binary
               cls
clus              0   1
  TOX MUTATED     5  10
  TOX WILD-TYPE 165 187
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED      5   10
  TOX WILD-TYPE  165  187
        clus
vv       TOX MUTATED TOX WILD-TYPE
  FEMALE           5           165
  MALE            10           187
[1] 2 2
[1] FALSE
D1532V8, binary
               cls
clus              0   1
  TOX MUTATED    14   0
  TOX WILD-TYPE 286   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     14    0
  TOX WILD-TYPE  286    8
     clus
vv    TOX MUTATED TOX WILD-TYPE
  NO           14           286
  YES           0             8
[1] 2 2
[1] FALSE
D1532V9, binary
               cls
clus              0   1
  TOX MUTATED    12   3
  TOX WILD-TYPE 302  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     12    3
  TOX WILD-TYPE  302   45
                               clus
vv                              TOX MUTATED TOX WILD-TYPE
  COLON ADENOCARCINOMA                   12           302
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TOX MUTATED    11   0   0   0
  TOX WILD-TYPE 248   3  22  21
D1532V10, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  R0          11           248
  R1           0             3
  R2           0            22
  RX           0            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"
D1532V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOX MUTATED                                  0     0
  TOX WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TOX MUTATED                           0     5
  TOX WILD-TYPE                        19   171
D1532V12, multiclass
                                  clus
vv                                 TOX MUTATED TOX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      5           171
[1] 4 2
[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 = ROCK1 MUTATION ANALYSIS
D1533V1, survival
                 sevent
clus2               0   1
  ROCK1 MUTATED    10   6
  ROCK1 WILD-TYPE 267  72
  ROCK1 MUTATED ROCK1 WILD-TYPE 
             16             339 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
              6              72 
$`ROCK1 MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-AA-3518 TCGA-AA-3666 TCGA-AA-3864 TCGA-AA-3977 
       24.00        79.69         1.02         2.01        53.00        25.02 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        10.98        83.24        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6162 TCGA-F4-6570 
       10.06        15.02        12.00         6.18 

$`ROCK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        15.02        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         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ROCK1 MUTATED ROCK1 WILD-TYPE 
           1.02            0.00 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
          83.24          148.01 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
          19.51           22.06 
[1] "1.0 - 83.2 (19.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1533V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ROCK1 MUTATED         1        0        2         8         2         0
  ROCK1 WILD-TYPE      63        1       24       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ROCK1 MUTATED           1          0          1          1        0         0
  ROCK1 WILD-TYPE        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  ROCK1 MUTATED           0
  ROCK1 WILD-TYPE         1
D1533V3, multiclass
            clus
vv           ROCK1 MUTATED ROCK1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ROCK1 MUTATED     0   2  13   2
  ROCK1 WILD-TYPE   9  65 236  39
D1533V4, multiclass
    clus
vv   ROCK1 MUTATED ROCK1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            13             236
  T4             2              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
  ROCK1 MUTATED    14   2   1
  ROCK1 WILD-TYPE 206  79  65
D1533V5, multiclass
    clus
vv   ROCK1 MUTATED ROCK1 WILD-TYPE
  N0            14             206
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1533V6, binary
                 cls
clus                0   1
  ROCK1 MUTATED    14   0
  ROCK1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED     14    0
  ROCK1 WILD-TYPE  271   48
   clus
vv  ROCK1 MUTATED ROCK1 WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D1533V7, binary
                 cls
clus                0   1
  ROCK1 MUTATED     9   8
  ROCK1 WILD-TYPE 161 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED      9    8
  ROCK1 WILD-TYPE  161  189
        clus
vv       ROCK1 MUTATED ROCK1 WILD-TYPE
  FEMALE             9             161
  MALE               8             189
[1] 2 2
[1] FALSE
D1533V8, binary
                 cls
clus                0   1
  ROCK1 MUTATED    14   0
  ROCK1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED     14    0
  ROCK1 WILD-TYPE  286    8
     clus
vv    ROCK1 MUTATED ROCK1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1533V9, binary
                 cls
clus                0   1
  ROCK1 MUTATED    13   4
  ROCK1 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED     13    4
  ROCK1 WILD-TYPE  301   44
                               clus
vv                              ROCK1 MUTATED ROCK1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ROCK1 MUTATED    12   0   0   3
  ROCK1 WILD-TYPE 247   3  22  18
D1533V10, multiclass
    clus
vv   ROCK1 MUTATED ROCK1 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             3              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"
D1533V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ROCK1 MUTATED                                  0     3
  ROCK1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ROCK1 MUTATED                           0     7
  ROCK1 WILD-TYPE                        19   169
D1533V12, multiclass
                                  clus
vv                                 ROCK1 MUTATED ROCK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = CCDC158 MUTATION ANALYSIS
D1534V1, survival
                   sevent
clus2                 0   1
  CCDC158 MUTATED    13   2
  CCDC158 WILD-TYPE 264  76
  CCDC158 MUTATED CCDC158 WILD-TYPE 
               15               340 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                2                76 
$`CCDC158 MUTATED`
TCGA-AA-3950 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3864 
       24.00        31.63        33.53         8.38        63.98        53.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       25.02        34.98        83.24        58.39        12.76        10.06 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6171 
       13.02        15.02        14.04 

$`CCDC158 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.75        36.53        32.91        30.44        29.19        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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CCDC158 MUTATED CCDC158 WILD-TYPE 
             8.38              0.00 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
            83.24            148.01 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
            25.02             22.01 
[1] "8.4 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1534V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC158 MUTATED         1        0        2        10         1         0
  CCDC158 WILD-TYPE      63        1       24        98         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC158 MUTATED           0          0          1          0        0
  CCDC158 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  CCDC158 MUTATED           0         0
  CCDC158 WILD-TYPE        12         1
D1534V3, multiclass
            clus
vv           CCDC158 MUTATED CCDC158 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA               10                98
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  CCDC158 MUTATED     0   2  13   1
  CCDC158 WILD-TYPE   9  65 236  40
D1534V4, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3              13               236
  T4               1                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
  CCDC158 MUTATED    15   1   0
  CCDC158 WILD-TYPE 205  80  66
D1534V5, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  N0              15               205
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1534V6, binary
                   cls
clus                  0   1
  CCDC158 MUTATED    15   0
  CCDC158 WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED     15    0
  CCDC158 WILD-TYPE  270   48
   clus
vv  CCDC158 MUTATED CCDC158 WILD-TYPE
  0              15               270
  1               0                48
[1] 2 2
[1] FALSE
D1534V7, binary
                   cls
clus                  0   1
  CCDC158 MUTATED     6  10
  CCDC158 WILD-TYPE 164 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      6   10
  CCDC158 WILD-TYPE  164  187
        clus
vv       CCDC158 MUTATED CCDC158 WILD-TYPE
  FEMALE               6               164
  MALE                10               187
[1] 2 2
[1] FALSE
D1534V8, binary
                   cls
clus                  0   1
  CCDC158 MUTATED    15   0
  CCDC158 WILD-TYPE 285   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED     15    0
  CCDC158 WILD-TYPE  285    8
     clus
vv    CCDC158 MUTATED CCDC158 WILD-TYPE
  NO               15               285
  YES               0                 8
[1] 2 2
[1] FALSE
D1534V9, binary
                   cls
clus                  0   1
  CCDC158 MUTATED    14   2
  CCDC158 WILD-TYPE 300  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED     14    2
  CCDC158 WILD-TYPE  300   46
                               clus
vv                              CCDC158 MUTATED CCDC158 WILD-TYPE
  COLON ADENOCARCINOMA                       14               300
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC158 MUTATED    12   0   0   2
  CCDC158 WILD-TYPE 247   3  22  19
D1534V10, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               2                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"
D1534V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC158 MUTATED                                  0     3
  CCDC158 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC158 MUTATED                           4     3
  CCDC158 WILD-TYPE                        15   173
D1534V12, multiclass
                                  clus
vv                                 CCDC158 MUTATED CCDC158 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      4                15
  WHITE                                          3               173
[1] 4 2
[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 = XPO4 MUTATION ANALYSIS
D1535V1, survival
                sevent
clus2              0   1
  XPO4 MUTATED    12   5
  XPO4 WILD-TYPE 265  73
  XPO4 MUTATED XPO4 WILD-TYPE 
            17            338 
  XPO4 MUTATED XPO4 WILD-TYPE 
             5             73 
$`XPO4 MUTATED`
TCGA-AA-3662 TCGA-DM-A285 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01P 
        6.05         5.88        63.98        25.02        34.98        38.07 
TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 
       17.82        49.41        12.76        10.06        85.45        15.62 
TCGA-CM-5861 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A28G TCGA-G4-6304 
       15.02        10.13        13.35        60.79        53.62 

$`XPO4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
      148.01        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        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         7.53        12.39        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       13.78        46.75 

  XPO4 MUTATED XPO4 WILD-TYPE 
          5.88           0.00 
  XPO4 MUTATED XPO4 WILD-TYPE 
         85.45         148.01 
  XPO4 MUTATED XPO4 WILD-TYPE 
        17.820         22.075 
[1] "5.9 - 85.5 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1535V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XPO4 MUTATED         0        0        2         6         2         0
  XPO4 WILD-TYPE      64        1       24       102         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XPO4 MUTATED           1          1          2          1        2         0
  XPO4 WILD-TYPE        17          5         42         32       33        12
                vv
clus             STAGE IVB
  XPO4 MUTATED           0
  XPO4 WILD-TYPE         1
D1535V3, multiclass
            clus
vv           XPO4 MUTATED XPO4 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  XPO4 MUTATED     0   1  13   4
  XPO4 WILD-TYPE   9  66 236  37
D1535V4, multiclass
    clus
vv   XPO4 MUTATED XPO4 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           13            236
  T4            4             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
  XPO4 MUTATED    11   4   3
  XPO4 WILD-TYPE 209  77  63
D1535V5, multiclass
    clus
vv   XPO4 MUTATED XPO4 WILD-TYPE
  N0           11            209
  N1            4             77
  N2            3             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"
D1535V6, binary
                cls
clus               0   1
  XPO4 MUTATED    14   2
  XPO4 WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     14    2
  XPO4 WILD-TYPE  271   46
   clus
vv  XPO4 MUTATED XPO4 WILD-TYPE
  0           14            271
  1            2             46
[1] 2 2
[1] FALSE
D1535V7, binary
                cls
clus               0   1
  XPO4 MUTATED    11   7
  XPO4 WILD-TYPE 159 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     11    7
  XPO4 WILD-TYPE  159  190
        clus
vv       XPO4 MUTATED XPO4 WILD-TYPE
  FEMALE           11            159
  MALE              7            190
[1] 2 2
[1] FALSE
D1535V8, binary
                cls
clus               0   1
  XPO4 MUTATED    14   0
  XPO4 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     14    0
  XPO4 WILD-TYPE  286    8
     clus
vv    XPO4 MUTATED XPO4 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1535V9, binary
                cls
clus               0   1
  XPO4 MUTATED    13   5
  XPO4 WILD-TYPE 301  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     13    5
  XPO4 WILD-TYPE  301   43
                               clus
vv                              XPO4 MUTATED XPO4 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  XPO4 MUTATED     9   1   1   3
  XPO4 WILD-TYPE 250   2  21  18
D1535V10, multiclass
    clus
vv   XPO4 MUTATED XPO4 WILD-TYPE
  R0            9            250
  R1            1              2
  R2            1             21
  RX            3             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"
D1535V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XPO4 MUTATED                                  0     2
  XPO4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XPO4 MUTATED                           2     8
  XPO4 WILD-TYPE                        17   168
D1535V12, multiclass
                                  clus
vv                                 XPO4 MUTATED XPO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       8            168
[1] 4 2
[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 = ULK2 MUTATION ANALYSIS
D1536V1, survival
                sevent
clus2              0   1
  ULK2 MUTATED     8   4
  ULK2 WILD-TYPE 269  74
  ULK2 MUTATED ULK2 WILD-TYPE 
            12            343 
  ULK2 MUTATED ULK2 WILD-TYPE 
             4             74 
$`ULK2 MUTATED`
TCGA-AZ-6601 TCGA-AA-3492 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-6004 
      100.01         3.02        15.95         4.01        35.01        27.09 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5861 TCGA-DM-A1HB TCGA-F4-6703 
       58.39        49.41        51.32        15.02       135.65        47.87 

$`ULK2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ULK2 MUTATED ULK2 WILD-TYPE 
          3.02           0.00 
  ULK2 MUTATED ULK2 WILD-TYPE 
        135.65         148.01 
  ULK2 MUTATED ULK2 WILD-TYPE 
         41.44          21.99 
[1] "3.0 - 135.7 (41.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1536V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ULK2 MUTATED         1        0        3         5         1         0
  ULK2 WILD-TYPE      63        1       23       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ULK2 MUTATED           1          0          1          0        0         0
  ULK2 WILD-TYPE        17          6         43         33       35        12
                vv
clus             STAGE IVB
  ULK2 MUTATED           0
  ULK2 WILD-TYPE         1
D1536V3, multiclass
            clus
vv           ULK2 MUTATED ULK2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ULK2 MUTATED     0   1  10   1
  ULK2 WILD-TYPE   9  66 239  40
D1536V4, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           10            239
  T4            1             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
  ULK2 MUTATED    10   1   1
  ULK2 WILD-TYPE 210  80  65
D1536V5, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1536V6, binary
                cls
clus               0   1
  ULK2 MUTATED    10   0
  ULK2 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED     10    0
  ULK2 WILD-TYPE  275   48
   clus
vv  ULK2 MUTATED ULK2 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1536V7, binary
                cls
clus               0   1
  ULK2 MUTATED     6   6
  ULK2 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      6    6
  ULK2 WILD-TYPE  164  191
        clus
vv       ULK2 MUTATED ULK2 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D1536V8, binary
                cls
clus               0   1
  ULK2 MUTATED     8   1
  ULK2 WILD-TYPE 292   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      8    1
  ULK2 WILD-TYPE  292    7
     clus
vv    ULK2 MUTATED ULK2 WILD-TYPE
  NO             8            292
  YES            1              7
[1] 2 2
[1] FALSE
D1536V9, binary
                cls
clus               0   1
  ULK2 MUTATED     9   2
  ULK2 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      9    2
  ULK2 WILD-TYPE  305   46
                               clus
vv                              ULK2 MUTATED ULK2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ULK2 MUTATED     8   0   0   1
  ULK2 WILD-TYPE 251   3  22  20
D1536V10, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            1             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"
D1536V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ULK2 MUTATED                                  0     0
  ULK2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ULK2 MUTATED                           0     8
  ULK2 WILD-TYPE                        19   168
D1536V12, multiclass
                                  clus
vv                                 ULK2 MUTATED ULK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = TMEM62 MUTATION ANALYSIS
D1537V1, survival
                  sevent
clus2                0   1
  TMEM62 MUTATED     3   2
  TMEM62 WILD-TYPE 274  76
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               5              350 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               2               76 
$`TMEM62 MUTATED`
TCGA-AZ-6608 TCGA-AA-3864 TCGA-CA-6717 TCGA-DM-A28C TCGA-DM-A28K 
        1.94        53.00        12.76        81.37        98.24 

$`TMEM62 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TMEM62 MUTATED TMEM62 WILD-TYPE 
            1.94             0.00 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
           98.24           148.01 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
          53.000           22.045 
[1] "1.9 - 98.2 (53.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1537V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM62 MUTATED         0        0        1         4         0         0
  TMEM62 WILD-TYPE      64        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM62 MUTATED           0          1          0          0        0
  TMEM62 WILD-TYPE        18          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM62 MUTATED           0         0
  TMEM62 WILD-TYPE        12         1
D1537V3, multiclass
            clus
vv           TMEM62 MUTATED TMEM62 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TMEM62 MUTATED     0   1   5   0
  TMEM62 WILD-TYPE   9  66 244  41
D1537V4, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              0               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
  TMEM62 MUTATED     5   1   0
  TMEM62 WILD-TYPE 215  80  66
D1537V5, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1537V6, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     6   0
  TMEM62 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      6    0
  TMEM62 WILD-TYPE  279   48
   clus
vv  TMEM62 MUTATED TMEM62 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1537V7, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     2   4
  TMEM62 WILD-TYPE 168 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      2    4
  TMEM62 WILD-TYPE  168  193
        clus
vv       TMEM62 MUTATED TMEM62 WILD-TYPE
  FEMALE              2              168
  MALE                4              193
[1] 2 2
[1] FALSE
D1537V8, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     3   0
  TMEM62 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      3    0
  TMEM62 WILD-TYPE  297    8
     clus
vv    TMEM62 MUTATED TMEM62 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1537V9, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     4   2
  TMEM62 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      4    2
  TMEM62 WILD-TYPE  310   46
                               clus
vv                              TMEM62 MUTATED TMEM62 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM62 MUTATED     2   0   0   1
  TMEM62 WILD-TYPE 257   3  22  20
D1537V10, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              1               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"
D1537V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM62 MUTATED                                  0     1
  TMEM62 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM62 MUTATED                           0     3
  TMEM62 WILD-TYPE                        19   173
D1537V12, multiclass
                                  clus
vv                                 TMEM62 MUTATED TMEM62 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ATR MUTATION ANALYSIS
D1538V1, survival
               sevent
clus2             0   1
  ATR MUTATED    20   7
  ATR WILD-TYPE 257  71
  ATR MUTATED ATR WILD-TYPE 
           27           328 
  ATR MUTATED ATR WILD-TYPE 
            7            71 
$`ATR MUTATED`
TCGA-AA-3496 TCGA-AA-3543 TCGA-AA-3713 TCGA-AZ-6608 TCGA-CK-5912 TCGA-A6-2676 
        1.02         0.99        19.04         1.94        49.08        42.90 
TCGA-A6-6648 TCGA-AA-3502 TCGA-AA-3664 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3977 
       25.18        35.01        54.02        10.06        53.00        25.02 
TCGA-AA-A010 TCGA-AY-4070 TCGA-AY-6197 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 
       34.98        16.31        21.44        12.36        12.76        10.06 
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        54.61        17.85 
TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6315 
       41.42        33.67        61.91 

$`ATR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 
       36.03         8.05        19.07        34.03        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 
       15.52        25.08        10.88       106.75       100.01         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.08        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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        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-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-D5-5539 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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       34.42        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  ATR MUTATED ATR WILD-TYPE 
         0.99          0.00 
  ATR MUTATED ATR WILD-TYPE 
       124.27        148.01 
  ATR MUTATED ATR WILD-TYPE 
       23.050        22.045 
[1] "1.0 - 124.3 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1538V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATR MUTATED         6        0        3         8         2         0
  ATR WILD-TYPE      58        1       23       100         6         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        17          5         43         32       33        11
               vv
clus            STAGE IVB
  ATR MUTATED           1
  ATR WILD-TYPE         0
D1538V3, multiclass
            clus
vv           ATR MUTATED ATR WILD-TYPE
  STAGE I              6            58
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            8           100
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           1             5
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             2            33
  STAGE IVA            1            11
  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     1   7  18   2
  ATR WILD-TYPE   8  60 231  39
D1538V4, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  T1           1             8
  T2           7            60
  T3          18           231
  T4           2            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
  ATR MUTATED    22   3   3
  ATR WILD-TYPE 198  78  63
D1538V5, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  N0          22           198
  N1           3            78
  N2           3            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"
D1538V6, binary
               cls
clus              0   1
  ATR MUTATED    20   4
  ATR WILD-TYPE 265  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     20    4
  ATR WILD-TYPE  265   44
   clus
vv  ATR MUTATED ATR WILD-TYPE
  0          20           265
  1           4            44
[1] 2 2
[1] FALSE
D1538V7, binary
               cls
clus              0   1
  ATR MUTATED    12  16
  ATR WILD-TYPE 158 181
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     12   16
  ATR WILD-TYPE  158  181
        clus
vv       ATR MUTATED ATR WILD-TYPE
  FEMALE          12           158
  MALE            16           181
[1] 2 2
[1] FALSE
D1538V8, binary
               cls
clus              0   1
  ATR MUTATED    24   2
  ATR WILD-TYPE 276   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     24    2
  ATR WILD-TYPE  276    6
     clus
vv    ATR MUTATED ATR WILD-TYPE
  NO           24           276
  YES           2             6
[1] 2 2
[1] FALSE
D1538V9, binary
               cls
clus              0   1
  ATR MUTATED    25   3
  ATR WILD-TYPE 289  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     25    3
  ATR WILD-TYPE  289   45
                               clus
vv                              ATR MUTATED ATR WILD-TYPE
  COLON ADENOCARCINOMA                   25           289
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATR MUTATED    18   1   1   5
  ATR WILD-TYPE 241   2  21  16
D1538V10, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  R0          18           241
  R1           1             2
  R2           1            21
  RX           5            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"
D1538V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATR MUTATED                                  0     3
  ATR WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATR MUTATED                           2    13
  ATR WILD-TYPE                        17   163
D1538V12, multiclass
                                  clus
vv                                 ATR MUTATED ATR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             7
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                     13           163
[1] 4 2
[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 = FABP2 MUTATION ANALYSIS
D1539V1, survival
                 sevent
clus2               0   1
  FABP2 MUTATED     6   1
  FABP2 WILD-TYPE 271  77
  FABP2 MUTATED FABP2 WILD-TYPE 
              7             348 
  FABP2 MUTATED FABP2 WILD-TYPE 
              1              77 
$`FABP2 MUTATED`
TCGA-A6-6137 TCGA-AA-3977 TCGA-AZ-6599 TCGA-CM-6677 TCGA-D5-5540 TCGA-D5-6540 
       27.09        25.02         6.77        11.08        56.09        16.14 
TCGA-G4-6309 
       85.48 

$`FABP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  FABP2 MUTATED FABP2 WILD-TYPE 
           6.77            0.00 
  FABP2 MUTATED FABP2 WILD-TYPE 
          85.48          148.01 
  FABP2 MUTATED FABP2 WILD-TYPE 
         25.020          22.045 
[1] "6.8 - 85.5 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1539V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FABP2 MUTATED         2        0        0         2         0         0
  FABP2 WILD-TYPE      62        1       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FABP2 MUTATED           0          0          2          0        0         0
  FABP2 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  FABP2 MUTATED           0
  FABP2 WILD-TYPE         1
D1539V3, multiclass
            clus
vv           FABP2 MUTATED FABP2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  FABP2 MUTATED     0   3   4   0
  FABP2 WILD-TYPE   9  64 245  41
D1539V4, multiclass
    clus
vv   FABP2 MUTATED FABP2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             4             245
  T4             0              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
  FABP2 MUTATED     5   2   0
  FABP2 WILD-TYPE 215  79  66
D1539V5, multiclass
    clus
vv   FABP2 MUTATED FABP2 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1539V6, binary
                 cls
clus                0   1
  FABP2 MUTATED     5   0
  FABP2 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      5    0
  FABP2 WILD-TYPE  280   48
   clus
vv  FABP2 MUTATED FABP2 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1539V7, binary
                 cls
clus                0   1
  FABP2 MUTATED     2   5
  FABP2 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      2    5
  FABP2 WILD-TYPE  168  192
        clus
vv       FABP2 MUTATED FABP2 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1539V8, binary
                 cls
clus                0   1
  FABP2 MUTATED     7   0
  FABP2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      7    0
  FABP2 WILD-TYPE  293    8
     clus
vv    FABP2 MUTATED FABP2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1539V9, binary
                 cls
clus                0   1
  FABP2 MUTATED     6   1
  FABP2 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      6    1
  FABP2 WILD-TYPE  308   47
                               clus
vv                              FABP2 MUTATED FABP2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FABP2 MUTATED     4   0   0   0
  FABP2 WILD-TYPE 255   3  22  21
D1539V10, multiclass
    clus
vv   FABP2 MUTATED FABP2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1539V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FABP2 MUTATED                                  0     0
  FABP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FABP2 MUTATED                           1     5
  FABP2 WILD-TYPE                        18   171
D1539V12, multiclass
                                  clus
vv                                 FABP2 MUTATED FABP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = CTNND1 MUTATION ANALYSIS
D1540V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    14   3
  CTNND1 WILD-TYPE 263  75
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              17              338 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               3               75 
$`CTNND1 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-AZ-6601 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 
       19.04        25.08       100.01        33.53        22.06        19.66 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       61.02         6.97        34.98        58.39        49.41        12.76 
TCGA-CM-4743 TCGA-CM-5864 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-F4-6856 
       23.05        15.02        13.35        13.32        35.31 

$`CTNND1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            6.97             0.00 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          100.01           148.01 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           23.05            22.01 
[1] "7.0 - 100.0 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1540V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTNND1 MUTATED         2        0        4         8         1         0
  CTNND1 WILD-TYPE      62        1       22       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           0          0          1          1        1
  CTNND1 WILD-TYPE        18          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CTNND1 MUTATED           0         0
  CTNND1 WILD-TYPE        12         1
D1540V3, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CTNND1 MUTATED     0   2  14   2
  CTNND1 WILD-TYPE   9  65 235  39
D1540V4, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             14              235
  T4              2               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
  CTNND1 MUTATED    16   2   0
  CTNND1 WILD-TYPE 204  79  66
D1540V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0             16              204
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1540V6, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    15   1
  CTNND1 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     15    1
  CTNND1 WILD-TYPE  270   47
   clus
vv  CTNND1 MUTATED CTNND1 WILD-TYPE
  0             15              270
  1              1               47
[1] 2 2
[1] FALSE
D1540V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     5  13
  CTNND1 WILD-TYPE 165 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      5   13
  CTNND1 WILD-TYPE  165  184
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              5              165
  MALE               13              184
[1] 2 2
[1] FALSE
D1540V8, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    15   1
  CTNND1 WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     15    1
  CTNND1 WILD-TYPE  285    7
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D1540V9, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    13   4
  CTNND1 WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     13    4
  CTNND1 WILD-TYPE  301   44
                               clus
vv                              CTNND1 MUTATED CTNND1 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    13   0   1   1
  CTNND1 WILD-TYPE 246   3  21  20
D1540V10, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              1               21
  RX              1               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"
D1540V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNND1 MUTATED                                  0     1
  CTNND1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNND1 MUTATED                           1    11
  CTNND1 WILD-TYPE                        18   165
D1540V12, multiclass
                                  clus
vv                                 CTNND1 MUTATED CTNND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        11              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(1541) Variable = NEDD9 MUTATION ANALYSIS
D1541V1, survival
                 sevent
clus2               0   1
  NEDD9 MUTATED    10   1
  NEDD9 WILD-TYPE 267  77
  NEDD9 MUTATED NEDD9 WILD-TYPE 
             11             344 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
              1              77 
$`NEDD9 MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3877 
       19.04        35.80        26.17        22.06         1.02        31.00 
TCGA-AA-3949 TCGA-AA-A010 TCGA-AZ-4315 TCGA-D5-6540 TCGA-F4-6805 
       26.01        34.98        58.39        16.14        34.42 

$`NEDD9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 
       27.02        18.05         2.01        24.00        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NEDD9 MUTATED NEDD9 WILD-TYPE 
           1.02            0.00 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
          58.39          148.01 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
          26.17           21.99 
[1] "1.0 - 58.4 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1541V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEDD9 MUTATED         2        0        1         6         2         0
  NEDD9 WILD-TYPE      62        1       25       102         6         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  NEDD9 MUTATED           0
  NEDD9 WILD-TYPE         1
D1541V3, multiclass
            clus
vv           NEDD9 MUTATED NEDD9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  NEDD9 MUTATED     1   1   8   2
  NEDD9 WILD-TYPE   8  66 241  39
D1541V4, multiclass
    clus
vv   NEDD9 MUTATED NEDD9 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             8             241
  T4             2              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
  NEDD9 MUTATED    11   1   0
  NEDD9 WILD-TYPE 209  80  66
D1541V5, multiclass
    clus
vv   NEDD9 MUTATED NEDD9 WILD-TYPE
  N0            11             209
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1541V6, binary
                 cls
clus                0   1
  NEDD9 MUTATED    11   0
  NEDD9 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED     11    0
  NEDD9 WILD-TYPE  274   48
   clus
vv  NEDD9 MUTATED NEDD9 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1541V7, binary
                 cls
clus                0   1
  NEDD9 MUTATED     9   3
  NEDD9 WILD-TYPE 161 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED      9    3
  NEDD9 WILD-TYPE  161  194
        clus
vv       NEDD9 MUTATED NEDD9 WILD-TYPE
  FEMALE             9             161
  MALE               3             194
[1] 2 2
[1] FALSE
D1541V8, binary
                 cls
clus                0   1
  NEDD9 MUTATED    10   0
  NEDD9 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED     10    0
  NEDD9 WILD-TYPE  290    8
     clus
vv    NEDD9 MUTATED NEDD9 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1541V9, binary
                 cls
clus                0   1
  NEDD9 MUTATED     9   3
  NEDD9 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED      9    3
  NEDD9 WILD-TYPE  305   45
                               clus
vv                              NEDD9 MUTATED NEDD9 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NEDD9 MUTATED    11   0   0   1
  NEDD9 WILD-TYPE 248   3  22  20
D1541V10, multiclass
    clus
vv   NEDD9 MUTATED NEDD9 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1541V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEDD9 MUTATED                                  0     0
  NEDD9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NEDD9 MUTATED                           0     7
  NEDD9 WILD-TYPE                        19   169
D1541V12, multiclass
                                  clus
vv                                 NEDD9 MUTATED NEDD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = HCFC1R1 MUTATION ANALYSIS
D1542V1, survival
                   sevent
clus2                 0   1
  HCFC1R1 MUTATED     3   2
  HCFC1R1 WILD-TYPE 274  76
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               350 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                2                76 
$`HCFC1R1 MUTATED`
TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3845 TCGA-DM-A1D7 
       35.80        22.06        19.66         0.00        13.32 

$`HCFC1R1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                0                 0 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
            35.80            148.01 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
            19.66             22.09 
[1] "0.0 - 35.8 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.9"
D1542V2, continuous
                   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      64        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCFC1R1 MUTATED           0          0          0          1        0
  HCFC1R1 WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  HCFC1R1 MUTATED           0         0
  HCFC1R1 WILD-TYPE        12         1
D1542V3, multiclass
            clus
vv           HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  HCFC1R1 MUTATED     0   0   4   1
  HCFC1R1 WILD-TYPE   9  67 245  40
D1542V4, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               4               245
  T4               1                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
  HCFC1R1 MUTATED     4   1   0
  HCFC1R1 WILD-TYPE 216  80  66
D1542V5, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1542V6, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     4   0
  HCFC1R1 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      4    0
  HCFC1R1 WILD-TYPE  281   48
   clus
vv  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1542V7, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     3   2
  HCFC1R1 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      3    2
  HCFC1R1 WILD-TYPE  167  195
        clus
vv       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1542V8, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     3   0
  HCFC1R1 WILD-TYPE 297   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      3    0
  HCFC1R1 WILD-TYPE  297    8
     clus
vv    HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  NO                3               297
  YES               0                 8
[1] 2 2
[1] FALSE
D1542V9, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     3   1
  HCFC1R1 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      3    1
  HCFC1R1 WILD-TYPE  311   47
                               clus
vv                              HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HCFC1R1 MUTATED     4   0   0   0
  HCFC1R1 WILD-TYPE 255   3  22  21
D1542V10, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1542V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCFC1R1 MUTATED                                  0     0
  HCFC1R1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HCFC1R1 MUTATED                           0     4
  HCFC1R1 WILD-TYPE                        19   172
D1542V12, multiclass
                                  clus
vv                                 HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = PRKCQ MUTATION ANALYSIS
D1543V1, survival
                 sevent
clus2               0   1
  PRKCQ MUTATED    12   3
  PRKCQ WILD-TYPE 265  75
  PRKCQ MUTATED PRKCQ WILD-TYPE 
             15             340 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
              3              75 
$`PRKCQ MUTATED`
TCGA-A6-6652 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AY-5543 
       24.69        31.00        25.02        30.02         4.01        33.01 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6674 TCGA-D5-6930 TCGA-DM-A28G 
       12.10        12.76        22.03        12.95        13.35        60.79 
TCGA-DM-A28H TCGA-F4-6704 TCGA-G4-6307 
      117.07         1.55        55.04 

$`PRKCQ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6653 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 
      139.17        81.37       119.93        35.97        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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  PRKCQ MUTATED PRKCQ WILD-TYPE 
           1.55            0.00 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
         117.07          148.01 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
         24.690          22.025 
[1] "1.6 - 117.1 (24.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1543V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKCQ MUTATED         1        0        0         5         1         0
  PRKCQ WILD-TYPE      63        1       26       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCQ MUTATED           0          0          2          2        1         2
  PRKCQ WILD-TYPE        18          6         42         31       34        10
                 vv
clus              STAGE IVB
  PRKCQ MUTATED           0
  PRKCQ WILD-TYPE         1
D1543V3, multiclass
            clus
vv           PRKCQ MUTATED PRKCQ WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              2              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
  PRKCQ MUTATED     1   1  11   2
  PRKCQ WILD-TYPE   8  66 238  39
D1543V4, multiclass
    clus
vv   PRKCQ MUTATED PRKCQ WILD-TYPE
  T1             1               8
  T2             1              66
  T3            11             238
  T4             2              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
  PRKCQ MUTATED     9   4   2
  PRKCQ WILD-TYPE 211  77  64
D1543V5, multiclass
    clus
vv   PRKCQ MUTATED PRKCQ WILD-TYPE
  N0             9             211
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1543V6, binary
                 cls
clus                0   1
  PRKCQ MUTATED    10   3
  PRKCQ WILD-TYPE 275  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCQ MUTATED     10    3
  PRKCQ WILD-TYPE  275   45
   clus
vv  PRKCQ MUTATED PRKCQ WILD-TYPE
  0            10             275
  1             3              45
[1] 2 2
[1] FALSE
D1543V7, binary
                 cls
clus                0   1
  PRKCQ MUTATED     4  11
  PRKCQ WILD-TYPE 166 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCQ MUTATED      4   11
  PRKCQ WILD-TYPE  166  186
        clus
vv       PRKCQ MUTATED PRKCQ WILD-TYPE
  FEMALE             4             166
  MALE              11             186
[1] 2 2
[1] FALSE
D1543V8, binary
                 cls
clus                0   1
  PRKCQ MUTATED    11   0
  PRKCQ WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCQ MUTATED     11    0
  PRKCQ WILD-TYPE  289    8
     clus
vv    PRKCQ MUTATED PRKCQ WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1543V9, binary
                 cls
clus                0   1
  PRKCQ MUTATED    10   5
  PRKCQ WILD-TYPE 304  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCQ MUTATED     10    5
  PRKCQ WILD-TYPE  304   43
                               clus
vv                              PRKCQ MUTATED PRKCQ WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKCQ MUTATED     9   0   0   1
  PRKCQ WILD-TYPE 250   3  22  20
D1543V10, multiclass
    clus
vv   PRKCQ MUTATED PRKCQ WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D1543V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCQ MUTATED                                  1     1
  PRKCQ WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCQ MUTATED                           3     6
  PRKCQ WILD-TYPE                        16   170
D1543V12, multiclass
                                  clus
vv                                 PRKCQ MUTATED PRKCQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                        6             170
[1] 4 2
[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 = CAMK1 MUTATION ANALYSIS
D1544V1, survival
                 sevent
clus2               0   1
  CAMK1 MUTATED     4   3
  CAMK1 WILD-TYPE 273  75
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              7             348 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              3              75 
$`CAMK1 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-AA-A00N TCGA-AD-6889 TCGA-AY-6386 TCGA-G4-6304 
       24.00       100.01         4.01        83.24        17.82        53.62 
TCGA-G4-6315 
       61.91 

$`CAMK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  CAMK1 MUTATED CAMK1 WILD-TYPE 
           4.01            0.00 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
         100.01          148.01 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
          53.62           22.01 
[1] "4.0 - 100.0 (53.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1544V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAMK1 MUTATED         0        0        1         2         2         0
  CAMK1 WILD-TYPE      64        1       25       106         6         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  CAMK1 MUTATED           0
  CAMK1 WILD-TYPE         1
D1544V3, multiclass
            clus
vv           CAMK1 MUTATED CAMK1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  CAMK1 MUTATED     0   0   5   2
  CAMK1 WILD-TYPE   9  67 244  39
D1544V4, multiclass
    clus
vv   CAMK1 MUTATED CAMK1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             2              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
  CAMK1 MUTATED     5   2   0
  CAMK1 WILD-TYPE 215  79  66
D1544V5, multiclass
    clus
vv   CAMK1 MUTATED CAMK1 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1544V6, binary
                 cls
clus                0   1
  CAMK1 MUTATED     6   1
  CAMK1 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      6    1
  CAMK1 WILD-TYPE  279   47
   clus
vv  CAMK1 MUTATED CAMK1 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1544V7, binary
                 cls
clus                0   1
  CAMK1 MUTATED     3   4
  CAMK1 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      3    4
  CAMK1 WILD-TYPE  167  193
        clus
vv       CAMK1 MUTATED CAMK1 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1544V8, binary
                 cls
clus                0   1
  CAMK1 MUTATED     6   0
  CAMK1 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      6    0
  CAMK1 WILD-TYPE  294    8
     clus
vv    CAMK1 MUTATED CAMK1 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1544V9, binary
                 cls
clus                0   1
  CAMK1 MUTATED     5   2
  CAMK1 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      5    2
  CAMK1 WILD-TYPE  309   46
                               clus
vv                              CAMK1 MUTATED CAMK1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CAMK1 MUTATED     6   0   0   0
  CAMK1 WILD-TYPE 253   3  22  21
D1544V10, multiclass
    clus
vv   CAMK1 MUTATED CAMK1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1544V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAMK1 MUTATED                                  0     1
  CAMK1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CAMK1 MUTATED                           1     3
  CAMK1 WILD-TYPE                        18   173
D1544V12, multiclass
                                  clus
vv                                 CAMK1 MUTATED CAMK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = VCX3A MUTATION ANALYSIS
D1545V1, survival
                 sevent
clus2               0   1
  VCX3A MUTATED     4   1
  VCX3A WILD-TYPE 273  77
  VCX3A MUTATED VCX3A WILD-TYPE 
              5             350 
  VCX3A MUTATED VCX3A WILD-TYPE 
              1              77 
$`VCX3A MUTATED`
TCGA-AA-3662 TCGA-AZ-4681 TCGA-A6-2671 TCGA-AY-6386 TCGA-D5-6922 
        6.05       106.75        43.76        17.82        10.13 

$`VCX3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  VCX3A MUTATED VCX3A WILD-TYPE 
           6.05            0.00 
  VCX3A MUTATED VCX3A WILD-TYPE 
         106.75          148.01 
  VCX3A MUTATED VCX3A WILD-TYPE 
         17.820          22.075 
[1] "6.0 - 106.8 (17.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1545V2, continuous
                 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      64        1       26       107         8         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        18          5         43         33       33        12
                 vv
clus              STAGE IVB
  VCX3A MUTATED           0
  VCX3A WILD-TYPE         1
D1545V3, multiclass
            clus
vv           VCX3A MUTATED VCX3A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  VCX3A MUTATED     0   0   4   1
  VCX3A WILD-TYPE   9  67 245  40
D1545V4, multiclass
    clus
vv   VCX3A MUTATED VCX3A WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  VCX3A MUTATED     1   2   2
  VCX3A WILD-TYPE 219  79  64
D1545V5, multiclass
    clus
vv   VCX3A MUTATED VCX3A WILD-TYPE
  N0             1             219
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1545V6, binary
                 cls
clus                0   1
  VCX3A MUTATED     3   2
  VCX3A WILD-TYPE 282  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      3    2
  VCX3A WILD-TYPE  282   46
   clus
vv  VCX3A MUTATED VCX3A WILD-TYPE
  0             3             282
  1             2              46
[1] 2 2
[1] FALSE
D1545V7, binary
                 cls
clus                0   1
  VCX3A MUTATED     3   2
  VCX3A WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      3    2
  VCX3A WILD-TYPE  167  195
        clus
vv       VCX3A MUTATED VCX3A WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1545V8, binary
                 cls
clus                0   1
  VCX3A MUTATED     5   0
  VCX3A WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      5    0
  VCX3A WILD-TYPE  295    8
     clus
vv    VCX3A MUTATED VCX3A WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1545V9, binary
                 cls
clus                0   1
  VCX3A MUTATED     5   0
  VCX3A WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      5    0
  VCX3A WILD-TYPE  309   48
                               clus
vv                              VCX3A MUTATED VCX3A WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VCX3A MUTATED     4   0   1   0
  VCX3A WILD-TYPE 255   3  21  21
D1545V10, multiclass
    clus
vv   VCX3A MUTATED VCX3A WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D1545V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VCX3A MUTATED                                  0     0
  VCX3A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VCX3A MUTATED                           1     3
  VCX3A WILD-TYPE                        18   173
D1545V12, multiclass
                                  clus
vv                                 VCX3A MUTATED VCX3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = ATAD1 MUTATION ANALYSIS
D1546V1, survival
                 sevent
clus2               0   1
  ATAD1 MUTATED     6   2
  ATAD1 WILD-TYPE 271  76
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              8             347 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              2              76 
$`ATAD1 MUTATED`
TCGA-AD-6895 TCGA-AA-3947 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6168 
       25.08        33.01        58.39        21.14        23.05        12.99 
TCGA-D5-6920 TCGA-DM-A28F 
       12.39        35.97 

$`ATAD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ATAD1 MUTATED ATAD1 WILD-TYPE 
          12.39            0.00 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
          58.39          148.01 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
         24.065          22.030 
[1] "12.4 - 58.4 (24.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1546V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD1 MUTATED         1        0        0         4         1         0
  ATAD1 WILD-TYPE      63        1       26       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATAD1 MUTATED           0          0          2          0        0         0
  ATAD1 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  ATAD1 MUTATED           0
  ATAD1 WILD-TYPE         1
D1546V3, multiclass
            clus
vv           ATAD1 MUTATED ATAD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ATAD1 MUTATED     1   0   6   1
  ATAD1 WILD-TYPE   8  67 243  40
D1546V4, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             6             243
  T4             1              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
  ATAD1 MUTATED     6   2   0
  ATAD1 WILD-TYPE 214  79  66
D1546V5, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1546V6, binary
                 cls
clus                0   1
  ATAD1 MUTATED     8   0
  ATAD1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      8    0
  ATAD1 WILD-TYPE  277   48
   clus
vv  ATAD1 MUTATED ATAD1 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1546V7, binary
                 cls
clus                0   1
  ATAD1 MUTATED     4   4
  ATAD1 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      4    4
  ATAD1 WILD-TYPE  166  193
        clus
vv       ATAD1 MUTATED ATAD1 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D1546V8, binary
                 cls
clus                0   1
  ATAD1 MUTATED     7   0
  ATAD1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      7    0
  ATAD1 WILD-TYPE  293    8
     clus
vv    ATAD1 MUTATED ATAD1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1546V9, binary
                 cls
clus                0   1
  ATAD1 MUTATED     7   1
  ATAD1 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      7    1
  ATAD1 WILD-TYPE  307   47
                               clus
vv                              ATAD1 MUTATED ATAD1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATAD1 MUTATED     6   0   0   1
  ATAD1 WILD-TYPE 253   3  22  20
D1546V10, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1546V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD1 MUTATED                                  0     0
  ATAD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD1 MUTATED                           1     6
  ATAD1 WILD-TYPE                        18   170
D1546V12, multiclass
                                  clus
vv                                 ATAD1 MUTATED ATAD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = C6ORF150 MUTATION ANALYSIS
D1547V1, survival
                    sevent
clus2                  0   1
  C6ORF150 MUTATED     7   2
  C6ORF150 WILD-TYPE 270  76
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 9                346 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 2                 76 
$`C6ORF150 MUTATED`
TCGA-AA-3496 TCGA-AZ-6601 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00A TCGA-AA-A010 
        1.02       100.01        63.98        53.00        38.04        34.98 
TCGA-AU-6004 TCGA-CM-5349 TCGA-D5-5538 
       27.09        30.08        54.61 

$`C6ORF150 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
              1.02               0.00 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
            100.01             148.01 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
             38.04              21.99 
[1] "1.0 - 100.0 (38.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1547V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF150 MUTATED         1        0        4         2         1         0
  C6ORF150 WILD-TYPE      63        1       22       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF150 MUTATED           0          0          1          0        0
  C6ORF150 WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF150 MUTATED           0         0
  C6ORF150 WILD-TYPE        12         1
D1547V3, multiclass
            clus
vv           C6ORF150 MUTATED C6ORF150 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                 2                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C6ORF150 MUTATED     0   1   7   1
  C6ORF150 WILD-TYPE   9  66 242  40
D1547V4, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                7                242
  T4                1                 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
  C6ORF150 MUTATED     8   1   0
  C6ORF150 WILD-TYPE 212  80  66
D1547V5, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  N0                8                212
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1547V6, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     9   0
  C6ORF150 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      9    0
  C6ORF150 WILD-TYPE  276   48
   clus
vv  C6ORF150 MUTATED C6ORF150 WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D1547V7, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     5   4
  C6ORF150 WILD-TYPE 165 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      5    4
  C6ORF150 WILD-TYPE  165  193
        clus
vv       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  FEMALE                5                165
  MALE                  4                193
[1] 2 2
[1] FALSE
D1547V8, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     7   0
  C6ORF150 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      7    0
  C6ORF150 WILD-TYPE  293    8
     clus
vv    C6ORF150 MUTATED C6ORF150 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1547V9, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     9   0
  C6ORF150 WILD-TYPE 305  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      9    0
  C6ORF150 WILD-TYPE  305   48
                               clus
vv                              C6ORF150 MUTATED C6ORF150 WILD-TYPE
  COLON ADENOCARCINOMA                         9                305
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C6ORF150 MUTATED     8   0   0   0
  C6ORF150 WILD-TYPE 251   3  22  21
D1547V10, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  R0                8                251
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1547V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF150 MUTATED                                  0     0
  C6ORF150 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF150 MUTATED                           0     4
  C6ORF150 WILD-TYPE                        19   172
D1547V12, multiclass
                                  clus
vv                                 C6ORF150 MUTATED C6ORF150 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = IGFN1 MUTATION ANALYSIS
D1548V1, survival
                 sevent
clus2               0   1
  IGFN1 MUTATED    11   4
  IGFN1 WILD-TYPE 266  74
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             15             340 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              4              74 
$`IGFN1 MUTATED`
TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-A00E 
       26.17        22.06         3.02        10.06        33.04        30.02 
TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6533 
       83.24        12.76        10.06        23.05        14.04        25.48 
TCGA-DM-A28K TCGA-G4-6293 TCGA-G4-6323 
       98.24       133.18        13.78 

$`IGFN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        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-G4-6626 
       85.48        61.91        36.00        46.75 

  IGFN1 MUTATED IGFN1 WILD-TYPE 
           3.02            0.00 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
         133.18          148.01 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
          23.05           22.01 
[1] "3.0 - 133.2 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1548V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFN1 MUTATED         1        1        1        10         0         0
  IGFN1 WILD-TYPE      63        0       25        98         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGFN1 MUTATED           2          0          0          0        0         0
  IGFN1 WILD-TYPE        16          6         44         33       35        12
                 vv
clus              STAGE IVB
  IGFN1 MUTATED           0
  IGFN1 WILD-TYPE         1
D1548V3, multiclass
            clus
vv           IGFN1 MUTATED IGFN1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA             10              98
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  IGFN1 MUTATED     0   1  13   1
  IGFN1 WILD-TYPE   9  66 236  40
D1548V4, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            13             236
  T4             1              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
  IGFN1 MUTATED    14   1   1
  IGFN1 WILD-TYPE 206  80  65
D1548V5, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  N0            14             206
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1548V6, binary
                 cls
clus                0   1
  IGFN1 MUTATED    15   0
  IGFN1 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     15    0
  IGFN1 WILD-TYPE  270   48
   clus
vv  IGFN1 MUTATED IGFN1 WILD-TYPE
  0            15             270
  1             0              48
[1] 2 2
[1] FALSE
D1548V7, binary
                 cls
clus                0   1
  IGFN1 MUTATED     9   7
  IGFN1 WILD-TYPE 161 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      9    7
  IGFN1 WILD-TYPE  161  190
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  FEMALE             9             161
  MALE               7             190
[1] 2 2
[1] FALSE
D1548V8, binary
                 cls
clus                0   1
  IGFN1 MUTATED    14   0
  IGFN1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     14    0
  IGFN1 WILD-TYPE  286    8
     clus
vv    IGFN1 MUTATED IGFN1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1548V9, binary
                 cls
clus                0   1
  IGFN1 MUTATED    14   2
  IGFN1 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     14    2
  IGFN1 WILD-TYPE  300   46
                               clus
vv                              IGFN1 MUTATED IGFN1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IGFN1 MUTATED    13   0   0   2
  IGFN1 WILD-TYPE 246   3  22  19
D1548V10, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             0              22
  RX             2              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"
D1548V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFN1 MUTATED                                  0     3
  IGFN1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGFN1 MUTATED                           1     7
  IGFN1 WILD-TYPE                        18   169
D1548V12, multiclass
                                  clus
vv                                 IGFN1 MUTATED IGFN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = CCDC14 MUTATION ANALYSIS
D1549V1, survival
                  sevent
clus2                0   1
  CCDC14 MUTATED     6   5
  CCDC14 WILD-TYPE 271  73
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              344 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
               5               73 
$`CCDC14 MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3977 
       19.04        10.88        30.44        63.98         0.00        25.02 
TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-F4-6570 
        4.01        58.39        12.76        10.06         6.18 

$`CCDC14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCDC14 MUTATED CCDC14 WILD-TYPE 
               0                0 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
           63.98           148.01 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
           12.76            22.09 
[1] "0.0 - 64.0 (12.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D1549V2, continuous
                  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      63        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC14 MUTATED           0          0          0          0        1
  CCDC14 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC14 MUTATED           0         0
  CCDC14 WILD-TYPE        12         1
D1549V3, multiclass
            clus
vv           CCDC14 MUTATED CCDC14 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CCDC14 MUTATED     0   2   7   2
  CCDC14 WILD-TYPE   9  65 242  39
D1549V4, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              2               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
  CCDC14 MUTATED    10   0   1
  CCDC14 WILD-TYPE 210  81  65
D1549V5, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  N0             10              210
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1549V6, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     8   1
  CCDC14 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      8    1
  CCDC14 WILD-TYPE  277   47
   clus
vv  CCDC14 MUTATED CCDC14 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1549V7, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     2   9
  CCDC14 WILD-TYPE 168 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      2    9
  CCDC14 WILD-TYPE  168  188
        clus
vv       CCDC14 MUTATED CCDC14 WILD-TYPE
  FEMALE              2              168
  MALE                9              188
[1] 2 2
[1] FALSE
D1549V8, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     8   1
  CCDC14 WILD-TYPE 292   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      8    1
  CCDC14 WILD-TYPE  292    7
     clus
vv    CCDC14 MUTATED CCDC14 WILD-TYPE
  NO               8              292
  YES              1                7
[1] 2 2
[1] FALSE
D1549V9, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     9   2
  CCDC14 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      9    2
  CCDC14 WILD-TYPE  305   46
                               clus
vv                              CCDC14 MUTATED CCDC14 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC14 MUTATED     6   0   1   2
  CCDC14 WILD-TYPE 253   3  21  19
D1549V10, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              2               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"
D1549V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC14 MUTATED                                  0     2
  CCDC14 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC14 MUTATED                           0     4
  CCDC14 WILD-TYPE                        19   172
D1549V12, multiclass
                                  clus
vv                                 CCDC14 MUTATED CCDC14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = ENPP3 MUTATION ANALYSIS
D1550V1, survival
                 sevent
clus2               0   1
  ENPP3 MUTATED     6   3
  ENPP3 WILD-TYPE 271  75
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              9             346 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              3              75 
$`ENPP3 MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-AA-3555 TCGA-AA-A00N TCGA-AZ-6598 TCGA-CA-6717 
       19.04        10.88        29.95         4.01        49.41        12.76 
TCGA-CM-5344 TCGA-D5-6928 TCGA-DM-A1HB 
       22.03        11.64       135.65 

$`ENPP3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ENPP3 MUTATED ENPP3 WILD-TYPE 
           4.01            0.00 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
         135.65          148.01 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
          19.04           22.09 
[1] "4.0 - 135.7 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1550V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPP3 MUTATED         0        0        1         3         1         0
  ENPP3 WILD-TYPE      64        1       25       105         7         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        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  ENPP3 MUTATED           0
  ENPP3 WILD-TYPE         1
D1550V3, multiclass
            clus
vv           ENPP3 MUTATED ENPP3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ENPP3 MUTATED     0   0   7   2
  ENPP3 WILD-TYPE   9  67 242  39
D1550V4, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             2              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
  ENPP3 MUTATED     6   2   1
  ENPP3 WILD-TYPE 214  79  65
D1550V5, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1550V6, binary
                 cls
clus                0   1
  ENPP3 MUTATED     6   1
  ENPP3 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      6    1
  ENPP3 WILD-TYPE  279   47
   clus
vv  ENPP3 MUTATED ENPP3 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1550V7, binary
                 cls
clus                0   1
  ENPP3 MUTATED     3   6
  ENPP3 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      3    6
  ENPP3 WILD-TYPE  167  191
        clus
vv       ENPP3 MUTATED ENPP3 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1550V8, binary
                 cls
clus                0   1
  ENPP3 MUTATED     6   1
  ENPP3 WILD-TYPE 294   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      6    1
  ENPP3 WILD-TYPE  294    7
     clus
vv    ENPP3 MUTATED ENPP3 WILD-TYPE
  NO              6             294
  YES             1               7
[1] 2 2
[1] FALSE
D1550V9, binary
                 cls
clus                0   1
  ENPP3 MUTATED     4   4
  ENPP3 WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      4    4
  ENPP3 WILD-TYPE  310   44
                               clus
vv                              ENPP3 MUTATED ENPP3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ENPP3 MUTATED     4   0   1   1
  ENPP3 WILD-TYPE 255   3  21  20
D1550V10, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             1              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"
D1550V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENPP3 MUTATED                                  0     1
  ENPP3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ENPP3 MUTATED                           0     5
  ENPP3 WILD-TYPE                        19   171
D1550V12, multiclass
                                  clus
vv                                 ENPP3 MUTATED ENPP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = TAB1 MUTATION ANALYSIS
D1551V1, survival
                sevent
clus2              0   1
  TAB1 MUTATED     2   1
  TAB1 WILD-TYPE 275  77
  TAB1 MUTATED TAB1 WILD-TYPE 
             3            352 
  TAB1 MUTATED TAB1 WILD-TYPE 
             1             77 
$`TAB1 MUTATED`
TCGA-AA-3672 TCGA-AD-6889 TCGA-CM-6171 
        0.92        83.24        14.04 

$`TAB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TAB1 MUTATED TAB1 WILD-TYPE 
          0.92           0.00 
  TAB1 MUTATED TAB1 WILD-TYPE 
         83.24         148.01 
  TAB1 MUTATED TAB1 WILD-TYPE 
        14.040         22.075 
[1] "0.9 - 83.2 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1551V2, continuous
[1] "Remove cluster labels:" "TAB1 MUTATED"          
clus
  TAB1 MUTATED TAB1 WILD-TYPE 
             2            364 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AA-3496 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3516     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-3527     TCGA-AA-3530 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552     TCGA-AA-3554 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562     TCGA-AA-3662 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3697     TCGA-AA-3713 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3814     TCGA-AA-3844     TCGA-AA-3860 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3870     TCGA-AA-3939     TCGA-AA-3950 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3972     TCGA-AA-3976     TCGA-AA-3979 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-A00L     TCGA-AA-A00Z     TCGA-AA-A024 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A285     TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-3810     TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5660     TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5665     TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6141     TCGA-A6-6142     TCGA-A6-6648     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-3502     TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3517     TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3526 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3542     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3555     TCGA-AA-3558     TCGA-AA-3561 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3663     TCGA-AA-3664 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3673     TCGA-AA-3678 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3811     TCGA-AA-3812 
"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-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-3861     TCGA-AA-3864 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3866     TCGA-AA-3869     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-3941     TCGA-AA-3947 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973     TCGA-AA-3975 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3980     TCGA-AA-3982     TCGA-AA-3984 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00K     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-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-A029 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6890     TCGA-AD-6899 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"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-5913     TCGA-CK-5914     TCGA-CK-5915 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6172     TCGA-CM-6674 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
                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      63        1       26       107         8         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        17          6         44         33       35        12
                vv
clus             STAGE IVB
  TAB1 MUTATED           0
  TAB1 WILD-TYPE         1
D1551V3, multiclass
            clus
vv           TAB1 MUTATED TAB1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TAB1 MUTATED     0   1   2   0
  TAB1 WILD-TYPE   9  66 247  41
D1551V4, multiclass
    clus
vv   TAB1 MUTATED TAB1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            0             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
  TAB1 MUTATED     2   1   0
  TAB1 WILD-TYPE 218  80  66
D1551V5, multiclass
    clus
vv   TAB1 MUTATED TAB1 WILD-TYPE
  N0            2            218
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1551V6, binary
                cls
clus               0   1
  TAB1 MUTATED     3   0
  TAB1 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      3    0
  TAB1 WILD-TYPE  282   48
   clus
vv  TAB1 MUTATED TAB1 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1551V7, binary
                cls
clus               0   1
  TAB1 MUTATED     2   1
  TAB1 WILD-TYPE 168 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      2    1
  TAB1 WILD-TYPE  168  196
        clus
vv       TAB1 MUTATED TAB1 WILD-TYPE
  FEMALE            2            168
  MALE              1            196
[1] 2 2
[1] FALSE
D1551V8, binary
                cls
clus               0   1
  TAB1 MUTATED     3   0
  TAB1 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      3    0
  TAB1 WILD-TYPE  297    8
     clus
vv    TAB1 MUTATED TAB1 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1551V9, binary
                cls
clus               0   1
  TAB1 MUTATED     3   0
  TAB1 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      3    0
  TAB1 WILD-TYPE  311   48
                               clus
vv                              TAB1 MUTATED TAB1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAB1 MUTATED     3   0   0   0
  TAB1 WILD-TYPE 256   3  22  21
D1551V10, multiclass
    clus
vv   TAB1 MUTATED TAB1 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1551V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAB1 MUTATED                                  0     1
  TAB1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAB1 MUTATED                           0     1
  TAB1 WILD-TYPE                        19   175
D1551V12, multiclass
[1] "Remove cluster labels:" "TAB1 MUTATED"          
clus
  TAB1 MUTATED TAB1 WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6890     TCGA-AD-6899 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"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-5913     TCGA-CK-5914     TCGA-CK-5915 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6172     TCGA-CM-6674 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 

Clustering(1552) Variable = CDK5RAP2 MUTATION ANALYSIS
D1552V1, survival
                    sevent
clus2                  0   1
  CDK5RAP2 MUTATED    20   2
  CDK5RAP2 WILD-TYPE 257  76
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                22                333 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                 2                 76 
$`CDK5RAP2 MUTATED`
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 
       35.80        79.69        30.44        22.06        32.71        24.39 
TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 
       63.98        25.02         4.01        34.98        12.16        83.24 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-5861 
       27.09        58.39        88.21        12.59        12.76        15.02 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6930 TCGA-G4-6293 
       12.99        12.95        13.35       133.18 

$`CDK5RAP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
              4.01               0.00 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
            133.18             148.01 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
            26.055             21.990 
[1] "4.0 - 133.2 (26.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.3"
D1552V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK5RAP2 MUTATED         6        0        2        10         2         1
  CDK5RAP2 WILD-TYPE      58        1       24        98         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDK5RAP2 MUTATED           1          0          0          0        0
  CDK5RAP2 WILD-TYPE        17          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  CDK5RAP2 MUTATED           0         0
  CDK5RAP2 WILD-TYPE        12         1
D1552V3, multiclass
            clus
vv           CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  STAGE I                   6                 58
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                10                 98
  STAGE IIB                 2                  6
  STAGE IIC                 1                  0
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  CDK5RAP2 MUTATED     1   6  12   4
  CDK5RAP2 WILD-TYPE   8  61 237  37
D1552V4, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  T1                1                  8
  T2                6                 61
  T3               12                237
  T4                4                 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
  CDK5RAP2 MUTATED    22   1   0
  CDK5RAP2 WILD-TYPE 198  80  66
D1552V5, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  N0               22                198
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1552V6, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    21   0
  CDK5RAP2 WILD-TYPE 264  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     21    0
  CDK5RAP2 WILD-TYPE  264   48
   clus
vv  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  0               21                264
  1                0                 48
[1] 2 2
[1] FALSE
D1552V7, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED     9  14
  CDK5RAP2 WILD-TYPE 161 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED      9   14
  CDK5RAP2 WILD-TYPE  161  183
        clus
vv       CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  FEMALE                9                161
  MALE                 14                183
[1] 2 2
[1] FALSE
D1552V8, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    20   0
  CDK5RAP2 WILD-TYPE 280   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     20    0
  CDK5RAP2 WILD-TYPE  280    8
     clus
vv    CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  NO                20                280
  YES                0                  8
[1] 2 2
[1] FALSE
D1552V9, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    19   4
  CDK5RAP2 WILD-TYPE 295  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     19    4
  CDK5RAP2 WILD-TYPE  295   44
                               clus
vv                              CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  COLON ADENOCARCINOMA                        19                295
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CDK5RAP2 MUTATED    18   0   0   1
  CDK5RAP2 WILD-TYPE 241   3  22  20
D1552V10, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  R0               18                241
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1552V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK5RAP2 MUTATED                                  0     3
  CDK5RAP2 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CDK5RAP2 MUTATED                           1    14
  CDK5RAP2 WILD-TYPE                        18   162
D1552V12, multiclass
                                  clus
vv                                 CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          14                162
[1] 4 2
[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 = CASP5 MUTATION ANALYSIS
D1553V1, survival
                 sevent
clus2               0   1
  CASP5 MUTATED     8   4
  CASP5 WILD-TYPE 269  74
  CASP5 MUTATED CASP5 WILD-TYPE 
             12             343 
  CASP5 MUTATED CASP5 WILD-TYPE 
              4              74 
$`CASP5 MUTATED`
TCGA-AD-6895 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3833 
       25.08         1.94        26.17        23.61        63.98        15.95 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CM-6676 TCGA-D5-6927 
       25.02         4.01        62.79        49.41        11.08         9.44 

$`CASP5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CASP5 MUTATED CASP5 WILD-TYPE 
           1.94            0.00 
  CASP5 MUTATED CASP5 WILD-TYPE 
          63.98          148.01 
  CASP5 MUTATED CASP5 WILD-TYPE 
         24.315          22.030 
[1] "1.9 - 64.0 (24.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1553V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP5 MUTATED         1        0        3         4         1         0
  CASP5 WILD-TYPE      63        1       23       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP5 MUTATED           0          1          1          0        0         1
  CASP5 WILD-TYPE        18          5         43         33       35        11
                 vv
clus              STAGE IVB
  CASP5 MUTATED           0
  CASP5 WILD-TYPE         1
D1553V3, multiclass
            clus
vv           CASP5 MUTATED CASP5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  CASP5 MUTATED     0   3   9   1
  CASP5 WILD-TYPE   9  64 240  40
D1553V4, multiclass
    clus
vv   CASP5 MUTATED CASP5 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             9             240
  T4             1              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
  CASP5 MUTATED    10   2   1
  CASP5 WILD-TYPE 210  79  65
D1553V5, multiclass
    clus
vv   CASP5 MUTATED CASP5 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1553V6, binary
                 cls
clus                0   1
  CASP5 MUTATED     9   1
  CASP5 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP5 MUTATED      9    1
  CASP5 WILD-TYPE  276   47
   clus
vv  CASP5 MUTATED CASP5 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1553V7, binary
                 cls
clus                0   1
  CASP5 MUTATED     5   8
  CASP5 WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP5 MUTATED      5    8
  CASP5 WILD-TYPE  165  189
        clus
vv       CASP5 MUTATED CASP5 WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D1553V8, binary
                 cls
clus                0   1
  CASP5 MUTATED    11   0
  CASP5 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP5 MUTATED     11    0
  CASP5 WILD-TYPE  289    8
     clus
vv    CASP5 MUTATED CASP5 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1553V9, binary
                 cls
clus                0   1
  CASP5 MUTATED    12   1
  CASP5 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP5 MUTATED     12    1
  CASP5 WILD-TYPE  302   47
                               clus
vv                              CASP5 MUTATED CASP5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP5 MUTATED     8   0   0   0
  CASP5 WILD-TYPE 251   3  22  21
D1553V10, multiclass
    clus
vv   CASP5 MUTATED CASP5 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1553V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP5 MUTATED                                  0     0
  CASP5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP5 MUTATED                           0     8
  CASP5 WILD-TYPE                        19   168
D1553V12, multiclass
                                  clus
vv                                 CASP5 MUTATED CASP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = NONO MUTATION ANALYSIS
D1554V1, survival
                sevent
clus2              0   1
  NONO MUTATED     9   2
  NONO WILD-TYPE 268  76
  NONO MUTATED NONO WILD-TYPE 
            11            344 
  NONO MUTATED NONO WILD-TYPE 
             2             76 
$`NONO MUTATED`
TCGA-CK-5912 TCGA-A6-6141 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-4948 
       49.08         8.38        34.98        83.24        58.39       148.01 
TCGA-CK-6751 TCGA-CM-6677 TCGA-D5-6539 TCGA-D5-6930 TCGA-G4-6306 
      124.27        11.08        12.49        13.35        44.68 

$`NONO WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NONO MUTATED NONO WILD-TYPE 
          8.38           0.00 
  NONO MUTATED NONO WILD-TYPE 
        148.01         140.38 
  NONO MUTATED NONO WILD-TYPE 
         44.68          22.01 
[1] "8.4 - 148.0 (44.7)" "0.0 - 140.4 (22.0)"
[1] "hr=" "2.1"
D1554V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NONO MUTATED         2        0        0         5         1         0
  NONO WILD-TYPE      62        1       26       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NONO MUTATED           1          0          0          0        0         0
  NONO WILD-TYPE        17          6         44         33       35        12
                vv
clus             STAGE IVB
  NONO MUTATED           0
  NONO WILD-TYPE         1
D1554V3, multiclass
            clus
vv           NONO MUTATED NONO WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  NONO MUTATED     0   3   7   1
  NONO WILD-TYPE   9  64 242  40
D1554V4, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  T1            0              9
  T2            3             64
  T3            7            242
  T4            1             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
  NONO MUTATED    10   1   0
  NONO WILD-TYPE 210  80  66
D1554V5, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  N0           10            210
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1554V6, binary
                cls
clus               0   1
  NONO MUTATED     9   0
  NONO WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      9    0
  NONO WILD-TYPE  276   48
   clus
vv  NONO MUTATED NONO WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D1554V7, binary
                cls
clus               0   1
  NONO MUTATED     5   6
  NONO WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      5    6
  NONO WILD-TYPE  165  191
        clus
vv       NONO MUTATED NONO WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D1554V8, binary
                cls
clus               0   1
  NONO MUTATED    11   0
  NONO WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED     11    0
  NONO WILD-TYPE  289    8
     clus
vv    NONO MUTATED NONO WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1554V9, binary
                cls
clus               0   1
  NONO MUTATED     9   2
  NONO WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      9    2
  NONO WILD-TYPE  305   46
                               clus
vv                              NONO MUTATED NONO WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NONO MUTATED     8   0   0   2
  NONO WILD-TYPE 251   3  22  19
D1554V10, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            2             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"
D1554V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NONO MUTATED                                  0     1
  NONO WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NONO MUTATED                           1     8
  NONO WILD-TYPE                        18   168
D1554V12, multiclass
                                  clus
vv                                 NONO MUTATED NONO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       8            168
[1] 4 2
[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 = SLC16A5 MUTATION ANALYSIS
D1555V1, survival
                   sevent
clus2                 0   1
  SLC16A5 MUTATED     8   1
  SLC16A5 WILD-TYPE 269  77
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
                9               346 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
                1                77 
$`SLC16A5 MUTATED`
TCGA-AA-3672 TCGA-A6-6651 TCGA-AA-3517 TCGA-AA-3815 TCGA-AA-3977 TCGA-CA-6717 
        0.92        21.76        38.99        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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  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            22.045 
[1] "0.9 - 46.8 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1555V2, continuous
                   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      63        1       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A5 MUTATED           1          1          1          0        0
  SLC16A5 WILD-TYPE        17          5         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A5 MUTATED           0         0
  SLC16A5 WILD-TYPE        12         1
D1555V3, multiclass
            clus
vv           SLC16A5 MUTATED SLC16A5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               1                 5
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC16A5 MUTATED     1   1   7   1
  SLC16A5 WILD-TYPE   8  66 242  40
D1555V4, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               7               242
  T4               1                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
  SLC16A5 MUTATED     7   3   0
  SLC16A5 WILD-TYPE 213  78  66
D1555V5, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  N0               7               213
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1555V6, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     8   0
  SLC16A5 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      8    0
  SLC16A5 WILD-TYPE  277   48
   clus
vv  SLC16A5 MUTATED SLC16A5 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D1555V7, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     5   5
  SLC16A5 WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      5    5
  SLC16A5 WILD-TYPE  165  192
        clus
vv       SLC16A5 MUTATED SLC16A5 WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D1555V8, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     9   0
  SLC16A5 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      9    0
  SLC16A5 WILD-TYPE  291    8
     clus
vv    SLC16A5 MUTATED SLC16A5 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D1555V9, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     8   2
  SLC16A5 WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      8    2
  SLC16A5 WILD-TYPE  306   46
                               clus
vv                              SLC16A5 MUTATED SLC16A5 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC16A5 MUTATED     7   0   0   1
  SLC16A5 WILD-TYPE 252   3  22  20
D1555V10, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               1                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"
D1555V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A5 MUTATED                                  0     1
  SLC16A5 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A5 MUTATED                           0     4
  SLC16A5 WILD-TYPE                        19   172
D1555V12, multiclass
                                  clus
vv                                 SLC16A5 MUTATED SLC16A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = GUCY2F MUTATION ANALYSIS
D1556V1, survival
                  sevent
clus2                0   1
  GUCY2F MUTATED    15   3
  GUCY2F WILD-TYPE 262  75
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              18              337 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               3               75 
$`GUCY2F MUTATED`
TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-6141 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3660 
        1.94        26.17         8.38         6.97        29.95        78.08 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A01P TCGA-AD-6965 TCGA-CM-5860 
       53.00        31.00        25.02        38.07        26.47        32.02 
TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DM-A28K 
       45.40        25.48         9.44        12.00       135.65        98.24 

$`GUCY2F WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        22.42        27.42        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        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        54.61 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GUCY2F MUTATED GUCY2F WILD-TYPE 
            1.94             0.00 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
          135.65           148.01 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
           28.21            21.99 
[1] "1.9 - 135.7 (28.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1556V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GUCY2F MUTATED         1        0        3         8         0         0
  GUCY2F WILD-TYPE      63        1       23       100         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GUCY2F MUTATED           1          1          1          2        0
  GUCY2F WILD-TYPE        17          5         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GUCY2F MUTATED           0         0
  GUCY2F WILD-TYPE        12         1
D1556V3, multiclass
            clus
vv           GUCY2F MUTATED GUCY2F WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               8              100
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  GUCY2F MUTATED     1   2  12   4
  GUCY2F WILD-TYPE   8  65 237  37
D1556V4, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  T1              1                8
  T2              2               65
  T3             12              237
  T4              4               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
  GUCY2F MUTATED    13   3   3
  GUCY2F WILD-TYPE 207  78  63
D1556V5, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  N0             13              207
  N1              3               78
  N2              3               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"
D1556V6, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    17   0
  GUCY2F WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     17    0
  GUCY2F WILD-TYPE  268   48
   clus
vv  GUCY2F MUTATED GUCY2F WILD-TYPE
  0             17              268
  1              0               48
[1] 2 2
[1] FALSE
D1556V7, binary
                  cls
clus                 0   1
  GUCY2F MUTATED     8  11
  GUCY2F WILD-TYPE 162 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      8   11
  GUCY2F WILD-TYPE  162  186
        clus
vv       GUCY2F MUTATED GUCY2F WILD-TYPE
  FEMALE              8              162
  MALE               11              186
[1] 2 2
[1] FALSE
D1556V8, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    16   0
  GUCY2F WILD-TYPE 284   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     16    0
  GUCY2F WILD-TYPE  284    8
     clus
vv    GUCY2F MUTATED GUCY2F WILD-TYPE
  NO              16              284
  YES              0                8
[1] 2 2
[1] FALSE
D1556V9, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    15   3
  GUCY2F WILD-TYPE 299  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     15    3
  GUCY2F WILD-TYPE  299   45
                               clus
vv                              GUCY2F MUTATED GUCY2F WILD-TYPE
  COLON ADENOCARCINOMA                      15              299
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GUCY2F MUTATED    12   1   0   1
  GUCY2F WILD-TYPE 247   2  22  20
D1556V10, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  R0             12              247
  R1              1                2
  R2              0               22
  RX              1               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"
D1556V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GUCY2F MUTATED                                  0     0
  GUCY2F WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GUCY2F MUTATED                           1    10
  GUCY2F WILD-TYPE                        18   166
D1556V12, multiclass
                                  clus
vv                                 GUCY2F MUTATED GUCY2F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(1557) Variable = CXCR7 MUTATION ANALYSIS
D1557V1, survival
                 sevent
clus2               0   1
  CXCR7 MUTATED    11   4
  CXCR7 WILD-TYPE 266  74
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             15             340 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              4              74 
$`CXCR7 MUTATED`
TCGA-AA-3522 TCGA-AA-3692 TCGA-CK-5912 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6780 
       37.05        36.00        49.08        35.80        26.17        20.12 
TCGA-A6-6781 TCGA-AA-3663 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-6598 TCGA-CM-5344 
       19.66         6.97        14.50         0.20        49.41        22.03 
TCGA-CM-6170 TCGA-D5-6927 TCGA-G4-6303 
       15.02         9.44        65.85 

$`CXCR7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 
        1.94         5.88        63.62        22.09        91.79        79.69 
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-A6-5656 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-A6-6648 
       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-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CXCR7 MUTATED CXCR7 WILD-TYPE 
            0.2             0.0 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          65.85          148.01 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
         22.030          22.075 
[1] "0.2 - 65.8 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1557V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CXCR7 MUTATED         2        0        3         8         0         0
  CXCR7 WILD-TYPE      62        1       23       100         8         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        18          6         43         31       32        12
                 vv
clus              STAGE IVB
  CXCR7 MUTATED           0
  CXCR7 WILD-TYPE         1
D1557V3, multiclass
            clus
vv           CXCR7 MUTATED CXCR7 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              0              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
  CXCR7 MUTATED     0   2  15   2
  CXCR7 WILD-TYPE   9  65 234  39
D1557V4, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            15             234
  T4             2              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
  CXCR7 MUTATED    13   3   3
  CXCR7 WILD-TYPE 207  78  63
D1557V5, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  N0            13             207
  N1             3              78
  N2             3              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"
D1557V6, binary
                 cls
clus                0   1
  CXCR7 MUTATED    11   3
  CXCR7 WILD-TYPE 274  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     11    3
  CXCR7 WILD-TYPE  274   45
   clus
vv  CXCR7 MUTATED CXCR7 WILD-TYPE
  0            11             274
  1             3              45
[1] 2 2
[1] FALSE
D1557V7, binary
                 cls
clus                0   1
  CXCR7 MUTATED    12   7
  CXCR7 WILD-TYPE 158 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     12    7
  CXCR7 WILD-TYPE  158  190
        clus
vv       CXCR7 MUTATED CXCR7 WILD-TYPE
  FEMALE            12             158
  MALE               7             190
[1] 2 2
[1] FALSE
D1557V8, binary
                 cls
clus                0   1
  CXCR7 MUTATED    13   1
  CXCR7 WILD-TYPE 287   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     13    1
  CXCR7 WILD-TYPE  287    7
     clus
vv    CXCR7 MUTATED CXCR7 WILD-TYPE
  NO             13             287
  YES             1               7
[1] 2 2
[1] FALSE
D1557V9, binary
                 cls
clus                0   1
  CXCR7 MUTATED    15   4
  CXCR7 WILD-TYPE 299  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     15    4
  CXCR7 WILD-TYPE  299   44
                               clus
vv                              CXCR7 MUTATED CXCR7 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CXCR7 MUTATED    14   0   2   1
  CXCR7 WILD-TYPE 245   3  20  20
D1557V10, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             2              20
  RX             1              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"
D1557V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXCR7 MUTATED                                  0     0
  CXCR7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXCR7 MUTATED                           0    12
  CXCR7 WILD-TYPE                        19   164
D1557V12, multiclass
                                  clus
vv                                 CXCR7 MUTATED CXCR7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = RELA MUTATION ANALYSIS
D1558V1, survival
                sevent
clus2              0   1
  RELA MUTATED     7   2
  RELA WILD-TYPE 270  76
  RELA MUTATED RELA WILD-TYPE 
             9            346 
  RELA MUTATED RELA WILD-TYPE 
             2             76 
$`RELA MUTATED`
TCGA-G4-6588 TCGA-AA-3511 TCGA-AA-3821 TCGA-AA-A01R TCGA-AY-6386 TCGA-AZ-6598 
       26.17         6.97         1.02        35.01        17.82        49.41 
TCGA-D5-6535 TCGA-D5-6540 TCGA-G4-6626 
       15.12        16.14        46.75 

$`RELA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  RELA MUTATED RELA WILD-TYPE 
          1.02           0.00 
  RELA MUTATED RELA WILD-TYPE 
         49.41         148.01 
  RELA MUTATED RELA WILD-TYPE 
        17.820         22.075 
[1] "1.0 - 49.4 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1558V2, continuous
                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      62        1       24       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELA MUTATED           1          0          2          0        0         0
  RELA WILD-TYPE        17          6         42         33       35        12
                vv
clus             STAGE IVB
  RELA MUTATED           0
  RELA WILD-TYPE         1
D1558V3, multiclass
            clus
vv           RELA MUTATED RELA WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RELA MUTATED     0   2   6   1
  RELA WILD-TYPE   9  65 243  40
D1558V4, multiclass
    clus
vv   RELA MUTATED RELA WILD-TYPE
  T1            0              9
  T2            2             65
  T3            6            243
  T4            1             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
  RELA MUTATED     6   2   1
  RELA WILD-TYPE 214  79  65
D1558V5, multiclass
    clus
vv   RELA MUTATED RELA WILD-TYPE
  N0            6            214
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1558V6, binary
                cls
clus               0   1
  RELA MUTATED     7   0
  RELA WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      7    0
  RELA WILD-TYPE  278   48
   clus
vv  RELA MUTATED RELA WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1558V7, binary
                cls
clus               0   1
  RELA MUTATED     5   4
  RELA WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      5    4
  RELA WILD-TYPE  165  193
        clus
vv       RELA MUTATED RELA WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D1558V8, binary
                cls
clus               0   1
  RELA MUTATED     8   1
  RELA WILD-TYPE 292   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      8    1
  RELA WILD-TYPE  292    7
     clus
vv    RELA MUTATED RELA WILD-TYPE
  NO             8            292
  YES            1              7
[1] 2 2
[1] FALSE
D1558V9, binary
                cls
clus               0   1
  RELA MUTATED     6   3
  RELA WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      6    3
  RELA WILD-TYPE  308   45
                               clus
vv                              RELA MUTATED RELA WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RELA MUTATED     7   0   0   1
  RELA WILD-TYPE 252   3  22  20
D1558V10, multiclass
    clus
vv   RELA MUTATED RELA WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D1558V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RELA MUTATED                                  0     0
  RELA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RELA MUTATED                           1     5
  RELA WILD-TYPE                        18   171
D1558V12, multiclass
                                  clus
vv                                 RELA MUTATED RELA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = WDR65 MUTATION ANALYSIS
D1559V1, survival
                 sevent
clus2               0   1
  WDR65 MUTATED     4   2
  WDR65 WILD-TYPE 273  76
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             349 
  WDR65 MUTATED WDR65 WILD-TYPE 
              2              76 
$`WDR65 MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-A6-6780 TCGA-AA-A00J TCGA-AD-6889 TCGA-CA-6718 
       24.00        79.69        20.12        18.05        83.24        10.06 

$`WDR65 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  WDR65 MUTATED WDR65 WILD-TYPE 
          10.06            0.00 
  WDR65 MUTATED WDR65 WILD-TYPE 
          83.24          148.01 
  WDR65 MUTATED WDR65 WILD-TYPE 
          22.06           22.06 
[1] "10.1 - 83.2 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1559V2, continuous
                 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      63        1       26       104         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  WDR65 MUTATED           0
  WDR65 WILD-TYPE         1
D1559V3, multiclass
            clus
vv           WDR65 MUTATED WDR65 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  WDR65 MUTATED     0   1   4   1
  WDR65 WILD-TYPE   9  66 245  40
D1559V4, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             1              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
  WDR65 MUTATED     5   1   0
  WDR65 WILD-TYPE 215  80  66
D1559V5, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1559V6, binary
                 cls
clus                0   1
  WDR65 MUTATED     5   0
  WDR65 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      5    0
  WDR65 WILD-TYPE  280   48
   clus
vv  WDR65 MUTATED WDR65 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1559V7, binary
                 cls
clus                0   1
  WDR65 MUTATED     1   5
  WDR65 WILD-TYPE 169 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      1    5
  WDR65 WILD-TYPE  169  192
        clus
vv       WDR65 MUTATED WDR65 WILD-TYPE
  FEMALE             1             169
  MALE               5             192
[1] 2 2
[1] FALSE
D1559V8, binary
                 cls
clus                0   1
  WDR65 MUTATED     6   0
  WDR65 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      6    0
  WDR65 WILD-TYPE  294    8
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1559V9, binary
                 cls
clus                0   1
  WDR65 MUTATED     3   3
  WDR65 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      3    3
  WDR65 WILD-TYPE  311   45
                               clus
vv                              WDR65 MUTATED WDR65 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR65 MUTATED     4   0   0   1
  WDR65 WILD-TYPE 255   3  22  20
D1559V10, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1559V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR65 MUTATED                                  0     2
  WDR65 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR65 MUTATED                           0     2
  WDR65 WILD-TYPE                        19   174
D1559V12, multiclass
                                  clus
vv                                 WDR65 MUTATED WDR65 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        2             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(1560) Variable = DTX3L MUTATION ANALYSIS
D1560V1, survival
                 sevent
clus2               0   1
  DTX3L MUTATED     5   4
  DTX3L WILD-TYPE 272  74
  DTX3L MUTATED DTX3L WILD-TYPE 
              9             346 
  DTX3L MUTATED DTX3L WILD-TYPE 
              4              74 
$`DTX3L MUTATED`
TCGA-AD-6964 TCGA-CK-5912 TCGA-G4-6586 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6599 
       10.88        49.08        35.80        25.02        34.98         6.77 
TCGA-CM-4743 TCGA-D5-6533 TCGA-DM-A1D4 
       23.05        25.48        92.75 

$`DTX3L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
      100.01         1.94         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  DTX3L MUTATED DTX3L WILD-TYPE 
           6.77            0.00 
  DTX3L MUTATED DTX3L WILD-TYPE 
          92.75          148.01 
  DTX3L MUTATED DTX3L WILD-TYPE 
          25.48           21.99 
[1] "6.8 - 92.8 (25.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1560V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DTX3L MUTATED         2        0        0         4         1         0
  DTX3L WILD-TYPE      62        1       26       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DTX3L MUTATED           0          0          0          0        0         0
  DTX3L WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  DTX3L MUTATED           0
  DTX3L WILD-TYPE         1
D1560V3, multiclass
            clus
vv           DTX3L MUTATED DTX3L WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DTX3L MUTATED     0   3   4   3
  DTX3L WILD-TYPE   9  64 245  38
D1560V4, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  T1             0               9
  T2             3              64
  T3             4             245
  T4             3              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
  DTX3L MUTATED     9   0   1
  DTX3L WILD-TYPE 211  81  65
D1560V5, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  N0             9             211
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1560V6, binary
                 cls
clus                0   1
  DTX3L MUTATED     6   0
  DTX3L WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      6    0
  DTX3L WILD-TYPE  279   48
   clus
vv  DTX3L MUTATED DTX3L WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1560V7, binary
                 cls
clus                0   1
  DTX3L MUTATED     4   6
  DTX3L WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      4    6
  DTX3L WILD-TYPE  166  191
        clus
vv       DTX3L MUTATED DTX3L WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1560V8, binary
                 cls
clus                0   1
  DTX3L MUTATED     8   0
  DTX3L WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      8    0
  DTX3L WILD-TYPE  292    8
     clus
vv    DTX3L MUTATED DTX3L WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1560V9, binary
                 cls
clus                0   1
  DTX3L MUTATED    10   0
  DTX3L WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED     10    0
  DTX3L WILD-TYPE  304   48
                               clus
vv                              DTX3L MUTATED DTX3L WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DTX3L MUTATED     5   0   0   1
  DTX3L WILD-TYPE 254   3  22  20
D1560V10, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D1560V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DTX3L MUTATED                                  0     0
  DTX3L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DTX3L MUTATED                           0     7
  DTX3L WILD-TYPE                        19   169
D1560V12, multiclass
                                  clus
vv                                 DTX3L MUTATED DTX3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = ARID4B MUTATION ANALYSIS
D1561V1, survival
                  sevent
clus2                0   1
  ARID4B MUTATED     9   1
  ARID4B WILD-TYPE 268  77
  ARID4B MUTATED ARID4B WILD-TYPE 
              10              345 
  ARID4B MUTATED ARID4B WILD-TYPE 
               1               77 
$`ARID4B MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6588 TCGA-AA-A00N TCGA-AU-6004 TCGA-AY-6196 
       19.04        25.08        26.17         4.01        27.09         0.20 
TCGA-CA-6716 TCGA-CM-5349 TCGA-D5-6536 TCGA-DM-A1HA 
       12.20        30.08        17.85       131.51 

$`ARID4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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-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-6717 
       12.69        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ARID4B MUTATED ARID4B WILD-TYPE 
             0.2              0.0 
  ARID4B MUTATED ARID4B WILD-TYPE 
          131.51           148.01 
  ARID4B MUTATED ARID4B WILD-TYPE 
           22.06            22.06 
[1] "0.2 - 131.5 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1561V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID4B MUTATED         1        0        0         5         1         0
  ARID4B WILD-TYPE      63        1       26       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID4B MUTATED           0          0          1          2        1
  ARID4B WILD-TYPE        18          6         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ARID4B MUTATED           0         0
  ARID4B WILD-TYPE        12         1
D1561V3, multiclass
            clus
vv           ARID4B MUTATED ARID4B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  ARID4B MUTATED     0   1   9   1
  ARID4B WILD-TYPE   9  66 240  40
D1561V4, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  T1              0                9
  T2              1               66
  T3              9              240
  T4              1               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
  ARID4B MUTATED     8   1   2
  ARID4B WILD-TYPE 212  80  64
D1561V5, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  N0              8              212
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1561V6, binary
                  cls
clus                 0   1
  ARID4B MUTATED     9   1
  ARID4B WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      9    1
  ARID4B WILD-TYPE  276   47
   clus
vv  ARID4B MUTATED ARID4B WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1561V7, binary
                  cls
clus                 0   1
  ARID4B MUTATED     4   7
  ARID4B WILD-TYPE 166 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      4    7
  ARID4B WILD-TYPE  166  190
        clus
vv       ARID4B MUTATED ARID4B WILD-TYPE
  FEMALE              4              166
  MALE                7              190
[1] 2 2
[1] FALSE
D1561V8, binary
                  cls
clus                 0   1
  ARID4B MUTATED     5   1
  ARID4B WILD-TYPE 295   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      5    1
  ARID4B WILD-TYPE  295    7
     clus
vv    ARID4B MUTATED ARID4B WILD-TYPE
  NO               5              295
  YES              1                7
[1] 2 2
[1] FALSE
D1561V9, binary
                  cls
clus                 0   1
  ARID4B MUTATED     9   2
  ARID4B WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      9    2
  ARID4B WILD-TYPE  305   46
                               clus
vv                              ARID4B MUTATED ARID4B WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID4B MUTATED     8   0   1   1
  ARID4B WILD-TYPE 251   3  21  20
D1561V10, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  R0              8              251
  R1              0                3
  R2              1               21
  RX              1               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"
D1561V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID4B MUTATED                                  0     1
  ARID4B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID4B MUTATED                           0     7
  ARID4B WILD-TYPE                        19   169
D1561V12, multiclass
                                  clus
vv                                 ARID4B MUTATED ARID4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = ZNF295 MUTATION ANALYSIS
D1562V1, survival
                  sevent
clus2                0   1
  ZNF295 MUTATED     7   2
  ZNF295 WILD-TYPE 270  76
  ZNF295 MUTATED ZNF295 WILD-TYPE 
               9              346 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
               2               76 
$`ZNF295 MUTATED`
TCGA-A6-2676 TCGA-A6-5666 TCGA-AA-3855 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6599 
       42.90        32.71        32.05        25.02        34.98         6.77 
TCGA-D5-6924 TCGA-D5-6931 TCGA-F4-6856 
       14.30        12.00        35.31 

$`ZNF295 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07         0.00        36.03         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF295 MUTATED ZNF295 WILD-TYPE 
            6.77             0.00 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           42.90           148.01 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           32.05            22.01 
[1] "6.8 - 42.9 (32.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1562V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF295 MUTATED         3        0        0         2         2         1
  ZNF295 WILD-TYPE      61        1       26       106         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF295 MUTATED           0          0          0          1        0
  ZNF295 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF295 MUTATED           0         0
  ZNF295 WILD-TYPE        12         1
D1562V3, multiclass
            clus
vv           ZNF295 MUTATED ZNF295 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF295 MUTATED     0   4   2   4
  ZNF295 WILD-TYPE   9  63 247  37
D1562V4, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  T1              0                9
  T2              4               63
  T3              2              247
  T4              4               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
  ZNF295 MUTATED     9   0   1
  ZNF295 WILD-TYPE 211  81  65
D1562V5, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1562V6, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     8   0
  ZNF295 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      8    0
  ZNF295 WILD-TYPE  277   48
   clus
vv  ZNF295 MUTATED ZNF295 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1562V7, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     3   7
  ZNF295 WILD-TYPE 167 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      3    7
  ZNF295 WILD-TYPE  167  190
        clus
vv       ZNF295 MUTATED ZNF295 WILD-TYPE
  FEMALE              3              167
  MALE                7              190
[1] 2 2
[1] FALSE
D1562V8, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     9   0
  ZNF295 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      9    0
  ZNF295 WILD-TYPE  291    8
     clus
vv    ZNF295 MUTATED ZNF295 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1562V9, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     9   1
  ZNF295 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      9    1
  ZNF295 WILD-TYPE  305   47
                               clus
vv                              ZNF295 MUTATED ZNF295 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF295 MUTATED     7   0   0   0
  ZNF295 WILD-TYPE 252   3  22  21
D1562V10, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1562V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF295 MUTATED                                  0     0
  ZNF295 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF295 MUTATED                           0     6
  ZNF295 WILD-TYPE                        19   170
D1562V12, multiclass
                                  clus
vv                                 ZNF295 MUTATED ZNF295 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = FBLIM1 MUTATION ANALYSIS
D1563V1, survival
                  sevent
clus2                0   1
  FBLIM1 MUTATED     4   1
  FBLIM1 WILD-TYPE 273  77
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               5              350 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               1               77 
$`FBLIM1 MUTATED`
TCGA-AA-3713 TCGA-AA-3837 TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-6171 
       19.04        38.99        49.41        15.02        14.04 

$`FBLIM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
           14.04             0.00 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
           49.41           148.01 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
          19.040           22.075 
[1] "14.0 - 49.4 (19.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1563V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBLIM1 MUTATED         1        0        1         2         0         0
  FBLIM1 WILD-TYPE      63        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBLIM1 MUTATED           0          0          0          0        1
  FBLIM1 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  FBLIM1 MUTATED           0         0
  FBLIM1 WILD-TYPE        12         1
D1563V3, multiclass
            clus
vv           FBLIM1 MUTATED FBLIM1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  FBLIM1 MUTATED     0   1   4   0
  FBLIM1 WILD-TYPE   9  66 245  41
D1563V4, multiclass
    clus
vv   FBLIM1 MUTATED FBLIM1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              4              245
  T4              0               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
  FBLIM1 MUTATED     5   0   0
  FBLIM1 WILD-TYPE 215  81  66
D1563V5, multiclass
    clus
vv   FBLIM1 MUTATED FBLIM1 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1563V6, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     3   1
  FBLIM1 WILD-TYPE 282  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      3    1
  FBLIM1 WILD-TYPE  282   47
   clus
vv  FBLIM1 MUTATED FBLIM1 WILD-TYPE
  0              3              282
  1              1               47
[1] 2 2
[1] FALSE
D1563V7, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     3   2
  FBLIM1 WILD-TYPE 167 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      3    2
  FBLIM1 WILD-TYPE  167  195
        clus
vv       FBLIM1 MUTATED FBLIM1 WILD-TYPE
  FEMALE              3              167
  MALE                2              195
[1] 2 2
[1] FALSE
D1563V8, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     4   1
  FBLIM1 WILD-TYPE 296   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      4    1
  FBLIM1 WILD-TYPE  296    7
     clus
vv    FBLIM1 MUTATED FBLIM1 WILD-TYPE
  NO               4              296
  YES              1                7
[1] 2 2
[1] FALSE
D1563V9, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     4   1
  FBLIM1 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      4    1
  FBLIM1 WILD-TYPE  310   47
                               clus
vv                              FBLIM1 MUTATED FBLIM1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBLIM1 MUTATED     3   0   1   0
  FBLIM1 WILD-TYPE 256   3  21  21
D1563V10, multiclass
    clus
vv   FBLIM1 MUTATED FBLIM1 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              1               21
  RX              0               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"
D1563V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBLIM1 MUTATED                                  0     0
  FBLIM1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBLIM1 MUTATED                           0     3
  FBLIM1 WILD-TYPE                        19   173
D1563V12, multiclass
                                  clus
vv                                 FBLIM1 MUTATED FBLIM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = WFDC10B MUTATION ANALYSIS
D1564V1, survival
                   sevent
clus2                 0   1
  WFDC10B MUTATED     4   1
  WFDC10B WILD-TYPE 273  77
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               350 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                1                77 
$`WFDC10B MUTATED`
TCGA-G4-6588 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-F4-6459 
       26.17        11.01        13.05        11.08         8.61 

$`WFDC10B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        14.04        12.95        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  WFDC10B MUTATED WFDC10B WILD-TYPE 
             8.61              0.00 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
            26.17            148.01 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
            11.08             22.09 
[1] "8.6 - 26.2 (11.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1564V2, continuous
                   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      63        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WFDC10B MUTATED           0          0          2          0        0
  WFDC10B WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  WFDC10B MUTATED           0         1
  WFDC10B WILD-TYPE        12         0
D1564V3, multiclass
            clus
vv           WFDC10B MUTATED WFDC10B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                12
  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   9  66 245  41
D1564V4, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               0                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
  WFDC10B MUTATED     2   1   2
  WFDC10B WILD-TYPE 218  80  64
D1564V5, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  N0               2               218
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1564V6, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     4   1
  WFDC10B WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      4    1
  WFDC10B WILD-TYPE  281   47
   clus
vv  WFDC10B MUTATED WFDC10B WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D1564V7, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     3   2
  WFDC10B WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      3    2
  WFDC10B WILD-TYPE  167  195
        clus
vv       WFDC10B MUTATED WFDC10B WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1564V8, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     5   0
  WFDC10B WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      5    0
  WFDC10B WILD-TYPE  295    8
     clus
vv    WFDC10B MUTATED WFDC10B WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1564V9, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     5   0
  WFDC10B WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      5    0
  WFDC10B WILD-TYPE  309   48
                               clus
vv                              WFDC10B MUTATED WFDC10B WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  WFDC10B MUTATED     5   0   0   0
  WFDC10B WILD-TYPE 254   3  22  21
D1564V10, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1564V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WFDC10B MUTATED                                  0     0
  WFDC10B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  WFDC10B MUTATED                           1     4
  WFDC10B WILD-TYPE                        18   172
D1564V12, multiclass
                                  clus
vv                                 WFDC10B MUTATED WFDC10B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = NAA15 MUTATION ANALYSIS
D1565V1, survival
                 sevent
clus2               0   1
  NAA15 MUTATED    11   3
  NAA15 WILD-TYPE 266  75
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             341 
  NAA15 MUTATED NAA15 WILD-TYPE 
              3              75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6704 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NAA15 MUTATED NAA15 WILD-TYPE 
              0               0 
  NAA15 MUTATED NAA15 WILD-TYPE 
          58.39          148.01 
  NAA15 MUTATED NAA15 WILD-TYPE 
          28.03           22.03 
[1] "0.0 - 58.4 (28.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1565V2, continuous
                 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      63        1       25       100         4         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        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  NAA15 MUTATED           0
  NAA15 WILD-TYPE         1
D1565V3, multiclass
            clus
vv           NAA15 MUTATED NAA15 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              8             100
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  NAA15 MUTATED     0   1  10   4
  NAA15 WILD-TYPE   9  66 239  37
D1565V4, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            10             239
  T4             4              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
  NAA15 MUTATED    14   0   1
  NAA15 WILD-TYPE 206  81  65
D1565V5, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  N0            14             206
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1565V6, binary
                 cls
clus                0   1
  NAA15 MUTATED    14   0
  NAA15 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED     14    0
  NAA15 WILD-TYPE  271   48
   clus
vv  NAA15 MUTATED NAA15 WILD-TYPE
  0            14             271
  1             0              48
[1] 2 2
[1] FALSE
D1565V7, binary
                 cls
clus                0   1
  NAA15 MUTATED     5  10
  NAA15 WILD-TYPE 165 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED      5   10
  NAA15 WILD-TYPE  165  187
        clus
vv       NAA15 MUTATED NAA15 WILD-TYPE
  FEMALE             5             165
  MALE              10             187
[1] 2 2
[1] FALSE
D1565V8, binary
                 cls
clus                0   1
  NAA15 MUTATED    11   1
  NAA15 WILD-TYPE 289   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED     11    1
  NAA15 WILD-TYPE  289    7
     clus
vv    NAA15 MUTATED NAA15 WILD-TYPE
  NO             11             289
  YES             1               7
[1] 2 2
[1] FALSE
D1565V9, binary
                 cls
clus                0   1
  NAA15 MUTATED    11   4
  NAA15 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED     11    4
  NAA15 WILD-TYPE  303   44
                               clus
vv                              NAA15 MUTATED NAA15 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NAA15 MUTATED    12   0   0   3
  NAA15 WILD-TYPE 247   3  22  18
D1565V10, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             3              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"
D1565V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAA15 MUTATED                                  0     2
  NAA15 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NAA15 MUTATED                           2     5
  NAA15 WILD-TYPE                        17   171
D1565V12, multiclass
                                  clus
vv                                 NAA15 MUTATED NAA15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        5             171
[1] 4 2
[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 = ACTL7B MUTATION ANALYSIS
D1566V1, survival
                  sevent
clus2                0   1
  ACTL7B MUTATED     3   1
  ACTL7B WILD-TYPE 274  77
  ACTL7B MUTATED ACTL7B WILD-TYPE 
               4              351 
  ACTL7B MUTATED ACTL7B WILD-TYPE 
               1               77 
$`ACTL7B MUTATED`
TCGA-AA-3994 TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-4752 
       27.02        34.98        83.24        13.02 

$`ACTL7B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ACTL7B MUTATED ACTL7B WILD-TYPE 
           13.02             0.00 
  ACTL7B MUTATED ACTL7B WILD-TYPE 
           83.24           148.01 
  ACTL7B MUTATED ACTL7B WILD-TYPE 
           31.00            22.03 
[1] "13.0 - 83.2 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1566V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTL7B MUTATED         0        0        0         2         1         0
  ACTL7B WILD-TYPE      64        1       26       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL7B MUTATED           0          0          1          0        0
  ACTL7B WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ACTL7B MUTATED           0         0
  ACTL7B WILD-TYPE        12         1
D1566V3, multiclass
            clus
vv           ACTL7B MUTATED ACTL7B WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ACTL7B MUTATED     0   0   3   1
  ACTL7B WILD-TYPE   9  67 246  40
D1566V4, multiclass
    clus
vv   ACTL7B MUTATED ACTL7B WILD-TYPE
  T1              0                9
  T2              0               67
  T3              3              246
  T4              1               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
  ACTL7B MUTATED     3   1   0
  ACTL7B WILD-TYPE 217  80  66
D1566V5, multiclass
    clus
vv   ACTL7B MUTATED ACTL7B WILD-TYPE
  N0              3              217
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1566V6, binary
                  cls
clus                 0   1
  ACTL7B MUTATED     4   0
  ACTL7B WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL7B MUTATED      4    0
  ACTL7B WILD-TYPE  281   48
   clus
vv  ACTL7B MUTATED ACTL7B WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1566V7, binary
                  cls
clus                 0   1
  ACTL7B MUTATED     1   3
  ACTL7B WILD-TYPE 169 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL7B MUTATED      1    3
  ACTL7B WILD-TYPE  169  194
        clus
vv       ACTL7B MUTATED ACTL7B WILD-TYPE
  FEMALE              1              169
  MALE                3              194
[1] 2 2
[1] FALSE
D1566V8, binary
                  cls
clus                 0   1
  ACTL7B MUTATED     4   0
  ACTL7B WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL7B MUTATED      4    0
  ACTL7B WILD-TYPE  296    8
     clus
vv    ACTL7B MUTATED ACTL7B WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1566V9, binary
                  cls
clus                 0   1
  ACTL7B MUTATED     3   1
  ACTL7B WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL7B MUTATED      3    1
  ACTL7B WILD-TYPE  311   47
                               clus
vv                              ACTL7B MUTATED ACTL7B WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACTL7B MUTATED     4   0   0   0
  ACTL7B WILD-TYPE 255   3  22  21
D1566V10, multiclass
    clus
vv   ACTL7B MUTATED ACTL7B WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D1566V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL7B MUTATED                                  0     1
  ACTL7B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTL7B MUTATED                           1     0
  ACTL7B WILD-TYPE                        18   176
D1566V12, multiclass
[1] "Remove cluster labels:" "ACTL7B MUTATED"        
clus
  ACTL7B MUTATED ACTL7B WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6890       TCGA-AD-6899 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" "ACTL7B WILD-TYPE" 

Clustering(1567) Variable = COL4A6 MUTATION ANALYSIS
D1567V1, survival
                  sevent
clus2                0   1
  COL4A6 MUTATED    17   3
  COL4A6 WILD-TYPE 260  75
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              20              335 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
               3               75 
$`COL4A6 MUTATED`
TCGA-AA-3672 TCGA-AA-A00Z TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3542 TCGA-AA-3846 
        0.92        21.99        33.53        32.71        12.99        17.03 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01Q TCGA-AD-5900 
       18.05         4.01        34.98        31.00         1.02        12.16 
TCGA-AZ-4323 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-5349 TCGA-CM-6162 
        1.41        12.76        51.32        21.99        30.08        12.00 
TCGA-DM-A0XD TCGA-F4-6807 
       24.43        43.04 

$`COL4A6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       50.99        26.01        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R 
       10.98        32.02        12.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 
       14.30        17.56       148.01        85.45        15.62        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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-F4-6808 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  COL4A6 MUTATED COL4A6 WILD-TYPE 
            0.92             0.00 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
           51.32           148.01 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
           20.02            22.09 
[1] "0.9 - 51.3 (20.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1567V2, continuous
                  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      63        1       25        99         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL4A6 MUTATED           1          0          2          3        1
  COL4A6 WILD-TYPE        17          6         42         30       34
                  vv
clus               STAGE IVA STAGE IVB
  COL4A6 MUTATED           0         0
  COL4A6 WILD-TYPE        12         1
D1567V3, multiclass
            clus
vv           COL4A6 MUTATED COL4A6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               9               99
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              3               30
  STAGE IV                1               34
  STAGE IVA               0               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
  COL4A6 MUTATED     0   1  16   4
  COL4A6 WILD-TYPE   9  66 233  37
D1567V4, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             16              233
  T4              4               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
  COL4A6 MUTATED    14   3   4
  COL4A6 WILD-TYPE 206  78  62
D1567V5, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  N0             14              206
  N1              3               78
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1567V6, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    17   1
  COL4A6 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     17    1
  COL4A6 WILD-TYPE  268   47
   clus
vv  COL4A6 MUTATED COL4A6 WILD-TYPE
  0             17              268
  1              1               47
[1] 2 2
[1] FALSE
D1567V7, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    11  10
  COL4A6 WILD-TYPE 159 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     11   10
  COL4A6 WILD-TYPE  159  187
        clus
vv       COL4A6 MUTATED COL4A6 WILD-TYPE
  FEMALE             11              159
  MALE               10              187
[1] 2 2
[1] FALSE
D1567V8, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    15   0
  COL4A6 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     15    0
  COL4A6 WILD-TYPE  285    8
     clus
vv    COL4A6 MUTATED COL4A6 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D1567V9, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    17   4
  COL4A6 WILD-TYPE 297  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     17    4
  COL4A6 WILD-TYPE  297   44
                               clus
vv                              COL4A6 MUTATED COL4A6 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  COL4A6 MUTATED    15   0   0   3
  COL4A6 WILD-TYPE 244   3  22  18
D1567V10, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  R0             15              244
  R1              0                3
  R2              0               22
  RX              3               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"
D1567V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL4A6 MUTATED                                  0     1
  COL4A6 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL4A6 MUTATED                           1     9
  COL4A6 WILD-TYPE                        18   167
D1567V12, multiclass
                                  clus
vv                                 COL4A6 MUTATED COL4A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(1568) Variable = FGD3 MUTATION ANALYSIS
D1568V1, survival
                sevent
clus2              0   1
  FGD3 MUTATED    10   3
  FGD3 WILD-TYPE 267  75
  FGD3 MUTATED FGD3 WILD-TYPE 
            13            342 
  FGD3 MUTATED FGD3 WILD-TYPE 
             3             75 
$`FGD3 MUTATED`
TCGA-DM-A285 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3966 TCGA-AU-6004 
        5.88        33.53        19.66        33.04         2.01        27.09 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CM-4743 TCGA-CM-5348 TCGA-D5-6927 TCGA-F4-6703 
       49.41        12.10        23.05        22.98         9.44        47.87 
TCGA-G4-6309 
       85.48 

$`FGD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
       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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  FGD3 MUTATED FGD3 WILD-TYPE 
          2.01           0.00 
  FGD3 MUTATED FGD3 WILD-TYPE 
         85.48         148.01 
  FGD3 MUTATED FGD3 WILD-TYPE 
         23.05          22.01 
[1] "2.0 - 85.5 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1568V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGD3 MUTATED         1        0        1         6         0         0
  FGD3 WILD-TYPE      63        1       25       102         8         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        18          6         42         32       33        12
                vv
clus             STAGE IVB
  FGD3 MUTATED           0
  FGD3 WILD-TYPE         1
D1568V3, multiclass
            clus
vv           FGD3 MUTATED FGD3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  FGD3 MUTATED     0   1  10   2
  FGD3 WILD-TYPE   9  66 239  39
D1568V4, multiclass
    clus
vv   FGD3 MUTATED FGD3 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           10            239
  T4            2             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
  FGD3 MUTATED     8   4   1
  FGD3 WILD-TYPE 212  77  65
D1568V5, multiclass
    clus
vv   FGD3 MUTATED FGD3 WILD-TYPE
  N0            8            212
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1568V6, binary
                cls
clus               0   1
  FGD3 MUTATED     9   2
  FGD3 WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED      9    2
  FGD3 WILD-TYPE  276   46
   clus
vv  FGD3 MUTATED FGD3 WILD-TYPE
  0            9            276
  1            2             46
[1] 2 2
[1] FALSE
D1568V7, binary
                cls
clus               0   1
  FGD3 MUTATED     7   6
  FGD3 WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED      7    6
  FGD3 WILD-TYPE  163  191
        clus
vv       FGD3 MUTATED FGD3 WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D1568V8, binary
                cls
clus               0   1
  FGD3 MUTATED    10   0
  FGD3 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED     10    0
  FGD3 WILD-TYPE  290    8
     clus
vv    FGD3 MUTATED FGD3 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1568V9, binary
                cls
clus               0   1
  FGD3 MUTATED    10   3
  FGD3 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED     10    3
  FGD3 WILD-TYPE  304   45
                               clus
vv                              FGD3 MUTATED FGD3 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FGD3 MUTATED     9   0   0   0
  FGD3 WILD-TYPE 250   3  22  21
D1568V10, multiclass
    clus
vv   FGD3 MUTATED FGD3 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            0             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"
D1568V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGD3 MUTATED                                  0     0
  FGD3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FGD3 MUTATED                           3     8
  FGD3 WILD-TYPE                        16   168
D1568V12, multiclass
                                  clus
vv                                 FGD3 MUTATED FGD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                       8            168
[1] 4 2
[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 = PHKB MUTATION ANALYSIS
D1569V1, survival
                sevent
clus2              0   1
  PHKB MUTATED     7   4
  PHKB WILD-TYPE 270  74
  PHKB MUTATED PHKB WILD-TYPE 
            11            344 
  PHKB MUTATED PHKB WILD-TYPE 
             4             74 
$`PHKB MUTATED`
TCGA-G4-6310 TCGA-AA-3492 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AD-6889 
       63.62         3.02         4.01        34.98        18.05        83.24 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-6747 TCGA-D5-6922 TCGA-DM-A28H 
       27.09        58.39        82.95        10.13       117.07 

$`PHKB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 
       41.00        39.98        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PHKB MUTATED PHKB WILD-TYPE 
          3.02           0.00 
  PHKB MUTATED PHKB WILD-TYPE 
        117.07         148.01 
  PHKB MUTATED PHKB WILD-TYPE 
         34.98          22.01 
[1] "3.0 - 117.1 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1569V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHKB MUTATED         1        0        1         3         3         0
  PHKB WILD-TYPE      63        1       25       105         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHKB MUTATED           1          1          1          1        0         0
  PHKB WILD-TYPE        17          5         43         32       35        12
                vv
clus             STAGE IVB
  PHKB MUTATED           0
  PHKB WILD-TYPE         1
D1569V3, multiclass
            clus
vv           PHKB MUTATED PHKB WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  PHKB MUTATED     0   1   8   3
  PHKB WILD-TYPE   9  66 241  38
D1569V4, multiclass
    clus
vv   PHKB MUTATED PHKB WILD-TYPE
  T1            0              9
  T2            1             66
  T3            8            241
  T4            3             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
  PHKB MUTATED     8   2   2
  PHKB WILD-TYPE 212  79  64
D1569V5, multiclass
    clus
vv   PHKB MUTATED PHKB WILD-TYPE
  N0            8            212
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1569V6, binary
                cls
clus               0   1
  PHKB MUTATED    10   0
  PHKB WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED     10    0
  PHKB WILD-TYPE  275   48
   clus
vv  PHKB MUTATED PHKB WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1569V7, binary
                cls
clus               0   1
  PHKB MUTATED     6   6
  PHKB WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED      6    6
  PHKB WILD-TYPE  164  191
        clus
vv       PHKB MUTATED PHKB WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D1569V8, binary
                cls
clus               0   1
  PHKB MUTATED     7   1
  PHKB WILD-TYPE 293   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED      7    1
  PHKB WILD-TYPE  293    7
     clus
vv    PHKB MUTATED PHKB WILD-TYPE
  NO             7            293
  YES            1              7
[1] 2 2
[1] FALSE
D1569V9, binary
                cls
clus               0   1
  PHKB MUTATED    10   2
  PHKB WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED     10    2
  PHKB WILD-TYPE  304   46
                               clus
vv                              PHKB MUTATED PHKB WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PHKB MUTATED     9   0   0   2
  PHKB WILD-TYPE 250   3  22  19
D1569V10, multiclass
    clus
vv   PHKB MUTATED PHKB WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            2             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"
D1569V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHKB MUTATED                                  0     1
  PHKB WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PHKB MUTATED                           0     7
  PHKB WILD-TYPE                        19   169
D1569V12, multiclass
                                  clus
vv                                 PHKB MUTATED PHKB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = CHD5 MUTATION ANALYSIS
D1570V1, survival
                sevent
clus2              0   1
  CHD5 MUTATED    22   4
  CHD5 WILD-TYPE 255  74
  CHD5 MUTATED CHD5 WILD-TYPE 
            26            329 
  CHD5 MUTATED CHD5 WILD-TYPE 
             4             74 
$`CHD5 MUTATED`
TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3672 TCGA-AD-6964 TCGA-A6-5665 TCGA-A6-6141 
       13.02        17.95         0.92        10.88        22.06         8.38 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3947 
       35.01        63.98        26.99        33.04        53.00        33.01 
TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4950 
       25.02        27.09        58.39        49.41        12.76        85.45 
TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-5868 TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6808 
       21.14        37.02        17.03        98.24        47.87        33.67 
TCGA-G4-6293 TCGA-G4-6307 
      133.18        55.04 

$`CHD5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04         3.02         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CHD5 MUTATED CHD5 WILD-TYPE 
          0.92           0.00 
  CHD5 MUTATED CHD5 WILD-TYPE 
        133.18         148.01 
  CHD5 MUTATED CHD5 WILD-TYPE 
        33.025         21.990 
[1] "0.9 - 133.2 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1570V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD5 MUTATED         5        0        4        10         1         0
  CHD5 WILD-TYPE      59        1       22        98         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD5 MUTATED           3          0          2          0        0         1
  CHD5 WILD-TYPE        15          6         42         33       35        11
                vv
clus             STAGE IVB
  CHD5 MUTATED           0
  CHD5 WILD-TYPE         1
D1570V3, multiclass
            clus
vv           CHD5 MUTATED CHD5 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            10             98
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             3             15
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  CHD5 MUTATED     2   4  18   4
  CHD5 WILD-TYPE   7  63 231  37
D1570V4, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  T1            2              7
  T2            4             63
  T3           18            231
  T4            4             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
  CHD5 MUTATED    21   5   2
  CHD5 WILD-TYPE 199  76  64
D1570V5, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  N0           21            199
  N1            5             76
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1570V6, binary
                cls
clus               0   1
  CHD5 MUTATED    24   1
  CHD5 WILD-TYPE 261  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     24    1
  CHD5 WILD-TYPE  261   47
   clus
vv  CHD5 MUTATED CHD5 WILD-TYPE
  0           24            261
  1            1             47
[1] 2 2
[1] FALSE
D1570V7, binary
                cls
clus               0   1
  CHD5 MUTATED    17  11
  CHD5 WILD-TYPE 153 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     17   11
  CHD5 WILD-TYPE  153  186
        clus
vv       CHD5 MUTATED CHD5 WILD-TYPE
  FEMALE           17            153
  MALE             11            186
[1] 2 2
[1] FALSE
D1570V8, binary
                cls
clus               0   1
  CHD5 MUTATED    24   0
  CHD5 WILD-TYPE 276   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     24    0
  CHD5 WILD-TYPE  276    8
     clus
vv    CHD5 MUTATED CHD5 WILD-TYPE
  NO            24            276
  YES            0              8
[1] 2 2
[1] FALSE
D1570V9, binary
                cls
clus               0   1
  CHD5 MUTATED    23   5
  CHD5 WILD-TYPE 291  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     23    5
  CHD5 WILD-TYPE  291   43
                               clus
vv                              CHD5 MUTATED CHD5 WILD-TYPE
  COLON ADENOCARCINOMA                    23            291
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD5 MUTATED    19   1   0   2
  CHD5 WILD-TYPE 240   2  22  19
D1570V10, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  R0           19            240
  R1            1              2
  R2            0             22
  RX            2             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"
D1570V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD5 MUTATED                                  0     1
  CHD5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD5 MUTATED                           3    12
  CHD5 WILD-TYPE                        16   164
D1570V12, multiclass
                                  clus
vv                                 CHD5 MUTATED CHD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      12            164
[1] 4 2
[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 = GSTA5 MUTATION ANALYSIS
D1571V1, survival
                 sevent
clus2               0   1
  GSTA5 MUTATED     5   1
  GSTA5 WILD-TYPE 272  77
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              6             349 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              1              77 
$`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 

$`GSTA5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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        25.48        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GSTA5 MUTATED GSTA5 WILD-TYPE 
          22.98            0.00 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
          85.05          148.01 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
          50.83           21.99 
[1] "23.0 - 85.0 (50.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1571V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSTA5 MUTATED         0        0        1         2         0         0
  GSTA5 WILD-TYPE      64        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSTA5 MUTATED           0          0          1          0        1         0
  GSTA5 WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  GSTA5 MUTATED           0
  GSTA5 WILD-TYPE         1
D1571V3, multiclass
            clus
vv           GSTA5 MUTATED GSTA5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GSTA5 MUTATED     0   1   5   0
  GSTA5 WILD-TYPE   9  66 244  41
D1571V4, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             0              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
  GSTA5 MUTATED     4   2   0
  GSTA5 WILD-TYPE 216  79  66
D1571V5, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  N0             4             216
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1571V6, binary
                 cls
clus                0   1
  GSTA5 MUTATED     4   1
  GSTA5 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      4    1
  GSTA5 WILD-TYPE  281   47
   clus
vv  GSTA5 MUTATED GSTA5 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1571V7, binary
                 cls
clus                0   1
  GSTA5 MUTATED     2   4
  GSTA5 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      2    4
  GSTA5 WILD-TYPE  168  193
        clus
vv       GSTA5 MUTATED GSTA5 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D1571V8, binary
                 cls
clus                0   1
  GSTA5 MUTATED     6   0
  GSTA5 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      6    0
  GSTA5 WILD-TYPE  294    8
     clus
vv    GSTA5 MUTATED GSTA5 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1571V9, binary
                 cls
clus                0   1
  GSTA5 MUTATED     5   1
  GSTA5 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      5    1
  GSTA5 WILD-TYPE  309   47
                               clus
vv                              GSTA5 MUTATED GSTA5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GSTA5 MUTATED     5   0   0   0
  GSTA5 WILD-TYPE 254   3  22  21
D1571V10, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1571V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSTA5 MUTATED                                  0     0
  GSTA5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GSTA5 MUTATED                           0     4
  GSTA5 WILD-TYPE                        19   172
D1571V12, multiclass
                                  clus
vv                                 GSTA5 MUTATED GSTA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = C5ORF42 MUTATION ANALYSIS
D1572V1, survival
                   sevent
clus2                 0   1
  C5ORF42 MUTATED    23   8
  C5ORF42 WILD-TYPE 254  70
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               31               324 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                8                70 
$`C5ORF42 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-6601 TCGA-A6-3809 TCGA-A6-5660 
       19.04        19.04        24.00       100.01        32.75        29.19 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-3664 
       33.53        22.06         8.38        24.39         6.97        54.02 
TCGA-AA-3710 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 
       26.99         2.01         4.01        34.98        38.07        12.16 
TCGA-AD-6963 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
       27.42        58.39         1.41        12.10        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 
       85.48 

$`C5ORF42 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-5662 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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        21.44        17.82         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       53.62        44.68        61.91        36.00        13.78        46.75 

  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
             1.41              0.00 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
           100.01            148.01 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            24.39             21.99 
[1] "1.4 - 100.0 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1572V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF42 MUTATED         3        0        4        14         3         0
  C5ORF42 WILD-TYPE      61        1       22        94         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF42 MUTATED           1          0          2          1        3
  C5ORF42 WILD-TYPE        17          6         42         32       32
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF42 MUTATED           0         0
  C5ORF42 WILD-TYPE        12         1
D1572V3, multiclass
            clus
vv           C5ORF42 MUTATED C5ORF42 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 4                22
  STAGE IIA               14                94
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 3                32
  STAGE IVA                0                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
  C5ORF42 MUTATED     0   3  23   6
  C5ORF42 WILD-TYPE   9  64 226  35
D1572V4, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              23               226
  T4               6                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
  C5ORF42 MUTATED    25   4   3
  C5ORF42 WILD-TYPE 195  77  63
D1572V5, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  N0              25               195
  N1               4                77
  N2               3                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"
D1572V6, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    25   3
  C5ORF42 WILD-TYPE 260  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     25    3
  C5ORF42 WILD-TYPE  260   45
   clus
vv  C5ORF42 MUTATED C5ORF42 WILD-TYPE
  0              25               260
  1               3                45
[1] 2 2
[1] FALSE
D1572V7, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    14  18
  C5ORF42 WILD-TYPE 156 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     14   18
  C5ORF42 WILD-TYPE  156  179
        clus
vv       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  FEMALE              14               156
  MALE                18               179
[1] 2 2
[1] FALSE
D1572V8, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    28   1
  C5ORF42 WILD-TYPE 272   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     28    1
  C5ORF42 WILD-TYPE  272    7
     clus
vv    C5ORF42 MUTATED C5ORF42 WILD-TYPE
  NO               28               272
  YES               1                 7
[1] 2 2
[1] FALSE
D1572V9, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    25   7
  C5ORF42 WILD-TYPE 289  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     25    7
  C5ORF42 WILD-TYPE  289   41
                               clus
vv                              C5ORF42 MUTATED C5ORF42 WILD-TYPE
  COLON ADENOCARCINOMA                       25               289
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C5ORF42 MUTATED    19   0   1   4
  C5ORF42 WILD-TYPE 240   3  21  17
D1572V10, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  R0              19               240
  R1               0                 3
  R2               1                21
  RX               4                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"
D1572V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF42 MUTATED                                  0     2
  C5ORF42 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF42 MUTATED                           6    13
  C5ORF42 WILD-TYPE                        13   163
D1572V12, multiclass
                                  clus
vv                                 C5ORF42 MUTATED C5ORF42 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      6                13
  WHITE                                         13               163
[1] 4 2
[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 = ESYT1 MUTATION ANALYSIS
D1573V1, survival
                 sevent
clus2               0   1
  ESYT1 MUTATED     6   2
  ESYT1 WILD-TYPE 271  76
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              8             347 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              2              76 
$`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        26.47        33.01        51.32 
TCGA-DM-A1DA TCGA-F4-6809 
        7.50        13.25 

$`ESYT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 
       83.24        24.53         5.79        22.42        27.42        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        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-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ESYT1 MUTATED ESYT1 WILD-TYPE 
            7.5             0.0 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
          53.00          148.01 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
          25.43           22.03 
[1] "7.5 - 53.0 (25.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1573V2, continuous
                 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      63        1       25       106         7         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        18          6         44         31       35        10
                 vv
clus              STAGE IVB
  ESYT1 MUTATED           0
  ESYT1 WILD-TYPE         1
D1573V3, multiclass
            clus
vv           ESYT1 MUTATED ESYT1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              2              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
  ESYT1 MUTATED     0   1   6   2
  ESYT1 WILD-TYPE   9  66 243  39
D1573V4, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             2              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
  ESYT1 MUTATED     5   2   2
  ESYT1 WILD-TYPE 215  79  64
D1573V5, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1573V6, binary
                 cls
clus                0   1
  ESYT1 MUTATED     4   2
  ESYT1 WILD-TYPE 281  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      4    2
  ESYT1 WILD-TYPE  281   46
   clus
vv  ESYT1 MUTATED ESYT1 WILD-TYPE
  0             4             281
  1             2              46
[1] 2 2
[1] FALSE
D1573V7, binary
                 cls
clus                0   1
  ESYT1 MUTATED     5   4
  ESYT1 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      5    4
  ESYT1 WILD-TYPE  165  193
        clus
vv       ESYT1 MUTATED ESYT1 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1573V8, binary
                 cls
clus                0   1
  ESYT1 MUTATED     7   0
  ESYT1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      7    0
  ESYT1 WILD-TYPE  293    8
     clus
vv    ESYT1 MUTATED ESYT1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1573V9, binary
                 cls
clus                0   1
  ESYT1 MUTATED     8   1
  ESYT1 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      8    1
  ESYT1 WILD-TYPE  306   47
                               clus
vv                              ESYT1 MUTATED ESYT1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESYT1 MUTATED     3   1   0   2
  ESYT1 WILD-TYPE 256   2  22  19
D1573V10, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  R0             3             256
  R1             1               2
  R2             0              22
  RX             2              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"
D1573V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESYT1 MUTATED                                  0     0
  ESYT1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESYT1 MUTATED                           1     7
  ESYT1 WILD-TYPE                        18   169
D1573V12, multiclass
                                  clus
vv                                 ESYT1 MUTATED ESYT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = ADAM30 MUTATION ANALYSIS
D1574V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     7   1
  ADAM30 WILD-TYPE 270  77
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               8              347 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               77 
$`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 
       13.32        35.31 

$`ADAM30 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            1.02             0.00 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           35.31           148.01 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           19.17            22.06 
[1] "1.0 - 35.3 (19.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1574V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM30 MUTATED         3        0        0         4         0         0
  ADAM30 WILD-TYPE      61        1       26       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED           0          0          0          0        0
  ADAM30 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ADAM30 MUTATED           0         0
  ADAM30 WILD-TYPE        12         1
D1574V3, multiclass
            clus
vv           ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ADAM30 MUTATED     1   3   4   0
  ADAM30 WILD-TYPE   8  64 245  41
D1574V4, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  T1              1                8
  T2              3               64
  T3              4              245
  T4              0               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
  ADAM30 MUTATED     8   0   0
  ADAM30 WILD-TYPE 212  81  66
D1574V5, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1574V6, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     7   0
  ADAM30 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      7    0
  ADAM30 WILD-TYPE  278   48
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1574V7, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     3   5
  ADAM30 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      3    5
  ADAM30 WILD-TYPE  167  192
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D1574V8, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     7   0
  ADAM30 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      7    0
  ADAM30 WILD-TYPE  293    8
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1574V9, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     3   4
  ADAM30 WILD-TYPE 311  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      3    4
  ADAM30 WILD-TYPE  311   44
                               clus
vv                              ADAM30 MUTATED ADAM30 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ADAM30 MUTATED     6   0   0   0
  ADAM30 WILD-TYPE 253   3  22  21
D1574V10, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1574V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM30 MUTATED                                  0     0
  ADAM30 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM30 MUTATED                           1     4
  ADAM30 WILD-TYPE                        18   172
D1574V12, multiclass
                                  clus
vv                                 ADAM30 MUTATED ADAM30 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1575) Variable = PNPLA5 MUTATION ANALYSIS
D1575V1, survival
                  sevent
clus2                0   1
  PNPLA5 MUTATED     7   1
  PNPLA5 WILD-TYPE 270  77
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
               8              347 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
               1               77 
$`PNPLA5 MUTATED`
TCGA-G4-6586 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3877 TCGA-AU-6004 
       35.80        79.69         3.02        63.98        31.00        27.09 
TCGA-CA-5254 TCGA-CK-5913 
       12.69        51.32 

$`PNPLA5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        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 
       12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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            21.99 
[1] "3.0 - 79.7 (33.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1575V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PNPLA5 MUTATED         3        0        2         3         1         0
  PNPLA5 WILD-TYPE      61        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA5 MUTATED           0          0          0          0        1
  PNPLA5 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PNPLA5 MUTATED           0         0
  PNPLA5 WILD-TYPE        12         1
D1575V3, multiclass
            clus
vv           PNPLA5 MUTATED PNPLA5 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  PNPLA5 MUTATED     1   2   6   1
  PNPLA5 WILD-TYPE   8  65 243  40
D1575V4, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  T1              1                8
  T2              2               65
  T3              6              243
  T4              1               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
  PNPLA5 MUTATED     9   0   1
  PNPLA5 WILD-TYPE 211  81  65
D1575V5, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  N0              9              211
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1575V6, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     7   1
  PNPLA5 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      7    1
  PNPLA5 WILD-TYPE  278   47
   clus
vv  PNPLA5 MUTATED PNPLA5 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D1575V7, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     8   2
  PNPLA5 WILD-TYPE 162 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      8    2
  PNPLA5 WILD-TYPE  162  195
        clus
vv       PNPLA5 MUTATED PNPLA5 WILD-TYPE
  FEMALE              8              162
  MALE                2              195
[1] 2 2
[1] FALSE
D1575V8, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     7   0
  PNPLA5 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      7    0
  PNPLA5 WILD-TYPE  293    8
     clus
vv    PNPLA5 MUTATED PNPLA5 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1575V9, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     9   1
  PNPLA5 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      9    1
  PNPLA5 WILD-TYPE  305   47
                               clus
vv                              PNPLA5 MUTATED PNPLA5 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PNPLA5 MUTATED     6   0   1   3
  PNPLA5 WILD-TYPE 253   3  21  18
D1575V10, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              3               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"
D1575V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PNPLA5 MUTATED                                  0     1
  PNPLA5 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PNPLA5 MUTATED                           0     5
  PNPLA5 WILD-TYPE                        19   171
D1575V12, multiclass
                                  clus
vv                                 PNPLA5 MUTATED PNPLA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = TMPRSS5 MUTATION ANALYSIS
D1576V1, survival
                   sevent
clus2                 0   1
  TMPRSS5 MUTATED     5   2
  TMPRSS5 WILD-TYPE 272  76
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               348 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                2                76 
$`TMPRSS5 MUTATED`
TCGA-AA-3715 TCGA-A6-6141 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-5860 
       19.04         8.38        25.02        27.09        49.41        32.02 
TCGA-CM-6162 
       12.00 

$`TMPRSS5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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            22.045 
[1] "8.4 - 49.4 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1576V2, continuous
                   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      63        1       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS5 MUTATED           0          0          1          0        0
  TMPRSS5 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  TMPRSS5 MUTATED           0         0
  TMPRSS5 WILD-TYPE        12         1
D1576V3, multiclass
            clus
vv           TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  TMPRSS5 MUTATED     0   2   5   0
  TMPRSS5 WILD-TYPE   9  65 244  41
D1576V4, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               0                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
  TMPRSS5 MUTATED     6   1   0
  TMPRSS5 WILD-TYPE 214  80  66
D1576V5, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  N0               6               214
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1576V6, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     5   0
  TMPRSS5 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      5    0
  TMPRSS5 WILD-TYPE  280   48
   clus
vv  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1576V7, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     3   4
  TMPRSS5 WILD-TYPE 167 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      3    4
  TMPRSS5 WILD-TYPE  167  193
        clus
vv       TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  FEMALE               3               167
  MALE                 4               193
[1] 2 2
[1] FALSE
D1576V8, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     6   0
  TMPRSS5 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      6    0
  TMPRSS5 WILD-TYPE  294    8
     clus
vv    TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1576V9, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     6   1
  TMPRSS5 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      6    1
  TMPRSS5 WILD-TYPE  308   47
                               clus
vv                              TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMPRSS5 MUTATED     4   0   0   0
  TMPRSS5 WILD-TYPE 255   3  22  21
D1576V10, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1576V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMPRSS5 MUTATED                                  0     0
  TMPRSS5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS5 MUTATED                           1     4
  TMPRSS5 WILD-TYPE                        18   172
D1576V12, multiclass
                                  clus
vv                                 TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = CSF3R MUTATION ANALYSIS
D1577V1, survival
                 sevent
clus2               0   1
  CSF3R MUTATED     8   6
  CSF3R WILD-TYPE 269  72
  CSF3R MUTATED CSF3R WILD-TYPE 
             14             341 
  CSF3R MUTATED CSF3R WILD-TYPE 
              6              72 
$`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        12.16        51.32        23.05        15.02        16.14 
TCGA-DM-A1DA TCGA-F4-6570 
        7.50         6.18 

$`CSF3R WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C 
      140.38        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CSF3R MUTATED CSF3R WILD-TYPE 
           4.01            0.00 
  CSF3R MUTATED CSF3R WILD-TYPE 
          53.00          148.01 
  CSF3R MUTATED CSF3R WILD-TYPE 
          15.58           22.09 
[1] "4.0 - 53.0 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D1577V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSF3R MUTATED         2        0        1         4         2         0
  CSF3R WILD-TYPE      62        1       25       104         6         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        16          6         43         31       35        12
                 vv
clus              STAGE IVB
  CSF3R MUTATED           0
  CSF3R WILD-TYPE         1
D1577V3, multiclass
            clus
vv           CSF3R MUTATED CSF3R WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  CSF3R MUTATED     0   2   9   3
  CSF3R WILD-TYPE   9  65 240  38
D1577V4, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             3              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
  CSF3R MUTATED     9   2   3
  CSF3R WILD-TYPE 211  79  63
D1577V5, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  N0             9             211
  N1             2              79
  N2             3              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"
D1577V6, binary
                 cls
clus                0   1
  CSF3R MUTATED    12   0
  CSF3R WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     12    0
  CSF3R WILD-TYPE  273   48
   clus
vv  CSF3R MUTATED CSF3R WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D1577V7, binary
                 cls
clus                0   1
  CSF3R MUTATED     7   7
  CSF3R WILD-TYPE 163 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      7    7
  CSF3R WILD-TYPE  163  190
        clus
vv       CSF3R MUTATED CSF3R WILD-TYPE
  FEMALE             7             163
  MALE               7             190
[1] 2 2
[1] FALSE
D1577V8, binary
                 cls
clus                0   1
  CSF3R MUTATED    12   0
  CSF3R WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     12    0
  CSF3R WILD-TYPE  288    8
     clus
vv    CSF3R MUTATED CSF3R WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1577V9, binary
                 cls
clus                0   1
  CSF3R MUTATED     9   5
  CSF3R WILD-TYPE 305  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      9    5
  CSF3R WILD-TYPE  305   43
                               clus
vv                              CSF3R MUTATED CSF3R WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CSF3R MUTATED    11   0   0   1
  CSF3R WILD-TYPE 248   3  22  20
D1577V10, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1577V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSF3R MUTATED                                  0     0
  CSF3R WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSF3R MUTATED                           0     7
  CSF3R WILD-TYPE                        19   169
D1577V12, multiclass
                                  clus
vv                                 CSF3R MUTATED CSF3R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = VANGL1 MUTATION ANALYSIS
D1578V1, survival
                  sevent
clus2                0   1
  VANGL1 MUTATED     6   3
  VANGL1 WILD-TYPE 271  75
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               9              346 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3               75 
$`VANGL1 MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-A00J TCGA-AZ-6600 TCGA-CM-4746 
       19.04       100.01        26.17        18.05        12.10        37.02 
TCGA-CM-4752 TCGA-D5-6535 TCGA-DM-A28H 
       13.02        15.12       117.07 

$`VANGL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  VANGL1 MUTATED VANGL1 WILD-TYPE 
            12.1              0.0 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
          117.07           148.01 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
          19.040           22.075 
[1] "12.1 - 117.1 (19.0)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.1"
D1578V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VANGL1 MUTATED         1        0        2         2         0         0
  VANGL1 WILD-TYPE      63        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VANGL1 MUTATED           1          0          2          1        1
  VANGL1 WILD-TYPE        17          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  VANGL1 MUTATED           0         0
  VANGL1 WILD-TYPE        12         1
D1578V3, multiclass
            clus
vv           VANGL1 MUTATED VANGL1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  VANGL1 MUTATED     0   1   7   2
  VANGL1 WILD-TYPE   9  66 242  39
D1578V4, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              2               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
  VANGL1 MUTATED     5   3   2
  VANGL1 WILD-TYPE 215  78  64
D1578V5, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  N0              5              215
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1578V6, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     8   1
  VANGL1 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      8    1
  VANGL1 WILD-TYPE  277   47
   clus
vv  VANGL1 MUTATED VANGL1 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1578V7, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     2   8
  VANGL1 WILD-TYPE 168 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      2    8
  VANGL1 WILD-TYPE  168  189
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  FEMALE              2              168
  MALE                8              189
[1] 2 2
[1] FALSE
D1578V8, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     8   0
  VANGL1 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      8    0
  VANGL1 WILD-TYPE  292    8
     clus
vv    VANGL1 MUTATED VANGL1 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1578V9, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     9   1
  VANGL1 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      9    1
  VANGL1 WILD-TYPE  305   47
                               clus
vv                              VANGL1 MUTATED VANGL1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  VANGL1 MUTATED     6   0   0   1
  VANGL1 WILD-TYPE 253   3  22  20
D1578V10, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1578V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VANGL1 MUTATED                                  0     0
  VANGL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VANGL1 MUTATED                           3     4
  VANGL1 WILD-TYPE                        16   172
D1578V12, multiclass
                                  clus
vv                                 VANGL1 MUTATED VANGL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         4              172
[1] 4 2
[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 = MST1R MUTATION ANALYSIS
D1579V1, survival
                 sevent
clus2               0   1
  MST1R MUTATED    11   3
  MST1R WILD-TYPE 266  75
  MST1R MUTATED MST1R WILD-TYPE 
             14             341 
  MST1R MUTATED MST1R WILD-TYPE 
              3              75 
$`MST1R MUTATED`
TCGA-A6-6138 TCGA-AA-3845 TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CK-4952 
       22.52         0.00        12.16         0.20         3.19        15.62 
TCGA-CK-6751 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A0XD 
      124.27        15.02        14.04        12.95        11.64        24.43 
TCGA-F4-6856 TCGA-G4-6315 
       35.31        61.91 

$`MST1R WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        36.00        13.78        46.75 

  MST1R MUTATED MST1R WILD-TYPE 
              0               0 
  MST1R MUTATED MST1R WILD-TYPE 
         124.27          148.01 
  MST1R MUTATED MST1R WILD-TYPE 
          14.53           22.09 
[1] "0.0 - 124.3 (14.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1579V2, continuous
                 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      59        1       26       103         8         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        18          6         44         31       33        12
                 vv
clus              STAGE IVB
  MST1R MUTATED           0
  MST1R WILD-TYPE         1
D1579V3, multiclass
            clus
vv           MST1R MUTATED MST1R WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               2              33
  STAGE IVA              0              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
  MST1R MUTATED     0   5   7   2
  MST1R WILD-TYPE   9  62 242  39
D1579V4, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  T1             0               9
  T2             5              62
  T3             7             242
  T4             2              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
  MST1R MUTATED    10   1   3
  MST1R WILD-TYPE 210  80  63
D1579V5, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  N0            10             210
  N1             1              80
  N2             3              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"
D1579V6, binary
                 cls
clus                0   1
  MST1R MUTATED     9   2
  MST1R WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      9    2
  MST1R WILD-TYPE  276   46
   clus
vv  MST1R MUTATED MST1R WILD-TYPE
  0             9             276
  1             2              46
[1] 2 2
[1] FALSE
D1579V7, binary
                 cls
clus                0   1
  MST1R MUTATED     5   9
  MST1R WILD-TYPE 165 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      5    9
  MST1R WILD-TYPE  165  188
        clus
vv       MST1R MUTATED MST1R WILD-TYPE
  FEMALE             5             165
  MALE               9             188
[1] 2 2
[1] FALSE
D1579V8, binary
                 cls
clus                0   1
  MST1R MUTATED    10   0
  MST1R WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED     10    0
  MST1R WILD-TYPE  290    8
     clus
vv    MST1R MUTATED MST1R WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1579V9, binary
                 cls
clus                0   1
  MST1R MUTATED     8   6
  MST1R WILD-TYPE 306  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      8    6
  MST1R WILD-TYPE  306   42
                               clus
vv                              MST1R MUTATED MST1R WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MST1R MUTATED     9   0   0   2
  MST1R WILD-TYPE 250   3  22  19
D1579V10, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D1579V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MST1R MUTATED                                  0     0
  MST1R WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MST1R MUTATED                           0    13
  MST1R WILD-TYPE                        19   163
D1579V12, multiclass
                                  clus
vv                                 MST1R MUTATED MST1R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       13             163
[1] 4 2
[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 = OR5H1 MUTATION ANALYSIS
D1580V1, survival
                 sevent
clus2               0   1
  OR5H1 MUTATED     6   3
  OR5H1 WILD-TYPE 271  75
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              9             346 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              3              75 
$`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        83.24 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-D5-6541 
       49.41        12.10        15.58 

$`OR5H1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  OR5H1 MUTATED OR5H1 WILD-TYPE 
           1.02            0.00 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
          83.24          148.01 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
          30.44           22.01 
[1] "1.0 - 83.2 (30.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1580V2, continuous
                 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      63        1       24       104         8         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  OR5H1 MUTATED           0
  OR5H1 WILD-TYPE         1
D1580V3, multiclass
            clus
vv           OR5H1 MUTATED OR5H1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  OR5H1 MUTATED     0   1   7   2
  OR5H1 WILD-TYPE   9  66 242  39
D1580V4, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             2              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
  OR5H1 MUTATED     8   2   0
  OR5H1 WILD-TYPE 212  79  66
D1580V5, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  N0             8             212
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1580V6, binary
                 cls
clus                0   1
  OR5H1 MUTATED     8   1
  OR5H1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      8    1
  OR5H1 WILD-TYPE  277   47
   clus
vv  OR5H1 MUTATED OR5H1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1580V7, binary
                 cls
clus                0   1
  OR5H1 MUTATED     5   5
  OR5H1 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      5    5
  OR5H1 WILD-TYPE  165  192
        clus
vv       OR5H1 MUTATED OR5H1 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1580V8, binary
                 cls
clus                0   1
  OR5H1 MUTATED     8   0
  OR5H1 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      8    0
  OR5H1 WILD-TYPE  292    8
     clus
vv    OR5H1 MUTATED OR5H1 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1580V9, binary
                 cls
clus                0   1
  OR5H1 MUTATED     9   1
  OR5H1 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      9    1
  OR5H1 WILD-TYPE  305   47
                               clus
vv                              OR5H1 MUTATED OR5H1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5H1 MUTATED     7   0   0   0
  OR5H1 WILD-TYPE 252   3  22  21
D1580V10, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1580V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5H1 MUTATED                                  0     1
  OR5H1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5H1 MUTATED                           2     4
  OR5H1 WILD-TYPE                        17   172
D1580V12, multiclass
                                  clus
vv                                 OR5H1 MUTATED OR5H1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        4             172
[1] 4 2
[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 = VWA5A MUTATION ANALYSIS
D1581V1, survival
                 sevent
clus2               0   1
  VWA5A MUTATED     8   3
  VWA5A WILD-TYPE 269  75
  VWA5A MUTATED VWA5A WILD-TYPE 
             11             344 
  VWA5A MUTATED VWA5A WILD-TYPE 
              3              75 
$`VWA5A MUTATED`
TCGA-AA-3522 TCGA-AA-3672 TCGA-A6-2683 TCGA-A6-6653 TCGA-AA-3821 TCGA-AA-3966 
       37.05         0.92        16.57        24.39         1.02         2.01 
TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-6168 TCGA-G4-6303 TCGA-G4-6307 
       34.98        49.41        12.99        65.85        55.04 

$`VWA5A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.90        42.28        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       74.56        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  VWA5A MUTATED VWA5A WILD-TYPE 
           0.92            0.00 
  VWA5A MUTATED VWA5A WILD-TYPE 
          65.85          148.01 
  VWA5A MUTATED VWA5A WILD-TYPE 
         24.390          22.045 
[1] "0.9 - 65.8 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1581V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VWA5A MUTATED         2        0        1         3         2         0
  VWA5A WILD-TYPE      62        1       25       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VWA5A MUTATED           1          0          1          0        2         0
  VWA5A WILD-TYPE        17          6         43         33       33        12
                 vv
clus              STAGE IVB
  VWA5A MUTATED           0
  VWA5A WILD-TYPE         1
D1581V3, multiclass
            clus
vv           VWA5A MUTATED VWA5A WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  VWA5A MUTATED     0   2   7   3
  VWA5A WILD-TYPE   9  65 242  38
D1581V4, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             3              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
  VWA5A MUTATED     9   3   0
  VWA5A WILD-TYPE 211  78  66
D1581V5, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  N0             9             211
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1581V6, binary
                 cls
clus                0   1
  VWA5A MUTATED     8   2
  VWA5A WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED      8    2
  VWA5A WILD-TYPE  277   46
   clus
vv  VWA5A MUTATED VWA5A WILD-TYPE
  0             8             277
  1             2              46
[1] 2 2
[1] FALSE
D1581V7, binary
                 cls
clus                0   1
  VWA5A MUTATED    10   2
  VWA5A WILD-TYPE 160 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     10    2
  VWA5A WILD-TYPE  160  195
        clus
vv       VWA5A MUTATED VWA5A WILD-TYPE
  FEMALE            10             160
  MALE               2             195
[1] 2 2
[1] FALSE
D1581V8, binary
                 cls
clus                0   1
  VWA5A MUTATED    10   0
  VWA5A WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     10    0
  VWA5A WILD-TYPE  290    8
     clus
vv    VWA5A MUTATED VWA5A WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1581V9, binary
                 cls
clus                0   1
  VWA5A MUTATED    10   2
  VWA5A WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     10    2
  VWA5A WILD-TYPE  304   46
                               clus
vv                              VWA5A MUTATED VWA5A WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VWA5A MUTATED     8   0   0   1
  VWA5A WILD-TYPE 251   3  22  20
D1581V10, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1581V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VWA5A MUTATED                                  0     0
  VWA5A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VWA5A MUTATED                           1     6
  VWA5A WILD-TYPE                        18   170
D1581V12, multiclass
                                  clus
vv                                 VWA5A MUTATED VWA5A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = ABCF3 MUTATION ANALYSIS
D1582V1, survival
                 sevent
clus2               0   1
  ABCF3 MUTATED    11   3
  ABCF3 WILD-TYPE 266  75
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             14             341 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              3              75 
$`ABCF3 MUTATED`
TCGA-AZ-6601 TCGA-G4-6310 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3852 TCGA-AA-A00J 
      100.01        63.62        19.66        33.04         0.00        18.05 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6161 TCGA-CM-6165 
       83.24        58.39        23.05        37.02        15.02        16.04 
TCGA-D5-6535 TCGA-G4-6293 
       15.12       133.18 

$`ABCF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      106.75         1.94        49.08         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-5861 TCGA-CM-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-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ABCF3 MUTATED ABCF3 WILD-TYPE 
              0               0 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
         133.18          148.01 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
         28.045          22.030 
[1] "0.0 - 133.2 (28.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1582V2, continuous
                 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      62        1       25       102         7         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        17          6         41         32       35        12
                 vv
clus              STAGE IVB
  ABCF3 MUTATED           0
  ABCF3 WILD-TYPE         1
D1582V3, multiclass
            clus
vv           ABCF3 MUTATED ABCF3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  ABCF3 MUTATED     0   2  10   3
  ABCF3 WILD-TYPE   9  65 239  38
D1582V4, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             3              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
  ABCF3 MUTATED    10   5   0
  ABCF3 WILD-TYPE 210  76  66
D1582V5, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  N0            10             210
  N1             5              76
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1582V6, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   0
  ABCF3 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    0
  ABCF3 WILD-TYPE  273   48
   clus
vv  ABCF3 MUTATED ABCF3 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D1582V7, binary
                 cls
clus                0   1
  ABCF3 MUTATED     5  10
  ABCF3 WILD-TYPE 165 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      5   10
  ABCF3 WILD-TYPE  165  187
        clus
vv       ABCF3 MUTATED ABCF3 WILD-TYPE
  FEMALE             5             165
  MALE              10             187
[1] 2 2
[1] FALSE
D1582V8, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   1
  ABCF3 WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    1
  ABCF3 WILD-TYPE  288    7
     clus
vv    ABCF3 MUTATED ABCF3 WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D1582V9, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   3
  ABCF3 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    3
  ABCF3 WILD-TYPE  302   45
                               clus
vv                              ABCF3 MUTATED ABCF3 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCF3 MUTATED    12   0   0   2
  ABCF3 WILD-TYPE 247   3  22  19
D1582V10, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             2              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"
D1582V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCF3 MUTATED                                  0     1
  ABCF3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCF3 MUTATED                           1    10
  ABCF3 WILD-TYPE                        18   166
D1582V12, multiclass
                                  clus
vv                                 ABCF3 MUTATED ABCF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       10             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(1583) Variable = CUBN MUTATION ANALYSIS
D1583V1, survival
                sevent
clus2              0   1
  CUBN MUTATED    36  12
  CUBN WILD-TYPE 241  66
  CUBN MUTATED CUBN WILD-TYPE 
            48            307 
  CUBN MUTATED CUBN WILD-TYPE 
            12             66 
$`CUBN MUTATED`
TCGA-A6-4105 TCGA-AA-3554 TCGA-AA-3672 TCGA-AD-6895 TCGA-G4-6588 TCGA-A6-2672 
       14.53        17.95         0.92        25.08        26.17        46.65 
TCGA-A6-2678 TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 
       42.28        30.44        22.52         8.38        19.66         3.02 
TCGA-AA-3544 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3846 TCGA-AA-3861 
       14.01        20.98         6.97        26.99        17.03        30.05 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 
       53.00        25.02         7.96        18.05         4.01        34.98 
TCGA-AA-A01K TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AY-6196 
       31.00        35.01        12.16        83.24        24.53         0.20 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6168 
       49.41        29.56        12.20        12.76        10.06        12.99 
TCGA-CM-6675 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6931 
       13.05        17.85         4.80        16.14         7.53        12.00 
TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6299 TCGA-G4-6315 
       24.43        13.32         6.18        47.87        74.56        61.91 

$`CUBN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        35.80        91.79        79.69 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        43.76        42.90        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6142 
       23.61        22.09        22.06        32.71        27.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        26.01        12.99        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       29.95        13.94        61.02        78.08        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       32.05         0.99        31.07        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I 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         1.02 
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-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.39        12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        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-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        43.04        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CUBN MUTATED CUBN WILD-TYPE 
           0.2            0.0 
  CUBN MUTATED CUBN WILD-TYPE 
         83.24         148.01 
  CUBN MUTATED CUBN WILD-TYPE 
         18.00          22.36 
[1] "0.2 - 83.2 (18.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D1583V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUBN MUTATED         7        0        5        19         2         0
  CUBN WILD-TYPE      57        1       21        89         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUBN MUTATED           2          0          4          5        4         0
  CUBN WILD-TYPE        16          6         40         28       31        12
                vv
clus             STAGE IVB
  CUBN MUTATED           1
  CUBN WILD-TYPE         0
D1583V3, multiclass
            clus
vv           CUBN MUTATED CUBN WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA            19             89
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            5             28
  STAGE IV              4             31
  STAGE IVA             0             12
  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   9  35   7
  CUBN WILD-TYPE   8  58 214  34
D1583V4, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  T1            1              8
  T2            9             58
  T3           35            214
  T4            7             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
  CUBN MUTATED    35   8   9
  CUBN WILD-TYPE 185  73  57
D1583V5, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  N0           35            185
  N1            8             73
  N2            9             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1583V6, binary
                cls
clus               0   1
  CUBN MUTATED    39   5
  CUBN WILD-TYPE 246  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     39    5
  CUBN WILD-TYPE  246   43
   clus
vv  CUBN MUTATED CUBN WILD-TYPE
  0           39            246
  1            5             43
[1] 2 2
[1] FALSE
D1583V7, binary
                cls
clus               0   1
  CUBN MUTATED    18  34
  CUBN WILD-TYPE 152 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     18   34
  CUBN WILD-TYPE  152  163
        clus
vv       CUBN MUTATED CUBN WILD-TYPE
  FEMALE           18            152
  MALE             34            163
[1] 2 2
[1] FALSE
D1583V8, binary
                cls
clus               0   1
  CUBN MUTATED    42   1
  CUBN WILD-TYPE 258   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     42    1
  CUBN WILD-TYPE  258    7
     clus
vv    CUBN MUTATED CUBN WILD-TYPE
  NO            42            258
  YES            1              7
[1] 2 2
[1] FALSE
D1583V9, binary
                cls
clus               0   1
  CUBN MUTATED    43   8
  CUBN WILD-TYPE 271  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     43    8
  CUBN WILD-TYPE  271   40
                               clus
vv                              CUBN MUTATED CUBN WILD-TYPE
  COLON ADENOCARCINOMA                    43            271
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CUBN MUTATED    36   0   4   3
  CUBN WILD-TYPE 223   3  18  18
D1583V10, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  R0           36            223
  R1            0              3
  R2            4             18
  RX            3             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"
D1583V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUBN MUTATED                                  0     4
  CUBN WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUBN MUTATED                           3    24
  CUBN WILD-TYPE                        16   152
D1583V12, multiclass
                                  clus
vv                                 CUBN MUTATED CUBN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              6
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      24            152
[1] 4 2
[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 = LIPH MUTATION ANALYSIS
D1584V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     8   1
  LIPH WILD-TYPE 269  77
  LIPH MUTATED LIPH WILD-TYPE 
             9            346 
  LIPH MUTATED LIPH WILD-TYPE 
             1             77 
$`LIPH MUTATED`
TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-6141 TCGA-AA-3947 TCGA-AA-A010 TCGA-CA-6717 
       22.09        26.17         8.38        33.01        34.98        12.76 
TCGA-CK-5913 TCGA-D5-6532 TCGA-G4-6626 
       51.32        18.25        46.75 

$`LIPH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  LIPH MUTATED LIPH WILD-TYPE 
          8.38           0.00 
  LIPH MUTATED LIPH WILD-TYPE 
         51.32         148.01 
  LIPH MUTATED LIPH WILD-TYPE 
         26.17          22.01 
[1] "8.4 - 51.3 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1584V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIPH MUTATED         0        0        0         6         2         0
  LIPH WILD-TYPE      64        1       26       102         6         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        17          6         44         33       35        12
                vv
clus             STAGE IVB
  LIPH MUTATED           0
  LIPH WILD-TYPE         1
D1584V3, multiclass
            clus
vv           LIPH MUTATED LIPH WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  LIPH MUTATED     0   1   6   2
  LIPH WILD-TYPE   9  66 243  39
D1584V4, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  T1            0              9
  T2            1             66
  T3            6            243
  T4            2             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
  LIPH MUTATED     8   1   0
  LIPH WILD-TYPE 212  80  66
D1584V5, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            8            212
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1584V6, binary
                cls
clus               0   1
  LIPH MUTATED     7   0
  LIPH WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      7    0
  LIPH WILD-TYPE  278   48
   clus
vv  LIPH MUTATED LIPH WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1584V7, binary
                cls
clus               0   1
  LIPH MUTATED     5   4
  LIPH WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      5    4
  LIPH WILD-TYPE  165  193
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D1584V8, binary
                cls
clus               0   1
  LIPH MUTATED     9   0
  LIPH WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      9    0
  LIPH WILD-TYPE  291    8
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1584V9, binary
                cls
clus               0   1
  LIPH MUTATED     7   2
  LIPH WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      7    2
  LIPH WILD-TYPE  307   46
                               clus
vv                              LIPH MUTATED LIPH WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LIPH MUTATED     6   0   0   2
  LIPH WILD-TYPE 253   3  22  19
D1584V10, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            2             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"
D1584V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIPH MUTATED                                  0     1
  LIPH WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIPH MUTATED                           1     5
  LIPH WILD-TYPE                        18   171
D1584V12, multiclass
                                  clus
vv                                 LIPH MUTATED LIPH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1585) Variable = SHQ1 MUTATION ANALYSIS
D1585V1, survival
                sevent
clus2              0   1
  SHQ1 MUTATED     6   2
  SHQ1 WILD-TYPE 271  76
  SHQ1 MUTATED SHQ1 WILD-TYPE 
             8            347 
  SHQ1 MUTATED SHQ1 WILD-TYPE 
             2             76 
$`SHQ1 MUTATED`
TCGA-A6-6654 TCGA-AA-3660 TCGA-AA-3982 TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-4315 
       23.87        78.08        27.02        34.98        38.07        58.39 
TCGA-D5-5538 TCGA-D5-6536 
       54.61        17.85 

$`SHQ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SHQ1 MUTATED SHQ1 WILD-TYPE 
         17.85           0.00 
  SHQ1 MUTATED SHQ1 WILD-TYPE 
         78.08         148.01 
  SHQ1 MUTATED SHQ1 WILD-TYPE 
        36.525         21.990 
[1] "17.9 - 78.1 (36.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1585V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SHQ1 MUTATED         0        0        1         2         1         0
  SHQ1 WILD-TYPE      64        1       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SHQ1 MUTATED           1          0          3          0        0         0
  SHQ1 WILD-TYPE        17          6         41         33       35        12
                vv
clus             STAGE IVB
  SHQ1 MUTATED           0
  SHQ1 WILD-TYPE         1
D1585V3, multiclass
            clus
vv           SHQ1 MUTATED SHQ1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  SHQ1 MUTATED     0   0   7   1
  SHQ1 WILD-TYPE   9  67 242  40
D1585V4, multiclass
    clus
vv   SHQ1 MUTATED SHQ1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            7            242
  T4            1             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
  SHQ1 MUTATED     4   4   0
  SHQ1 WILD-TYPE 216  77  66
D1585V5, multiclass
    clus
vv   SHQ1 MUTATED SHQ1 WILD-TYPE
  N0            4            216
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1585V6, binary
                cls
clus               0   1
  SHQ1 MUTATED     8   0
  SHQ1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SHQ1 MUTATED      8    0
  SHQ1 WILD-TYPE  277   48
   clus
vv  SHQ1 MUTATED SHQ1 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1585V7, binary
                cls
clus               0   1
  SHQ1 MUTATED     5   3
  SHQ1 WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  SHQ1 MUTATED      5    3
  SHQ1 WILD-TYPE  165  194
        clus
vv       SHQ1 MUTATED SHQ1 WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D1585V8, binary
                cls
clus               0   1
  SHQ1 MUTATED     8   0
  SHQ1 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SHQ1 MUTATED      8    0
  SHQ1 WILD-TYPE  292    8
     clus
vv    SHQ1 MUTATED SHQ1 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1585V9, binary
                cls
clus               0   1
  SHQ1 MUTATED     8   0
  SHQ1 WILD-TYPE 306  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SHQ1 MUTATED      8    0
  SHQ1 WILD-TYPE  306   48
                               clus
vv                              SHQ1 MUTATED SHQ1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SHQ1 MUTATED     6   0   0   0
  SHQ1 WILD-TYPE 253   3  22  21
D1585V10, multiclass
    clus
vv   SHQ1 MUTATED SHQ1 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D1585V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SHQ1 MUTATED                                  0     0
  SHQ1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SHQ1 MUTATED                           0     4
  SHQ1 WILD-TYPE                        19   172
D1585V12, multiclass
                                  clus
vv                                 SHQ1 MUTATED SHQ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = DAB2 MUTATION ANALYSIS
D1586V1, survival
                sevent
clus2              0   1
  DAB2 MUTATED    12   1
  DAB2 WILD-TYPE 265  77
  DAB2 MUTATED DAB2 WILD-TYPE 
            13            342 
  DAB2 MUTATED DAB2 WILD-TYPE 
             1             77 
$`DAB2 MUTATED`
TCGA-G4-6586 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-A01G 
       35.80         8.38        63.98        47.01        37.05        12.00 
TCGA-AZ-4315 TCGA-CK-6751 TCGA-CM-6165 TCGA-CM-6167 TCGA-D5-6927 TCGA-DM-A28H 
       58.39       124.27        16.04        14.99         9.44       117.07 
TCGA-F4-6570 
        6.18 

$`DAB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       14.01        50.04        15.02        11.01         5.98         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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-CM-4743 
       51.32        21.99        21.14        82.95         2.01        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        14.04        29.03 
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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K 
      139.17        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DAB2 MUTATED DAB2 WILD-TYPE 
          6.18           0.00 
  DAB2 MUTATED DAB2 WILD-TYPE 
        124.27         148.01 
  DAB2 MUTATED DAB2 WILD-TYPE 
        35.800         22.045 
[1] "6.2 - 124.3 (35.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "4.3"
D1586V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DAB2 MUTATED         1        0        2         7         0         0
  DAB2 WILD-TYPE      63        1       24       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DAB2 MUTATED           1          0          0          2        0         0
  DAB2 WILD-TYPE        17          6         44         31       35        12
                vv
clus             STAGE IVB
  DAB2 MUTATED           0
  DAB2 WILD-TYPE         1
D1586V3, multiclass
            clus
vv           DAB2 MUTATED DAB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  DAB2 MUTATED     0   2  11   0
  DAB2 WILD-TYPE   9  65 238  41
D1586V4, multiclass
    clus
vv   DAB2 MUTATED DAB2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           11            238
  T4            0             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
  DAB2 MUTATED    10   1   2
  DAB2 WILD-TYPE 210  80  64
D1586V5, multiclass
    clus
vv   DAB2 MUTATED DAB2 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1586V6, binary
                cls
clus               0   1
  DAB2 MUTATED    12   0
  DAB2 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAB2 MUTATED     12    0
  DAB2 WILD-TYPE  273   48
   clus
vv  DAB2 MUTATED DAB2 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D1586V7, binary
                cls
clus               0   1
  DAB2 MUTATED     5   8
  DAB2 WILD-TYPE 165 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAB2 MUTATED      5    8
  DAB2 WILD-TYPE  165  189
        clus
vv       DAB2 MUTATED DAB2 WILD-TYPE
  FEMALE            5            165
  MALE              8            189
[1] 2 2
[1] FALSE
D1586V8, binary
                cls
clus               0   1
  DAB2 MUTATED    12   0
  DAB2 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAB2 MUTATED     12    0
  DAB2 WILD-TYPE  288    8
     clus
vv    DAB2 MUTATED DAB2 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1586V9, binary
                cls
clus               0   1
  DAB2 MUTATED    11   2
  DAB2 WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAB2 MUTATED     11    2
  DAB2 WILD-TYPE  303   46
                               clus
vv                              DAB2 MUTATED DAB2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DAB2 MUTATED    10   0   0   1
  DAB2 WILD-TYPE 249   3  22  20
D1586V10, multiclass
    clus
vv   DAB2 MUTATED DAB2 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D1586V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DAB2 MUTATED                                  0     0
  DAB2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DAB2 MUTATED                           2     7
  DAB2 WILD-TYPE                        17   169
D1586V12, multiclass
                                  clus
vv                                 DAB2 MUTATED DAB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       7            169
[1] 4 2
[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 = IFLTD1 MUTATION ANALYSIS
D1587V1, survival
                  sevent
clus2                0   1
  IFLTD1 MUTATED    11   0
  IFLTD1 WILD-TYPE 266  78
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              11              344 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
               0               78 
$`IFLTD1 MUTATED`
TCGA-AA-3524 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 
       36.03        29.19        22.06        26.99        53.00        25.02 
TCGA-AY-6386 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6675 
       17.82        12.76        30.08        15.02        13.05 

$`IFLTD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
           12.76             0.00 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
           53.00           148.01 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
           25.02            22.01 
[1] "12.8 - 53.0 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.5e+07"
D1587V2, continuous
                  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      64        1       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFLTD1 MUTATED           1          0          1          1        0
  IFLTD1 WILD-TYPE        17          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  IFLTD1 MUTATED           0         1
  IFLTD1 WILD-TYPE        12         0
D1587V3, multiclass
            clus
vv           IFLTD1 MUTATED IFLTD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               12
  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  11   0
  IFLTD1 WILD-TYPE   9  66 238  41
D1587V4, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             11              238
  T4              0               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
  IFLTD1 MUTATED     8   1   3
  IFLTD1 WILD-TYPE 212  80  63
D1587V5, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              3               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"
D1587V6, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    10   1
  IFLTD1 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     10    1
  IFLTD1 WILD-TYPE  275   47
   clus
vv  IFLTD1 MUTATED IFLTD1 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D1587V7, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED     5   7
  IFLTD1 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED      5    7
  IFLTD1 WILD-TYPE  165  190
        clus
vv       IFLTD1 MUTATED IFLTD1 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D1587V8, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    11   0
  IFLTD1 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     11    0
  IFLTD1 WILD-TYPE  289    8
     clus
vv    IFLTD1 MUTATED IFLTD1 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1587V9, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    11   1
  IFLTD1 WILD-TYPE 303  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     11    1
  IFLTD1 WILD-TYPE  303   47
                               clus
vv                              IFLTD1 MUTATED IFLTD1 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IFLTD1 MUTATED     9   0   0   1
  IFLTD1 WILD-TYPE 250   3  22  20
D1587V10, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              1               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"
D1587V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFLTD1 MUTATED                                  0     1
  IFLTD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFLTD1 MUTATED                           3     3
  IFLTD1 WILD-TYPE                        16   173
D1587V12, multiclass
                                  clus
vv                                 IFLTD1 MUTATED IFLTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                         3              173
[1] 4 2
[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 = TEX11 MUTATION ANALYSIS
D1588V1, survival
                 sevent
clus2               0   1
  TEX11 MUTATED    12   4
  TEX11 WILD-TYPE 265  74
  TEX11 MUTATED TEX11 WILD-TYPE 
             16             339 
  TEX11 MUTATED TEX11 WILD-TYPE 
              4              74 
$`TEX11 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-DM-A285 TCGA-G4-6321 TCGA-A6-2678 TCGA-A6-5666 
       13.02         0.92         5.88        22.09        42.28        32.71 
TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-4743 
        4.01        21.44        49.41        14.30        51.32        23.05 
TCGA-CM-6163 TCGA-CM-6171 TCGA-D5-5540 TCGA-D5-6540 
       14.04        14.04        56.09        16.14 

$`TEX11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        1.94        49.08        63.62        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TEX11 MUTATED TEX11 WILD-TYPE 
           0.92            0.00 
  TEX11 MUTATED TEX11 WILD-TYPE 
          56.09          148.01 
  TEX11 MUTATED TEX11 WILD-TYPE 
          18.79           22.09 
[1] "0.9 - 56.1 (18.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1588V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TEX11 MUTATED         3        0        1         5         1         1
  TEX11 WILD-TYPE      61        1       25       103         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEX11 MUTATED           4          0          1          0        1         0
  TEX11 WILD-TYPE        14          6         43         33       34        12
                 vv
clus              STAGE IVB
  TEX11 MUTATED           0
  TEX11 WILD-TYPE         1
D1588V3, multiclass
            clus
vv           TEX11 MUTATED TEX11 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              4              14
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TEX11 MUTATED     1   3  11   2
  TEX11 WILD-TYPE   8  64 238  39
D1588V4, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            11             238
  T4             2              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
  TEX11 MUTATED    11   3   3
  TEX11 WILD-TYPE 209  78  63
D1588V5, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  N0            11             209
  N1             3              78
  N2             3              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"
D1588V6, binary
                 cls
clus                0   1
  TEX11 MUTATED    12   1
  TEX11 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     12    1
  TEX11 WILD-TYPE  273   47
   clus
vv  TEX11 MUTATED TEX11 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D1588V7, binary
                 cls
clus                0   1
  TEX11 MUTATED     8   9
  TEX11 WILD-TYPE 162 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED      8    9
  TEX11 WILD-TYPE  162  188
        clus
vv       TEX11 MUTATED TEX11 WILD-TYPE
  FEMALE             8             162
  MALE               9             188
[1] 2 2
[1] FALSE
D1588V8, binary
                 cls
clus                0   1
  TEX11 MUTATED    14   0
  TEX11 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     14    0
  TEX11 WILD-TYPE  286    8
     clus
vv    TEX11 MUTATED TEX11 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1588V9, binary
                 cls
clus                0   1
  TEX11 MUTATED    13   4
  TEX11 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     13    4
  TEX11 WILD-TYPE  301   44
                               clus
vv                              TEX11 MUTATED TEX11 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TEX11 MUTATED    11   0   0   2
  TEX11 WILD-TYPE 248   3  22  19
D1588V10, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             2              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"
D1588V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEX11 MUTATED                                  0     1
  TEX11 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TEX11 MUTATED                           0    12
  TEX11 WILD-TYPE                        19   164
D1588V12, multiclass
                                  clus
vv                                 TEX11 MUTATED TEX11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = GOLGA1 MUTATION ANALYSIS
D1589V1, survival
                  sevent
clus2                0   1
  GOLGA1 MUTATED     3   3
  GOLGA1 WILD-TYPE 274  75
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               6              349 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               3               75 
$`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        54.61 

$`GOLGA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-D5-6532 
       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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
            4.01             0.00 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
           54.61           148.01 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
          12.575           22.090 
[1] "4.0 - 54.6 (12.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3"  
D1589V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLGA1 MUTATED         1        0        1         1         1         0
  GOLGA1 WILD-TYPE      63        1       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLGA1 MUTATED           0          0          1          0        1
  GOLGA1 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  GOLGA1 MUTATED           0         1
  GOLGA1 WILD-TYPE        12         0
D1589V3, multiclass
            clus
vv           GOLGA1 MUTATED GOLGA1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               12
  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   4   2
  GOLGA1 WILD-TYPE   8  67 245  39
D1589V4, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              4              245
  T4              2               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
  GOLGA1 MUTATED     4   2   1
  GOLGA1 WILD-TYPE 216  79  65
D1589V5, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  N0              4              216
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1589V6, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     5   2
  GOLGA1 WILD-TYPE 280  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      5    2
  GOLGA1 WILD-TYPE  280   46
   clus
vv  GOLGA1 MUTATED GOLGA1 WILD-TYPE
  0              5              280
  1              2               46
[1] 2 2
[1] FALSE
D1589V7, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     3   4
  GOLGA1 WILD-TYPE 167 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      3    4
  GOLGA1 WILD-TYPE  167  193
        clus
vv       GOLGA1 MUTATED GOLGA1 WILD-TYPE
  FEMALE              3              167
  MALE                4              193
[1] 2 2
[1] FALSE
D1589V8, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     5   0
  GOLGA1 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      5    0
  GOLGA1 WILD-TYPE  295    8
     clus
vv    GOLGA1 MUTATED GOLGA1 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1589V9, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     5   2
  GOLGA1 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      5    2
  GOLGA1 WILD-TYPE  309   46
                               clus
vv                              GOLGA1 MUTATED GOLGA1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GOLGA1 MUTATED     6   0   0   0
  GOLGA1 WILD-TYPE 253   3  22  21
D1589V10, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              0               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"
D1589V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLGA1 MUTATED                                  0     0
  GOLGA1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GOLGA1 MUTATED                           2     1
  GOLGA1 WILD-TYPE                        17   175
D1589V12, multiclass
                                  clus
vv                                 GOLGA1 MUTATED GOLGA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         1              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(1590) Variable = ZHX2 MUTATION ANALYSIS
D1590V1, survival
                sevent
clus2              0   1
  ZHX2 MUTATED    14   1
  ZHX2 WILD-TYPE 263  77
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            15            340 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             1             77 
$`ZHX2 MUTATED`
TCGA-AA-3976 TCGA-AA-3979 TCGA-A6-2672 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 
       26.01        24.00        46.65        33.53         3.02        63.98 
TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 TCGA-AU-6004 
        6.97        25.02        38.04         0.99        34.98        27.09 
TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1HB 
       12.76        12.00       135.65 

$`ZHX2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
        2.01        50.99        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        79.69        43.76        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       42.02        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ZHX2 MUTATED ZHX2 WILD-TYPE 
          0.99           0.00 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
        135.65         148.01 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
         26.01          21.99 
[1] "1.0 - 135.7 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.6"
D1590V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZHX2 MUTATED         2        0        4         4         2         0
  ZHX2 WILD-TYPE      62        1       22       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX2 MUTATED           0          1          3          0        0         0
  ZHX2 WILD-TYPE        18          5         41         33       35        12
                vv
clus             STAGE IVB
  ZHX2 MUTATED           0
  ZHX2 WILD-TYPE         1
D1590V3, multiclass
            clus
vv           ZHX2 MUTATED ZHX2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             4            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            3             41
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ZHX2 MUTATED     0   4  10   3
  ZHX2 WILD-TYPE   9  63 239  38
D1590V4, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           10            239
  T4            3             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
  ZHX2 MUTATED    13   4   0
  ZHX2 WILD-TYPE 207  77  66
D1590V5, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  N0           13            207
  N1            4             77
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1590V6, binary
                cls
clus               0   1
  ZHX2 MUTATED    15   0
  ZHX2 WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     15    0
  ZHX2 WILD-TYPE  270   48
   clus
vv  ZHX2 MUTATED ZHX2 WILD-TYPE
  0           15            270
  1            0             48
[1] 2 2
[1] FALSE
D1590V7, binary
                cls
clus               0   1
  ZHX2 MUTATED     9   8
  ZHX2 WILD-TYPE 161 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED      9    8
  ZHX2 WILD-TYPE  161  189
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  FEMALE            9            161
  MALE              8            189
[1] 2 2
[1] FALSE
D1590V8, binary
                cls
clus               0   1
  ZHX2 MUTATED    12   0
  ZHX2 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     12    0
  ZHX2 WILD-TYPE  288    8
     clus
vv    ZHX2 MUTATED ZHX2 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1590V9, binary
                cls
clus               0   1
  ZHX2 MUTATED    14   2
  ZHX2 WILD-TYPE 300  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     14    2
  ZHX2 WILD-TYPE  300   46
                               clus
vv                              ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ZHX2 MUTATED    13   0   0   2
  ZHX2 WILD-TYPE 246   3  22  19
D1590V10, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            2             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"
D1590V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZHX2 MUTATED                                  0     1
  ZHX2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZHX2 MUTATED                           1     5
  ZHX2 WILD-TYPE                        18   171
D1590V12, multiclass
                                  clus
vv                                 ZHX2 MUTATED ZHX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = FAM167B MUTATION ANALYSIS
D1591V1, survival
                   sevent
clus2                 0   1
  FAM167B MUTATED     2   1
  FAM167B WILD-TYPE 275  77
  FAM167B MUTATED FAM167B WILD-TYPE 
                3               352 
  FAM167B MUTATED FAM167B WILD-TYPE 
                1                77 
$`FAM167B MUTATED`
TCGA-A6-6780 TCGA-CK-4952 TCGA-DM-A1D7 
       20.12        15.62        13.32 

$`FAM167B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
       10.06        14.30        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FAM167B MUTATED FAM167B WILD-TYPE 
            13.32              0.00 
  FAM167B MUTATED FAM167B WILD-TYPE 
            20.12            148.01 
  FAM167B MUTATED FAM167B WILD-TYPE 
            15.62             22.09 
[1] "13.3 - 20.1 (15.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1591V2, continuous
                   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      64        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM167B MUTATED           0          0          0          1        0
  FAM167B WILD-TYPE        18          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM167B MUTATED           0         0
  FAM167B WILD-TYPE        12         1
D1591V3, multiclass
            clus
vv           FAM167B MUTATED FAM167B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM167B MUTATED     0   0   3   1
  FAM167B WILD-TYPE   9  67 246  40
D1591V4, multiclass
    clus
vv   FAM167B MUTATED FAM167B WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               3               246
  T4               1                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
  FAM167B MUTATED     3   0   1
  FAM167B WILD-TYPE 217  81  65
D1591V5, multiclass
    clus
vv   FAM167B MUTATED FAM167B WILD-TYPE
  N0               3               217
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1591V6, binary
                   cls
clus                  0   1
  FAM167B MUTATED     3   0
  FAM167B WILD-TYPE 282  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      3    0
  FAM167B WILD-TYPE  282   48
   clus
vv  FAM167B MUTATED FAM167B WILD-TYPE
  0               3               282
  1               0                48
[1] 2 2
[1] FALSE
D1591V7, binary
                   cls
clus                  0   1
  FAM167B MUTATED     2   2
  FAM167B WILD-TYPE 168 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      2    2
  FAM167B WILD-TYPE  168  195
        clus
vv       FAM167B MUTATED FAM167B WILD-TYPE
  FEMALE               2               168
  MALE                 2               195
[1] 2 2
[1] FALSE
D1591V8, binary
                   cls
clus                  0   1
  FAM167B MUTATED     1   0
  FAM167B WILD-TYPE 299   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      1    0
  FAM167B WILD-TYPE  299    8
     clus
vv    FAM167B MUTATED FAM167B WILD-TYPE
  NO                1               299
  YES               0                 8
[1] 2 2
[1] FALSE
D1591V9, binary
                   cls
clus                  0   1
  FAM167B MUTATED     1   2
  FAM167B WILD-TYPE 313  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      1    2
  FAM167B WILD-TYPE  313   46
                               clus
vv                              FAM167B MUTATED FAM167B WILD-TYPE
  COLON ADENOCARCINOMA                        1               313
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM167B MUTATED     1   0   0   1
  FAM167B WILD-TYPE 258   3  22  20
D1591V10, multiclass
[1] "Remove cluster labels:" "FAM167B MUTATED"       
clus
  FAM167B MUTATED FAM167B WILD-TYPE 
                2               303 
       TCGA-A6-2677        TCGA-AA-3496        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-3527 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3543        TCGA-AA-3552 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3562 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3662        TCGA-AA-3672        TCGA-AA-3688        TCGA-AA-3692 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3814 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3860        TCGA-AA-3867        TCGA-AA-3870 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3972 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-A00L 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A024        TCGA-AD-6548        TCGA-AD-6888 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AD-6895        TCGA-AZ-4681        TCGA-CK-5912        TCGA-G4-6310 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-2676        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-3502        TCGA-AA-3510 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3526        TCGA-AA-3529        TCGA-AA-3532 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3544 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3553        TCGA-AA-3555 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3561        TCGA-AA-3655        TCGA-AA-3660 
"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-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3693 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3712 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3815        TCGA-AA-3818 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3842        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-3861        TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3955 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3973 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3975        TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00N        TCGA-AA-A00O 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"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-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6889 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4682        TCGA-CA-5254 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-5913 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6315 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
D1591V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM167B MUTATED                                  0     0
  FAM167B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM167B MUTATED                           0     3
  FAM167B WILD-TYPE                        19   173
D1591V12, multiclass
                                  clus
vv                                 FAM167B MUTATED FAM167B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = UFSP2 MUTATION ANALYSIS
D1592V1, survival
                 sevent
clus2               0   1
  UFSP2 MUTATED     2   2
  UFSP2 WILD-TYPE 275  76
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              4             351 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              2              76 
$`UFSP2 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A00N TCGA-AD-6889 
       63.98         6.97         4.01        83.24 

$`UFSP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  UFSP2 MUTATED UFSP2 WILD-TYPE 
           4.01            0.00 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
          83.24          148.01 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
         35.475          22.060 
[1] "4.0 - 83.2 (35.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1592V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UFSP2 MUTATED         0        0        2         1         1         0
  UFSP2 WILD-TYPE      64        1       24       107         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  UFSP2 MUTATED           0
  UFSP2 WILD-TYPE         1
D1592V3, multiclass
            clus
vv           UFSP2 MUTATED UFSP2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  UFSP2 MUTATED     0   0   3   1
  UFSP2 WILD-TYPE   9  67 246  40
D1592V4, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             1              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
  UFSP2 MUTATED     4   0   0
  UFSP2 WILD-TYPE 216  81  66
D1592V5, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1592V6, binary
                 cls
clus                0   1
  UFSP2 MUTATED     4   0
  UFSP2 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      4    0
  UFSP2 WILD-TYPE  281   48
   clus
vv  UFSP2 MUTATED UFSP2 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1592V7, binary
                 cls
clus                0   1
  UFSP2 MUTATED     0   4
  UFSP2 WILD-TYPE 170 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      0    4
  UFSP2 WILD-TYPE  170  193
        clus
vv       UFSP2 MUTATED UFSP2 WILD-TYPE
  FEMALE             0             170
  MALE               4             193
[1] 2 2
[1] FALSE
D1592V8, binary
                 cls
clus                0   1
  UFSP2 MUTATED     3   0
  UFSP2 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      3    0
  UFSP2 WILD-TYPE  297    8
     clus
vv    UFSP2 MUTATED UFSP2 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1592V9, binary
                 cls
clus                0   1
  UFSP2 MUTATED     3   1
  UFSP2 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      3    1
  UFSP2 WILD-TYPE  311   47
                               clus
vv                              UFSP2 MUTATED UFSP2 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UFSP2 MUTATED     4   0   0   0
  UFSP2 WILD-TYPE 255   3  22  21
D1592V10, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1592V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UFSP2 MUTATED                                  0     1
  UFSP2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UFSP2 MUTATED                           0     0
  UFSP2 WILD-TYPE                        19   176
D1592V12, multiclass
[1] "Remove cluster labels:" "UFSP2 MUTATED"         
clus
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              1             205 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6890      TCGA-AD-6899 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"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-5913      TCGA-CK-5914      TCGA-CK-5915 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6626 
"UFSP2 WILD-TYPE" 

Clustering(1593) Variable = BTBD11 MUTATION ANALYSIS
D1593V1, survival
                  sevent
clus2                0   1
  BTBD11 MUTATED    12   9
  BTBD11 WILD-TYPE 265  69
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              21              334 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               9               69 
$`BTBD11 MUTATED`
TCGA-AA-3525 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3952 TCGA-AZ-6601 TCGA-AZ-6608 
        8.05        19.04        19.04         2.01       100.01         1.94 
TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 
       42.90        20.12         3.02        63.98        29.95         6.97 
TCGA-AA-3811 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       10.06        25.02        58.39        12.76        10.06        21.14 
TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6674 
       23.05        15.02        12.95 

$`BTBD11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       19.00        36.00        85.05        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99        24.00        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       25.08        10.88       106.75        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.39        23.87        19.66        20.28         7.04        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
            1.94             0.00 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
          100.01           148.01 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           19.04            22.39 
[1] "1.9 - 100.0 (19.0)" "0.0 - 148.0 (22.4)"
[1] "hr=" "2.3"
D1593V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTBD11 MUTATED         2        0        5         8         1         0
  BTBD11 WILD-TYPE      62        1       21       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD11 MUTATED           1          1          1          1        1
  BTBD11 WILD-TYPE        17          5         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  BTBD11 MUTATED           0         0
  BTBD11 WILD-TYPE        12         1
D1593V3, multiclass
            clus
vv           BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  BTBD11 MUTATED     1   3  17   1
  BTBD11 WILD-TYPE   8  64 232  40
D1593V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             17              232
  T4              1               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
  BTBD11 MUTATED    18   2   2
  BTBD11 WILD-TYPE 202  79  64
D1593V5, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  N0             18              202
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1593V6, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    19   1
  BTBD11 WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     19    1
  BTBD11 WILD-TYPE  266   47
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D1593V7, binary
                  cls
clus                 0   1
  BTBD11 MUTATED     7  15
  BTBD11 WILD-TYPE 163 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      7   15
  BTBD11 WILD-TYPE  163  182
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE              7              163
  MALE               15              182
[1] 2 2
[1] FALSE
D1593V8, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    19   1
  BTBD11 WILD-TYPE 281   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     19    1
  BTBD11 WILD-TYPE  281    7
     clus
vv    BTBD11 MUTATED BTBD11 WILD-TYPE
  NO              19              281
  YES              1                7
[1] 2 2
[1] FALSE
D1593V9, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    19   3
  BTBD11 WILD-TYPE 295  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     19    3
  BTBD11 WILD-TYPE  295   45
                               clus
vv                              BTBD11 MUTATED BTBD11 WILD-TYPE
  COLON ADENOCARCINOMA                      19              295
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BTBD11 MUTATED    14   0   1   3
  BTBD11 WILD-TYPE 245   3  21  18
D1593V10, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              1               21
  RX              3               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"
D1593V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTBD11 MUTATED                                  0     2
  BTBD11 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BTBD11 MUTATED                           0     9
  BTBD11 WILD-TYPE                        19   167
D1593V12, multiclass
                                  clus
vv                                 BTBD11 MUTATED BTBD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         9              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(1594) Variable = BFAR MUTATION ANALYSIS
D1594V1, survival
                sevent
clus2              0   1
  BFAR MUTATED     7   1
  BFAR WILD-TYPE 270  77
  BFAR MUTATED BFAR WILD-TYPE 
             8            347 
  BFAR MUTATED BFAR WILD-TYPE 
             1             77 
$`BFAR MUTATED`
TCGA-AA-3672 TCGA-AZ-4681 TCGA-G4-6321 TCGA-AD-6963 TCGA-AU-6004 TCGA-CA-6717 
        0.92       106.75        22.09        27.42        27.09        12.76 
TCGA-CA-6718 TCGA-CK-4947 
       10.06        17.56 

$`BFAR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        22.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       12.20        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  BFAR MUTATED BFAR WILD-TYPE 
          0.92           0.00 
  BFAR MUTATED BFAR WILD-TYPE 
        106.75         148.01 
  BFAR MUTATED BFAR WILD-TYPE 
        19.825         22.060 
[1] "0.9 - 106.8 (19.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1594V2, continuous
                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      63        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BFAR MUTATED           2          0          1          0        0         0
  BFAR WILD-TYPE        16          6         43         33       35        12
                vv
clus             STAGE IVB
  BFAR MUTATED           0
  BFAR WILD-TYPE         1
D1594V3, multiclass
            clus
vv           BFAR MUTATED BFAR WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  BFAR MUTATED     0   2   5   1
  BFAR WILD-TYPE   9  65 244  40
D1594V4, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  T1            0              9
  T2            2             65
  T3            5            244
  T4            1             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
  BFAR MUTATED     5   3   0
  BFAR WILD-TYPE 215  78  66
D1594V5, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  N0            5            215
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1594V6, binary
                cls
clus               0   1
  BFAR MUTATED     6   0
  BFAR WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      6    0
  BFAR WILD-TYPE  279   48
   clus
vv  BFAR MUTATED BFAR WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1594V7, binary
                cls
clus               0   1
  BFAR MUTATED     5   3
  BFAR WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      5    3
  BFAR WILD-TYPE  165  194
        clus
vv       BFAR MUTATED BFAR WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D1594V8, binary
                cls
clus               0   1
  BFAR MUTATED     7   0
  BFAR WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      7    0
  BFAR WILD-TYPE  293    8
     clus
vv    BFAR MUTATED BFAR WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1594V9, binary
                cls
clus               0   1
  BFAR MUTATED     7   1
  BFAR WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      7    1
  BFAR WILD-TYPE  307   47
                               clus
vv                              BFAR MUTATED BFAR WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BFAR MUTATED     4   0   0   3
  BFAR WILD-TYPE 255   3  22  18
D1594V10, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            3             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"
D1594V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BFAR MUTATED                                  0     2
  BFAR WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BFAR MUTATED                           0     5
  BFAR WILD-TYPE                        19   171
D1594V12, multiclass
                                  clus
vv                                 BFAR MUTATED BFAR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = SBNO1 MUTATION ANALYSIS
D1595V1, survival
                 sevent
clus2               0   1
  SBNO1 MUTATED    13   2
  SBNO1 WILD-TYPE 264  76
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             15             340 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              2              76 
$`SBNO1 MUTATED`
TCGA-AA-3672 TCGA-AA-3688 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-6653 TCGA-A6-6781 
        0.92        19.00       100.01        26.17        24.39        19.66 
TCGA-AA-3864 TCGA-AA-A010 TCGA-AZ-5407 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 
       53.00        34.98        88.21        10.06        15.62        23.05 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 
       22.03        30.08        17.03 

$`SBNO1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SBNO1 MUTATED SBNO1 WILD-TYPE 
           0.92            0.00 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
         100.01          148.01 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
         23.050          22.025 
[1] "0.9 - 100.0 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1595V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SBNO1 MUTATED         2        0        2         4         1         0
  SBNO1 WILD-TYPE      62        1       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBNO1 MUTATED           1          0          1          2        1         1
  SBNO1 WILD-TYPE        17          6         43         31       34        11
                 vv
clus              STAGE IVB
  SBNO1 MUTATED           0
  SBNO1 WILD-TYPE         1
D1595V3, multiclass
            clus
vv           SBNO1 MUTATED SBNO1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  SBNO1 MUTATED     1   1   9   4
  SBNO1 WILD-TYPE   8  66 240  37
D1595V4, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             9             240
  T4             4              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
  SBNO1 MUTATED     9   5   1
  SBNO1 WILD-TYPE 211  76  65
D1595V5, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  N0             9             211
  N1             5              76
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1595V6, binary
                 cls
clus                0   1
  SBNO1 MUTATED    12   2
  SBNO1 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     12    2
  SBNO1 WILD-TYPE  273   46
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0            12             273
  1             2              46
[1] 2 2
[1] FALSE
D1595V7, binary
                 cls
clus                0   1
  SBNO1 MUTATED     8   7
  SBNO1 WILD-TYPE 162 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      8    7
  SBNO1 WILD-TYPE  162  190
        clus
vv       SBNO1 MUTATED SBNO1 WILD-TYPE
  FEMALE             8             162
  MALE               7             190
[1] 2 2
[1] FALSE
D1595V8, binary
                 cls
clus                0   1
  SBNO1 MUTATED    14   0
  SBNO1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     14    0
  SBNO1 WILD-TYPE  286    8
     clus
vv    SBNO1 MUTATED SBNO1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1595V9, binary
                 cls
clus                0   1
  SBNO1 MUTATED    13   2
  SBNO1 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     13    2
  SBNO1 WILD-TYPE  301   46
                               clus
vv                              SBNO1 MUTATED SBNO1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SBNO1 MUTATED     9   0   1   2
  SBNO1 WILD-TYPE 250   3  21  19
D1595V10, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             2              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"
D1595V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBNO1 MUTATED                                  0     1
  SBNO1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SBNO1 MUTATED                           0    10
  SBNO1 WILD-TYPE                        19   166
D1595V12, multiclass
                                  clus
vv                                 SBNO1 MUTATED SBNO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1596) Variable = MR1 MUTATION ANALYSIS
D1596V1, survival
               sevent
clus2             0   1
  MR1 MUTATED     4   1
  MR1 WILD-TYPE 273  77
  MR1 MUTATED MR1 WILD-TYPE 
            5           350 
  MR1 MUTATED MR1 WILD-TYPE 
            1            77 
$`MR1 MUTATED`
TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 
       20.28        63.98        25.02        12.76        10.06 

$`MR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        19.66         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  MR1 MUTATED MR1 WILD-TYPE 
        10.06          0.00 
  MR1 MUTATED MR1 WILD-TYPE 
        63.98        148.01 
  MR1 MUTATED MR1 WILD-TYPE 
       20.280        22.075 
[1] "10.1 - 64.0 (20.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1596V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MR1 MUTATED         0        0        1         2         1         0
  MR1 WILD-TYPE      64        1       25       106         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MR1 MUTATED           0          0          0          0        0         0
  MR1 WILD-TYPE        18          6         44         33       35        12
               vv
clus            STAGE IVB
  MR1 MUTATED           0
  MR1 WILD-TYPE         1
D1596V3, multiclass
            clus
vv           MR1 MUTATED MR1 WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            2           106
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  MR1 MUTATED     0   1   3   1
  MR1 WILD-TYPE   9  66 246  40
D1596V4, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  T1           0             9
  T2           1            66
  T3           3           246
  T4           1            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
  MR1 MUTATED     5   0   0
  MR1 WILD-TYPE 215  81  66
D1596V5, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  N0           5           215
  N1           0            81
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1596V6, binary
               cls
clus              0   1
  MR1 MUTATED     3   0
  MR1 WILD-TYPE 282  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      3    0
  MR1 WILD-TYPE  282   48
   clus
vv  MR1 MUTATED MR1 WILD-TYPE
  0           3           282
  1           0            48
[1] 2 2
[1] FALSE
D1596V7, binary
               cls
clus              0   1
  MR1 MUTATED     0   5
  MR1 WILD-TYPE 170 192
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      0    5
  MR1 WILD-TYPE  170  192
        clus
vv       MR1 MUTATED MR1 WILD-TYPE
  FEMALE           0           170
  MALE             5           192
[1] 2 2
[1] FALSE
D1596V8, binary
               cls
clus              0   1
  MR1 MUTATED     5   0
  MR1 WILD-TYPE 295   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      5    0
  MR1 WILD-TYPE  295    8
     clus
vv    MR1 MUTATED MR1 WILD-TYPE
  NO            5           295
  YES           0             8
[1] 2 2
[1] FALSE
D1596V9, binary
               cls
clus              0   1
  MR1 MUTATED     4   1
  MR1 WILD-TYPE 310  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      4    1
  MR1 WILD-TYPE  310   47
                               clus
vv                              MR1 MUTATED MR1 WILD-TYPE
  COLON ADENOCARCINOMA                    4           310
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MR1 MUTATED     1   0   0   2
  MR1 WILD-TYPE 258   3  22  19
D1596V10, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  R0           1           258
  R1           0             3
  R2           0            22
  RX           2            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"
D1596V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MR1 MUTATED                                  0     2
  MR1 WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MR1 MUTATED                           0     1
  MR1 WILD-TYPE                        19   175
D1596V12, multiclass
                                  clus
vv                                 MR1 MUTATED MR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      1           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(1597) Variable = OR5R1 MUTATION ANALYSIS
D1597V1, survival
                 sevent
clus2               0   1
  OR5R1 MUTATED     9   4
  OR5R1 WILD-TYPE 268  74
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             13             342 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
              4              74 
$`OR5R1 MUTATED`
TCGA-AA-3950 TCGA-AZ-4681 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3955 TCGA-AZ-6598 
       24.00       106.75        63.98         0.00        20.98        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        25.48        13.41         0.53 
TCGA-G4-6626 
       46.75 

$`OR5R1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  OR5R1 MUTATED OR5R1 WILD-TYPE 
              0               0 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
         106.75          148.01 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
         20.980          22.075 
[1] "0.0 - 106.8 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1597V2, continuous
                 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      63        1       24       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5R1 MUTATED           0          0          2          0        1         0
  OR5R1 WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  OR5R1 MUTATED           0
  OR5R1 WILD-TYPE         1
D1597V3, multiclass
            clus
vv           OR5R1 MUTATED OR5R1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  OR5R1 MUTATED     0   2  10   2
  OR5R1 WILD-TYPE   9  65 239  39
D1597V4, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             2              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
  OR5R1 MUTATED    11   2   1
  OR5R1 WILD-TYPE 209  79  65
D1597V5, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  N0            11             209
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1597V6, binary
                 cls
clus                0   1
  OR5R1 MUTATED    11   1
  OR5R1 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     11    1
  OR5R1 WILD-TYPE  274   47
   clus
vv  OR5R1 MUTATED OR5R1 WILD-TYPE
  0            11             274
  1             1              47
[1] 2 2
[1] FALSE
D1597V7, binary
                 cls
clus                0   1
  OR5R1 MUTATED     9   5
  OR5R1 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED      9    5
  OR5R1 WILD-TYPE  161  192
        clus
vv       OR5R1 MUTATED OR5R1 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D1597V8, binary
                 cls
clus                0   1
  OR5R1 MUTATED    12   0
  OR5R1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     12    0
  OR5R1 WILD-TYPE  288    8
     clus
vv    OR5R1 MUTATED OR5R1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1597V9, binary
                 cls
clus                0   1
  OR5R1 MUTATED    12   2
  OR5R1 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     12    2
  OR5R1 WILD-TYPE  302   46
                               clus
vv                              OR5R1 MUTATED OR5R1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5R1 MUTATED    10   0   0   2
  OR5R1 WILD-TYPE 249   3  22  19
D1597V10, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D1597V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5R1 MUTATED                                  0     1
  OR5R1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5R1 MUTATED                           0     8
  OR5R1 WILD-TYPE                        19   168
D1597V12, multiclass
                                  clus
vv                                 OR5R1 MUTATED OR5R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = RIMS2 MUTATION ANALYSIS
D1598V1, survival
                 sevent
clus2               0   1
  RIMS2 MUTATED    26   9
  RIMS2 WILD-TYPE 251  69
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             35             320 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
              9              69 
$`RIMS2 MUTATED`
TCGA-AA-3672 TCGA-AA-A024 TCGA-AD-6964 TCGA-G4-6588 TCGA-A6-5660 TCGA-A6-6141 
        0.92        39.06        10.88        26.17        29.19         8.38 
TCGA-AA-3680 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3930 TCGA-AA-3949 TCGA-AA-3977 
       11.01        25.02         1.02         2.01        26.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
        4.01        34.98        14.50        58.39        88.21        49.41 
TCGA-AZ-6600 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4952 
       12.10        12.59        12.76        10.06        17.56        15.62 
TCGA-CM-4747 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6541 
       25.02        12.95        25.48        15.12        16.14        15.58 
TCGA-D5-6928 TCGA-DM-A28G TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6323 
       11.64        60.79        55.04        85.48        13.78 

$`RIMS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        33.04         0.99        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       53.00        17.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        27.09        16.31         0.95        33.01         0.20 
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-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
       12.36        12.39        12.59        12.20        14.30       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6626 
       36.00        46.75 

  RIMS2 MUTATED RIMS2 WILD-TYPE 
           0.92            0.00 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
          88.21          148.01 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
         15.620          22.225 
[1] "0.9 - 88.2 (15.6)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D1598V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RIMS2 MUTATED         3        1        2        12         2         0
  RIMS2 WILD-TYPE      61        0       24        96         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIMS2 MUTATED           1          0          6          2        3         1
  RIMS2 WILD-TYPE        17          6         38         31       32        11
                 vv
clus              STAGE IVB
  RIMS2 MUTATED           0
  RIMS2 WILD-TYPE         1
D1598V3, multiclass
            clus
vv           RIMS2 MUTATED RIMS2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               2              24
  STAGE IIA             12              96
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              1              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
  RIMS2 MUTATED     1   3  22   9
  RIMS2 WILD-TYPE   8  64 227  32
D1598V4, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            22             227
  T4             9              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
  RIMS2 MUTATED    22   9   5
  RIMS2 WILD-TYPE 198  72  61
D1598V5, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  N0            22             198
  N1             9              72
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1598V6, binary
                 cls
clus                0   1
  RIMS2 MUTATED    27   4
  RIMS2 WILD-TYPE 258  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     27    4
  RIMS2 WILD-TYPE  258   44
   clus
vv  RIMS2 MUTATED RIMS2 WILD-TYPE
  0            27             258
  1             4              44
[1] 2 2
[1] FALSE
D1598V7, binary
                 cls
clus                0   1
  RIMS2 MUTATED    17  19
  RIMS2 WILD-TYPE 153 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     17   19
  RIMS2 WILD-TYPE  153  178
        clus
vv       RIMS2 MUTATED RIMS2 WILD-TYPE
  FEMALE            17             153
  MALE              19             178
[1] 2 2
[1] FALSE
D1598V8, binary
                 cls
clus                0   1
  RIMS2 MUTATED    32   0
  RIMS2 WILD-TYPE 268   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     32    0
  RIMS2 WILD-TYPE  268    8
     clus
vv    RIMS2 MUTATED RIMS2 WILD-TYPE
  NO             32             268
  YES             0               8
[1] 2 2
[1] FALSE
D1598V9, binary
                 cls
clus                0   1
  RIMS2 MUTATED    28   8
  RIMS2 WILD-TYPE 286  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     28    8
  RIMS2 WILD-TYPE  286   40
                               clus
vv                              RIMS2 MUTATED RIMS2 WILD-TYPE
  COLON ADENOCARCINOMA                     28             286
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RIMS2 MUTATED    20   0   2   6
  RIMS2 WILD-TYPE 239   3  20  15
D1598V10, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  R0            20             239
  R1             0               3
  R2             2              20
  RX             6              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"
D1598V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMS2 MUTATED                                  0     3
  RIMS2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RIMS2 MUTATED                           5    17
  RIMS2 WILD-TYPE                        14   159
D1598V12, multiclass
                                  clus
vv                                 RIMS2 MUTATED RIMS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    5              14
  WHITE                                       17             159
[1] 4 2
[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 = ZNF660 MUTATION ANALYSIS
D1599V1, survival
                  sevent
clus2                0   1
  ZNF660 MUTATED     5   2
  ZNF660 WILD-TYPE 272  76
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               7              348 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               2               76 
$`ZNF660 MUTATED`
TCGA-G4-6588 TCGA-AA-3510 TCGA-AA-3555 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5861 
       26.17        63.98        29.95        10.06        21.14        15.02 
TCGA-G4-6299 
       74.56 

$`ZNF660 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF660 MUTATED ZNF660 WILD-TYPE 
           10.06             0.00 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
           74.56           148.01 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
          26.170           22.045 
[1] "10.1 - 74.6 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1599V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF660 MUTATED         1        0        1         4         0         0
  ZNF660 WILD-TYPE      63        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF660 MUTATED           0          0          0          1        0
  ZNF660 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF660 MUTATED           0         0
  ZNF660 WILD-TYPE        12         1
D1599V3, multiclass
            clus
vv           ZNF660 MUTATED ZNF660 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF660 MUTATED     1   0   6   0
  ZNF660 WILD-TYPE   8  67 243  41
D1599V4, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              6              243
  T4              0               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
  ZNF660 MUTATED     6   0   1
  ZNF660 WILD-TYPE 214  81  65
D1599V5, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  N0              6              214
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1599V6, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     7   0
  ZNF660 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      7    0
  ZNF660 WILD-TYPE  278   48
   clus
vv  ZNF660 MUTATED ZNF660 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1599V7, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     4   3
  ZNF660 WILD-TYPE 166 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      4    3
  ZNF660 WILD-TYPE  166  194
        clus
vv       ZNF660 MUTATED ZNF660 WILD-TYPE
  FEMALE              4              166
  MALE                3              194
[1] 2 2
[1] FALSE
D1599V8, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     7   0
  ZNF660 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      7    0
  ZNF660 WILD-TYPE  293    8
     clus
vv    ZNF660 MUTATED ZNF660 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1599V9, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     6   1
  ZNF660 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      6    1
  ZNF660 WILD-TYPE  308   47
                               clus
vv                              ZNF660 MUTATED ZNF660 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF660 MUTATED     5   0   0   2
  ZNF660 WILD-TYPE 254   3  22  19
D1599V10, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D1599V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF660 MUTATED                                  0     1
  ZNF660 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF660 MUTATED                           0     4
  ZNF660 WILD-TYPE                        19   172
D1599V12, multiclass
                                  clus
vv                                 ZNF660 MUTATED ZNF660 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = GSS MUTATION ANALYSIS
D1600V1, survival
               sevent
clus2             0   1
  GSS MUTATED     5   2
  GSS WILD-TYPE 272  76
  GSS MUTATED GSS WILD-TYPE 
            7           348 
  GSS MUTATED GSS WILD-TYPE 
            2            76 
$`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 
       13.41 

$`GSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GSS MUTATED GSS WILD-TYPE 
         4.01          0.00 
  GSS MUTATED GSS WILD-TYPE 
        38.04        148.01 
  GSS MUTATED GSS WILD-TYPE 
        14.04         22.09 
[1] "4.0 - 38.0 (14.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1600V2, continuous
               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      63        1       25       106         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSS MUTATED           0          0          1          0        1         0
  GSS WILD-TYPE        18          6         43         33       34        12
               vv
clus            STAGE IVB
  GSS MUTATED           0
  GSS WILD-TYPE         1
D1600V3, multiclass
            clus
vv           GSS MUTATED GSS WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            2           106
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  GSS MUTATED     0   1   3   4
  GSS WILD-TYPE   9  66 246  37
D1600V4, multiclass
    clus
vv   GSS MUTATED GSS WILD-TYPE
  T1           0             9
  T2           1            66
  T3           3           246
  T4           4            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
  GSS MUTATED     6   2   0
  GSS WILD-TYPE 214  79  66
D1600V5, multiclass
    clus
vv   GSS MUTATED GSS WILD-TYPE
  N0           6           214
  N1           2            79
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1600V6, binary
               cls
clus              0   1
  GSS MUTATED     7   1
  GSS WILD-TYPE 278  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      7    1
  GSS WILD-TYPE  278   47
   clus
vv  GSS MUTATED GSS WILD-TYPE
  0           7           278
  1           1            47
[1] 2 2
[1] FALSE
D1600V7, binary
               cls
clus              0   1
  GSS MUTATED     5   3
  GSS WILD-TYPE 165 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      5    3
  GSS WILD-TYPE  165  194
        clus
vv       GSS MUTATED GSS WILD-TYPE
  FEMALE           5           165
  MALE             3           194
[1] 2 2
[1] FALSE
D1600V8, binary
               cls
clus              0   1
  GSS MUTATED     6   0
  GSS WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      6    0
  GSS WILD-TYPE  294    8
     clus
vv    GSS MUTATED GSS WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D1600V9, binary
               cls
clus              0   1
  GSS MUTATED     7   1
  GSS WILD-TYPE 307  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      7    1
  GSS WILD-TYPE  307   47
                               clus
vv                              GSS MUTATED GSS WILD-TYPE
  COLON ADENOCARCINOMA                    7           307
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  GSS MUTATED     7   0   0   0
  GSS WILD-TYPE 252   3  22  21
D1600V10, multiclass
    clus
vv   GSS MUTATED GSS WILD-TYPE
  R0           7           252
  R1           0             3
  R2           0            22
  RX           0            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"
D1600V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSS MUTATED                                  0     0
  GSS WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GSS MUTATED                           0     4
  GSS WILD-TYPE                        19   172
D1600V12, multiclass
                                  clus
vv                                 GSS MUTATED GSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      4           172
[1] 4 2
[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 = SLC38A9 MUTATION ANALYSIS
D1601V1, survival
                   sevent
clus2                 0   1
  SLC38A9 MUTATED     9   1
  SLC38A9 WILD-TYPE 268  77
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               10               345 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
                1                77 
$`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 
       10.06        23.05        37.02        11.64 

$`SLC38A9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
             6.97              0.00 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
            58.39            148.01 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
            25.07             21.99 
[1] "7.0 - 58.4 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D1601V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC38A9 MUTATED         2        0        2         7         0         0
  SLC38A9 WILD-TYPE      62        1       24       101         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A9 MUTATED           0          0          0          0        0
  SLC38A9 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC38A9 MUTATED           0         0
  SLC38A9 WILD-TYPE        12         1
D1601V3, multiclass
            clus
vv           SLC38A9 MUTATED SLC38A9 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                7               101
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC38A9 MUTATED     0   2   9   0
  SLC38A9 WILD-TYPE   9  65 240  41
D1601V4, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               9               240
  T4               0                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
  SLC38A9 MUTATED    11   0   0
  SLC38A9 WILD-TYPE 209  81  66
D1601V5, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  N0              11               209
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1601V6, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    11   0
  SLC38A9 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     11    0
  SLC38A9 WILD-TYPE  274   48
   clus
vv  SLC38A9 MUTATED SLC38A9 WILD-TYPE
  0              11               274
  1               0                48
[1] 2 2
[1] FALSE
D1601V7, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED     4   7
  SLC38A9 WILD-TYPE 166 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED      4    7
  SLC38A9 WILD-TYPE  166  190
        clus
vv       SLC38A9 MUTATED SLC38A9 WILD-TYPE
  FEMALE               4               166
  MALE                 7               190
[1] 2 2
[1] FALSE
D1601V8, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED     9   0
  SLC38A9 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED      9    0
  SLC38A9 WILD-TYPE  291    8
     clus
vv    SLC38A9 MUTATED SLC38A9 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D1601V9, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    10   1
  SLC38A9 WILD-TYPE 304  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     10    1
  SLC38A9 WILD-TYPE  304   47
                               clus
vv                              SLC38A9 MUTATED SLC38A9 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC38A9 MUTATED    10   0   0   1
  SLC38A9 WILD-TYPE 249   3  22  20
D1601V10, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               1                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"
D1601V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC38A9 MUTATED                                  0     1
  SLC38A9 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC38A9 MUTATED                           1     5
  SLC38A9 WILD-TYPE                        18   171
D1601V12, multiclass
                                  clus
vv                                 SLC38A9 MUTATED SLC38A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = VPS72 MUTATION ANALYSIS
D1602V1, survival
                 sevent
clus2               0   1
  VPS72 MUTATED     8   0
  VPS72 WILD-TYPE 269  78
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             347 
  VPS72 MUTATED VPS72 WILD-TYPE 
              0              78 
$`VPS72 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AD-5900 TCGA-CM-5348 TCGA-CM-6171 TCGA-D5-6927 
       22.06        53.00        12.16        22.98        14.04         9.44 
TCGA-D5-6931 TCGA-G4-6309 
       12.00        85.48 

$`VPS72 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  VPS72 MUTATED VPS72 WILD-TYPE 
           9.44            0.00 
  VPS72 MUTATED VPS72 WILD-TYPE 
          85.48          148.01 
  VPS72 MUTATED VPS72 WILD-TYPE 
          18.05           22.09 
[1] "9.4 - 85.5 (18.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D1602V2, continuous
                 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      62        1       25       106         8         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        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  VPS72 MUTATED           0
  VPS72 WILD-TYPE         1
D1602V3, multiclass
            clus
vv           VPS72 MUTATED VPS72 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  VPS72 MUTATED     0   2   5   1
  VPS72 WILD-TYPE   9  65 244  40
D1602V4, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             5             244
  T4             1              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
  VPS72 MUTATED     5   2   1
  VPS72 WILD-TYPE 215  79  65
D1602V5, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1602V6, binary
                 cls
clus                0   1
  VPS72 MUTATED     7   0
  VPS72 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      7    0
  VPS72 WILD-TYPE  278   48
   clus
vv  VPS72 MUTATED VPS72 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1602V7, binary
                 cls
clus                0   1
  VPS72 MUTATED     3   5
  VPS72 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      3    5
  VPS72 WILD-TYPE  167  192
        clus
vv       VPS72 MUTATED VPS72 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D1602V8, binary
                 cls
clus                0   1
  VPS72 MUTATED     8   0
  VPS72 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      8    0
  VPS72 WILD-TYPE  292    8
     clus
vv    VPS72 MUTATED VPS72 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1602V9, binary
                 cls
clus                0   1
  VPS72 MUTATED     7   1
  VPS72 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      7    1
  VPS72 WILD-TYPE  307   47
                               clus
vv                              VPS72 MUTATED VPS72 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VPS72 MUTATED     8   0   0   0
  VPS72 WILD-TYPE 251   3  22  21
D1602V10, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1602V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS72 MUTATED                                  0     0
  VPS72 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VPS72 MUTATED                           1     6
  VPS72 WILD-TYPE                        18   170
D1602V12, multiclass
                                  clus
vv                                 VPS72 MUTATED VPS72 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = LCK MUTATION ANALYSIS
D1603V1, survival
               sevent
clus2             0   1
  LCK MUTATED     6   1
  LCK WILD-TYPE 271  77
  LCK MUTATED LCK WILD-TYPE 
            7           348 
  LCK MUTATED LCK WILD-TYPE 
            1            77 
$`LCK MUTATED`
TCGA-A6-2676 TCGA-A6-6781 TCGA-AY-6197 TCGA-CM-6678 TCGA-CM-6680 TCGA-DM-A1D9 
       42.90        19.66        21.44        11.01        12.03       140.38 
TCGA-F4-6703 
       47.87 

$`LCK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  LCK MUTATED LCK WILD-TYPE 
        11.01          0.00 
  LCK MUTATED LCK WILD-TYPE 
       140.38        148.01 
  LCK MUTATED LCK WILD-TYPE 
       21.440        22.075 
[1] "11.0 - 140.4 (21.4)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "2.1"
D1603V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LCK MUTATED         0        0        0         4         1         0
  LCK WILD-TYPE      64        1       26       104         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LCK MUTATED           0          0          1          1        0         1
  LCK WILD-TYPE        18          6         43         32       35        11
               vv
clus            STAGE IVB
  LCK MUTATED           0
  LCK WILD-TYPE         1
D1603V3, multiclass
            clus
vv           LCK MUTATED LCK WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            4           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            1            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
  LCK MUTATED     0   0   5   3
  LCK WILD-TYPE   9  67 244  38
D1603V4, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  T1           0             9
  T2           0            67
  T3           5           244
  T4           3            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
  LCK MUTATED     5   2   1
  LCK WILD-TYPE 215  79  65
D1603V5, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  N0           5           215
  N1           2            79
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1603V6, binary
               cls
clus              0   1
  LCK MUTATED     5   1
  LCK WILD-TYPE 280  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      5    1
  LCK WILD-TYPE  280   47
   clus
vv  LCK MUTATED LCK WILD-TYPE
  0           5           280
  1           1            47
[1] 2 2
[1] FALSE
D1603V7, binary
               cls
clus              0   1
  LCK MUTATED     5   3
  LCK WILD-TYPE 165 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      5    3
  LCK WILD-TYPE  165  194
        clus
vv       LCK MUTATED LCK WILD-TYPE
  FEMALE           5           165
  MALE             3           194
[1] 2 2
[1] FALSE
D1603V8, binary
               cls
clus              0   1
  LCK MUTATED     6   0
  LCK WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      6    0
  LCK WILD-TYPE  294    8
     clus
vv    LCK MUTATED LCK WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D1603V9, binary
               cls
clus              0   1
  LCK MUTATED     7   1
  LCK WILD-TYPE 307  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      7    1
  LCK WILD-TYPE  307   47
                               clus
vv                              LCK MUTATED LCK WILD-TYPE
  COLON ADENOCARCINOMA                    7           307
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  LCK MUTATED     7   0   0   0
  LCK WILD-TYPE 252   3  22  21
D1603V10, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  R0           7           252
  R1           0             3
  R2           0            22
  RX           0            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"
D1603V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCK MUTATED                                  0     0
  LCK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LCK MUTATED                           0     7
  LCK WILD-TYPE                        19   169
D1603V12, multiclass
                                  clus
vv                                 LCK MUTATED LCK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      7           169
[1] 4 2
[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 = AGTPBP1 MUTATION ANALYSIS
D1604V1, survival
                   sevent
clus2                 0   1
  AGTPBP1 MUTATED    13   3
  AGTPBP1 WILD-TYPE 264  75
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               16               339 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
                3                75 
$`AGTPBP1 MUTATED`
TCGA-A6-6649 TCGA-AD-6964 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6780 
       24.16        10.88        33.53        23.61        32.71        20.12 
TCGA-AA-3510 TCGA-AA-A00J TCGA-AA-A02J TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
       63.98        18.05         5.03        21.44        58.39        12.76 
TCGA-CM-5349 TCGA-D5-6534 TCGA-DM-A1HA TCGA-F4-6570 
       30.08        43.27       131.51         6.18 

$`AGTPBP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        29.19        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-A6-6781 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
             5.03              0.00 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
           131.51            148.01 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
           23.885            22.030 
[1] "5.0 - 131.5 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1604V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGTPBP1 MUTATED         0        0        2         8         0         1
  AGTPBP1 WILD-TYPE      64        1       24       100         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGTPBP1 MUTATED           0          0          2          1        1
  AGTPBP1 WILD-TYPE        18          6         42         32       34
                   vv
clus                STAGE IVA STAGE IVB
  AGTPBP1 MUTATED           1         0
  AGTPBP1 WILD-TYPE        11         1
D1604V3, multiclass
            clus
vv           AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                8               100
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                1                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
  AGTPBP1 MUTATED     0   0  13   4
  AGTPBP1 WILD-TYPE   9  67 236  37
D1604V4, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3              13               236
  T4               4                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
  AGTPBP1 MUTATED    12   2   3
  AGTPBP1 WILD-TYPE 208  79  63
D1604V5, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  N0              12               208
  N1               2                79
  N2               3                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"
D1604V6, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    12   2
  AGTPBP1 WILD-TYPE 273  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     12    2
  AGTPBP1 WILD-TYPE  273   46
   clus
vv  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  0              12               273
  1               2                46
[1] 2 2
[1] FALSE
D1604V7, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED     6  11
  AGTPBP1 WILD-TYPE 164 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED      6   11
  AGTPBP1 WILD-TYPE  164  186
        clus
vv       AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  FEMALE               6               164
  MALE                11               186
[1] 2 2
[1] FALSE
D1604V8, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    14   0
  AGTPBP1 WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     14    0
  AGTPBP1 WILD-TYPE  286    8
     clus
vv    AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D1604V9, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    13   4
  AGTPBP1 WILD-TYPE 301  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     13    4
  AGTPBP1 WILD-TYPE  301   44
                               clus
vv                              AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  AGTPBP1 MUTATED     9   0   1   1
  AGTPBP1 WILD-TYPE 250   3  21  20
D1604V10, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               1                21
  RX               1                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"
D1604V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGTPBP1 MUTATED                                  0     1
  AGTPBP1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AGTPBP1 MUTATED                           1    11
  AGTPBP1 WILD-TYPE                        18   165
D1604V12, multiclass
                                  clus
vv                                 AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               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(1605) Variable = GRIN2A MUTATION ANALYSIS
D1605V1, survival
                  sevent
clus2                0   1
  GRIN2A MUTATED    31   9
  GRIN2A WILD-TYPE 246  69
  GRIN2A MUTATED GRIN2A WILD-TYPE 
              40              315 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
               9               69 
$`GRIN2A MUTATED`
TCGA-AA-3530 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-A00L 
       19.07         6.05         0.92        19.00        19.04        38.04 
TCGA-AZ-4681 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5664 TCGA-AA-3510 
      106.75        35.80        26.17        79.69        22.09        63.98 
TCGA-AA-3833 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A00E TCGA-AA-A00N 
       15.95        13.05        25.02        27.02        30.02         4.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AD-6889 TCGA-AY-6386 
       34.98        38.07         1.02        35.01        83.24        17.82 
TCGA-AZ-5403 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5344 
       62.79        12.20        12.76        10.06        15.62        22.03 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6537 
       16.04        13.02        11.01        19.59        18.25         4.80 
TCGA-D5-6928 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-G4-6626 
       11.64        44.32       135.65        46.75 

$`GRIN2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3697 
       17.95        23.01        19.99        19.99        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-5665 
       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-A6-6142 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 
       34.03         2.01        21.99        16.08        34.06        27.02 
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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13        22.36        88.21        49.41         6.77 
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-6719 TCGA-CK-4947 
       12.36        12.39        12.59        12.59        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        29.03        21.99        14.99        12.99        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-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       20.19        25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.50       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  GRIN2A MUTATED GRIN2A WILD-TYPE 
            0.92             0.00 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
          135.65           148.01 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
           19.33            22.36 
[1] "0.9 - 135.7 (19.3)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1"  
D1605V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRIN2A MUTATED         2        0        4        16         3         0
  GRIN2A WILD-TYPE      62        1       22        92         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRIN2A MUTATED           3          1          6          2        3
  GRIN2A WILD-TYPE        15          5         38         31       32
                  vv
clus               STAGE IVA STAGE IVB
  GRIN2A MUTATED           0         0
  GRIN2A WILD-TYPE        12         1
D1605V3, multiclass
            clus
vv           GRIN2A MUTATED GRIN2A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA              16               92
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               3               15
  STAGE IIIA              1                5
  STAGE IIIB              6               38
  STAGE IIIC              2               31
  STAGE IV                3               32
  STAGE IVA               0               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
  GRIN2A MUTATED     0   3  31   7
  GRIN2A WILD-TYPE   9  64 218  34
D1605V4, multiclass
    clus
vv   GRIN2A MUTATED GRIN2A WILD-TYPE
  T1              0                9
  T2              3               64
  T3             31              218
  T4              7               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
  GRIN2A MUTATED    26  11   4
  GRIN2A WILD-TYPE 194  70  62
D1605V5, multiclass
    clus
vv   GRIN2A MUTATED GRIN2A WILD-TYPE
  N0             26              194
  N1             11               70
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1605V6, binary
                  cls
clus                 0   1
  GRIN2A MUTATED    33   3
  GRIN2A WILD-TYPE 252  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2A MUTATED     33    3
  GRIN2A WILD-TYPE  252   45
   clus
vv  GRIN2A MUTATED GRIN2A WILD-TYPE
  0             33              252
  1              3               45
[1] 2 2
[1] FALSE
D1605V7, binary
                  cls
clus                 0   1
  GRIN2A MUTATED    14  27
  GRIN2A WILD-TYPE 156 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2A MUTATED     14   27
  GRIN2A WILD-TYPE  156  170
        clus
vv       GRIN2A MUTATED GRIN2A WILD-TYPE
  FEMALE             14              156
  MALE               27              170
[1] 2 2
[1] FALSE
D1605V8, binary
                  cls
clus                 0   1
  GRIN2A MUTATED    34   1
  GRIN2A WILD-TYPE 266   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2A MUTATED     34    1
  GRIN2A WILD-TYPE  266    7
     clus
vv    GRIN2A MUTATED GRIN2A WILD-TYPE
  NO              34              266
  YES              1                7
[1] 2 2
[1] FALSE
D1605V9, binary
                  cls
clus                 0   1
  GRIN2A MUTATED    34   6
  GRIN2A WILD-TYPE 280  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2A MUTATED     34    6
  GRIN2A WILD-TYPE  280   42
                               clus
vv                              GRIN2A MUTATED GRIN2A WILD-TYPE
  COLON ADENOCARCINOMA                      34              280
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GRIN2A MUTATED    27   0   3   5
  GRIN2A WILD-TYPE 232   3  19  16
D1605V10, multiclass
    clus
vv   GRIN2A MUTATED GRIN2A WILD-TYPE
  R0             27              232
  R1              0                3
  R2              3               19
  RX              5               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"
D1605V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRIN2A MUTATED                                  0     4
  GRIN2A WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GRIN2A MUTATED                           3    17
  GRIN2A WILD-TYPE                        16   159
D1605V12, multiclass
                                  clus
vv                                 GRIN2A MUTATED GRIN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                     3               16
  WHITE                                        17              159
[1] 4 2
[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 = FGD1 MUTATION ANALYSIS
D1606V1, survival
                sevent
clus2              0   1
  FGD1 MUTATED     9   7
  FGD1 WILD-TYPE 268  71
  FGD1 MUTATED FGD1 WILD-TYPE 
            16            339 
  FGD1 MUTATED FGD1 WILD-TYPE 
             7             71 
$`FGD1 MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-AA-3492 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3947 
      100.01        35.80         3.02        50.04        10.06        33.01 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5913 
       17.03        15.02        12.16        83.24        27.09        51.32 
TCGA-CK-5916 TCGA-D5-6539 TCGA-F4-6459 TCGA-F4-6570 
       21.14        12.49         8.61         6.18 

$`FGD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       18.05         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       85.45        15.62        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6460 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FGD1 MUTATED FGD1 WILD-TYPE 
          3.02           0.00 
  FGD1 MUTATED FGD1 WILD-TYPE 
        100.01         148.01 
  FGD1 MUTATED FGD1 WILD-TYPE 
        19.085         22.090 
[1] "3.0 - 100.0 (19.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1606V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGD1 MUTATED         3        0        3         5         1         0
  FGD1 WILD-TYPE      61        1       23       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGD1 MUTATED           1          0          2          0        0         0
  FGD1 WILD-TYPE        17          6         42         33       35        12
                vv
clus             STAGE IVB
  FGD1 MUTATED           0
  FGD1 WILD-TYPE         1
D1606V3, multiclass
            clus
vv           FGD1 MUTATED FGD1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  FGD1 MUTATED     1   2  12   1
  FGD1 WILD-TYPE   8  65 237  40
D1606V4, multiclass
    clus
vv   FGD1 MUTATED FGD1 WILD-TYPE
  T1            1              8
  T2            2             65
  T3           12            237
  T4            1             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
  FGD1 MUTATED    13   1   2
  FGD1 WILD-TYPE 207  80  64
D1606V5, multiclass
    clus
vv   FGD1 MUTATED FGD1 WILD-TYPE
  N0           13            207
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1606V6, binary
                cls
clus               0   1
  FGD1 MUTATED    14   0
  FGD1 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD1 MUTATED     14    0
  FGD1 WILD-TYPE  271   48
   clus
vv  FGD1 MUTATED FGD1 WILD-TYPE
  0           14            271
  1            0             48
[1] 2 2
[1] FALSE
D1606V7, binary
                cls
clus               0   1
  FGD1 MUTATED    12   4
  FGD1 WILD-TYPE 158 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD1 MUTATED     12    4
  FGD1 WILD-TYPE  158  193
        clus
vv       FGD1 MUTATED FGD1 WILD-TYPE
  FEMALE           12            158
  MALE              4            193
[1] 2 2
[1] FALSE
D1606V8, binary
                cls
clus               0   1
  FGD1 MUTATED    15   0
  FGD1 WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD1 MUTATED     15    0
  FGD1 WILD-TYPE  285    8
     clus
vv    FGD1 MUTATED FGD1 WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D1606V9, binary
                cls
clus               0   1
  FGD1 MUTATED    14   2
  FGD1 WILD-TYPE 300  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD1 MUTATED     14    2
  FGD1 WILD-TYPE  300   46
                               clus
vv                              FGD1 MUTATED FGD1 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FGD1 MUTATED    13   0   0   2
  FGD1 WILD-TYPE 246   3  22  19
D1606V10, multiclass
    clus
vv   FGD1 MUTATED FGD1 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            2             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"
D1606V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGD1 MUTATED                                  0     1
  FGD1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FGD1 MUTATED                           0     9
  FGD1 WILD-TYPE                        19   167
D1606V12, multiclass
                                  clus
vv                                 FGD1 MUTATED FGD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(1607) Variable = ZNF286A MUTATION ANALYSIS
D1607V1, survival
                   sevent
clus2                 0   1
  ZNF286A MUTATED     5   1
  ZNF286A WILD-TYPE 272  77
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                6               349 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                1                77 
$`ZNF286A MUTATED`
TCGA-AZ-6601 TCGA-A6-6141 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 
      100.01         8.38        34.98        12.16        58.39        12.76 

$`ZNF286A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ZNF286A MUTATED ZNF286A WILD-TYPE 
             8.38              0.00 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
           100.01            148.01 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
            23.87             22.06 
[1] "8.4 - 100.0 (23.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1607V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF286A MUTATED         1        0        1         4         1         0
  ZNF286A WILD-TYPE      63        1       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF286A MUTATED           0          0          0          0        0
  ZNF286A WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF286A MUTATED           0         0
  ZNF286A WILD-TYPE        12         1
D1607V3, multiclass
            clus
vv           ZNF286A MUTATED ZNF286A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                4               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ZNF286A MUTATED     0   1   5   1
  ZNF286A WILD-TYPE   9  66 244  40
D1607V4, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               5               244
  T4               1                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
  ZNF286A MUTATED     7   0   0
  ZNF286A WILD-TYPE 213  81  66
D1607V5, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  N0               7               213
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1607V6, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     6   0
  ZNF286A WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      6    0
  ZNF286A WILD-TYPE  279   48
   clus
vv  ZNF286A MUTATED ZNF286A WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1607V7, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     2   5
  ZNF286A WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      2    5
  ZNF286A WILD-TYPE  168  192
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D1607V8, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     6   0
  ZNF286A WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      6    0
  ZNF286A WILD-TYPE  294    8
     clus
vv    ZNF286A MUTATED ZNF286A WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1607V9, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     5   2
  ZNF286A WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      5    2
  ZNF286A WILD-TYPE  309   46
                               clus
vv                              ZNF286A MUTATED ZNF286A WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF286A MUTATED     4   0   0   1
  ZNF286A WILD-TYPE 255   3  22  20
D1607V10, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               1                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"
D1607V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF286A MUTATED                                  0     1
  ZNF286A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF286A MUTATED                           1     3
  ZNF286A WILD-TYPE                        18   173
D1607V12, multiclass
                                  clus
vv                                 ZNF286A MUTATED ZNF286A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               173
[1] 4 2
[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 = BRCA1 MUTATION ANALYSIS
D1608V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED    16   9
  BRCA1 WILD-TYPE 261  69
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             25             330 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              9              69 
$`BRCA1 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-A6-3809 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 
        1.02        19.04        32.75        20.28         3.02        63.98 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6599 
       25.02        30.02        34.98        83.24        49.41         6.77 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-5862 TCGA-CM-5864 
       12.59        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 
       36.00 

$`BRCA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.12        19.66         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       12.69        12.36        12.39        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56        85.45        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        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 
       14.04        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-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        61.91        13.78        46.75 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           1.02            0.00 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         148.01          140.38 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         20.280          22.075 
[1] "1.0 - 148.0 (20.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.4"
D1608V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRCA1 MUTATED         3        0        5         9         3         0
  BRCA1 WILD-TYPE      61        1       21        99         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA1 MUTATED           1          0          1          2        0         1
  BRCA1 WILD-TYPE        17          6         43         31       35        11
                 vv
clus              STAGE IVB
  BRCA1 MUTATED           0
  BRCA1 WILD-TYPE         1
D1608V3, multiclass
            clus
vv           BRCA1 MUTATED BRCA1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA              9              99
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              1              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
  BRCA1 MUTATED     0   4  18   4
  BRCA1 WILD-TYPE   9  63 231  37
D1608V4, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            18             231
  T4             4              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
  BRCA1 MUTATED    20   3   3
  BRCA1 WILD-TYPE 200  78  63
D1608V5, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  N0            20             200
  N1             3              78
  N2             3              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"
D1608V6, binary
                 cls
clus                0   1
  BRCA1 MUTATED    19   1
  BRCA1 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     19    1
  BRCA1 WILD-TYPE  266   47
   clus
vv  BRCA1 MUTATED BRCA1 WILD-TYPE
  0            19             266
  1             1              47
[1] 2 2
[1] FALSE
D1608V7, binary
                 cls
clus                0   1
  BRCA1 MUTATED    11  15
  BRCA1 WILD-TYPE 159 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     11   15
  BRCA1 WILD-TYPE  159  182
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  FEMALE            11             159
  MALE              15             182
[1] 2 2
[1] FALSE
D1608V8, binary
                 cls
clus                0   1
  BRCA1 MUTATED    21   0
  BRCA1 WILD-TYPE 279   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     21    0
  BRCA1 WILD-TYPE  279    8
     clus
vv    BRCA1 MUTATED BRCA1 WILD-TYPE
  NO             21             279
  YES             0               8
[1] 2 2
[1] FALSE
D1608V9, binary
                 cls
clus                0   1
  BRCA1 MUTATED    20   5
  BRCA1 WILD-TYPE 294  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     20    5
  BRCA1 WILD-TYPE  294   43
                               clus
vv                              BRCA1 MUTATED BRCA1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRCA1 MUTATED    17   0   0   3
  BRCA1 WILD-TYPE 242   3  22  18
D1608V10, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  R0            17             242
  R1             0               3
  R2             0              22
  RX             3              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"
D1608V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA1 MUTATED                                  0     3
  BRCA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA1 MUTATED                           0    15
  BRCA1 WILD-TYPE                        19   161
D1608V12, multiclass
                                  clus
vv                                 BRCA1 MUTATED BRCA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       15             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(1609) Variable = AOX1 MUTATION ANALYSIS
D1609V1, survival
                sevent
clus2              0   1
  AOX1 MUTATED     9   3
  AOX1 WILD-TYPE 268  75
  AOX1 MUTATED AOX1 WILD-TYPE 
            12            343 
  AOX1 MUTATED AOX1 WILD-TYPE 
             3             75 
$`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 
       83.24        27.09        12.76        21.14        15.02        35.97 

$`AOX1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       31.07        30.05        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  AOX1 MUTATED AOX1 WILD-TYPE 
          2.01           0.00 
  AOX1 MUTATED AOX1 WILD-TYPE 
         83.24         148.01 
  AOX1 MUTATED AOX1 WILD-TYPE 
        26.055         21.990 
[1] "2.0 - 83.2 (26.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1609V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AOX1 MUTATED         4        0        1         4         1         0
  AOX1 WILD-TYPE      60        1       25       104         7         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  AOX1 MUTATED           0
  AOX1 WILD-TYPE         1
D1609V3, multiclass
            clus
vv           AOX1 MUTATED AOX1 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  AOX1 MUTATED     2   3   6   1
  AOX1 WILD-TYPE   7  64 243  40
D1609V4, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  T1            2              7
  T2            3             64
  T3            6            243
  T4            1             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
  AOX1 MUTATED    11   1   0
  AOX1 WILD-TYPE 209  80  66
D1609V5, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  N0           11            209
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1609V6, binary
                cls
clus               0   1
  AOX1 MUTATED    11   0
  AOX1 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED     11    0
  AOX1 WILD-TYPE  274   48
   clus
vv  AOX1 MUTATED AOX1 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D1609V7, binary
                cls
clus               0   1
  AOX1 MUTATED     7   5
  AOX1 WILD-TYPE 163 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      7    5
  AOX1 WILD-TYPE  163  192
        clus
vv       AOX1 MUTATED AOX1 WILD-TYPE
  FEMALE            7            163
  MALE              5            192
[1] 2 2
[1] FALSE
D1609V8, binary
                cls
clus               0   1
  AOX1 MUTATED     9   0
  AOX1 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      9    0
  AOX1 WILD-TYPE  291    8
     clus
vv    AOX1 MUTATED AOX1 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1609V9, binary
                cls
clus               0   1
  AOX1 MUTATED     8   4
  AOX1 WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      8    4
  AOX1 WILD-TYPE  306   44
                               clus
vv                              AOX1 MUTATED AOX1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AOX1 MUTATED     7   0   0   2
  AOX1 WILD-TYPE 252   3  22  19
D1609V10, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            2             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"
D1609V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AOX1 MUTATED                                  0     2
  AOX1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AOX1 MUTATED                           0     5
  AOX1 WILD-TYPE                        19   171
D1609V12, multiclass
                                  clus
vv                                 AOX1 MUTATED AOX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1610) Variable = ZNF323 MUTATION ANALYSIS
D1610V1, survival
                  sevent
clus2                0   1
  ZNF323 MUTATED     9   1
  ZNF323 WILD-TYPE 268  77
  ZNF323 MUTATED ZNF323 WILD-TYPE 
              10              345 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
               1               77 
$`ZNF323 MUTATED`
TCGA-G4-6628 TCGA-A6-3809 TCGA-AA-3502 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A02O 
       79.69        32.75        35.01         6.97        34.98         0.92 
TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-5541 TCGA-D5-6533 
       10.06        51.32        55.92        25.48 

$`ZNF323 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF323 MUTATED ZNF323 WILD-TYPE 
            0.92             0.00 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
           79.69           148.01 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
          33.865           21.990 
[1] "0.9 - 79.7 (33.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D1610V2, continuous
                  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      62        1       24       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF323 MUTATED           0          0          1          0        0
  ZNF323 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF323 MUTATED           0         0
  ZNF323 WILD-TYPE        12         1
D1610V3, multiclass
            clus
vv           ZNF323 MUTATED ZNF323 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF323 MUTATED     0   2   5   3
  ZNF323 WILD-TYPE   9  65 244  38
D1610V4, multiclass
    clus
vv   ZNF323 MUTATED ZNF323 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              3               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
  ZNF323 MUTATED     9   1   0
  ZNF323 WILD-TYPE 211  80  66
D1610V5, multiclass
    clus
vv   ZNF323 MUTATED ZNF323 WILD-TYPE
  N0              9              211
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1610V6, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     9   0
  ZNF323 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      9    0
  ZNF323 WILD-TYPE  276   48
   clus
vv  ZNF323 MUTATED ZNF323 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1610V7, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     4   6
  ZNF323 WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      4    6
  ZNF323 WILD-TYPE  166  191
        clus
vv       ZNF323 MUTATED ZNF323 WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D1610V8, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     9   0
  ZNF323 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      9    0
  ZNF323 WILD-TYPE  291    8
     clus
vv    ZNF323 MUTATED ZNF323 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1610V9, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     9   1
  ZNF323 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      9    1
  ZNF323 WILD-TYPE  305   47
                               clus
vv                              ZNF323 MUTATED ZNF323 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF323 MUTATED     8   0   0   2
  ZNF323 WILD-TYPE 251   3  22  19
D1610V10, multiclass
    clus
vv   ZNF323 MUTATED ZNF323 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              2               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"
D1610V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF323 MUTATED                                  0     1
  ZNF323 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF323 MUTATED                           0     5
  ZNF323 WILD-TYPE                        19   171
D1610V12, multiclass
                                  clus
vv                                 ZNF323 MUTATED ZNF323 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = ESR1 MUTATION ANALYSIS
D1611V1, survival
                sevent
clus2              0   1
  ESR1 MUTATED    15   3
  ESR1 WILD-TYPE 262  75
  ESR1 MUTATED ESR1 WILD-TYPE 
            18            337 
  ESR1 MUTATED ESR1 WILD-TYPE 
             3             75 
$`ESR1 MUTATED`
TCGA-AA-3525 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 
        8.05       100.01        26.17        22.06        19.66         3.02 
TCGA-AA-3858 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A00N 
       31.07        33.01        26.01        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-CM-4743 TCGA-CM-5861 TCGA-F4-6569 TCGA-G4-6315 
       34.98         1.02        23.05        15.02        35.74        61.91 

$`ESR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00         2.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        85.48        36.00        13.78 
TCGA-G4-6626 
       46.75 

  ESR1 MUTATED ESR1 WILD-TYPE 
          1.02           0.00 
  ESR1 MUTATED ESR1 WILD-TYPE 
        100.01         148.01 
  ESR1 MUTATED ESR1 WILD-TYPE 
        25.515         21.990 
[1] "1.0 - 100.0 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1611V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESR1 MUTATED         2        0        4         4         3         0
  ESR1 WILD-TYPE      62        1       22       104         5         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        18          6         41         32       34        12
                vv
clus             STAGE IVB
  ESR1 MUTATED           0
  ESR1 WILD-TYPE         1
D1611V3, multiclass
            clus
vv           ESR1 MUTATED ESR1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             4            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  ESR1 MUTATED     0   3  11   5
  ESR1 WILD-TYPE   9  64 238  36
D1611V4, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           11            238
  T4            5             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
  ESR1 MUTATED    14   5   0
  ESR1 WILD-TYPE 206  76  66
D1611V5, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  N0           14            206
  N1            5             76
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1611V6, binary
                cls
clus               0   1
  ESR1 MUTATED    16   1
  ESR1 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     16    1
  ESR1 WILD-TYPE  269   47
   clus
vv  ESR1 MUTATED ESR1 WILD-TYPE
  0           16            269
  1            1             47
[1] 2 2
[1] FALSE
D1611V7, binary
                cls
clus               0   1
  ESR1 MUTATED     9  10
  ESR1 WILD-TYPE 161 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED      9   10
  ESR1 WILD-TYPE  161  187
        clus
vv       ESR1 MUTATED ESR1 WILD-TYPE
  FEMALE            9            161
  MALE             10            187
[1] 2 2
[1] FALSE
D1611V8, binary
                cls
clus               0   1
  ESR1 MUTATED    16   0
  ESR1 WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     16    0
  ESR1 WILD-TYPE  284    8
     clus
vv    ESR1 MUTATED ESR1 WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D1611V9, binary
                cls
clus               0   1
  ESR1 MUTATED    15   4
  ESR1 WILD-TYPE 299  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     15    4
  ESR1 WILD-TYPE  299   44
                               clus
vv                              ESR1 MUTATED ESR1 WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ESR1 MUTATED    16   0   0   0
  ESR1 WILD-TYPE 243   3  22  21
D1611V10, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            0             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"
D1611V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESR1 MUTATED                                  0     0
  ESR1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ESR1 MUTATED                           0     8
  ESR1 WILD-TYPE                        19   168
D1611V12, multiclass
                                  clus
vv                                 ESR1 MUTATED ESR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = LDLRAD3 MUTATION ANALYSIS
D1612V1, survival
                   sevent
clus2                 0   1
  LDLRAD3 MUTATED     3   1
  LDLRAD3 WILD-TYPE 274  77
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                4               351 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                1                77 
$`LDLRAD3 MUTATED`
TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3949 TCGA-AZ-4315 
        3.02        53.00        26.01        58.39 

$`LDLRAD3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
             3.02              0.00 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
            58.39            148.01 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
           39.505            22.030 
[1] "3.0 - 58.4 (39.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1612V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LDLRAD3 MUTATED         0        0        2         1         1         0
  LDLRAD3 WILD-TYPE      64        1       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LDLRAD3 MUTATED           0          0          1          0        0
  LDLRAD3 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  LDLRAD3 MUTATED           0         0
  LDLRAD3 WILD-TYPE        12         1
D1612V3, multiclass
            clus
vv           LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                1               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  LDLRAD3 MUTATED     0   0   4   1
  LDLRAD3 WILD-TYPE   9  67 245  40
D1612V4, multiclass
    clus
vv   LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               4               245
  T4               1                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
  LDLRAD3 MUTATED     4   1   0
  LDLRAD3 WILD-TYPE 216  80  66
D1612V5, multiclass
    clus
vv   LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  N0               4               216
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1612V6, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     4   0
  LDLRAD3 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      4    0
  LDLRAD3 WILD-TYPE  281   48
   clus
vv  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  0               4               281
  1               0                48
[1] 2 2
[1] FALSE
D1612V7, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     3   2
  LDLRAD3 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      3    2
  LDLRAD3 WILD-TYPE  167  195
        clus
vv       LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1612V8, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     4   0
  LDLRAD3 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      4    0
  LDLRAD3 WILD-TYPE  296    8
     clus
vv    LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D1612V9, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     4   1
  LDLRAD3 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      4    1
  LDLRAD3 WILD-TYPE  310   47
                               clus
vv                              LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  LDLRAD3 MUTATED     4   0   0   1
  LDLRAD3 WILD-TYPE 255   3  22  20
D1612V10, multiclass
    clus
vv   LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               1                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"
D1612V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LDLRAD3 MUTATED                                  0     0
  LDLRAD3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LDLRAD3 MUTATED                           0     2
  LDLRAD3 WILD-TYPE                        19   174
D1612V12, multiclass
[1] "Remove cluster labels:" "LDLRAD3 MUTATED"       
clus
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"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-5913        TCGA-CK-5914        TCGA-CK-5915 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 

Clustering(1613) Variable = BAZ1B MUTATION ANALYSIS
D1613V1, survival
                 sevent
clus2               0   1
  BAZ1B MUTATED    14   6
  BAZ1B WILD-TYPE 263  72
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             20             335 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
              6              72 
$`BAZ1B MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3663 TCGA-AA-3930 TCGA-AA-3947 
       19.04       100.01        26.17         6.97         2.01        33.01 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       38.04         4.01        12.16        49.41        12.76        10.06 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6926 
       12.00        14.04        18.25        16.14         7.53         9.04 
TCGA-D5-6930 TCGA-DM-A1D6 
       13.35        49.91 

$`BAZ1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3949 
       17.03        27.02        18.05        31.00        24.00        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        43.27        15.12 
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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  BAZ1B MUTATED BAZ1B WILD-TYPE 
           2.01            0.00 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
         100.01          148.01 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
         13.695          22.420 
[1] "2.0 - 100.0 (13.7)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D1613V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAZ1B MUTATED         4        0        3         8         2         0
  BAZ1B WILD-TYPE      60        1       23       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAZ1B MUTATED           0          0          2          0        2         0
  BAZ1B WILD-TYPE        18          6         42         33       33        12
                 vv
clus              STAGE IVB
  BAZ1B MUTATED           0
  BAZ1B WILD-TYPE         1
D1613V3, multiclass
            clus
vv           BAZ1B MUTATED BAZ1B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  BAZ1B MUTATED     0   4  14   3
  BAZ1B WILD-TYPE   9  63 235  38
D1613V4, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  T1             0               9
  T2             4              63
  T3            14             235
  T4             3              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
  BAZ1B MUTATED    18   2   1
  BAZ1B WILD-TYPE 202  79  65
D1613V5, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  N0            18             202
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1613V6, binary
                 cls
clus                0   1
  BAZ1B MUTATED    17   2
  BAZ1B WILD-TYPE 268  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     17    2
  BAZ1B WILD-TYPE  268   46
   clus
vv  BAZ1B MUTATED BAZ1B WILD-TYPE
  0            17             268
  1             2              46
[1] 2 2
[1] FALSE
D1613V7, binary
                 cls
clus                0   1
  BAZ1B MUTATED     7  14
  BAZ1B WILD-TYPE 163 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED      7   14
  BAZ1B WILD-TYPE  163  183
        clus
vv       BAZ1B MUTATED BAZ1B WILD-TYPE
  FEMALE             7             163
  MALE              14             183
[1] 2 2
[1] FALSE
D1613V8, binary
                 cls
clus                0   1
  BAZ1B MUTATED    16   2
  BAZ1B WILD-TYPE 284   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     16    2
  BAZ1B WILD-TYPE  284    6
     clus
vv    BAZ1B MUTATED BAZ1B WILD-TYPE
  NO             16             284
  YES             2               6
[1] 2 2
[1] FALSE
D1613V9, binary
                 cls
clus                0   1
  BAZ1B MUTATED    13   8
  BAZ1B WILD-TYPE 301  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     13    8
  BAZ1B WILD-TYPE  301   40
                               clus
vv                              BAZ1B MUTATED BAZ1B WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BAZ1B MUTATED    14   0   2   2
  BAZ1B WILD-TYPE 245   3  20  19
D1613V10, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  R0            14             245
  R1             0               3
  R2             2              20
  RX             2              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"
D1613V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAZ1B MUTATED                                  0     2
  BAZ1B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BAZ1B MUTATED                           0    12
  BAZ1B WILD-TYPE                        19   164
D1613V12, multiclass
                                  clus
vv                                 BAZ1B MUTATED BAZ1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1614) Variable = SLAMF9 MUTATION ANALYSIS
D1614V1, survival
                  sevent
clus2                0   1
  SLAMF9 MUTATED     5   1
  SLAMF9 WILD-TYPE 272  77
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               6              349 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               1               77 
$`SLAMF9 MUTATED`
TCGA-A6-5662 TCGA-AA-3555 TCGA-AA-3949 TCGA-CA-6717 TCGA-CM-4743 TCGA-G4-6626 
       23.61        29.95        26.01        12.76        23.05        46.75 

$`SLAMF9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           12.76             0.00 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           46.75           148.01 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           24.81            21.99 
[1] "12.8 - 46.8 (24.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1614V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLAMF9 MUTATED         0        0        0         4         0         0
  SLAMF9 WILD-TYPE      64        1       26       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLAMF9 MUTATED           0          0          1          0        0
  SLAMF9 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SLAMF9 MUTATED           1         0
  SLAMF9 WILD-TYPE        11         1
D1614V3, multiclass
            clus
vv           SLAMF9 MUTATED SLAMF9 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  SLAMF9 MUTATED     0   0   6   0
  SLAMF9 WILD-TYPE   9  67 243  41
D1614V4, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              0               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
  SLAMF9 MUTATED     4   1   1
  SLAMF9 WILD-TYPE 216  80  65
D1614V5, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1614V6, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     5   1
  SLAMF9 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      5    1
  SLAMF9 WILD-TYPE  280   47
   clus
vv  SLAMF9 MUTATED SLAMF9 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D1614V7, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     2   4
  SLAMF9 WILD-TYPE 168 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      2    4
  SLAMF9 WILD-TYPE  168  193
        clus
vv       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  FEMALE              2              168
  MALE                4              193
[1] 2 2
[1] FALSE
D1614V8, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     6   0
  SLAMF9 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      6    0
  SLAMF9 WILD-TYPE  294    8
     clus
vv    SLAMF9 MUTATED SLAMF9 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1614V9, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     3   3
  SLAMF9 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      3    3
  SLAMF9 WILD-TYPE  311   45
                               clus
vv                              SLAMF9 MUTATED SLAMF9 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLAMF9 MUTATED     4   0   0   1
  SLAMF9 WILD-TYPE 255   3  22  20
D1614V10, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              1               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"
D1614V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLAMF9 MUTATED                                  0     1
  SLAMF9 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLAMF9 MUTATED                           0     3
  SLAMF9 WILD-TYPE                        19   173
D1614V12, multiclass
                                  clus
vv                                 SLAMF9 MUTATED SLAMF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = C6ORF203 MUTATION ANALYSIS
D1615V1, survival
                    sevent
clus2                  0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 273  78
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 4                351 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 0                 78 
$`C6ORF203 MUTATED`
TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A010 TCGA-CM-4743 
        6.97        53.00        34.98        23.05 

$`C6ORF203 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
              6.97               0.00 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
             53.00             148.01 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
            29.015             22.030 
[1] "7.0 - 53.0 (29.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1615V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF203 MUTATED         0        0        2         1         1         0
  C6ORF203 WILD-TYPE      64        1       24       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF203 MUTATED           0          0          0          0        0
  C6ORF203 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF203 MUTATED           0         0
  C6ORF203 WILD-TYPE        12         1
D1615V3, multiclass
            clus
vv           C6ORF203 MUTATED C6ORF203 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 1                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C6ORF203 MUTATED     0   0   3   1
  C6ORF203 WILD-TYPE   9  67 246  40
D1615V4, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                3                246
  T4                1                 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
  C6ORF203 MUTATED     4   0   0
  C6ORF203 WILD-TYPE 216  81  66
D1615V5, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  N0                4                216
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1615V6, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    0
  C6ORF203 WILD-TYPE  281   48
   clus
vv  C6ORF203 MUTATED C6ORF203 WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D1615V7, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     1   3
  C6ORF203 WILD-TYPE 169 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      1    3
  C6ORF203 WILD-TYPE  169  194
        clus
vv       C6ORF203 MUTATED C6ORF203 WILD-TYPE
  FEMALE                1                169
  MALE                  3                194
[1] 2 2
[1] FALSE
D1615V8, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 296   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    0
  C6ORF203 WILD-TYPE  296    8
     clus
vv    C6ORF203 MUTATED C6ORF203 WILD-TYPE
  NO                 4                296
  YES                0                  8
[1] 2 2
[1] FALSE
D1615V9, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 310  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    0
  C6ORF203 WILD-TYPE  310   48
                               clus
vv                              C6ORF203 MUTATED C6ORF203 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C6ORF203 MUTATED     4   0   0   0
  C6ORF203 WILD-TYPE 255   3  22  21
D1615V10, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  R0                4                255
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1615V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF203 MUTATED                                  0     0
  C6ORF203 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF203 MUTATED                           0     1
  C6ORF203 WILD-TYPE                        19   175
D1615V12, multiclass
[1] "Remove cluster labels:" "C6ORF203 MUTATED"      
clus
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 1                205 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4744 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0X9         TCGA-DM-A0XD 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A0XF         TCGA-DM-A1D0         TCGA-DM-A1D4 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1D6         TCGA-DM-A1D7         TCGA-DM-A1D8 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1DB 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1HA         TCGA-DM-A1HB         TCGA-DM-A282 
"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-G4-6315         TCGA-G4-6317         TCGA-G4-6323 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6626 
"C6ORF203 WILD-TYPE" 

Clustering(1616) Variable = CCPG1 MUTATION ANALYSIS
D1616V1, survival
                 sevent
clus2               0   1
  CCPG1 MUTATED     7   4
  CCPG1 WILD-TYPE 270  74
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             11             344 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              4              74 
$`CCPG1 MUTATED`
TCGA-AA-3672 TCGA-AD-6964 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00N 
        0.92        10.88        19.66         6.97        25.02         4.01 
TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-4315 TCGA-CA-6718 TCGA-DM-A1HB 
       34.98         0.95        58.39        10.06       135.65 

$`CCPG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       27.42        26.47        14.50        27.09        16.31        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCPG1 MUTATED CCPG1 WILD-TYPE 
           0.92            0.00 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
         135.65          148.01 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
          10.88           22.09 
[1] "0.9 - 135.7 (10.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1616V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCPG1 MUTATED         1        0        1         2         2         0
  CCPG1 WILD-TYPE      63        1       25       106         6         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        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  CCPG1 MUTATED           0
  CCPG1 WILD-TYPE         1
D1616V3, multiclass
            clus
vv           CCPG1 MUTATED CCPG1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CCPG1 MUTATED     1   1   5   4
  CCPG1 WILD-TYPE   8  66 244  37
D1616V4, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             5             244
  T4             4              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
  CCPG1 MUTATED     7   3   1
  CCPG1 WILD-TYPE 213  78  65
D1616V5, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1616V6, binary
                 cls
clus                0   1
  CCPG1 MUTATED     7   0
  CCPG1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      7    0
  CCPG1 WILD-TYPE  278   48
   clus
vv  CCPG1 MUTATED CCPG1 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1616V7, binary
                 cls
clus                0   1
  CCPG1 MUTATED     3   8
  CCPG1 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      3    8
  CCPG1 WILD-TYPE  167  189
        clus
vv       CCPG1 MUTATED CCPG1 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1616V8, binary
                 cls
clus                0   1
  CCPG1 MUTATED     9   0
  CCPG1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      9    0
  CCPG1 WILD-TYPE  291    8
     clus
vv    CCPG1 MUTATED CCPG1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1616V9, binary
                 cls
clus                0   1
  CCPG1 MUTATED     7   2
  CCPG1 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      7    2
  CCPG1 WILD-TYPE  307   46
                               clus
vv                              CCPG1 MUTATED CCPG1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCPG1 MUTATED     7   0   0   1
  CCPG1 WILD-TYPE 252   3  22  20
D1616V10, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1616V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCPG1 MUTATED                                  0     1
  CCPG1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCPG1 MUTATED                           0     5
  CCPG1 WILD-TYPE                        19   171
D1616V12, multiclass
                                  clus
vv                                 CCPG1 MUTATED CCPG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1617) Variable = RIC8B MUTATION ANALYSIS
D1617V1, survival
                 sevent
clus2               0   1
  RIC8B MUTATED     7   2
  RIC8B WILD-TYPE 270  76
  RIC8B MUTATED RIC8B WILD-TYPE 
              9             346 
  RIC8B MUTATED RIC8B WILD-TYPE 
              2              76 
$`RIC8B MUTATED`
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-A00J TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 
       63.98         1.02        18.05        49.41        12.76        15.62 
TCGA-CM-5349 TCGA-CM-5860 TCGA-G4-6626 
       30.08        32.02        46.75 

$`RIC8B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 
       85.48        61.91        36.00        13.78 

  RIC8B MUTATED RIC8B WILD-TYPE 
           1.02            0.00 
  RIC8B MUTATED RIC8B WILD-TYPE 
          63.98          148.01 
  RIC8B MUTATED RIC8B WILD-TYPE 
         30.080          22.045 
[1] "1.0 - 64.0 (30.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1617V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RIC8B MUTATED         0        0        2         5         0         0
  RIC8B WILD-TYPE      64        1       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIC8B MUTATED           0          0          1          1        0         0
  RIC8B WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  RIC8B MUTATED           0
  RIC8B WILD-TYPE         1
D1617V3, multiclass
            clus
vv           RIC8B MUTATED RIC8B WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RIC8B MUTATED     0   0   7   2
  RIC8B WILD-TYPE   9  67 242  39
D1617V4, multiclass
    clus
vv   RIC8B MUTATED RIC8B WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             2              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
  RIC8B MUTATED     7   1   1
  RIC8B WILD-TYPE 213  80  65
D1617V5, multiclass
    clus
vv   RIC8B MUTATED RIC8B WILD-TYPE
  N0             7             213
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1617V6, binary
                 cls
clus                0   1
  RIC8B MUTATED     8   0
  RIC8B WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIC8B MUTATED      8    0
  RIC8B WILD-TYPE  277   48
   clus
vv  RIC8B MUTATED RIC8B WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1617V7, binary
                 cls
clus                0   1
  RIC8B MUTATED     4   5
  RIC8B WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIC8B MUTATED      4    5
  RIC8B WILD-TYPE  166  192
        clus
vv       RIC8B MUTATED RIC8B WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1617V8, binary
                 cls
clus                0   1
  RIC8B MUTATED     7   0
  RIC8B WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIC8B MUTATED      7    0
  RIC8B WILD-TYPE  293    8
     clus
vv    RIC8B MUTATED RIC8B WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1617V9, binary
                 cls
clus                0   1
  RIC8B MUTATED     6   3
  RIC8B WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIC8B MUTATED      6    3
  RIC8B WILD-TYPE  308   45
                               clus
vv                              RIC8B MUTATED RIC8B WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RIC8B MUTATED     6   0   0   2
  RIC8B WILD-TYPE 253   3  22  19
D1617V10, multiclass
    clus
vv   RIC8B MUTATED RIC8B WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1617V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIC8B MUTATED                                  0     1
  RIC8B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RIC8B MUTATED                           0     5
  RIC8B WILD-TYPE                        19   171
D1617V12, multiclass
                                  clus
vv                                 RIC8B MUTATED RIC8B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = KIAA1429 MUTATION ANALYSIS
D1618V1, survival
                    sevent
clus2                  0   1
  KIAA1429 MUTATED    11   4
  KIAA1429 WILD-TYPE 266  74
  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
                15                340 
  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
                 4                 74 
$`KIAA1429 MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6601 TCGA-A6-2676 
        1.02         0.92        19.04        24.00       100.01        42.90 
TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6718 
       53.00         4.01        34.98        27.09        58.39        10.06 
TCGA-CM-6162 TCGA-D5-7000 TCGA-F4-6856 
       12.00        10.26        35.31 

$`KIAA1429 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        85.05        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-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-G4-6293 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
              0.92               0.00 
  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
            100.01             148.01 
  KIAA1429 MUTATED KIAA1429 WILD-TYPE 
            24.000             22.045 
[1] "0.9 - 100.0 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1618V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1429 MUTATED         3        0        4         4         3         0
  KIAA1429 WILD-TYPE      61        1       22       104         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1429 MUTATED           1          0          1          0        1
  KIAA1429 WILD-TYPE        17          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1429 MUTATED           0         0
  KIAA1429 WILD-TYPE        12         1
D1618V3, multiclass
            clus
vv           KIAA1429 MUTATED KIAA1429 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                 4                104
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  KIAA1429 MUTATED     0   3  10   4
  KIAA1429 WILD-TYPE   9  64 239  37
D1618V4, multiclass
    clus
vv   KIAA1429 MUTATED KIAA1429 WILD-TYPE
  T1                0                  9
  T2                3                 64
  T3               10                239
  T4                4                 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
  KIAA1429 MUTATED    15   2   0
  KIAA1429 WILD-TYPE 205  79  66
D1618V5, multiclass
    clus
vv   KIAA1429 MUTATED KIAA1429 WILD-TYPE
  N0               15                205
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1618V6, binary
                    cls
clus                   0   1
  KIAA1429 MUTATED    16   1
  KIAA1429 WILD-TYPE 269  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1429 MUTATED     16    1
  KIAA1429 WILD-TYPE  269   47
   clus
vv  KIAA1429 MUTATED KIAA1429 WILD-TYPE
  0               16                269
  1                1                 47
[1] 2 2
[1] FALSE
D1618V7, binary
                    cls
clus                   0   1
  KIAA1429 MUTATED    10   7
  KIAA1429 WILD-TYPE 160 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1429 MUTATED     10    7
  KIAA1429 WILD-TYPE  160  190
        clus
vv       KIAA1429 MUTATED KIAA1429 WILD-TYPE
  FEMALE               10                160
  MALE                  7                190
[1] 2 2
[1] FALSE
D1618V8, binary
                    cls
clus                   0   1
  KIAA1429 MUTATED    11   1
  KIAA1429 WILD-TYPE 289   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1429 MUTATED     11    1
  KIAA1429 WILD-TYPE  289    7
     clus
vv    KIAA1429 MUTATED KIAA1429 WILD-TYPE
  NO                11                289
  YES                1                  7
[1] 2 2
[1] FALSE
D1618V9, binary
                    cls
clus                   0   1
  KIAA1429 MUTATED    12   5
  KIAA1429 WILD-TYPE 302  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1429 MUTATED     12    5
  KIAA1429 WILD-TYPE  302   43
                               clus
vv                              KIAA1429 MUTATED KIAA1429 WILD-TYPE
  COLON ADENOCARCINOMA                        12                302
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1429 MUTATED    14   0   1   1
  KIAA1429 WILD-TYPE 245   3  21  20
D1618V10, multiclass
    clus
vv   KIAA1429 MUTATED KIAA1429 WILD-TYPE
  R0               14                245
  R1                0                  3
  R2                1                 21
  RX                1                 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"
D1618V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1429 MUTATED                                  0     1
  KIAA1429 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1429 MUTATED                           0     7
  KIAA1429 WILD-TYPE                        19   169
D1618V12, multiclass
                                  clus
vv                                 KIAA1429 MUTATED KIAA1429 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           7                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1619) Variable = SPATA6 MUTATION ANALYSIS
D1619V1, survival
                  sevent
clus2                0   1
  SPATA6 MUTATED     4   2
  SPATA6 WILD-TYPE 273  76
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               6              349 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               2               76 
$`SPATA6 MUTATED`
TCGA-AA-3496 TCGA-AA-3949 TCGA-CK-6751 TCGA-CM-5863 TCGA-D5-6537 TCGA-G4-6303 
        1.02        26.01       124.27        15.02         4.80        65.85 

$`SPATA6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95         2.01        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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SPATA6 MUTATED SPATA6 WILD-TYPE 
            1.02             0.00 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
          124.27           148.01 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
          20.515           22.060 
[1] "1.0 - 124.3 (20.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1619V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPATA6 MUTATED         1        0        1         0         0         0
  SPATA6 WILD-TYPE      63        1       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA6 MUTATED           0          0          3          0        1
  SPATA6 WILD-TYPE        18          6         41         33       34
                  vv
clus               STAGE IVA STAGE IVB
  SPATA6 MUTATED           0         0
  SPATA6 WILD-TYPE        12         1
D1619V3, multiclass
            clus
vv           SPATA6 MUTATED SPATA6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  SPATA6 MUTATED     0   1   5   0
  SPATA6 WILD-TYPE   9  66 244  41
D1619V4, multiclass
    clus
vv   SPATA6 MUTATED SPATA6 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              5              244
  T4              0               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
  SPATA6 MUTATED     2   4   0
  SPATA6 WILD-TYPE 218  77  66
D1619V5, multiclass
    clus
vv   SPATA6 MUTATED SPATA6 WILD-TYPE
  N0              2              218
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1619V6, binary
                  cls
clus                 0   1
  SPATA6 MUTATED     3   1
  SPATA6 WILD-TYPE 282  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA6 MUTATED      3    1
  SPATA6 WILD-TYPE  282   47
   clus
vv  SPATA6 MUTATED SPATA6 WILD-TYPE
  0              3              282
  1              1               47
[1] 2 2
[1] FALSE
D1619V7, binary
                  cls
clus                 0   1
  SPATA6 MUTATED     5   1
  SPATA6 WILD-TYPE 165 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA6 MUTATED      5    1
  SPATA6 WILD-TYPE  165  196
        clus
vv       SPATA6 MUTATED SPATA6 WILD-TYPE
  FEMALE              5              165
  MALE                1              196
[1] 2 2
[1] FALSE
D1619V8, binary
                  cls
clus                 0   1
  SPATA6 MUTATED     5   0
  SPATA6 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA6 MUTATED      5    0
  SPATA6 WILD-TYPE  295    8
     clus
vv    SPATA6 MUTATED SPATA6 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1619V9, binary
                  cls
clus                 0   1
  SPATA6 MUTATED     3   3
  SPATA6 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA6 MUTATED      3    3
  SPATA6 WILD-TYPE  311   45
                               clus
vv                              SPATA6 MUTATED SPATA6 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SPATA6 MUTATED     5   0   0   1
  SPATA6 WILD-TYPE 254   3  22  20
D1619V10, multiclass
    clus
vv   SPATA6 MUTATED SPATA6 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D1619V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPATA6 MUTATED                                  0     0
  SPATA6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SPATA6 MUTATED                           0     4
  SPATA6 WILD-TYPE                        19   172
D1619V12, multiclass
                                  clus
vv                                 SPATA6 MUTATED SPATA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = PIGN MUTATION ANALYSIS
D1620V1, survival
                sevent
clus2              0   1
  PIGN MUTATED     6   1
  PIGN WILD-TYPE 271  77
  PIGN MUTATED PIGN WILD-TYPE 
             7            348 
  PIGN MUTATED PIGN WILD-TYPE 
             1             77 
$`PIGN MUTATED`
TCGA-AA-3950 TCGA-AD-6964 TCGA-AA-3966 TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-6928 
       24.00        10.88         2.01        22.98        15.02        11.64 
TCGA-F4-6703 
       47.87 

$`PIGN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PIGN MUTATED PIGN WILD-TYPE 
          2.01           0.00 
  PIGN MUTATED PIGN WILD-TYPE 
         47.87         148.01 
  PIGN MUTATED PIGN WILD-TYPE 
        15.020         22.075 
[1] "2.0 - 47.9 (15.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1620V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGN MUTATED         0        0        0         5         0         0
  PIGN WILD-TYPE      64        1       26       103         8         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  PIGN MUTATED           0
  PIGN WILD-TYPE         1
D1620V3, multiclass
            clus
vv           PIGN MUTATED PIGN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PIGN MUTATED     0   0   6   1
  PIGN WILD-TYPE   9  67 243  40
D1620V4, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            1             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
  PIGN MUTATED     5   1   1
  PIGN WILD-TYPE 215  80  65
D1620V5, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  N0            5            215
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1620V6, binary
                cls
clus               0   1
  PIGN MUTATED     6   0
  PIGN WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      6    0
  PIGN WILD-TYPE  279   48
   clus
vv  PIGN MUTATED PIGN WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1620V7, binary
                cls
clus               0   1
  PIGN MUTATED     3   4
  PIGN WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      3    4
  PIGN WILD-TYPE  167  193
        clus
vv       PIGN MUTATED PIGN WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D1620V8, binary
                cls
clus               0   1
  PIGN MUTATED     6   0
  PIGN WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      6    0
  PIGN WILD-TYPE  294    8
     clus
vv    PIGN MUTATED PIGN WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1620V9, binary
                cls
clus               0   1
  PIGN MUTATED     4   3
  PIGN WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      4    3
  PIGN WILD-TYPE  310   45
                               clus
vv                              PIGN MUTATED PIGN WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PIGN MUTATED     5   0   0   0
  PIGN WILD-TYPE 254   3  22  21
D1620V10, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1620V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGN MUTATED                                  0     0
  PIGN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGN MUTATED                           0     5
  PIGN WILD-TYPE                        19   171
D1620V12, multiclass
                                  clus
vv                                 PIGN MUTATED PIGN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = OR4N2 MUTATION ANALYSIS
D1621V1, survival
                 sevent
clus2               0   1
  OR4N2 MUTATED     6   4
  OR4N2 WILD-TYPE 271  74
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             345 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              4              74 
$`OR4N2 MUTATED`
TCGA-AA-3715 TCGA-G4-6586 TCGA-AA-3858 TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6537 
       19.04        35.80        31.07        58.39        15.62         4.80 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6309 
       12.00        92.75         6.18        85.48 

$`OR4N2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 
       33.07         0.00        36.03        32.05         0.99        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.060 
[1] "4.8 - 92.8 (25.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1621V2, continuous
                 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      63        1       25       104         8         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        18          6         42         31       35        12
                 vv
clus              STAGE IVB
  OR4N2 MUTATED           0
  OR4N2 WILD-TYPE         1
D1621V3, multiclass
            clus
vv           OR4N2 MUTATED OR4N2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  OR4N2 MUTATED     0   1   7   2
  OR4N2 WILD-TYPE   9  66 242  39
D1621V4, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             2              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
  OR4N2 MUTATED     6   2   2
  OR4N2 WILD-TYPE 214  79  64
D1621V5, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1621V6, binary
                 cls
clus                0   1
  OR4N2 MUTATED     9   0
  OR4N2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      9    0
  OR4N2 WILD-TYPE  276   48
   clus
vv  OR4N2 MUTATED OR4N2 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1621V7, binary
                 cls
clus                0   1
  OR4N2 MUTATED     4   6
  OR4N2 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      4    6
  OR4N2 WILD-TYPE  166  191
        clus
vv       OR4N2 MUTATED OR4N2 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1621V8, binary
                 cls
clus                0   1
  OR4N2 MUTATED     8   0
  OR4N2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      8    0
  OR4N2 WILD-TYPE  292    8
     clus
vv    OR4N2 MUTATED OR4N2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1621V9, binary
                 cls
clus                0   1
  OR4N2 MUTATED     9   1
  OR4N2 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      9    1
  OR4N2 WILD-TYPE  305   47
                               clus
vv                              OR4N2 MUTATED OR4N2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4N2 MUTATED     8   0   0   1
  OR4N2 WILD-TYPE 251   3  22  20
D1621V10, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1621V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4N2 MUTATED                                  0     0
  OR4N2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4N2 MUTATED                           1     7
  OR4N2 WILD-TYPE                        18   169
D1621V12, multiclass
                                  clus
vv                                 OR4N2 MUTATED OR4N2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = RALA MUTATION ANALYSIS
D1622V1, survival
                sevent
clus2              0   1
  RALA MUTATED     6   1
  RALA WILD-TYPE 271  77
  RALA MUTATED RALA WILD-TYPE 
             7            348 
  RALA MUTATED RALA WILD-TYPE 
             1             77 
$`RALA MUTATED`
TCGA-AA-3697 TCGA-AA-3510 TCGA-AU-6004 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4752 
       85.05        63.98        27.09        10.06        51.32        13.02 
TCGA-CM-6163 
       14.04 

$`RALA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RALA MUTATED RALA WILD-TYPE 
         10.06           0.00 
  RALA MUTATED RALA WILD-TYPE 
         85.05         148.01 
  RALA MUTATED RALA WILD-TYPE 
        27.090         22.045 
[1] "10.1 - 85.0 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D1622V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RALA MUTATED         2        0        2         3         0         0
  RALA WILD-TYPE      62        1       24       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RALA MUTATED           0          0          0          0        0         0
  RALA WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  RALA MUTATED           0
  RALA WILD-TYPE         1
D1622V3, multiclass
            clus
vv           RALA MUTATED RALA WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  RALA MUTATED     1   1   5   0
  RALA WILD-TYPE   8  66 244  41
D1622V4, multiclass
    clus
vv   RALA MUTATED RALA WILD-TYPE
  T1            1              8
  T2            1             66
  T3            5            244
  T4            0             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
  RALA MUTATED     7   0   0
  RALA WILD-TYPE 213  81  66
D1622V5, multiclass
    clus
vv   RALA MUTATED RALA WILD-TYPE
  N0            7            213
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1622V6, binary
                cls
clus               0   1
  RALA MUTATED     6   0
  RALA WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      6    0
  RALA WILD-TYPE  279   48
   clus
vv  RALA MUTATED RALA WILD-TYPE
  0            6            279
  1            0             48
[1] 2 2
[1] FALSE
D1622V7, binary
                cls
clus               0   1
  RALA MUTATED     2   5
  RALA WILD-TYPE 168 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      2    5
  RALA WILD-TYPE  168  192
        clus
vv       RALA MUTATED RALA WILD-TYPE
  FEMALE            2            168
  MALE              5            192
[1] 2 2
[1] FALSE
D1622V8, binary
                cls
clus               0   1
  RALA MUTATED     6   0
  RALA WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      6    0
  RALA WILD-TYPE  294    8
     clus
vv    RALA MUTATED RALA WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1622V9, binary
                cls
clus               0   1
  RALA MUTATED     7   0
  RALA WILD-TYPE 307  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      7    0
  RALA WILD-TYPE  307   48
                               clus
vv                              RALA MUTATED RALA WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RALA MUTATED     5   0   0   2
  RALA WILD-TYPE 254   3  22  19
D1622V10, multiclass
    clus
vv   RALA MUTATED RALA WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            2             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"
D1622V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RALA MUTATED                                  0     1
  RALA WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RALA MUTATED                           1     3
  RALA WILD-TYPE                        18   173
D1622V12, multiclass
                                  clus
vv                                 RALA MUTATED RALA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       3            173
[1] 4 2
[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 = MUS81 MUTATION ANALYSIS
D1623V1, survival
                 sevent
clus2               0   1
  MUS81 MUTATED     6   1
  MUS81 WILD-TYPE 271  77
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             348 
  MUS81 MUTATED MUS81 WILD-TYPE 
              1              77 
$`MUS81 MUTATED`
TCGA-A6-5665 TCGA-AA-3877 TCGA-AD-6889 TCGA-AY-6197 TCGA-CK-4947 TCGA-CM-5861 
       22.06        31.00        83.24        21.44        17.56        15.02 
TCGA-CM-5864 
       15.02 

$`MUS81 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MUS81 MUTATED MUS81 WILD-TYPE 
          15.02            0.00 
  MUS81 MUTATED MUS81 WILD-TYPE 
          83.24          148.01 
  MUS81 MUTATED MUS81 WILD-TYPE 
          21.44           22.09 
[1] "15.0 - 83.2 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1623V2, continuous
                 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      62        1       26       104         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  MUS81 MUTATED           0
  MUS81 WILD-TYPE         1
D1623V3, multiclass
            clus
vv           MUS81 MUTATED MUS81 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MUS81 MUTATED     1   1   4   1
  MUS81 WILD-TYPE   8  66 245  40
D1623V4, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             4             245
  T4             1              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
  MUS81 MUTATED     6   1   0
  MUS81 WILD-TYPE 214  80  66
D1623V5, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1623V6, binary
                 cls
clus                0   1
  MUS81 MUTATED     6   0
  MUS81 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      6    0
  MUS81 WILD-TYPE  279   48
   clus
vv  MUS81 MUTATED MUS81 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1623V7, binary
                 cls
clus                0   1
  MUS81 MUTATED     4   3
  MUS81 WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      4    3
  MUS81 WILD-TYPE  166  194
        clus
vv       MUS81 MUTATED MUS81 WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1623V8, binary
                 cls
clus                0   1
  MUS81 MUTATED     7   0
  MUS81 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      7    0
  MUS81 WILD-TYPE  293    8
     clus
vv    MUS81 MUTATED MUS81 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1623V9, binary
                 cls
clus                0   1
  MUS81 MUTATED     6   1
  MUS81 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      6    1
  MUS81 WILD-TYPE  308   47
                               clus
vv                              MUS81 MUTATED MUS81 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MUS81 MUTATED     6   0   0   1
  MUS81 WILD-TYPE 253   3  22  20
D1623V10, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1623V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUS81 MUTATED                                  0     1
  MUS81 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUS81 MUTATED                           0     5
  MUS81 WILD-TYPE                        19   171
D1623V12, multiclass
                                  clus
vv                                 MUS81 MUTATED MUS81 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = CDHR5 MUTATION ANALYSIS
D1624V1, survival
                 sevent
clus2               0   1
  CDHR5 MUTATED    10   1
  CDHR5 WILD-TYPE 267  77
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             344 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              1              77 
$`CDHR5 MUTATED`
TCGA-AA-3950 TCGA-G4-6586 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3864 
       24.00        35.80        24.39        19.66        33.04        53.00 
TCGA-AA-3877 TCGA-AA-3968 TCGA-AA-A03F TCGA-AY-6197 TCGA-DM-A0X9 
       31.00        21.99        18.05        21.44       119.70 

$`CDHR5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        24.69        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CDHR5 MUTATED CDHR5 WILD-TYPE 
          18.05            0.00 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
         119.70          148.01 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
          24.39           22.01 
[1] "18.1 - 119.7 (24.4)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "3"  
D1624V2, continuous
                 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      61        1       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDHR5 MUTATED           1          0          0          1        0         0
  CDHR5 WILD-TYPE        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  CDHR5 MUTATED           0
  CDHR5 WILD-TYPE         1
D1624V3, multiclass
            clus
vv           CDHR5 MUTATED CDHR5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CDHR5 MUTATED     1   2   7   1
  CDHR5 WILD-TYPE   8  65 242  40
D1624V4, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             7             242
  T4             1              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
  CDHR5 MUTATED     9   1   1
  CDHR5 WILD-TYPE 211  80  65
D1624V5, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1624V6, binary
                 cls
clus                0   1
  CDHR5 MUTATED     9   0
  CDHR5 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      9    0
  CDHR5 WILD-TYPE  276   48
   clus
vv  CDHR5 MUTATED CDHR5 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1624V7, binary
                 cls
clus                0   1
  CDHR5 MUTATED     7   4
  CDHR5 WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      7    4
  CDHR5 WILD-TYPE  163  193
        clus
vv       CDHR5 MUTATED CDHR5 WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D1624V8, binary
                 cls
clus                0   1
  CDHR5 MUTATED    10   0
  CDHR5 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED     10    0
  CDHR5 WILD-TYPE  290    8
     clus
vv    CDHR5 MUTATED CDHR5 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1624V9, binary
                 cls
clus                0   1
  CDHR5 MUTATED     7   4
  CDHR5 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      7    4
  CDHR5 WILD-TYPE  307   44
                               clus
vv                              CDHR5 MUTATED CDHR5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDHR5 MUTATED     9   0   0   0
  CDHR5 WILD-TYPE 250   3  22  21
D1624V10, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1624V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDHR5 MUTATED                                  0     0
  CDHR5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDHR5 MUTATED                           0     5
  CDHR5 WILD-TYPE                        19   171
D1624V12, multiclass
                                  clus
vv                                 CDHR5 MUTATED CDHR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = ZNF318 MUTATION ANALYSIS
D1625V1, survival
                  sevent
clus2                0   1
  ZNF318 MUTATED    22   6
  ZNF318 WILD-TYPE 255  72
  ZNF318 MUTATED ZNF318 WILD-TYPE 
              28              327 
  ZNF318 MUTATED ZNF318 WILD-TYPE 
               6               72 
$`ZNF318 MUTATED`
TCGA-AA-3525 TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6964 TCGA-A6-5661 TCGA-A6-6653 
        8.05        19.04        24.00        10.88        33.53        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3518 
       23.87        20.12        19.66         3.02        63.98         1.02 
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       29.95         6.97        33.04        53.00        25.02         4.01 
TCGA-AA-A03F TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6676 
       18.05        58.39        12.76        29.03        12.99        11.08 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6923 TCGA-G4-6626 
       17.85        16.14        12.43        46.75 

$`ZNF318 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       21.76        24.69        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       24.00        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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-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 
       54.61        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 
       25.48        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-D5-6926 
       15.58         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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 
       61.91        36.00        13.78 

  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            22.09 
[1] "1.0 - 64.0 (19.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1625V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF318 MUTATED         4        0        5        12         1         0
  ZNF318 WILD-TYPE      60        1       21        96         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF318 MUTATED           1          0          2          1        0
  ZNF318 WILD-TYPE        17          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF318 MUTATED           0         0
  ZNF318 WILD-TYPE        12         1
D1625V3, multiclass
            clus
vv           ZNF318 MUTATED ZNF318 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                5               21
  STAGE IIA              12               96
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF318 MUTATED     0   5  20   3
  ZNF318 WILD-TYPE   9  62 229  38
D1625V4, multiclass
    clus
vv   ZNF318 MUTATED ZNF318 WILD-TYPE
  T1              0                9
  T2              5               62
  T3             20              229
  T4              3               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
  ZNF318 MUTATED    23   3   2
  ZNF318 WILD-TYPE 197  78  64
D1625V5, multiclass
    clus
vv   ZNF318 MUTATED ZNF318 WILD-TYPE
  N0             23              197
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1625V6, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    24   0
  ZNF318 WILD-TYPE 261  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     24    0
  ZNF318 WILD-TYPE  261   48
   clus
vv  ZNF318 MUTATED ZNF318 WILD-TYPE
  0             24              261
  1              0               48
[1] 2 2
[1] FALSE
D1625V7, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    10  18
  ZNF318 WILD-TYPE 160 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     10   18
  ZNF318 WILD-TYPE  160  179
        clus
vv       ZNF318 MUTATED ZNF318 WILD-TYPE
  FEMALE             10              160
  MALE               18              179
[1] 2 2
[1] FALSE
D1625V8, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    26   0
  ZNF318 WILD-TYPE 274   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     26    0
  ZNF318 WILD-TYPE  274    8
     clus
vv    ZNF318 MUTATED ZNF318 WILD-TYPE
  NO              26              274
  YES              0                8
[1] 2 2
[1] FALSE
D1625V9, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    20   8
  ZNF318 WILD-TYPE 294  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     20    8
  ZNF318 WILD-TYPE  294   40
                               clus
vv                              ZNF318 MUTATED ZNF318 WILD-TYPE
  COLON ADENOCARCINOMA                      20              294
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF318 MUTATED    22   0   0   1
  ZNF318 WILD-TYPE 237   3  22  20
D1625V10, multiclass
    clus
vv   ZNF318 MUTATED ZNF318 WILD-TYPE
  R0             22              237
  R1              0                3
  R2              0               22
  RX              1               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"
D1625V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF318 MUTATED                                  0     1
  ZNF318 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF318 MUTATED                           2    12
  ZNF318 WILD-TYPE                        17   164
D1625V12, multiclass
                                  clus
vv                                 ZNF318 MUTATED ZNF318 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        12              164
[1] 4 2
[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 = IL7R MUTATION ANALYSIS
D1626V1, survival
                sevent
clus2              0   1
  IL7R MUTATED     7   3
  IL7R WILD-TYPE 270  75
  IL7R MUTATED IL7R WILD-TYPE 
            10            345 
  IL7R MUTATED IL7R WILD-TYPE 
             3             75 
$`IL7R MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A01F TCGA-AZ-5403 TCGA-CA-6718 
       30.44        63.98         4.01        32.02        62.79        10.06 
TCGA-CM-6168 TCGA-D5-6920 TCGA-F4-6703 TCGA-G4-6317 
       12.99        12.39        47.87        36.00 

$`IL7R WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         7.53        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  IL7R MUTATED IL7R WILD-TYPE 
          4.01           0.00 
  IL7R MUTATED IL7R WILD-TYPE 
         63.98         148.01 
  IL7R MUTATED IL7R WILD-TYPE 
         31.23          22.03 
[1] "4.0 - 64.0 (31.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1626V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL7R MUTATED         2        0        2         4         1         0
  IL7R WILD-TYPE      62        1       24       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL7R MUTATED           0          0          1          1        0         0
  IL7R WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  IL7R MUTATED           0
  IL7R WILD-TYPE         1
D1626V3, multiclass
            clus
vv           IL7R MUTATED IL7R WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  IL7R MUTATED     0   2   8   1
  IL7R WILD-TYPE   9  65 241  40
D1626V4, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            1             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
  IL7R MUTATED     9   1   1
  IL7R WILD-TYPE 211  80  65
D1626V5, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  N0            9            211
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1626V6, binary
                cls
clus               0   1
  IL7R MUTATED     8   0
  IL7R WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      8    0
  IL7R WILD-TYPE  277   48
   clus
vv  IL7R MUTATED IL7R WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1626V7, binary
                cls
clus               0   1
  IL7R MUTATED     3   8
  IL7R WILD-TYPE 167 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      3    8
  IL7R WILD-TYPE  167  189
        clus
vv       IL7R MUTATED IL7R WILD-TYPE
  FEMALE            3            167
  MALE              8            189
[1] 2 2
[1] FALSE
D1626V8, binary
                cls
clus               0   1
  IL7R MUTATED     9   0
  IL7R WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      9    0
  IL7R WILD-TYPE  291    8
     clus
vv    IL7R MUTATED IL7R WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1626V9, binary
                cls
clus               0   1
  IL7R MUTATED    10   1
  IL7R WILD-TYPE 304  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED     10    1
  IL7R WILD-TYPE  304   47
                               clus
vv                              IL7R MUTATED IL7R WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IL7R MUTATED     8   0   0   2
  IL7R WILD-TYPE 251   3  22  19
D1626V10, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            2             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"
D1626V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL7R MUTATED                                  0     1
  IL7R WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IL7R MUTATED                           1     6
  IL7R WILD-TYPE                        18   170
D1626V12, multiclass
                                  clus
vv                                 IL7R MUTATED IL7R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       6            170
[1] 4 2
[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 = LRRTM2 MUTATION ANALYSIS
D1627V1, survival
                  sevent
clus2                0   1
  LRRTM2 MUTATED     5   0
  LRRTM2 WILD-TYPE 272  78
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               5              350 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               0               78 
$`LRRTM2 MUTATED`
TCGA-AA-3833 TCGA-AU-3779 TCGA-D5-6529 TCGA-F4-6856 TCGA-G4-6304 
       15.95        14.50        20.19        35.31        53.62 

$`LRRTM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
            14.5              0.0 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
           53.62           148.01 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
          20.190           22.075 
[1] "14.5 - 53.6 (20.2)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1627V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRTM2 MUTATED         1        0        0         3         1         0
  LRRTM2 WILD-TYPE      63        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRTM2 MUTATED           0          0          0          0        0
  LRRTM2 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRTM2 MUTATED           0         0
  LRRTM2 WILD-TYPE        12         1
D1627V3, multiclass
            clus
vv           LRRTM2 MUTATED LRRTM2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  LRRTM2 MUTATED     0   1   3   1
  LRRTM2 WILD-TYPE   9  66 246  40
D1627V4, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              3              246
  T4              1               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
  LRRTM2 MUTATED     5   0   0
  LRRTM2 WILD-TYPE 215  81  66
D1627V5, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1627V6, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     5   0
  LRRTM2 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      5    0
  LRRTM2 WILD-TYPE  280   48
   clus
vv  LRRTM2 MUTATED LRRTM2 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1627V7, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     3   2
  LRRTM2 WILD-TYPE 167 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      3    2
  LRRTM2 WILD-TYPE  167  195
        clus
vv       LRRTM2 MUTATED LRRTM2 WILD-TYPE
  FEMALE              3              167
  MALE                2              195
[1] 2 2
[1] FALSE
D1627V8, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     5   0
  LRRTM2 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      5    0
  LRRTM2 WILD-TYPE  295    8
     clus
vv    LRRTM2 MUTATED LRRTM2 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1627V9, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     4   1
  LRRTM2 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      4    1
  LRRTM2 WILD-TYPE  310   47
                               clus
vv                              LRRTM2 MUTATED LRRTM2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LRRTM2 MUTATED     5   0   0   0
  LRRTM2 WILD-TYPE 254   3  22  21
D1627V10, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1627V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRTM2 MUTATED                                  0     0
  LRRTM2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRTM2 MUTATED                           0     4
  LRRTM2 WILD-TYPE                        19   172
D1627V12, multiclass
                                  clus
vv                                 LRRTM2 MUTATED LRRTM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = IGSF1 MUTATION ANALYSIS
D1628V1, survival
                 sevent
clus2               0   1
  IGSF1 MUTATED    14   6
  IGSF1 WILD-TYPE 263  72
  IGSF1 MUTATED IGSF1 WILD-TYPE 
             20             335 
  IGSF1 MUTATED IGSF1 WILD-TYPE 
              6              72 
$`IGSF1 MUTATED`
TCGA-AA-3516 TCGA-AD-6964 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6628 
       13.02        10.88         5.88        22.09        35.80        79.69 
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3666 TCGA-AA-3949 TCGA-AA-3975 TCGA-AA-3977 
       32.75        22.06         2.01        26.01        34.06        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-5861 
        4.01        34.98        49.41        12.76        21.99        15.02 
TCGA-CM-6162 TCGA-F4-6856 
       12.00        35.31 

$`IGSF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 
        1.94        49.08        63.62        26.17        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  IGSF1 MUTATED IGSF1 WILD-TYPE 
           2.01            0.00 
  IGSF1 MUTATED IGSF1 WILD-TYPE 
          79.69          148.01 
  IGSF1 MUTATED IGSF1 WILD-TYPE 
         22.075          22.030 
[1] "2.0 - 79.7 (22.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1628V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGSF1 MUTATED         3        0        1         5         3         0
  IGSF1 WILD-TYPE      61        1       25       103         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGSF1 MUTATED           3          0          3          0        1         0
  IGSF1 WILD-TYPE        15          6         41         33       34        12
                 vv
clus              STAGE IVB
  IGSF1 MUTATED           0
  IGSF1 WILD-TYPE         1
D1628V3, multiclass
            clus
vv           IGSF1 MUTATED IGSF1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              15
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  IGSF1 MUTATED     0   5  12   4
  IGSF1 WILD-TYPE   9  62 237  37
D1628V4, multiclass
    clus
vv   IGSF1 MUTATED IGSF1 WILD-TYPE
  T1             0               9
  T2             5              62
  T3            12             237
  T4             4              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
  IGSF1 MUTATED    13   5   3
  IGSF1 WILD-TYPE 207  76  63
D1628V5, multiclass
    clus
vv   IGSF1 MUTATED IGSF1 WILD-TYPE
  N0            13             207
  N1             5              76
  N2             3              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"
D1628V6, binary
                 cls
clus                0   1
  IGSF1 MUTATED    15   1
  IGSF1 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF1 MUTATED     15    1
  IGSF1 WILD-TYPE  270   47
   clus
vv  IGSF1 MUTATED IGSF1 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D1628V7, binary
                 cls
clus                0   1
  IGSF1 MUTATED    12   9
  IGSF1 WILD-TYPE 158 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF1 MUTATED     12    9
  IGSF1 WILD-TYPE  158  188
        clus
vv       IGSF1 MUTATED IGSF1 WILD-TYPE
  FEMALE            12             158
  MALE               9             188
[1] 2 2
[1] FALSE
D1628V8, binary
                 cls
clus                0   1
  IGSF1 MUTATED    16   0
  IGSF1 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF1 MUTATED     16    0
  IGSF1 WILD-TYPE  284    8
     clus
vv    IGSF1 MUTATED IGSF1 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D1628V9, binary
                 cls
clus                0   1
  IGSF1 MUTATED    13   8
  IGSF1 WILD-TYPE 301  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF1 MUTATED     13    8
  IGSF1 WILD-TYPE  301   40
                               clus
vv                              IGSF1 MUTATED IGSF1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IGSF1 MUTATED    14   0   0   2
  IGSF1 WILD-TYPE 245   3  22  19
D1628V10, multiclass
    clus
vv   IGSF1 MUTATED IGSF1 WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             2              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"
D1628V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGSF1 MUTATED                                  0     1
  IGSF1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGSF1 MUTATED                           0    12
  IGSF1 WILD-TYPE                        19   164
D1628V12, multiclass
                                  clus
vv                                 IGSF1 MUTATED IGSF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = GCC2 MUTATION ANALYSIS
D1629V1, survival
                sevent
clus2              0   1
  GCC2 MUTATED    10   0
  GCC2 WILD-TYPE 267  78
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            345 
  GCC2 MUTATED GCC2 WILD-TYPE 
             0             78 
$`GCC2 MUTATED`
TCGA-AA-3496 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
        1.02        19.04         1.02        25.02        34.98        12.16 
TCGA-AY-6196 TCGA-CA-6717 TCGA-CM-6674 TCGA-F4-6569 
        0.20        12.76        12.95        35.74 

$`GCC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 
       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GCC2 MUTATED GCC2 WILD-TYPE 
           0.2            0.0 
  GCC2 MUTATED GCC2 WILD-TYPE 
         35.74         148.01 
  GCC2 MUTATED GCC2 WILD-TYPE 
        12.855         22.090 
[1] "0.2 - 35.7 (12.9)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D1629V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GCC2 MUTATED         3        0        1         2         1         0
  GCC2 WILD-TYPE      61        1       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCC2 MUTATED           0          0          0          1        1         0
  GCC2 WILD-TYPE        18          6         44         32       34        12
                vv
clus             STAGE IVB
  GCC2 MUTATED           0
  GCC2 WILD-TYPE         1
D1629V3, multiclass
            clus
vv           GCC2 MUTATED GCC2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  GCC2 MUTATED     0   4   5   1
  GCC2 WILD-TYPE   9  63 244  40
D1629V4, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  T1            0              9
  T2            4             63
  T3            5            244
  T4            1             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
  GCC2 MUTATED     9   0   1
  GCC2 WILD-TYPE 211  81  65
D1629V5, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  N0            9            211
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1629V6, binary
                cls
clus               0   1
  GCC2 MUTATED     6   1
  GCC2 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      6    1
  GCC2 WILD-TYPE  279   47
   clus
vv  GCC2 MUTATED GCC2 WILD-TYPE
  0            6            279
  1            1             47
[1] 2 2
[1] FALSE
D1629V7, binary
                cls
clus               0   1
  GCC2 MUTATED     3   7
  GCC2 WILD-TYPE 167 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      3    7
  GCC2 WILD-TYPE  167  190
        clus
vv       GCC2 MUTATED GCC2 WILD-TYPE
  FEMALE            3            167
  MALE              7            190
[1] 2 2
[1] FALSE
D1629V8, binary
                cls
clus               0   1
  GCC2 MUTATED     7   1
  GCC2 WILD-TYPE 293   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      7    1
  GCC2 WILD-TYPE  293    7
     clus
vv    GCC2 MUTATED GCC2 WILD-TYPE
  NO             7            293
  YES            1              7
[1] 2 2
[1] FALSE
D1629V9, binary
                cls
clus               0   1
  GCC2 MUTATED     6   4
  GCC2 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      6    4
  GCC2 WILD-TYPE  308   44
                               clus
vv                              GCC2 MUTATED GCC2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GCC2 MUTATED     7   0   1   1
  GCC2 WILD-TYPE 252   3  21  20
D1629V10, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            1             21
  RX            1             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"
D1629V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GCC2 MUTATED                                  0     1
  GCC2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GCC2 MUTATED                           0     4
  GCC2 WILD-TYPE                        19   172
D1629V12, multiclass
                                  clus
vv                                 GCC2 MUTATED GCC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = ATRNL1 MUTATION ANALYSIS
D1630V1, survival
                  sevent
clus2                0   1
  ATRNL1 MUTATED    16   4
  ATRNL1 WILD-TYPE 261  74
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
              20              335 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
               4               74 
$`ATRNL1 MUTATED`
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 
        1.94         5.88        79.69        33.53        29.95         6.97 
TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6196 TCGA-AY-6197 
       15.95        25.02         4.01        24.53         0.20        21.44 
TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6928 
       58.39        12.59        12.76        14.04        15.12        11.64 
TCGA-DM-A0XF TCGA-DM-A1HB 
       38.20       135.65 

$`ATRNL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      106.75       100.01        49.08        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24         5.79        22.42        27.42        26.47        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-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        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-CA-5254 
       12.10        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 
       12.36        12.39        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
             0.2              0.0 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
          135.65           148.01 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
          15.535           22.090 
[1] "0.2 - 135.7 (15.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1630V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATRNL1 MUTATED         2        0        2         9         1         0
  ATRNL1 WILD-TYPE      62        1       24        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATRNL1 MUTATED           0          1          2          2        1
  ATRNL1 WILD-TYPE        18          5         42         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ATRNL1 MUTATED           0         0
  ATRNL1 WILD-TYPE        12         1
D1630V3, multiclass
            clus
vv           ATRNL1 MUTATED ATRNL1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               9               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  ATRNL1 MUTATED     1   4  15   2
  ATRNL1 WILD-TYPE   8  63 234  39
D1630V4, multiclass
    clus
vv   ATRNL1 MUTATED ATRNL1 WILD-TYPE
  T1              1                8
  T2              4               63
  T3             15              234
  T4              2               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
  ATRNL1 MUTATED    16   3   3
  ATRNL1 WILD-TYPE 204  78  63
D1630V5, multiclass
    clus
vv   ATRNL1 MUTATED ATRNL1 WILD-TYPE
  N0             16              204
  N1              3               78
  N2              3               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"
D1630V6, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    16   1
  ATRNL1 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     16    1
  ATRNL1 WILD-TYPE  269   47
   clus
vv  ATRNL1 MUTATED ATRNL1 WILD-TYPE
  0             16              269
  1              1               47
[1] 2 2
[1] FALSE
D1630V7, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    10  12
  ATRNL1 WILD-TYPE 160 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     10   12
  ATRNL1 WILD-TYPE  160  185
        clus
vv       ATRNL1 MUTATED ATRNL1 WILD-TYPE
  FEMALE             10              160
  MALE               12              185
[1] 2 2
[1] FALSE
D1630V8, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    15   0
  ATRNL1 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     15    0
  ATRNL1 WILD-TYPE  285    8
     clus
vv    ATRNL1 MUTATED ATRNL1 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D1630V9, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    14   6
  ATRNL1 WILD-TYPE 300  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     14    6
  ATRNL1 WILD-TYPE  300   42
                               clus
vv                              ATRNL1 MUTATED ATRNL1 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATRNL1 MUTATED    14   0   0   2
  ATRNL1 WILD-TYPE 245   3  22  19
D1630V10, multiclass
    clus
vv   ATRNL1 MUTATED ATRNL1 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              0               22
  RX              2               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"
D1630V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATRNL1 MUTATED                                  0     2
  ATRNL1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATRNL1 MUTATED                           1    12
  ATRNL1 WILD-TYPE                        18   164
D1630V12, multiclass
                                  clus
vv                                 ATRNL1 MUTATED ATRNL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        12              164
[1] 4 2
[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 = ERN1 MUTATION ANALYSIS
D1631V1, survival
                sevent
clus2              0   1
  ERN1 MUTATED     2   1
  ERN1 WILD-TYPE 275  77
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            352 
  ERN1 MUTATED ERN1 WILD-TYPE 
             1             77 
$`ERN1 MUTATED`
TCGA-AZ-6601 TCGA-AA-3968 TCGA-CM-5860 
      100.01        21.99        32.02 

$`ERN1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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         22.045 
[1] "22.0 - 100.0 (32.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.2"
D1631V2, continuous
                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      63        1       25       107         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ERN1 MUTATED           0
  ERN1 WILD-TYPE         1
D1631V3, multiclass
            clus
vv           ERN1 MUTATED ERN1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ERN1 MUTATED     0   1   2   0
  ERN1 WILD-TYPE   9  66 247  41
D1631V4, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            0             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
  ERN1 MUTATED     3   0   0
  ERN1 WILD-TYPE 217  81  66
D1631V5, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  N0            3            217
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1631V6, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  282   48
   clus
vv  ERN1 MUTATED ERN1 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1631V7, binary
                cls
clus               0   1
  ERN1 MUTATED     1   2
  ERN1 WILD-TYPE 169 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      1    2
  ERN1 WILD-TYPE  169  195
        clus
vv       ERN1 MUTATED ERN1 WILD-TYPE
  FEMALE            1            169
  MALE              2            195
[1] 2 2
[1] FALSE
D1631V8, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  297    8
     clus
vv    ERN1 MUTATED ERN1 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1631V9, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  311   48
                               clus
vv                              ERN1 MUTATED ERN1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ERN1 MUTATED     2   0   0   0
  ERN1 WILD-TYPE 257   3  22  21
D1631V10, multiclass
[1] "Remove cluster labels:" "ERN1 MUTATED"          
clus
  ERN1 MUTATED ERN1 WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     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-3527 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-2676     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-3502     TCGA-AA-3510 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660 
"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-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     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-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3971     TCGA-AA-3973     TCGA-AA-3975 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N     TCGA-AA-A00O 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"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-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6889 
"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-4682     TCGA-CA-5254 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
D1631V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERN1 MUTATED                                  0     0
  ERN1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ERN1 MUTATED                           0     2
  ERN1 WILD-TYPE                        19   174
D1631V12, multiclass
[1] "Remove cluster labels:" "ERN1 MUTATED"          
clus
  ERN1 MUTATED ERN1 WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285     TCGA-G4-6310 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-2676     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-A6-5656 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660     TCGA-A6-5661 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665     TCGA-A6-5666 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141     TCGA-A6-6142 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6648     TCGA-A6-6651     TCGA-A6-6652     TCGA-A6-6653 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781     TCGA-A6-6782 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6899 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"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-5913     TCGA-CK-5914     TCGA-CK-5915 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5861     TCGA-CM-5862 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 

Clustering(1632) Variable = BTBD7 MUTATION ANALYSIS
D1632V1, survival
                 sevent
clus2               0   1
  BTBD7 MUTATED    10   1
  BTBD7 WILD-TYPE 267  77
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             11             344 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        32.75        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       23.87        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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 
       36.00        13.78 

  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           22.06 
[1] "1.0 - 46.8 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1632V2, continuous
                 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      62        1       25       102         7         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  BTBD7 MUTATED           1
  BTBD7 WILD-TYPE         0
D1632V3, multiclass
            clus
vv           BTBD7 MUTATED BTBD7 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              12
  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   9  65 241  39
D1632V4, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             2              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
  BTBD7 MUTATED    10   1   1
  BTBD7 WILD-TYPE 210  80  65
D1632V5, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1632V6, binary
                 cls
clus                0   1
  BTBD7 MUTATED     9   1
  BTBD7 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      9    1
  BTBD7 WILD-TYPE  276   47
   clus
vv  BTBD7 MUTATED BTBD7 WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1632V7, binary
                 cls
clus                0   1
  BTBD7 MUTATED     5   7
  BTBD7 WILD-TYPE 165 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      5    7
  BTBD7 WILD-TYPE  165  190
        clus
vv       BTBD7 MUTATED BTBD7 WILD-TYPE
  FEMALE             5             165
  MALE               7             190
[1] 2 2
[1] FALSE
D1632V8, binary
                 cls
clus                0   1
  BTBD7 MUTATED    10   0
  BTBD7 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     10    0
  BTBD7 WILD-TYPE  290    8
     clus
vv    BTBD7 MUTATED BTBD7 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1632V9, binary
                 cls
clus                0   1
  BTBD7 MUTATED     9   3
  BTBD7 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      9    3
  BTBD7 WILD-TYPE  305   45
                               clus
vv                              BTBD7 MUTATED BTBD7 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BTBD7 MUTATED    11   0   0   0
  BTBD7 WILD-TYPE 248   3  22  21
D1632V10, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             0              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"
D1632V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTBD7 MUTATED                                  0     0
  BTBD7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTBD7 MUTATED                           1     7
  BTBD7 WILD-TYPE                        18   169
D1632V12, multiclass
                                  clus
vv                                 BTBD7 MUTATED BTBD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = COL11A1 MUTATION ANALYSIS
D1633V1, survival
                   sevent
clus2                 0   1
  COL11A1 MUTATED    34   8
  COL11A1 WILD-TYPE 243  70
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               42               313 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
                8                70 
$`COL11A1 MUTATED`
TCGA-AA-3552 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3715 TCGA-AD-6895 TCGA-G4-6586 
       13.02         6.05         0.92        19.04        25.08        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6648 TCGA-AA-3492 
       26.17        79.69        22.06        22.52        25.18         3.02 
TCGA-AA-3510 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-3968 
       63.98        37.05         5.03        26.99        33.01        21.99 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AD-6889 
       25.02        34.98        15.02         1.02        12.16        83.24 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 
       27.42        14.50        21.44        58.39         1.41        88.21 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6171 TCGA-D5-6924 
        6.77        12.76        32.02        17.03        14.04        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-DM-A28K TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6626 
        9.44        11.64        98.24        53.62        85.48        46.75 

$`COL11A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99        19.99        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       63.62        22.09        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       23.61        22.09        32.71        27.09         8.38        25.08 
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-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       11.01         5.98        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        0.20        17.82         5.13        22.36        62.79        49.41 
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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       10.13        12.43         9.04        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 
       74.56        65.85        44.68        55.04        61.91        36.00 
TCGA-G4-6323 
       13.78 

  COL11A1 MUTATED COL11A1 WILD-TYPE 
             0.92              0.00 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
            98.24            148.01 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
            22.29             22.03 
[1] "0.9 - 98.2 (22.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1633V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL11A1 MUTATED         7        0        6        17         4         0
  COL11A1 WILD-TYPE      57        1       20        91         4         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL11A1 MUTATED           1          0          2          1        3
  COL11A1 WILD-TYPE        17          6         42         32       32
                   vv
clus                STAGE IVA STAGE IVB
  COL11A1 MUTATED           2         0
  COL11A1 WILD-TYPE        10         1
D1633V3, multiclass
            clus
vv           COL11A1 MUTATED COL11A1 WILD-TYPE
  STAGE I                  7                57
  STAGE IA                 0                 1
  STAGE II                 6                20
  STAGE IIA               17                91
  STAGE IIB                4                 4
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 3                32
  STAGE IVA                2                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
  COL11A1 MUTATED     1   7  29   8
  COL11A1 WILD-TYPE   8  60 220  33
D1633V4, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  T1               1                 8
  T2               7                60
  T3              29               220
  T4               8                33
[1] 4 2
[1] TRUE
[1] "dimension 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    37   5   3
  COL11A1 WILD-TYPE 183  76  63
D1633V5, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  N0              37               183
  N1               5                76
  N2               3                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"
D1633V6, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    34   5
  COL11A1 WILD-TYPE 251  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     34    5
  COL11A1 WILD-TYPE  251   43
   clus
vv  COL11A1 MUTATED COL11A1 WILD-TYPE
  0              34               251
  1               5                43
[1] 2 2
[1] FALSE
D1633V7, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    22  23
  COL11A1 WILD-TYPE 148 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     22   23
  COL11A1 WILD-TYPE  148  174
        clus
vv       COL11A1 MUTATED COL11A1 WILD-TYPE
  FEMALE              22               148
  MALE                23               174
[1] 2 2
[1] FALSE
D1633V8, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    40   0
  COL11A1 WILD-TYPE 260   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     40    0
  COL11A1 WILD-TYPE  260    8
     clus
vv    COL11A1 MUTATED COL11A1 WILD-TYPE
  NO               40               260
  YES               0                 8
[1] 2 2
[1] FALSE
D1633V9, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    40   5
  COL11A1 WILD-TYPE 274  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     40    5
  COL11A1 WILD-TYPE  274   43
                               clus
vv                              COL11A1 MUTATED COL11A1 WILD-TYPE
  COLON ADENOCARCINOMA                       40               274
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  COL11A1 MUTATED    33   0   2   2
  COL11A1 WILD-TYPE 226   3  20  19
D1633V10, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  R0              33               226
  R1               0                 3
  R2               2                20
  RX               2                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"
D1633V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL11A1 MUTATED                                  0     2
  COL11A1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COL11A1 MUTATED                           1    25
  COL11A1 WILD-TYPE                        18   151
D1633V12, multiclass
                                  clus
vv                                 COL11A1 MUTATED COL11A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         25               151
[1] 4 2
[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 = TTLL13 MUTATION ANALYSIS
D1634V1, survival
                  sevent
clus2                0   1
  TTLL13 MUTATED     5   0
  TTLL13 WILD-TYPE 272  78
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               5              350 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               0               78 
$`TTLL13 MUTATED`
TCGA-AA-3713 TCGA-A6-5661 TCGA-AA-3815 TCGA-AA-3947 TCGA-CA-6717 
       19.04        33.53        33.04        33.01        12.76 

$`TTLL13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TTLL13 MUTATED TTLL13 WILD-TYPE 
           12.76             0.00 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
           33.53           148.01 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
          33.010           22.045 
[1] "12.8 - 33.5 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1634V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTLL13 MUTATED         0        0        0         3         1         0
  TTLL13 WILD-TYPE      64        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TTLL13 MUTATED           0          0          0          0        1
  TTLL13 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  TTLL13 MUTATED           0         0
  TTLL13 WILD-TYPE        12         1
D1634V3, multiclass
            clus
vv           TTLL13 MUTATED TTLL13 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  TTLL13 MUTATED     0   0   4   1
  TTLL13 WILD-TYPE   9  67 245  40
D1634V4, multiclass
    clus
vv   TTLL13 MUTATED TTLL13 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              1               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
  TTLL13 MUTATED     5   0   0
  TTLL13 WILD-TYPE 215  81  66
D1634V5, multiclass
    clus
vv   TTLL13 MUTATED TTLL13 WILD-TYPE
  N0              5              215
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1634V6, binary
                  cls
clus                 0   1
  TTLL13 MUTATED     4   1
  TTLL13 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTLL13 MUTATED      4    1
  TTLL13 WILD-TYPE  281   47
   clus
vv  TTLL13 MUTATED TTLL13 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1634V7, binary
                  cls
clus                 0   1
  TTLL13 MUTATED     3   2
  TTLL13 WILD-TYPE 167 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTLL13 MUTATED      3    2
  TTLL13 WILD-TYPE  167  195
        clus
vv       TTLL13 MUTATED TTLL13 WILD-TYPE
  FEMALE              3              167
  MALE                2              195
[1] 2 2
[1] FALSE
D1634V8, binary
                  cls
clus                 0   1
  TTLL13 MUTATED     4   1
  TTLL13 WILD-TYPE 296   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTLL13 MUTATED      4    1
  TTLL13 WILD-TYPE  296    7
     clus
vv    TTLL13 MUTATED TTLL13 WILD-TYPE
  NO               4              296
  YES              1                7
[1] 2 2
[1] FALSE
D1634V9, binary
                  cls
clus                 0   1
  TTLL13 MUTATED     3   2
  TTLL13 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTLL13 MUTATED      3    2
  TTLL13 WILD-TYPE  311   46
                               clus
vv                              TTLL13 MUTATED TTLL13 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TTLL13 MUTATED     3   0   1   1
  TTLL13 WILD-TYPE 256   3  21  20
D1634V10, multiclass
    clus
vv   TTLL13 MUTATED TTLL13 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              1               21
  RX              1               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"
D1634V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTLL13 MUTATED                                  0     1
  TTLL13 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TTLL13 MUTATED                           1     0
  TTLL13 WILD-TYPE                        18   176
D1634V12, multiclass
[1] "Remove cluster labels:" "TTLL13 MUTATED"        
clus
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665       TCGA-A6-5666 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652       TCGA-A6-6653 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6718       TCGA-CA-6719 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 

Clustering(1635) Variable = RPS6KC1 MUTATION ANALYSIS
D1635V1, survival
                   sevent
clus2                 0   1
  RPS6KC1 MUTATED    10   3
  RPS6KC1 WILD-TYPE 267  75
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
               13               342 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
                3                75 
$`RPS6KC1 MUTATED`
TCGA-AA-3713 TCGA-A6-6780 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 
       19.04        20.12        53.00        33.01        25.02        34.98 
TCGA-AA-A02K TCGA-AD-6889 TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-5537 
       14.01        83.24        21.44        12.76        15.02        45.40 
TCGA-D5-6532 
       18.25 

$`RPS6KC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
            12.76              0.00 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
            83.24            148.01 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
           21.440            22.075 
[1] "12.8 - 83.2 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1635V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPS6KC1 MUTATED         0        0        1         7         3         0
  RPS6KC1 WILD-TYPE      64        1       25       101         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KC1 MUTATED           1          0          0          0        2
  RPS6KC1 WILD-TYPE        17          6         44         33       33
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KC1 MUTATED           0         0
  RPS6KC1 WILD-TYPE        12         1
D1635V3, multiclass
            clus
vv           RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                7               101
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 2                33
  STAGE IVA                0                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
  RPS6KC1 MUTATED     0   1  10   4
  RPS6KC1 WILD-TYPE   9  66 239  37
D1635V4, multiclass
    clus
vv   RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              10               239
  T4               4                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
  RPS6KC1 MUTATED    12   0   3
  RPS6KC1 WILD-TYPE 208  81  63
D1635V5, multiclass
    clus
vv   RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  N0              12               208
  N1               0                81
  N2               3                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"
D1635V6, binary
                   cls
clus                  0   1
  RPS6KC1 MUTATED     8   2
  RPS6KC1 WILD-TYPE 277  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KC1 MUTATED      8    2
  RPS6KC1 WILD-TYPE  277   46
   clus
vv  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  0               8               277
  1               2                46
[1] 2 2
[1] FALSE
D1635V7, binary
                   cls
clus                  0   1
  RPS6KC1 MUTATED     4  11
  RPS6KC1 WILD-TYPE 166 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KC1 MUTATED      4   11
  RPS6KC1 WILD-TYPE  166  186
        clus
vv       RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  FEMALE               4               166
  MALE                11               186
[1] 2 2
[1] FALSE
D1635V8, binary
                   cls
clus                  0   1
  RPS6KC1 MUTATED    12   1
  RPS6KC1 WILD-TYPE 288   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KC1 MUTATED     12    1
  RPS6KC1 WILD-TYPE  288    7
     clus
vv    RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  NO               12               288
  YES               1                 7
[1] 2 2
[1] FALSE
D1635V9, binary
                   cls
clus                  0   1
  RPS6KC1 MUTATED    12   3
  RPS6KC1 WILD-TYPE 302  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KC1 MUTATED     12    3
  RPS6KC1 WILD-TYPE  302   45
                               clus
vv                              RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  COLON ADENOCARCINOMA                       12               302
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RPS6KC1 MUTATED     8   0   2   3
  RPS6KC1 WILD-TYPE 251   3  20  18
D1635V10, multiclass
    clus
vv   RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               2                20
  RX               3                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"
D1635V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KC1 MUTATED                                  0     2
  RPS6KC1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KC1 MUTATED                           0     6
  RPS6KC1 WILD-TYPE                        19   170
D1635V12, multiclass
                                  clus
vv                                 RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = ZNF350 MUTATION ANALYSIS
D1636V1, survival
                  sevent
clus2                0   1
  ZNF350 MUTATED     7   1
  ZNF350 WILD-TYPE 270  77
  ZNF350 MUTATED ZNF350 WILD-TYPE 
               8              347 
  ZNF350 MUTATED ZNF350 WILD-TYPE 
               1               77 
$`ZNF350 MUTATED`
TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6718 
        0.92        25.02        18.05        34.98        58.39        10.06 
TCGA-CM-6162 TCGA-F4-6806 
       12.00        41.42 

$`ZNF350 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF350 MUTATED ZNF350 WILD-TYPE 
            0.92             0.00 
  ZNF350 MUTATED ZNF350 WILD-TYPE 
           58.39           148.01 
  ZNF350 MUTATED ZNF350 WILD-TYPE 
          21.535           22.060 
[1] "0.9 - 58.4 (21.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1636V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF350 MUTATED         1        0        0         3         1         0
  ZNF350 WILD-TYPE      63        1       26       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF350 MUTATED           1          0          2          0        0
  ZNF350 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF350 MUTATED           0         0
  ZNF350 WILD-TYPE        12         1
D1636V3, multiclass
            clus
vv           ZNF350 MUTATED ZNF350 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF350 MUTATED     0   2   5   2
  ZNF350 WILD-TYPE   9  65 244  39
D1636V4, multiclass
    clus
vv   ZNF350 MUTATED ZNF350 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              2               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
  ZNF350 MUTATED     6   3   0
  ZNF350 WILD-TYPE 214  78  66
D1636V5, multiclass
    clus
vv   ZNF350 MUTATED ZNF350 WILD-TYPE
  N0              6              214
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1636V6, binary
                  cls
clus                 0   1
  ZNF350 MUTATED     8   0
  ZNF350 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF350 MUTATED      8    0
  ZNF350 WILD-TYPE  277   48
   clus
vv  ZNF350 MUTATED ZNF350 WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1636V7, binary
                  cls
clus                 0   1
  ZNF350 MUTATED     5   4
  ZNF350 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF350 MUTATED      5    4
  ZNF350 WILD-TYPE  165  193
        clus
vv       ZNF350 MUTATED ZNF350 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1636V8, binary
                  cls
clus                 0   1
  ZNF350 MUTATED     8   0
  ZNF350 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF350 MUTATED      8    0
  ZNF350 WILD-TYPE  292    8
     clus
vv    ZNF350 MUTATED ZNF350 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1636V9, binary
                  cls
clus                 0   1
  ZNF350 MUTATED     7   2
  ZNF350 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF350 MUTATED      7    2
  ZNF350 WILD-TYPE  307   46
                               clus
vv                              ZNF350 MUTATED ZNF350 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF350 MUTATED     7   0   0   1
  ZNF350 WILD-TYPE 252   3  22  20
D1636V10, multiclass
    clus
vv   ZNF350 MUTATED ZNF350 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1636V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF350 MUTATED                                  0     1
  ZNF350 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF350 MUTATED                           0     3
  ZNF350 WILD-TYPE                        19   173
D1636V12, multiclass
                                  clus
vv                                 ZNF350 MUTATED ZNF350 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ITPRIPL1 MUTATION ANALYSIS
D1637V1, survival
                    sevent
clus2                  0   1
  ITPRIPL1 MUTATED     7   0
  ITPRIPL1 WILD-TYPE 270  78
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 7                348 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 0                 78 
$`ITPRIPL1 MUTATED`
TCGA-G4-6625 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3949 TCGA-AZ-4315 TCGA-D5-6927 
       91.79        19.66        35.01        26.01        58.39         9.44 
TCGA-D5-6930 
       13.35 

$`ITPRIPL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
              9.44               0.00 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
             91.79             148.01 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
            26.010             22.045 
[1] "9.4 - 91.8 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1637V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITPRIPL1 MUTATED         1        0        0         4         0         0
  ITPRIPL1 WILD-TYPE      63        1       26       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITPRIPL1 MUTATED           0          0          1          1        0
  ITPRIPL1 WILD-TYPE        18          6         43         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  ITPRIPL1 MUTATED           0         0
  ITPRIPL1 WILD-TYPE        12         1
D1637V3, multiclass
            clus
vv           ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  ITPRIPL1 MUTATED     0   1   5   1
  ITPRIPL1 WILD-TYPE   9  66 244  40
D1637V4, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                5                244
  T4                1                 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
  ITPRIPL1 MUTATED     5   2   0
  ITPRIPL1 WILD-TYPE 215  79  66
D1637V5, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  N0                5                215
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1637V6, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     6   0
  ITPRIPL1 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      6    0
  ITPRIPL1 WILD-TYPE  279   48
   clus
vv  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D1637V7, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     2   5
  ITPRIPL1 WILD-TYPE 168 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      2    5
  ITPRIPL1 WILD-TYPE  168  192
        clus
vv       ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  FEMALE                2                168
  MALE                  5                192
[1] 2 2
[1] FALSE
D1637V8, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     7   0
  ITPRIPL1 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      7    0
  ITPRIPL1 WILD-TYPE  293    8
     clus
vv    ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1637V9, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     4   3
  ITPRIPL1 WILD-TYPE 310  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      4    3
  ITPRIPL1 WILD-TYPE  310   45
                               clus
vv                              ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ITPRIPL1 MUTATED     7   0   0   0
  ITPRIPL1 WILD-TYPE 252   3  22  21
D1637V10, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1637V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITPRIPL1 MUTATED                                  0     0
  ITPRIPL1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ITPRIPL1 MUTATED                           0     5
  ITPRIPL1 WILD-TYPE                        19   171
D1637V12, multiclass
                                  clus
vv                                 ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                171
[1] 4 2
[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 = CCDC18 MUTATION ANALYSIS
D1638V1, survival
                  sevent
clus2                0   1
  CCDC18 MUTATED     8   2
  CCDC18 WILD-TYPE 269  76
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              10              345 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
               2               76 
$`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 
       21.99        11.08        13.41        81.37 

$`CCDC18 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        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-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CCDC18 MUTATED CCDC18 WILD-TYPE 
            5.79             0.00 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
           81.37           148.01 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
           22.52            22.06 
[1] "5.8 - 81.4 (22.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1638V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC18 MUTATED         1        0        1         5         1         0
  CCDC18 WILD-TYPE      63        1       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC18 MUTATED           0          0          0          1        1
  CCDC18 WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC18 MUTATED           0         0
  CCDC18 WILD-TYPE        12         1
D1638V3, multiclass
            clus
vv           CCDC18 MUTATED CCDC18 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CCDC18 MUTATED     0   2   7   2
  CCDC18 WILD-TYPE   9  65 242  39
D1638V4, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              2               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
  CCDC18 MUTATED     9   1   1
  CCDC18 WILD-TYPE 211  80  65
D1638V5, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  N0              9              211
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1638V6, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     8   1
  CCDC18 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      8    1
  CCDC18 WILD-TYPE  277   47
   clus
vv  CCDC18 MUTATED CCDC18 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1638V7, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     6   5
  CCDC18 WILD-TYPE 164 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      6    5
  CCDC18 WILD-TYPE  164  192
        clus
vv       CCDC18 MUTATED CCDC18 WILD-TYPE
  FEMALE              6              164
  MALE                5              192
[1] 2 2
[1] FALSE
D1638V8, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     9   0
  CCDC18 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      9    0
  CCDC18 WILD-TYPE  291    8
     clus
vv    CCDC18 MUTATED CCDC18 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1638V9, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     9   2
  CCDC18 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      9    2
  CCDC18 WILD-TYPE  305   46
                               clus
vv                              CCDC18 MUTATED CCDC18 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC18 MUTATED     7   0   0   1
  CCDC18 WILD-TYPE 252   3  22  20
D1638V10, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              1               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"
D1638V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC18 MUTATED                                  0     1
  CCDC18 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC18 MUTATED                           0     6
  CCDC18 WILD-TYPE                        19   170
D1638V12, multiclass
                                  clus
vv                                 CCDC18 MUTATED CCDC18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = CUTC MUTATION ANALYSIS
D1639V1, survival
                sevent
clus2              0   1
  CUTC MUTATED     3   1
  CUTC WILD-TYPE 274  77
  CUTC MUTATED CUTC WILD-TYPE 
             4            351 
  CUTC MUTATED CUTC WILD-TYPE 
             1             77 
$`CUTC MUTATED`
TCGA-AZ-6608 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-5666 
        1.94        79.69        22.06        32.71 

$`CUTC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       23.61        22.09        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CUTC MUTATED CUTC WILD-TYPE 
          1.94           0.00 
  CUTC MUTATED CUTC WILD-TYPE 
         79.69         148.01 
  CUTC MUTATED CUTC WILD-TYPE 
        27.385         22.030 
[1] "1.9 - 79.7 (27.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1639V2, continuous
                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      63        1       26       106         8         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        18          5         44         33       35        12
                vv
clus             STAGE IVB
  CUTC MUTATED           0
  CUTC WILD-TYPE         1
D1639V3, multiclass
            clus
vv           CUTC MUTATED CUTC WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CUTC MUTATED     0   2   2   1
  CUTC WILD-TYPE   9  65 247  40
D1639V4, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  T1            0              9
  T2            2             65
  T3            2            247
  T4            1             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
  CUTC MUTATED     4   1   0
  CUTC WILD-TYPE 216  80  66
D1639V5, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  N0            4            216
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1639V6, binary
                cls
clus               0   1
  CUTC MUTATED     5   0
  CUTC WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      5    0
  CUTC WILD-TYPE  280   48
   clus
vv  CUTC MUTATED CUTC WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1639V7, binary
                cls
clus               0   1
  CUTC MUTATED     3   2
  CUTC WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      3    2
  CUTC WILD-TYPE  167  195
        clus
vv       CUTC MUTATED CUTC WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D1639V8, binary
                cls
clus               0   1
  CUTC MUTATED     4   0
  CUTC WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      4    0
  CUTC WILD-TYPE  296    8
     clus
vv    CUTC MUTATED CUTC WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1639V9, binary
                cls
clus               0   1
  CUTC MUTATED     5   0
  CUTC WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      5    0
  CUTC WILD-TYPE  309   48
                               clus
vv                              CUTC MUTATED CUTC WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CUTC MUTATED     3   0   0   0
  CUTC WILD-TYPE 256   3  22  21
D1639V10, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1639V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUTC MUTATED                                  0     0
  CUTC WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUTC MUTATED                           0     4
  CUTC WILD-TYPE                        19   172
D1639V12, multiclass
                                  clus
vv                                 CUTC MUTATED CUTC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = GON4L MUTATION ANALYSIS
D1640V1, survival
                 sevent
clus2               0   1
  GON4L MUTATED    16   3
  GON4L WILD-TYPE 261  75
  GON4L MUTATED GON4L WILD-TYPE 
             19             336 
  GON4L MUTATED GON4L WILD-TYPE 
              3              75 
$`GON4L MUTATED`
TCGA-G4-6586 TCGA-G4-6628 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6780 
       35.80        79.69        32.75        22.06        21.76        20.12 
TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 
       63.98         0.00        31.00        34.98         1.02        83.24 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5341 TCGA-D5-6928 TCGA-DM-A1HA 
       88.21        49.41        12.76        29.06        11.64       131.51 
TCGA-G4-6323 
       13.78 

$`GON4L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  GON4L MUTATED GON4L WILD-TYPE 
              0               0 
  GON4L MUTATED GON4L WILD-TYPE 
         131.51          148.01 
  GON4L MUTATED GON4L WILD-TYPE 
          31.00           21.99 
[1] "0.0 - 131.5 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1640V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GON4L MUTATED         3        1        3         8         2         0
  GON4L WILD-TYPE      61        0       23       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GON4L MUTATED           0          1          1          1        0         0
  GON4L WILD-TYPE        18          5         43         32       35        12
                 vv
clus              STAGE IVB
  GON4L MUTATED           0
  GON4L WILD-TYPE         1
D1640V3, multiclass
            clus
vv           GON4L MUTATED GON4L WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               3              23
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  GON4L MUTATED     2   2  13   2
  GON4L WILD-TYPE   7  65 236  39
D1640V4, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  T1             2               7
  T2             2              65
  T3            13             236
  T4             2              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
  GON4L MUTATED    17   2   1
  GON4L WILD-TYPE 203  79  65
D1640V5, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  N0            17             203
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1640V6, binary
                 cls
clus                0   1
  GON4L MUTATED    16   0
  GON4L WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     16    0
  GON4L WILD-TYPE  269   48
   clus
vv  GON4L MUTATED GON4L WILD-TYPE
  0            16             269
  1             0              48
[1] 2 2
[1] FALSE
D1640V7, binary
                 cls
clus                0   1
  GON4L MUTATED    12   8
  GON4L WILD-TYPE 158 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     12    8
  GON4L WILD-TYPE  158  189
        clus
vv       GON4L MUTATED GON4L WILD-TYPE
  FEMALE            12             158
  MALE               8             189
[1] 2 2
[1] FALSE
D1640V8, binary
                 cls
clus                0   1
  GON4L MUTATED    16   0
  GON4L WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     16    0
  GON4L WILD-TYPE  284    8
     clus
vv    GON4L MUTATED GON4L WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D1640V9, binary
                 cls
clus                0   1
  GON4L MUTATED    15   5
  GON4L WILD-TYPE 299  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     15    5
  GON4L WILD-TYPE  299   43
                               clus
vv                              GON4L MUTATED GON4L WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GON4L MUTATED    14   0   0   1
  GON4L WILD-TYPE 245   3  22  20
D1640V10, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  R0            14             245
  R1             0               3
  R2             0              22
  RX             1              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"
D1640V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GON4L MUTATED                                  0     2
  GON4L WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GON4L MUTATED                           1    11
  GON4L WILD-TYPE                        18   165
D1640V12, multiclass
                                  clus
vv                                 GON4L MUTATED GON4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(1641) Variable = PLCG2 MUTATION ANALYSIS
D1641V1, survival
                 sevent
clus2               0   1
  PLCG2 MUTATED    14   4
  PLCG2 WILD-TYPE 263  74
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             18             337 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
              4              74 
$`PLCG2 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-6138 TCGA-AA-3492 
        6.05        19.04        35.80        26.17        22.52         3.02 
TCGA-AA-3510 TCGA-AA-3812 TCGA-AA-3855 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 
       63.98        35.05        32.05        33.01         4.01        34.98 
TCGA-AA-A01P TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-6930 
       38.07        58.39        12.76        29.03        14.04        13.35 

$`PLCG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 
       20.28         7.04        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07         0.00        36.03         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PLCG2 MUTATED PLCG2 WILD-TYPE 
           3.02            0.00 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
          63.98          148.01 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
          27.60           21.99 
[1] "3.0 - 64.0 (27.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1641V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCG2 MUTATED         3        0        3         7         3         0
  PLCG2 WILD-TYPE      61        1       23       101         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCG2 MUTATED           1          0          0          0        1         0
  PLCG2 WILD-TYPE        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  PLCG2 MUTATED           0
  PLCG2 WILD-TYPE         1
D1641V3, multiclass
            clus
vv           PLCG2 MUTATED PLCG2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  PLCG2 MUTATED     0   3  11   4
  PLCG2 WILD-TYPE   9  64 238  37
D1641V4, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            11             238
  T4             4              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
  PLCG2 MUTATED    16   1   1
  PLCG2 WILD-TYPE 204  80  65
D1641V5, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  N0            16             204
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1641V6, binary
                 cls
clus                0   1
  PLCG2 MUTATED    17   1
  PLCG2 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     17    1
  PLCG2 WILD-TYPE  268   47
   clus
vv  PLCG2 MUTATED PLCG2 WILD-TYPE
  0            17             268
  1             1              47
[1] 2 2
[1] FALSE
D1641V7, binary
                 cls
clus                0   1
  PLCG2 MUTATED    10   8
  PLCG2 WILD-TYPE 160 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     10    8
  PLCG2 WILD-TYPE  160  189
        clus
vv       PLCG2 MUTATED PLCG2 WILD-TYPE
  FEMALE            10             160
  MALE               8             189
[1] 2 2
[1] FALSE
D1641V8, binary
                 cls
clus                0   1
  PLCG2 MUTATED    17   0
  PLCG2 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     17    0
  PLCG2 WILD-TYPE  283    8
     clus
vv    PLCG2 MUTATED PLCG2 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D1641V9, binary
                 cls
clus                0   1
  PLCG2 MUTATED    14   4
  PLCG2 WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     14    4
  PLCG2 WILD-TYPE  300   44
                               clus
vv                              PLCG2 MUTATED PLCG2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PLCG2 MUTATED    15   0   1   1
  PLCG2 WILD-TYPE 244   3  21  20
D1641V10, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             1              21
  RX             1              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"
D1641V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCG2 MUTATED                                  0     1
  PLCG2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCG2 MUTATED                           0     7
  PLCG2 WILD-TYPE                        19   169
D1641V12, multiclass
                                  clus
vv                                 PLCG2 MUTATED PLCG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = GLTSCR1 MUTATION ANALYSIS
D1642V1, survival
                   sevent
clus2                 0   1
  GLTSCR1 MUTATED     8   3
  GLTSCR1 WILD-TYPE 269  75
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               11               344 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                3                75 
$`GLTSCR1 MUTATED`
TCGA-AA-3870 TCGA-AA-3950 TCGA-AD-6548 TCGA-AZ-6601 TCGA-AA-3663 TCGA-AD-6889 
       29.98        24.00        21.37       100.01         6.97        83.24 
TCGA-CK-6751 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HA 
      124.27        54.61        16.14        13.35       131.51 

$`GLTSCR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        24.03        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
             6.97              0.00 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
           131.51            148.01 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
            29.98             22.01 
[1] "7.0 - 131.5 (30.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1642V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLTSCR1 MUTATED         3        0        2         3         0         0
  GLTSCR1 WILD-TYPE      61        1       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLTSCR1 MUTATED           0          0          1          1        1
  GLTSCR1 WILD-TYPE        18          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  GLTSCR1 MUTATED           0         0
  GLTSCR1 WILD-TYPE        12         1
D1642V3, multiclass
            clus
vv           GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  GLTSCR1 MUTATED     0   3   8   0
  GLTSCR1 WILD-TYPE   9  64 241  41
D1642V4, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               8               241
  T4               0                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
  GLTSCR1 MUTATED     8   1   2
  GLTSCR1 WILD-TYPE 212  80  64
D1642V5, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  N0               8               212
  N1               1                80
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1642V6, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     9   1
  GLTSCR1 WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      9    1
  GLTSCR1 WILD-TYPE  276   47
   clus
vv  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  0               9               276
  1               1                47
[1] 2 2
[1] FALSE
D1642V7, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     5   6
  GLTSCR1 WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      5    6
  GLTSCR1 WILD-TYPE  165  191
        clus
vv       GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D1642V8, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     9   0
  GLTSCR1 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      9    0
  GLTSCR1 WILD-TYPE  291    8
     clus
vv    GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D1642V9, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     7   4
  GLTSCR1 WILD-TYPE 307  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      7    4
  GLTSCR1 WILD-TYPE  307   44
                               clus
vv                              GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GLTSCR1 MUTATED     8   0   0   1
  GLTSCR1 WILD-TYPE 251   3  22  20
D1642V10, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               0                22
  RX               1                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"
D1642V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLTSCR1 MUTATED                                  0     1
  GLTSCR1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GLTSCR1 MUTATED                           0     7
  GLTSCR1 WILD-TYPE                        19   169
D1642V12, multiclass
                                  clus
vv                                 GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = OR9G4 MUTATION ANALYSIS
D1643V1, survival
                 sevent
clus2               0   1
  OR9G4 MUTATED     7   1
  OR9G4 WILD-TYPE 270  77
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             347 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              1              77 
$`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        12.39        12.76        15.12 
TCGA-F4-6807 TCGA-F4-6808 
       43.04        33.67 

$`OR9G4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19        12.69        12.36        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       34.42        41.42        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR9G4 MUTATED OR9G4 WILD-TYPE 
           4.01            0.00 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
          43.04          148.01 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
         24.395          22.060 
[1] "4.0 - 43.0 (24.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1643V2, continuous
                 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      62        1       26       106         6         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  OR9G4 MUTATED           0
  OR9G4 WILD-TYPE         1
D1643V3, multiclass
            clus
vv           OR9G4 MUTATED OR9G4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OR9G4 MUTATED     1   1   4   2
  OR9G4 WILD-TYPE   8  66 245  39
D1643V4, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  T1             1               8
  T2             1              66
  T3             4             245
  T4             2              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
  OR9G4 MUTATED     6   1   1
  OR9G4 WILD-TYPE 214  80  65
D1643V5, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1643V6, binary
                 cls
clus                0   1
  OR9G4 MUTATED     7   0
  OR9G4 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      7    0
  OR9G4 WILD-TYPE  278   48
   clus
vv  OR9G4 MUTATED OR9G4 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1643V7, binary
                 cls
clus                0   1
  OR9G4 MUTATED     5   3
  OR9G4 WILD-TYPE 165 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      5    3
  OR9G4 WILD-TYPE  165  194
        clus
vv       OR9G4 MUTATED OR9G4 WILD-TYPE
  FEMALE             5             165
  MALE               3             194
[1] 2 2
[1] FALSE
D1643V8, binary
                 cls
clus                0   1
  OR9G4 MUTATED     7   0
  OR9G4 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      7    0
  OR9G4 WILD-TYPE  293    8
     clus
vv    OR9G4 MUTATED OR9G4 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1643V9, binary
                 cls
clus                0   1
  OR9G4 MUTATED     5   3
  OR9G4 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      5    3
  OR9G4 WILD-TYPE  309   45
                               clus
vv                              OR9G4 MUTATED OR9G4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR9G4 MUTATED     6   0   0   2
  OR9G4 WILD-TYPE 253   3  22  19
D1643V10, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1643V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR9G4 MUTATED                                  0     2
  OR9G4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR9G4 MUTATED                           0     3
  OR9G4 WILD-TYPE                        19   173
D1643V12, multiclass
                                  clus
vv                                 OR9G4 MUTATED OR9G4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = NFATC2IP MUTATION ANALYSIS
D1644V1, survival
                    sevent
clus2                  0   1
  NFATC2IP MUTATED     1   1
  NFATC2IP WILD-TYPE 276  77
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
                 2                353 
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
                 1                 77 
$`NFATC2IP MUTATED`
TCGA-AZ-6598 TCGA-D5-5539 
       49.41        19.59 

$`NFATC2IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
             19.59               0.00 
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
             49.41             148.01 
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
             34.50              22.06 
[1] "19.6 - 49.4 (34.5)" "0.0 - 148.0 (22.1)"
[1] "Remove cluster labels:" "NFATC2IP MUTATED"      
D1644V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFATC2IP MUTATED         0        0        1         0         1         0
  NFATC2IP WILD-TYPE      64        1       25       108         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFATC2IP MUTATED           0          1          0          0        0
  NFATC2IP WILD-TYPE        18          5         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  NFATC2IP MUTATED           0         0
  NFATC2IP WILD-TYPE        12         1
D1644V3, multiclass
            clus
vv           NFATC2IP MUTATED NFATC2IP WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 0                108
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  NFATC2IP MUTATED     0   0   2   1
  NFATC2IP WILD-TYPE   9  67 247  40
D1644V4, multiclass
    clus
vv   NFATC2IP MUTATED NFATC2IP WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                2                247
  T4                1                 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
  NFATC2IP MUTATED     2   1   0
  NFATC2IP WILD-TYPE 218  80  66
D1644V5, multiclass
    clus
vv   NFATC2IP MUTATED NFATC2IP WILD-TYPE
  N0                2                218
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1644V6, binary
                    cls
clus                   0   1
  NFATC2IP MUTATED     1   0
  NFATC2IP WILD-TYPE 284  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NFATC2IP MUTATED      1    0
  NFATC2IP WILD-TYPE  284   48
   clus
vv  NFATC2IP MUTATED NFATC2IP WILD-TYPE
  0                1                284
  1                0                 48
[1] 2 2
[1] FALSE
D1644V7, binary
                    cls
clus                   0   1
  NFATC2IP MUTATED     2   1
  NFATC2IP WILD-TYPE 168 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NFATC2IP MUTATED      2    1
  NFATC2IP WILD-TYPE  168  196
        clus
vv       NFATC2IP MUTATED NFATC2IP WILD-TYPE
  FEMALE                2                168
  MALE                  1                196
[1] 2 2
[1] FALSE
D1644V8, binary
                    cls
clus                   0   1
  NFATC2IP MUTATED     2   0
  NFATC2IP WILD-TYPE 298   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NFATC2IP MUTATED      2    0
  NFATC2IP WILD-TYPE  298    8
     clus
vv    NFATC2IP MUTATED NFATC2IP WILD-TYPE
  NO                 2                298
  YES                0                  8
[1] 2 2
[1] FALSE
D1644V9, binary
                    cls
clus                   0   1
  NFATC2IP MUTATED     2   1
  NFATC2IP WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NFATC2IP MUTATED      2    1
  NFATC2IP WILD-TYPE  312   47
                               clus
vv                              NFATC2IP MUTATED NFATC2IP WILD-TYPE
  COLON ADENOCARCINOMA                         2                312
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  NFATC2IP MUTATED     1   0   0   1
  NFATC2IP WILD-TYPE 258   3  22  20
D1644V10, multiclass
[1] "Remove cluster labels:" "NFATC2IP MUTATED"      
clus
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
                 2                303 
        TCGA-A6-2677         TCGA-AA-3496         TCGA-AA-3520 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3527         TCGA-AA-3530 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3662         TCGA-AA-3672 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3697 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3814 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3860         TCGA-AA-3867 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3939         TCGA-AA-3950 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3972         TCGA-AA-3976 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3986         TCGA-AA-A00L 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A024         TCGA-AD-6548 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AZ-4681 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CK-5912         TCGA-G4-6310         TCGA-G4-6321 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6586         TCGA-G4-6588         TCGA-G4-6625 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6628         TCGA-A6-2671         TCGA-A6-2672 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2678 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3510         TCGA-AA-3511 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3517         TCGA-AA-3518 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3526         TCGA-AA-3529 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3544         TCGA-AA-3548 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3553         TCGA-AA-3555 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3561         TCGA-AA-3655 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3663         TCGA-AA-3664 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3673 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3678         TCGA-AA-3679         TCGA-AA-3680 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3684         TCGA-AA-3685 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3712         TCGA-AA-3811 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3815         TCGA-AA-3818 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3842 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3861         TCGA-AA-3864 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3869         TCGA-AA-3872 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3968 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3973         TCGA-AA-3975 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3989         TCGA-AA-3994 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00N         TCGA-AA-A00O 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A010         TCGA-AA-A017 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A029 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6889         TCGA-AD-6965 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AZ-4682         TCGA-CA-5254         TCGA-CA-5255 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CA-5796         TCGA-CA-5797         TCGA-CA-6715 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CA-6716         TCGA-CA-6717         TCGA-CA-6718 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4947         TCGA-CK-4948 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5913 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-F4-6459 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6315 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
D1644V11, continuous
[1] "Remove cluster labels:" "NFATC2IP MUTATED"      
clus
  NFATC2IP MUTATED NFATC2IP WILD-TYPE 
                 2                344 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3516         TCGA-AA-3520 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3527         TCGA-AA-3530 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3662         TCGA-AA-3672 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3697 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3814 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3860         TCGA-AA-3867 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3939         TCGA-AA-3950 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3972         TCGA-AA-3976 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3986         TCGA-AA-A00L 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A024         TCGA-AD-6548 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AD-6964 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6608         TCGA-DM-A285 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3510         TCGA-AA-3511 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3517         TCGA-AA-3518 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3526         TCGA-AA-3529 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3544         TCGA-AA-3548 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3553         TCGA-AA-3555 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3655         TCGA-AA-3660 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3663         TCGA-AA-3664         TCGA-AA-3666 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3673         TCGA-AA-3678 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3693 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3811         TCGA-AA-3812 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         TCGA-AA-3845 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3861         TCGA-AA-3864         TCGA-AA-3866 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3872         TCGA-AA-3875 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3941 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3955 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3973         TCGA-AA-3975 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3980         TCGA-AA-3982 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3989         TCGA-AA-3994 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00N         TCGA-AA-A00O 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A010         TCGA-AA-A017 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A029 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6889         TCGA-AD-6890 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AD-6899         TCGA-AD-6901         TCGA-AD-6963 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AD-6965         TCGA-AU-3779         TCGA-AU-6004 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4682 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6599 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-6715 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CK-4952         TCGA-CM-4743         TCGA-CM-4744 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5540         TCGA-D5-5541 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A28C 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6806 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6807         TCGA-F4-6808         TCGA-F4-6809 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-F4-6854         TCGA-F4-6855         TCGA-F4-6856 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6293         TCGA-G4-6299         TCGA-G4-6303 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6306         TCGA-G4-6307 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6309         TCGA-G4-6315         TCGA-G4-6317 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6626 
"NFATC2IP WILD-TYPE" "NFATC2IP WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFATC2IP MUTATED                                  0     0
  NFATC2IP WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  NFATC2IP MUTATED                           0     3
  NFATC2IP WILD-TYPE                        19   173
D1644V12, multiclass
                                  clus
vv                                 NFATC2IP MUTATED NFATC2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1645) Variable = C14ORF180 MUTATION ANALYSIS
D1645V1, survival
                     sevent
clus2                   0   1
  C14ORF180 MUTATED     2   2
  C14ORF180 WILD-TYPE 275  76
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 351 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  2                  76 
$`C14ORF180 MUTATED`
TCGA-G4-6628 TCGA-AU-6004 TCGA-AZ-6598 TCGA-DM-A1D7 
       79.69        27.09        49.41        13.32 

$`C14ORF180 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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               22.03 
[1] "13.3 - 79.7 (38.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1645V2, continuous
                     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      62        1       25       107         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF180 MUTATED           0          0          0          0        0
  C14ORF180 WILD-TYPE        18          6         44         33       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF180 MUTATED           0         0
  C14ORF180 WILD-TYPE        12         1
D1645V3, multiclass
            clus
vv           C14ORF180 MUTATED C14ORF180 WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  25
  STAGE IIA                  1                 107
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 0                  44
  STAGE IIIC                 0                  33
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C14ORF180 MUTATED     0   2   2   0
  C14ORF180 WILD-TYPE   9  65 247  41
D1645V4, multiclass
    clus
vv   C14ORF180 MUTATED C14ORF180 WILD-TYPE
  T1                 0                   9
  T2                 2                  65
  T3                 2                 247
  T4                 0                  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
  C14ORF180 MUTATED     4   0   0
  C14ORF180 WILD-TYPE 216  81  66
D1645V5, multiclass
    clus
vv   C14ORF180 MUTATED C14ORF180 WILD-TYPE
  N0                 4                 216
  N1                 0                  81
  N2                 0                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1645V6, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     3   0
  C14ORF180 WILD-TYPE 282  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      3    0
  C14ORF180 WILD-TYPE  282   48
   clus
vv  C14ORF180 MUTATED C14ORF180 WILD-TYPE
  0                 3                 282
  1                 0                  48
[1] 2 2
[1] FALSE
D1645V7, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     2   2
  C14ORF180 WILD-TYPE 168 195
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      2    2
  C14ORF180 WILD-TYPE  168  195
        clus
vv       C14ORF180 MUTATED C14ORF180 WILD-TYPE
  FEMALE                 2                 168
  MALE                   2                 195
[1] 2 2
[1] FALSE
D1645V8, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     2   0
  C14ORF180 WILD-TYPE 298   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      2    0
  C14ORF180 WILD-TYPE  298    8
     clus
vv    C14ORF180 MUTATED C14ORF180 WILD-TYPE
  NO                  2                 298
  YES                 0                   8
[1] 2 2
[1] FALSE
D1645V9, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     3   0
  C14ORF180 WILD-TYPE 311  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      3    0
  C14ORF180 WILD-TYPE  311   48
                               clus
vv                              C14ORF180 MUTATED C14ORF180 WILD-TYPE
  COLON ADENOCARCINOMA                          3                 311
  COLON MUCINOUS ADENOCARCINOMA                 0                  48
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF180 MUTATED     2   0   0   0
  C14ORF180 WILD-TYPE 257   3  22  21
D1645V10, multiclass
[1] "Remove cluster labels:" "C14ORF180 MUTATED"     
clus
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  2                 303 
         TCGA-A6-2677          TCGA-AA-3496          TCGA-AA-3520 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3527          TCGA-AA-3530 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3543          TCGA-AA-3552 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3554          TCGA-AA-3556          TCGA-AA-3560 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3562          TCGA-AA-3662          TCGA-AA-3672 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3697 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3713          TCGA-AA-3715          TCGA-AA-3814 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3860          TCGA-AA-3867 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3870          TCGA-AA-3939          TCGA-AA-3950 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3972          TCGA-AA-3976 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3979          TCGA-AA-3986          TCGA-AA-A00L 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A024          TCGA-AD-6548 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6895          TCGA-AZ-4681 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-5912          TCGA-G4-6310          TCGA-G4-6321 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6586          TCGA-G4-6588          TCGA-G4-6625 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2678          TCGA-A6-2683 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5657          TCGA-A6-5659 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-5661          TCGA-A6-5665          TCGA-A6-6781 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3489          TCGA-AA-3492          TCGA-AA-3502 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3510          TCGA-AA-3511          TCGA-AA-3514 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3517          TCGA-AA-3518          TCGA-AA-3519 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3526          TCGA-AA-3529          TCGA-AA-3532 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3534          TCGA-AA-3538          TCGA-AA-3542 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3544          TCGA-AA-3548          TCGA-AA-3549 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3555          TCGA-AA-3558 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3655          TCGA-AA-3660 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3663          TCGA-AA-3664          TCGA-AA-3666 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3667          TCGA-AA-3673          TCGA-AA-3678 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3693 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3695          TCGA-AA-3696          TCGA-AA-3710 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3811          TCGA-AA-3812 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3845 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3846          TCGA-AA-3848          TCGA-AA-3850 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3851          TCGA-AA-3852          TCGA-AA-3854 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3855          TCGA-AA-3856          TCGA-AA-3858 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3861          TCGA-AA-3864          TCGA-AA-3866 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3872          TCGA-AA-3875 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3877          TCGA-AA-3930          TCGA-AA-3941 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3947          TCGA-AA-3949          TCGA-AA-3955 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3956          TCGA-AA-3968          TCGA-AA-3971 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3973          TCGA-AA-3975          TCGA-AA-3984 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3989          TCGA-AA-3994          TCGA-AA-A004 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"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-A010          TCGA-AA-A017          TCGA-AA-A01D 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01F          TCGA-AA-A01G          TCGA-AA-A01I 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01K          TCGA-AA-A01P          TCGA-AA-A01Q 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01R          TCGA-AA-A01S          TCGA-AA-A01T 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01V          TCGA-AA-A01X          TCGA-AA-A01Z 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A022          TCGA-AA-A029          TCGA-AA-A02F 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A02H          TCGA-AA-A02J          TCGA-AA-A02K 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A02O          TCGA-AA-A02W          TCGA-AA-A02Y 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A03F          TCGA-AA-A03J          TCGA-AD-5900 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AD-6889          TCGA-AD-6965          TCGA-AU-3779 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AZ-4315          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-5913          TCGA-CK-5914          TCGA-CK-5915 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-5916          TCGA-CK-6746          TCGA-CK-6747 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-6748          TCGA-CK-6751          TCGA-CM-4743 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-4744          TCGA-CM-4746          TCGA-CM-4747 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-4752          TCGA-CM-5341          TCGA-CM-5344 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5348          TCGA-CM-5349          TCGA-CM-5860 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5861          TCGA-CM-5862          TCGA-CM-5863 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5864          TCGA-CM-5868          TCGA-CM-6161 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6162          TCGA-CM-6163          TCGA-CM-6164 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6165          TCGA-CM-6166          TCGA-CM-6167 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6168          TCGA-CM-6169          TCGA-CM-6170 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6171          TCGA-CM-6172          TCGA-CM-6674 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6675          TCGA-CM-6676          TCGA-CM-6677 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6678          TCGA-CM-6679          TCGA-CM-6680 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-5537          TCGA-D5-5538          TCGA-D5-5539 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-5540          TCGA-D5-5541          TCGA-D5-6529 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6532          TCGA-D5-6533          TCGA-D5-6534 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6535          TCGA-D5-6536          TCGA-D5-6537 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6538          TCGA-D5-6539          TCGA-D5-6540 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6541          TCGA-D5-6898          TCGA-D5-6920 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6922          TCGA-D5-6923          TCGA-D5-6924 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6926          TCGA-D5-6927          TCGA-D5-6928 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6929          TCGA-D5-6930          TCGA-D5-6931 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-F4-6459 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6460          TCGA-F4-6569          TCGA-F4-6570 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6703          TCGA-F4-6704          TCGA-F4-6805 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6806          TCGA-F4-6807          TCGA-F4-6808 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6809          TCGA-F4-6854          TCGA-F4-6855 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6856          TCGA-G4-6293          TCGA-G4-6299 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6315 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6323          TCGA-G4-6626 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
D1645V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF180 MUTATED                                  0     0
  C14ORF180 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF180 MUTATED                           0     4
  C14ORF180 WILD-TYPE                        19   172
D1645V12, multiclass
                                  clus
vv                                 C14ORF180 MUTATED C14ORF180 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            4                 172
[1] 4 2
[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 = MYLK4 MUTATION ANALYSIS
D1646V1, survival
                 sevent
clus2               0   1
  MYLK4 MUTATED    11   1
  MYLK4 WILD-TYPE 266  77
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             12             343 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
              1              77 
$`MYLK4 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-AZ-6601 TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3511 
       85.05        19.04       100.01        23.61        63.98         6.97 
TCGA-AA-3815 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6539 
       33.04        12.76        21.99        32.02        15.02        12.49 

$`MYLK4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3514 
       19.66        20.28         7.04         3.02        35.01         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYLK4 MUTATED MYLK4 WILD-TYPE 
           6.97            0.00 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
         100.01          148.01 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
          22.80           22.06 
[1] "7.0 - 100.0 (22.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "3.5"
D1646V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYLK4 MUTATED         0        0        4         4         0         0
  MYLK4 WILD-TYPE      64        1       22       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYLK4 MUTATED           0          0          1          0        1         1
  MYLK4 WILD-TYPE        18          6         43         33       34        11
                 vv
clus              STAGE IVB
  MYLK4 MUTATED           0
  MYLK4 WILD-TYPE         1
D1646V3, multiclass
            clus
vv           MYLK4 MUTATED MYLK4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  MYLK4 MUTATED     0   0  11   1
  MYLK4 WILD-TYPE   9  67 238  40
D1646V4, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            11             238
  T4             1              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
  MYLK4 MUTATED    10   1   1
  MYLK4 WILD-TYPE 210  80  65
D1646V5, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1646V6, binary
                 cls
clus                0   1
  MYLK4 MUTATED     9   2
  MYLK4 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED      9    2
  MYLK4 WILD-TYPE  276   46
   clus
vv  MYLK4 MUTATED MYLK4 WILD-TYPE
  0             9             276
  1             2              46
[1] 2 2
[1] FALSE
D1646V7, binary
                 cls
clus                0   1
  MYLK4 MUTATED     3   9
  MYLK4 WILD-TYPE 167 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED      3    9
  MYLK4 WILD-TYPE  167  188
        clus
vv       MYLK4 MUTATED MYLK4 WILD-TYPE
  FEMALE             3             167
  MALE               9             188
[1] 2 2
[1] FALSE
D1646V8, binary
                 cls
clus                0   1
  MYLK4 MUTATED    10   1
  MYLK4 WILD-TYPE 290   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED     10    1
  MYLK4 WILD-TYPE  290    7
     clus
vv    MYLK4 MUTATED MYLK4 WILD-TYPE
  NO             10             290
  YES             1               7
[1] 2 2
[1] FALSE
D1646V9, binary
                 cls
clus                0   1
  MYLK4 MUTATED    11   1
  MYLK4 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED     11    1
  MYLK4 WILD-TYPE  303   47
                               clus
vv                              MYLK4 MUTATED MYLK4 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYLK4 MUTATED     7   0   1   2
  MYLK4 WILD-TYPE 252   3  21  19
D1646V10, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             2              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"
D1646V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYLK4 MUTATED                                  0     1
  MYLK4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYLK4 MUTATED                           0     6
  MYLK4 WILD-TYPE                        19   170
D1646V12, multiclass
                                  clus
vv                                 MYLK4 MUTATED MYLK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = CENPJ MUTATION ANALYSIS
D1647V1, survival
                 sevent
clus2               0   1
  CENPJ MUTATED    13   6
  CENPJ WILD-TYPE 264  72
  CENPJ MUTATED CENPJ WILD-TYPE 
             19             336 
  CENPJ MUTATED CENPJ WILD-TYPE 
              6              72 
$`CENPJ MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-6141 TCGA-A6-6651 
        0.92        19.04        22.09        79.69         8.38        21.76 
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3851 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 
       19.66         6.97        33.07         4.01        34.98        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6537 TCGA-F4-6570 TCGA-G4-6303 
       12.76        10.06        14.04         4.80         6.18        65.85 
TCGA-G4-6323 
       13.78 

$`CENPJ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6652 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6626 
       44.68        55.04        85.48        61.91        36.00        46.75 

  CENPJ MUTATED CENPJ WILD-TYPE 
           0.92            0.00 
  CENPJ MUTATED CENPJ WILD-TYPE 
          79.69          148.01 
  CENPJ MUTATED CENPJ WILD-TYPE 
          14.04           22.47 
[1] "0.9 - 79.7 (14.0)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.8"
D1647V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CENPJ MUTATED         2        1        3         7         2         0
  CENPJ WILD-TYPE      62        0       23       101         6         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        16          6         42         32       34        12
                 vv
clus              STAGE IVB
  CENPJ MUTATED           0
  CENPJ WILD-TYPE         1
D1647V3, multiclass
            clus
vv           CENPJ MUTATED CENPJ WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  CENPJ MUTATED     0   3  13   4
  CENPJ WILD-TYPE   9  64 236  37
D1647V4, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  T1             0               9
  T2             3              64
  T3            13             236
  T4             4              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
  CENPJ MUTATED    15   6   0
  CENPJ WILD-TYPE 205  75  66
D1647V5, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  N0            15             205
  N1             6              75
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1647V6, binary
                 cls
clus                0   1
  CENPJ MUTATED    15   1
  CENPJ WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     15    1
  CENPJ WILD-TYPE  270   47
   clus
vv  CENPJ MUTATED CENPJ WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D1647V7, binary
                 cls
clus                0   1
  CENPJ MUTATED     9  12
  CENPJ WILD-TYPE 161 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED      9   12
  CENPJ WILD-TYPE  161  185
        clus
vv       CENPJ MUTATED CENPJ WILD-TYPE
  FEMALE             9             161
  MALE              12             185
[1] 2 2
[1] FALSE
D1647V8, binary
                 cls
clus                0   1
  CENPJ MUTATED    18   0
  CENPJ WILD-TYPE 282   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     18    0
  CENPJ WILD-TYPE  282    8
     clus
vv    CENPJ MUTATED CENPJ WILD-TYPE
  NO             18             282
  YES             0               8
[1] 2 2
[1] FALSE
D1647V9, binary
                 cls
clus                0   1
  CENPJ MUTATED    18   3
  CENPJ WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     18    3
  CENPJ WILD-TYPE  296   45
                               clus
vv                              CENPJ MUTATED CENPJ WILD-TYPE
  COLON ADENOCARCINOMA                     18             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CENPJ MUTATED    17   0   0   2
  CENPJ WILD-TYPE 242   3  22  19
D1647V10, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  R0            17             242
  R1             0               3
  R2             0              22
  RX             2              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"
D1647V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CENPJ MUTATED                                  0     2
  CENPJ WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CENPJ MUTATED                           2     9
  CENPJ WILD-TYPE                        17   167
D1647V12, multiclass
                                  clus
vv                                 CENPJ MUTATED CENPJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        9             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(1648) Variable = CHMP4B MUTATION ANALYSIS
D1648V1, survival
                  sevent
clus2                0   1
  CHMP4B MUTATED     2   1
  CHMP4B WILD-TYPE 275  77
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              352 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               1               77 
$`CHMP4B MUTATED`
TCGA-A6-6780 TCGA-AA-3811 TCGA-D5-6540 
       20.12        10.06        16.14 

$`CHMP4B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CHMP4B MUTATED CHMP4B WILD-TYPE 
           10.06             0.00 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
           20.12           148.01 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
           16.14            22.09 
[1] "10.1 - 20.1 (16.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D1648V2, continuous
                  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      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP4B MUTATED           1          0          0          0        0
  CHMP4B WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  CHMP4B MUTATED           0         0
  CHMP4B WILD-TYPE        12         1
D1648V3, multiclass
            clus
vv           CHMP4B MUTATED CHMP4B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  CHMP4B MUTATED     0   1   2   0
  CHMP4B WILD-TYPE   9  66 247  41
D1648V4, multiclass
    clus
vv   CHMP4B MUTATED CHMP4B WILD-TYPE
  T1              0                9
  T2              1               66
  T3              2              247
  T4              0               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
  CHMP4B MUTATED     2   0   1
  CHMP4B WILD-TYPE 218  81  65
D1648V5, multiclass
    clus
vv   CHMP4B MUTATED CHMP4B WILD-TYPE
  N0              2              218
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1648V6, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     2   0
  CHMP4B WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      2    0
  CHMP4B WILD-TYPE  283   48
   clus
vv  CHMP4B MUTATED CHMP4B WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D1648V7, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     1   2
  CHMP4B WILD-TYPE 169 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      1    2
  CHMP4B WILD-TYPE  169  195
        clus
vv       CHMP4B MUTATED CHMP4B WILD-TYPE
  FEMALE              1              169
  MALE                2              195
[1] 2 2
[1] FALSE
D1648V8, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     3   0
  CHMP4B WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      3    0
  CHMP4B WILD-TYPE  297    8
     clus
vv    CHMP4B MUTATED CHMP4B WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1648V9, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     1   2
  CHMP4B WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      1    2
  CHMP4B WILD-TYPE  313   46
                               clus
vv                              CHMP4B MUTATED CHMP4B WILD-TYPE
  COLON ADENOCARCINOMA                       1              313
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHMP4B MUTATED     2   0   0   0
  CHMP4B WILD-TYPE 257   3  22  21
D1648V10, multiclass
[1] "Remove cluster labels:" "CHMP4B MUTATED"        
clus
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               2              303 
      TCGA-A6-2677       TCGA-AA-3496       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-3527 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-2676       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-3502       TCGA-AA-3510 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660 
"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-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3842       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-3861 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       TCGA-AA-3872 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3941 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N       TCGA-AA-A00O 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"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-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6889 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682       TCGA-CA-5254 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
D1648V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHMP4B MUTATED                                  0     0
  CHMP4B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHMP4B MUTATED                           0     2
  CHMP4B WILD-TYPE                        19   174
D1648V12, multiclass
[1] "Remove cluster labels:" "CHMP4B MUTATED"        
clus
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6781       TCGA-A6-6782 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"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-5913       TCGA-CK-5914       TCGA-CK-5915 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 

Clustering(1649) Variable = C20ORF43 MUTATION ANALYSIS
D1649V1, survival
                    sevent
clus2                  0   1
  C20ORF43 MUTATED     3   0
  C20ORF43 WILD-TYPE 274  78
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                352 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 0                 78 
$`C20ORF43 MUTATED`
TCGA-AA-3510 TCGA-AY-6196 TCGA-CK-4947 
       63.98         0.20        17.56 

$`C20ORF43 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
               0.2                0.0 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
             63.98             148.01 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
            17.560             22.075 
[1] "0.2 - 64.0 (17.6)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "3300000"
D1649V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF43 MUTATED         0        0        1         0         0         0
  C20ORF43 WILD-TYPE      64        1       25       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF43 MUTATED           0          0          1          1        0
  C20ORF43 WILD-TYPE        18          6         43         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C20ORF43 MUTATED           0         0
  C20ORF43 WILD-TYPE        12         1
D1649V3, multiclass
            clus
vv           C20ORF43 MUTATED C20ORF43 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 0                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C20ORF43 MUTATED     0   0   2   1
  C20ORF43 WILD-TYPE   9  67 247  40
D1649V4, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                2                247
  T4                1                 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
  C20ORF43 MUTATED     1   1   1
  C20ORF43 WILD-TYPE 219  80  65
D1649V5, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  N0                1                219
  N1                1                 80
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1649V6, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     2   0
  C20ORF43 WILD-TYPE 283  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      2    0
  C20ORF43 WILD-TYPE  283   48
   clus
vv  C20ORF43 MUTATED C20ORF43 WILD-TYPE
  0                2                283
  1                0                 48
[1] 2 2
[1] FALSE
D1649V7, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     1   2
  C20ORF43 WILD-TYPE 169 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      1    2
  C20ORF43 WILD-TYPE  169  195
        clus
vv       C20ORF43 MUTATED C20ORF43 WILD-TYPE
  FEMALE                1                169
  MALE                  2                195
[1] 2 2
[1] FALSE
D1649V8, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     2   0
  C20ORF43 WILD-TYPE 298   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      2    0
  C20ORF43 WILD-TYPE  298    8
     clus
vv    C20ORF43 MUTATED C20ORF43 WILD-TYPE
  NO                 2                298
  YES                0                  8
[1] 2 2
[1] FALSE
D1649V9, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     2   1
  C20ORF43 WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      2    1
  C20ORF43 WILD-TYPE  312   47
                               clus
vv                              C20ORF43 MUTATED C20ORF43 WILD-TYPE
  COLON ADENOCARCINOMA                         2                312
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C20ORF43 MUTATED     2   0   0   1
  C20ORF43 WILD-TYPE 257   3  22  20
D1649V10, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  R0                2                257
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1649V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF43 MUTATED                                  0     0
  C20ORF43 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C20ORF43 MUTATED                           0     2
  C20ORF43 WILD-TYPE                        19   174
D1649V12, multiclass
[1] "Remove cluster labels:" "C20ORF43 MUTATED"      
clus
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6197         TCGA-AY-6386 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4323         TCGA-AZ-4616 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"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-CA-5254         TCGA-CA-5255 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-5796         TCGA-CA-5797         TCGA-CA-6715 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-6716         TCGA-CA-6717         TCGA-CA-6718 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4948         TCGA-CK-4950 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5913         TCGA-CK-5914 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 

Clustering(1650) Variable = CIZ1 MUTATION ANALYSIS
D1650V1, survival
                sevent
clus2              0   1
  CIZ1 MUTATED    12   2
  CIZ1 WILD-TYPE 265  76
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            14            341 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
             2             76 
$`CIZ1 MUTATED`
TCGA-AA-3715 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3542 TCGA-AA-3558 
       19.04        22.06        32.71        24.39        12.99        20.98 
TCGA-AA-3877 TCGA-AA-3980 TCGA-AA-3982 TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-6598 
       31.00        27.02        27.02        12.16        33.01        49.41 
TCGA-CK-6751 TCGA-CM-6162 
      124.27        12.00 

$`CIZ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        23.61        22.09        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        29.95        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CIZ1 MUTATED CIZ1 WILD-TYPE 
            12              0 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
        124.27         148.01 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
        25.705         21.990 
[1] "12.0 - 124.3 (25.7)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.7"
D1650V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CIZ1 MUTATED         6        0        3         1         0         1
  CIZ1 WILD-TYPE      58        1       23       107         8         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        18          6         42         32       35        11
                vv
clus             STAGE IVB
  CIZ1 MUTATED           0
  CIZ1 WILD-TYPE         1
D1650V3, multiclass
            clus
vv           CIZ1 MUTATED CIZ1 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             1             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
  CIZ1 MUTATED     1   5   7   2
  CIZ1 WILD-TYPE   8  62 242  39
D1650V4, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  T1            1              8
  T2            5             62
  T3            7            242
  T4            2             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
  CIZ1 MUTATED    11   3   1
  CIZ1 WILD-TYPE 209  78  65
D1650V5, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  N0           11            209
  N1            3             78
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1650V6, binary
                cls
clus               0   1
  CIZ1 MUTATED    11   1
  CIZ1 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     11    1
  CIZ1 WILD-TYPE  274   47
   clus
vv  CIZ1 MUTATED CIZ1 WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D1650V7, binary
                cls
clus               0   1
  CIZ1 MUTATED     8   7
  CIZ1 WILD-TYPE 162 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED      8    7
  CIZ1 WILD-TYPE  162  190
        clus
vv       CIZ1 MUTATED CIZ1 WILD-TYPE
  FEMALE            8            162
  MALE              7            190
[1] 2 2
[1] FALSE
D1650V8, binary
                cls
clus               0   1
  CIZ1 MUTATED    14   0
  CIZ1 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     14    0
  CIZ1 WILD-TYPE  286    8
     clus
vv    CIZ1 MUTATED CIZ1 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1650V9, binary
                cls
clus               0   1
  CIZ1 MUTATED    11   4
  CIZ1 WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     11    4
  CIZ1 WILD-TYPE  303   44
                               clus
vv                              CIZ1 MUTATED CIZ1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CIZ1 MUTATED     8   0   1   1
  CIZ1 WILD-TYPE 251   3  21  20
D1650V10, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            1             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"
D1650V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIZ1 MUTATED                                  0     0
  CIZ1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CIZ1 MUTATED                           1     7
  CIZ1 WILD-TYPE                        18   169
D1650V12, multiclass
                                  clus
vv                                 CIZ1 MUTATED CIZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       7            169
[1] 4 2
[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 = ZNF416 MUTATION ANALYSIS
D1651V1, survival
                  sevent
clus2                0   1
  ZNF416 MUTATED     4   3
  ZNF416 WILD-TYPE 273  75
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               7              348 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               3               75 
$`ZNF416 MUTATED`
TCGA-AZ-6601 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
      100.01        34.98        21.44        58.39        12.76        10.06 
TCGA-F4-6570 
        6.18 

$`ZNF416 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF416 MUTATED ZNF416 WILD-TYPE 
            6.18             0.00 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
          100.01           148.01 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
          21.440           22.075 
[1] "6.2 - 100.0 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1651V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF416 MUTATED         0        0        2         5         1         0
  ZNF416 WILD-TYPE      64        1       24       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF416 MUTATED           0          0          0          0        0
  ZNF416 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF416 MUTATED           0         0
  ZNF416 WILD-TYPE        12         1
D1651V3, multiclass
            clus
vv           ZNF416 MUTATED ZNF416 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF416 MUTATED     0   0   6   2
  ZNF416 WILD-TYPE   9  67 243  39
D1651V4, multiclass
    clus
vv   ZNF416 MUTATED ZNF416 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              2               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
  ZNF416 MUTATED     8   0   0
  ZNF416 WILD-TYPE 212  81  66
D1651V5, multiclass
    clus
vv   ZNF416 MUTATED ZNF416 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1651V6, binary
                  cls
clus                 0   1
  ZNF416 MUTATED     7   0
  ZNF416 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF416 MUTATED      7    0
  ZNF416 WILD-TYPE  278   48
   clus
vv  ZNF416 MUTATED ZNF416 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1651V7, binary
                  cls
clus                 0   1
  ZNF416 MUTATED     3   5
  ZNF416 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF416 MUTATED      3    5
  ZNF416 WILD-TYPE  167  192
        clus
vv       ZNF416 MUTATED ZNF416 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D1651V8, binary
                  cls
clus                 0   1
  ZNF416 MUTATED     7   0
  ZNF416 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF416 MUTATED      7    0
  ZNF416 WILD-TYPE  293    8
     clus
vv    ZNF416 MUTATED ZNF416 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1651V9, binary
                  cls
clus                 0   1
  ZNF416 MUTATED     7   1
  ZNF416 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF416 MUTATED      7    1
  ZNF416 WILD-TYPE  307   47
                               clus
vv                              ZNF416 MUTATED ZNF416 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF416 MUTATED     5   0   0   2
  ZNF416 WILD-TYPE 254   3  22  19
D1651V10, multiclass
    clus
vv   ZNF416 MUTATED ZNF416 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              2               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"
D1651V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF416 MUTATED                                  0     2
  ZNF416 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF416 MUTATED                           0     4
  ZNF416 WILD-TYPE                        19   172
D1651V12, multiclass
                                  clus
vv                                 ZNF416 MUTATED ZNF416 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = RBM16 MUTATION ANALYSIS
D1652V1, survival
                 sevent
clus2               0   1
  RBM16 MUTATED    11   4
  RBM16 WILD-TYPE 266  74
  RBM16 MUTATED RBM16 WILD-TYPE 
             15             340 
  RBM16 MUTATED RBM16 WILD-TYPE 
              4              74 
$`RBM16 MUTATED`
TCGA-AD-6964 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3821 
       10.88        32.75        32.71         6.97        26.99         1.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        4.01        34.98        83.24        58.39        49.41        12.76 
TCGA-CM-5861 TCGA-CM-6164 TCGA-DM-A1HA 
       15.02        29.03       131.51 

$`RBM16 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  RBM16 MUTATED RBM16 WILD-TYPE 
           1.02            0.00 
  RBM16 MUTATED RBM16 WILD-TYPE 
         131.51          148.01 
  RBM16 MUTATED RBM16 WILD-TYPE 
          29.03           22.01 
[1] "1.0 - 131.5 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1652V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM16 MUTATED         1        0        2         6         3         1
  RBM16 WILD-TYPE      63        1       24       102         5         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  RBM16 MUTATED           0
  RBM16 WILD-TYPE         1
D1652V3, multiclass
            clus
vv           RBM16 MUTATED RBM16 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  RBM16 MUTATED     0   1   9   5
  RBM16 WILD-TYPE   9  66 240  36
D1652V4, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             5              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
  RBM16 MUTATED    13   0   2
  RBM16 WILD-TYPE 207  81  64
D1652V5, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  N0            13             207
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1652V6, binary
                 cls
clus                0   1
  RBM16 MUTATED    13   0
  RBM16 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     13    0
  RBM16 WILD-TYPE  272   48
   clus
vv  RBM16 MUTATED RBM16 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D1652V7, binary
                 cls
clus                0   1
  RBM16 MUTATED     7   8
  RBM16 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      7    8
  RBM16 WILD-TYPE  163  189
        clus
vv       RBM16 MUTATED RBM16 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D1652V8, binary
                 cls
clus                0   1
  RBM16 MUTATED    13   0
  RBM16 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     13    0
  RBM16 WILD-TYPE  287    8
     clus
vv    RBM16 MUTATED RBM16 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D1652V9, binary
                 cls
clus                0   1
  RBM16 MUTATED    11   4
  RBM16 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     11    4
  RBM16 WILD-TYPE  303   44
                               clus
vv                              RBM16 MUTATED RBM16 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBM16 MUTATED    10   0   0   1
  RBM16 WILD-TYPE 249   3  22  20
D1652V10, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             1              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"
D1652V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM16 MUTATED                                  0     2
  RBM16 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM16 MUTATED                           0     8
  RBM16 WILD-TYPE                        19   168
D1652V12, multiclass
                                  clus
vv                                 RBM16 MUTATED RBM16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1653) Variable = MORC1 MUTATION ANALYSIS
D1653V1, survival
                 sevent
clus2               0   1
  MORC1 MUTATED    10   2
  MORC1 WILD-TYPE 267  76
  MORC1 MUTATED MORC1 WILD-TYPE 
             12             343 
  MORC1 MUTATED MORC1 WILD-TYPE 
              2              76 
$`MORC1 MUTATED`
TCGA-G4-6588 TCGA-A6-2676 TCGA-AA-3538 TCGA-AA-A00A TCGA-AA-A010 TCGA-AZ-4315 
       26.17        42.90        26.01        38.04        34.98        58.39 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5868 TCGA-D5-6533 
       12.59        12.76        10.06        13.02        17.03        25.48 

$`MORC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        19.00        30.02 
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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69        12.36        12.39        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-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        14.04        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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MORC1 MUTATED MORC1 WILD-TYPE 
          10.06            0.00 
  MORC1 MUTATED MORC1 WILD-TYPE 
          58.39          148.01 
  MORC1 MUTATED MORC1 WILD-TYPE 
         25.745          22.030 
[1] "10.1 - 58.4 (25.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1653V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MORC1 MUTATED         1        0        0         8         2         0
  MORC1 WILD-TYPE      63        1       26       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MORC1 MUTATED           0          0          0          0        0         1
  MORC1 WILD-TYPE        18          6         44         33       35        11
                 vv
clus              STAGE IVB
  MORC1 MUTATED           0
  MORC1 WILD-TYPE         1
D1653V3, multiclass
            clus
vv           MORC1 MUTATED MORC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              8             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  MORC1 MUTATED     0   1   8   4
  MORC1 WILD-TYPE   9  66 241  37
D1653V4, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             4              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
  MORC1 MUTATED    12   1   0
  MORC1 WILD-TYPE 208  80  66
D1653V5, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  N0            12             208
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1653V6, binary
                 cls
clus                0   1
  MORC1 MUTATED    12   1
  MORC1 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     12    1
  MORC1 WILD-TYPE  273   47
   clus
vv  MORC1 MUTATED MORC1 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D1653V7, binary
                 cls
clus                0   1
  MORC1 MUTATED     7   6
  MORC1 WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED      7    6
  MORC1 WILD-TYPE  163  191
        clus
vv       MORC1 MUTATED MORC1 WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D1653V8, binary
                 cls
clus                0   1
  MORC1 MUTATED    12   0
  MORC1 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     12    0
  MORC1 WILD-TYPE  288    8
     clus
vv    MORC1 MUTATED MORC1 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1653V9, binary
                 cls
clus                0   1
  MORC1 MUTATED    12   1
  MORC1 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     12    1
  MORC1 WILD-TYPE  302   47
                               clus
vv                              MORC1 MUTATED MORC1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MORC1 MUTATED    11   0   0   2
  MORC1 WILD-TYPE 248   3  22  19
D1653V10, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             2              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"
D1653V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MORC1 MUTATED                                  0     3
  MORC1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MORC1 MUTATED                           1     5
  MORC1 WILD-TYPE                        18   171
D1653V12, multiclass
                                  clus
vv                                 MORC1 MUTATED MORC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = ROR1 MUTATION ANALYSIS
D1654V1, survival
                sevent
clus2              0   1
  ROR1 MUTATED    18   1
  ROR1 WILD-TYPE 259  77
  ROR1 MUTATED ROR1 WILD-TYPE 
            19            336 
  ROR1 MUTATED ROR1 WILD-TYPE 
             1             77 
$`ROR1 MUTATED`
TCGA-AA-3697 TCGA-AA-3972 TCGA-G4-6588 TCGA-A6-2676 TCGA-AA-3502 TCGA-AA-3660 
       85.05        50.99        26.17        42.90        35.01        78.08 
TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A01R TCGA-AD-6963 TCGA-AU-6004 TCGA-AZ-4315 
       25.02        13.94        35.01        27.42        27.09        58.39 
TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6540 
       17.56        23.05        12.99        12.95        19.59        16.14 
TCGA-G4-6307 
       55.04 

$`ROR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
       91.79        79.69        43.76        46.65        43.76        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-A6-6651 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-3510 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        27.02        27.02         7.96        27.02        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        22.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       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        14.04        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        85.48        61.91        36.00        13.78        46.75 

  ROR1 MUTATED ROR1 WILD-TYPE 
         12.95           0.00 
  ROR1 MUTATED ROR1 WILD-TYPE 
         85.05         148.01 
  ROR1 MUTATED ROR1 WILD-TYPE 
         27.09          21.99 
[1] "12.9 - 85.0 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "5.5"
D1654V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ROR1 MUTATED         3        0        2         7         1         0
  ROR1 WILD-TYPE      61        1       24       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ROR1 MUTATED           1          1          2          0        1         0
  ROR1 WILD-TYPE        17          5         42         33       34        12
                vv
clus             STAGE IVB
  ROR1 MUTATED           0
  ROR1 WILD-TYPE         1
D1654V3, multiclass
            clus
vv           ROR1 MUTATED ROR1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  ROR1 MUTATED     0   4  14   2
  ROR1 WILD-TYPE   9  63 235  39
D1654V4, multiclass
    clus
vv   ROR1 MUTATED ROR1 WILD-TYPE
  T1            0              9
  T2            4             63
  T3           14            235
  T4            2             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
  ROR1 MUTATED    15   4   1
  ROR1 WILD-TYPE 205  77  65
D1654V5, multiclass
    clus
vv   ROR1 MUTATED ROR1 WILD-TYPE
  N0           15            205
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1654V6, binary
                cls
clus               0   1
  ROR1 MUTATED    17   1
  ROR1 WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED     17    1
  ROR1 WILD-TYPE  268   47
   clus
vv  ROR1 MUTATED ROR1 WILD-TYPE
  0           17            268
  1            1             47
[1] 2 2
[1] FALSE
D1654V7, binary
                cls
clus               0   1
  ROR1 MUTATED     8  12
  ROR1 WILD-TYPE 162 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED      8   12
  ROR1 WILD-TYPE  162  185
        clus
vv       ROR1 MUTATED ROR1 WILD-TYPE
  FEMALE            8            162
  MALE             12            185
[1] 2 2
[1] FALSE
D1654V8, binary
                cls
clus               0   1
  ROR1 MUTATED    17   1
  ROR1 WILD-TYPE 283   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED     17    1
  ROR1 WILD-TYPE  283    7
     clus
vv    ROR1 MUTATED ROR1 WILD-TYPE
  NO            17            283
  YES            1              7
[1] 2 2
[1] FALSE
D1654V9, binary
                cls
clus               0   1
  ROR1 MUTATED    17   3
  ROR1 WILD-TYPE 297  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED     17    3
  ROR1 WILD-TYPE  297   45
                               clus
vv                              ROR1 MUTATED ROR1 WILD-TYPE
  COLON ADENOCARCINOMA                    17            297
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ROR1 MUTATED    16   0   1   1
  ROR1 WILD-TYPE 243   3  21  20
D1654V10, multiclass
    clus
vv   ROR1 MUTATED ROR1 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            1             21
  RX            1             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"
D1654V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ROR1 MUTATED                                  0     0
  ROR1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ROR1 MUTATED                           1    11
  ROR1 WILD-TYPE                        18   165
D1654V12, multiclass
                                  clus
vv                                 ROR1 MUTATED ROR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      11            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(1655) Variable = HSPA4L MUTATION ANALYSIS
D1655V1, survival
                  sevent
clus2                0   1
  HSPA4L MUTATED     7   1
  HSPA4L WILD-TYPE 270  77
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               8              347 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               1               77 
$`HSPA4L MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6310 TCGA-AA-3555 TCGA-AA-3663 TCGA-AZ-4315 
       19.04        24.00        63.62        29.95         6.97        58.39 
TCGA-CA-6717 TCGA-DM-A28H 
       12.76       117.07 

$`HSPA4L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  HSPA4L MUTATED HSPA4L WILD-TYPE 
            6.97             0.00 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
          117.07           148.01 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
          26.975           22.030 
[1] "7.0 - 117.1 (27.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D1655V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HSPA4L MUTATED         0        0        2         4         0         0
  HSPA4L WILD-TYPE      64        1       24       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPA4L MUTATED           0          0          1          1        0
  HSPA4L WILD-TYPE        18          6         43         32       35
                  vv
clus               STAGE IVA STAGE IVB
  HSPA4L MUTATED           0         0
  HSPA4L WILD-TYPE        12         1
D1655V3, multiclass
            clus
vv           HSPA4L MUTATED HSPA4L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  HSPA4L MUTATED     0   0   8   0
  HSPA4L WILD-TYPE   9  67 241  41
D1655V4, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  T1              0                9
  T2              0               67
  T3              8              241
  T4              0               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
  HSPA4L MUTATED     6   1   1
  HSPA4L WILD-TYPE 214  80  65
D1655V5, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  N0              6              214
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1655V6, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     8   0
  HSPA4L WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      8    0
  HSPA4L WILD-TYPE  277   48
   clus
vv  HSPA4L MUTATED HSPA4L WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1655V7, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     2   6
  HSPA4L WILD-TYPE 168 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      2    6
  HSPA4L WILD-TYPE  168  191
        clus
vv       HSPA4L MUTATED HSPA4L WILD-TYPE
  FEMALE              2              168
  MALE                6              191
[1] 2 2
[1] FALSE
D1655V8, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     6   1
  HSPA4L WILD-TYPE 294   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      6    1
  HSPA4L WILD-TYPE  294    7
     clus
vv    HSPA4L MUTATED HSPA4L WILD-TYPE
  NO               6              294
  YES              1                7
[1] 2 2
[1] FALSE
D1655V9, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     5   3
  HSPA4L WILD-TYPE 309  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      5    3
  HSPA4L WILD-TYPE  309   45
                               clus
vv                              HSPA4L MUTATED HSPA4L WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HSPA4L MUTATED     6   0   0   1
  HSPA4L WILD-TYPE 253   3  22  20
D1655V10, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  R0              6              253
  R1              0                3
  R2              0               22
  RX              1               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"
D1655V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPA4L MUTATED                                  0     1
  HSPA4L WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HSPA4L MUTATED                           0     3
  HSPA4L WILD-TYPE                        19   173
D1655V12, multiclass
                                  clus
vv                                 HSPA4L MUTATED HSPA4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = GSG2 MUTATION ANALYSIS
D1656V1, survival
                sevent
clus2              0   1
  GSG2 MUTATED     4   1
  GSG2 WILD-TYPE 273  77
  GSG2 MUTATED GSG2 WILD-TYPE 
             5            350 
  GSG2 MUTATED GSG2 WILD-TYPE 
             1             77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3858 TCGA-AA-3861 
       33.07         0.00        36.03        32.05        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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         22.225 
[1] "1.0 - 22.1 (15.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.8"
D1656V2, continuous
                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      64        1       26       102         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  GSG2 MUTATED           0
  GSG2 WILD-TYPE         1
D1656V3, multiclass
            clus
vv           GSG2 MUTATED GSG2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GSG2 MUTATED     0   0   6   0
  GSG2 WILD-TYPE   9  67 243  41
D1656V4, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            6            243
  T4            0             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
  GSG2 MUTATED     6   0   0
  GSG2 WILD-TYPE 214  81  66
D1656V5, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  N0            6            214
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1656V6, binary
                cls
clus               0   1
  GSG2 MUTATED     5   0
  GSG2 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      5    0
  GSG2 WILD-TYPE  280   48
   clus
vv  GSG2 MUTATED GSG2 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1656V7, binary
                cls
clus               0   1
  GSG2 MUTATED     4   2
  GSG2 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      4    2
  GSG2 WILD-TYPE  166  195
        clus
vv       GSG2 MUTATED GSG2 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D1656V8, binary
                cls
clus               0   1
  GSG2 MUTATED     4   0
  GSG2 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      4    0
  GSG2 WILD-TYPE  296    8
     clus
vv    GSG2 MUTATED GSG2 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1656V9, binary
                cls
clus               0   1
  GSG2 MUTATED     5   1
  GSG2 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      5    1
  GSG2 WILD-TYPE  309   47
                               clus
vv                              GSG2 MUTATED GSG2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GSG2 MUTATED     5   0   0   0
  GSG2 WILD-TYPE 254   3  22  21
D1656V10, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            0             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"
D1656V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSG2 MUTATED                                  0     0
  GSG2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GSG2 MUTATED                           0     4
  GSG2 WILD-TYPE                        19   172
D1656V12, multiclass
                                  clus
vv                                 GSG2 MUTATED GSG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = MIPEP MUTATION ANALYSIS
D1657V1, survival
                 sevent
clus2               0   1
  MIPEP MUTATED     7   0
  MIPEP WILD-TYPE 270  78
  MIPEP MUTATED MIPEP WILD-TYPE 
              7             348 
  MIPEP MUTATED MIPEP WILD-TYPE 
              0              78 
$`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 
       17.85 

$`MIPEP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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-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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MIPEP MUTATED MIPEP WILD-TYPE 
          12.03            0.00 
  MIPEP MUTATED MIPEP WILD-TYPE 
         124.27          148.01 
  MIPEP MUTATED MIPEP WILD-TYPE 
         29.950          22.045 
[1] "12.0 - 124.3 (29.9)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1657V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIPEP MUTATED         1        0        3         3         0         0
  MIPEP WILD-TYPE      63        1       23       105         8         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  MIPEP MUTATED           0
  MIPEP WILD-TYPE         1
D1657V3, multiclass
            clus
vv           MIPEP MUTATED MIPEP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  MIPEP MUTATED     0   1   6   1
  MIPEP WILD-TYPE   9  66 243  40
D1657V4, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             1              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
  MIPEP MUTATED     7   0   1
  MIPEP WILD-TYPE 213  81  65
D1657V5, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  N0             7             213
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1657V6, binary
                 cls
clus                0   1
  MIPEP MUTATED     7   0
  MIPEP WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      7    0
  MIPEP WILD-TYPE  278   48
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1657V7, binary
                 cls
clus                0   1
  MIPEP MUTATED     4   4
  MIPEP WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      4    4
  MIPEP WILD-TYPE  166  193
        clus
vv       MIPEP MUTATED MIPEP WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D1657V8, binary
                 cls
clus                0   1
  MIPEP MUTATED     7   0
  MIPEP WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      7    0
  MIPEP WILD-TYPE  293    8
     clus
vv    MIPEP MUTATED MIPEP WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1657V9, binary
                 cls
clus                0   1
  MIPEP MUTATED     6   2
  MIPEP WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      6    2
  MIPEP WILD-TYPE  308   46
                               clus
vv                              MIPEP MUTATED MIPEP WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MIPEP MUTATED     7   0   0   1
  MIPEP WILD-TYPE 252   3  22  20
D1657V10, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1657V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIPEP MUTATED                                  0     0
  MIPEP WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MIPEP MUTATED                           1     3
  MIPEP WILD-TYPE                        18   173
D1657V12, multiclass
                                  clus
vv                                 MIPEP MUTATED MIPEP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = CENPA MUTATION ANALYSIS
D1658V1, survival
                 sevent
clus2               0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 272  78
  CENPA MUTATED CENPA WILD-TYPE 
              5             350 
  CENPA MUTATED CENPA WILD-TYPE 
              0              78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CENPA MUTATED CENPA WILD-TYPE 
          32.75            0.00 
  CENPA MUTATED CENPA WILD-TYPE 
          58.39          148.01 
  CENPA MUTATED CENPA WILD-TYPE 
          38.04           21.99 
[1] "32.8 - 58.4 (38.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1658V2, continuous
                 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      64        1       25       106         6         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  CENPA MUTATED           0
  CENPA WILD-TYPE         1
D1658V3, multiclass
            clus
vv           CENPA MUTATED CENPA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CENPA MUTATED     0   0   3   2
  CENPA WILD-TYPE   9  67 246  39
D1658V4, multiclass
    clus
vv   CENPA MUTATED CENPA WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             2              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
  CENPA MUTATED     5   0   0
  CENPA WILD-TYPE 215  81  66
D1658V5, multiclass
    clus
vv   CENPA MUTATED CENPA WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1658V6, binary
                 cls
clus                0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      5    0
  CENPA WILD-TYPE  280   48
   clus
vv  CENPA MUTATED CENPA WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1658V7, binary
                 cls
clus                0   1
  CENPA MUTATED     2   3
  CENPA WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      2    3
  CENPA WILD-TYPE  168  194
        clus
vv       CENPA MUTATED CENPA WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D1658V8, binary
                 cls
clus                0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      5    0
  CENPA WILD-TYPE  295    8
     clus
vv    CENPA MUTATED CENPA WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1658V9, binary
                 cls
clus                0   1
  CENPA MUTATED     4   1
  CENPA WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      4    1
  CENPA WILD-TYPE  310   47
                               clus
vv                              CENPA MUTATED CENPA WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CENPA MUTATED     5   0   0   0
  CENPA WILD-TYPE 254   3  22  21
D1658V10, multiclass
    clus
vv   CENPA MUTATED CENPA WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1658V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CENPA MUTATED                                  0     0
  CENPA WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CENPA MUTATED                           0     2
  CENPA WILD-TYPE                        19   174
D1658V12, multiclass
[1] "Remove cluster labels:" "CENPA MUTATED"         
clus
  CENPA MUTATED CENPA WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810      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-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4323 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6603 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      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-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 

Clustering(1659) Variable = OTUD4 MUTATION ANALYSIS
D1659V1, survival
                 sevent
clus2               0   1
  OTUD4 MUTATED    13   5
  OTUD4 WILD-TYPE 264  73
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             18             337 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              5              73 
$`OTUD4 MUTATED`
TCGA-AA-3715 TCGA-AD-6895 TCGA-AZ-6608 TCGA-G4-6586 TCGA-G4-6628 TCGA-AA-3510 
       19.04        25.08         1.94        35.80        79.69        63.98 
TCGA-AA-3655 TCGA-AA-3845 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       61.02         0.00        18.05         4.01        34.98        83.24 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4743 TCGA-D5-6931 
       33.01        58.39        12.59       148.01        23.05        12.00 

$`OTUD4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        13.35        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  OTUD4 MUTATED OTUD4 WILD-TYPE 
              0               0 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
         148.01          140.38 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
         29.045          21.990 
[1] "0.0 - 148.0 (29.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D1659V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OTUD4 MUTATED         1        0        3         5         3         0
  OTUD4 WILD-TYPE      63        1       23       103         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OTUD4 MUTATED           1          1          3          1        0         1
  OTUD4 WILD-TYPE        17          5         41         32       35        11
                 vv
clus              STAGE IVB
  OTUD4 MUTATED           0
  OTUD4 WILD-TYPE         1
D1659V3, multiclass
            clus
vv           OTUD4 MUTATED OTUD4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              5             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  OTUD4 MUTATED     0   2  12   5
  OTUD4 WILD-TYPE   9  65 237  36
D1659V4, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            12             237
  T4             5              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
  OTUD4 MUTATED    12   6   1
  OTUD4 WILD-TYPE 208  75  65
D1659V5, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  N0            12             208
  N1             6              75
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1659V6, binary
                 cls
clus                0   1
  OTUD4 MUTATED    17   1
  OTUD4 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     17    1
  OTUD4 WILD-TYPE  268   47
   clus
vv  OTUD4 MUTATED OTUD4 WILD-TYPE
  0            17             268
  1             1              47
[1] 2 2
[1] FALSE
D1659V7, binary
                 cls
clus                0   1
  OTUD4 MUTATED     7  12
  OTUD4 WILD-TYPE 163 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      7   12
  OTUD4 WILD-TYPE  163  185
        clus
vv       OTUD4 MUTATED OTUD4 WILD-TYPE
  FEMALE             7             163
  MALE              12             185
[1] 2 2
[1] FALSE
D1659V8, binary
                 cls
clus                0   1
  OTUD4 MUTATED    16   0
  OTUD4 WILD-TYPE 284   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     16    0
  OTUD4 WILD-TYPE  284    8
     clus
vv    OTUD4 MUTATED OTUD4 WILD-TYPE
  NO             16             284
  YES             0               8
[1] 2 2
[1] FALSE
D1659V9, binary
                 cls
clus                0   1
  OTUD4 MUTATED    17   2
  OTUD4 WILD-TYPE 297  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     17    2
  OTUD4 WILD-TYPE  297   46
                               clus
vv                              OTUD4 MUTATED OTUD4 WILD-TYPE
  COLON ADENOCARCINOMA                     17             297
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OTUD4 MUTATED    16   0   0   2
  OTUD4 WILD-TYPE 243   3  22  19
D1659V10, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             2              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"
D1659V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OTUD4 MUTATED                                  0     2
  OTUD4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OTUD4 MUTATED                           1     9
  OTUD4 WILD-TYPE                        18   167
D1659V12, multiclass
                                  clus
vv                                 OTUD4 MUTATED OTUD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(1660) Variable = CASC4 MUTATION ANALYSIS
D1660V1, survival
                 sevent
clus2               0   1
  CASC4 MUTATED     5   0
  CASC4 WILD-TYPE 272  78
  CASC4 MUTATED CASC4 WILD-TYPE 
              5             350 
  CASC4 MUTATED CASC4 WILD-TYPE 
              0              78 
$`CASC4 MUTATED`
TCGA-AA-3554 TCGA-A6-6651 TCGA-AA-A010 TCGA-CM-4746 TCGA-D5-6533 
       17.95        21.76        34.98        37.02        25.48 

$`CASC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CASC4 MUTATED CASC4 WILD-TYPE 
          17.95            0.00 
  CASC4 MUTATED CASC4 WILD-TYPE 
          37.02          148.01 
  CASC4 MUTATED CASC4 WILD-TYPE 
         25.480          22.045 
[1] "17.9 - 37.0 (25.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1660V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASC4 MUTATED         1        0        0         1         1         0
  CASC4 WILD-TYPE      63        1       26       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC4 MUTATED           0          0          1          0        0         0
  CASC4 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  CASC4 MUTATED           0
  CASC4 WILD-TYPE         1
D1660V3, multiclass
            clus
vv           CASC4 MUTATED CASC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CASC4 MUTATED     0   1   2   2
  CASC4 WILD-TYPE   9  66 247  39
D1660V4, multiclass
    clus
vv   CASC4 MUTATED CASC4 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             2             247
  T4             2              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
  CASC4 MUTATED     4   1   0
  CASC4 WILD-TYPE 216  80  66
D1660V5, multiclass
    clus
vv   CASC4 MUTATED CASC4 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1660V6, binary
                 cls
clus                0   1
  CASC4 MUTATED     4   0
  CASC4 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC4 MUTATED      4    0
  CASC4 WILD-TYPE  281   48
   clus
vv  CASC4 MUTATED CASC4 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1660V7, binary
                 cls
clus                0   1
  CASC4 MUTATED     4   1
  CASC4 WILD-TYPE 166 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC4 MUTATED      4    1
  CASC4 WILD-TYPE  166  196
        clus
vv       CASC4 MUTATED CASC4 WILD-TYPE
  FEMALE             4             166
  MALE               1             196
[1] 2 2
[1] FALSE
D1660V8, binary
                 cls
clus                0   1
  CASC4 MUTATED     5   0
  CASC4 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC4 MUTATED      5    0
  CASC4 WILD-TYPE  295    8
     clus
vv    CASC4 MUTATED CASC4 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1660V9, binary
                 cls
clus                0   1
  CASC4 MUTATED     5   0
  CASC4 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC4 MUTATED      5    0
  CASC4 WILD-TYPE  309   48
                               clus
vv                              CASC4 MUTATED CASC4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASC4 MUTATED     4   0   0   0
  CASC4 WILD-TYPE 255   3  22  21
D1660V10, multiclass
    clus
vv   CASC4 MUTATED CASC4 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1660V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASC4 MUTATED                                  0     0
  CASC4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASC4 MUTATED                           1     2
  CASC4 WILD-TYPE                        18   174
D1660V12, multiclass
                                  clus
vv                                 CASC4 MUTATED CASC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(1661) Variable = OR2F2 MUTATION ANALYSIS
D1661V1, survival
                 sevent
clus2               0   1
  OR2F2 MUTATED     5   2
  OR2F2 WILD-TYPE 272  76
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              7             348 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              2              76 
$`OR2F2 MUTATED`
TCGA-AZ-6601 TCGA-AA-3877 TCGA-AA-3966 TCGA-CA-6717 TCGA-D5-6930 TCGA-DM-A1HA 
      100.01        31.00         2.01        12.76        13.35       131.51 
TCGA-F4-6809 
       13.25 

$`OR2F2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  OR2F2 MUTATED OR2F2 WILD-TYPE 
           2.01            0.00 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
         131.51          148.01 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
         13.350          22.075 
[1] "2.0 - 131.5 (13.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1661V2, continuous
                 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      63        1       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2F2 MUTATED           0          0          0          1        0         1
  OR2F2 WILD-TYPE        18          6         44         32       35        11
                 vv
clus              STAGE IVB
  OR2F2 MUTATED           0
  OR2F2 WILD-TYPE         1
D1661V3, multiclass
            clus
vv           OR2F2 MUTATED OR2F2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  OR2F2 MUTATED     1   0   6   0
  OR2F2 WILD-TYPE   8  67 243  41
D1661V4, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  T1             1               8
  T2             0              67
  T3             6             243
  T4             0              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
  OR2F2 MUTATED     5   1   1
  OR2F2 WILD-TYPE 215  80  65
D1661V5, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1661V6, binary
                 cls
clus                0   1
  OR2F2 MUTATED     6   1
  OR2F2 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      6    1
  OR2F2 WILD-TYPE  279   47
   clus
vv  OR2F2 MUTATED OR2F2 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1661V7, binary
                 cls
clus                0   1
  OR2F2 MUTATED     3   4
  OR2F2 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      3    4
  OR2F2 WILD-TYPE  167  193
        clus
vv       OR2F2 MUTATED OR2F2 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1661V8, binary
                 cls
clus                0   1
  OR2F2 MUTATED     5   0
  OR2F2 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      5    0
  OR2F2 WILD-TYPE  295    8
     clus
vv    OR2F2 MUTATED OR2F2 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1661V9, binary
                 cls
clus                0   1
  OR2F2 MUTATED     3   4
  OR2F2 WILD-TYPE 311  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      3    4
  OR2F2 WILD-TYPE  311   44
                               clus
vv                              OR2F2 MUTATED OR2F2 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2F2 MUTATED     3   0   0   1
  OR2F2 WILD-TYPE 256   3  22  20
D1661V10, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1661V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2F2 MUTATED                                  0     1
  OR2F2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2F2 MUTATED                           0     4
  OR2F2 WILD-TYPE                        19   172
D1661V12, multiclass
                                  clus
vv                                 OR2F2 MUTATED OR2F2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = MPZL1 MUTATION ANALYSIS
D1662V1, survival
                 sevent
clus2               0   1
  MPZL1 MUTATED     4   3
  MPZL1 WILD-TYPE 273  75
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             348 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              3              75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 

  MPZL1 MUTATED MPZL1 WILD-TYPE 
            7.5             0.0 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
         135.65          148.01 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
          32.75           22.01 
[1] "7.5 - 135.7 (32.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1662V2, continuous
                 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      64        1       26       106         7         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        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  MPZL1 MUTATED           0
  MPZL1 WILD-TYPE         1
D1662V3, multiclass
            clus
vv           MPZL1 MUTATED MPZL1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  MPZL1 MUTATED     0   0   6   1
  MPZL1 WILD-TYPE   9  67 243  40
D1662V4, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  MPZL1 MUTATED     4   1   2
  MPZL1 WILD-TYPE 216  80  64
D1662V5, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1662V6, binary
                 cls
clus                0   1
  MPZL1 MUTATED     6   0
  MPZL1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      6    0
  MPZL1 WILD-TYPE  279   48
   clus
vv  MPZL1 MUTATED MPZL1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1662V7, binary
                 cls
clus                0   1
  MPZL1 MUTATED     2   5
  MPZL1 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      2    5
  MPZL1 WILD-TYPE  168  192
        clus
vv       MPZL1 MUTATED MPZL1 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1662V8, binary
                 cls
clus                0   1
  MPZL1 MUTATED     4   1
  MPZL1 WILD-TYPE 296   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      4    1
  MPZL1 WILD-TYPE  296    7
     clus
vv    MPZL1 MUTATED MPZL1 WILD-TYPE
  NO              4             296
  YES             1               7
[1] 2 2
[1] FALSE
D1662V9, binary
                 cls
clus                0   1
  MPZL1 MUTATED     4   2
  MPZL1 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      4    2
  MPZL1 WILD-TYPE  310   46
                               clus
vv                              MPZL1 MUTATED MPZL1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MPZL1 MUTATED     3   0   0   1
  MPZL1 WILD-TYPE 256   3  22  20
D1662V10, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1662V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPZL1 MUTATED                                  0     1
  MPZL1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MPZL1 MUTATED                           0     5
  MPZL1 WILD-TYPE                        19   171
D1662V12, multiclass
                                  clus
vv                                 MPZL1 MUTATED MPZL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = VN1R4 MUTATION ANALYSIS
D1663V1, survival
                 sevent
clus2               0   1
  VN1R4 MUTATED     5   1
  VN1R4 WILD-TYPE 272  77
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              6             349 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              1              77 
$`VN1R4 MUTATED`
TCGA-AZ-6601 TCGA-AA-3815 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 
      100.01        33.04        34.98        12.76        15.62        22.98 

$`VN1R4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  VN1R4 MUTATED VN1R4 WILD-TYPE 
          12.76            0.00 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
         100.01          148.01 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
          28.01           22.03 
[1] "12.8 - 100.0 (28.0)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.7"
D1663V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VN1R4 MUTATED         0        0        1         2         1         0
  VN1R4 WILD-TYPE      64        1       25       106         7         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  VN1R4 MUTATED           0
  VN1R4 WILD-TYPE         1
D1663V3, multiclass
            clus
vv           VN1R4 MUTATED VN1R4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  VN1R4 MUTATED     0   0   4   2
  VN1R4 WILD-TYPE   9  67 245  39
D1663V4, multiclass
    clus
vv   VN1R4 MUTATED VN1R4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             2              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
  VN1R4 MUTATED     4   1   1
  VN1R4 WILD-TYPE 216  80  65
D1663V5, multiclass
    clus
vv   VN1R4 MUTATED VN1R4 WILD-TYPE
  N0             4             216
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1663V6, binary
                 cls
clus                0   1
  VN1R4 MUTATED     6   0
  VN1R4 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      6    0
  VN1R4 WILD-TYPE  279   48
   clus
vv  VN1R4 MUTATED VN1R4 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1663V7, binary
                 cls
clus                0   1
  VN1R4 MUTATED     3   3
  VN1R4 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      3    3
  VN1R4 WILD-TYPE  167  194
        clus
vv       VN1R4 MUTATED VN1R4 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1663V8, binary
                 cls
clus                0   1
  VN1R4 MUTATED     5   0
  VN1R4 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      5    0
  VN1R4 WILD-TYPE  295    8
     clus
vv    VN1R4 MUTATED VN1R4 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1663V9, binary
                 cls
clus                0   1
  VN1R4 MUTATED     4   2
  VN1R4 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      4    2
  VN1R4 WILD-TYPE  310   46
                               clus
vv                              VN1R4 MUTATED VN1R4 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VN1R4 MUTATED     3   0   0   2
  VN1R4 WILD-TYPE 256   3  22  19
D1663V10, multiclass
    clus
vv   VN1R4 MUTATED VN1R4 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             2              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"
D1663V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VN1R4 MUTATED                                  0     1
  VN1R4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VN1R4 MUTATED                           0     3
  VN1R4 WILD-TYPE                        19   173
D1663V12, multiclass
                                  clus
vv                                 VN1R4 MUTATED VN1R4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = KIF14 MUTATION ANALYSIS
D1664V1, survival
                 sevent
clus2               0   1
  KIF14 MUTATED     9   2
  KIF14 WILD-TYPE 268  76
  KIF14 MUTATED KIF14 WILD-TYPE 
             11             344 
  KIF14 MUTATED KIF14 WILD-TYPE 
              2              76 
$`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 
       34.98        12.76       131.51        98.24        47.41 

$`KIF14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-3492 
       24.39        23.87        20.12        19.66        20.28         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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       135.65       139.17        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        43.04        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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KIF14 MUTATED KIF14 WILD-TYPE 
           2.01            0.00 
  KIF14 MUTATED KIF14 WILD-TYPE 
         131.51          148.01 
  KIF14 MUTATED KIF14 WILD-TYPE 
         25.020          22.045 
[1] "2.0 - 131.5 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1664V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF14 MUTATED         0        0        2         5         2         0
  KIF14 WILD-TYPE      64        1       24       103         6         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        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  KIF14 MUTATED           0
  KIF14 WILD-TYPE         1
D1664V3, multiclass
            clus
vv           KIF14 MUTATED KIF14 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  KIF14 MUTATED     0   1   8   2
  KIF14 WILD-TYPE   9  66 241  39
D1664V4, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             2              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
  KIF14 MUTATED    10   0   1
  KIF14 WILD-TYPE 210  81  65
D1664V5, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  N0            10             210
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1664V6, binary
                 cls
clus                0   1
  KIF14 MUTATED    10   0
  KIF14 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED     10    0
  KIF14 WILD-TYPE  275   48
   clus
vv  KIF14 MUTATED KIF14 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1664V7, binary
                 cls
clus                0   1
  KIF14 MUTATED     3   8
  KIF14 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED      3    8
  KIF14 WILD-TYPE  167  189
        clus
vv       KIF14 MUTATED KIF14 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1664V8, binary
                 cls
clus                0   1
  KIF14 MUTATED     7   0
  KIF14 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED      7    0
  KIF14 WILD-TYPE  293    8
     clus
vv    KIF14 MUTATED KIF14 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1664V9, binary
                 cls
clus                0   1
  KIF14 MUTATED     7   4
  KIF14 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED      7    4
  KIF14 WILD-TYPE  307   44
                               clus
vv                              KIF14 MUTATED KIF14 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KIF14 MUTATED     5   0   0   1
  KIF14 WILD-TYPE 254   3  22  20
D1664V10, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D1664V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF14 MUTATED                                  0     1
  KIF14 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF14 MUTATED                           1     3
  KIF14 WILD-TYPE                        18   173
D1664V12, multiclass
                                  clus
vv                                 KIF14 MUTATED KIF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = TRIM33 MUTATION ANALYSIS
D1665V1, survival
                  sevent
clus2                0   1
  TRIM33 MUTATED    12   2
  TRIM33 WILD-TYPE 265  76
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              14              341 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
               2               76 
$`TRIM33 MUTATED`
TCGA-AA-3525 TCGA-G4-6588 TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3811 TCGA-AA-3864 
        8.05        26.17        29.19        33.53        10.06        53.00 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6171 TCGA-D5-6930 
       34.98        21.44        49.41        21.99        14.04        13.35 
TCGA-F4-6856 TCGA-G4-6307 
       35.31        55.04 

$`TRIM33 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TRIM33 MUTATED TRIM33 WILD-TYPE 
            8.05             0.00 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
           55.04           148.01 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
           27.68            22.03 
[1] "8.1 - 55.0 (27.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1665V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM33 MUTATED         2        0        2         4         2         0
  TRIM33 WILD-TYPE      62        1       24       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM33 MUTATED           1          0          3          1        0
  TRIM33 WILD-TYPE        17          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM33 MUTATED           0         0
  TRIM33 WILD-TYPE        12         1
D1665V3, multiclass
            clus
vv           TRIM33 MUTATED TRIM33 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  TRIM33 MUTATED     0   2  11   2
  TRIM33 WILD-TYPE   9  65 238  39
D1665V4, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             11              238
  T4              2               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
  TRIM33 MUTATED    10   3   2
  TRIM33 WILD-TYPE 210  78  64
D1665V5, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  N0             10              210
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1665V6, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    11   0
  TRIM33 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     11    0
  TRIM33 WILD-TYPE  274   48
   clus
vv  TRIM33 MUTATED TRIM33 WILD-TYPE
  0             11              274
  1              0               48
[1] 2 2
[1] FALSE
D1665V7, binary
                  cls
clus                 0   1
  TRIM33 MUTATED     8   7
  TRIM33 WILD-TYPE 162 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED      8    7
  TRIM33 WILD-TYPE  162  190
        clus
vv       TRIM33 MUTATED TRIM33 WILD-TYPE
  FEMALE              8              162
  MALE                7              190
[1] 2 2
[1] FALSE
D1665V8, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    13   0
  TRIM33 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     13    0
  TRIM33 WILD-TYPE  287    8
     clus
vv    TRIM33 MUTATED TRIM33 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1665V9, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    13   2
  TRIM33 WILD-TYPE 301  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     13    2
  TRIM33 WILD-TYPE  301   46
                               clus
vv                              TRIM33 MUTATED TRIM33 WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM33 MUTATED    11   0   0   2
  TRIM33 WILD-TYPE 248   3  22  19
D1665V10, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              2               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"
D1665V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM33 MUTATED                                  0     0
  TRIM33 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM33 MUTATED                           2     9
  TRIM33 WILD-TYPE                        17   167
D1665V12, multiclass
                                  clus
vv                                 TRIM33 MUTATED TRIM33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         9              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(1666) Variable = XRCC6 MUTATION ANALYSIS
D1666V1, survival
                 sevent
clus2               0   1
  XRCC6 MUTATED     5   2
  XRCC6 WILD-TYPE 272  76
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             348 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              2              76 
$`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 
      135.65 

$`XRCC6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  XRCC6 MUTATED XRCC6 WILD-TYPE 
          11.64            0.00 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
         135.65          148.01 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
         19.040          22.075 
[1] "11.6 - 135.7 (19.0)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1"  
D1666V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XRCC6 MUTATED         1        0        1         3         1         0
  XRCC6 WILD-TYPE      63        1       25       105         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  XRCC6 MUTATED           0
  XRCC6 WILD-TYPE         1
D1666V3, multiclass
            clus
vv           XRCC6 MUTATED XRCC6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  XRCC6 MUTATED     0   1   5   1
  XRCC6 WILD-TYPE   9  66 244  40
D1666V4, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             1              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
  XRCC6 MUTATED     6   1   0
  XRCC6 WILD-TYPE 214  80  66
D1666V5, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1666V6, binary
                 cls
clus                0   1
  XRCC6 MUTATED     7   0
  XRCC6 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      7    0
  XRCC6 WILD-TYPE  278   48
   clus
vv  XRCC6 MUTATED XRCC6 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1666V7, binary
                 cls
clus                0   1
  XRCC6 MUTATED     2   5
  XRCC6 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      2    5
  XRCC6 WILD-TYPE  168  192
        clus
vv       XRCC6 MUTATED XRCC6 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1666V8, binary
                 cls
clus                0   1
  XRCC6 MUTATED     5   0
  XRCC6 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      5    0
  XRCC6 WILD-TYPE  295    8
     clus
vv    XRCC6 MUTATED XRCC6 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1666V9, binary
                 cls
clus                0   1
  XRCC6 MUTATED     4   2
  XRCC6 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      4    2
  XRCC6 WILD-TYPE  310   46
                               clus
vv                              XRCC6 MUTATED XRCC6 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  XRCC6 MUTATED     5   0   0   0
  XRCC6 WILD-TYPE 254   3  22  21
D1666V10, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1666V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XRCC6 MUTATED                                  0     0
  XRCC6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  XRCC6 MUTATED                           0     5
  XRCC6 WILD-TYPE                        19   171
D1666V12, multiclass
                                  clus
vv                                 XRCC6 MUTATED XRCC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = GTDC1 MUTATION ANALYSIS
D1667V1, survival
                 sevent
clus2               0   1
  GTDC1 MUTATED     6   2
  GTDC1 WILD-TYPE 271  76
  GTDC1 MUTATED GTDC1 WILD-TYPE 
              8             347 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
              2              76 
$`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        25.48 
TCGA-D5-6927 TCGA-D5-6930 
        9.44        13.35 

$`GTDC1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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         7.53        12.39        10.13 
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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GTDC1 MUTATED GTDC1 WILD-TYPE 
           4.01            0.00 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
          49.41          148.01 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
          15.70           22.09 
[1] "4.0 - 49.4 (15.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1667V2, continuous
                 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      64        1       25       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GTDC1 MUTATED           0          0          1          0        0         0
  GTDC1 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  GTDC1 MUTATED           0
  GTDC1 WILD-TYPE         1
D1667V3, multiclass
            clus
vv           GTDC1 MUTATED GTDC1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GTDC1 MUTATED     0   1   4   4
  GTDC1 WILD-TYPE   9  66 245  37
D1667V4, multiclass
    clus
vv   GTDC1 MUTATED GTDC1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             4              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
  GTDC1 MUTATED     8   1   0
  GTDC1 WILD-TYPE 212  80  66
D1667V5, multiclass
    clus
vv   GTDC1 MUTATED GTDC1 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1667V6, binary
                 cls
clus                0   1
  GTDC1 MUTATED     6   0
  GTDC1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      6    0
  GTDC1 WILD-TYPE  279   48
   clus
vv  GTDC1 MUTATED GTDC1 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1667V7, binary
                 cls
clus                0   1
  GTDC1 MUTATED     3   6
  GTDC1 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      3    6
  GTDC1 WILD-TYPE  167  191
        clus
vv       GTDC1 MUTATED GTDC1 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1667V8, binary
                 cls
clus                0   1
  GTDC1 MUTATED     7   0
  GTDC1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      7    0
  GTDC1 WILD-TYPE  293    8
     clus
vv    GTDC1 MUTATED GTDC1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1667V9, binary
                 cls
clus                0   1
  GTDC1 MUTATED     5   4
  GTDC1 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      5    4
  GTDC1 WILD-TYPE  309   44
                               clus
vv                              GTDC1 MUTATED GTDC1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GTDC1 MUTATED     5   0   0   2
  GTDC1 WILD-TYPE 254   3  22  19
D1667V10, multiclass
    clus
vv   GTDC1 MUTATED GTDC1 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D1667V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTDC1 MUTATED                                  0     1
  GTDC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GTDC1 MUTATED                           0     5
  GTDC1 WILD-TYPE                        19   171
D1667V12, multiclass
                                  clus
vv                                 GTDC1 MUTATED GTDC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = SERPINB10 MUTATION ANALYSIS
D1668V1, survival
                     sevent
clus2                   0   1
  SERPINB10 MUTATED     7   3
  SERPINB10 WILD-TYPE 270  75
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 10                 345 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  3                  75 
$`SERPINB10 MUTATED`
TCGA-A6-6649 TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-4681 TCGA-G4-6628 TCGA-AA-3660 
       24.16        24.00        10.88       106.75        79.69        78.08 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-6717 
        4.01        34.98        49.41        12.76 

$`SERPINB10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        25.08       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
               4.01                0.00 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
             106.75              148.01 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
              29.57               21.99 
[1] "4.0 - 106.8 (29.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1668V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SERPINB10 MUTATED         1        0        2         3         2         0
  SERPINB10 WILD-TYPE      63        1       24       105         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB10 MUTATED           0          0          1          0        0
  SERPINB10 WILD-TYPE        18          6         43         33       35
                     vv
clus                  STAGE IVA STAGE IVB
  SERPINB10 MUTATED           0         0
  SERPINB10 WILD-TYPE        12         1
D1668V3, multiclass
            clus
vv           SERPINB10 MUTATED SERPINB10 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   2                  24
  STAGE IIA                  3                 105
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 1                  43
  STAGE IIIC                 0                  33
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  SERPINB10 MUTATED     0   1   6   3
  SERPINB10 WILD-TYPE   9  66 243  38
D1668V4, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  T1                 0                   9
  T2                 1                  66
  T3                 6                 243
  T4                 3                  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
  SERPINB10 MUTATED     8   1   1
  SERPINB10 WILD-TYPE 212  80  65
D1668V5, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  N0                 8                 212
  N1                 1                  80
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1668V6, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     8   0
  SERPINB10 WILD-TYPE 277  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      8    0
  SERPINB10 WILD-TYPE  277   48
   clus
vv  SERPINB10 MUTATED SERPINB10 WILD-TYPE
  0                 8                 277
  1                 0                  48
[1] 2 2
[1] FALSE
D1668V7, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     5   5
  SERPINB10 WILD-TYPE 165 192
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      5    5
  SERPINB10 WILD-TYPE  165  192
        clus
vv       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  FEMALE                 5                 165
  MALE                   5                 192
[1] 2 2
[1] FALSE
D1668V8, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     9   0
  SERPINB10 WILD-TYPE 291   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      9    0
  SERPINB10 WILD-TYPE  291    8
     clus
vv    SERPINB10 MUTATED SERPINB10 WILD-TYPE
  NO                  9                 291
  YES                 0                   8
[1] 2 2
[1] FALSE
D1668V9, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     7   3
  SERPINB10 WILD-TYPE 307  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      7    3
  SERPINB10 WILD-TYPE  307   45
                               clus
vv                              SERPINB10 MUTATED SERPINB10 WILD-TYPE
  COLON ADENOCARCINOMA                          7                 307
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  SERPINB10 MUTATED     6   0   0   1
  SERPINB10 WILD-TYPE 253   3  22  20
D1668V10, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  R0                 6                 253
  R1                 0                   3
  R2                 0                  22
  RX                 1                  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"
D1668V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB10 MUTATED                                  0     1
  SERPINB10 WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  SERPINB10 MUTATED                           0     5
  SERPINB10 WILD-TYPE                        19   171
D1668V12, multiclass
                                  clus
vv                                 SERPINB10 MUTATED SERPINB10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                   9
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            5                 171
[1] 4 2
[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 = PCDHGA8 MUTATION ANALYSIS
D1669V1, survival
                   sevent
clus2                 0   1
  PCDHGA8 MUTATED    10   4
  PCDHGA8 WILD-TYPE 267  74
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
               14               341 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
                4                74 
$`PCDHGA8 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 
        0.92        19.04        33.53         3.02        63.98         6.97 
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 
       53.62        85.48 

$`PCDHGA8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
             0.92              0.00 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
            85.48            148.01 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
           27.335            22.060 
[1] "0.9 - 85.5 (27.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1669V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGA8 MUTATED         1        0        5         4         2         0
  PCDHGA8 WILD-TYPE      63        1       21       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA8 MUTATED           1          0          1          0        0
  PCDHGA8 WILD-TYPE        17          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGA8 MUTATED           0         0
  PCDHGA8 WILD-TYPE        12         1
D1669V3, multiclass
            clus
vv           PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 5                21
  STAGE IIA                4               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  PCDHGA8 MUTATED     1   0  11   2
  PCDHGA8 WILD-TYPE   8  67 238  39
D1669V4, multiclass
    clus
vv   PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  T1               1                 8
  T2               0                67
  T3              11               238
  T4               2                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
  PCDHGA8 MUTATED    12   2   0
  PCDHGA8 WILD-TYPE 208  79  66
D1669V5, multiclass
    clus
vv   PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  N0              12               208
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1669V6, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    13   0
  PCDHGA8 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     13    0
  PCDHGA8 WILD-TYPE  272   48
   clus
vv  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  0              13               272
  1               0                48
[1] 2 2
[1] FALSE
D1669V7, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED     8   6
  PCDHGA8 WILD-TYPE 162 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED      8    6
  PCDHGA8 WILD-TYPE  162  191
        clus
vv       PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  FEMALE               8               162
  MALE                 6               191
[1] 2 2
[1] FALSE
D1669V8, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    14   0
  PCDHGA8 WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     14    0
  PCDHGA8 WILD-TYPE  286    8
     clus
vv    PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D1669V9, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    13   1
  PCDHGA8 WILD-TYPE 301  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     13    1
  PCDHGA8 WILD-TYPE  301   47
                               clus
vv                              PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PCDHGA8 MUTATED    10   0   0   3
  PCDHGA8 WILD-TYPE 249   3  22  18
D1669V10, multiclass
    clus
vv   PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               3                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"
D1669V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA8 MUTATED                                  0     2
  PCDHGA8 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA8 MUTATED                           2     4
  PCDHGA8 WILD-TYPE                        17   172
D1669V12, multiclass
                                  clus
vv                                 PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          4               172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1670) Variable = F2R MUTATION ANALYSIS
D1670V1, survival
               sevent
clus2             0   1
  F2R MUTATED    10   1
  F2R WILD-TYPE 267  77
  F2R MUTATED F2R WILD-TYPE 
           11           344 
  F2R MUTATED F2R WILD-TYPE 
            1            77 
$`F2R MUTATED`
TCGA-AA-3950 TCGA-A6-6780 TCGA-AA-3511 TCGA-AA-3663 TCGA-AZ-6599 TCGA-CA-6717 
       24.00        20.12         6.97         6.97         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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-5864 
       22.03        22.98        32.02         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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  F2R MUTATED F2R WILD-TYPE 
         6.77          0.00 
  F2R MUTATED F2R WILD-TYPE 
        85.45        148.01 
  F2R MUTATED F2R WILD-TYPE 
       15.020        22.225 
[1] "6.8 - 85.5 (15.0)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "2"  
D1670V2, continuous
               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      61        1       24       103         8         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        18          6         43         33       35        12
               vv
clus            STAGE IVB
  F2R MUTATED           0
  F2R WILD-TYPE         1
D1670V3, multiclass
            clus
vv           F2R MUTATED F2R WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             2            24
  STAGE IIA            5           103
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  F2R MUTATED     0   3   7   1
  F2R WILD-TYPE   9  64 242  40
D1670V4, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  T1           0             9
  T2           3            64
  T3           7           242
  T4           1            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
  F2R MUTATED    10   1   0
  F2R WILD-TYPE 210  80  66
D1670V5, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  N0          10           210
  N1           1            80
  N2           0            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1670V6, binary
               cls
clus              0   1
  F2R MUTATED     9   0
  F2R WILD-TYPE 276  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      9    0
  F2R WILD-TYPE  276   48
   clus
vv  F2R MUTATED F2R WILD-TYPE
  0           9           276
  1           0            48
[1] 2 2
[1] FALSE
D1670V7, binary
               cls
clus              0   1
  F2R MUTATED     5   6
  F2R WILD-TYPE 165 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      5    6
  F2R WILD-TYPE  165  191
        clus
vv       F2R MUTATED F2R WILD-TYPE
  FEMALE           5           165
  MALE             6           191
[1] 2 2
[1] FALSE
D1670V8, binary
               cls
clus              0   1
  F2R MUTATED    11   0
  F2R WILD-TYPE 289   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED     11    0
  F2R WILD-TYPE  289    8
     clus
vv    F2R MUTATED F2R WILD-TYPE
  NO           11           289
  YES           0             8
[1] 2 2
[1] FALSE
D1670V9, binary
               cls
clus              0   1
  F2R MUTATED     6   5
  F2R WILD-TYPE 308  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      6    5
  F2R WILD-TYPE  308   43
                               clus
vv                              F2R MUTATED F2R WILD-TYPE
  COLON ADENOCARCINOMA                    6           308
  COLON MUCINOUS ADENOCARCINOMA           5            43
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  F2R MUTATED     7   1   0   1
  F2R WILD-TYPE 252   2  22  20
D1670V10, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  R0           7           252
  R1           1             2
  R2           0            22
  RX           1            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"
D1670V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  F2R MUTATED                                  0     1
  F2R WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  F2R MUTATED                           1     6
  F2R WILD-TYPE                        18   170
D1670V12, multiclass
                                  clus
vv                                 F2R MUTATED F2R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      6           170
[1] 4 2
[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 = C17ORF58 MUTATION ANALYSIS
D1671V1, survival
                    sevent
clus2                  0   1
  C17ORF58 MUTATED     2   1
  C17ORF58 WILD-TYPE 275  77
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 3                352 
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 1                 77 
$`C17ORF58 MUTATED`
TCGA-AD-6964 TCGA-G4-6588 TCGA-AA-3663 
       10.88        26.17         6.97 

$`C17ORF58 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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             22.075 
[1] "7.0 - 26.2 (10.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.7"
D1671V2, continuous
                    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      64        1       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF58 MUTATED           0          0          0          0        0
  C17ORF58 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF58 MUTATED           0         0
  C17ORF58 WILD-TYPE        12         1
D1671V3, multiclass
[1] "Remove cluster labels:" "C17ORF58 MUTATED"      
clus
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 2                355 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3516         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-3527         TCGA-AA-3530 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3662         TCGA-AA-3672 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3697 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3814 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3860         TCGA-AA-3867 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3939         TCGA-AA-3950 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3972         TCGA-AA-3976 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3986         TCGA-AA-A00L 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A024         TCGA-AD-6548 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AZ-4681 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6608         TCGA-CK-5912 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A285         TCGA-G4-6310         TCGA-G4-6321 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6586         TCGA-G4-6625         TCGA-G4-6628 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-3502         TCGA-AA-3510         TCGA-AA-3511 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3517         TCGA-AA-3518 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3526         TCGA-AA-3529 
"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-3544         TCGA-AA-3548 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3553         TCGA-AA-3555 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3561         TCGA-AA-3655 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3664         TCGA-AA-3666 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3667         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-3693 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3811         TCGA-AA-3812 
"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-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-3861         TCGA-AA-3864         TCGA-AA-3866 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3872         TCGA-AA-3875 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3941 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3955 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3973         TCGA-AA-3975 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3980         TCGA-AA-3982         TCGA-AA-3984 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"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-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-A029         TCGA-AA-A02F 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02K 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02O         TCGA-AA-A02W         TCGA-AA-A02Y 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A03F         TCGA-AA-A03J         TCGA-AD-5900 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6899         TCGA-AD-6965 
"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-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-6605 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         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-5913         TCGA-CK-5914         TCGA-CK-5915 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6534         TCGA-D5-6535 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"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-A28C         TCGA-DM-A28E 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A28F         TCGA-DM-A28G         TCGA-DM-A28H 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A28K         TCGA-F4-6459         TCGA-F4-6460 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6569         TCGA-F4-6570         TCGA-F4-6703 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6704         TCGA-F4-6805         TCGA-F4-6806 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6807         TCGA-F4-6808         TCGA-F4-6809 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6854         TCGA-F4-6855         TCGA-F4-6856 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6293         TCGA-G4-6299         TCGA-G4-6303 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6307         TCGA-G4-6309 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6323 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6626 
"C17ORF58 WILD-TYPE" 
                    vv
clus                  T1  T2  T3  T4
  C17ORF58 MUTATED     0   0   2   1
  C17ORF58 WILD-TYPE   9  67 247  40
D1671V4, multiclass
    clus
vv   C17ORF58 MUTATED C17ORF58 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                2                247
  T4                1                 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
  C17ORF58 MUTATED     2   0   1
  C17ORF58 WILD-TYPE 218  81  65
D1671V5, multiclass
    clus
vv   C17ORF58 MUTATED C17ORF58 WILD-TYPE
  N0                2                218
  N1                0                 81
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1671V6, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     2   0
  C17ORF58 WILD-TYPE 283  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      2    0
  C17ORF58 WILD-TYPE  283   48
   clus
vv  C17ORF58 MUTATED C17ORF58 WILD-TYPE
  0                2                283
  1                0                 48
[1] 2 2
[1] FALSE
D1671V7, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     1   2
  C17ORF58 WILD-TYPE 169 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      1    2
  C17ORF58 WILD-TYPE  169  195
        clus
vv       C17ORF58 MUTATED C17ORF58 WILD-TYPE
  FEMALE                1                169
  MALE                  2                195
[1] 2 2
[1] FALSE
D1671V8, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     3   0
  C17ORF58 WILD-TYPE 297   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      3    0
  C17ORF58 WILD-TYPE  297    8
     clus
vv    C17ORF58 MUTATED C17ORF58 WILD-TYPE
  NO                 3                297
  YES                0                  8
[1] 2 2
[1] FALSE
D1671V9, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     3   0
  C17ORF58 WILD-TYPE 311  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      3    0
  C17ORF58 WILD-TYPE  311   48
                               clus
vv                              C17ORF58 MUTATED C17ORF58 WILD-TYPE
  COLON ADENOCARCINOMA                         3                311
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C17ORF58 MUTATED     2   0   0   0
  C17ORF58 WILD-TYPE 257   3  22  21
D1671V10, multiclass
[1] "Remove cluster labels:" "C17ORF58 MUTATED"      
clus
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 2                303 
        TCGA-A6-2677         TCGA-AA-3496         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-3527         TCGA-AA-3530 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3543         TCGA-AA-3552 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3556         TCGA-AA-3560 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3662         TCGA-AA-3672 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3697 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3814 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3860         TCGA-AA-3867 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3939         TCGA-AA-3950 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3972         TCGA-AA-3976 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3986         TCGA-AA-A00L 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A024         TCGA-AD-6548 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AZ-4681 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5912         TCGA-G4-6310         TCGA-G4-6321 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6586         TCGA-G4-6625         TCGA-G4-6628 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5657         TCGA-A6-5659 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5661         TCGA-A6-5665         TCGA-A6-6781 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3489         TCGA-AA-3492         TCGA-AA-3502 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3510         TCGA-AA-3511         TCGA-AA-3514 
"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-3526         TCGA-AA-3529         TCGA-AA-3532 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3534         TCGA-AA-3538         TCGA-AA-3542 
"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-3553         TCGA-AA-3555         TCGA-AA-3558 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3655         TCGA-AA-3660 
"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-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-3693         TCGA-AA-3695 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3712 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         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-3845         TCGA-AA-3846 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3861 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3869 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3941         TCGA-AA-3947 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3955         TCGA-AA-3956 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3973 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3984         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-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-A010 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01D         TCGA-AA-A01F 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01R 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01S         TCGA-AA-A01T         TCGA-AA-A01V 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01X         TCGA-AA-A01Z         TCGA-AA-A022 
"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-6889 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6965         TCGA-AU-3779         TCGA-AU-6004 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-4315         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-5913         TCGA-CK-5914         TCGA-CK-5915 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         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-G4-6315 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
D1671V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C17ORF58 MUTATED                                  0     0
  C17ORF58 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C17ORF58 MUTATED                           0     2
  C17ORF58 WILD-TYPE                        19   174
D1671V12, multiclass
[1] "Remove cluster labels:" "C17ORF58 MUTATED"      
clus
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-6601         TCGA-AZ-6608 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5912         TCGA-DM-A285         TCGA-G4-6310 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6586         TCGA-G4-6625 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6628         TCGA-A6-2671         TCGA-A6-2672 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         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-A6-5656 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5657         TCGA-A6-5659         TCGA-A6-5660 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5661         TCGA-A6-5662         TCGA-A6-5664 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5665         TCGA-A6-5666         TCGA-A6-6137 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6138         TCGA-A6-6141         TCGA-A6-6142 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6651         TCGA-A6-6652 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6653         TCGA-A6-6654         TCGA-A6-6780 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6781         TCGA-A6-6782         TCGA-AD-5900 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6890         TCGA-AD-6899 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6901         TCGA-AD-6963         TCGA-AD-6965 
"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-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-6603 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-4952         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-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-G4-6315 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 

Clustering(1672) Variable = TEX13A MUTATION ANALYSIS
D1672V1, survival
                  sevent
clus2                0   1
  TEX13A MUTATED     8   1
  TEX13A WILD-TYPE 269  77
  TEX13A MUTATED TEX13A WILD-TYPE 
               9              346 
  TEX13A MUTATED TEX13A WILD-TYPE 
               1               77 
$`TEX13A MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AA-3979 TCGA-G4-6586 TCGA-AA-3815 TCGA-AA-3989 
        0.92        24.00        24.00        35.80        33.04         7.96 
TCGA-AY-6386 TCGA-CM-6167 TCGA-D5-6930 
       17.82        14.99        13.35 

$`TEX13A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 
       13.05        34.06        25.02        27.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TEX13A MUTATED TEX13A WILD-TYPE 
            0.92             0.00 
  TEX13A MUTATED TEX13A WILD-TYPE 
           35.80           148.01 
  TEX13A MUTATED TEX13A WILD-TYPE 
          17.820           22.075 
[1] "0.9 - 35.8 (17.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1672V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TEX13A MUTATED         0        0        0         6         0         0
  TEX13A WILD-TYPE      64        1       26       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TEX13A MUTATED           1          0          1          1        1
  TEX13A WILD-TYPE        17          6         43         32       34
                  vv
clus               STAGE IVA STAGE IVB
  TEX13A MUTATED           0         0
  TEX13A WILD-TYPE        12         1
D1672V3, multiclass
            clus
vv           TEX13A MUTATED TEX13A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  TEX13A MUTATED     0   0  10   0
  TEX13A WILD-TYPE   9  67 239  41
D1672V4, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  T1              0                9
  T2              0               67
  T3             10              239
  T4              0               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
  TEX13A MUTATED     6   2   2
  TEX13A WILD-TYPE 214  79  64
D1672V5, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  N0              6              214
  N1              2               79
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1672V6, binary
                  cls
clus                 0   1
  TEX13A MUTATED     9   1
  TEX13A WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      9    1
  TEX13A WILD-TYPE  276   47
   clus
vv  TEX13A MUTATED TEX13A WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1672V7, binary
                  cls
clus                 0   1
  TEX13A MUTATED     7   3
  TEX13A WILD-TYPE 163 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      7    3
  TEX13A WILD-TYPE  163  194
        clus
vv       TEX13A MUTATED TEX13A WILD-TYPE
  FEMALE              7              163
  MALE                3              194
[1] 2 2
[1] FALSE
D1672V8, binary
                  cls
clus                 0   1
  TEX13A MUTATED     9   0
  TEX13A WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      9    0
  TEX13A WILD-TYPE  291    8
     clus
vv    TEX13A MUTATED TEX13A WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1672V9, binary
                  cls
clus                 0   1
  TEX13A MUTATED     8   2
  TEX13A WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      8    2
  TEX13A WILD-TYPE  306   46
                               clus
vv                              TEX13A MUTATED TEX13A WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TEX13A MUTATED     9   0   1   0
  TEX13A WILD-TYPE 250   3  21  21
D1672V10, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              0               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"
D1672V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEX13A MUTATED                                  0     0
  TEX13A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TEX13A MUTATED                           2     2
  TEX13A WILD-TYPE                        17   174
D1672V12, multiclass
                                  clus
vv                                 TEX13A MUTATED TEX13A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         2              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(1673) Variable = LCT MUTATION ANALYSIS
D1673V1, survival
               sevent
clus2             0   1
  LCT MUTATED    23   9
  LCT WILD-TYPE 254  69
  LCT MUTATED LCT WILD-TYPE 
           32           323 
  LCT MUTATED LCT WILD-TYPE 
            9            69 
$`LCT MUTATED`
TCGA-A6-4105 TCGA-AA-3950 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6588 TCGA-A6-5662 
       14.53        24.00       100.01         5.88        26.17        23.61 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3977 
       19.66         3.02        29.95        78.08        26.99        25.02 
TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R 
       38.04        18.05         4.01        34.98         1.02        35.01 
TCGA-AA-A03F TCGA-AD-6901 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
       18.05        22.42        58.39        12.59        12.76        10.06 
TCGA-CM-6165 TCGA-CM-6677 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6929 TCGA-F4-6459 
       16.04        11.08        16.14         9.44        13.41         8.61 
TCGA-G4-6304 TCGA-G4-6307 
       53.62        55.04 

$`LCT WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       49.08        63.62        22.09        35.80        91.79        79.69 
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-A6-5656 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-A6-5664 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       13.94        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6460 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        43.04        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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LCT MUTATED LCT WILD-TYPE 
         1.02          0.00 
  LCT MUTATED LCT WILD-TYPE 
       100.01        148.01 
  LCT MUTATED LCT WILD-TYPE 
       18.855        22.090 
[1] "1.0 - 100.0 (18.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1673V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LCT MUTATED         1        0        4        14         3         0
  LCT WILD-TYPE      63        1       22        94         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LCT MUTATED           2          0          3          1        2         1
  LCT WILD-TYPE        16          6         41         32       33        11
               vv
clus            STAGE IVB
  LCT MUTATED           0
  LCT WILD-TYPE         1
D1673V3, multiclass
            clus
vv           LCT MUTATED LCT WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             4            22
  STAGE IIA           14            94
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            2            16
  STAGE IIIA           0             6
  STAGE IIIB           3            41
  STAGE IIIC           1            32
  STAGE IV             2            33
  STAGE IVA            1            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
  LCT MUTATED     0   2  26   5
  LCT WILD-TYPE   9  65 223  36
D1673V4, multiclass
    clus
vv   LCT MUTATED LCT WILD-TYPE
  T1           0             9
  T2           2            65
  T3          26           223
  T4           5            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
  LCT MUTATED    24   4   5
  LCT WILD-TYPE 196  77  61
D1673V5, multiclass
    clus
vv   LCT MUTATED LCT WILD-TYPE
  N0          24           196
  N1           4            77
  N2           5            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1673V6, binary
               cls
clus              0   1
  LCT MUTATED    27   3
  LCT WILD-TYPE 258  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCT MUTATED     27    3
  LCT WILD-TYPE  258   45
   clus
vv  LCT MUTATED LCT WILD-TYPE
  0          27           258
  1           3            45
[1] 2 2
[1] FALSE
D1673V7, binary
               cls
clus              0   1
  LCT MUTATED    16  17
  LCT WILD-TYPE 154 180
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCT MUTATED     16   17
  LCT WILD-TYPE  154  180
        clus
vv       LCT MUTATED LCT WILD-TYPE
  FEMALE          16           154
  MALE            17           180
[1] 2 2
[1] FALSE
D1673V8, binary
               cls
clus              0   1
  LCT MUTATED    28   1
  LCT WILD-TYPE 272   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCT MUTATED     28    1
  LCT WILD-TYPE  272    7
     clus
vv    LCT MUTATED LCT WILD-TYPE
  NO           28           272
  YES           1             7
[1] 2 2
[1] FALSE
D1673V9, binary
               cls
clus              0   1
  LCT MUTATED    23  10
  LCT WILD-TYPE 291  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCT MUTATED     23   10
  LCT WILD-TYPE  291   38
                               clus
vv                              LCT MUTATED LCT WILD-TYPE
  COLON ADENOCARCINOMA                   23           291
  COLON MUCINOUS ADENOCARCINOMA          10            38
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  LCT MUTATED    25   0   0   2
  LCT WILD-TYPE 234   3  22  19
D1673V10, multiclass
    clus
vv   LCT MUTATED LCT WILD-TYPE
  R0          25           234
  R1           0             3
  R2           0            22
  RX           2            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"
D1673V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCT MUTATED                                  0     3
  LCT WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LCT MUTATED                           0    16
  LCT WILD-TYPE                        19   160
D1673V12, multiclass
                                  clus
vv                                 LCT MUTATED LCT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             7
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                     16           160
[1] 4 2
[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 = IDI1 MUTATION ANALYSIS
D1674V1, survival
                sevent
clus2              0   1
  IDI1 MUTATED     1   2
  IDI1 WILD-TYPE 276  76
  IDI1 MUTATED IDI1 WILD-TYPE 
             3            352 
  IDI1 MUTATED IDI1 WILD-TYPE 
             2             76 
$`IDI1 MUTATED`
TCGA-AZ-6598 TCGA-F4-6570 TCGA-G4-6304 
       49.41         6.18        53.62 

$`IDI1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  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         22.045 
[1] "6.2 - 53.6 (49.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.2"
D1674V2, continuous
                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      64        1       25       106         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  IDI1 MUTATED           0
  IDI1 WILD-TYPE         1
D1674V3, multiclass
            clus
vv           IDI1 MUTATED IDI1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             2            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  IDI1 MUTATED     0   0   3   1
  IDI1 WILD-TYPE   9  67 246  40
D1674V4, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            3            246
  T4            1             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
  IDI1 MUTATED     4   0   0
  IDI1 WILD-TYPE 216  81  66
D1674V5, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1674V6, binary
                cls
clus               0   1
  IDI1 MUTATED     3   0
  IDI1 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      3    0
  IDI1 WILD-TYPE  282   48
   clus
vv  IDI1 MUTATED IDI1 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1674V7, binary
                cls
clus               0   1
  IDI1 MUTATED     4   0
  IDI1 WILD-TYPE 166 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      4    0
  IDI1 WILD-TYPE  166  197
        clus
vv       IDI1 MUTATED IDI1 WILD-TYPE
  FEMALE            4            166
  MALE              0            197
[1] 2 2
[1] FALSE
D1674V8, binary
                cls
clus               0   1
  IDI1 MUTATED     3   0
  IDI1 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      3    0
  IDI1 WILD-TYPE  297    8
     clus
vv    IDI1 MUTATED IDI1 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1674V9, binary
                cls
clus               0   1
  IDI1 MUTATED     4   0
  IDI1 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      4    0
  IDI1 WILD-TYPE  310   48
                               clus
vv                              IDI1 MUTATED IDI1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDI1 MUTATED     3   0   0   0
  IDI1 WILD-TYPE 256   3  22  21
D1674V10, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1674V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDI1 MUTATED                                  0     0
  IDI1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDI1 MUTATED                           0     3
  IDI1 WILD-TYPE                        19   173
D1674V12, multiclass
                                  clus
vv                                 IDI1 MUTATED IDI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = C6ORF15 MUTATION ANALYSIS
D1675V1, survival
                   sevent
clus2                 0   1
  C6ORF15 MUTATED     5   1
  C6ORF15 WILD-TYPE 272  77
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                6               349 
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.090 
[1] "10.1 - 58.4 (15.5)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1675V2, continuous
                   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      62        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF15 MUTATED           0          0          0          0        0
  C6ORF15 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C6ORF15 MUTATED           0         0
  C6ORF15 WILD-TYPE        12         1
D1675V3, multiclass
            clus
vv           C6ORF15 MUTATED C6ORF15 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C6ORF15 MUTATED     1   1   4   0
  C6ORF15 WILD-TYPE   8  66 245  41
D1675V4, multiclass
    clus
vv   C6ORF15 MUTATED C6ORF15 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               4               245
  T4               0                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
  C6ORF15 MUTATED     6   0   0
  C6ORF15 WILD-TYPE 214  81  66
D1675V5, multiclass
    clus
vv   C6ORF15 MUTATED C6ORF15 WILD-TYPE
  N0               6               214
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1675V6, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     6   0
  C6ORF15 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      6    0
  C6ORF15 WILD-TYPE  279   48
   clus
vv  C6ORF15 MUTATED C6ORF15 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1675V7, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     4   2
  C6ORF15 WILD-TYPE 166 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      4    2
  C6ORF15 WILD-TYPE  166  195
        clus
vv       C6ORF15 MUTATED C6ORF15 WILD-TYPE
  FEMALE               4               166
  MALE                 2               195
[1] 2 2
[1] FALSE
D1675V8, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     6   0
  C6ORF15 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      6    0
  C6ORF15 WILD-TYPE  294    8
     clus
vv    C6ORF15 MUTATED C6ORF15 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1675V9, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     5   1
  C6ORF15 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      5    1
  C6ORF15 WILD-TYPE  309   47
                               clus
vv                              C6ORF15 MUTATED C6ORF15 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C6ORF15 MUTATED     5   0   0   1
  C6ORF15 WILD-TYPE 254   3  22  20
D1675V10, multiclass
    clus
vv   C6ORF15 MUTATED C6ORF15 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               1                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"
D1675V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF15 MUTATED                                  0     1
  C6ORF15 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C6ORF15 MUTATED                           0     3
  C6ORF15 WILD-TYPE                        19   173
D1675V12, multiclass
                                  clus
vv                                 C6ORF15 MUTATED C6ORF15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = MYO3A MUTATION ANALYSIS
D1676V1, survival
                 sevent
clus2               0   1
  MYO3A MUTATED    27   9
  MYO3A WILD-TYPE 250  69
  MYO3A MUTATED MYO3A WILD-TYPE 
             36             319 
  MYO3A MUTATED MYO3A WILD-TYPE 
              9              69 
$`MYO3A MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-6138 
      100.01        26.17        32.75        36.53        33.53        22.52 
TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 
       24.69        20.12        19.66        63.98         6.97        10.06 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       33.01         2.01        25.02         4.01        34.98         1.02 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       83.24         5.79        58.39        12.76        10.06       148.01 
TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6163 
       23.05        22.03        22.98        15.02        15.02        14.04 
TCGA-D5-6535 TCGA-D5-6537 TCGA-DM-A28G TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6626 
       15.12         4.80        60.79        41.42        33.67        46.75 

$`MYO3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-5656 
       42.90        42.28        16.57        34.65        33.34        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09         8.38        25.08        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       24.39        23.87        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6901 TCGA-AD-6963 
       18.05        40.96        12.16        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       25.48        43.27        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       13.78 

  MYO3A MUTATED MYO3A WILD-TYPE 
           1.02            0.00 
  MYO3A MUTATED MYO3A WILD-TYPE 
         148.01          140.38 
  MYO3A MUTATED MYO3A WILD-TYPE 
         23.015          21.990 
[1] "1.0 - 148.0 (23.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D1676V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO3A MUTATED         6        0        4        13         4         0
  MYO3A WILD-TYPE      58        1       22        95         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3A MUTATED           2          0          4          2        0         1
  MYO3A WILD-TYPE        16          6         40         31       35        11
                 vv
clus              STAGE IVB
  MYO3A MUTATED           0
  MYO3A WILD-TYPE         1
D1676V3, multiclass
            clus
vv           MYO3A MUTATED MYO3A WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA             13              95
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              1              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
  MYO3A MUTATED     2   5  24   6
  MYO3A WILD-TYPE   7  62 225  35
D1676V4, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  T1             2               7
  T2             5              62
  T3            24             225
  T4             6              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
  MYO3A MUTATED    29   6   2
  MYO3A WILD-TYPE 191  75  64
D1676V5, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  N0            29             191
  N1             6              75
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1676V6, binary
                 cls
clus                0   1
  MYO3A MUTATED    29   1
  MYO3A WILD-TYPE 256  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     29    1
  MYO3A WILD-TYPE  256   47
   clus
vv  MYO3A MUTATED MYO3A WILD-TYPE
  0            29             256
  1             1              47
[1] 2 2
[1] FALSE
D1676V7, binary
                 cls
clus                0   1
  MYO3A MUTATED    15  22
  MYO3A WILD-TYPE 155 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     15   22
  MYO3A WILD-TYPE  155  175
        clus
vv       MYO3A MUTATED MYO3A WILD-TYPE
  FEMALE            15             155
  MALE              22             175
[1] 2 2
[1] FALSE
D1676V8, binary
                 cls
clus                0   1
  MYO3A MUTATED    32   0
  MYO3A WILD-TYPE 268   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     32    0
  MYO3A WILD-TYPE  268    8
     clus
vv    MYO3A MUTATED MYO3A WILD-TYPE
  NO             32             268
  YES             0               8
[1] 2 2
[1] FALSE
D1676V9, binary
                 cls
clus                0   1
  MYO3A MUTATED    29   8
  MYO3A WILD-TYPE 285  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     29    8
  MYO3A WILD-TYPE  285   40
                               clus
vv                              MYO3A MUTATED MYO3A WILD-TYPE
  COLON ADENOCARCINOMA                     29             285
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYO3A MUTATED    25   0   0   4
  MYO3A WILD-TYPE 234   3  22  17
D1676V10, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  R0            25             234
  R1             0               3
  R2             0              22
  RX             4              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"
D1676V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO3A MUTATED                                  0     3
  MYO3A WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO3A MUTATED                           2    23
  MYO3A WILD-TYPE                        17   153
D1676V12, multiclass
                                  clus
vv                                 MYO3A MUTATED MYO3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       23             153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1677) Variable = C5 MUTATION ANALYSIS
D1677V1, survival
              sevent
clus2            0   1
  C5 MUTATED    12   5
  C5 WILD-TYPE 265  73
  C5 MUTATED C5 WILD-TYPE 
          17          338 
  C5 MUTATED C5 WILD-TYPE 
           5           73 
$`C5 MUTATED`
TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3950 TCGA-AA-3979 TCGA-G4-6628 TCGA-AA-3877 
       19.07        13.02        24.00        24.00        79.69        31.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AZ-4315 TCGA-CA-6719 TCGA-CM-5344 
        4.01        34.98        14.01        58.39        14.30        22.03 
TCGA-CM-6674 TCGA-D5-6927 TCGA-DM-A1DA TCGA-F4-6809 TCGA-G4-6299 
       12.95         9.44         7.50        13.25        74.56 

$`C5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       37.05        36.03         8.05        34.03         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
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-A6-5656 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-A6-6648 
       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-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-F4-6459 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        43.04 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       33.67         0.53        47.41        35.31       133.18        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  C5 MUTATED C5 WILD-TYPE 
        4.01         0.00 
  C5 MUTATED C5 WILD-TYPE 
       79.69       148.01 
  C5 MUTATED C5 WILD-TYPE 
       19.07        22.09 
[1] "4.0 - 79.7 (19.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1677V2, continuous
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5 MUTATED         3        0        0         6         2         0
  C5 WILD-TYPE      61        1       26       102         6         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C5 MUTATED           0          0          1          3        1         1
  C5 WILD-TYPE        18          6         43         30       34        11
              vv
clus           STAGE IVB
  C5 MUTATED           0
  C5 WILD-TYPE         1
D1677V3, multiclass
            clus
vv           C5 MUTATED C5 WILD-TYPE
  STAGE I             3           61
  STAGE IA            0            1
  STAGE II            0           26
  STAGE IIA           6          102
  STAGE IIB           2            6
  STAGE IIC           0            1
  STAGE III           0           18
  STAGE IIIA          0            6
  STAGE IIIB          1           43
  STAGE IIIC          3           30
  STAGE IV            1           34
  STAGE IVA           1           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
  C5 MUTATED     1   2  11   3
  C5 WILD-TYPE   8  65 238  38
D1677V4, multiclass
    clus
vv   C5 MUTATED C5 WILD-TYPE
  T1          1            8
  T2          2           65
  T3         11          238
  T4          3           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
  C5 MUTATED    11   2   4
  C5 WILD-TYPE 209  79  62
D1677V5, multiclass
    clus
vv   C5 MUTATED C5 WILD-TYPE
  N0         11          209
  N1          2           79
  N2          4           62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1677V6, binary
              cls
clus             0   1
  C5 MUTATED    15   2
  C5 WILD-TYPE 270  46
[1] "tbl2"
              cls
clus           [,1] [,2]
  C5 MUTATED     15    2
  C5 WILD-TYPE  270   46
   clus
vv  C5 MUTATED C5 WILD-TYPE
  0         15          270
  1          2           46
[1] 2 2
[1] FALSE
D1677V7, binary
              cls
clus             0   1
  C5 MUTATED     6  11
  C5 WILD-TYPE 164 186
[1] "tbl2"
              cls
clus           [,1] [,2]
  C5 MUTATED      6   11
  C5 WILD-TYPE  164  186
        clus
vv       C5 MUTATED C5 WILD-TYPE
  FEMALE          6          164
  MALE           11          186
[1] 2 2
[1] FALSE
D1677V8, binary
              cls
clus             0   1
  C5 MUTATED    15   0
  C5 WILD-TYPE 285   8
[1] "tbl2"
              cls
clus           [,1] [,2]
  C5 MUTATED     15    0
  C5 WILD-TYPE  285    8
     clus
vv    C5 MUTATED C5 WILD-TYPE
  NO          15          285
  YES          0            8
[1] 2 2
[1] FALSE
D1677V9, binary
              cls
clus             0   1
  C5 MUTATED    14   3
  C5 WILD-TYPE 300  45
[1] "tbl2"
              cls
clus           [,1] [,2]
  C5 MUTATED     14    3
  C5 WILD-TYPE  300   45
                               clus
vv                              C5 MUTATED C5 WILD-TYPE
  COLON ADENOCARCINOMA                  14          300
  COLON MUCINOUS ADENOCARCINOMA          3           45
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  C5 MUTATED    14   0   1   1
  C5 WILD-TYPE 245   3  21  20
D1677V10, multiclass
    clus
vv   C5 MUTATED C5 WILD-TYPE
  R0         14          245
  R1          0            3
  R2          1           21
  RX          1           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"
D1677V11, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  C5 MUTATED                                  0     1                         0
  C5 WILD-TYPE                                1     9                        19
              vv
clus           WHITE
  C5 MUTATED       8
  C5 WILD-TYPE   168
D1677V12, multiclass
                                  clus
vv                                 C5 MUTATED C5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     1            9
  BLACK OR AFRICAN AMERICAN                 0           19
  WHITE                                     8          168
[1] 4 2
[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 = MICAL1 MUTATION ANALYSIS
D1678V1, survival
                  sevent
clus2                0   1
  MICAL1 MUTATED     7   1
  MICAL1 WILD-TYPE 270  77
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               8              347 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               1               77 
$`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        83.24        27.09 
TCGA-CM-6162 TCGA-D5-6927 
       12.00         9.44 

$`MICAL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  MICAL1 MUTATED MICAL1 WILD-TYPE 
            1.02             0.00 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
           83.24           148.01 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
           10.72            22.09 
[1] "1.0 - 83.2 (10.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1678V2, continuous
                  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      61        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MICAL1 MUTATED           0          0          1          0        0
  MICAL1 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MICAL1 MUTATED           0         0
  MICAL1 WILD-TYPE        12         1
D1678V3, multiclass
            clus
vv           MICAL1 MUTATED MICAL1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MICAL1 MUTATED     0   3   5   1
  MICAL1 WILD-TYPE   9  64 244  40
D1678V4, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              5              244
  T4              1               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
  MICAL1 MUTATED     8   1   0
  MICAL1 WILD-TYPE 212  80  66
D1678V5, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1678V6, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     9   0
  MICAL1 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      9    0
  MICAL1 WILD-TYPE  276   48
   clus
vv  MICAL1 MUTATED MICAL1 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1678V7, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     4   5
  MICAL1 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      4    5
  MICAL1 WILD-TYPE  166  192
        clus
vv       MICAL1 MUTATED MICAL1 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D1678V8, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     7   0
  MICAL1 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      7    0
  MICAL1 WILD-TYPE  293    8
     clus
vv    MICAL1 MUTATED MICAL1 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1678V9, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     7   2
  MICAL1 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      7    2
  MICAL1 WILD-TYPE  307   46
                               clus
vv                              MICAL1 MUTATED MICAL1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MICAL1 MUTATED     7   0   0   0
  MICAL1 WILD-TYPE 252   3  22  21
D1678V10, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1678V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MICAL1 MUTATED                                  0     1
  MICAL1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MICAL1 MUTATED                           1     4
  MICAL1 WILD-TYPE                        18   172
D1678V12, multiclass
                                  clus
vv                                 MICAL1 MUTATED MICAL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1679) Variable = PTPN13 MUTATION ANALYSIS
D1679V1, survival
                  sevent
clus2                0   1
  PTPN13 MUTATED    17   5
  PTPN13 WILD-TYPE 260  73
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              22              333 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
               5               73 
$`PTPN13 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 
       85.05        19.04        26.17        33.53         3.02        63.98 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A02H 
       33.01        20.98         4.01        34.98        38.07         2.01 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6171 TCGA-D5-6929 TCGA-D5-6930 
       58.39        12.76        30.08        14.04        13.41        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-G4-6323 
       12.00        10.26        24.43        13.78 

$`PTPN13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3956 
       18.05        31.00         2.01        24.00        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.64        11.38       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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        46.75 

  PTPN13 MUTATED PTPN13 WILD-TYPE 
            2.01             0.00 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
           85.05           148.01 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
           20.01            22.09 
[1] "2.0 - 85.0 (20.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1679V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN13 MUTATED         2        1        3         7         3         0
  PTPN13 WILD-TYPE      62        0       23       101         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN13 MUTATED           1          0          1          1        3
  PTPN13 WILD-TYPE        17          6         43         32       32
                  vv
clus               STAGE IVA STAGE IVB
  PTPN13 MUTATED           0         0
  PTPN13 WILD-TYPE        12         1
D1679V3, multiclass
            clus
vv           PTPN13 MUTATED PTPN13 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                3               23
  STAGE IIA               7              101
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                3               32
  STAGE IVA               0               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
  PTPN13 MUTATED     0   3  14   4
  PTPN13 WILD-TYPE   9  64 235  37
D1679V4, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             14              235
  T4              4               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
  PTPN13 MUTATED    17   2   3
  PTPN13 WILD-TYPE 203  79  63
D1679V5, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  N0             17              203
  N1              2               79
  N2              3               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"
D1679V6, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    18   3
  PTPN13 WILD-TYPE 267  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     18    3
  PTPN13 WILD-TYPE  267   45
   clus
vv  PTPN13 MUTATED PTPN13 WILD-TYPE
  0             18              267
  1              3               45
[1] 2 2
[1] FALSE
D1679V7, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    11  11
  PTPN13 WILD-TYPE 159 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     11   11
  PTPN13 WILD-TYPE  159  186
        clus
vv       PTPN13 MUTATED PTPN13 WILD-TYPE
  FEMALE             11              159
  MALE               11              186
[1] 2 2
[1] FALSE
D1679V8, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    18   1
  PTPN13 WILD-TYPE 282   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     18    1
  PTPN13 WILD-TYPE  282    7
     clus
vv    PTPN13 MUTATED PTPN13 WILD-TYPE
  NO              18              282
  YES              1                7
[1] 2 2
[1] FALSE
D1679V9, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    17   5
  PTPN13 WILD-TYPE 297  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     17    5
  PTPN13 WILD-TYPE  297   43
                               clus
vv                              PTPN13 MUTATED PTPN13 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPN13 MUTATED    18   0   2   1
  PTPN13 WILD-TYPE 241   3  20  20
D1679V10, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  R0             18              241
  R1              0                3
  R2              2               20
  RX              1               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"
D1679V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN13 MUTATED                                  0     1
  PTPN13 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN13 MUTATED                           2     9
  PTPN13 WILD-TYPE                        17   167
D1679V12, multiclass
                                  clus
vv                                 PTPN13 MUTATED PTPN13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         9              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(1680) Variable = TMPRSS15 MUTATION ANALYSIS
D1680V1, survival
                    sevent
clus2                  0   1
  TMPRSS15 MUTATED    15   7
  TMPRSS15 WILD-TYPE 262  71
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                22                333 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                 7                 71 
$`TMPRSS15 MUTATED`
TCGA-AA-3516 TCGA-AA-3715 TCGA-AD-6888 TCGA-A6-6137 TCGA-AA-3518 TCGA-AA-3555 
       13.02        19.04        15.52        27.09         1.02        29.95 
TCGA-AA-3558 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6599 
       20.98        53.00        34.98        17.82        49.41         6.77 
TCGA-CA-5797 TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-6166 
       12.59        10.06         2.01        37.02        13.02        21.99 
TCGA-D5-6536 TCGA-D5-6931 TCGA-DM-A28F TCGA-G4-6309 
       17.85        12.00        35.97        85.48 

$`TMPRSS15 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       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-A6-6651 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       21.01        24.00        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.20        12.76 
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-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
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-6167 TCGA-CM-6168 
       12.00        14.04        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 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
              1.02               0.00 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
             85.48             148.01 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
            18.445             22.360 
[1] "1.0 - 85.5 (18.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.7"
D1680V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMPRSS15 MUTATED         4        0        3         6         1         0
  TMPRSS15 WILD-TYPE      60        1       23       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS15 MUTATED           1          0          5          1        1
  TMPRSS15 WILD-TYPE        17          6         39         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  TMPRSS15 MUTATED           0         0
  TMPRSS15 WILD-TYPE        12         1
D1680V3, multiclass
            clus
vv           TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  3                 23
  STAGE IIA                 6                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                5                 39
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  TMPRSS15 MUTATED     0   4  16   2
  TMPRSS15 WILD-TYPE   9  63 233  39
D1680V4, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  T1                0                  9
  T2                4                 63
  T3               16                233
  T4                2                 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
  TMPRSS15 MUTATED    14   6   2
  TMPRSS15 WILD-TYPE 206  75  64
D1680V5, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  N0               14                206
  N1                6                 75
  N2                2                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1680V6, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    19   1
  TMPRSS15 WILD-TYPE 266  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     19    1
  TMPRSS15 WILD-TYPE  266   47
   clus
vv  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  0               19                266
  1                1                 47
[1] 2 2
[1] FALSE
D1680V7, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED     9  13
  TMPRSS15 WILD-TYPE 161 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED      9   13
  TMPRSS15 WILD-TYPE  161  184
        clus
vv       TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  FEMALE                9                161
  MALE                 13                184
[1] 2 2
[1] FALSE
D1680V8, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    20   0
  TMPRSS15 WILD-TYPE 280   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     20    0
  TMPRSS15 WILD-TYPE  280    8
     clus
vv    TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  NO                20                280
  YES                0                  8
[1] 2 2
[1] FALSE
D1680V9, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    19   3
  TMPRSS15 WILD-TYPE 295  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     19    3
  TMPRSS15 WILD-TYPE  295   45
                               clus
vv                              TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  COLON ADENOCARCINOMA                        19                295
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TMPRSS15 MUTATED    14   0   1   2
  TMPRSS15 WILD-TYPE 245   3  21  19
D1680V10, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  R0               14                245
  R1                0                  3
  R2                1                 21
  RX                2                 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"
D1680V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMPRSS15 MUTATED                                  0     2
  TMPRSS15 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS15 MUTATED                           4     9
  TMPRSS15 WILD-TYPE                        15   167
D1680V12, multiclass
                                  clus
vv                                 TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       4                 15
  WHITE                                           9                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(1681) Variable = C17ORF71 MUTATION ANALYSIS
D1681V1, survival
                    sevent
clus2                  0   1
  C17ORF71 MUTATED     7   2
  C17ORF71 WILD-TYPE 270  76
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 9                346 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 2                 76 
$`C17ORF71 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-6654 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 
       19.04        19.04        23.87        33.04         4.01        34.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6679 
       30.08        32.02        10.06 

$`C17ORF71 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
              4.01               0.00 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
             34.98             148.01 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
            23.870             22.045 
[1] "4.0 - 35.0 (23.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1681V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C17ORF71 MUTATED         0        0        1         4         2         0
  C17ORF71 WILD-TYPE      64        1       25       104         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF71 MUTATED           0          0          1          0        1
  C17ORF71 WILD-TYPE        18          6         43         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF71 MUTATED           0         0
  C17ORF71 WILD-TYPE        12         1
D1681V3, multiclass
            clus
vv           C17ORF71 MUTATED C17ORF71 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  C17ORF71 MUTATED     0   0   7   2
  C17ORF71 WILD-TYPE   9  67 242  39
D1681V4, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                7                242
  T4                2                 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
  C17ORF71 MUTATED     8   1   0
  C17ORF71 WILD-TYPE 212  80  66
D1681V5, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  N0                8                212
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1681V6, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     8   1
  C17ORF71 WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      8    1
  C17ORF71 WILD-TYPE  277   47
   clus
vv  C17ORF71 MUTATED C17ORF71 WILD-TYPE
  0                8                277
  1                1                 47
[1] 2 2
[1] FALSE
D1681V7, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     4   5
  C17ORF71 WILD-TYPE 166 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      4    5
  C17ORF71 WILD-TYPE  166  192
        clus
vv       C17ORF71 MUTATED C17ORF71 WILD-TYPE
  FEMALE                4                166
  MALE                  5                192
[1] 2 2
[1] FALSE
D1681V8, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     7   1
  C17ORF71 WILD-TYPE 293   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      7    1
  C17ORF71 WILD-TYPE  293    7
     clus
vv    C17ORF71 MUTATED C17ORF71 WILD-TYPE
  NO                 7                293
  YES                1                  7
[1] 2 2
[1] FALSE
D1681V9, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     8   1
  C17ORF71 WILD-TYPE 306  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      8    1
  C17ORF71 WILD-TYPE  306   47
                               clus
vv                              C17ORF71 MUTATED C17ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C17ORF71 MUTATED     7   0   1   0
  C17ORF71 WILD-TYPE 252   3  21  21
D1681V10, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D1681V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C17ORF71 MUTATED                                  0     0
  C17ORF71 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C17ORF71 MUTATED                           0     4
  C17ORF71 WILD-TYPE                        19   172
D1681V12, multiclass
                                  clus
vv                                 C17ORF71 MUTATED C17ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = WDR17 MUTATION ANALYSIS
D1682V1, survival
                 sevent
clus2               0   1
  WDR17 MUTATED    18   4
  WDR17 WILD-TYPE 259  74
  WDR17 MUTATED WDR17 WILD-TYPE 
             22             333 
  WDR17 MUTATED WDR17 WILD-TYPE 
              4              74 
$`WDR17 MUTATED`
TCGA-AA-3554 TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3851 
       17.95        10.88        22.06        63.98        29.95        33.07 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 
        2.01        25.02         4.01        34.98        35.01        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        12.39        10.13 
TCGA-D5-6928 TCGA-DM-A1D6 TCGA-G4-6293 TCGA-G4-6317 
       11.64        49.91       133.18        36.00 

$`WDR17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        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-6718 
       12.36        12.39        12.59        12.59        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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 
       43.04        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-G4-6315 TCGA-G4-6323 TCGA-G4-6626 
       61.91        13.78        46.75 

  WDR17 MUTATED WDR17 WILD-TYPE 
           2.01            0.00 
  WDR17 MUTATED WDR17 WILD-TYPE 
         133.18          148.01 
  WDR17 MUTATED WDR17 WILD-TYPE 
         20.005          22.090 
[1] "2.0 - 133.2 (20.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1682V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR17 MUTATED         0        0        1        12         2         0
  WDR17 WILD-TYPE      64        1       25        96         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR17 MUTATED           2          1          1          1        1         0
  WDR17 WILD-TYPE        16          5         43         32       34        12
                 vv
clus              STAGE IVB
  WDR17 MUTATED           0
  WDR17 WILD-TYPE         1
D1682V3, multiclass
            clus
vv           WDR17 MUTATED WDR17 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA             12              96
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  WDR17 MUTATED     0   1  17   5
  WDR17 WILD-TYPE   9  66 232  36
D1682V4, multiclass
    clus
vv   WDR17 MUTATED WDR17 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            17             232
  T4             5              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
  WDR17 MUTATED    16   3   4
  WDR17 WILD-TYPE 204  78  62
D1682V5, multiclass
    clus
vv   WDR17 MUTATED WDR17 WILD-TYPE
  N0            16             204
  N1             3              78
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1682V6, binary
                 cls
clus                0   1
  WDR17 MUTATED    19   1
  WDR17 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     19    1
  WDR17 WILD-TYPE  266   47
   clus
vv  WDR17 MUTATED WDR17 WILD-TYPE
  0            19             266
  1             1              47
[1] 2 2
[1] FALSE
D1682V7, binary
                 cls
clus                0   1
  WDR17 MUTATED    11  12
  WDR17 WILD-TYPE 159 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     11   12
  WDR17 WILD-TYPE  159  185
        clus
vv       WDR17 MUTATED WDR17 WILD-TYPE
  FEMALE            11             159
  MALE              12             185
[1] 2 2
[1] FALSE
D1682V8, binary
                 cls
clus                0   1
  WDR17 MUTATED    18   1
  WDR17 WILD-TYPE 282   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     18    1
  WDR17 WILD-TYPE  282    7
     clus
vv    WDR17 MUTATED WDR17 WILD-TYPE
  NO             18             282
  YES             1               7
[1] 2 2
[1] FALSE
D1682V9, binary
                 cls
clus                0   1
  WDR17 MUTATED    16   7
  WDR17 WILD-TYPE 298  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     16    7
  WDR17 WILD-TYPE  298   41
                               clus
vv                              WDR17 MUTATED WDR17 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR17 MUTATED    16   0   0   2
  WDR17 WILD-TYPE 243   3  22  19
D1682V10, multiclass
    clus
vv   WDR17 MUTATED WDR17 WILD-TYPE
  R0            16             243
  R1             0               3
  R2             0              22
  RX             2              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"
D1682V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR17 MUTATED                                  0     1
  WDR17 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR17 MUTATED                           1    11
  WDR17 WILD-TYPE                        18   165
D1682V12, multiclass
                                  clus
vv                                 WDR17 MUTATED WDR17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(1683) Variable = FBXO40 MUTATION ANALYSIS
D1683V1, survival
                  sevent
clus2                0   1
  FBXO40 MUTATED    13   3
  FBXO40 WILD-TYPE 264  75
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              16              339 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
               3               75 
$`FBXO40 MUTATED`
TCGA-AA-3543 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3710 
        0.99       100.01        26.17        32.71         6.97        26.99 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6718 
        0.99        34.98        27.09        21.44        49.41        10.06 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-6930 
       29.03        13.02        15.02        13.35 

$`FBXO40 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6171 
       14.04        16.04        21.99        14.99        12.99        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FBXO40 MUTATED FBXO40 WILD-TYPE 
            0.99             0.00 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
          100.01           148.01 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
          23.805           22.060 
[1] "1.0 - 100.0 (23.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1683V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO40 MUTATED         4        0        3         7         1         1
  FBXO40 WILD-TYPE      60        1       23       101         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO40 MUTATED           0          0          0          0        0
  FBXO40 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXO40 MUTATED           0         0
  FBXO40 WILD-TYPE        12         1
D1683V3, multiclass
            clus
vv           FBXO40 MUTATED FBXO40 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  FBXO40 MUTATED     0   4  10   2
  FBXO40 WILD-TYPE   9  63 239  39
D1683V4, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             10              239
  T4              2               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
  FBXO40 MUTATED    16   0   0
  FBXO40 WILD-TYPE 204  81  66
D1683V5, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  N0             16              204
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1683V6, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    14   0
  FBXO40 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     14    0
  FBXO40 WILD-TYPE  271   48
   clus
vv  FBXO40 MUTATED FBXO40 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D1683V7, binary
                  cls
clus                 0   1
  FBXO40 MUTATED     8   8
  FBXO40 WILD-TYPE 162 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED      8    8
  FBXO40 WILD-TYPE  162  189
        clus
vv       FBXO40 MUTATED FBXO40 WILD-TYPE
  FEMALE              8              162
  MALE                8              189
[1] 2 2
[1] FALSE
D1683V8, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    14   0
  FBXO40 WILD-TYPE 286   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     14    0
  FBXO40 WILD-TYPE  286    8
     clus
vv    FBXO40 MUTATED FBXO40 WILD-TYPE
  NO              14              286
  YES              0                8
[1] 2 2
[1] FALSE
D1683V9, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    14   2
  FBXO40 WILD-TYPE 300  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     14    2
  FBXO40 WILD-TYPE  300   46
                               clus
vv                              FBXO40 MUTATED FBXO40 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXO40 MUTATED    12   0   0   1
  FBXO40 WILD-TYPE 247   3  22  20
D1683V10, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              1               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"
D1683V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO40 MUTATED                                  0     1
  FBXO40 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO40 MUTATED                           1     9
  FBXO40 WILD-TYPE                        18   167
D1683V12, multiclass
                                  clus
vv                                 FBXO40 MUTATED FBXO40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(1684) Variable = PDK1 MUTATION ANALYSIS
D1684V1, survival
                sevent
clus2              0   1
  PDK1 MUTATED     4   0
  PDK1 WILD-TYPE 273  78
  PDK1 MUTATED PDK1 WILD-TYPE 
             4            351 
  PDK1 MUTATED PDK1 WILD-TYPE 
             0             78 
$`PDK1 MUTATED`
TCGA-AA-3713 TCGA-AZ-4315 TCGA-CM-6166 TCGA-G4-6293 
       19.04        58.39        21.99       133.18 

$`PDK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PDK1 MUTATED PDK1 WILD-TYPE 
         19.04           0.00 
  PDK1 MUTATED PDK1 WILD-TYPE 
        133.18         148.01 
  PDK1 MUTATED PDK1 WILD-TYPE 
         40.19          22.06 
[1] "19.0 - 133.2 (40.2)" "0.0 - 148.0 (22.1)" 
[1] "hr="     "9300000"
D1684V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDK1 MUTATED         1        0        0         1         1         0
  PDK1 WILD-TYPE      63        1       26       107         7         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        17          6         44         33       34        12
                vv
clus             STAGE IVB
  PDK1 MUTATED           0
  PDK1 WILD-TYPE         1
D1684V3, multiclass
            clus
vv           PDK1 MUTATED PDK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  PDK1 MUTATED     0   1   3   1
  PDK1 WILD-TYPE   9  66 246  40
D1684V4, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            3            246
  T4            1             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
  PDK1 MUTATED     4   1   0
  PDK1 WILD-TYPE 216  80  66
D1684V5, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  N0            4            216
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1684V6, binary
                cls
clus               0   1
  PDK1 MUTATED     3   1
  PDK1 WILD-TYPE 282  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      3    1
  PDK1 WILD-TYPE  282   47
   clus
vv  PDK1 MUTATED PDK1 WILD-TYPE
  0            3            282
  1            1             47
[1] 2 2
[1] FALSE
D1684V7, binary
                cls
clus               0   1
  PDK1 MUTATED     3   2
  PDK1 WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      3    2
  PDK1 WILD-TYPE  167  195
        clus
vv       PDK1 MUTATED PDK1 WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D1684V8, binary
                cls
clus               0   1
  PDK1 MUTATED     3   1
  PDK1 WILD-TYPE 297   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      3    1
  PDK1 WILD-TYPE  297    7
     clus
vv    PDK1 MUTATED PDK1 WILD-TYPE
  NO             3            297
  YES            1              7
[1] 2 2
[1] FALSE
D1684V9, binary
                cls
clus               0   1
  PDK1 MUTATED     5   0
  PDK1 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      5    0
  PDK1 WILD-TYPE  309   48
                               clus
vv                              PDK1 MUTATED PDK1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PDK1 MUTATED     3   0   1   1
  PDK1 WILD-TYPE 256   3  21  20
D1684V10, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            1             21
  RX            1             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"
D1684V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDK1 MUTATED                                  0     0
  PDK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PDK1 MUTATED                           0     4
  PDK1 WILD-TYPE                        19   172
D1684V12, multiclass
                                  clus
vv                                 PDK1 MUTATED PDK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1685) Variable = FAM81B MUTATION ANALYSIS
D1685V1, survival
                  sevent
clus2                0   1
  FAM81B MUTATED     4   3
  FAM81B WILD-TYPE 273  75
  FAM81B MUTATED FAM81B WILD-TYPE 
               7              348 
  FAM81B MUTATED FAM81B WILD-TYPE 
               3               75 
$`FAM81B MUTATED`
TCGA-A6-4105 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3861 TCGA-D5-6930 
       14.53        20.12         7.04         3.02        30.05        13.35 
TCGA-G4-6299 
       74.56 

$`FAM81B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3510 
       24.39        23.87        19.66        20.28        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  FAM81B MUTATED FAM81B WILD-TYPE 
            3.02             0.00 
  FAM81B MUTATED FAM81B WILD-TYPE 
           74.56           148.01 
  FAM81B MUTATED FAM81B WILD-TYPE 
           14.53            22.09 
[1] "3.0 - 74.6 (14.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1685V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM81B MUTATED         0        0        2         5         0         0
  FAM81B WILD-TYPE      64        1       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM81B MUTATED           1          0          0          1        0
  FAM81B WILD-TYPE        17          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM81B MUTATED           0         0
  FAM81B WILD-TYPE        12         1
D1685V3, multiclass
            clus
vv           FAM81B MUTATED FAM81B WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  FAM81B MUTATED     0   0   9   0
  FAM81B WILD-TYPE   9  67 240  41
D1685V4, multiclass
    clus
vv   FAM81B MUTATED FAM81B WILD-TYPE
  T1              0                9
  T2              0               67
  T3              9              240
  T4              0               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
  FAM81B MUTATED     7   0   2
  FAM81B WILD-TYPE 213  81  64
D1685V5, multiclass
    clus
vv   FAM81B MUTATED FAM81B WILD-TYPE
  N0              7              213
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1685V6, binary
                  cls
clus                 0   1
  FAM81B MUTATED     8   0
  FAM81B WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM81B MUTATED      8    0
  FAM81B WILD-TYPE  277   48
   clus
vv  FAM81B MUTATED FAM81B WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1685V7, binary
                  cls
clus                 0   1
  FAM81B MUTATED     2   7
  FAM81B WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM81B MUTATED      2    7
  FAM81B WILD-TYPE  168  190
        clus
vv       FAM81B MUTATED FAM81B WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D1685V8, binary
                  cls
clus                 0   1
  FAM81B MUTATED     7   0
  FAM81B WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM81B MUTATED      7    0
  FAM81B WILD-TYPE  293    8
     clus
vv    FAM81B MUTATED FAM81B WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1685V9, binary
                  cls
clus                 0   1
  FAM81B MUTATED     7   2
  FAM81B WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM81B MUTATED      7    2
  FAM81B WILD-TYPE  307   46
                               clus
vv                              FAM81B MUTATED FAM81B WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM81B MUTATED     7   0   0   0
  FAM81B WILD-TYPE 252   3  22  21
D1685V10, multiclass
    clus
vv   FAM81B MUTATED FAM81B WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1685V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM81B MUTATED                                  0     0
  FAM81B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM81B MUTATED                           0     4
  FAM81B WILD-TYPE                        19   172
D1685V12, multiclass
                                  clus
vv                                 FAM81B MUTATED FAM81B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = HIP1 MUTATION ANALYSIS
D1686V1, survival
                sevent
clus2              0   1
  HIP1 MUTATED     7   5
  HIP1 WILD-TYPE 270  73
  HIP1 MUTATED HIP1 WILD-TYPE 
            12            343 
  HIP1 MUTATED HIP1 WILD-TYPE 
             5             73 
$`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 

$`HIP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        62.79        49.41         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  HIP1 MUTATED HIP1 WILD-TYPE 
          2.01           0.00 
  HIP1 MUTATED HIP1 WILD-TYPE 
         88.21         148.01 
  HIP1 MUTATED HIP1 WILD-TYPE 
        26.975         22.030 
[1] "2.0 - 88.2 (27.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1686V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIP1 MUTATED         2        0        2         2         3         0
  HIP1 WILD-TYPE      62        1       24       106         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIP1 MUTATED           0          0          1          0        1         0
  HIP1 WILD-TYPE        18          6         43         33       34        12
                vv
clus             STAGE IVB
  HIP1 MUTATED           0
  HIP1 WILD-TYPE         1
D1686V3, multiclass
            clus
vv           HIP1 MUTATED HIP1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             2            106
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  HIP1 MUTATED     1   2   6   3
  HIP1 WILD-TYPE   8  65 243  38
D1686V4, multiclass
    clus
vv   HIP1 MUTATED HIP1 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            6            243
  T4            3             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
  HIP1 MUTATED     9   2   1
  HIP1 WILD-TYPE 211  79  65
D1686V5, multiclass
    clus
vv   HIP1 MUTATED HIP1 WILD-TYPE
  N0            9            211
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1686V6, binary
                cls
clus               0   1
  HIP1 MUTATED    10   1
  HIP1 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED     10    1
  HIP1 WILD-TYPE  275   47
   clus
vv  HIP1 MUTATED HIP1 WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D1686V7, binary
                cls
clus               0   1
  HIP1 MUTATED     8   4
  HIP1 WILD-TYPE 162 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED      8    4
  HIP1 WILD-TYPE  162  193
        clus
vv       HIP1 MUTATED HIP1 WILD-TYPE
  FEMALE            8            162
  MALE              4            193
[1] 2 2
[1] FALSE
D1686V8, binary
                cls
clus               0   1
  HIP1 MUTATED    10   0
  HIP1 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED     10    0
  HIP1 WILD-TYPE  290    8
     clus
vv    HIP1 MUTATED HIP1 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1686V9, binary
                cls
clus               0   1
  HIP1 MUTATED    11   1
  HIP1 WILD-TYPE 303  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED     11    1
  HIP1 WILD-TYPE  303   47
                               clus
vv                              HIP1 MUTATED HIP1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HIP1 MUTATED     8   0   1   0
  HIP1 WILD-TYPE 251   3  21  21
D1686V10, multiclass
    clus
vv   HIP1 MUTATED HIP1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            1             21
  RX            0             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"
D1686V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIP1 MUTATED                                  0     0
  HIP1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HIP1 MUTATED                           0     7
  HIP1 WILD-TYPE                        19   169
D1686V12, multiclass
                                  clus
vv                                 HIP1 MUTATED HIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = PHLDB2 MUTATION ANALYSIS
D1687V1, survival
                  sevent
clus2                0   1
  PHLDB2 MUTATED    15   2
  PHLDB2 WILD-TYPE 262  76
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              17              338 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
               2               76 
$`PHLDB2 MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3697 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3819 
       13.02         8.05        85.05        22.06        63.98        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 
       13.02        15.12       117.07        53.62        85.48 

$`PHLDB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       36.00        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        10.06        35.05        33.04         0.99         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 
       74.56        65.85        44.68        55.04        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
            4.01             0.00 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
          117.07           148.01 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
           25.02            22.01 
[1] "4.0 - 117.1 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.7"
D1687V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHLDB2 MUTATED         1        0        2         6         3         0
  PHLDB2 WILD-TYPE      63        1       24       102         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHLDB2 MUTATED           1          0          3          2        0
  PHLDB2 WILD-TYPE        17          6         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PHLDB2 MUTATED           0         0
  PHLDB2 WILD-TYPE        12         1
D1687V3, multiclass
            clus
vv           PHLDB2 MUTATED PHLDB2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  PHLDB2 MUTATED     0   1  13   4
  PHLDB2 WILD-TYPE   9  66 236  37
D1687V4, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3             13              236
  T4              4               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
  PHLDB2 MUTATED    12   3   3
  PHLDB2 WILD-TYPE 208  78  63
D1687V5, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  N0             12              208
  N1              3               78
  N2              3               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"
D1687V6, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    17   0
  PHLDB2 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     17    0
  PHLDB2 WILD-TYPE  268   48
   clus
vv  PHLDB2 MUTATED PHLDB2 WILD-TYPE
  0             17              268
  1              0               48
[1] 2 2
[1] FALSE
D1687V7, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    10   8
  PHLDB2 WILD-TYPE 160 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     10    8
  PHLDB2 WILD-TYPE  160  189
        clus
vv       PHLDB2 MUTATED PHLDB2 WILD-TYPE
  FEMALE             10              160
  MALE                8              189
[1] 2 2
[1] FALSE
D1687V8, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    13   0
  PHLDB2 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     13    0
  PHLDB2 WILD-TYPE  287    8
     clus
vv    PHLDB2 MUTATED PHLDB2 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1687V9, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    14   4
  PHLDB2 WILD-TYPE 300  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     14    4
  PHLDB2 WILD-TYPE  300   44
                               clus
vv                              PHLDB2 MUTATED PHLDB2 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PHLDB2 MUTATED    13   0   0   3
  PHLDB2 WILD-TYPE 246   3  22  18
D1687V10, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              3               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"
D1687V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHLDB2 MUTATED                                  0     1
  PHLDB2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PHLDB2 MUTATED                           2     7
  PHLDB2 WILD-TYPE                        17   169
D1687V12, multiclass
                                  clus
vv                                 PHLDB2 MUTATED PHLDB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         7              169
[1] 4 2
[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 = TATDN2 MUTATION ANALYSIS
D1688V1, survival
                  sevent
clus2                0   1
  TATDN2 MUTATED     8   1
  TATDN2 WILD-TYPE 269  77
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               9              346 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               1               77 
$`TATDN2 MUTATED`
TCGA-AA-3554 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A00N 
       17.95        22.06        24.39         2.01        18.05         4.01 
TCGA-AA-A010 TCGA-CM-6674 TCGA-CM-6676 
       34.98        12.95        11.08 

$`TATDN2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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-6677 TCGA-CM-6678 
       15.02        14.04        11.01        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  TATDN2 MUTATED TATDN2 WILD-TYPE 
            2.01             0.00 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
           34.98           148.01 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
          17.950           22.225 
[1] "2.0 - 35.0 (17.9)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D1688V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TATDN2 MUTATED         2        0        0         4         2         0
  TATDN2 WILD-TYPE      62        1       26       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TATDN2 MUTATED           0          0          1          0        0
  TATDN2 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TATDN2 MUTATED           0         0
  TATDN2 WILD-TYPE        12         1
D1688V3, multiclass
            clus
vv           TATDN2 MUTATED TATDN2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  TATDN2 MUTATED     0   2   4   3
  TATDN2 WILD-TYPE   9  65 245  38
D1688V4, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              3               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
  TATDN2 MUTATED     8   1   0
  TATDN2 WILD-TYPE 212  80  66
D1688V5, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1688V6, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     9   0
  TATDN2 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      9    0
  TATDN2 WILD-TYPE  276   48
   clus
vv  TATDN2 MUTATED TATDN2 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1688V7, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     4   5
  TATDN2 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      4    5
  TATDN2 WILD-TYPE  166  192
        clus
vv       TATDN2 MUTATED TATDN2 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D1688V8, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     7   0
  TATDN2 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      7    0
  TATDN2 WILD-TYPE  293    8
     clus
vv    TATDN2 MUTATED TATDN2 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1688V9, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     6   3
  TATDN2 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      6    3
  TATDN2 WILD-TYPE  308   45
                               clus
vv                              TATDN2 MUTATED TATDN2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TATDN2 MUTATED     7   0   0   0
  TATDN2 WILD-TYPE 252   3  22  21
D1688V10, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  R0              7              252
  R1              0                3
  R2              0               22
  RX              0               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"
D1688V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TATDN2 MUTATED                                  0     0
  TATDN2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TATDN2 MUTATED                           0     4
  TATDN2 WILD-TYPE                        19   172
D1688V12, multiclass
                                  clus
vv                                 TATDN2 MUTATED TATDN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = SFRP2 MUTATION ANALYSIS
D1689V1, survival
                 sevent
clus2               0   1
  SFRP2 MUTATED     7   1
  SFRP2 WILD-TYPE 270  77
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              8             347 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              1              77 
$`SFRP2 MUTATED`
TCGA-AA-3697 TCGA-AZ-6601 TCGA-A6-3810 TCGA-AD-6963 TCGA-CK-4947 TCGA-CM-4743 
       85.05       100.01        36.53        27.42        17.56        23.05 
TCGA-D5-6930 TCGA-F4-6854 
       13.35         0.53 

$`SFRP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        22.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-F4-6855 TCGA-F4-6856 
       41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SFRP2 MUTATED SFRP2 WILD-TYPE 
           0.53            0.00 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
         100.01          148.01 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
         25.235          22.030 
[1] "0.5 - 100.0 (25.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1689V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRP2 MUTATED         0        0        2         4         0         0
  SFRP2 WILD-TYPE      64        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SFRP2 MUTATED           0          0          1          0        0         0
  SFRP2 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  SFRP2 MUTATED           0
  SFRP2 WILD-TYPE         1
D1689V3, multiclass
            clus
vv           SFRP2 MUTATED SFRP2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  SFRP2 MUTATED     0   0   7   1
  SFRP2 WILD-TYPE   9  67 242  40
D1689V4, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  SFRP2 MUTATED     7   1   0
  SFRP2 WILD-TYPE 213  80  66
D1689V5, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1689V6, binary
                 cls
clus                0   1
  SFRP2 MUTATED     7   0
  SFRP2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      7    0
  SFRP2 WILD-TYPE  278   48
   clus
vv  SFRP2 MUTATED SFRP2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1689V7, binary
                 cls
clus                0   1
  SFRP2 MUTATED     2   6
  SFRP2 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      2    6
  SFRP2 WILD-TYPE  168  191
        clus
vv       SFRP2 MUTATED SFRP2 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D1689V8, binary
                 cls
clus                0   1
  SFRP2 MUTATED     8   0
  SFRP2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      8    0
  SFRP2 WILD-TYPE  292    8
     clus
vv    SFRP2 MUTATED SFRP2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1689V9, binary
                 cls
clus                0   1
  SFRP2 MUTATED     7   1
  SFRP2 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      7    1
  SFRP2 WILD-TYPE  307   47
                               clus
vv                              SFRP2 MUTATED SFRP2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SFRP2 MUTATED     5   0   0   1
  SFRP2 WILD-TYPE 254   3  22  20
D1689V10, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D1689V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRP2 MUTATED                                  0     0
  SFRP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SFRP2 MUTATED                           0     7
  SFRP2 WILD-TYPE                        19   169
D1689V12, multiclass
                                  clus
vv                                 SFRP2 MUTATED SFRP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = EPRS MUTATION ANALYSIS
D1690V1, survival
                sevent
clus2              0   1
  EPRS MUTATED    14   3
  EPRS WILD-TYPE 263  75
  EPRS MUTATED EPRS WILD-TYPE 
            17            338 
  EPRS MUTATED EPRS WILD-TYPE 
             3             75 
$`EPRS MUTATED`
TCGA-AD-6895 TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-3710 TCGA-AA-3811 
       25.08        22.06        24.69        20.12        26.99        10.06 
TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6890 TCGA-CA-6717 
        2.01        18.05         4.01        34.98        24.53        12.76 
TCGA-CM-4747 TCGA-CM-5864 TCGA-CM-6674 TCGA-D5-6929 TCGA-DM-A0XF 
       25.02        15.02        12.95        13.41        38.20 

$`EPRS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.08        25.18        21.76        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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.35        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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  EPRS MUTATED EPRS WILD-TYPE 
          2.01           0.00 
  EPRS MUTATED EPRS WILD-TYPE 
         38.20         148.01 
  EPRS MUTATED EPRS WILD-TYPE 
         20.12          22.09 
[1] "2.0 - 38.2 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1690V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPRS MUTATED         1        0        0         7         3         0
  EPRS WILD-TYPE      63        1       26       101         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPRS MUTATED           1          0          2          1        1         2
  EPRS WILD-TYPE        17          6         42         32       34        10
                vv
clus             STAGE IVB
  EPRS MUTATED           0
  EPRS WILD-TYPE         1
D1690V3, multiclass
            clus
vv           EPRS MUTATED EPRS WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             2             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
  EPRS MUTATED     1   1  12   5
  EPRS WILD-TYPE   8  66 237  36
D1690V4, multiclass
    clus
vv   EPRS MUTATED EPRS WILD-TYPE
  T1            1              8
  T2            1             66
  T3           12            237
  T4            5             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
  EPRS MUTATED    13   4   2
  EPRS WILD-TYPE 207  77  64
D1690V5, multiclass
    clus
vv   EPRS MUTATED EPRS WILD-TYPE
  N0           13            207
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1690V6, binary
                cls
clus               0   1
  EPRS MUTATED    13   3
  EPRS WILD-TYPE 272  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     13    3
  EPRS WILD-TYPE  272   45
   clus
vv  EPRS MUTATED EPRS WILD-TYPE
  0           13            272
  1            3             45
[1] 2 2
[1] FALSE
D1690V7, binary
                cls
clus               0   1
  EPRS MUTATED     9  10
  EPRS WILD-TYPE 161 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED      9   10
  EPRS WILD-TYPE  161  187
        clus
vv       EPRS MUTATED EPRS WILD-TYPE
  FEMALE            9            161
  MALE             10            187
[1] 2 2
[1] FALSE
D1690V8, binary
                cls
clus               0   1
  EPRS MUTATED    14   0
  EPRS WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     14    0
  EPRS WILD-TYPE  286    8
     clus
vv    EPRS MUTATED EPRS WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1690V9, binary
                cls
clus               0   1
  EPRS MUTATED    13   5
  EPRS WILD-TYPE 301  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     13    5
  EPRS WILD-TYPE  301   43
                               clus
vv                              EPRS MUTATED EPRS WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EPRS MUTATED    12   0   0   2
  EPRS WILD-TYPE 247   3  22  19
D1690V10, multiclass
    clus
vv   EPRS MUTATED EPRS WILD-TYPE
  R0           12            247
  R1            0              3
  R2            0             22
  RX            2             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"
D1690V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPRS MUTATED                                  0     1
  EPRS WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EPRS MUTATED                           1    10
  EPRS WILD-TYPE                        18   166
D1690V12, multiclass
                                  clus
vv                                 EPRS MUTATED EPRS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(1691) Variable = CELSR1 MUTATION ANALYSIS
D1691V1, survival
                  sevent
clus2                0   1
  CELSR1 MUTATED    20   2
  CELSR1 WILD-TYPE 257  76
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              22              333 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
               2               76 
$`CELSR1 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3819 
       19.04        25.08        79.69        24.39         6.97        25.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A01Q TCGA-AA-A02O TCGA-AD-5900 
       18.05        31.00        33.01         1.02         0.92        12.16 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-5861 
       83.24        27.09        49.41        23.05        29.06        15.02 
TCGA-CM-6674 TCGA-DM-A1D9 TCGA-F4-6856 TCGA-G4-6306 
       12.95       140.38        35.31        44.68 

$`CELSR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99        10.06        35.05        33.04         0.99         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W 
       51.98        39.98         2.01         5.03        14.01        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        18.05        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       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-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-G4-6293 
       43.04        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-G4-6315 
       74.56        65.85        53.62        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CELSR1 MUTATED CELSR1 WILD-TYPE 
            0.92             0.00 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          140.38           148.01 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
           25.05            21.99 
[1] "0.9 - 140.4 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.8"
D1691V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CELSR1 MUTATED         7        0        4         6         1         0
  CELSR1 WILD-TYPE      57        1       22       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CELSR1 MUTATED           0          1          1          0        1
  CELSR1 WILD-TYPE        18          5         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CELSR1 MUTATED           0         0
  CELSR1 WILD-TYPE        12         1
D1691V3, multiclass
            clus
vv           CELSR1 MUTATED CELSR1 WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CELSR1 MUTATED     2   7  12   1
  CELSR1 WILD-TYPE   7  60 237  40
D1691V4, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  T1              2                7
  T2              7               60
  T3             12              237
  T4              1               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
  CELSR1 MUTATED    20   2   0
  CELSR1 WILD-TYPE 200  79  66
D1691V5, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  N0             20              200
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1691V6, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    19   1
  CELSR1 WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     19    1
  CELSR1 WILD-TYPE  266   47
   clus
vv  CELSR1 MUTATED CELSR1 WILD-TYPE
  0             19              266
  1              1               47
[1] 2 2
[1] FALSE
D1691V7, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    10  12
  CELSR1 WILD-TYPE 160 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     10   12
  CELSR1 WILD-TYPE  160  185
        clus
vv       CELSR1 MUTATED CELSR1 WILD-TYPE
  FEMALE             10              160
  MALE               12              185
[1] 2 2
[1] FALSE
D1691V8, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    17   1
  CELSR1 WILD-TYPE 283   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     17    1
  CELSR1 WILD-TYPE  283    7
     clus
vv    CELSR1 MUTATED CELSR1 WILD-TYPE
  NO              17              283
  YES              1                7
[1] 2 2
[1] FALSE
D1691V9, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    18   4
  CELSR1 WILD-TYPE 296  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     18    4
  CELSR1 WILD-TYPE  296   44
                               clus
vv                              CELSR1 MUTATED CELSR1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CELSR1 MUTATED    18   0   1   0
  CELSR1 WILD-TYPE 241   3  21  21
D1691V10, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  R0             18              241
  R1              0                3
  R2              1               21
  RX              0               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"
D1691V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CELSR1 MUTATED                                  0     1
  CELSR1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CELSR1 MUTATED                           0    13
  CELSR1 WILD-TYPE                        19   163
D1691V12, multiclass
                                  clus
vv                                 CELSR1 MUTATED CELSR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        13              163
[1] 4 2
[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 = PIAS2 MUTATION ANALYSIS
D1692V1, survival
                 sevent
clus2               0   1
  PIAS2 MUTATED     2   1
  PIAS2 WILD-TYPE 275  77
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              3             352 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              1              77 
$`PIAS2 MUTATED`
TCGA-AA-3555 TCGA-CA-6718 TCGA-CM-5860 
       29.95        10.06        32.02 

$`PIAS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PIAS2 MUTATED PIAS2 WILD-TYPE 
          10.06            0.00 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
          32.02          148.01 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
         29.950          22.045 
[1] "10.1 - 32.0 (29.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1692V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIAS2 MUTATED         0        0        0         4         0         0
  PIAS2 WILD-TYPE      64        1       26       104         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  PIAS2 MUTATED           0
  PIAS2 WILD-TYPE         1
D1692V3, multiclass
            clus
vv           PIAS2 MUTATED PIAS2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PIAS2 MUTATED     0   0   4   0
  PIAS2 WILD-TYPE   9  67 245  41
D1692V4, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             0              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
  PIAS2 MUTATED     4   0   0
  PIAS2 WILD-TYPE 216  81  66
D1692V5, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1692V6, binary
                 cls
clus                0   1
  PIAS2 MUTATED     4   0
  PIAS2 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      4    0
  PIAS2 WILD-TYPE  281   48
   clus
vv  PIAS2 MUTATED PIAS2 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1692V7, binary
                 cls
clus                0   1
  PIAS2 MUTATED     2   2
  PIAS2 WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      2    2
  PIAS2 WILD-TYPE  168  195
        clus
vv       PIAS2 MUTATED PIAS2 WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D1692V8, binary
                 cls
clus                0   1
  PIAS2 MUTATED     3   0
  PIAS2 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      3    0
  PIAS2 WILD-TYPE  297    8
     clus
vv    PIAS2 MUTATED PIAS2 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1692V9, binary
                 cls
clus                0   1
  PIAS2 MUTATED     3   1
  PIAS2 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      3    1
  PIAS2 WILD-TYPE  311   47
                               clus
vv                              PIAS2 MUTATED PIAS2 WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PIAS2 MUTATED     3   0   0   1
  PIAS2 WILD-TYPE 256   3  22  20
D1692V10, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1692V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIAS2 MUTATED                                  0     1
  PIAS2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PIAS2 MUTATED                           0     1
  PIAS2 WILD-TYPE                        19   175
D1692V12, multiclass
[1] "Remove cluster labels:" "PIAS2 MUTATED"         
clus
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6607      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-5913      TCGA-CK-5914      TCGA-CK-5915 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5861      TCGA-CM-5862 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 

Clustering(1693) Variable = CNGA3 MUTATION ANALYSIS
D1693V1, survival
                 sevent
clus2               0   1
  CNGA3 MUTATED    11   1
  CNGA3 WILD-TYPE 266  77
  CNGA3 MUTATED CNGA3 WILD-TYPE 
             12             343 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
              1              77 
$`CNGA3 MUTATED`
TCGA-AA-3672 TCGA-G4-6586 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A00E 
        0.92        35.80        63.98         1.02        25.02        30.02 
TCGA-AA-A010 TCGA-CK-4947 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5541 TCGA-D5-6537 
       34.98        17.56        15.02        14.04        55.92         4.80 

$`CNGA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        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-D5-6529 
       12.03        45.40        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CNGA3 MUTATED CNGA3 WILD-TYPE 
           0.92            0.00 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
          63.98          148.01 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
          21.29           22.06 
[1] "0.9 - 64.0 (21.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D1693V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNGA3 MUTATED         2        0        1         3         1         0
  CNGA3 WILD-TYPE      62        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNGA3 MUTATED           2          0          3          0        0         0
  CNGA3 WILD-TYPE        16          6         41         33       35        12
                 vv
clus              STAGE IVB
  CNGA3 MUTATED           0
  CNGA3 WILD-TYPE         1
D1693V3, multiclass
            clus
vv           CNGA3 MUTATED CNGA3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CNGA3 MUTATED     0   3   8   2
  CNGA3 WILD-TYPE   9  64 241  39
D1693V4, multiclass
    clus
vv   CNGA3 MUTATED CNGA3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             8             241
  T4             2              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
  CNGA3 MUTATED     8   4   1
  CNGA3 WILD-TYPE 212  77  65
D1693V5, multiclass
    clus
vv   CNGA3 MUTATED CNGA3 WILD-TYPE
  N0             8             212
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1693V6, binary
                 cls
clus                0   1
  CNGA3 MUTATED    11   0
  CNGA3 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED     11    0
  CNGA3 WILD-TYPE  274   48
   clus
vv  CNGA3 MUTATED CNGA3 WILD-TYPE
  0            11             274
  1             0              48
[1] 2 2
[1] FALSE
D1693V7, binary
                 cls
clus                0   1
  CNGA3 MUTATED     7   6
  CNGA3 WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED      7    6
  CNGA3 WILD-TYPE  163  191
        clus
vv       CNGA3 MUTATED CNGA3 WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D1693V8, binary
                 cls
clus                0   1
  CNGA3 MUTATED    12   0
  CNGA3 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED     12    0
  CNGA3 WILD-TYPE  288    8
     clus
vv    CNGA3 MUTATED CNGA3 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1693V9, binary
                 cls
clus                0   1
  CNGA3 MUTATED    12   1
  CNGA3 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED     12    1
  CNGA3 WILD-TYPE  302   47
                               clus
vv                              CNGA3 MUTATED CNGA3 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CNGA3 MUTATED    11   0   0   1
  CNGA3 WILD-TYPE 248   3  22  20
D1693V10, multiclass
    clus
vv   CNGA3 MUTATED CNGA3 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1693V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNGA3 MUTATED                                  0     0
  CNGA3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNGA3 MUTATED                           0     6
  CNGA3 WILD-TYPE                        19   170
D1693V12, multiclass
                                  clus
vv                                 CNGA3 MUTATED CNGA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = OR51E2 MUTATION ANALYSIS
D1694V1, survival
                  sevent
clus2                0   1
  OR51E2 MUTATED     5   0
  OR51E2 WILD-TYPE 272  78
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               5              350 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               0               78 
$`OR51E2 MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-CM-6677 TCGA-CM-6678 TCGA-F4-6569 
       63.98        35.01        11.08        11.01        35.74 

$`OR51E2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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-6679 
       14.04        11.01        12.95        13.05        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6570 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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  OR51E2 MUTATED OR51E2 WILD-TYPE 
           11.01             0.00 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
           63.98           148.01 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
          35.010           22.045 
[1] "11.0 - 64.0 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1694V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51E2 MUTATED         1        0        1         1         0         0
  OR51E2 WILD-TYPE      63        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51E2 MUTATED           1          0          0          0        0
  OR51E2 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51E2 MUTATED           1         0
  OR51E2 WILD-TYPE        11         1
D1694V3, multiclass
            clus
vv           OR51E2 MUTATED OR51E2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  OR51E2 MUTATED     0   1   3   1
  OR51E2 WILD-TYPE   9  66 246  40
D1694V4, multiclass
    clus
vv   OR51E2 MUTATED OR51E2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              3              246
  T4              1               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
  OR51E2 MUTATED     3   1   1
  OR51E2 WILD-TYPE 217  80  65
D1694V5, multiclass
    clus
vv   OR51E2 MUTATED OR51E2 WILD-TYPE
  N0              3              217
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1694V6, binary
                  cls
clus                 0   1
  OR51E2 MUTATED     4   1
  OR51E2 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E2 MUTATED      4    1
  OR51E2 WILD-TYPE  281   47
   clus
vv  OR51E2 MUTATED OR51E2 WILD-TYPE
  0              4              281
  1              1               47
[1] 2 2
[1] FALSE
D1694V7, binary
                  cls
clus                 0   1
  OR51E2 MUTATED     2   3
  OR51E2 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E2 MUTATED      2    3
  OR51E2 WILD-TYPE  168  194
        clus
vv       OR51E2 MUTATED OR51E2 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D1694V8, binary
                  cls
clus                 0   1
  OR51E2 MUTATED     4   1
  OR51E2 WILD-TYPE 296   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E2 MUTATED      4    1
  OR51E2 WILD-TYPE  296    7
     clus
vv    OR51E2 MUTATED OR51E2 WILD-TYPE
  NO               4              296
  YES              1                7
[1] 2 2
[1] FALSE
D1694V9, binary
                  cls
clus                 0   1
  OR51E2 MUTATED     4   1
  OR51E2 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E2 MUTATED      4    1
  OR51E2 WILD-TYPE  310   47
                               clus
vv                              OR51E2 MUTATED OR51E2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51E2 MUTATED     5   0   0   0
  OR51E2 WILD-TYPE 254   3  22  21
D1694V10, multiclass
    clus
vv   OR51E2 MUTATED OR51E2 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1694V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51E2 MUTATED                                  0     0
  OR51E2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51E2 MUTATED                           0     3
  OR51E2 WILD-TYPE                        19   173
D1694V12, multiclass
                                  clus
vv                                 OR51E2 MUTATED OR51E2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = OR6C1 MUTATION ANALYSIS
D1695V1, survival
                 sevent
clus2               0   1
  OR6C1 MUTATED     5   2
  OR6C1 WILD-TYPE 272  76
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              7             348 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              2              76 
$`OR6C1 MUTATED`
TCGA-DM-A285 TCGA-A6-6651 TCGA-A6-6782 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        5.88        21.76        20.28        58.39        12.76        10.06 
TCGA-DM-A28E 
      119.93 

$`OR6C1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01         1.94        49.08        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  OR6C1 MUTATED OR6C1 WILD-TYPE 
           5.88            0.00 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
         119.93          148.01 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
          20.28           22.09 
[1] "5.9 - 119.9 (20.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1695V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR6C1 MUTATED         0        0        0         4         1         0
  OR6C1 WILD-TYPE      64        1       26       104         7         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        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  OR6C1 MUTATED           0
  OR6C1 WILD-TYPE         1
D1695V3, multiclass
            clus
vv           OR6C1 MUTATED OR6C1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  OR6C1 MUTATED     0   0   6   1
  OR6C1 WILD-TYPE   9  67 243  40
D1695V4, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  OR6C1 MUTATED     5   1   1
  OR6C1 WILD-TYPE 215  80  65
D1695V5, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1695V6, binary
                 cls
clus                0   1
  OR6C1 MUTATED     4   1
  OR6C1 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      4    1
  OR6C1 WILD-TYPE  281   47
   clus
vv  OR6C1 MUTATED OR6C1 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1695V7, binary
                 cls
clus                0   1
  OR6C1 MUTATED     3   4
  OR6C1 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      3    4
  OR6C1 WILD-TYPE  167  193
        clus
vv       OR6C1 MUTATED OR6C1 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1695V8, binary
                 cls
clus                0   1
  OR6C1 MUTATED     5   0
  OR6C1 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      5    0
  OR6C1 WILD-TYPE  295    8
     clus
vv    OR6C1 MUTATED OR6C1 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1695V9, binary
                 cls
clus                0   1
  OR6C1 MUTATED     5   2
  OR6C1 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      5    2
  OR6C1 WILD-TYPE  309   46
                               clus
vv                              OR6C1 MUTATED OR6C1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR6C1 MUTATED     1   0   0   2
  OR6C1 WILD-TYPE 258   3  22  19
D1695V10, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  R0             1             258
  R1             0               3
  R2             0              22
  RX             2              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"
D1695V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6C1 MUTATED                                  0     2
  OR6C1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6C1 MUTATED                           0     5
  OR6C1 WILD-TYPE                        19   171
D1695V12, multiclass
                                  clus
vv                                 OR6C1 MUTATED OR6C1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1696) Variable = EVI2A MUTATION ANALYSIS
D1696V1, survival
                 sevent
clus2               0   1
  EVI2A MUTATED     6   0
  EVI2A WILD-TYPE 271  78
  EVI2A MUTATED EVI2A WILD-TYPE 
              6             349 
  EVI2A MUTATED EVI2A WILD-TYPE 
              0              78 
$`EVI2A MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-A00A TCGA-DM-A1D9 TCGA-DM-A282 TCGA-G4-6304 
       30.44        24.39        38.04       140.38       139.17        53.62 

$`EVI2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  EVI2A MUTATED EVI2A WILD-TYPE 
          24.39            0.00 
  EVI2A MUTATED EVI2A WILD-TYPE 
         140.38          148.01 
  EVI2A MUTATED EVI2A WILD-TYPE 
          45.83           21.99 
[1] "24.4 - 140.4 (45.8)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "2.6e+07"
D1696V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EVI2A MUTATED         2        0        0         3         1         0
  EVI2A WILD-TYPE      62        1       26       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EVI2A MUTATED           1          0          0          0        0         0
  EVI2A WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  EVI2A MUTATED           0
  EVI2A WILD-TYPE         1
D1696V3, multiclass
            clus
vv           EVI2A MUTATED EVI2A WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  EVI2A MUTATED     0   2   4   1
  EVI2A WILD-TYPE   9  65 245  40
D1696V4, multiclass
    clus
vv   EVI2A MUTATED EVI2A WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             1              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
  EVI2A MUTATED     6   0   1
  EVI2A WILD-TYPE 214  81  65
D1696V5, multiclass
    clus
vv   EVI2A MUTATED EVI2A WILD-TYPE
  N0             6             214
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1696V6, binary
                 cls
clus                0   1
  EVI2A MUTATED     7   0
  EVI2A WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      7    0
  EVI2A WILD-TYPE  278   48
   clus
vv  EVI2A MUTATED EVI2A WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1696V7, binary
                 cls
clus                0   1
  EVI2A MUTATED     3   4
  EVI2A WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      3    4
  EVI2A WILD-TYPE  167  193
        clus
vv       EVI2A MUTATED EVI2A WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1696V8, binary
                 cls
clus                0   1
  EVI2A MUTATED     4   0
  EVI2A WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      4    0
  EVI2A WILD-TYPE  296    8
     clus
vv    EVI2A MUTATED EVI2A WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1696V9, binary
                 cls
clus                0   1
  EVI2A MUTATED     7   0
  EVI2A WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      7    0
  EVI2A WILD-TYPE  307   48
                               clus
vv                              EVI2A MUTATED EVI2A WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EVI2A MUTATED     4   0   0   0
  EVI2A WILD-TYPE 255   3  22  21
D1696V10, multiclass
    clus
vv   EVI2A MUTATED EVI2A WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1696V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EVI2A MUTATED                                  0     0
  EVI2A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EVI2A MUTATED                           0     5
  EVI2A WILD-TYPE                        19   171
D1696V12, multiclass
                                  clus
vv                                 EVI2A MUTATED EVI2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = KIAA0415 MUTATION ANALYSIS
D1697V1, survival
                    sevent
clus2                  0   1
  KIAA0415 MUTATED     9   3
  KIAA0415 WILD-TYPE 268  75
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                12                343 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                 3                 75 
$`KIAA0415 MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3811 TCGA-AD-6889 
       25.08        79.69        24.39         6.97        10.06        83.24 
TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6674 TCGA-G4-6304 TCGA-G4-6309 
       21.44        12.76        21.14        12.95        53.62        85.48 

$`KIAA0415 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       65.85        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
              6.97               0.00 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
             85.48             148.01 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
            22.915             22.060 
[1] "7.0 - 85.5 (22.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1697V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0415 MUTATED         3        0        1         4         1         0
  KIAA0415 WILD-TYPE      61        1       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0415 MUTATED           1          0          2          0        0
  KIAA0415 WILD-TYPE        17          6         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0415 MUTATED           0         0
  KIAA0415 WILD-TYPE        12         1
D1697V3, multiclass
            clus
vv           KIAA0415 MUTATED KIAA0415 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA0415 MUTATED     1   2   8   1
  KIAA0415 WILD-TYPE   8  65 241  40
D1697V4, multiclass
    clus
vv   KIAA0415 MUTATED KIAA0415 WILD-TYPE
  T1                1                  8
  T2                2                 65
  T3                8                241
  T4                1                 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
  KIAA0415 MUTATED     9   2   1
  KIAA0415 WILD-TYPE 211  79  65
D1697V5, multiclass
    clus
vv   KIAA0415 MUTATED KIAA0415 WILD-TYPE
  N0                9                211
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1697V6, binary
                    cls
clus                   0   1
  KIAA0415 MUTATED    11   0
  KIAA0415 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0415 MUTATED     11    0
  KIAA0415 WILD-TYPE  274   48
   clus
vv  KIAA0415 MUTATED KIAA0415 WILD-TYPE
  0               11                274
  1                0                 48
[1] 2 2
[1] FALSE
D1697V7, binary
                    cls
clus                   0   1
  KIAA0415 MUTATED     4   8
  KIAA0415 WILD-TYPE 166 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0415 MUTATED      4    8
  KIAA0415 WILD-TYPE  166  189
        clus
vv       KIAA0415 MUTATED KIAA0415 WILD-TYPE
  FEMALE                4                166
  MALE                  8                189
[1] 2 2
[1] FALSE
D1697V8, binary
                    cls
clus                   0   1
  KIAA0415 MUTATED    12   0
  KIAA0415 WILD-TYPE 288   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0415 MUTATED     12    0
  KIAA0415 WILD-TYPE  288    8
     clus
vv    KIAA0415 MUTATED KIAA0415 WILD-TYPE
  NO                12                288
  YES                0                  8
[1] 2 2
[1] FALSE
D1697V9, binary
                    cls
clus                   0   1
  KIAA0415 MUTATED    11   1
  KIAA0415 WILD-TYPE 303  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0415 MUTATED     11    1
  KIAA0415 WILD-TYPE  303   47
                               clus
vv                              KIAA0415 MUTATED KIAA0415 WILD-TYPE
  COLON ADENOCARCINOMA                        11                303
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0415 MUTATED     9   0   0   2
  KIAA0415 WILD-TYPE 250   3  22  19
D1697V10, multiclass
    clus
vv   KIAA0415 MUTATED KIAA0415 WILD-TYPE
  R0                9                250
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1697V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0415 MUTATED                                  0     2
  KIAA0415 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0415 MUTATED                           1     7
  KIAA0415 WILD-TYPE                        18   169
D1697V12, multiclass
                                  clus
vv                                 KIAA0415 MUTATED KIAA0415 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           7                169
[1] 4 2
[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 = ELANE MUTATION ANALYSIS
D1698V1, survival
                 sevent
clus2               0   1
  ELANE MUTATED     6   1
  ELANE WILD-TYPE 271  77
  ELANE MUTATED ELANE WILD-TYPE 
              7             348 
  ELANE MUTATED ELANE WILD-TYPE 
              1              77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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          22.045 
[1] "7.0 - 58.4 (23.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1698V2, continuous
                 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      63        1       25       106         6         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  ELANE MUTATED           0
  ELANE WILD-TYPE         1
D1698V3, multiclass
            clus
vv           ELANE MUTATED ELANE WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  ELANE MUTATED     1   0   4   2
  ELANE WILD-TYPE   8  67 245  39
D1698V4, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  T1             1               8
  T2             0              67
  T3             4             245
  T4             2              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
  ELANE MUTATED     6   1   0
  ELANE WILD-TYPE 214  80  66
D1698V5, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1698V6, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  278   48
   clus
vv  ELANE MUTATED ELANE WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1698V7, binary
                 cls
clus                0   1
  ELANE MUTATED     5   2
  ELANE WILD-TYPE 165 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      5    2
  ELANE WILD-TYPE  165  195
        clus
vv       ELANE MUTATED ELANE WILD-TYPE
  FEMALE             5             165
  MALE               2             195
[1] 2 2
[1] FALSE
D1698V8, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  293    8
     clus
vv    ELANE MUTATED ELANE WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1698V9, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  307   48
                               clus
vv                              ELANE MUTATED ELANE WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ELANE MUTATED     5   0   0   1
  ELANE WILD-TYPE 254   3  22  20
D1698V10, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             1              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"
D1698V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELANE MUTATED                                  0     0
  ELANE WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ELANE MUTATED                           0     5
  ELANE WILD-TYPE                        19   171
D1698V12, multiclass
                                  clus
vv                                 ELANE MUTATED ELANE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = UGGT1 MUTATION ANALYSIS
D1699V1, survival
                 sevent
clus2               0   1
  UGGT1 MUTATED    11   6
  UGGT1 WILD-TYPE 266  72
  UGGT1 MUTATED UGGT1 WILD-TYPE 
             17             338 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
              6              72 
$`UGGT1 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3968 
       13.02         0.92        32.75         8.38         3.02        21.99 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6748 
        4.01        34.98        11.74        12.76        10.06         2.01 
TCGA-CK-6751 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6459 
      124.27        16.14        11.64       135.65         8.61 

$`UGGT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        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-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        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-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  UGGT1 MUTATED UGGT1 WILD-TYPE 
           0.92            0.00 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
         135.65          148.01 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
          11.74           22.47 
[1] "0.9 - 135.7 (11.7)" "0.0 - 148.0 (22.5)"
[1] "hr=" "2"  
D1699V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGGT1 MUTATED         3        0        2         4         3         0
  UGGT1 WILD-TYPE      61        1       24       104         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UGGT1 MUTATED           2          0          2          0        2         0
  UGGT1 WILD-TYPE        16          6         42         33       33        12
                 vv
clus              STAGE IVB
  UGGT1 MUTATED           0
  UGGT1 WILD-TYPE         1
D1699V3, multiclass
            clus
vv           UGGT1 MUTATED UGGT1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  UGGT1 MUTATED     0   3  10   5
  UGGT1 WILD-TYPE   9  64 239  36
D1699V4, multiclass
    clus
vv   UGGT1 MUTATED UGGT1 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            10             239
  T4             5              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
  UGGT1 MUTATED    12   3   3
  UGGT1 WILD-TYPE 208  78  63
D1699V5, multiclass
    clus
vv   UGGT1 MUTATED UGGT1 WILD-TYPE
  N0            12             208
  N1             3              78
  N2             3              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"
D1699V6, binary
                 cls
clus                0   1
  UGGT1 MUTATED    15   2
  UGGT1 WILD-TYPE 270  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED     15    2
  UGGT1 WILD-TYPE  270   46
   clus
vv  UGGT1 MUTATED UGGT1 WILD-TYPE
  0            15             270
  1             2              46
[1] 2 2
[1] FALSE
D1699V7, binary
                 cls
clus                0   1
  UGGT1 MUTATED    10   8
  UGGT1 WILD-TYPE 160 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED     10    8
  UGGT1 WILD-TYPE  160  189
        clus
vv       UGGT1 MUTATED UGGT1 WILD-TYPE
  FEMALE            10             160
  MALE               8             189
[1] 2 2
[1] FALSE
D1699V8, binary
                 cls
clus                0   1
  UGGT1 MUTATED    15   0
  UGGT1 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED     15    0
  UGGT1 WILD-TYPE  285    8
     clus
vv    UGGT1 MUTATED UGGT1 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D1699V9, binary
                 cls
clus                0   1
  UGGT1 MUTATED     9   8
  UGGT1 WILD-TYPE 305  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED      9    8
  UGGT1 WILD-TYPE  305   40
                               clus
vv                              UGGT1 MUTATED UGGT1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UGGT1 MUTATED    10   0   0   4
  UGGT1 WILD-TYPE 249   3  22  17
D1699V10, multiclass
    clus
vv   UGGT1 MUTATED UGGT1 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             4              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"
D1699V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGGT1 MUTATED                                  0     2
  UGGT1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UGGT1 MUTATED                           1     8
  UGGT1 WILD-TYPE                        18   168
D1699V12, multiclass
                                  clus
vv                                 UGGT1 MUTATED UGGT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = CCDC19 MUTATION ANALYSIS
D1700V1, survival
                  sevent
clus2                0   1
  CCDC19 MUTATED    11   3
  CCDC19 WILD-TYPE 266  75
  CCDC19 MUTATED CCDC19 WILD-TYPE 
              14              341 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
               3               75 
$`CCDC19 MUTATED`
TCGA-G4-6628 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-A00E TCGA-AA-A010 TCGA-AA-A01F 
       79.69         8.38        19.66        30.02        34.98        32.02 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6928 TCGA-D5-7000 
       58.39        49.41        12.76        10.06        11.64        10.26 
TCGA-DM-A1HB TCGA-G4-6303 
      135.65        65.85 

$`CCDC19 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41        13.35        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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CCDC19 MUTATED CCDC19 WILD-TYPE 
            8.38             0.00 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
          135.65           148.01 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
           31.02            22.03 
[1] "8.4 - 135.7 (31.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1700V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC19 MUTATED         2        0        1         7         1         0
  CCDC19 WILD-TYPE      62        1       25       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC19 MUTATED           0          0          2          1        1
  CCDC19 WILD-TYPE        18          6         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC19 MUTATED           0         0
  CCDC19 WILD-TYPE        12         1
D1700V3, multiclass
            clus
vv           CCDC19 MUTATED CCDC19 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  CCDC19 MUTATED     0   2  11   2
  CCDC19 WILD-TYPE   9  65 238  39
D1700V4, multiclass
    clus
vv   CCDC19 MUTATED CCDC19 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             11              238
  T4              2               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
  CCDC19 MUTATED    11   4   0
  CCDC19 WILD-TYPE 209  77  66
D1700V5, multiclass
    clus
vv   CCDC19 MUTATED CCDC19 WILD-TYPE
  N0             11              209
  N1              4               77
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1700V6, binary
                  cls
clus                 0   1
  CCDC19 MUTATED    12   1
  CCDC19 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC19 MUTATED     12    1
  CCDC19 WILD-TYPE  273   47
   clus
vv  CCDC19 MUTATED CCDC19 WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D1700V7, binary
                  cls
clus                 0   1
  CCDC19 MUTATED     5  10
  CCDC19 WILD-TYPE 165 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC19 MUTATED      5   10
  CCDC19 WILD-TYPE  165  187
        clus
vv       CCDC19 MUTATED CCDC19 WILD-TYPE
  FEMALE              5              165
  MALE               10              187
[1] 2 2
[1] FALSE
D1700V8, binary
                  cls
clus                 0   1
  CCDC19 MUTATED    13   0
  CCDC19 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC19 MUTATED     13    0
  CCDC19 WILD-TYPE  287    8
     clus
vv    CCDC19 MUTATED CCDC19 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1700V9, binary
                  cls
clus                 0   1
  CCDC19 MUTATED    10   4
  CCDC19 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC19 MUTATED     10    4
  CCDC19 WILD-TYPE  304   44
                               clus
vv                              CCDC19 MUTATED CCDC19 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC19 MUTATED    10   0   0   2
  CCDC19 WILD-TYPE 249   3  22  19
D1700V10, multiclass
    clus
vv   CCDC19 MUTATED CCDC19 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              2               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"
D1700V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC19 MUTATED                                  0     2
  CCDC19 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC19 MUTATED                           1     8
  CCDC19 WILD-TYPE                        18   168
D1700V12, multiclass
                                  clus
vv                                 CCDC19 MUTATED CCDC19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         8              168
[1] 4 2
[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 = C13ORF23 MUTATION ANALYSIS
D1701V1, survival
                    sevent
clus2                  0   1
  C13ORF23 MUTATED     9   3
  C13ORF23 WILD-TYPE 268  75
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                12                343 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                 3                 75 
$`C13ORF23 MUTATED`
TCGA-AA-3543 TCGA-G4-6628 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 
        0.99        79.69        18.05        34.98        83.24        27.42 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6928 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-G4-6293 
       49.41        12.76        11.64       140.38        44.32       133.18 

$`C13ORF23 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59         7.50       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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
              0.99               0.00 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
            140.38             148.01 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
             39.65              21.99 
[1] "1.0 - 140.4 (39.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1701V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C13ORF23 MUTATED         2        0        1         5         1         0
  C13ORF23 WILD-TYPE      62        1       25       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF23 MUTATED           1          0          1          0        0
  C13ORF23 WILD-TYPE        17          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  C13ORF23 MUTATED           0         0
  C13ORF23 WILD-TYPE        12         1
D1701V3, multiclass
            clus
vv           C13ORF23 MUTATED C13ORF23 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 17
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C13ORF23 MUTATED     0   2   8   2
  C13ORF23 WILD-TYPE   9  65 241  39
D1701V4, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                8                241
  T4                2                 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
  C13ORF23 MUTATED    10   2   0
  C13ORF23 WILD-TYPE 210  79  66
D1701V5, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  N0               10                210
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1701V6, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED    10   0
  C13ORF23 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED     10    0
  C13ORF23 WILD-TYPE  275   48
   clus
vv  C13ORF23 MUTATED C13ORF23 WILD-TYPE
  0               10                275
  1                0                 48
[1] 2 2
[1] FALSE
D1701V7, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED     4   8
  C13ORF23 WILD-TYPE 166 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED      4    8
  C13ORF23 WILD-TYPE  166  189
        clus
vv       C13ORF23 MUTATED C13ORF23 WILD-TYPE
  FEMALE                4                166
  MALE                  8                189
[1] 2 2
[1] FALSE
D1701V8, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED    10   0
  C13ORF23 WILD-TYPE 290   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED     10    0
  C13ORF23 WILD-TYPE  290    8
     clus
vv    C13ORF23 MUTATED C13ORF23 WILD-TYPE
  NO                10                290
  YES                0                  8
[1] 2 2
[1] FALSE
D1701V9, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED     8   4
  C13ORF23 WILD-TYPE 306  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED      8    4
  C13ORF23 WILD-TYPE  306   44
                               clus
vv                              C13ORF23 MUTATED C13ORF23 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C13ORF23 MUTATED     7   0   0   1
  C13ORF23 WILD-TYPE 252   3  22  20
D1701V10, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  R0                7                252
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1701V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C13ORF23 MUTATED                                  0     2
  C13ORF23 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C13ORF23 MUTATED                           0     7
  C13ORF23 WILD-TYPE                        19   169
D1701V12, multiclass
                                  clus
vv                                 C13ORF23 MUTATED C13ORF23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           7                169
[1] 4 2
[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 = SMC4 MUTATION ANALYSIS
D1702V1, survival
                sevent
clus2              0   1
  SMC4 MUTATED    12   4
  SMC4 WILD-TYPE 265  74
  SMC4 MUTATED SMC4 WILD-TYPE 
            16            339 
  SMC4 MUTATED SMC4 WILD-TYPE 
             4             74 
$`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 
       58.39         6.77        51.32        25.48 

$`SMC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3846 
        1.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       25.02        27.02        27.02         7.96        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SMC4 MUTATED SMC4 WILD-TYPE 
             0              0 
  SMC4 MUTATED SMC4 WILD-TYPE 
         63.98         148.01 
  SMC4 MUTATED SMC4 WILD-TYPE 
         26.25          22.03 
[1] "0.0 - 64.0 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1702V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC4 MUTATED         3        0        5         6         1         0
  SMC4 WILD-TYPE      61        1       21       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC4 MUTATED           0          0          1          1        0         0
  SMC4 WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  SMC4 MUTATED           0
  SMC4 WILD-TYPE         1
D1702V3, multiclass
            clus
vv           SMC4 MUTATED SMC4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA             6            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  SMC4 MUTATED     2   1  11   4
  SMC4 WILD-TYPE   7  66 238  37
D1702V4, multiclass
    clus
vv   SMC4 MUTATED SMC4 WILD-TYPE
  T1            2              7
  T2            1             66
  T3           11            238
  T4            4             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
  SMC4 MUTATED    16   2   0
  SMC4 WILD-TYPE 204  79  66
D1702V5, multiclass
    clus
vv   SMC4 MUTATED SMC4 WILD-TYPE
  N0           16            204
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1702V6, binary
                cls
clus               0   1
  SMC4 MUTATED    14   0
  SMC4 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     14    0
  SMC4 WILD-TYPE  271   48
   clus
vv  SMC4 MUTATED SMC4 WILD-TYPE
  0           14            271
  1            0             48
[1] 2 2
[1] FALSE
D1702V7, binary
                cls
clus               0   1
  SMC4 MUTATED    11   7
  SMC4 WILD-TYPE 159 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     11    7
  SMC4 WILD-TYPE  159  190
        clus
vv       SMC4 MUTATED SMC4 WILD-TYPE
  FEMALE           11            159
  MALE              7            190
[1] 2 2
[1] FALSE
D1702V8, binary
                cls
clus               0   1
  SMC4 MUTATED    14   0
  SMC4 WILD-TYPE 286   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     14    0
  SMC4 WILD-TYPE  286    8
     clus
vv    SMC4 MUTATED SMC4 WILD-TYPE
  NO            14            286
  YES            0              8
[1] 2 2
[1] FALSE
D1702V9, binary
                cls
clus               0   1
  SMC4 MUTATED    14   3
  SMC4 WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     14    3
  SMC4 WILD-TYPE  300   45
                               clus
vv                              SMC4 MUTATED SMC4 WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMC4 MUTATED    16   0   0   1
  SMC4 WILD-TYPE 243   3  22  20
D1702V10, multiclass
    clus
vv   SMC4 MUTATED SMC4 WILD-TYPE
  R0           16            243
  R1            0              3
  R2            0             22
  RX            1             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"
D1702V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC4 MUTATED                                  0     0
  SMC4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMC4 MUTATED                           0     6
  SMC4 WILD-TYPE                        19   170
D1702V12, multiclass
                                  clus
vv                                 SMC4 MUTATED SMC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = KIF13A MUTATION ANALYSIS
D1703V1, survival
                  sevent
clus2                0   1
  KIF13A MUTATED    17   3
  KIF13A WILD-TYPE 260  75
  KIF13A MUTATED KIF13A WILD-TYPE 
              20              335 
  KIF13A MUTATED KIF13A WILD-TYPE 
               3               75 
$`KIF13A MUTATED`
TCGA-AA-3688 TCGA-AA-3713 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3680 TCGA-AA-3966 
       19.00        19.04        22.06        19.66        11.01         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        12.16        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        10.13        13.35 
TCGA-D5-6932 TCGA-DM-A1HB 
       11.38       135.65 

$`KIF13A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       14.01        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       15.62        21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        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 
       13.41        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KIF13A MUTATED KIF13A WILD-TYPE 
            0.92             0.00 
  KIF13A MUTATED KIF13A WILD-TYPE 
          135.65           148.01 
  KIF13A MUTATED KIF13A WILD-TYPE 
           17.01            23.01 
[1] "0.9 - 135.7 (17.0)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1.2"
D1703V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF13A MUTATED         2        0        1         9         2         0
  KIF13A WILD-TYPE      62        1       25        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF13A MUTATED           0          2          1          1        3
  KIF13A WILD-TYPE        18          4         43         32       32
                  vv
clus               STAGE IVA STAGE IVB
  KIF13A MUTATED           0         0
  KIF13A WILD-TYPE        12         1
D1703V3, multiclass
            clus
vv           KIF13A MUTATED KIF13A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               9               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              2                4
  STAGE IIIB              1               43
  STAGE IIIC              1               32
  STAGE IV                3               32
  STAGE IVA               0               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
  KIF13A MUTATED     1   1  15   4
  KIF13A WILD-TYPE   8  66 234  37
D1703V4, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  T1              1                8
  T2              1               66
  T3             15              234
  T4              4               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
  KIF13A MUTATED    15   5   1
  KIF13A WILD-TYPE 205  76  65
D1703V5, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  N0             15              205
  N1              5               76
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1703V6, binary
                  cls
clus                 0   1
  KIF13A MUTATED    14   3
  KIF13A WILD-TYPE 271  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     14    3
  KIF13A WILD-TYPE  271   45
   clus
vv  KIF13A MUTATED KIF13A WILD-TYPE
  0             14              271
  1              3               45
[1] 2 2
[1] FALSE
D1703V7, binary
                  cls
clus                 0   1
  KIF13A MUTATED     8  13
  KIF13A WILD-TYPE 162 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      8   13
  KIF13A WILD-TYPE  162  184
        clus
vv       KIF13A MUTATED KIF13A WILD-TYPE
  FEMALE              8              162
  MALE               13              184
[1] 2 2
[1] FALSE
D1703V8, binary
                  cls
clus                 0   1
  KIF13A MUTATED    15   1
  KIF13A WILD-TYPE 285   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     15    1
  KIF13A WILD-TYPE  285    7
     clus
vv    KIF13A MUTATED KIF13A WILD-TYPE
  NO              15              285
  YES              1                7
[1] 2 2
[1] FALSE
D1703V9, binary
                  cls
clus                 0   1
  KIF13A MUTATED    13   7
  KIF13A WILD-TYPE 301  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     13    7
  KIF13A WILD-TYPE  301   41
                               clus
vv                              KIF13A MUTATED KIF13A WILD-TYPE
  COLON ADENOCARCINOMA                      13              301
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIF13A MUTATED    13   0   3   3
  KIF13A WILD-TYPE 246   3  19  18
D1703V10, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  R0             13              246
  R1              0                3
  R2              3               19
  RX              3               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"
D1703V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF13A MUTATED                                  0     1
  KIF13A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF13A MUTATED                           0    12
  KIF13A WILD-TYPE                        19   164
D1703V12, multiclass
                                  clus
vv                                 KIF13A MUTATED KIF13A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        12              164
[1] 4 2
[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 = DONSON MUTATION ANALYSIS
D1704V1, survival
                  sevent
clus2                0   1
  DONSON MUTATED     2   2
  DONSON WILD-TYPE 275  76
  DONSON MUTATED DONSON WILD-TYPE 
               4              351 
  DONSON MUTATED DONSON WILD-TYPE 
               2               76 
$`DONSON MUTATED`
TCGA-G4-6588 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-DM-A1D9 
       26.17        49.41         6.77       140.38 

$`DONSON WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79        88.21        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DONSON MUTATED DONSON WILD-TYPE 
            6.77             0.00 
  DONSON MUTATED DONSON WILD-TYPE 
          140.38           148.01 
  DONSON MUTATED DONSON WILD-TYPE 
           37.79            22.03 
[1] "6.8 - 140.4 (37.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1704V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DONSON MUTATED         1        0        1         2         0         0
  DONSON WILD-TYPE      63        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DONSON MUTATED           0          0          0          0        0
  DONSON WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  DONSON MUTATED           0         0
  DONSON WILD-TYPE        12         1
D1704V3, multiclass
            clus
vv           DONSON MUTATED DONSON WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  DONSON MUTATED     0   1   3   0
  DONSON WILD-TYPE   9  66 246  41
D1704V4, multiclass
    clus
vv   DONSON MUTATED DONSON WILD-TYPE
  T1              0                9
  T2              1               66
  T3              3              246
  T4              0               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
  DONSON MUTATED     4   0   0
  DONSON WILD-TYPE 216  81  66
D1704V5, multiclass
    clus
vv   DONSON MUTATED DONSON WILD-TYPE
  N0              4              216
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1704V6, binary
                  cls
clus                 0   1
  DONSON MUTATED     2   0
  DONSON WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DONSON MUTATED      2    0
  DONSON WILD-TYPE  283   48
   clus
vv  DONSON MUTATED DONSON WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D1704V7, binary
                  cls
clus                 0   1
  DONSON MUTATED     3   1
  DONSON WILD-TYPE 167 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DONSON MUTATED      3    1
  DONSON WILD-TYPE  167  196
        clus
vv       DONSON MUTATED DONSON WILD-TYPE
  FEMALE              3              167
  MALE                1              196
[1] 2 2
[1] FALSE
D1704V8, binary
                  cls
clus                 0   1
  DONSON MUTATED     3   0
  DONSON WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DONSON MUTATED      3    0
  DONSON WILD-TYPE  297    8
     clus
vv    DONSON MUTATED DONSON WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1704V9, binary
                  cls
clus                 0   1
  DONSON MUTATED     4   0
  DONSON WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DONSON MUTATED      4    0
  DONSON WILD-TYPE  310   48
                               clus
vv                              DONSON MUTATED DONSON WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DONSON MUTATED     1   0   0   0
  DONSON WILD-TYPE 258   3  22  21
D1704V10, multiclass
[1] "Remove cluster labels:" "DONSON MUTATED"        
clus
  DONSON MUTATED DONSON WILD-TYPE 
               1              304 
      TCGA-A6-2677       TCGA-AA-3496       TCGA-AA-3520       TCGA-AA-3521 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6625       TCGA-G4-6628 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657       TCGA-A6-5659 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781       TCGA-AA-3489 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518       TCGA-AA-3519 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532       TCGA-AA-3534 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544       TCGA-AA-3548 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555       TCGA-AA-3558 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3663 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3673 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693       TCGA-AA-3695 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3811 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3861 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       TCGA-AA-3872 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3941 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N       TCGA-AA-A00O 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6889 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682       TCGA-CA-5254 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
D1704V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DONSON MUTATED                                  0     0
  DONSON WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DONSON MUTATED                           0     4
  DONSON WILD-TYPE                        19   172
D1704V12, multiclass
                                  clus
vv                                 DONSON MUTATED DONSON WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = SLC26A7 MUTATION ANALYSIS
D1705V1, survival
                   sevent
clus2                 0   1
  SLC26A7 MUTATED    12   5
  SLC26A7 WILD-TYPE 265  73
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               17               338 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
                5                73 
$`SLC26A7 MUTATED`
TCGA-AA-3979 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-A00J 
       24.00        22.06        63.98        10.06         2.01        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 
       12.76        10.06        15.58       135.65        35.31 

$`SLC26A7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O 
       37.02        51.98        39.98         2.01        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
             2.01              0.00 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
           135.65            148.01 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
            18.05             22.09 
[1] "2.0 - 135.7 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1705V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC26A7 MUTATED         1        0        2         8         2         0
  SLC26A7 WILD-TYPE      63        1       24       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A7 MUTATED           1          0          2          0        1
  SLC26A7 WILD-TYPE        17          6         42         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC26A7 MUTATED           0         0
  SLC26A7 WILD-TYPE        12         1
D1705V3, multiclass
            clus
vv           SLC26A7 MUTATED SLC26A7 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                8               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  SLC26A7 MUTATED     0   1  13   3
  SLC26A7 WILD-TYPE   9  66 236  38
D1705V4, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              13               236
  T4               3                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
  SLC26A7 MUTATED    14   2   1
  SLC26A7 WILD-TYPE 206  79  65
D1705V5, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  N0              14               206
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1705V6, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    15   1
  SLC26A7 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     15    1
  SLC26A7 WILD-TYPE  270   47
   clus
vv  SLC26A7 MUTATED SLC26A7 WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D1705V7, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     6  11
  SLC26A7 WILD-TYPE 164 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      6   11
  SLC26A7 WILD-TYPE  164  186
        clus
vv       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  FEMALE               6               164
  MALE                11               186
[1] 2 2
[1] FALSE
D1705V8, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    13   0
  SLC26A7 WILD-TYPE 287   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     13    0
  SLC26A7 WILD-TYPE  287    8
     clus
vv    SLC26A7 MUTATED SLC26A7 WILD-TYPE
  NO               13               287
  YES               0                 8
[1] 2 2
[1] FALSE
D1705V9, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    10   6
  SLC26A7 WILD-TYPE 304  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     10    6
  SLC26A7 WILD-TYPE  304   42
                               clus
vv                              SLC26A7 MUTATED SLC26A7 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC26A7 MUTATED    11   0   1   2
  SLC26A7 WILD-TYPE 248   3  21  19
D1705V10, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  R0              11               248
  R1               0                 3
  R2               1                21
  RX               2                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"
D1705V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A7 MUTATED                                  0     2
  SLC26A7 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC26A7 MUTATED                           0     6
  SLC26A7 WILD-TYPE                        19   170
D1705V12, multiclass
                                  clus
vv                                 SLC26A7 MUTATED SLC26A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = ACSL3 MUTATION ANALYSIS
D1706V1, survival
                 sevent
clus2               0   1
  ACSL3 MUTATED     8   1
  ACSL3 WILD-TYPE 269  77
  ACSL3 MUTATED ACSL3 WILD-TYPE 
              9             346 
  ACSL3 MUTATED ACSL3 WILD-TYPE 
              1              77 
$`ACSL3 MUTATED`
TCGA-AA-3713 TCGA-G4-6625 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01G 
       19.04        91.79         0.00        25.02        34.98        12.00 
TCGA-CM-5861 TCGA-D5-6535 TCGA-G4-6304 
       15.02        15.12        53.62 

$`ACSL3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ACSL3 MUTATED ACSL3 WILD-TYPE 
              0               0 
  ACSL3 MUTATED ACSL3 WILD-TYPE 
          91.79          148.01 
  ACSL3 MUTATED ACSL3 WILD-TYPE 
         19.040          22.075 
[1] "0.0 - 91.8 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1706V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACSL3 MUTATED         0        0        0         5         2         0
  ACSL3 WILD-TYPE      64        1       26       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACSL3 MUTATED           0          0          1          0        1         0
  ACSL3 WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  ACSL3 MUTATED           0
  ACSL3 WILD-TYPE         1
D1706V3, multiclass
            clus
vv           ACSL3 MUTATED ACSL3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ACSL3 MUTATED     0   1   7   2
  ACSL3 WILD-TYPE   9  66 242  39
D1706V4, multiclass
    clus
vv   ACSL3 MUTATED ACSL3 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             2              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
  ACSL3 MUTATED     9   1   0
  ACSL3 WILD-TYPE 211  80  66
D1706V5, multiclass
    clus
vv   ACSL3 MUTATED ACSL3 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1706V6, binary
                 cls
clus                0   1
  ACSL3 MUTATED     7   1
  ACSL3 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL3 MUTATED      7    1
  ACSL3 WILD-TYPE  278   47
   clus
vv  ACSL3 MUTATED ACSL3 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D1706V7, binary
                 cls
clus                0   1
  ACSL3 MUTATED     7   3
  ACSL3 WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL3 MUTATED      7    3
  ACSL3 WILD-TYPE  163  194
        clus
vv       ACSL3 MUTATED ACSL3 WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D1706V8, binary
                 cls
clus                0   1
  ACSL3 MUTATED     7   1
  ACSL3 WILD-TYPE 293   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL3 MUTATED      7    1
  ACSL3 WILD-TYPE  293    7
     clus
vv    ACSL3 MUTATED ACSL3 WILD-TYPE
  NO              7             293
  YES             1               7
[1] 2 2
[1] FALSE
D1706V9, binary
                 cls
clus                0   1
  ACSL3 MUTATED     9   1
  ACSL3 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL3 MUTATED      9    1
  ACSL3 WILD-TYPE  305   47
                               clus
vv                              ACSL3 MUTATED ACSL3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACSL3 MUTATED     7   0   1   1
  ACSL3 WILD-TYPE 252   3  21  20
D1706V10, multiclass
    clus
vv   ACSL3 MUTATED ACSL3 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             1              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"
D1706V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACSL3 MUTATED                                  0     0
  ACSL3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACSL3 MUTATED                           0     4
  ACSL3 WILD-TYPE                        19   172
D1706V12, multiclass
                                  clus
vv                                 ACSL3 MUTATED ACSL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = CDC7 MUTATION ANALYSIS
D1707V1, survival
                sevent
clus2              0   1
  CDC7 MUTATED     7   2
  CDC7 WILD-TYPE 270  76
  CDC7 MUTATED CDC7 WILD-TYPE 
             9            346 
  CDC7 MUTATED CDC7 WILD-TYPE 
             2             76 
$`CDC7 MUTATED`
TCGA-AA-3496 TCGA-A6-2672 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6599 TCGA-CA-5255 
        1.02        46.65        25.02        27.09         6.77        12.36 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6676 
       12.76        10.06        11.08 

$`CDC7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CDC7 MUTATED CDC7 WILD-TYPE 
          1.02           0.00 
  CDC7 MUTATED CDC7 WILD-TYPE 
         46.65         148.01 
  CDC7 MUTATED CDC7 WILD-TYPE 
         12.36          22.09 
[1] "1.0 - 46.6 (12.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1707V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC7 MUTATED         4        0        1         3         0         0
  CDC7 WILD-TYPE      60        1       25       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC7 MUTATED           0          0          1          0        0         0
  CDC7 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  CDC7 MUTATED           0
  CDC7 WILD-TYPE         1
D1707V3, multiclass
            clus
vv           CDC7 MUTATED CDC7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CDC7 MUTATED     0   5   5   0
  CDC7 WILD-TYPE   9  62 244  41
D1707V4, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  T1            0              9
  T2            5             62
  T3            5            244
  T4            0             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
  CDC7 MUTATED     9   1   0
  CDC7 WILD-TYPE 211  80  66
D1707V5, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  N0            9            211
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1707V6, binary
                cls
clus               0   1
  CDC7 MUTATED     7   0
  CDC7 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      7    0
  CDC7 WILD-TYPE  278   48
   clus
vv  CDC7 MUTATED CDC7 WILD-TYPE
  0            7            278
  1            0             48
[1] 2 2
[1] FALSE
D1707V7, binary
                cls
clus               0   1
  CDC7 MUTATED     3   7
  CDC7 WILD-TYPE 167 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      3    7
  CDC7 WILD-TYPE  167  190
        clus
vv       CDC7 MUTATED CDC7 WILD-TYPE
  FEMALE            3            167
  MALE              7            190
[1] 2 2
[1] FALSE
D1707V8, binary
                cls
clus               0   1
  CDC7 MUTATED     6   1
  CDC7 WILD-TYPE 294   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      6    1
  CDC7 WILD-TYPE  294    7
     clus
vv    CDC7 MUTATED CDC7 WILD-TYPE
  NO             6            294
  YES            1              7
[1] 2 2
[1] FALSE
D1707V9, binary
                cls
clus               0   1
  CDC7 MUTATED     9   1
  CDC7 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      9    1
  CDC7 WILD-TYPE  305   47
                               clus
vv                              CDC7 MUTATED CDC7 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDC7 MUTATED     4   0   0   4
  CDC7 WILD-TYPE 255   3  22  17
D1707V10, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            4             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"
D1707V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC7 MUTATED                                  0     3
  CDC7 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDC7 MUTATED                           0     5
  CDC7 WILD-TYPE                        19   171
D1707V12, multiclass
                                  clus
vv                                 CDC7 MUTATED CDC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = C12ORF51 MUTATION ANALYSIS
D1708V1, survival
                    sevent
clus2                  0   1
  C12ORF51 MUTATED    22   9
  C12ORF51 WILD-TYPE 255  69
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                31                324 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                 9                 69 
$`C12ORF51 MUTATED`
TCGA-AA-A024 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 
       39.06        35.80        26.17        22.06        24.39        19.66 
TCGA-AA-3510 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3845 
       63.98         5.98        10.06        33.04         1.02         0.00 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01P 
       53.00        33.01         2.01        25.02        34.98        38.07 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 
       41.00        22.42        58.39        49.41        12.10        12.76 
TCGA-CA-6718 TCGA-CM-4746 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6460 
       10.06        37.02        16.14         9.44       135.65        31.96 
TCGA-G4-6309 
       85.48 

$`C12ORF51 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       25.18        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        37.05         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 
       25.02        17.98        15.95        38.99        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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-F4-6569 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                 0                  0 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
            135.65             148.01 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
             26.17              21.99 
[1] "0.0 - 135.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1708V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF51 MUTATED         5        0        4        10         2         0
  C12ORF51 WILD-TYPE      59        1       22        98         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF51 MUTATED           3          0          3          1        1
  C12ORF51 WILD-TYPE        15          6         41         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF51 MUTATED           0         0
  C12ORF51 WILD-TYPE        12         1
D1708V3, multiclass
            clus
vv           C12ORF51 MUTATED C12ORF51 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  4                 22
  STAGE IIA                10                 98
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 3                 15
  STAGE IIIA                0                  6
  STAGE IIIB                3                 41
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  C12ORF51 MUTATED     0   6  21   4
  C12ORF51 WILD-TYPE   9  61 228  37
D1708V4, multiclass
    clus
vv   C12ORF51 MUTATED C12ORF51 WILD-TYPE
  T1                0                  9
  T2                6                 61
  T3               21                228
  T4                4                 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
  C12ORF51 MUTATED    23   7   1
  C12ORF51 WILD-TYPE 197  74  65
D1708V5, multiclass
    clus
vv   C12ORF51 MUTATED C12ORF51 WILD-TYPE
  N0               23                197
  N1                7                 74
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1708V6, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED    26   1
  C12ORF51 WILD-TYPE 259  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED     26    1
  C12ORF51 WILD-TYPE  259   47
   clus
vv  C12ORF51 MUTATED C12ORF51 WILD-TYPE
  0               26                259
  1                1                 47
[1] 2 2
[1] FALSE
D1708V7, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED    16  15
  C12ORF51 WILD-TYPE 154 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED     16   15
  C12ORF51 WILD-TYPE  154  182
        clus
vv       C12ORF51 MUTATED C12ORF51 WILD-TYPE
  FEMALE               16                154
  MALE                 15                182
[1] 2 2
[1] FALSE
D1708V8, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED    28   0
  C12ORF51 WILD-TYPE 272   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED     28    0
  C12ORF51 WILD-TYPE  272    8
     clus
vv    C12ORF51 MUTATED C12ORF51 WILD-TYPE
  NO                28                272
  YES                0                  8
[1] 2 2
[1] FALSE
D1708V9, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED    23   7
  C12ORF51 WILD-TYPE 291  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED     23    7
  C12ORF51 WILD-TYPE  291   41
                               clus
vv                              C12ORF51 MUTATED C12ORF51 WILD-TYPE
  COLON ADENOCARCINOMA                        23                291
  COLON MUCINOUS ADENOCARCINOMA                7                 41
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF51 MUTATED    22   0   0   2
  C12ORF51 WILD-TYPE 237   3  22  19
D1708V10, multiclass
    clus
vv   C12ORF51 MUTATED C12ORF51 WILD-TYPE
  R0               22                237
  R1                0                  3
  R2                0                 22
  RX                2                 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"
D1708V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF51 MUTATED                                  0     2
  C12ORF51 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF51 MUTATED                           3    12
  C12ORF51 WILD-TYPE                        16   164
D1708V12, multiclass
                                  clus
vv                                 C12ORF51 MUTATED C12ORF51 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       3                 16
  WHITE                                          12                164
[1] 4 2
[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 = LARP7 MUTATION ANALYSIS
D1709V1, survival
                 sevent
clus2               0   1
  LARP7 MUTATED     6   2
  LARP7 WILD-TYPE 271  76
  LARP7 MUTATED LARP7 WILD-TYPE 
              8             347 
  LARP7 MUTATED LARP7 WILD-TYPE 
              2              76 
$`LARP7 MUTATED`
TCGA-AD-6895 TCGA-G4-6628 TCGA-AA-3492 TCGA-AZ-6603 TCGA-CA-6717 TCGA-D5-6535 
       25.08        79.69         3.02        29.56        12.76        15.12 
TCGA-DM-A28K TCGA-F4-6703 
       98.24        47.87 

$`LARP7 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6605 
       62.79        88.21        49.41         6.77        12.10         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  LARP7 MUTATED LARP7 WILD-TYPE 
           3.02            0.00 
  LARP7 MUTATED LARP7 WILD-TYPE 
          98.24          148.01 
  LARP7 MUTATED LARP7 WILD-TYPE 
          27.32           22.03 
[1] "3.0 - 98.2 (27.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1709V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LARP7 MUTATED         1        0        1         3         0         0
  LARP7 WILD-TYPE      63        1       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LARP7 MUTATED           0          0          2          0        0         0
  LARP7 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  LARP7 MUTATED           0
  LARP7 WILD-TYPE         1
D1709V3, multiclass
            clus
vv           LARP7 MUTATED LARP7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LARP7 MUTATED     0   2   6   0
  LARP7 WILD-TYPE   9  65 243  41
D1709V4, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             0              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
  LARP7 MUTATED     5   3   0
  LARP7 WILD-TYPE 215  78  66
D1709V5, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  N0             5             215
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1709V6, binary
                 cls
clus                0   1
  LARP7 MUTATED     6   0
  LARP7 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      6    0
  LARP7 WILD-TYPE  279   48
   clus
vv  LARP7 MUTATED LARP7 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1709V7, binary
                 cls
clus                0   1
  LARP7 MUTATED     3   5
  LARP7 WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      3    5
  LARP7 WILD-TYPE  167  192
        clus
vv       LARP7 MUTATED LARP7 WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D1709V8, binary
                 cls
clus                0   1
  LARP7 MUTATED     7   0
  LARP7 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      7    0
  LARP7 WILD-TYPE  293    8
     clus
vv    LARP7 MUTATED LARP7 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1709V9, binary
                 cls
clus                0   1
  LARP7 MUTATED     6   2
  LARP7 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      6    2
  LARP7 WILD-TYPE  308   46
                               clus
vv                              LARP7 MUTATED LARP7 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LARP7 MUTATED     4   0   0   2
  LARP7 WILD-TYPE 255   3  22  19
D1709V10, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             2              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"
D1709V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LARP7 MUTATED                                  0     1
  LARP7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LARP7 MUTATED                           0     6
  LARP7 WILD-TYPE                        19   170
D1709V12, multiclass
                                  clus
vv                                 LARP7 MUTATED LARP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = TRIP6 MUTATION ANALYSIS
D1710V1, survival
                 sevent
clus2               0   1
  TRIP6 MUTATED     8   2
  TRIP6 WILD-TYPE 269  76
  TRIP6 MUTATED TRIP6 WILD-TYPE 
             10             345 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
              2              76 
$`TRIP6 MUTATED`
TCGA-AA-3522 TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6780 TCGA-AD-5900 
       37.05        25.08        79.69        22.06        20.12        12.16 
TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 
       49.41        10.06        15.62        51.32 

$`TRIP6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 
       14.30        17.56       148.01        85.45        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TRIP6 MUTATED TRIP6 WILD-TYPE 
          10.06            0.00 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
          79.69          148.01 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
          23.57           22.03 
[1] "10.1 - 79.7 (23.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1710V2, continuous
                 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      62        1       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIP6 MUTATED           0          0          1          1        0         0
  TRIP6 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  TRIP6 MUTATED           0
  TRIP6 WILD-TYPE         1
D1710V3, multiclass
            clus
vv           TRIP6 MUTATED TRIP6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TRIP6 MUTATED     0   2   7   1
  TRIP6 WILD-TYPE   9  65 242  40
D1710V4, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             1              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
  TRIP6 MUTATED     8   1   1
  TRIP6 WILD-TYPE 212  80  65
D1710V5, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1710V6, binary
                 cls
clus                0   1
  TRIP6 MUTATED     6   0
  TRIP6 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      6    0
  TRIP6 WILD-TYPE  279   48
   clus
vv  TRIP6 MUTATED TRIP6 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1710V7, binary
                 cls
clus                0   1
  TRIP6 MUTATED     4   6
  TRIP6 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      4    6
  TRIP6 WILD-TYPE  166  191
        clus
vv       TRIP6 MUTATED TRIP6 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1710V8, binary
                 cls
clus                0   1
  TRIP6 MUTATED     9   0
  TRIP6 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      9    0
  TRIP6 WILD-TYPE  291    8
     clus
vv    TRIP6 MUTATED TRIP6 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1710V9, binary
                 cls
clus                0   1
  TRIP6 MUTATED     7   3
  TRIP6 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      7    3
  TRIP6 WILD-TYPE  307   45
                               clus
vv                              TRIP6 MUTATED TRIP6 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRIP6 MUTATED     5   0   0   3
  TRIP6 WILD-TYPE 254   3  22  18
D1710V10, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             3              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"
D1710V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP6 MUTATED                                  0     1
  TRIP6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRIP6 MUTATED                           0     8
  TRIP6 WILD-TYPE                        19   168
D1710V12, multiclass
                                  clus
vv                                 TRIP6 MUTATED TRIP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1711) Variable = FOLR3 MUTATION ANALYSIS
D1711V1, survival
                 sevent
clus2               0   1
  FOLR3 MUTATED     6   0
  FOLR3 WILD-TYPE 271  78
  FOLR3 MUTATED FOLR3 WILD-TYPE 
              6             349 
  FOLR3 MUTATED FOLR3 WILD-TYPE 
              0              78 
$`FOLR3 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-G4-6625 TCGA-AA-3855 TCGA-AA-3947 TCGA-CM-5861 
        0.92        19.04        91.79        32.05        33.01        15.02 

$`FOLR3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  FOLR3 MUTATED FOLR3 WILD-TYPE 
           0.92            0.00 
  FOLR3 MUTATED FOLR3 WILD-TYPE 
          91.79          148.01 
  FOLR3 MUTATED FOLR3 WILD-TYPE 
         25.545          22.060 
[1] "0.9 - 91.8 (25.5)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9200000"
D1711V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FOLR3 MUTATED         1        0        0         2         1         0
  FOLR3 WILD-TYPE      63        1       26       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOLR3 MUTATED           1          0          0          0        1         0
  FOLR3 WILD-TYPE        17          6         44         33       34        12
                 vv
clus              STAGE IVB
  FOLR3 MUTATED           0
  FOLR3 WILD-TYPE         1
D1711V3, multiclass
            clus
vv           FOLR3 MUTATED FOLR3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  FOLR3 MUTATED     0   1   4   1
  FOLR3 WILD-TYPE   9  66 245  40
D1711V4, multiclass
    clus
vv   FOLR3 MUTATED FOLR3 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             1              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
  FOLR3 MUTATED     5   1   0
  FOLR3 WILD-TYPE 215  80  66
D1711V5, multiclass
    clus
vv   FOLR3 MUTATED FOLR3 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1711V6, binary
                 cls
clus                0   1
  FOLR3 MUTATED     5   1
  FOLR3 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLR3 MUTATED      5    1
  FOLR3 WILD-TYPE  280   47
   clus
vv  FOLR3 MUTATED FOLR3 WILD-TYPE
  0             5             280
  1             1              47
[1] 2 2
[1] FALSE
D1711V7, binary
                 cls
clus                0   1
  FOLR3 MUTATED     4   2
  FOLR3 WILD-TYPE 166 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLR3 MUTATED      4    2
  FOLR3 WILD-TYPE  166  195
        clus
vv       FOLR3 MUTATED FOLR3 WILD-TYPE
  FEMALE             4             166
  MALE               2             195
[1] 2 2
[1] FALSE
D1711V8, binary
                 cls
clus                0   1
  FOLR3 MUTATED     5   1
  FOLR3 WILD-TYPE 295   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLR3 MUTATED      5    1
  FOLR3 WILD-TYPE  295    7
     clus
vv    FOLR3 MUTATED FOLR3 WILD-TYPE
  NO              5             295
  YES             1               7
[1] 2 2
[1] FALSE
D1711V9, binary
                 cls
clus                0   1
  FOLR3 MUTATED     5   1
  FOLR3 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLR3 MUTATED      5    1
  FOLR3 WILD-TYPE  309   47
                               clus
vv                              FOLR3 MUTATED FOLR3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOLR3 MUTATED     5   0   1   0
  FOLR3 WILD-TYPE 254   3  21  21
D1711V10, multiclass
    clus
vv   FOLR3 MUTATED FOLR3 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             0              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"
D1711V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOLR3 MUTATED                                  0     0
  FOLR3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOLR3 MUTATED                           0     2
  FOLR3 WILD-TYPE                        19   174
D1711V12, multiclass
[1] "Remove cluster labels:" "FOLR3 MUTATED"         
clus
  FOLR3 MUTATED FOLR3 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5656 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5862 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" "FOLR3 WILD-TYPE" 

Clustering(1712) Variable = ANKRD40 MUTATION ANALYSIS
D1712V1, survival
                   sevent
clus2                 0   1
  ANKRD40 MUTATED     5   3
  ANKRD40 WILD-TYPE 272  75
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                8               347 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                3                75 
$`ANKRD40 MUTATED`
TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3968 TCGA-AD-5900 
       79.69         3.02        10.06         1.02        21.99        12.16 
TCGA-AY-6197 TCGA-AZ-6598 
       21.44        49.41 

$`ANKRD40 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       33.01        26.01        20.98        34.03         2.01        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01         0.20        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
             1.02              0.00 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            79.69            148.01 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            16.80             22.09 
[1] "1.0 - 79.7 (16.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1712V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD40 MUTATED         4        0        2         1         0         0
  ANKRD40 WILD-TYPE      60        1       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD40 MUTATED           1          0          0          0        0
  ANKRD40 WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD40 MUTATED           0         0
  ANKRD40 WILD-TYPE        12         1
D1712V3, multiclass
            clus
vv           ANKRD40 MUTATED ANKRD40 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  ANKRD40 MUTATED     0   4   4   0
  ANKRD40 WILD-TYPE   9  63 245  41
D1712V4, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               4               245
  T4               0                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
  ANKRD40 MUTATED     7   0   1
  ANKRD40 WILD-TYPE 213  81  65
D1712V5, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  N0               7               213
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1712V6, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     5   0
  ANKRD40 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      5    0
  ANKRD40 WILD-TYPE  280   48
   clus
vv  ANKRD40 MUTATED ANKRD40 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1712V7, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     5   3
  ANKRD40 WILD-TYPE 165 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      5    3
  ANKRD40 WILD-TYPE  165  194
        clus
vv       ANKRD40 MUTATED ANKRD40 WILD-TYPE
  FEMALE               5               165
  MALE                 3               194
[1] 2 2
[1] FALSE
D1712V8, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     8   0
  ANKRD40 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      8    0
  ANKRD40 WILD-TYPE  292    8
     clus
vv    ANKRD40 MUTATED ANKRD40 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1712V9, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     6   2
  ANKRD40 WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      6    2
  ANKRD40 WILD-TYPE  308   46
                               clus
vv                              ANKRD40 MUTATED ANKRD40 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD40 MUTATED     7   0   0   0
  ANKRD40 WILD-TYPE 252   3  22  21
D1712V10, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               0                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"
D1712V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD40 MUTATED                                  0     0
  ANKRD40 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD40 MUTATED                           0     4
  ANKRD40 WILD-TYPE                        19   172
D1712V12, multiclass
                                  clus
vv                                 ANKRD40 MUTATED ANKRD40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = MRPL10 MUTATION ANALYSIS
D1713V1, survival
                  sevent
clus2                0   1
  MRPL10 MUTATED     3   1
  MRPL10 WILD-TYPE 274  77
  MRPL10 MUTATED MRPL10 WILD-TYPE 
               4              351 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
               1               77 
$`MRPL10 MUTATED`
TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-4752 TCGA-CM-5344 
        4.01        12.16        13.02        22.03 

$`MRPL10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       124.27        23.05 
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-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MRPL10 MUTATED MRPL10 WILD-TYPE 
            4.01             0.00 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
           22.03           148.01 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
           12.59            22.09 
[1] "4.0 - 22.0 (12.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1713V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPL10 MUTATED         1        0        0         1         1         0
  MRPL10 WILD-TYPE      63        1       26       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL10 MUTATED           0          0          1          0        0
  MRPL10 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MRPL10 MUTATED           0         0
  MRPL10 WILD-TYPE        12         1
D1713V3, multiclass
            clus
vv           MRPL10 MUTATED MRPL10 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MRPL10 MUTATED     0   1   2   1
  MRPL10 WILD-TYPE   9  66 247  40
D1713V4, multiclass
    clus
vv   MRPL10 MUTATED MRPL10 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              2              247
  T4              1               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
  MRPL10 MUTATED     3   1   0
  MRPL10 WILD-TYPE 217  80  66
D1713V5, multiclass
    clus
vv   MRPL10 MUTATED MRPL10 WILD-TYPE
  N0              3              217
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1713V6, binary
                  cls
clus                 0   1
  MRPL10 MUTATED     3   0
  MRPL10 WILD-TYPE 282  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL10 MUTATED      3    0
  MRPL10 WILD-TYPE  282   48
   clus
vv  MRPL10 MUTATED MRPL10 WILD-TYPE
  0              3              282
  1              0               48
[1] 2 2
[1] FALSE
D1713V7, binary
                  cls
clus                 0   1
  MRPL10 MUTATED     1   3
  MRPL10 WILD-TYPE 169 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL10 MUTATED      1    3
  MRPL10 WILD-TYPE  169  194
        clus
vv       MRPL10 MUTATED MRPL10 WILD-TYPE
  FEMALE              1              169
  MALE                3              194
[1] 2 2
[1] FALSE
D1713V8, binary
                  cls
clus                 0   1
  MRPL10 MUTATED     3   0
  MRPL10 WILD-TYPE 297   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL10 MUTATED      3    0
  MRPL10 WILD-TYPE  297    8
     clus
vv    MRPL10 MUTATED MRPL10 WILD-TYPE
  NO               3              297
  YES              0                8
[1] 2 2
[1] FALSE
D1713V9, binary
                  cls
clus                 0   1
  MRPL10 MUTATED     2   2
  MRPL10 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL10 MUTATED      2    2
  MRPL10 WILD-TYPE  312   46
                               clus
vv                              MRPL10 MUTATED MRPL10 WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MRPL10 MUTATED     4   0   0   0
  MRPL10 WILD-TYPE 255   3  22  21
D1713V10, multiclass
    clus
vv   MRPL10 MUTATED MRPL10 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D1713V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPL10 MUTATED                                  0     0
  MRPL10 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPL10 MUTATED                           1     2
  MRPL10 WILD-TYPE                        18   174
D1713V12, multiclass
                                  clus
vv                                 MRPL10 MUTATED MRPL10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         2              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(1714) Variable = ACADVL MUTATION ANALYSIS
D1714V1, survival
                  sevent
clus2                0   1
  ACADVL MUTATED     4   1
  ACADVL WILD-TYPE 273  77
  ACADVL MUTATED ACADVL WILD-TYPE 
               5              350 
  ACADVL MUTATED ACADVL WILD-TYPE 
               1               77 
$`ACADVL MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AA-3544 TCGA-DM-A1D8 
       35.80        26.17        79.69        14.01        12.59 

$`ACADVL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       22.09        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ACADVL MUTATED ACADVL WILD-TYPE 
           12.59             0.00 
  ACADVL MUTATED ACADVL WILD-TYPE 
           79.69           148.01 
  ACADVL MUTATED ACADVL WILD-TYPE 
          26.170           22.045 
[1] "12.6 - 79.7 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1714V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACADVL MUTATED         2        0        0         2         0         0
  ACADVL WILD-TYPE      62        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACADVL MUTATED           1          0          0          0        0
  ACADVL WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ACADVL MUTATED           0         0
  ACADVL WILD-TYPE        12         1
D1714V3, multiclass
            clus
vv           ACADVL MUTATED ACADVL WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ACADVL MUTATED     0   2   4   0
  ACADVL WILD-TYPE   9  65 245  41
D1714V4, multiclass
    clus
vv   ACADVL MUTATED ACADVL WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              0               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
  ACADVL MUTATED     4   1   1
  ACADVL WILD-TYPE 216  80  65
D1714V5, multiclass
    clus
vv   ACADVL MUTATED ACADVL WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1714V6, binary
                  cls
clus                 0   1
  ACADVL MUTATED     5   0
  ACADVL WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACADVL MUTATED      5    0
  ACADVL WILD-TYPE  280   48
   clus
vv  ACADVL MUTATED ACADVL WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1714V7, binary
                  cls
clus                 0   1
  ACADVL MUTATED     3   3
  ACADVL WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACADVL MUTATED      3    3
  ACADVL WILD-TYPE  167  194
        clus
vv       ACADVL MUTATED ACADVL WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D1714V8, binary
                  cls
clus                 0   1
  ACADVL MUTATED     4   0
  ACADVL WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACADVL MUTATED      4    0
  ACADVL WILD-TYPE  296    8
     clus
vv    ACADVL MUTATED ACADVL WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1714V9, binary
                  cls
clus                 0   1
  ACADVL MUTATED     6   0
  ACADVL WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACADVL MUTATED      6    0
  ACADVL WILD-TYPE  308   48
                               clus
vv                              ACADVL MUTATED ACADVL WILD-TYPE
  COLON ADENOCARCINOMA                       6              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACADVL MUTATED     5   0   0   0
  ACADVL WILD-TYPE 254   3  22  21
D1714V10, multiclass
    clus
vv   ACADVL MUTATED ACADVL WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1714V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACADVL MUTATED                                  0     0
  ACADVL WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACADVL MUTATED                           0     4
  ACADVL WILD-TYPE                        19   172
D1714V12, multiclass
                                  clus
vv                                 ACADVL MUTATED ACADVL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = SLIT3 MUTATION ANALYSIS
D1715V1, survival
                 sevent
clus2               0   1
  SLIT3 MUTATED    20   4
  SLIT3 WILD-TYPE 257  74
  SLIT3 MUTATED SLIT3 WILD-TYPE 
             24             331 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
              4              74 
$`SLIT3 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3986 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2672 
        0.92        19.04        19.07        35.80        26.17        46.65 
TCGA-A6-6781 TCGA-AA-3517 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3866 
       19.66        38.99        61.02         6.97         1.02        17.03 
TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-5543 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6167 
        4.01        24.53        33.01        12.76        15.02        14.99 
TCGA-CM-6171 TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6309 
       14.04        81.37        35.97         6.18       133.18        85.48 

$`SLIT3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        63.62        22.09        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
        3.02        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        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-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-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       25.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 
       32.05         0.99        31.07        30.05        53.00        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       26.47        14.50        27.09        16.31         0.95         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E 
        7.50        44.32       131.51       135.65       139.17       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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLIT3 MUTATED SLIT3 WILD-TYPE 
           0.92            0.00 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
         133.18          148.01 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
         19.365          22.090 
[1] "0.9 - 133.2 (19.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1715V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLIT3 MUTATED         4        0        2         7         2         0
  SLIT3 WILD-TYPE      60        1       24       101         6         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        16          6         41         31       34        11
                 vv
clus              STAGE IVB
  SLIT3 MUTATED           0
  SLIT3 WILD-TYPE         1
D1715V3, multiclass
            clus
vv           SLIT3 MUTATED SLIT3 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  SLIT3 MUTATED     1   4  17   3
  SLIT3 WILD-TYPE   8  63 232  38
D1715V4, multiclass
    clus
vv   SLIT3 MUTATED SLIT3 WILD-TYPE
  T1             1               8
  T2             4              63
  T3            17             232
  T4             3              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
  SLIT3 MUTATED    17   7   1
  SLIT3 WILD-TYPE 203  74  65
D1715V5, multiclass
    clus
vv   SLIT3 MUTATED SLIT3 WILD-TYPE
  N0            17             203
  N1             7              74
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1715V6, binary
                 cls
clus                0   1
  SLIT3 MUTATED    20   2
  SLIT3 WILD-TYPE 265  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     20    2
  SLIT3 WILD-TYPE  265   46
   clus
vv  SLIT3 MUTATED SLIT3 WILD-TYPE
  0            20             265
  1             2              46
[1] 2 2
[1] FALSE
D1715V7, binary
                 cls
clus                0   1
  SLIT3 MUTATED    14  11
  SLIT3 WILD-TYPE 156 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     14   11
  SLIT3 WILD-TYPE  156  186
        clus
vv       SLIT3 MUTATED SLIT3 WILD-TYPE
  FEMALE            14             156
  MALE              11             186
[1] 2 2
[1] FALSE
D1715V8, binary
                 cls
clus                0   1
  SLIT3 MUTATED    20   1
  SLIT3 WILD-TYPE 280   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     20    1
  SLIT3 WILD-TYPE  280    7
     clus
vv    SLIT3 MUTATED SLIT3 WILD-TYPE
  NO             20             280
  YES             1               7
[1] 2 2
[1] FALSE
D1715V9, binary
                 cls
clus                0   1
  SLIT3 MUTATED    21   4
  SLIT3 WILD-TYPE 293  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     21    4
  SLIT3 WILD-TYPE  293   44
                               clus
vv                              SLIT3 MUTATED SLIT3 WILD-TYPE
  COLON ADENOCARCINOMA                     21             293
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SLIT3 MUTATED    19   0   1   2
  SLIT3 WILD-TYPE 240   3  21  19
D1715V10, multiclass
    clus
vv   SLIT3 MUTATED SLIT3 WILD-TYPE
  R0            19             240
  R1             0               3
  R2             1              21
  RX             2              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"
D1715V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLIT3 MUTATED                                  0     1
  SLIT3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SLIT3 MUTATED                           3    12
  SLIT3 WILD-TYPE                        16   164
D1715V12, multiclass
                                  clus
vv                                 SLIT3 MUTATED SLIT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       12             164
[1] 4 2
[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 = CCL14 MUTATION ANALYSIS
D1716V1, survival
                 sevent
clus2               0   1
  CCL14 MUTATED     3   2
  CCL14 WILD-TYPE 274  76
  CCL14 MUTATED CCL14 WILD-TYPE 
              5             350 
  CCL14 MUTATED CCL14 WILD-TYPE 
              2              76 
$`CCL14 MUTATED`
TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-A00N TCGA-AZ-6598 TCGA-CM-5861 
       26.17        22.06         4.01        49.41        15.02 

$`CCL14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCL14 MUTATED CCL14 WILD-TYPE 
           4.01            0.00 
  CCL14 MUTATED CCL14 WILD-TYPE 
          49.41          148.01 
  CCL14 MUTATED CCL14 WILD-TYPE 
          22.06           22.06 
[1] "4.0 - 49.4 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1716V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCL14 MUTATED         0        0        1         3         1         0
  CCL14 WILD-TYPE      64        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCL14 MUTATED           0          0          0          0        0         0
  CCL14 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  CCL14 MUTATED           0
  CCL14 WILD-TYPE         1
D1716V3, multiclass
            clus
vv           CCL14 MUTATED CCL14 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  CCL14 MUTATED     0   0   4   1
  CCL14 WILD-TYPE   9  67 245  40
D1716V4, multiclass
    clus
vv   CCL14 MUTATED CCL14 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             1              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
  CCL14 MUTATED     5   0   0
  CCL14 WILD-TYPE 215  81  66
D1716V5, multiclass
    clus
vv   CCL14 MUTATED CCL14 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1716V6, binary
                 cls
clus                0   1
  CCL14 MUTATED     4   0
  CCL14 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCL14 MUTATED      4    0
  CCL14 WILD-TYPE  281   48
   clus
vv  CCL14 MUTATED CCL14 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1716V7, binary
                 cls
clus                0   1
  CCL14 MUTATED     4   1
  CCL14 WILD-TYPE 166 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCL14 MUTATED      4    1
  CCL14 WILD-TYPE  166  196
        clus
vv       CCL14 MUTATED CCL14 WILD-TYPE
  FEMALE             4             166
  MALE               1             196
[1] 2 2
[1] FALSE
D1716V8, binary
                 cls
clus                0   1
  CCL14 MUTATED     4   0
  CCL14 WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCL14 MUTATED      4    0
  CCL14 WILD-TYPE  296    8
     clus
vv    CCL14 MUTATED CCL14 WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1716V9, binary
                 cls
clus                0   1
  CCL14 MUTATED     4   1
  CCL14 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCL14 MUTATED      4    1
  CCL14 WILD-TYPE  310   47
                               clus
vv                              CCL14 MUTATED CCL14 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCL14 MUTATED     4   0   0   0
  CCL14 WILD-TYPE 255   3  22  21
D1716V10, multiclass
    clus
vv   CCL14 MUTATED CCL14 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1716V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCL14 MUTATED                                  0     0
  CCL14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCL14 MUTATED                           0     4
  CCL14 WILD-TYPE                        19   172
D1716V12, multiclass
                                  clus
vv                                 CCL14 MUTATED CCL14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = KLK11 MUTATION ANALYSIS
D1717V1, survival
                 sevent
clus2               0   1
  KLK11 MUTATED     5   0
  KLK11 WILD-TYPE 272  78
  KLK11 MUTATED KLK11 WILD-TYPE 
              5             350 
  KLK11 MUTATED KLK11 WILD-TYPE 
              0              78 
$`KLK11 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6588 TCGA-AA-3663 TCGA-AA-A01R 
       19.04        25.08        26.17         6.97        35.01 

$`KLK11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KLK11 MUTATED KLK11 WILD-TYPE 
           6.97            0.00 
  KLK11 MUTATED KLK11 WILD-TYPE 
          35.01          148.01 
  KLK11 MUTATED KLK11 WILD-TYPE 
         25.080          22.045 
[1] "7.0 - 35.0 (25.1)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1717V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLK11 MUTATED         0        0        1         1         0         0
  KLK11 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLK11 MUTATED           1          0          1          0        1         0
  KLK11 WILD-TYPE        17          6         43         33       34        12
                 vv
clus              STAGE IVB
  KLK11 MUTATED           0
  KLK11 WILD-TYPE         1
D1717V3, multiclass
            clus
vv           KLK11 MUTATED KLK11 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  KLK11 MUTATED     0   0   5   0
  KLK11 WILD-TYPE   9  67 244  41
D1717V4, multiclass
    clus
vv   KLK11 MUTATED KLK11 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             0              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
  KLK11 MUTATED     3   1   1
  KLK11 WILD-TYPE 217  80  65
D1717V5, multiclass
    clus
vv   KLK11 MUTATED KLK11 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1717V6, binary
                 cls
clus                0   1
  KLK11 MUTATED     4   1
  KLK11 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK11 MUTATED      4    1
  KLK11 WILD-TYPE  281   47
   clus
vv  KLK11 MUTATED KLK11 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1717V7, binary
                 cls
clus                0   1
  KLK11 MUTATED     1   4
  KLK11 WILD-TYPE 169 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK11 MUTATED      1    4
  KLK11 WILD-TYPE  169  193
        clus
vv       KLK11 MUTATED KLK11 WILD-TYPE
  FEMALE             1             169
  MALE               4             193
[1] 2 2
[1] FALSE
D1717V8, binary
                 cls
clus                0   1
  KLK11 MUTATED     3   2
  KLK11 WILD-TYPE 297   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK11 MUTATED      3    2
  KLK11 WILD-TYPE  297    6
     clus
vv    KLK11 MUTATED KLK11 WILD-TYPE
  NO              3             297
  YES             2               6
[1] 2 2
[1] FALSE
D1717V9, binary
                 cls
clus                0   1
  KLK11 MUTATED     4   1
  KLK11 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK11 MUTATED      4    1
  KLK11 WILD-TYPE  310   47
                               clus
vv                              KLK11 MUTATED KLK11 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLK11 MUTATED     4   0   1   0
  KLK11 WILD-TYPE 255   3  21  21
D1717V10, multiclass
    clus
vv   KLK11 MUTATED KLK11 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             1              21
  RX             0              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"
D1717V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLK11 MUTATED                                  0     0
  KLK11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLK11 MUTATED                           0     2
  KLK11 WILD-TYPE                        19   174
D1717V12, multiclass
[1] "Remove cluster labels:" "KLK11 MUTATED"         
clus
  KLK11 MUTATED KLK11 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6964      TCGA-AZ-4681      TCGA-AZ-6601 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285      TCGA-G4-6310 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6628 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5656      TCGA-A6-5657 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661      TCGA-A6-5662 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666      TCGA-A6-6137 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142      TCGA-A6-6648 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-6651      TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899      TCGA-AD-6901 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6603 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-CA-5254 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" "KLK11 WILD-TYPE" 

Clustering(1718) Variable = UBR5 MUTATION ANALYSIS
D1718V1, survival
                sevent
clus2              0   1
  UBR5 MUTATED    17   9
  UBR5 WILD-TYPE 260  69
  UBR5 MUTATED UBR5 WILD-TYPE 
            26            329 
  UBR5 MUTATED UBR5 WILD-TYPE 
             9             69 
$`UBR5 MUTATED`
TCGA-AA-3713 TCGA-A6-2676 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-A010 
       19.04        42.90         8.38        20.12         6.97        34.98 
TCGA-AA-A01F TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       32.02        21.44        58.39        49.41        12.76        10.06 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6679 TCGA-D5-5538 
       51.32        21.14        15.02        12.00        10.06        54.61 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6570 
      119.70        38.20        13.32        60.79       117.07         6.18 
TCGA-G4-6315 TCGA-G4-6323 
       61.91        13.78 

$`UBR5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6142 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       15.62        21.99        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        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-D5-5539 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 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D0 
       13.35        12.00        11.38        10.26        24.43       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-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        46.75 

  UBR5 MUTATED UBR5 WILD-TYPE 
          6.18           0.00 
  UBR5 MUTATED UBR5 WILD-TYPE 
        119.70         148.01 
  UBR5 MUTATED UBR5 WILD-TYPE 
         21.29          22.09 
[1] "6.2 - 119.7 (21.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1718V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBR5 MUTATED         1        1        2        14         3         0
  UBR5 WILD-TYPE      63        0       24        94         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR5 MUTATED           0          0          3          2        2         0
  UBR5 WILD-TYPE        18          6         41         31       33        12
                vv
clus             STAGE IVB
  UBR5 MUTATED           0
  UBR5 WILD-TYPE         1
D1718V3, multiclass
            clus
vv           UBR5 MUTATED UBR5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              2             24
  STAGE IIA            14             94
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            2             31
  STAGE IV              2             33
  STAGE IVA             0             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
  UBR5 MUTATED     1   0  23   3
  UBR5 WILD-TYPE   8  67 226  38
D1718V4, multiclass
    clus
vv   UBR5 MUTATED UBR5 WILD-TYPE
  T1            1              8
  T2            0             67
  T3           23            226
  T4            3             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
  UBR5 MUTATED    22   4   2
  UBR5 WILD-TYPE 198  77  64
D1718V5, multiclass
    clus
vv   UBR5 MUTATED UBR5 WILD-TYPE
  N0           22            198
  N1            4             77
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1718V6, binary
                cls
clus               0   1
  UBR5 MUTATED    20   2
  UBR5 WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR5 MUTATED     20    2
  UBR5 WILD-TYPE  265   46
   clus
vv  UBR5 MUTATED UBR5 WILD-TYPE
  0           20            265
  1            2             46
[1] 2 2
[1] FALSE
D1718V7, binary
                cls
clus               0   1
  UBR5 MUTATED    13  15
  UBR5 WILD-TYPE 157 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR5 MUTATED     13   15
  UBR5 WILD-TYPE  157  182
        clus
vv       UBR5 MUTATED UBR5 WILD-TYPE
  FEMALE           13            157
  MALE             15            182
[1] 2 2
[1] FALSE
D1718V8, binary
                cls
clus               0   1
  UBR5 MUTATED    20   1
  UBR5 WILD-TYPE 280   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR5 MUTATED     20    1
  UBR5 WILD-TYPE  280    7
     clus
vv    UBR5 MUTATED UBR5 WILD-TYPE
  NO            20            280
  YES            1              7
[1] 2 2
[1] FALSE
D1718V9, binary
                cls
clus               0   1
  UBR5 MUTATED    23   3
  UBR5 WILD-TYPE 291  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR5 MUTATED     23    3
  UBR5 WILD-TYPE  291   45
                               clus
vv                              UBR5 MUTATED UBR5 WILD-TYPE
  COLON ADENOCARCINOMA                    23            291
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UBR5 MUTATED    14   0   1   5
  UBR5 WILD-TYPE 245   3  21  16
D1718V10, multiclass
    clus
vv   UBR5 MUTATED UBR5 WILD-TYPE
  R0           14            245
  R1            0              3
  R2            1             21
  RX            5             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"
D1718V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBR5 MUTATED                                  0     2
  UBR5 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBR5 MUTATED                           2    19
  UBR5 WILD-TYPE                        17   157
D1718V12, multiclass
                                  clus
vv                                 UBR5 MUTATED UBR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                      19            157
[1] 4 2
[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 = ZNF557 MUTATION ANALYSIS
D1719V1, survival
                  sevent
clus2                0   1
  ZNF557 MUTATED     8   0
  ZNF557 WILD-TYPE 269  78
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               8              347 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               0               78 
$`ZNF557 MUTATED`
TCGA-AD-6895 TCGA-G4-6586 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3949 TCGA-AZ-4315 
       25.08        35.80        33.53        63.98        26.01        58.39 
TCGA-CM-6171 TCGA-G4-6304 
       14.04        53.62 

$`ZNF557 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ZNF557 MUTATED ZNF557 WILD-TYPE 
           14.04             0.00 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
           63.98           148.01 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
          34.665           21.990 
[1] "14.0 - 64.0 (34.7)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D1719V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF557 MUTATED         1        0        1         3         1         0
  ZNF557 WILD-TYPE      63        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF557 MUTATED           1          0          2          0        0
  ZNF557 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF557 MUTATED           0         0
  ZNF557 WILD-TYPE        12         1
D1719V3, multiclass
            clus
vv           ZNF557 MUTATED ZNF557 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF557 MUTATED     0   1   7   1
  ZNF557 WILD-TYPE   9  66 242  40
D1719V4, multiclass
    clus
vv   ZNF557 MUTATED ZNF557 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              1               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
  ZNF557 MUTATED     6   2   1
  ZNF557 WILD-TYPE 214  79  65
D1719V5, multiclass
    clus
vv   ZNF557 MUTATED ZNF557 WILD-TYPE
  N0              6              214
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1719V6, binary
                  cls
clus                 0   1
  ZNF557 MUTATED     9   0
  ZNF557 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF557 MUTATED      9    0
  ZNF557 WILD-TYPE  276   48
   clus
vv  ZNF557 MUTATED ZNF557 WILD-TYPE
  0              9              276
  1              0               48
[1] 2 2
[1] FALSE
D1719V7, binary
                  cls
clus                 0   1
  ZNF557 MUTATED     5   4
  ZNF557 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF557 MUTATED      5    4
  ZNF557 WILD-TYPE  165  193
        clus
vv       ZNF557 MUTATED ZNF557 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1719V8, binary
                  cls
clus                 0   1
  ZNF557 MUTATED     8   0
  ZNF557 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF557 MUTATED      8    0
  ZNF557 WILD-TYPE  292    8
     clus
vv    ZNF557 MUTATED ZNF557 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1719V9, binary
                  cls
clus                 0   1
  ZNF557 MUTATED     8   1
  ZNF557 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF557 MUTATED      8    1
  ZNF557 WILD-TYPE  306   47
                               clus
vv                              ZNF557 MUTATED ZNF557 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF557 MUTATED     9   0   0   0
  ZNF557 WILD-TYPE 250   3  22  21
D1719V10, multiclass
    clus
vv   ZNF557 MUTATED ZNF557 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D1719V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF557 MUTATED                                  0     0
  ZNF557 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF557 MUTATED                           1     5
  ZNF557 WILD-TYPE                        18   171
D1719V12, multiclass
                                  clus
vv                                 ZNF557 MUTATED ZNF557 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = UVRAG MUTATION ANALYSIS
D1720V1, survival
                 sevent
clus2               0   1
  UVRAG MUTATED     5   1
  UVRAG WILD-TYPE 272  77
  UVRAG MUTATED UVRAG WILD-TYPE 
              6             349 
  UVRAG MUTATED UVRAG WILD-TYPE 
              1              77 
$`UVRAG MUTATED`
TCGA-AA-3697 TCGA-AA-3510 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-D5-6929 
       85.05        63.98        12.76        10.06        14.30        13.41 

$`UVRAG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 
       12.39        12.59        12.59        12.20        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  UVRAG MUTATED UVRAG WILD-TYPE 
          10.06            0.00 
  UVRAG MUTATED UVRAG WILD-TYPE 
          85.05          148.01 
  UVRAG MUTATED UVRAG WILD-TYPE 
         13.855          22.090 
[1] "10.1 - 85.0 (13.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1720V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UVRAG MUTATED         0        0        2         4         0         0
  UVRAG WILD-TYPE      64        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UVRAG MUTATED           0          0          0          0        1         0
  UVRAG WILD-TYPE        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  UVRAG MUTATED           0
  UVRAG WILD-TYPE         1
D1720V3, multiclass
            clus
vv           UVRAG MUTATED UVRAG WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  UVRAG MUTATED     0   0   7   0
  UVRAG WILD-TYPE   9  67 242  41
D1720V4, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             0              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
  UVRAG MUTATED     6   1   0
  UVRAG WILD-TYPE 214  80  66
D1720V5, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  N0             6             214
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1720V6, binary
                 cls
clus                0   1
  UVRAG MUTATED     6   1
  UVRAG WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      6    1
  UVRAG WILD-TYPE  279   47
   clus
vv  UVRAG MUTATED UVRAG WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1720V7, binary
                 cls
clus                0   1
  UVRAG MUTATED     2   5
  UVRAG WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      2    5
  UVRAG WILD-TYPE  168  192
        clus
vv       UVRAG MUTATED UVRAG WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1720V8, binary
                 cls
clus                0   1
  UVRAG MUTATED     6   0
  UVRAG WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      6    0
  UVRAG WILD-TYPE  294    8
     clus
vv    UVRAG MUTATED UVRAG WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1720V9, binary
                 cls
clus                0   1
  UVRAG MUTATED     6   1
  UVRAG WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      6    1
  UVRAG WILD-TYPE  308   47
                               clus
vv                              UVRAG MUTATED UVRAG WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UVRAG MUTATED     4   0   0   3
  UVRAG WILD-TYPE 255   3  22  18
D1720V10, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             3              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"
D1720V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UVRAG MUTATED                                  0     3
  UVRAG WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UVRAG MUTATED                           0     1
  UVRAG WILD-TYPE                        19   175
D1720V12, multiclass
                                  clus
vv                                 UVRAG MUTATED UVRAG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        1             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(1721) Variable = C14ORF118 MUTATION ANALYSIS
D1721V1, survival
                     sevent
clus2                   0   1
  C14ORF118 MUTATED     7   1
  C14ORF118 WILD-TYPE 270  77
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  8                 347 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  1                  77 
$`C14ORF118 MUTATED`
TCGA-G4-6310 TCGA-G4-6586 TCGA-AA-A010 TCGA-AA-A01K TCGA-CM-6163 TCGA-D5-6529 
       63.62        35.80        34.98        31.00        14.04        20.19 
TCGA-D5-6535 TCGA-DM-A28F 
       15.12        35.97 

$`C14ORF118 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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        54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              14.04                0.00 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              63.62              148.01 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              32.99               22.03 
[1] "14.0 - 63.6 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1721V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF118 MUTATED         1        0        0         3         1         0
  C14ORF118 WILD-TYPE      63        1       26       105         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF118 MUTATED           0          0          3          1        0
  C14ORF118 WILD-TYPE        18          6         41         32       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF118 MUTATED           0         0
  C14ORF118 WILD-TYPE        12         1
D1721V3, multiclass
            clus
vv           C14ORF118 MUTATED C14ORF118 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  26
  STAGE IIA                  3                 105
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  18
  STAGE IIIA                 0                   6
  STAGE IIIB                 3                  41
  STAGE IIIC                 1                  32
  STAGE IV                   0                  35
  STAGE IVA                  0                  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
  C14ORF118 MUTATED     1   0   7   1
  C14ORF118 WILD-TYPE   8  67 242  40
D1721V4, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  T1                 1                   8
  T2                 0                  67
  T3                 7                 242
  T4                 1                  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
  C14ORF118 MUTATED     5   3   1
  C14ORF118 WILD-TYPE 215  78  65
D1721V5, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  N0                 5                 215
  N1                 3                  78
  N2                 1                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1721V6, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     8   0
  C14ORF118 WILD-TYPE 277  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      8    0
  C14ORF118 WILD-TYPE  277   48
   clus
vv  C14ORF118 MUTATED C14ORF118 WILD-TYPE
  0                 8                 277
  1                 0                  48
[1] 2 2
[1] FALSE
D1721V7, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     5   4
  C14ORF118 WILD-TYPE 165 193
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      5    4
  C14ORF118 WILD-TYPE  165  193
        clus
vv       C14ORF118 MUTATED C14ORF118 WILD-TYPE
  FEMALE                 5                 165
  MALE                   4                 193
[1] 2 2
[1] FALSE
D1721V8, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     6   1
  C14ORF118 WILD-TYPE 294   7
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      6    1
  C14ORF118 WILD-TYPE  294    7
     clus
vv    C14ORF118 MUTATED C14ORF118 WILD-TYPE
  NO                  6                 294
  YES                 1                   7
[1] 2 2
[1] FALSE
D1721V9, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     9   0
  C14ORF118 WILD-TYPE 305  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      9    0
  C14ORF118 WILD-TYPE  305   48
                               clus
vv                              C14ORF118 MUTATED C14ORF118 WILD-TYPE
  COLON ADENOCARCINOMA                          9                 305
  COLON MUCINOUS ADENOCARCINOMA                 0                  48
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF118 MUTATED     7   0   0   1
  C14ORF118 WILD-TYPE 252   3  22  20
D1721V10, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  R0                 7                 252
  R1                 0                   3
  R2                 0                  22
  RX                 1                  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"
D1721V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF118 MUTATED                                  0     0
  C14ORF118 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF118 MUTATED                           0     6
  C14ORF118 WILD-TYPE                        19   170
D1721V12, multiclass
                                  clus
vv                                 C14ORF118 MUTATED C14ORF118 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        0                  19
  WHITE                                            6                 170
[1] 4 2
[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 = XKR3 MUTATION ANALYSIS
D1722V1, survival
                sevent
clus2              0   1
  XKR3 MUTATED    10   1
  XKR3 WILD-TYPE 267  77
  XKR3 MUTATED XKR3 WILD-TYPE 
            11            344 
  XKR3 MUTATED XKR3 WILD-TYPE 
             1             77 
$`XKR3 MUTATED`
TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3821 
      100.01        79.69        20.12        78.08        26.99         1.02 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-5541 TCGA-G4-6307 
       58.39        12.76        15.02        55.92        55.04 

$`XKR3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  XKR3 MUTATED XKR3 WILD-TYPE 
          1.02           0.00 
  XKR3 MUTATED XKR3 WILD-TYPE 
        100.01         148.01 
  XKR3 MUTATED XKR3 WILD-TYPE 
         55.04          22.01 
[1] "1.0 - 100.0 (55.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "4.2"
D1722V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XKR3 MUTATED         2        0        2         6         0         0
  XKR3 WILD-TYPE      62        1       24       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XKR3 MUTATED           0          0          2          0        0         0
  XKR3 WILD-TYPE        18          6         42         33       35        12
                vv
clus             STAGE IVB
  XKR3 MUTATED           0
  XKR3 WILD-TYPE         1
D1722V3, multiclass
            clus
vv           XKR3 MUTATED XKR3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  XKR3 MUTATED     0   2  10   0
  XKR3 WILD-TYPE   9  65 239  41
D1722V4, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           10            239
  T4            0             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
  XKR3 MUTATED    10   2   0
  XKR3 WILD-TYPE 210  79  66
D1722V5, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  N0           10            210
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1722V6, binary
                cls
clus               0   1
  XKR3 MUTATED    11   0
  XKR3 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED     11    0
  XKR3 WILD-TYPE  274   48
   clus
vv  XKR3 MUTATED XKR3 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D1722V7, binary
                cls
clus               0   1
  XKR3 MUTATED     6   6
  XKR3 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED      6    6
  XKR3 WILD-TYPE  164  191
        clus
vv       XKR3 MUTATED XKR3 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D1722V8, binary
                cls
clus               0   1
  XKR3 MUTATED    11   0
  XKR3 WILD-TYPE 289   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED     11    0
  XKR3 WILD-TYPE  289    8
     clus
vv    XKR3 MUTATED XKR3 WILD-TYPE
  NO            11            289
  YES            0              8
[1] 2 2
[1] FALSE
D1722V9, binary
                cls
clus               0   1
  XKR3 MUTATED     9   3
  XKR3 WILD-TYPE 305  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED      9    3
  XKR3 WILD-TYPE  305   45
                               clus
vv                              XKR3 MUTATED XKR3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  XKR3 MUTATED     9   0   0   1
  XKR3 WILD-TYPE 250   3  22  20
D1722V10, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            1             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"
D1722V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XKR3 MUTATED                                  0     1
  XKR3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XKR3 MUTATED                           0     7
  XKR3 WILD-TYPE                        19   169
D1722V12, multiclass
                                  clus
vv                                 XKR3 MUTATED XKR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = EPHA4 MUTATION ANALYSIS
D1723V1, survival
                 sevent
clus2               0   1
  EPHA4 MUTATED    12   6
  EPHA4 WILD-TYPE 265  72
  EPHA4 MUTATED EPHA4 WILD-TYPE 
             18             337 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
              6              72 
$`EPHA4 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6586 TCGA-AA-3555 TCGA-AA-3663 
       19.04        19.04        24.00        35.80        29.95         6.97 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-A01V TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
       10.06        33.04         1.02        83.24        21.44        58.39 
TCGA-CA-6719 TCGA-CM-5861 TCGA-D5-6537 TCGA-D5-6928 TCGA-DM-A28F TCGA-F4-6570 
       14.30        15.02         4.80        11.64        35.97         6.18 

$`EPHA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        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-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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  EPHA4 MUTATED EPHA4 WILD-TYPE 
           1.02            0.00 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
          83.24          148.01 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
          19.04           22.09 
[1] "1.0 - 83.2 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1723V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA4 MUTATED         1        0        2        11         1         0
  EPHA4 WILD-TYPE      63        1       24        97         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA4 MUTATED           1          0          2          0        1         0
  EPHA4 WILD-TYPE        17          6         42         33       34        12
                 vv
clus              STAGE IVB
  EPHA4 MUTATED           0
  EPHA4 WILD-TYPE         1
D1723V3, multiclass
            clus
vv           EPHA4 MUTATED EPHA4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             11              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  EPHA4 MUTATED     0   1  17   1
  EPHA4 WILD-TYPE   9  66 232  40
D1723V4, multiclass
    clus
vv   EPHA4 MUTATED EPHA4 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            17             232
  T4             1              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
  EPHA4 MUTATED    16   2   1
  EPHA4 WILD-TYPE 204  79  65
D1723V5, multiclass
    clus
vv   EPHA4 MUTATED EPHA4 WILD-TYPE
  N0            16             204
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1723V6, binary
                 cls
clus                0   1
  EPHA4 MUTATED    15   1
  EPHA4 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     15    1
  EPHA4 WILD-TYPE  270   47
   clus
vv  EPHA4 MUTATED EPHA4 WILD-TYPE
  0            15             270
  1             1              47
[1] 2 2
[1] FALSE
D1723V7, binary
                 cls
clus                0   1
  EPHA4 MUTATED     8  11
  EPHA4 WILD-TYPE 162 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED      8   11
  EPHA4 WILD-TYPE  162  186
        clus
vv       EPHA4 MUTATED EPHA4 WILD-TYPE
  FEMALE             8             162
  MALE              11             186
[1] 2 2
[1] FALSE
D1723V8, binary
                 cls
clus                0   1
  EPHA4 MUTATED    15   1
  EPHA4 WILD-TYPE 285   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     15    1
  EPHA4 WILD-TYPE  285    7
     clus
vv    EPHA4 MUTATED EPHA4 WILD-TYPE
  NO             15             285
  YES             1               7
[1] 2 2
[1] FALSE
D1723V9, binary
                 cls
clus                0   1
  EPHA4 MUTATED    16   3
  EPHA4 WILD-TYPE 298  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     16    3
  EPHA4 WILD-TYPE  298   45
                               clus
vv                              EPHA4 MUTATED EPHA4 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA4 MUTATED    15   0   1   2
  EPHA4 WILD-TYPE 244   3  21  19
D1723V10, multiclass
    clus
vv   EPHA4 MUTATED EPHA4 WILD-TYPE
  R0            15             244
  R1             0               3
  R2             1              21
  RX             2              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"
D1723V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA4 MUTATED                                  0     2
  EPHA4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA4 MUTATED                           0     9
  EPHA4 WILD-TYPE                        19   167
D1723V12, multiclass
                                  clus
vv                                 EPHA4 MUTATED EPHA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(1724) Variable = PARVB MUTATION ANALYSIS
D1724V1, survival
                 sevent
clus2               0   1
  PARVB MUTATED     8   1
  PARVB WILD-TYPE 269  77
  PARVB MUTATED PARVB WILD-TYPE 
              9             346 
  PARVB MUTATED PARVB WILD-TYPE 
              1              77 
$`PARVB MUTATED`
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3664 TCGA-AA-3864 TCGA-AA-3877 TCGA-AU-6004 
       13.02         1.02        54.02        53.00        31.00        27.09 
TCGA-CM-5341 TCGA-CM-5864 TCGA-DM-A1HB 
       29.06        15.02       135.65 

$`PARVB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PARVB MUTATED PARVB WILD-TYPE 
           1.02            0.00 
  PARVB MUTATED PARVB WILD-TYPE 
         135.65          148.01 
  PARVB MUTATED PARVB WILD-TYPE 
          29.06           22.01 
[1] "1.0 - 135.7 (29.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.6"
D1724V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARVB MUTATED         3        0        2         1         0         0
  PARVB WILD-TYPE      61        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PARVB MUTATED           1          1          1          0        0         0
  PARVB WILD-TYPE        17          5         43         33       35        12
                 vv
clus              STAGE IVB
  PARVB MUTATED           0
  PARVB WILD-TYPE         1
D1724V3, multiclass
            clus
vv           PARVB MUTATED PARVB WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PARVB MUTATED     1   3   5   0
  PARVB WILD-TYPE   8  64 244  41
D1724V4, multiclass
    clus
vv   PARVB MUTATED PARVB WILD-TYPE
  T1             1               8
  T2             3              64
  T3             5             244
  T4             0              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
  PARVB MUTATED     6   2   1
  PARVB WILD-TYPE 214  79  65
D1724V5, multiclass
    clus
vv   PARVB MUTATED PARVB WILD-TYPE
  N0             6             214
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1724V6, binary
                 cls
clus                0   1
  PARVB MUTATED     9   0
  PARVB WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARVB MUTATED      9    0
  PARVB WILD-TYPE  276   48
   clus
vv  PARVB MUTATED PARVB WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1724V7, binary
                 cls
clus                0   1
  PARVB MUTATED     6   3
  PARVB WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARVB MUTATED      6    3
  PARVB WILD-TYPE  164  194
        clus
vv       PARVB MUTATED PARVB WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D1724V8, binary
                 cls
clus                0   1
  PARVB MUTATED     6   0
  PARVB WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARVB MUTATED      6    0
  PARVB WILD-TYPE  294    8
     clus
vv    PARVB MUTATED PARVB WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1724V9, binary
                 cls
clus                0   1
  PARVB MUTATED     6   2
  PARVB WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARVB MUTATED      6    2
  PARVB WILD-TYPE  308   46
                               clus
vv                              PARVB MUTATED PARVB WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PARVB MUTATED     7   0   0   0
  PARVB WILD-TYPE 252   3  22  21
D1724V10, multiclass
    clus
vv   PARVB MUTATED PARVB WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1724V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARVB MUTATED                                  0     0
  PARVB WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PARVB MUTATED                           0     4
  PARVB WILD-TYPE                        19   172
D1724V12, multiclass
                                  clus
vv                                 PARVB MUTATED PARVB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = TAF2 MUTATION ANALYSIS
D1725V1, survival
                sevent
clus2              0   1
  TAF2 MUTATED    14   3
  TAF2 WILD-TYPE 263  75
  TAF2 MUTATED TAF2 WILD-TYPE 
            17            338 
  TAF2 MUTATED TAF2 WILD-TYPE 
             3             75 
$`TAF2 MUTATED`
TCGA-AZ-6601 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3561 
      100.01        24.39        20.12        63.98        29.95        13.94 
TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-A010 TCGA-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 
        1.02        31.00        34.98         0.20        58.39        12.76 
TCGA-CA-6718 TCGA-CK-4948 TCGA-D5-6539 TCGA-DM-A1D7 TCGA-G4-6315 
       10.06       148.01        12.49        13.32        61.91 

$`TAF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6654 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       12.20        14.30        17.56        85.45        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TAF2 MUTATED TAF2 WILD-TYPE 
           0.2            0.0 
  TAF2 MUTATED TAF2 WILD-TYPE 
        148.01         140.38 
  TAF2 MUTATED TAF2 WILD-TYPE 
        24.390         22.045 
[1] "0.2 - 148.0 (24.4)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.6"
D1725V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF2 MUTATED         3        0        2         7         1         0
  TAF2 WILD-TYPE      61        1       24       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF2 MUTATED           1          0          0          1        1         0
  TAF2 WILD-TYPE        17          6         44         32       34        12
                vv
clus             STAGE IVB
  TAF2 MUTATED           0
  TAF2 WILD-TYPE         1
D1725V3, multiclass
            clus
vv           TAF2 MUTATED TAF2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  TAF2 MUTATED     1   2  13   1
  TAF2 WILD-TYPE   8  65 236  40
D1725V4, multiclass
    clus
vv   TAF2 MUTATED TAF2 WILD-TYPE
  T1            1              8
  T2            2             65
  T3           13            236
  T4            1             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
  TAF2 MUTATED    14   2   1
  TAF2 WILD-TYPE 206  79  65
D1725V5, multiclass
    clus
vv   TAF2 MUTATED TAF2 WILD-TYPE
  N0           14            206
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1725V6, binary
                cls
clus               0   1
  TAF2 MUTATED    14   1
  TAF2 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED     14    1
  TAF2 WILD-TYPE  271   47
   clus
vv  TAF2 MUTATED TAF2 WILD-TYPE
  0           14            271
  1            1             47
[1] 2 2
[1] FALSE
D1725V7, binary
                cls
clus               0   1
  TAF2 MUTATED     6  11
  TAF2 WILD-TYPE 164 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED      6   11
  TAF2 WILD-TYPE  164  186
        clus
vv       TAF2 MUTATED TAF2 WILD-TYPE
  FEMALE            6            164
  MALE             11            186
[1] 2 2
[1] FALSE
D1725V8, binary
                cls
clus               0   1
  TAF2 MUTATED    15   0
  TAF2 WILD-TYPE 285   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED     15    0
  TAF2 WILD-TYPE  285    8
     clus
vv    TAF2 MUTATED TAF2 WILD-TYPE
  NO            15            285
  YES            0              8
[1] 2 2
[1] FALSE
D1725V9, binary
                cls
clus               0   1
  TAF2 MUTATED    10   6
  TAF2 WILD-TYPE 304  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED     10    6
  TAF2 WILD-TYPE  304   42
                               clus
vv                              TAF2 MUTATED TAF2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAF2 MUTATED    11   0   0   2
  TAF2 WILD-TYPE 248   3  22  19
D1725V10, multiclass
    clus
vv   TAF2 MUTATED TAF2 WILD-TYPE
  R0           11            248
  R1            0              3
  R2            0             22
  RX            2             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"
D1725V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF2 MUTATED                                  0     2
  TAF2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF2 MUTATED                           0     9
  TAF2 WILD-TYPE                        19   167
D1725V12, multiclass
                                  clus
vv                                 TAF2 MUTATED TAF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(1726) Variable = KIAA0196 MUTATION ANALYSIS
D1726V1, survival
                    sevent
clus2                  0   1
  KIAA0196 MUTATED     7   3
  KIAA0196 WILD-TYPE 270  75
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                10                345 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                 3                 75 
$`KIAA0196 MUTATED`
TCGA-AA-3525 TCGA-AZ-6608 TCGA-AA-3518 TCGA-AA-A010 TCGA-AY-6197 TCGA-CA-6716 
        8.05         1.94         1.02        34.98        21.44        12.20 
TCGA-CM-6162 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-F4-6856 
       12.00        92.75        13.32        35.31 

$`KIAA0196 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        49.91        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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
              1.02               0.00 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
             92.75             148.01 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
             12.76              22.09 
[1] "1.0 - 92.8 (12.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1726V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0196 MUTATED         1        0        0         5         1         0
  KIAA0196 WILD-TYPE      63        1       26       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0196 MUTATED           0          1          2          0        0
  KIAA0196 WILD-TYPE        18          5         42         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0196 MUTATED           0         0
  KIAA0196 WILD-TYPE        12         1
D1726V3, multiclass
            clus
vv           KIAA0196 MUTATED KIAA0196 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 5                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                1                  5
  STAGE IIIB                2                 42
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  KIAA0196 MUTATED     0   2   7   1
  KIAA0196 WILD-TYPE   9  65 242  40
D1726V4, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  T1                0                  9
  T2                2                 65
  T3                7                242
  T4                1                 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
  KIAA0196 MUTATED     7   3   0
  KIAA0196 WILD-TYPE 213  78  66
D1726V5, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  N0                7                213
  N1                3                 78
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1726V6, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     9   0
  KIAA0196 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      9    0
  KIAA0196 WILD-TYPE  276   48
   clus
vv  KIAA0196 MUTATED KIAA0196 WILD-TYPE
  0                9                276
  1                0                 48
[1] 2 2
[1] FALSE
D1726V7, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     4   6
  KIAA0196 WILD-TYPE 166 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      4    6
  KIAA0196 WILD-TYPE  166  191
        clus
vv       KIAA0196 MUTATED KIAA0196 WILD-TYPE
  FEMALE                4                166
  MALE                  6                191
[1] 2 2
[1] FALSE
D1726V8, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     7   0
  KIAA0196 WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      7    0
  KIAA0196 WILD-TYPE  293    8
     clus
vv    KIAA0196 MUTATED KIAA0196 WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1726V9, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     7   2
  KIAA0196 WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      7    2
  KIAA0196 WILD-TYPE  307   46
                               clus
vv                              KIAA0196 MUTATED KIAA0196 WILD-TYPE
  COLON ADENOCARCINOMA                         7                307
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0196 MUTATED     6   0   0   1
  KIAA0196 WILD-TYPE 253   3  22  20
D1726V10, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1726V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0196 MUTATED                                  0     1
  KIAA0196 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0196 MUTATED                           0     6
  KIAA0196 WILD-TYPE                        19   170
D1726V12, multiclass
                                  clus
vv                                 KIAA0196 MUTATED KIAA0196 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = FRY MUTATION ANALYSIS
D1727V1, survival
               sevent
clus2             0   1
  FRY MUTATED    30   8
  FRY WILD-TYPE 247  70
  FRY MUTATED FRY WILD-TYPE 
           38           317 
  FRY MUTATED FRY WILD-TYPE 
            8            70 
$`FRY MUTATED`
TCGA-A6-4105 TCGA-G4-6628 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 
       14.53        79.69        33.34        32.75        33.53        22.06 
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        8.38         3.02         6.97        53.00        31.00        33.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02O 
       25.02         4.01        34.98        38.07        35.01         0.92 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 
       18.05        12.16        27.09        21.44        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5861 
       12.76        10.06        37.02        25.02        32.02        15.02 
TCGA-CM-6168 TCGA-D5-6538 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-F4-6703 TCGA-F4-6806 
       12.99        17.13       119.70         7.50        47.87        41.42 
TCGA-F4-6855 TCGA-G4-6307 
       47.41        55.04 

$`FRY WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       42.90        42.28        16.57        34.65        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-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       17.03        27.02        18.05         2.01        24.00        26.01 
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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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-A029 
        1.02        33.04         1.02        26.01        37.02        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-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       20.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        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-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        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-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  FRY MUTATED FRY WILD-TYPE 
         0.92          0.00 
  FRY MUTATED FRY WILD-TYPE 
       119.70        148.01 
  FRY MUTATED FRY WILD-TYPE 
       29.045        21.990 
[1] "0.9 - 119.7 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1727V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRY MUTATED         6        0        5        15         4         0
  FRY WILD-TYPE      58        1       21        93         4         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRY MUTATED           3          0          2          1        0         1
  FRY WILD-TYPE        15          6         42         32       35        11
               vv
clus            STAGE IVB
  FRY MUTATED           0
  FRY WILD-TYPE         1
D1727V3, multiclass
            clus
vv           FRY MUTATED FRY WILD-TYPE
  STAGE I              6            58
  STAGE IA             0             1
  STAGE II             5            21
  STAGE IIA           15            93
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            3            15
  STAGE IIIA           0             6
  STAGE IIIB           2            42
  STAGE IIIC           1            32
  STAGE IV             0            35
  STAGE IVA            1            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
  FRY MUTATED     1   6  26   5
  FRY WILD-TYPE   8  61 223  36
D1727V4, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  T1           1             8
  T2           6            61
  T3          26           223
  T4           5            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
  FRY MUTATED    31   3   4
  FRY WILD-TYPE 189  78  62
D1727V5, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  N0          31           189
  N1           3            78
  N2           4            62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1727V6, binary
               cls
clus              0   1
  FRY MUTATED    33   1
  FRY WILD-TYPE 252  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     33    1
  FRY WILD-TYPE  252   47
   clus
vv  FRY MUTATED FRY WILD-TYPE
  0          33           252
  1           1            47
[1] 2 2
[1] FALSE
D1727V7, binary
               cls
clus              0   1
  FRY MUTATED    19  19
  FRY WILD-TYPE 151 178
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     19   19
  FRY WILD-TYPE  151  178
        clus
vv       FRY MUTATED FRY WILD-TYPE
  FEMALE          19           151
  MALE            19           178
[1] 2 2
[1] FALSE
D1727V8, binary
               cls
clus              0   1
  FRY MUTATED    32   1
  FRY WILD-TYPE 268   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     32    1
  FRY WILD-TYPE  268    7
     clus
vv    FRY MUTATED FRY WILD-TYPE
  NO           32           268
  YES           1             7
[1] 2 2
[1] FALSE
D1727V9, binary
               cls
clus              0   1
  FRY MUTATED    30   8
  FRY WILD-TYPE 284  40
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     30    8
  FRY WILD-TYPE  284   40
                               clus
vv                              FRY MUTATED FRY WILD-TYPE
  COLON ADENOCARCINOMA                   30           284
  COLON MUCINOUS ADENOCARCINOMA           8            40
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FRY MUTATED    30   0   0   2
  FRY WILD-TYPE 229   3  22  19
D1727V10, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  R0          30           229
  R1           0             3
  R2           0            22
  RX           2            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"
D1727V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRY MUTATED                                  0     2
  FRY WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FRY MUTATED                           4    20
  FRY WILD-TYPE                        15   156
D1727V12, multiclass
                                  clus
vv                                 FRY MUTATED FRY WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  4            15
  WHITE                                     20           156
[1] 4 2
[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 = EIF2AK3 MUTATION ANALYSIS
D1728V1, survival
                   sevent
clus2                 0   1
  EIF2AK3 MUTATED     7   4
  EIF2AK3 WILD-TYPE 270  74
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               11               344 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                4                74 
$`EIF2AK3 MUTATED`
TCGA-AZ-4681 TCGA-A6-6141 TCGA-AA-3966 TCGA-AD-6899 TCGA-AZ-4323 TCGA-CA-6717 
      106.75         8.38         2.01         5.79         1.41        12.76 
TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6674 TCGA-F4-6570 TCGA-F4-6856 
        5.03        12.00        12.95         6.18        35.31 

$`EIF2AK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         5.13        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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
             1.41              0.00 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
           106.75            148.01 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
             8.38             22.39 
[1] "1.4 - 106.8 (8.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.4"
D1728V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2AK3 MUTATED         1        0        0         6         0         0
  EIF2AK3 WILD-TYPE      63        1       26       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2AK3 MUTATED           0          0          1          1        1
  EIF2AK3 WILD-TYPE        18          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  EIF2AK3 MUTATED           1         0
  EIF2AK3 WILD-TYPE        11         1
D1728V3, multiclass
            clus
vv           EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                6               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                1                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
  EIF2AK3 MUTATED     0   1   8   2
  EIF2AK3 WILD-TYPE   9  66 241  39
D1728V4, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               8               241
  T4               2                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
  EIF2AK3 MUTATED     7   2   2
  EIF2AK3 WILD-TYPE 213  79  64
D1728V5, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  N0               7               213
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1728V6, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     8   2
  EIF2AK3 WILD-TYPE 277  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      8    2
  EIF2AK3 WILD-TYPE  277   46
   clus
vv  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  0               8               277
  1               2                46
[1] 2 2
[1] FALSE
D1728V7, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     4   7
  EIF2AK3 WILD-TYPE 166 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      4    7
  EIF2AK3 WILD-TYPE  166  190
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  FEMALE               4               166
  MALE                 7               190
[1] 2 2
[1] FALSE
D1728V8, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED    10   0
  EIF2AK3 WILD-TYPE 290   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED     10    0
  EIF2AK3 WILD-TYPE  290    8
     clus
vv    EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  NO               10               290
  YES               0                 8
[1] 2 2
[1] FALSE
D1728V9, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     6   5
  EIF2AK3 WILD-TYPE 308  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      6    5
  EIF2AK3 WILD-TYPE  308   43
                               clus
vv                              EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EIF2AK3 MUTATED     6   0   0   1
  EIF2AK3 WILD-TYPE 253   3  22  20
D1728V10, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               1                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"
D1728V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2AK3 MUTATED                                  0     1
  EIF2AK3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EIF2AK3 MUTATED                           1     8
  EIF2AK3 WILD-TYPE                        18   168
D1728V12, multiclass
                                  clus
vv                                 EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          8               168
[1] 4 2
[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 = IFI35 MUTATION ANALYSIS
D1729V1, survival
                 sevent
clus2               0   1
  IFI35 MUTATED     4   4
  IFI35 WILD-TYPE 273  74
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             347 
  IFI35 MUTATED IFI35 WILD-TYPE 
              4              74 
$`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-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6626 
       44.68        55.04        85.48        61.91        46.75 

  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          22.060 
[1] "4.0 - 130.7 (21.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2"  
D1729V2, continuous
                 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      64        0       25       105         7         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        18          6         44         31       35        12
                 vv
clus              STAGE IVB
  IFI35 MUTATED           0
  IFI35 WILD-TYPE         1
D1729V3, multiclass
            clus
vv           IFI35 MUTATED IFI35 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  IFI35 MUTATED     0   0   6   1
  IFI35 WILD-TYPE   9  67 243  40
D1729V4, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  IFI35 MUTATED     6   0   2
  IFI35 WILD-TYPE 214  81  64
D1729V5, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  N0             6             214
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1729V6, binary
                 cls
clus                0   1
  IFI35 MUTATED     6   0
  IFI35 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      6    0
  IFI35 WILD-TYPE  279   48
   clus
vv  IFI35 MUTATED IFI35 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1729V7, binary
                 cls
clus                0   1
  IFI35 MUTATED     4   4
  IFI35 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      4    4
  IFI35 WILD-TYPE  166  193
        clus
vv       IFI35 MUTATED IFI35 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D1729V8, binary
                 cls
clus                0   1
  IFI35 MUTATED     5   0
  IFI35 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      5    0
  IFI35 WILD-TYPE  295    8
     clus
vv    IFI35 MUTATED IFI35 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1729V9, binary
                 cls
clus                0   1
  IFI35 MUTATED     7   1
  IFI35 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      7    1
  IFI35 WILD-TYPE  307   47
                               clus
vv                              IFI35 MUTATED IFI35 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IFI35 MUTATED     6   0   0   0
  IFI35 WILD-TYPE 253   3  22  21
D1729V10, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1729V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFI35 MUTATED                                  0     0
  IFI35 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFI35 MUTATED                           1     5
  IFI35 WILD-TYPE                        18   171
D1729V12, multiclass
                                  clus
vv                                 IFI35 MUTATED IFI35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = MYPN MUTATION ANALYSIS
D1730V1, survival
                sevent
clus2              0   1
  MYPN MUTATED    15   3
  MYPN WILD-TYPE 262  75
  MYPN MUTATED MYPN WILD-TYPE 
            18            337 
  MYPN MUTATED MYPN WILD-TYPE 
             3             75 
$`MYPN MUTATED`
TCGA-AA-3530 TCGA-AA-3672 TCGA-AZ-6608 TCGA-G4-6588 TCGA-A6-6141 TCGA-A6-6781 
       19.07         0.92         1.94        26.17         8.38        19.66 
TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3851 TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-A00N 
        3.02        33.04        33.07        33.01        34.03         4.01 
TCGA-AA-A01I TCGA-CA-6717 TCGA-CM-6676 TCGA-D5-6930 TCGA-DM-A28H TCGA-G4-6309 
       31.00        12.76        11.08        13.35       117.07        85.48 

$`MYPN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         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-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        26.01        20.98         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MYPN MUTATED MYPN WILD-TYPE 
          0.92           0.00 
  MYPN MUTATED MYPN WILD-TYPE 
        117.07         148.01 
  MYPN MUTATED MYPN WILD-TYPE 
        19.365         22.090 
[1] "0.9 - 117.1 (19.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1730V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYPN MUTATED         3        0        1         8         2         0
  MYPN WILD-TYPE      61        1       25       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYPN MUTATED           1          1          1          2        0         0
  MYPN WILD-TYPE        17          5         43         31       35        12
                vv
clus             STAGE IVB
  MYPN MUTATED           0
  MYPN WILD-TYPE         1
D1730V3, multiclass
            clus
vv           MYPN MUTATED MYPN WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             8            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            1              5
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  MYPN MUTATED     0   4  12   3
  MYPN WILD-TYPE   9  63 237  38
D1730V4, multiclass
    clus
vv   MYPN MUTATED MYPN WILD-TYPE
  T1            0              9
  T2            4             63
  T3           12            237
  T4            3             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
  MYPN MUTATED    14   4   1
  MYPN WILD-TYPE 206  77  65
D1730V5, multiclass
    clus
vv   MYPN MUTATED MYPN WILD-TYPE
  N0           14            206
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1730V6, binary
                cls
clus               0   1
  MYPN MUTATED    18   0
  MYPN WILD-TYPE 267  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYPN MUTATED     18    0
  MYPN WILD-TYPE  267   48
   clus
vv  MYPN MUTATED MYPN WILD-TYPE
  0           18            267
  1            0             48
[1] 2 2
[1] FALSE
D1730V7, binary
                cls
clus               0   1
  MYPN MUTATED     8  11
  MYPN WILD-TYPE 162 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYPN MUTATED      8   11
  MYPN WILD-TYPE  162  186
        clus
vv       MYPN MUTATED MYPN WILD-TYPE
  FEMALE            8            162
  MALE             11            186
[1] 2 2
[1] FALSE
D1730V8, binary
                cls
clus               0   1
  MYPN MUTATED    16   0
  MYPN WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYPN MUTATED     16    0
  MYPN WILD-TYPE  284    8
     clus
vv    MYPN MUTATED MYPN WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D1730V9, binary
                cls
clus               0   1
  MYPN MUTATED    14   5
  MYPN WILD-TYPE 300  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYPN MUTATED     14    5
  MYPN WILD-TYPE  300   43
                               clus
vv                              MYPN MUTATED MYPN WILD-TYPE
  COLON ADENOCARCINOMA                    14            300
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYPN MUTATED    15   0   0   1
  MYPN WILD-TYPE 244   3  22  20
D1730V10, multiclass
    clus
vv   MYPN MUTATED MYPN WILD-TYPE
  R0           15            244
  R1            0              3
  R2            0             22
  RX            1             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"
D1730V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYPN MUTATED                                  0     1
  MYPN WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYPN MUTATED                           2     6
  MYPN WILD-TYPE                        17   170
D1730V12, multiclass
                                  clus
vv                                 MYPN MUTATED MYPN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             17
  WHITE                                       6            170
[1] 4 2
[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 = DTD1 MUTATION ANALYSIS
D1731V1, survival
                sevent
clus2              0   1
  DTD1 MUTATED     2   2
  DTD1 WILD-TYPE 275  76
  DTD1 MUTATED DTD1 WILD-TYPE 
             4            351 
  DTD1 MUTATED DTD1 WILD-TYPE 
             2             76 
$`DTD1 MUTATED`
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6600 TCGA-DM-A1D9 
       83.24        21.44        12.10       140.38 

$`DTD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DTD1 MUTATED DTD1 WILD-TYPE 
          12.1            0.0 
  DTD1 MUTATED DTD1 WILD-TYPE 
        140.38         148.01 
  DTD1 MUTATED DTD1 WILD-TYPE 
         52.34          22.06 
[1] "12.1 - 140.4 (52.3)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.2"
D1731V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DTD1 MUTATED         0        0        0         3         0         0
  DTD1 WILD-TYPE      64        1       26       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DTD1 MUTATED           0          0          0          0        2         0
  DTD1 WILD-TYPE        18          6         44         33       33        12
                vv
clus             STAGE IVB
  DTD1 MUTATED           0
  DTD1 WILD-TYPE         1
D1731V3, multiclass
            clus
vv           DTD1 MUTATED DTD1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              2             33
  STAGE IVA             0             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
  DTD1 MUTATED     0   0   3   2
  DTD1 WILD-TYPE   9  67 246  39
D1731V4, multiclass
    clus
vv   DTD1 MUTATED DTD1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            3            246
  T4            2             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
  DTD1 MUTATED     3   2   0
  DTD1 WILD-TYPE 217  79  66
D1731V5, multiclass
    clus
vv   DTD1 MUTATED DTD1 WILD-TYPE
  N0            3            217
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1731V6, binary
                cls
clus               0   1
  DTD1 MUTATED     2   2
  DTD1 WILD-TYPE 283  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTD1 MUTATED      2    2
  DTD1 WILD-TYPE  283   46
   clus
vv  DTD1 MUTATED DTD1 WILD-TYPE
  0            2            283
  1            2             46
[1] 2 2
[1] FALSE
D1731V7, binary
                cls
clus               0   1
  DTD1 MUTATED     2   3
  DTD1 WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTD1 MUTATED      2    3
  DTD1 WILD-TYPE  168  194
        clus
vv       DTD1 MUTATED DTD1 WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D1731V8, binary
                cls
clus               0   1
  DTD1 MUTATED     3   0
  DTD1 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTD1 MUTATED      3    0
  DTD1 WILD-TYPE  297    8
     clus
vv    DTD1 MUTATED DTD1 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1731V9, binary
                cls
clus               0   1
  DTD1 MUTATED     5   0
  DTD1 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTD1 MUTATED      5    0
  DTD1 WILD-TYPE  309   48
                               clus
vv                              DTD1 MUTATED DTD1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DTD1 MUTATED     2   0   1   0
  DTD1 WILD-TYPE 257   3  21  21
D1731V10, multiclass
    clus
vv   DTD1 MUTATED DTD1 WILD-TYPE
  R0            2            257
  R1            0              3
  R2            1             21
  RX            0             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"
D1731V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DTD1 MUTATED                                  0     1
  DTD1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DTD1 MUTATED                           1     2
  DTD1 WILD-TYPE                        18   174
D1731V12, multiclass
                                  clus
vv                                 DTD1 MUTATED DTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       2            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(1732) Variable = MGAT5 MUTATION ANALYSIS
D1732V1, survival
                 sevent
clus2               0   1
  MGAT5 MUTATED     9   3
  MGAT5 WILD-TYPE 268  75
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             12             343 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
              3              75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6323 
       65.85        53.62        44.68        55.04        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.030 
[1] "3.0 - 85.5 (31.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1732V2, continuous
                 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      64        1       23       105         7         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        18          6         39         33       34        12
                 vv
clus              STAGE IVB
  MGAT5 MUTATED           0
  MGAT5 WILD-TYPE         1
D1732V3, multiclass
            clus
vv           MGAT5 MUTATED MGAT5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  MGAT5 MUTATED     0   0  11   2
  MGAT5 WILD-TYPE   9  67 238  39
D1732V4, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            11             238
  T4             2              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
  MGAT5 MUTATED     7   6   0
  MGAT5 WILD-TYPE 213  75  66
D1732V5, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  N0             7             213
  N1             6              75
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1732V6, binary
                 cls
clus                0   1
  MGAT5 MUTATED    10   1
  MGAT5 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     10    1
  MGAT5 WILD-TYPE  275   47
   clus
vv  MGAT5 MUTATED MGAT5 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1732V7, binary
                 cls
clus                0   1
  MGAT5 MUTATED     5   8
  MGAT5 WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED      5    8
  MGAT5 WILD-TYPE  165  189
        clus
vv       MGAT5 MUTATED MGAT5 WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D1732V8, binary
                 cls
clus                0   1
  MGAT5 MUTATED    12   0
  MGAT5 WILD-TYPE 288   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     12    0
  MGAT5 WILD-TYPE  288    8
     clus
vv    MGAT5 MUTATED MGAT5 WILD-TYPE
  NO             12             288
  YES             0               8
[1] 2 2
[1] FALSE
D1732V9, binary
                 cls
clus                0   1
  MGAT5 MUTATED    11   2
  MGAT5 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     11    2
  MGAT5 WILD-TYPE  303   46
                               clus
vv                              MGAT5 MUTATED MGAT5 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MGAT5 MUTATED     9   0   0   2
  MGAT5 WILD-TYPE 250   3  22  19
D1732V10, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             2              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"
D1732V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGAT5 MUTATED                                  0     1
  MGAT5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MGAT5 MUTATED                           1     7
  MGAT5 WILD-TYPE                        18   169
D1732V12, multiclass
                                  clus
vv                                 MGAT5 MUTATED MGAT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = GLUD2 MUTATION ANALYSIS
D1733V1, survival
                 sevent
clus2               0   1
  GLUD2 MUTATED    15   5
  GLUD2 WILD-TYPE 262  73
  GLUD2 MUTATED GLUD2 WILD-TYPE 
             20             335 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
              5              73 
$`GLUD2 MUTATED`
TCGA-AD-6895 TCGA-G4-6586 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3558 TCGA-AA-3663 
       25.08        35.80        32.75         3.02        20.98         6.97 
TCGA-AA-3956 TCGA-AA-3994 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-4950 
       34.03        27.02         4.01        27.09        12.76        85.45 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-D5-6537 TCGA-DM-A0X9 TCGA-F4-6459 
       82.95       124.27        23.05         4.80       119.70         8.61 
TCGA-G4-6303 TCGA-G4-6309 
       65.85        85.48 

$`GLUD2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        27.02         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4744 
       15.62        51.32        21.99        21.14         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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-F4-6460 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  GLUD2 MUTATED GLUD2 WILD-TYPE 
           3.02            0.00 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
         124.27          148.01 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
         27.055          21.990 
[1] "3.0 - 124.3 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1733V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLUD2 MUTATED         3        0        2         6         2         0
  GLUD2 WILD-TYPE      61        1       24       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLUD2 MUTATED           0          0          6          0        1         0
  GLUD2 WILD-TYPE        18          6         38         33       34        12
                 vv
clus              STAGE IVB
  GLUD2 MUTATED           0
  GLUD2 WILD-TYPE         1
D1733V3, multiclass
            clus
vv           GLUD2 MUTATED GLUD2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             6              38
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  GLUD2 MUTATED     0   3  15   2
  GLUD2 WILD-TYPE   9  64 234  39
D1733V4, multiclass
    clus
vv   GLUD2 MUTATED GLUD2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            15             234
  T4             2              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
  GLUD2 MUTATED    13   6   1
  GLUD2 WILD-TYPE 207  75  65
D1733V5, multiclass
    clus
vv   GLUD2 MUTATED GLUD2 WILD-TYPE
  N0            13             207
  N1             6              75
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1733V6, binary
                 cls
clus                0   1
  GLUD2 MUTATED    16   1
  GLUD2 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLUD2 MUTATED     16    1
  GLUD2 WILD-TYPE  269   47
   clus
vv  GLUD2 MUTATED GLUD2 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D1733V7, binary
                 cls
clus                0   1
  GLUD2 MUTATED    11   9
  GLUD2 WILD-TYPE 159 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLUD2 MUTATED     11    9
  GLUD2 WILD-TYPE  159  188
        clus
vv       GLUD2 MUTATED GLUD2 WILD-TYPE
  FEMALE            11             159
  MALE               9             188
[1] 2 2
[1] FALSE
D1733V8, binary
                 cls
clus                0   1
  GLUD2 MUTATED    17   0
  GLUD2 WILD-TYPE 283   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLUD2 MUTATED     17    0
  GLUD2 WILD-TYPE  283    8
     clus
vv    GLUD2 MUTATED GLUD2 WILD-TYPE
  NO             17             283
  YES             0               8
[1] 2 2
[1] FALSE
D1733V9, binary
                 cls
clus                0   1
  GLUD2 MUTATED    14   6
  GLUD2 WILD-TYPE 300  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLUD2 MUTATED     14    6
  GLUD2 WILD-TYPE  300   42
                               clus
vv                              GLUD2 MUTATED GLUD2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GLUD2 MUTATED    14   1   1   3
  GLUD2 WILD-TYPE 245   2  21  18
D1733V10, multiclass
    clus
vv   GLUD2 MUTATED GLUD2 WILD-TYPE
  R0            14             245
  R1             1               2
  R2             1              21
  RX             3              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"
D1733V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLUD2 MUTATED                                  0     1
  GLUD2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GLUD2 MUTATED                           2    11
  GLUD2 WILD-TYPE                        17   165
D1733V12, multiclass
                                  clus
vv                                 GLUD2 MUTATED GLUD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                       11             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(1734) Variable = PTPRZ1 MUTATION ANALYSIS
D1734V1, survival
                  sevent
clus2                0   1
  PTPRZ1 MUTATED    21   7
  PTPRZ1 WILD-TYPE 256  71
  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
              28              327 
  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
               7               71 
$`PTPRZ1 MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3715 TCGA-A6-5665 TCGA-A6-6653 
        1.02        13.02         0.92        19.04        22.06        24.39 
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00W 
       63.98        29.95        34.03        25.02         4.01        14.99 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4616 
       34.98        12.16        22.42         0.20        17.82         5.13 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-6164 TCGA-CM-6678 TCGA-D5-6922 TCGA-D5-6930 
       12.76        85.45        29.03        11.01        10.13        13.35 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A28E TCGA-DM-A28K 
       92.75        13.32       119.93        98.24 

$`PTPRZ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        5.88        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       17.03        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       40.96        83.24        24.53         5.79        27.42        26.47 
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-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41        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        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        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 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28F 
       44.32       131.51       135.65       139.17        81.37        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
             0.2              0.0 
  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
          119.93           148.01 
  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE 
           18.43            22.09 
[1] "0.2 - 119.9 (18.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1734V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRZ1 MUTATED         3        0        3        10         2         0
  PTPRZ1 WILD-TYPE      61        1       23        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPRZ1 MUTATED           2          1          2          1        1
  PTPRZ1 WILD-TYPE        16          5         42         32       34
                  vv
clus               STAGE IVA STAGE IVB
  PTPRZ1 MUTATED           1         0
  PTPRZ1 WILD-TYPE        11         1
D1734V3, multiclass
            clus
vv           PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA              10               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              1                5
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  PTPRZ1 MUTATED     1   3  21   3
  PTPRZ1 WILD-TYPE   8  64 228  38
D1734V4, multiclass
    clus
vv   PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  T1              1                8
  T2              3               64
  T3             21              228
  T4              3               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
  PTPRZ1 MUTATED    20   5   3
  PTPRZ1 WILD-TYPE 200  76  63
D1734V5, multiclass
    clus
vv   PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  N0             20              200
  N1              5               76
  N2              3               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"
D1734V6, binary
                  cls
clus                 0   1
  PTPRZ1 MUTATED    22   2
  PTPRZ1 WILD-TYPE 263  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPRZ1 MUTATED     22    2
  PTPRZ1 WILD-TYPE  263   46
   clus
vv  PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  0             22              263
  1              2               46
[1] 2 2
[1] FALSE
D1734V7, binary
                  cls
clus                 0   1
  PTPRZ1 MUTATED    12  16
  PTPRZ1 WILD-TYPE 158 181
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPRZ1 MUTATED     12   16
  PTPRZ1 WILD-TYPE  158  181
        clus
vv       PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  FEMALE             12              158
  MALE               16              181
[1] 2 2
[1] FALSE
D1734V8, binary
                  cls
clus                 0   1
  PTPRZ1 MUTATED    21   0
  PTPRZ1 WILD-TYPE 279   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPRZ1 MUTATED     21    0
  PTPRZ1 WILD-TYPE  279    8
     clus
vv    PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  NO              21              279
  YES              0                8
[1] 2 2
[1] FALSE
D1734V9, binary
                  cls
clus                 0   1
  PTPRZ1 MUTATED    18   9
  PTPRZ1 WILD-TYPE 296  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPRZ1 MUTATED     18    9
  PTPRZ1 WILD-TYPE  296   39
                               clus
vv                              PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              296
  COLON MUCINOUS ADENOCARCINOMA              9               39
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPRZ1 MUTATED    17   1   0   1
  PTPRZ1 WILD-TYPE 242   2  22  20
D1734V10, multiclass
    clus
vv   PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  R0             17              242
  R1              1                2
  R2              0               22
  RX              1               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"
D1734V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRZ1 MUTATED                                  0     1
  PTPRZ1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPRZ1 MUTATED                           2    14
  PTPRZ1 WILD-TYPE                        17   162
D1734V12, multiclass
                                  clus
vv                                 PTPRZ1 MUTATED PTPRZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                        14              162
[1] 4 2
[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 = C3ORF27 MUTATION ANALYSIS
D1735V1, survival
                   sevent
clus2                 0   1
  C3ORF27 MUTATED     2   1
  C3ORF27 WILD-TYPE 275  77
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               352 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                1                77 
$`C3ORF27 MUTATED`
TCGA-AA-3850 TCGA-AA-A010 TCGA-D5-6923 
        0.00        34.98        12.43 

$`C3ORF27 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                0                 0 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
            34.98            148.01 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
           12.430            22.075 
[1] "0.0 - 35.0 (12.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.9"
D1735V2, continuous
                   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      62        1       26       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF27 MUTATED           0          0          0          0        0
  C3ORF27 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C3ORF27 MUTATED           0         0
  C3ORF27 WILD-TYPE        12         1
D1735V3, multiclass
            clus
vv           C3ORF27 MUTATED C3ORF27 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                0               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C3ORF27 MUTATED     0   2   0   1
  C3ORF27 WILD-TYPE   9  65 249  40
D1735V4, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               0               249
  T4               1                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
  C3ORF27 MUTATED     3   0   0
  C3ORF27 WILD-TYPE 217  81  66
D1735V5, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  N0               3               217
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1735V6, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     3   0
  C3ORF27 WILD-TYPE 282  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      3    0
  C3ORF27 WILD-TYPE  282   48
   clus
vv  C3ORF27 MUTATED C3ORF27 WILD-TYPE
  0               3               282
  1               0                48
[1] 2 2
[1] FALSE
D1735V7, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     1   2
  C3ORF27 WILD-TYPE 169 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      1    2
  C3ORF27 WILD-TYPE  169  195
        clus
vv       C3ORF27 MUTATED C3ORF27 WILD-TYPE
  FEMALE               1               169
  MALE                 2               195
[1] 2 2
[1] FALSE
D1735V8, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     2   0
  C3ORF27 WILD-TYPE 298   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      2    0
  C3ORF27 WILD-TYPE  298    8
     clus
vv    C3ORF27 MUTATED C3ORF27 WILD-TYPE
  NO                2               298
  YES               0                 8
[1] 2 2
[1] FALSE
D1735V9, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     3   0
  C3ORF27 WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      3    0
  C3ORF27 WILD-TYPE  311   48
                               clus
vv                              C3ORF27 MUTATED C3ORF27 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C3ORF27 MUTATED     3   0   0   0
  C3ORF27 WILD-TYPE 256   3  22  21
D1735V10, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D1735V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3ORF27 MUTATED                                  0     0
  C3ORF27 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C3ORF27 MUTATED                           0     1
  C3ORF27 WILD-TYPE                        19   175
D1735V12, multiclass
[1] "Remove cluster labels:" "C3ORF27 MUTATED"       
clus
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                1               205 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6600        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6607        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-5913        TCGA-CK-5914 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6924 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6309        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6626 
"C3ORF27 WILD-TYPE" 

Clustering(1736) Variable = CCT4 MUTATION ANALYSIS
D1736V1, survival
                sevent
clus2              0   1
  CCT4 MUTATED    10   1
  CCT4 WILD-TYPE 267  77
  CCT4 MUTATED CCT4 WILD-TYPE 
            11            344 
  CCT4 MUTATED CCT4 WILD-TYPE 
             1             77 
$`CCT4 MUTATED`
TCGA-AA-3496 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6310 TCGA-G4-6628 
        1.02        19.04        24.00        25.08        63.62        79.69 
TCGA-A6-6780 TCGA-CM-5341 TCGA-D5-5538 TCGA-D5-6536 TCGA-D5-6538 
       20.12        29.06        54.61        17.85        17.13 

$`CCT4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 
        5.88        22.09        35.80        26.17        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCT4 MUTATED CCT4 WILD-TYPE 
          1.02           0.00 
  CCT4 MUTATED CCT4 WILD-TYPE 
         79.69         148.01 
  CCT4 MUTATED CCT4 WILD-TYPE 
        24.000         22.045 
[1] "1.0 - 79.7 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.9"
D1736V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCT4 MUTATED         1        0        1         4         0         0
  CCT4 WILD-TYPE      63        1       25       104         8         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        18          5         40         33       34        12
                vv
clus             STAGE IVB
  CCT4 MUTATED           0
  CCT4 WILD-TYPE         1
D1736V3, multiclass
            clus
vv           CCT4 MUTATED CCT4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            4             40
  STAGE IIIC            0             33
  STAGE IV              1             34
  STAGE IVA             0             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
  CCT4 MUTATED     0   2  10   0
  CCT4 WILD-TYPE   9  65 239  41
D1736V4, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           10            239
  T4            0             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
  CCT4 MUTATED     7   4   1
  CCT4 WILD-TYPE 213  77  65
D1736V5, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  N0            7            213
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1736V6, binary
                cls
clus               0   1
  CCT4 MUTATED    10   1
  CCT4 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED     10    1
  CCT4 WILD-TYPE  275   47
   clus
vv  CCT4 MUTATED CCT4 WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D1736V7, binary
                cls
clus               0   1
  CCT4 MUTATED     6   6
  CCT4 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED      6    6
  CCT4 WILD-TYPE  164  191
        clus
vv       CCT4 MUTATED CCT4 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D1736V8, binary
                cls
clus               0   1
  CCT4 MUTATED     8   2
  CCT4 WILD-TYPE 292   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED      8    2
  CCT4 WILD-TYPE  292    6
     clus
vv    CCT4 MUTATED CCT4 WILD-TYPE
  NO             8            292
  YES            2              6
[1] 2 2
[1] FALSE
D1736V9, binary
                cls
clus               0   1
  CCT4 MUTATED    10   2
  CCT4 WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED     10    2
  CCT4 WILD-TYPE  304   46
                               clus
vv                              CCT4 MUTATED CCT4 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCT4 MUTATED    10   0   1   0
  CCT4 WILD-TYPE 249   3  21  21
D1736V10, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            0             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"
D1736V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCT4 MUTATED                                  0     0
  CCT4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCT4 MUTATED                           0     8
  CCT4 WILD-TYPE                        19   168
D1736V12, multiclass
                                  clus
vv                                 CCT4 MUTATED CCT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = PON3 MUTATION ANALYSIS
D1737V1, survival
                sevent
clus2              0   1
  PON3 MUTATED     7   3
  PON3 WILD-TYPE 270  75
  PON3 MUTATED PON3 WILD-TYPE 
            10            345 
  PON3 MUTATED PON3 WILD-TYPE 
             3             75 
$`PON3 MUTATED`
TCGA-AA-3715 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3511 
       19.04        26.17        79.69        30.44        63.98         6.97 
TCGA-AA-3971 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       16.08        12.76        10.06        21.14 

$`PON3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-3502 TCGA-AA-3514 
       19.66        20.28         7.04         3.02        35.01         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  PON3 MUTATED PON3 WILD-TYPE 
          6.97           0.00 
  PON3 MUTATED PON3 WILD-TYPE 
         79.69         148.01 
  PON3 MUTATED PON3 WILD-TYPE 
         20.09          22.09 
[1] "7.0 - 79.7 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1737V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PON3 MUTATED         3        0        3         3         0         0
  PON3 WILD-TYPE      61        1       23       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PON3 MUTATED           1          0          0          0        0         0
  PON3 WILD-TYPE        17          6         44         33       35        12
                vv
clus             STAGE IVB
  PON3 MUTATED           0
  PON3 WILD-TYPE         1
D1737V3, multiclass
            clus
vv           PON3 MUTATED PON3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PON3 MUTATED     1   2   6   1
  PON3 WILD-TYPE   8  65 243  40
D1737V4, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  T1            1              8
  T2            2             65
  T3            6            243
  T4            1             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
  PON3 MUTATED     9   1   0
  PON3 WILD-TYPE 211  80  66
D1737V5, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  N0            9            211
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1737V6, binary
                cls
clus               0   1
  PON3 MUTATED    10   0
  PON3 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED     10    0
  PON3 WILD-TYPE  275   48
   clus
vv  PON3 MUTATED PON3 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1737V7, binary
                cls
clus               0   1
  PON3 MUTATED     2   8
  PON3 WILD-TYPE 168 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      2    8
  PON3 WILD-TYPE  168  189
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  FEMALE            2            168
  MALE              8            189
[1] 2 2
[1] FALSE
D1737V8, binary
                cls
clus               0   1
  PON3 MUTATED    10   0
  PON3 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED     10    0
  PON3 WILD-TYPE  290    8
     clus
vv    PON3 MUTATED PON3 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1737V9, binary
                cls
clus               0   1
  PON3 MUTATED     9   1
  PON3 WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      9    1
  PON3 WILD-TYPE  305   47
                               clus
vv                              PON3 MUTATED PON3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PON3 MUTATED     7   0   0   3
  PON3 WILD-TYPE 252   3  22  18
D1737V10, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            3             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"
D1737V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PON3 MUTATED                                  0     2
  PON3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PON3 MUTATED                           0     4
  PON3 WILD-TYPE                        19   172
D1737V12, multiclass
                                  clus
vv                                 PON3 MUTATED PON3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = TGM1 MUTATION ANALYSIS
D1738V1, survival
                sevent
clus2              0   1
  TGM1 MUTATED     8   3
  TGM1 WILD-TYPE 269  75
  TGM1 MUTATED TGM1 WILD-TYPE 
            11            344 
  TGM1 MUTATED TGM1 WILD-TYPE 
             3             75 
$`TGM1 MUTATED`
TCGA-AA-3554 TCGA-AA-3715 TCGA-A6-5665 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 
       17.95        19.04        22.06        35.01        12.16        83.24 
TCGA-AZ-6599 TCGA-CM-4743 TCGA-CM-6165 TCGA-DM-A28K TCGA-G4-6307 
        6.77        23.05        16.04        98.24        55.04 

$`TGM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6890 TCGA-AD-6899 
       41.00        39.98        18.05        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       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-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TGM1 MUTATED TGM1 WILD-TYPE 
          6.77           0.00 
  TGM1 MUTATED TGM1 WILD-TYPE 
         98.24         148.01 
  TGM1 MUTATED TGM1 WILD-TYPE 
         22.06          22.06 
[1] "6.8 - 98.2 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1738V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGM1 MUTATED         2        0        1         6         0         0
  TGM1 WILD-TYPE      62        1       25       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TGM1 MUTATED           1          0          1          0        0         0
  TGM1 WILD-TYPE        17          6         43         33       35        12
                vv
clus             STAGE IVB
  TGM1 MUTATED           0
  TGM1 WILD-TYPE         1
D1738V3, multiclass
            clus
vv           TGM1 MUTATED TGM1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  TGM1 MUTATED     0   2   9   0
  TGM1 WILD-TYPE   9  65 240  41
D1738V4, multiclass
    clus
vv   TGM1 MUTATED TGM1 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            9            240
  T4            0             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
  TGM1 MUTATED     9   1   1
  TGM1 WILD-TYPE 211  80  65
D1738V5, multiclass
    clus
vv   TGM1 MUTATED TGM1 WILD-TYPE
  N0            9            211
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1738V6, binary
                cls
clus               0   1
  TGM1 MUTATED     9   0
  TGM1 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM1 MUTATED      9    0
  TGM1 WILD-TYPE  276   48
   clus
vv  TGM1 MUTATED TGM1 WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D1738V7, binary
                cls
clus               0   1
  TGM1 MUTATED     3   8
  TGM1 WILD-TYPE 167 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM1 MUTATED      3    8
  TGM1 WILD-TYPE  167  189
        clus
vv       TGM1 MUTATED TGM1 WILD-TYPE
  FEMALE            3            167
  MALE              8            189
[1] 2 2
[1] FALSE
D1738V8, binary
                cls
clus               0   1
  TGM1 MUTATED     9   1
  TGM1 WILD-TYPE 291   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM1 MUTATED      9    1
  TGM1 WILD-TYPE  291    7
     clus
vv    TGM1 MUTATED TGM1 WILD-TYPE
  NO             9            291
  YES            1              7
[1] 2 2
[1] FALSE
D1738V9, binary
                cls
clus               0   1
  TGM1 MUTATED     8   3
  TGM1 WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM1 MUTATED      8    3
  TGM1 WILD-TYPE  306   45
                               clus
vv                              TGM1 MUTATED TGM1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TGM1 MUTATED     9   0   0   0
  TGM1 WILD-TYPE 250   3  22  21
D1738V10, multiclass
    clus
vv   TGM1 MUTATED TGM1 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            0             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"
D1738V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGM1 MUTATED                                  0     1
  TGM1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TGM1 MUTATED                           0     7
  TGM1 WILD-TYPE                        19   169
D1738V12, multiclass
                                  clus
vv                                 TGM1 MUTATED TGM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = NEK3 MUTATION ANALYSIS
D1739V1, survival
                sevent
clus2              0   1
  NEK3 MUTATED     5   4
  NEK3 WILD-TYPE 272  74
  NEK3 MUTATED NEK3 WILD-TYPE 
             9            346 
  NEK3 MUTATED NEK3 WILD-TYPE 
             4             74 
$`NEK3 MUTATED`
TCGA-G4-6588 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5254 TCGA-CA-6718 
       26.17        25.02         4.01        34.98        12.69        10.06 
TCGA-CM-5862 TCGA-D5-6930 TCGA-DM-A28F 
        5.03        13.35        35.97 

$`NEK3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  NEK3 MUTATED NEK3 WILD-TYPE 
          4.01           0.00 
  NEK3 MUTATED NEK3 WILD-TYPE 
         35.97         148.01 
  NEK3 MUTATED NEK3 WILD-TYPE 
        13.350         22.075 
[1] "4.0 - 36.0 (13.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "3.3"
D1739V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEK3 MUTATED         1        0        0         5         2         0
  NEK3 WILD-TYPE      63        1       26       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEK3 MUTATED           0          0          1          0        0         1
  NEK3 WILD-TYPE        18          6         43         33       35        11
                vv
clus             STAGE IVB
  NEK3 MUTATED           0
  NEK3 WILD-TYPE         1
D1739V3, multiclass
            clus
vv           NEK3 MUTATED NEK3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  NEK3 MUTATED     0   2   7   2
  NEK3 WILD-TYPE   9  65 242  39
D1739V4, multiclass
    clus
vv   NEK3 MUTATED NEK3 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            7            242
  T4            2             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
  NEK3 MUTATED     9   2   0
  NEK3 WILD-TYPE 211  79  66
D1739V5, multiclass
    clus
vv   NEK3 MUTATED NEK3 WILD-TYPE
  N0            9            211
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1739V6, binary
                cls
clus               0   1
  NEK3 MUTATED     8   1
  NEK3 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK3 MUTATED      8    1
  NEK3 WILD-TYPE  277   47
   clus
vv  NEK3 MUTATED NEK3 WILD-TYPE
  0            8            277
  1            1             47
[1] 2 2
[1] FALSE
D1739V7, binary
                cls
clus               0   1
  NEK3 MUTATED     4   7
  NEK3 WILD-TYPE 166 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK3 MUTATED      4    7
  NEK3 WILD-TYPE  166  190
        clus
vv       NEK3 MUTATED NEK3 WILD-TYPE
  FEMALE            4            166
  MALE              7            190
[1] 2 2
[1] FALSE
D1739V8, binary
                cls
clus               0   1
  NEK3 MUTATED     7   0
  NEK3 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK3 MUTATED      7    0
  NEK3 WILD-TYPE  293    8
     clus
vv    NEK3 MUTATED NEK3 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1739V9, binary
                cls
clus               0   1
  NEK3 MUTATED     9   2
  NEK3 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK3 MUTATED      9    2
  NEK3 WILD-TYPE  305   46
                               clus
vv                              NEK3 MUTATED NEK3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEK3 MUTATED     6   0   0   3
  NEK3 WILD-TYPE 253   3  22  18
D1739V10, multiclass
    clus
vv   NEK3 MUTATED NEK3 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            3             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"
D1739V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEK3 MUTATED                                  0     2
  NEK3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEK3 MUTATED                           0     5
  NEK3 WILD-TYPE                        19   171
D1739V12, multiclass
                                  clus
vv                                 NEK3 MUTATED NEK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[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 = GSTM5 MUTATION ANALYSIS
D1740V1, survival
                 sevent
clus2               0   1
  GSTM5 MUTATED     5   0
  GSTM5 WILD-TYPE 272  78
  GSTM5 MUTATED GSTM5 WILD-TYPE 
              5             350 
  GSTM5 MUTATED GSTM5 WILD-TYPE 
              0              78 
$`GSTM5 MUTATED`
TCGA-AA-A03J TCGA-CM-5861 TCGA-CM-6677 TCGA-F4-6856 TCGA-G4-6323 
       40.96        15.02        11.08        35.31        13.78 

$`GSTM5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6626 
       36.00        46.75 

  GSTM5 MUTATED GSTM5 WILD-TYPE 
          11.08            0.00 
  GSTM5 MUTATED GSTM5 WILD-TYPE 
          40.96          148.01 
  GSTM5 MUTATED GSTM5 WILD-TYPE 
         15.020          22.075 
[1] "11.1 - 41.0 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1740V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSTM5 MUTATED         2        1        0         2         0         0
  GSTM5 WILD-TYPE      62        0       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSTM5 MUTATED           0          0          0          0        0         0
  GSTM5 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  GSTM5 MUTATED           0
  GSTM5 WILD-TYPE         1
D1740V3, multiclass
            clus
vv           GSTM5 MUTATED GSTM5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GSTM5 MUTATED     0   2   2   0
  GSTM5 WILD-TYPE   9  65 247  41
D1740V4, multiclass
    clus
vv   GSTM5 MUTATED GSTM5 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             2             247
  T4             0              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
  GSTM5 MUTATED     5   0   0
  GSTM5 WILD-TYPE 215  81  66
D1740V5, multiclass
    clus
vv   GSTM5 MUTATED GSTM5 WILD-TYPE
  N0             5             215
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1740V6, binary
                 cls
clus                0   1
  GSTM5 MUTATED     4   0
  GSTM5 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM5 MUTATED      4    0
  GSTM5 WILD-TYPE  281   48
   clus
vv  GSTM5 MUTATED GSTM5 WILD-TYPE
  0             4             281
  1             0              48
[1] 2 2
[1] FALSE
D1740V7, binary
                 cls
clus                0   1
  GSTM5 MUTATED     3   2
  GSTM5 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM5 MUTATED      3    2
  GSTM5 WILD-TYPE  167  195
        clus
vv       GSTM5 MUTATED GSTM5 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1740V8, binary
                 cls
clus                0   1
  GSTM5 MUTATED     5   0
  GSTM5 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM5 MUTATED      5    0
  GSTM5 WILD-TYPE  295    8
     clus
vv    GSTM5 MUTATED GSTM5 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1740V9, binary
                 cls
clus                0   1
  GSTM5 MUTATED     4   1
  GSTM5 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM5 MUTATED      4    1
  GSTM5 WILD-TYPE  310   47
                               clus
vv                              GSTM5 MUTATED GSTM5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GSTM5 MUTATED     5   0   0   0
  GSTM5 WILD-TYPE 254   3  22  21
D1740V10, multiclass
    clus
vv   GSTM5 MUTATED GSTM5 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1740V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSTM5 MUTATED                                  0     0
  GSTM5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GSTM5 MUTATED                           1     3
  GSTM5 WILD-TYPE                        18   173
D1740V12, multiclass
                                  clus
vv                                 GSTM5 MUTATED GSTM5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        3             173
[1] 4 2
[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 = CLEC1A MUTATION ANALYSIS
D1741V1, survival
                  sevent
clus2                0   1
  CLEC1A MUTATED     7   1
  CLEC1A WILD-TYPE 270  77
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               8              347 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               1               77 
$`CLEC1A MUTATED`
TCGA-AA-3662 TCGA-G4-6586 TCGA-G4-6628 TCGA-AA-3977 TCGA-AA-A010 TCGA-CA-6718 
        6.05        35.80        79.69        25.02        34.98        10.06 
TCGA-CM-6168 TCGA-DM-A282 
       12.99       139.17 

$`CLEC1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  CLEC1A MUTATED CLEC1A WILD-TYPE 
            6.05             0.00 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
          139.17           148.01 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
           30.00            22.03 
[1] "6.0 - 139.2 (30.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1741V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLEC1A MUTATED         1        0        0         4         1         0
  CLEC1A WILD-TYPE      63        1       26       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLEC1A MUTATED           0          0          0          0        1
  CLEC1A WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CLEC1A MUTATED           0         0
  CLEC1A WILD-TYPE        12         1
D1741V3, multiclass
            clus
vv           CLEC1A MUTATED CLEC1A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CLEC1A MUTATED     0   2   4   2
  CLEC1A WILD-TYPE   9  65 245  39
D1741V4, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  T1              0                9
  T2              2               65
  T3              4              245
  T4              2               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
  CLEC1A MUTATED     7   0   1
  CLEC1A WILD-TYPE 213  81  65
D1741V5, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  N0              7              213
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1741V6, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     6   1
  CLEC1A WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      6    1
  CLEC1A WILD-TYPE  279   47
   clus
vv  CLEC1A MUTATED CLEC1A WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D1741V7, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     5   3
  CLEC1A WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      5    3
  CLEC1A WILD-TYPE  165  194
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1741V8, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     7   0
  CLEC1A WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      7    0
  CLEC1A WILD-TYPE  293    8
     clus
vv    CLEC1A MUTATED CLEC1A WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1741V9, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     8   0
  CLEC1A WILD-TYPE 306  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      8    0
  CLEC1A WILD-TYPE  306   48
                               clus
vv                              CLEC1A MUTATED CLEC1A WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLEC1A MUTATED     4   0   1   1
  CLEC1A WILD-TYPE 255   3  21  20
D1741V10, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  R0              4              255
  R1              0                3
  R2              1               21
  RX              1               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"
D1741V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLEC1A MUTATED                                  0     1
  CLEC1A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLEC1A MUTATED                           1     3
  CLEC1A WILD-TYPE                        18   173
D1741V12, multiclass
                                  clus
vv                                 CLEC1A MUTATED CLEC1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = CCDC64B MUTATION ANALYSIS
D1742V1, survival
                   sevent
clus2                 0   1
  CCDC64B MUTATED     3   2
  CCDC64B WILD-TYPE 274  76
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                5               350 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                2                76 
$`CCDC64B MUTATED`
TCGA-AZ-6601 TCGA-A6-2671 TCGA-AA-3815 TCGA-AA-3821 TCGA-DM-A1HB 
      100.01        43.76        33.04         1.02       135.65 

$`CCDC64B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CCDC64B MUTATED CCDC64B WILD-TYPE 
             1.02              0.00 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
           135.65            148.01 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
            43.76             22.01 
[1] "1.0 - 135.7 (43.8)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1742V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC64B MUTATED         1        0        1         1         0         0
  CCDC64B WILD-TYPE      63        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC64B MUTATED           0          0          1          0        1
  CCDC64B WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC64B MUTATED           0         0
  CCDC64B WILD-TYPE        12         1
D1742V3, multiclass
            clus
vv           CCDC64B MUTATED CCDC64B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  CCDC64B MUTATED     0   1   4   0
  CCDC64B WILD-TYPE   9  66 245  41
D1742V4, multiclass
    clus
vv   CCDC64B MUTATED CCDC64B WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               0                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
  CCDC64B MUTATED     3   1   1
  CCDC64B WILD-TYPE 217  80  65
D1742V5, multiclass
    clus
vv   CCDC64B MUTATED CCDC64B WILD-TYPE
  N0               3               217
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1742V6, binary
                   cls
clus                  0   1
  CCDC64B MUTATED     4   1
  CCDC64B WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC64B MUTATED      4    1
  CCDC64B WILD-TYPE  281   47
   clus
vv  CCDC64B MUTATED CCDC64B WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D1742V7, binary
                   cls
clus                  0   1
  CCDC64B MUTATED     2   3
  CCDC64B WILD-TYPE 168 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC64B MUTATED      2    3
  CCDC64B WILD-TYPE  168  194
        clus
vv       CCDC64B MUTATED CCDC64B WILD-TYPE
  FEMALE               2               168
  MALE                 3               194
[1] 2 2
[1] FALSE
D1742V8, binary
                   cls
clus                  0   1
  CCDC64B MUTATED     4   0
  CCDC64B WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC64B MUTATED      4    0
  CCDC64B WILD-TYPE  296    8
     clus
vv    CCDC64B MUTATED CCDC64B WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D1742V9, binary
                   cls
clus                  0   1
  CCDC64B MUTATED     3   1
  CCDC64B WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC64B MUTATED      3    1
  CCDC64B WILD-TYPE  311   47
                               clus
vv                              CCDC64B MUTATED CCDC64B WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC64B MUTATED     3   0   0   0
  CCDC64B WILD-TYPE 256   3  22  21
D1742V10, multiclass
    clus
vv   CCDC64B MUTATED CCDC64B WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               0                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"
D1742V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC64B MUTATED                                  0     0
  CCDC64B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC64B MUTATED                           0     3
  CCDC64B WILD-TYPE                        19   173
D1742V12, multiclass
                                  clus
vv                                 CCDC64B MUTATED CCDC64B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = TEK MUTATION ANALYSIS
D1743V1, survival
               sevent
clus2             0   1
  TEK MUTATED    16  11
  TEK WILD-TYPE 261  67
  TEK MUTATED TEK WILD-TYPE 
           27           328 
  TEK MUTATED TEK WILD-TYPE 
           11            67 
$`TEK MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-A6-2676 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3660 
       19.04       100.01        42.90        31.63        33.53        78.08 
TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A010 
        0.00        33.01         7.96         4.01        42.02        34.98 
TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4948 
       12.16         0.20        58.39        49.41        10.06       148.01 
TCGA-CM-6171 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6537 TCGA-DM-A1D4 TCGA-DM-A1HB 
       14.04        20.19        17.85         4.80        92.75       135.65 
TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6315 
       35.97         6.18        61.91 

$`TEK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00R 
       30.02        34.03        18.05        18.05        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        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-4682 
       33.01        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.20        12.76        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        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-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 
       43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        36.00        13.78        46.75 

  TEK MUTATED TEK WILD-TYPE 
            0             0 
  TEK MUTATED TEK WILD-TYPE 
       148.01        140.38 
  TEK MUTATED TEK WILD-TYPE 
        33.01         22.01 
[1] "0.0 - 148.0 (33.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D1743V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TEK MUTATED         2        0        3         9         4         0
  TEK WILD-TYPE      62        1       23        99         4         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEK MUTATED           1          0          5          1        3         0
  TEK WILD-TYPE        17          6         39         32       32        12
               vv
clus            STAGE IVB
  TEK MUTATED           0
  TEK WILD-TYPE         1
D1743V3, multiclass
            clus
vv           TEK MUTATED TEK WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            9            99
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           5            39
  STAGE IIIC           1            32
  STAGE IV             3            32
  STAGE IVA            0            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
  TEK MUTATED     0   2  21   5
  TEK WILD-TYPE   9  65 228  36
D1743V4, multiclass
    clus
vv   TEK MUTATED TEK WILD-TYPE
  T1           0             9
  T2           2            65
  T3          21           228
  T4           5            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
  TEK MUTATED    19   7   2
  TEK WILD-TYPE 201  74  64
D1743V5, multiclass
    clus
vv   TEK MUTATED TEK WILD-TYPE
  N0          19           201
  N1           7            74
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1743V6, binary
               cls
clus              0   1
  TEK MUTATED    21   3
  TEK WILD-TYPE 264  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEK MUTATED     21    3
  TEK WILD-TYPE  264   45
   clus
vv  TEK MUTATED TEK WILD-TYPE
  0          21           264
  1           3            45
[1] 2 2
[1] FALSE
D1743V7, binary
               cls
clus              0   1
  TEK MUTATED    12  16
  TEK WILD-TYPE 158 181
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEK MUTATED     12   16
  TEK WILD-TYPE  158  181
        clus
vv       TEK MUTATED TEK WILD-TYPE
  FEMALE          12           158
  MALE            16           181
[1] 2 2
[1] FALSE
D1743V8, binary
               cls
clus              0   1
  TEK MUTATED    20   1
  TEK WILD-TYPE 280   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEK MUTATED     20    1
  TEK WILD-TYPE  280    7
     clus
vv    TEK MUTATED TEK WILD-TYPE
  NO           20           280
  YES           1             7
[1] 2 2
[1] FALSE
D1743V9, binary
               cls
clus              0   1
  TEK MUTATED    23   4
  TEK WILD-TYPE 291  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEK MUTATED     23    4
  TEK WILD-TYPE  291   44
                               clus
vv                              TEK MUTATED TEK WILD-TYPE
  COLON ADENOCARCINOMA                   23           291
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TEK MUTATED    20   0   2   1
  TEK WILD-TYPE 239   3  20  20
D1743V10, multiclass
    clus
vv   TEK MUTATED TEK WILD-TYPE
  R0          20           239
  R1           0             3
  R2           2            20
  RX           1            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"
D1743V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEK MUTATED                                  0     1
  TEK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TEK MUTATED                           2    16
  TEK WILD-TYPE                        17   160
D1743V12, multiclass
                                  clus
vv                                 TEK MUTATED TEK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                     16           160
[1] 4 2
[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 = IL8 MUTATION ANALYSIS
D1744V1, survival
               sevent
clus2             0   1
  IL8 MUTATED     2   2
  IL8 WILD-TYPE 275  76
  IL8 MUTATED IL8 WILD-TYPE 
            4           351 
  IL8 MUTATED IL8 WILD-TYPE 
            2            76 
$`IL8 MUTATED`
TCGA-A6-6781 TCGA-AZ-6607 TCGA-CK-5916 TCGA-D5-6926 
       19.66         3.19        21.14         9.04 

$`IL8 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  IL8 MUTATED IL8 WILD-TYPE 
         3.19          0.00 
  IL8 MUTATED IL8 WILD-TYPE 
        21.14        148.01 
  IL8 MUTATED IL8 WILD-TYPE 
        14.35         22.09 
[1] "3.2 - 21.1 (14.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "4.4"
D1744V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL8 MUTATED         1        0        0         0         1         0
  IL8 WILD-TYPE      63        1       26       108         7         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        18          6         43         32       34        12
               vv
clus            STAGE IVB
  IL8 MUTATED           0
  IL8 WILD-TYPE         1
D1744V3, multiclass
            clus
vv           IL8 MUTATED IL8 WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            0           108
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           1            32
  STAGE IV             1            34
  STAGE IVA            0            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
  IL8 MUTATED     1   0   0   4
  IL8 WILD-TYPE   8  67 249  37
D1744V4, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  T1           1             8
  T2           0            67
  T3           0           249
  T4           4            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
  IL8 MUTATED     2   2   1
  IL8 WILD-TYPE 218  79  65
D1744V5, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  N0           2           218
  N1           2            79
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1744V6, binary
               cls
clus              0   1
  IL8 MUTATED     2   1
  IL8 WILD-TYPE 283  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      2    1
  IL8 WILD-TYPE  283   47
   clus
vv  IL8 MUTATED IL8 WILD-TYPE
  0           2           283
  1           1            47
[1] 2 2
[1] FALSE
D1744V7, binary
               cls
clus              0   1
  IL8 MUTATED     2   3
  IL8 WILD-TYPE 168 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      2    3
  IL8 WILD-TYPE  168  194
        clus
vv       IL8 MUTATED IL8 WILD-TYPE
  FEMALE           2           168
  MALE             3           194
[1] 2 2
[1] FALSE
D1744V8, binary
               cls
clus              0   1
  IL8 MUTATED     3   1
  IL8 WILD-TYPE 297   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      3    1
  IL8 WILD-TYPE  297    7
     clus
vv    IL8 MUTATED IL8 WILD-TYPE
  NO            3           297
  YES           1             7
[1] 2 2
[1] FALSE
D1744V9, binary
               cls
clus              0   1
  IL8 MUTATED     4   1
  IL8 WILD-TYPE 310  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      4    1
  IL8 WILD-TYPE  310   47
                               clus
vv                              IL8 MUTATED IL8 WILD-TYPE
  COLON ADENOCARCINOMA                    4           310
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  IL8 MUTATED     2   0   0   2
  IL8 WILD-TYPE 257   3  22  19
D1744V10, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  R0           2           257
  R1           0             3
  R2           0            22
  RX           2            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"
D1744V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL8 MUTATED                                  0     0
  IL8 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IL8 MUTATED                           0     5
  IL8 WILD-TYPE                        19   171
D1744V12, multiclass
                                  clus
vv                                 IL8 MUTATED IL8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      5           171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1745) Variable = ADCY9 MUTATION ANALYSIS
D1745V1, survival
                 sevent
clus2               0   1
  ADCY9 MUTATED    15   1
  ADCY9 WILD-TYPE 262  77
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             16             339 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
              1              77 
$`ADCY9 MUTATED`
TCGA-AA-3713 TCGA-AA-3867 TCGA-AA-3972 TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-3977 
       19.04        24.03        50.99        24.39         6.97        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 
       12.00        25.48        16.14        47.87 

$`ADCY9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 
       31.07        29.98        12.99        24.00         2.01        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ADCY9 MUTATED ADCY9 WILD-TYPE 
           6.97            0.00 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
          88.21          148.01 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
          24.21           22.03 
[1] "7.0 - 88.2 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3.9"
D1745V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADCY9 MUTATED         3        0        1         4         1         0
  ADCY9 WILD-TYPE      61        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADCY9 MUTATED           2          0          1          1        3         0
  ADCY9 WILD-TYPE        16          6         43         32       32        12
                 vv
clus              STAGE IVB
  ADCY9 MUTATED           0
  ADCY9 WILD-TYPE         1
D1745V3, multiclass
            clus
vv           ADCY9 MUTATED ADCY9 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               3              32
  STAGE IVA              0              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
  ADCY9 MUTATED     1   3  10   4
  ADCY9 WILD-TYPE   8  64 239  37
D1745V4, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  T1             1               8
  T2             3              64
  T3            10             239
  T4             4              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
  ADCY9 MUTATED    12   2   4
  ADCY9 WILD-TYPE 208  79  62
D1745V5, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             4              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1745V6, binary
                 cls
clus                0   1
  ADCY9 MUTATED    13   3
  ADCY9 WILD-TYPE 272  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     13    3
  ADCY9 WILD-TYPE  272   45
   clus
vv  ADCY9 MUTATED ADCY9 WILD-TYPE
  0            13             272
  1             3              45
[1] 2 2
[1] FALSE
D1745V7, binary
                 cls
clus                0   1
  ADCY9 MUTATED     5  13
  ADCY9 WILD-TYPE 165 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED      5   13
  ADCY9 WILD-TYPE  165  184
        clus
vv       ADCY9 MUTATED ADCY9 WILD-TYPE
  FEMALE             5             165
  MALE              13             184
[1] 2 2
[1] FALSE
D1745V8, binary
                 cls
clus                0   1
  ADCY9 MUTATED    13   2
  ADCY9 WILD-TYPE 287   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     13    2
  ADCY9 WILD-TYPE  287    6
     clus
vv    ADCY9 MUTATED ADCY9 WILD-TYPE
  NO             13             287
  YES             2               6
[1] 2 2
[1] FALSE
D1745V9, binary
                 cls
clus                0   1
  ADCY9 MUTATED    13   5
  ADCY9 WILD-TYPE 301  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     13    5
  ADCY9 WILD-TYPE  301   43
                               clus
vv                              ADCY9 MUTATED ADCY9 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ADCY9 MUTATED     8   0   3   4
  ADCY9 WILD-TYPE 251   3  19  17
D1745V10, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             3              19
  RX             4              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"
D1745V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADCY9 MUTATED                                  0     2
  ADCY9 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADCY9 MUTATED                           0     9
  ADCY9 WILD-TYPE                        19   167
D1745V12, multiclass
                                  clus
vv                                 ADCY9 MUTATED ADCY9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(1746) Variable = TNXB MUTATION ANALYSIS
D1746V1, survival
                sevent
clus2              0   1
  TNXB MUTATED    29   7
  TNXB WILD-TYPE 248  71
  TNXB MUTATED TNXB WILD-TYPE 
            36            319 
  TNXB MUTATED TNXB WILD-TYPE 
             7             71 
$`TNXB MUTATED`
TCGA-AA-3662 TCGA-G4-6628 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5665 
        6.05        79.69        36.53        32.91        33.53        22.06 
TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       25.08        19.66        35.01        78.08         6.97         2.01 
TCGA-AA-3837 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00N 
       38.99         0.00        53.00        31.00        33.01         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        83.24        17.82        58.39        49.41        12.76 
TCGA-CK-4952 TCGA-CM-5862 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6674 TCGA-D5-6538 
       15.62         5.03        14.99        15.02        12.95        17.13 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6293 
       11.64        13.35       139.17         6.18        35.31       133.18 

$`TNXB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       13.94        61.02        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        37.02         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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       30.05        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        12.99        13.02        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       135.65        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TNXB MUTATED TNXB WILD-TYPE 
             0              0 
  TNXB MUTATED TNXB WILD-TYPE 
        139.17         148.01 
  TNXB MUTATED TNXB WILD-TYPE 
         23.57          22.03 
[1] "0.0 - 139.2 (23.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1746V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNXB MUTATED         8        0        4        13         4         0
  TNXB WILD-TYPE      56        1       22        95         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNXB MUTATED           2          0          2          3        1         2
  TNXB WILD-TYPE        16          6         42         30       34        10
                vv
clus             STAGE IVB
  TNXB MUTATED           0
  TNXB WILD-TYPE         1
D1746V3, multiclass
            clus
vv           TNXB MUTATED TNXB WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            13             95
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            3             30
  STAGE IV              1             34
  STAGE IVA             2             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
  TNXB MUTATED     1   7  24   7
  TNXB WILD-TYPE   8  60 225  34
D1746V4, multiclass
    clus
vv   TNXB MUTATED TNXB WILD-TYPE
  T1            1              8
  T2            7             60
  T3           24            225
  T4            7             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
  TNXB MUTATED    29   6   4
  TNXB WILD-TYPE 191  75  62
D1746V5, multiclass
    clus
vv   TNXB MUTATED TNXB WILD-TYPE
  N0           29            191
  N1            6             75
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1746V6, binary
                cls
clus               0   1
  TNXB MUTATED    32   3
  TNXB WILD-TYPE 253  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     32    3
  TNXB WILD-TYPE  253   45
   clus
vv  TNXB MUTATED TNXB WILD-TYPE
  0           32            253
  1            3             45
[1] 2 2
[1] FALSE
D1746V7, binary
                cls
clus               0   1
  TNXB MUTATED    19  20
  TNXB WILD-TYPE 151 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     19   20
  TNXB WILD-TYPE  151  177
        clus
vv       TNXB MUTATED TNXB WILD-TYPE
  FEMALE           19            151
  MALE             20            177
[1] 2 2
[1] FALSE
D1746V8, binary
                cls
clus               0   1
  TNXB MUTATED    31   0
  TNXB WILD-TYPE 269   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     31    0
  TNXB WILD-TYPE  269    8
     clus
vv    TNXB MUTATED TNXB WILD-TYPE
  NO            31            269
  YES            0              8
[1] 2 2
[1] FALSE
D1746V9, binary
                cls
clus               0   1
  TNXB MUTATED    29  10
  TNXB WILD-TYPE 285  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     29   10
  TNXB WILD-TYPE  285   38
                               clus
vv                              TNXB MUTATED TNXB WILD-TYPE
  COLON ADENOCARCINOMA                    29            285
  COLON MUCINOUS ADENOCARCINOMA           10             38
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TNXB MUTATED    30   0   1   4
  TNXB WILD-TYPE 229   3  21  17
D1746V10, multiclass
    clus
vv   TNXB MUTATED TNXB WILD-TYPE
  R0           30            229
  R1            0              3
  R2            1             21
  RX            4             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"
D1746V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNXB MUTATED                                  0     2
  TNXB WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TNXB MUTATED                           3    21
  TNXB WILD-TYPE                        16   155
D1746V12, multiclass
                                  clus
vv                                 TNXB MUTATED TNXB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   3             16
  WHITE                                      21            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(1747) Variable = MOGAT3 MUTATION ANALYSIS
D1747V1, survival
                  sevent
clus2                0   1
  MOGAT3 MUTATED     6   0
  MOGAT3 WILD-TYPE 271  78
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
               6              349 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
               0               78 
$`MOGAT3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A01Q TCGA-DM-A1HB TCGA-F4-6855 
       33.53        22.06        63.98         1.02       135.65        47.41 

$`MOGAT3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
            1.02             0.00 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
          135.65           148.01 
  MOGAT3 MUTATED MOGAT3 WILD-TYPE 
           40.47            21.99 
[1] "1.0 - 135.7 (40.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D1747V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOGAT3 MUTATED         0        0        2         3         0         0
  MOGAT3 WILD-TYPE      64        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOGAT3 MUTATED           0          0          1          0        0
  MOGAT3 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MOGAT3 MUTATED           0         0
  MOGAT3 WILD-TYPE        12         1
D1747V3, multiclass
            clus
vv           MOGAT3 MUTATED MOGAT3 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MOGAT3 MUTATED     0   0   6   0
  MOGAT3 WILD-TYPE   9  67 243  41
D1747V4, multiclass
    clus
vv   MOGAT3 MUTATED MOGAT3 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              6              243
  T4              0               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
  MOGAT3 MUTATED     5   1   0
  MOGAT3 WILD-TYPE 215  80  66
D1747V5, multiclass
    clus
vv   MOGAT3 MUTATED MOGAT3 WILD-TYPE
  N0              5              215
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1747V6, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     6   0
  MOGAT3 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      6    0
  MOGAT3 WILD-TYPE  279   48
   clus
vv  MOGAT3 MUTATED MOGAT3 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1747V7, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     4   2
  MOGAT3 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      4    2
  MOGAT3 WILD-TYPE  166  195
        clus
vv       MOGAT3 MUTATED MOGAT3 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D1747V8, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     4   0
  MOGAT3 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      4    0
  MOGAT3 WILD-TYPE  296    8
     clus
vv    MOGAT3 MUTATED MOGAT3 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1747V9, binary
                  cls
clus                 0   1
  MOGAT3 MUTATED     5   0
  MOGAT3 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT3 MUTATED      5    0
  MOGAT3 WILD-TYPE  309   48
                               clus
vv                              MOGAT3 MUTATED MOGAT3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              309
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MOGAT3 MUTATED     5   0   0   0
  MOGAT3 WILD-TYPE 254   3  22  21
D1747V10, multiclass
    clus
vv   MOGAT3 MUTATED MOGAT3 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1747V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOGAT3 MUTATED                                  0     0
  MOGAT3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MOGAT3 MUTATED                           1     3
  MOGAT3 WILD-TYPE                        18   173
D1747V12, multiclass
                                  clus
vv                                 MOGAT3 MUTATED MOGAT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = HIST1H3B MUTATION ANALYSIS
D1748V1, survival
                    sevent
clus2                  0   1
  HIST1H3B MUTATED     1   3
  HIST1H3B WILD-TYPE 276  75
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                351 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 3                 75 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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             22.090 
[1] "3.0 - 44.3 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "4.4"
D1748V2, continuous
                    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      63        1       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H3B MUTATED           0          0          1          0        0
  HIST1H3B WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H3B MUTATED           0         0
  HIST1H3B WILD-TYPE        12         1
D1748V3, multiclass
            clus
vv           HIST1H3B MUTATED HIST1H3B WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 1                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  HIST1H3B MUTATED     1   0   2   1
  HIST1H3B WILD-TYPE   8  67 247  40
D1748V4, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  T1                1                  8
  T2                0                 67
  T3                2                247
  T4                1                 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
  HIST1H3B MUTATED     3   1   0
  HIST1H3B WILD-TYPE 217  80  66
D1748V5, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  N0                3                217
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1748V6, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     4   0
  HIST1H3B WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      4    0
  HIST1H3B WILD-TYPE  281   48
   clus
vv  HIST1H3B MUTATED HIST1H3B WILD-TYPE
  0                4                281
  1                0                 48
[1] 2 2
[1] FALSE
D1748V7, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     2   2
  HIST1H3B WILD-TYPE 168 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      2    2
  HIST1H3B WILD-TYPE  168  195
        clus
vv       HIST1H3B MUTATED HIST1H3B WILD-TYPE
  FEMALE                2                168
  MALE                  2                195
[1] 2 2
[1] FALSE
D1748V8, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     3   0
  HIST1H3B WILD-TYPE 297   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      3    0
  HIST1H3B WILD-TYPE  297    8
     clus
vv    HIST1H3B MUTATED HIST1H3B WILD-TYPE
  NO                 3                297
  YES                0                  8
[1] 2 2
[1] FALSE
D1748V9, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     3   1
  HIST1H3B WILD-TYPE 311  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      3    1
  HIST1H3B WILD-TYPE  311   47
                               clus
vv                              HIST1H3B MUTATED HIST1H3B WILD-TYPE
  COLON ADENOCARCINOMA                         3                311
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H3B MUTATED     2   0   0   1
  HIST1H3B WILD-TYPE 257   3  22  20
D1748V10, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  R0                2                257
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1748V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H3B MUTATED                                  0     0
  HIST1H3B WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H3B MUTATED                           0     2
  HIST1H3B WILD-TYPE                        19   174
D1748V12, multiclass
[1] "Remove cluster labels:" "HIST1H3B MUTATED"      
clus
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 2                204 
        TCGA-A6-2677         TCGA-A6-4105         TCGA-A6-6649 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6895 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6964         TCGA-AZ-4681         TCGA-AZ-6601 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6321         TCGA-G4-6586 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2678         TCGA-A6-2683 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-3807         TCGA-A6-3808         TCGA-A6-3809 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-5656         TCGA-A6-5657 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5660         TCGA-A6-5661 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5662         TCGA-A6-5664         TCGA-A6-5665 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5666         TCGA-A6-6137         TCGA-A6-6138 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"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-6889 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0X9         TCGA-DM-A0XD 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A0XF         TCGA-DM-A1D0         TCGA-DM-A1D4 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1D6         TCGA-DM-A1D7         TCGA-DM-A1D8 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1HA 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         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-G4-6315 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6323         TCGA-G4-6626 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 

Clustering(1749) Variable = ERCC6L MUTATION ANALYSIS
D1749V1, survival
                  sevent
clus2                0   1
  ERCC6L MUTATED     9   2
  ERCC6L WILD-TYPE 268  76
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              11              344 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               2               76 
$`ERCC6L MUTATED`
TCGA-AA-3860 TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-2672 
       31.07        24.00        25.08       100.01        35.80        46.65 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-A01D 
       33.53        22.06         8.38        78.08        10.98 

$`ERCC6L WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       14.93        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        15.52        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  ERCC6L MUTATED ERCC6L WILD-TYPE 
            8.38             0.00 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
          100.01           148.01 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
           31.07            21.99 
[1] "8.4 - 100.0 (31.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1749V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC6L MUTATED         0        0        2         6         0         0
  ERCC6L WILD-TYPE      64        1       24       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERCC6L MUTATED           0          0          3          1        0
  ERCC6L WILD-TYPE        18          6         41         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ERCC6L MUTATED           0         0
  ERCC6L WILD-TYPE        12         1
D1749V3, multiclass
            clus
vv           ERCC6L MUTATED ERCC6L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ERCC6L MUTATED     0   0  12   0
  ERCC6L WILD-TYPE   9  67 237  41
D1749V4, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  T1              0                9
  T2              0               67
  T3             12              237
  T4              0               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
  ERCC6L MUTATED     8   3   1
  ERCC6L WILD-TYPE 212  78  65
D1749V5, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  N0              8              212
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1749V6, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    12   0
  ERCC6L WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     12    0
  ERCC6L WILD-TYPE  273   48
   clus
vv  ERCC6L MUTATED ERCC6L WILD-TYPE
  0             12              273
  1              0               48
[1] 2 2
[1] FALSE
D1749V7, binary
                  cls
clus                 0   1
  ERCC6L MUTATED     9   3
  ERCC6L WILD-TYPE 161 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED      9    3
  ERCC6L WILD-TYPE  161  194
        clus
vv       ERCC6L MUTATED ERCC6L WILD-TYPE
  FEMALE              9              161
  MALE                3              194
[1] 2 2
[1] FALSE
D1749V8, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    11   0
  ERCC6L WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     11    0
  ERCC6L WILD-TYPE  289    8
     clus
vv    ERCC6L MUTATED ERCC6L WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1749V9, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    10   2
  ERCC6L WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     10    2
  ERCC6L WILD-TYPE  304   46
                               clus
vv                              ERCC6L MUTATED ERCC6L WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ERCC6L MUTATED    10   0   0   0
  ERCC6L WILD-TYPE 249   3  22  21
D1749V10, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              0               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"
D1749V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC6L MUTATED                                  0     0
  ERCC6L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ERCC6L MUTATED                           2     5
  ERCC6L WILD-TYPE                        17   171
D1749V12, multiclass
                                  clus
vv                                 ERCC6L MUTATED ERCC6L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         5              171
[1] 4 2
[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 = SBF1 MUTATION ANALYSIS
D1750V1, survival
                sevent
clus2              0   1
  SBF1 MUTATED     9   5
  SBF1 WILD-TYPE 268  73
  SBF1 MUTATED SBF1 WILD-TYPE 
            14            341 
  SBF1 MUTATED SBF1 WILD-TYPE 
             5             73 
$`SBF1 MUTATED`
TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 
       10.88        22.06         3.02        63.98         6.97        10.06 
TCGA-AA-3877 TCGA-AA-A02K TCGA-AZ-6598 TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A1HA 
       31.00        14.01        49.41         9.44        13.35       131.51 
TCGA-DM-A1HB TCGA-F4-6703 
      135.65        47.87 

$`SBF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38         7.50        44.32       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-F4-6704 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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  SBF1 MUTATED SBF1 WILD-TYPE 
          3.02           0.00 
  SBF1 MUTATED SBF1 WILD-TYPE 
        135.65         148.01 
  SBF1 MUTATED SBF1 WILD-TYPE 
        18.035         22.090 
[1] "3.0 - 135.7 (18.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1750V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SBF1 MUTATED         1        0        4         4         0         0
  SBF1 WILD-TYPE      63        1       22       104         8         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        17          6         43         32       34        12
                vv
clus             STAGE IVB
  SBF1 MUTATED           0
  SBF1 WILD-TYPE         1
D1750V3, multiclass
            clus
vv           SBF1 MUTATED SBF1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  SBF1 MUTATED     1   0  11   2
  SBF1 WILD-TYPE   8  67 238  39
D1750V4, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  T1            1              8
  T2            0             67
  T3           11            238
  T4            2             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
  SBF1 MUTATED     9   1   4
  SBF1 WILD-TYPE 211  80  62
D1750V5, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  N0            9            211
  N1            1             80
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1750V6, binary
                cls
clus               0   1
  SBF1 MUTATED    11   1
  SBF1 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     11    1
  SBF1 WILD-TYPE  274   47
   clus
vv  SBF1 MUTATED SBF1 WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D1750V7, binary
                cls
clus               0   1
  SBF1 MUTATED     5   9
  SBF1 WILD-TYPE 165 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED      5    9
  SBF1 WILD-TYPE  165  188
        clus
vv       SBF1 MUTATED SBF1 WILD-TYPE
  FEMALE            5            165
  MALE              9            188
[1] 2 2
[1] FALSE
D1750V8, binary
                cls
clus               0   1
  SBF1 MUTATED    12   0
  SBF1 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     12    0
  SBF1 WILD-TYPE  288    8
     clus
vv    SBF1 MUTATED SBF1 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1750V9, binary
                cls
clus               0   1
  SBF1 MUTATED    11   2
  SBF1 WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     11    2
  SBF1 WILD-TYPE  303   46
                               clus
vv                              SBF1 MUTATED SBF1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SBF1 MUTATED     9   0   1   0
  SBF1 WILD-TYPE 250   3  21  21
D1750V10, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            1             21
  RX            0             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"
D1750V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBF1 MUTATED                                  0     0
  SBF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBF1 MUTATED                           0     8
  SBF1 WILD-TYPE                        19   168
D1750V12, multiclass
                                  clus
vv                                 SBF1 MUTATED SBF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       8            168
[1] 4 2
[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 = ZNF391 MUTATION ANALYSIS
D1751V1, survival
                  sevent
clus2                0   1
  ZNF391 MUTATED     6   1
  ZNF391 WILD-TYPE 271  77
  ZNF391 MUTATED ZNF391 WILD-TYPE 
               7              348 
  ZNF391 MUTATED ZNF391 WILD-TYPE 
               1               77 
$`ZNF391 MUTATED`
TCGA-AA-3950 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-5254 TCGA-D5-6929 TCGA-DM-A1D0 
       24.00        25.02        58.39        12.69        13.41       130.65 
TCGA-F4-6570 
        6.18 

$`ZNF391 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         3.19        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ZNF391 MUTATED ZNF391 WILD-TYPE 
            6.18             0.00 
  ZNF391 MUTATED ZNF391 WILD-TYPE 
          130.65           148.01 
  ZNF391 MUTATED ZNF391 WILD-TYPE 
          24.000           22.045 
[1] "6.2 - 130.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1751V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF391 MUTATED         0        0        0         6         0         0
  ZNF391 WILD-TYPE      64        1       26       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF391 MUTATED           0          0          0          0        1
  ZNF391 WILD-TYPE        18          6         44         33       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF391 MUTATED           0         0
  ZNF391 WILD-TYPE        12         1
D1751V3, multiclass
            clus
vv           ZNF391 MUTATED ZNF391 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               6              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  ZNF391 MUTATED     0   1   7   0
  ZNF391 WILD-TYPE   9  66 242  41
D1751V4, multiclass
    clus
vv   ZNF391 MUTATED ZNF391 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              0               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
  ZNF391 MUTATED     7   1   0
  ZNF391 WILD-TYPE 213  80  66
D1751V5, multiclass
    clus
vv   ZNF391 MUTATED ZNF391 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1751V6, binary
                  cls
clus                 0   1
  ZNF391 MUTATED     6   1
  ZNF391 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF391 MUTATED      6    1
  ZNF391 WILD-TYPE  279   47
   clus
vv  ZNF391 MUTATED ZNF391 WILD-TYPE
  0              6              279
  1              1               47
[1] 2 2
[1] FALSE
D1751V7, binary
                  cls
clus                 0   1
  ZNF391 MUTATED     6   2
  ZNF391 WILD-TYPE 164 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF391 MUTATED      6    2
  ZNF391 WILD-TYPE  164  195
        clus
vv       ZNF391 MUTATED ZNF391 WILD-TYPE
  FEMALE              6              164
  MALE                2              195
[1] 2 2
[1] FALSE
D1751V8, binary
                  cls
clus                 0   1
  ZNF391 MUTATED     6   0
  ZNF391 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF391 MUTATED      6    0
  ZNF391 WILD-TYPE  294    8
     clus
vv    ZNF391 MUTATED ZNF391 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1751V9, binary
                  cls
clus                 0   1
  ZNF391 MUTATED     7   1
  ZNF391 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF391 MUTATED      7    1
  ZNF391 WILD-TYPE  307   47
                               clus
vv                              ZNF391 MUTATED ZNF391 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF391 MUTATED     5   0   0   1
  ZNF391 WILD-TYPE 254   3  22  20
D1751V10, multiclass
    clus
vv   ZNF391 MUTATED ZNF391 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D1751V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF391 MUTATED                                  0     1
  ZNF391 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF391 MUTATED                           0     4
  ZNF391 WILD-TYPE                        19   172
D1751V12, multiclass
                                  clus
vv                                 ZNF391 MUTATED ZNF391 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = SORBS1 MUTATION ANALYSIS
D1752V1, survival
                  sevent
clus2                0   1
  SORBS1 MUTATED     7   2
  SORBS1 WILD-TYPE 270  76
  SORBS1 MUTATED SORBS1 WILD-TYPE 
               9              346 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
               2               76 
$`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 
       83.24        21.44        58.39 

$`SORBS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
        2.01        21.99        13.05        34.06        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SORBS1 MUTATED SORBS1 WILD-TYPE 
           16.08             0.00 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
           83.24           148.01 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
           34.98            22.01 
[1] "16.1 - 83.2 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1752V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SORBS1 MUTATED         1        0        0         3         2         0
  SORBS1 WILD-TYPE      63        1       26       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SORBS1 MUTATED           1          0          2          0        0
  SORBS1 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SORBS1 MUTATED           0         0
  SORBS1 WILD-TYPE        12         1
D1752V3, multiclass
            clus
vv           SORBS1 MUTATED SORBS1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SORBS1 MUTATED     0   2   5   3
  SORBS1 WILD-TYPE   9  65 244  38
D1752V4, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              3               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
  SORBS1 MUTATED     7   3   0
  SORBS1 WILD-TYPE 213  78  66
D1752V5, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  N0              7              213
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1752V6, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     7   0
  SORBS1 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      7    0
  SORBS1 WILD-TYPE  278   48
   clus
vv  SORBS1 MUTATED SORBS1 WILD-TYPE
  0              7              278
  1              0               48
[1] 2 2
[1] FALSE
D1752V7, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     3   7
  SORBS1 WILD-TYPE 167 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      3    7
  SORBS1 WILD-TYPE  167  190
        clus
vv       SORBS1 MUTATED SORBS1 WILD-TYPE
  FEMALE              3              167
  MALE                7              190
[1] 2 2
[1] FALSE
D1752V8, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     9   0
  SORBS1 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      9    0
  SORBS1 WILD-TYPE  291    8
     clus
vv    SORBS1 MUTATED SORBS1 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1752V9, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     9   1
  SORBS1 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      9    1
  SORBS1 WILD-TYPE  305   47
                               clus
vv                              SORBS1 MUTATED SORBS1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SORBS1 MUTATED     8   0   0   1
  SORBS1 WILD-TYPE 251   3  22  20
D1752V10, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              1               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"
D1752V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SORBS1 MUTATED                                  0     1
  SORBS1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SORBS1 MUTATED                           0     5
  SORBS1 WILD-TYPE                        19   171
D1752V12, multiclass
                                  clus
vv                                 SORBS1 MUTATED SORBS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = MOGAT1 MUTATION ANALYSIS
D1753V1, survival
                  sevent
clus2                0   1
  MOGAT1 MUTATED     3   1
  MOGAT1 WILD-TYPE 274  77
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
               4              351 
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
               1               77 
$`MOGAT1 MUTATED`
TCGA-AA-3877 TCGA-CA-6718 TCGA-D5-6924 TCGA-F4-6805 
       31.00        10.06        14.30        34.42 

$`MOGAT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
           10.06             0.00 
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
           34.42           148.01 
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
           22.65            22.06 
[1] "10.1 - 34.4 (22.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1753V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOGAT1 MUTATED         1        0        0         3         0         0
  MOGAT1 WILD-TYPE      63        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOGAT1 MUTATED           0          0          0          0        0
  MOGAT1 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  MOGAT1 MUTATED           0         0
  MOGAT1 WILD-TYPE        12         1
D1753V3, multiclass
            clus
vv           MOGAT1 MUTATED MOGAT1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  MOGAT1 MUTATED     1   0   3   0
  MOGAT1 WILD-TYPE   8  67 246  41
D1753V4, multiclass
    clus
vv   MOGAT1 MUTATED MOGAT1 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              3              246
  T4              0               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
  MOGAT1 MUTATED     4   0   0
  MOGAT1 WILD-TYPE 216  81  66
D1753V5, multiclass
    clus
vv   MOGAT1 MUTATED MOGAT1 WILD-TYPE
  N0              4              216
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1753V6, binary
                  cls
clus                 0   1
  MOGAT1 MUTATED     4   0
  MOGAT1 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT1 MUTATED      4    0
  MOGAT1 WILD-TYPE  281   48
   clus
vv  MOGAT1 MUTATED MOGAT1 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1753V7, binary
                  cls
clus                 0   1
  MOGAT1 MUTATED     2   2
  MOGAT1 WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT1 MUTATED      2    2
  MOGAT1 WILD-TYPE  168  195
        clus
vv       MOGAT1 MUTATED MOGAT1 WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D1753V8, binary
                  cls
clus                 0   1
  MOGAT1 MUTATED     4   0
  MOGAT1 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT1 MUTATED      4    0
  MOGAT1 WILD-TYPE  296    8
     clus
vv    MOGAT1 MUTATED MOGAT1 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1753V9, binary
                  cls
clus                 0   1
  MOGAT1 MUTATED     3   1
  MOGAT1 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MOGAT1 MUTATED      3    1
  MOGAT1 WILD-TYPE  311   47
                               clus
vv                              MOGAT1 MUTATED MOGAT1 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MOGAT1 MUTATED     3   0   0   1
  MOGAT1 WILD-TYPE 256   3  22  20
D1753V10, multiclass
    clus
vv   MOGAT1 MUTATED MOGAT1 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              1               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"
D1753V11, continuous
[1] "Remove cluster labels:" "MOGAT1 MUTATED"        
clus
  MOGAT1 MUTATED MOGAT1 WILD-TYPE 
               2              344 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527       TCGA-AA-3530 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AD-6964       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-DM-A285 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3655       TCGA-AA-3660 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3930       TCGA-AA-3941 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3977       TCGA-AA-3980       TCGA-AA-3982 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N       TCGA-AA-A00O 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6889 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-CA-6715       TCGA-CK-4947       TCGA-CK-4948 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806       TCGA-F4-6807 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" "MOGAT1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOGAT1 MUTATED                                  0     1
  MOGAT1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MOGAT1 MUTATED                           0     2
  MOGAT1 WILD-TYPE                        19   174
D1753V12, multiclass
                                  clus
vv                                 MOGAT1 MUTATED MOGAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         2              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(1754) Variable = GAB3 MUTATION ANALYSIS
D1754V1, survival
                sevent
clus2              0   1
  GAB3 MUTATED     8   2
  GAB3 WILD-TYPE 269  76
  GAB3 MUTATED GAB3 WILD-TYPE 
            10            345 
  GAB3 MUTATED GAB3 WILD-TYPE 
             2             76 
$`GAB3 MUTATED`
TCGA-AZ-6601 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3534 TCGA-AA-3663 TCGA-AA-A00R 
      100.01        63.98         1.02        29.00         6.97         0.99 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-D5-6534 TCGA-DM-A28F 
       34.98         1.02        43.27        35.97 

$`GAB3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        3.02        35.01         6.97        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28G 
      131.51       135.65       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GAB3 MUTATED GAB3 WILD-TYPE 
          0.99           0.00 
  GAB3 MUTATED GAB3 WILD-TYPE 
        100.01         148.01 
  GAB3 MUTATED GAB3 WILD-TYPE 
         31.99          22.03 
[1] "1.0 - 100.0 (32.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1754V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAB3 MUTATED         2        0        4         3         1         0
  GAB3 WILD-TYPE      62        1       22       105         7         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        18          6         43         33       35        12
                vv
clus             STAGE IVB
  GAB3 MUTATED           0
  GAB3 WILD-TYPE         1
D1754V3, multiclass
            clus
vv           GAB3 MUTATED GAB3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA             3            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  GAB3 MUTATED     0   2   8   1
  GAB3 WILD-TYPE   9  65 241  40
D1754V4, multiclass
    clus
vv   GAB3 MUTATED GAB3 WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            1             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
  GAB3 MUTATED    10   1   0
  GAB3 WILD-TYPE 210  80  66
D1754V5, multiclass
    clus
vv   GAB3 MUTATED GAB3 WILD-TYPE
  N0           10            210
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1754V6, binary
                cls
clus               0   1
  GAB3 MUTATED    11   0
  GAB3 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED     11    0
  GAB3 WILD-TYPE  274   48
   clus
vv  GAB3 MUTATED GAB3 WILD-TYPE
  0           11            274
  1            0             48
[1] 2 2
[1] FALSE
D1754V7, binary
                cls
clus               0   1
  GAB3 MUTATED     7   4
  GAB3 WILD-TYPE 163 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED      7    4
  GAB3 WILD-TYPE  163  193
        clus
vv       GAB3 MUTATED GAB3 WILD-TYPE
  FEMALE            7            163
  MALE              4            193
[1] 2 2
[1] FALSE
D1754V8, binary
                cls
clus               0   1
  GAB3 MUTATED     7   0
  GAB3 WILD-TYPE 293   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED      7    0
  GAB3 WILD-TYPE  293    8
     clus
vv    GAB3 MUTATED GAB3 WILD-TYPE
  NO             7            293
  YES            0              8
[1] 2 2
[1] FALSE
D1754V9, binary
                cls
clus               0   1
  GAB3 MUTATED    10   1
  GAB3 WILD-TYPE 304  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED     10    1
  GAB3 WILD-TYPE  304   47
                               clus
vv                              GAB3 MUTATED GAB3 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAB3 MUTATED     9   0   0   0
  GAB3 WILD-TYPE 250   3  22  21
D1754V10, multiclass
    clus
vv   GAB3 MUTATED GAB3 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            0             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"
D1754V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAB3 MUTATED                                  0     0
  GAB3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAB3 MUTATED                           0     3
  GAB3 WILD-TYPE                        19   173
D1754V12, multiclass
                                  clus
vv                                 GAB3 MUTATED GAB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = SIGLEC14 MUTATION ANALYSIS
D1755V1, survival
                    sevent
clus2                  0   1
  SIGLEC14 MUTATED     5   2
  SIGLEC14 WILD-TYPE 272  76
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 7                348 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 76 
$`SIGLEC14 MUTATED`
TCGA-AZ-6601 TCGA-G4-6588 TCGA-AA-3977 TCGA-AZ-6598 TCGA-CM-4752 TCGA-D5-6927 
      100.01        26.17        25.02        49.41        13.02         9.44 
TCGA-DM-A282 
      139.17 

$`SIGLEC14 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              9.44               0.00 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
            139.17             148.01 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             26.17              22.01 
[1] "9.4 - 139.2 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1755V2, continuous
                    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      64        1       24       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIGLEC14 MUTATED           0          0          0          0        0
  SIGLEC14 WILD-TYPE        18          6         44         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  SIGLEC14 MUTATED           0         0
  SIGLEC14 WILD-TYPE        12         1
D1755V3, multiclass
            clus
vv           SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 5                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  SIGLEC14 MUTATED     0   1   7   0
  SIGLEC14 WILD-TYPE   9  66 242  41
D1755V4, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                7                242
  T4                0                 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
  SIGLEC14 MUTATED     8   0   0
  SIGLEC14 WILD-TYPE 212  81  66
D1755V5, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  N0                8                212
  N1                0                 81
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1755V6, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     6   0
  SIGLEC14 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      6    0
  SIGLEC14 WILD-TYPE  279   48
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D1755V7, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     4   4
  SIGLEC14 WILD-TYPE 166 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      4    4
  SIGLEC14 WILD-TYPE  166  193
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  FEMALE                4                166
  MALE                  4                193
[1] 2 2
[1] FALSE
D1755V8, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     6   0
  SIGLEC14 WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      6    0
  SIGLEC14 WILD-TYPE  294    8
     clus
vv    SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D1755V9, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     8   0
  SIGLEC14 WILD-TYPE 306  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      8    0
  SIGLEC14 WILD-TYPE  306   48
                               clus
vv                              SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  COLON ADENOCARCINOMA                         8                306
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SIGLEC14 MUTATED     4   0   0   0
  SIGLEC14 WILD-TYPE 255   3  22  21
D1755V10, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  R0                4                255
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1755V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIGLEC14 MUTATED                                  0     0
  SIGLEC14 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC14 MUTATED                           1     5
  SIGLEC14 WILD-TYPE                        18   171
D1755V12, multiclass
                                  clus
vv                                 SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           5                171
[1] 4 2
[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 = GBA2 MUTATION ANALYSIS
D1756V1, survival
                sevent
clus2              0   1
  GBA2 MUTATED    10   4
  GBA2 WILD-TYPE 267  74
  GBA2 MUTATED GBA2 WILD-TYPE 
            14            341 
  GBA2 MUTATED GBA2 WILD-TYPE 
             4             74 
$`GBA2 MUTATED`
TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 
       19.04       100.01        35.80        22.06        20.12         6.97 
TCGA-AA-3833 TCGA-AA-3966 TCGA-AA-A00J TCGA-AU-6004 TCGA-AY-6197 TCGA-DM-A1DA 
       15.95         2.01        18.05        27.09        21.44         7.50 
TCGA-DM-A28K TCGA-F4-6460 
       98.24        31.96 

$`GBA2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GBA2 MUTATED GBA2 WILD-TYPE 
          2.01           0.00 
  GBA2 MUTATED GBA2 WILD-TYPE 
        100.01         148.01 
  GBA2 MUTATED GBA2 WILD-TYPE 
         20.78          22.09 
[1] "2.0 - 100.0 (20.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1756V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GBA2 MUTATED         1        0        3         7         0         0
  GBA2 WILD-TYPE      63        1       23       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GBA2 MUTATED           0          0          2          1        1         0
  GBA2 WILD-TYPE        18          6         42         32       34        12
                vv
clus             STAGE IVB
  GBA2 MUTATED           0
  GBA2 WILD-TYPE         1
D1756V3, multiclass
            clus
vv           GBA2 MUTATED GBA2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             7            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  GBA2 MUTATED     0   1  13   1
  GBA2 WILD-TYPE   9  66 236  40
D1756V4, multiclass
    clus
vv   GBA2 MUTATED GBA2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           13            236
  T4            1             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
  GBA2 MUTATED    11   2   2
  GBA2 WILD-TYPE 209  79  64
D1756V5, multiclass
    clus
vv   GBA2 MUTATED GBA2 WILD-TYPE
  N0           11            209
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1756V6, binary
                cls
clus               0   1
  GBA2 MUTATED    12   1
  GBA2 WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBA2 MUTATED     12    1
  GBA2 WILD-TYPE  273   47
   clus
vv  GBA2 MUTATED GBA2 WILD-TYPE
  0           12            273
  1            1             47
[1] 2 2
[1] FALSE
D1756V7, binary
                cls
clus               0   1
  GBA2 MUTATED     8   7
  GBA2 WILD-TYPE 162 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBA2 MUTATED      8    7
  GBA2 WILD-TYPE  162  190
        clus
vv       GBA2 MUTATED GBA2 WILD-TYPE
  FEMALE            8            162
  MALE              7            190
[1] 2 2
[1] FALSE
D1756V8, binary
                cls
clus               0   1
  GBA2 MUTATED    10   0
  GBA2 WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBA2 MUTATED     10    0
  GBA2 WILD-TYPE  290    8
     clus
vv    GBA2 MUTATED GBA2 WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1756V9, binary
                cls
clus               0   1
  GBA2 MUTATED    11   4
  GBA2 WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBA2 MUTATED     11    4
  GBA2 WILD-TYPE  303   44
                               clus
vv                              GBA2 MUTATED GBA2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            303
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GBA2 MUTATED     9   0   1   0
  GBA2 WILD-TYPE 250   3  21  21
D1756V10, multiclass
    clus
vv   GBA2 MUTATED GBA2 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            1             21
  RX            0             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"
D1756V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GBA2 MUTATED                                  0     0
  GBA2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GBA2 MUTATED                           0     9
  GBA2 WILD-TYPE                        19   167
D1756V12, multiclass
                                  clus
vv                                 GBA2 MUTATED GBA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(1757) Variable = RTTN MUTATION ANALYSIS
D1757V1, survival
                sevent
clus2              0   1
  RTTN MUTATED    12   5
  RTTN WILD-TYPE 265  73
  RTTN MUTATED RTTN WILD-TYPE 
            17            338 
  RTTN MUTATED RTTN WILD-TYPE 
             5             73 
$`RTTN MUTATED`
TCGA-AA-3672 TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6625 TCGA-A6-5665 
        0.92        25.08       100.01        35.80        91.79        22.06 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-6197 
        3.02        63.98        26.01        34.98        38.07        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6931 TCGA-DM-A28G 
       58.39        12.76        10.06        12.00        60.79 

$`RTTN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       39.06        21.37        15.52        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 
       49.08         5.88        63.62        22.09        26.17        79.69 
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-A6-5656 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  RTTN MUTATED RTTN WILD-TYPE 
          0.92           0.00 
  RTTN MUTATED RTTN WILD-TYPE 
        100.01         148.01 
  RTTN MUTATED RTTN WILD-TYPE 
         26.01          21.99 
[1] "0.9 - 100.0 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1757V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RTTN MUTATED         0        0        3         8         1         0
  RTTN WILD-TYPE      64        1       23       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTTN MUTATED           2          0          2          1        0         0
  RTTN WILD-TYPE        16          6         42         32       35        12
                vv
clus             STAGE IVB
  RTTN MUTATED           0
  RTTN WILD-TYPE         1
D1757V3, multiclass
            clus
vv           RTTN MUTATED RTTN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  RTTN MUTATED     0   0  15   2
  RTTN WILD-TYPE   9  67 234  39
D1757V4, multiclass
    clus
vv   RTTN MUTATED RTTN WILD-TYPE
  T1            0              9
  T2            0             67
  T3           15            234
  T4            2             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
  RTTN MUTATED    12   4   1
  RTTN WILD-TYPE 208  77  65
D1757V5, multiclass
    clus
vv   RTTN MUTATED RTTN WILD-TYPE
  N0           12            208
  N1            4             77
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1757V6, binary
                cls
clus               0   1
  RTTN MUTATED    16   0
  RTTN WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED     16    0
  RTTN WILD-TYPE  269   48
   clus
vv  RTTN MUTATED RTTN WILD-TYPE
  0           16            269
  1            0             48
[1] 2 2
[1] FALSE
D1757V7, binary
                cls
clus               0   1
  RTTN MUTATED     8   9
  RTTN WILD-TYPE 162 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      8    9
  RTTN WILD-TYPE  162  188
        clus
vv       RTTN MUTATED RTTN WILD-TYPE
  FEMALE            8            162
  MALE              9            188
[1] 2 2
[1] FALSE
D1757V8, binary
                cls
clus               0   1
  RTTN MUTATED    16   0
  RTTN WILD-TYPE 284   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED     16    0
  RTTN WILD-TYPE  284    8
     clus
vv    RTTN MUTATED RTTN WILD-TYPE
  NO            16            284
  YES            0              8
[1] 2 2
[1] FALSE
D1757V9, binary
                cls
clus               0   1
  RTTN MUTATED    15   2
  RTTN WILD-TYPE 299  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED     15    2
  RTTN WILD-TYPE  299   46
                               clus
vv                              RTTN MUTATED RTTN WILD-TYPE
  COLON ADENOCARCINOMA                    15            299
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RTTN MUTATED    13   0   0   2
  RTTN WILD-TYPE 246   3  22  19
D1757V10, multiclass
    clus
vv   RTTN MUTATED RTTN WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            2             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"
D1757V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RTTN MUTATED                                  0     2
  RTTN WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RTTN MUTATED                           0     9
  RTTN WILD-TYPE                        19   167
D1757V12, multiclass
                                  clus
vv                                 RTTN MUTATED RTTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       9            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(1758) Variable = SFRS12IP1 MUTATION ANALYSIS
D1758V1, survival
                     sevent
clus2                   0   1
  SFRS12IP1 MUTATED     3   0
  SFRS12IP1 WILD-TYPE 274  78
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  3                 352 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  0                  78 
$`SFRS12IP1 MUTATED`
TCGA-G4-6628 TCGA-AD-6890 TCGA-G4-6309 
       79.69        24.53        85.48 

$`SFRS12IP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
              24.53                0.00 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
              85.48              148.01 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
              79.69               22.01 
[1] "24.5 - 85.5 (79.7)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9300000"
D1758V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS12IP1 MUTATED         1        0        0         0         0         0
  SFRS12IP1 WILD-TYPE      63        1       26       108         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS12IP1 MUTATED           0          0          1          0        0
  SFRS12IP1 WILD-TYPE        18          6         43         33       35
                     vv
clus                  STAGE IVA STAGE IVB
  SFRS12IP1 MUTATED           0         0
  SFRS12IP1 WILD-TYPE        12         1
D1758V3, multiclass
[1] "Remove cluster labels:" "SFRS12IP1 MUTATED"     
clus
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  2                 355 
         TCGA-A6-2677          TCGA-A6-4105          TCGA-A6-6649 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3516          TCGA-AA-3520 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3527          TCGA-AA-3530 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3543          TCGA-AA-3552 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3554          TCGA-AA-3556          TCGA-AA-3560 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3562          TCGA-AA-3662          TCGA-AA-3672 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3697 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3713          TCGA-AA-3715          TCGA-AA-3814 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3860          TCGA-AA-3867 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3870          TCGA-AA-3939          TCGA-AA-3950 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3972          TCGA-AA-3976 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3979          TCGA-AA-3986          TCGA-AA-A00L 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A024          TCGA-AD-6548 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6895          TCGA-AZ-4681 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AZ-6601          TCGA-AZ-6608          TCGA-CK-5912 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A285          TCGA-G4-6310          TCGA-G4-6321 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6586          TCGA-G4-6588          TCGA-G4-6625 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2678          TCGA-A6-2683 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5656          TCGA-A6-5657 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5660          TCGA-A6-5661 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-5662          TCGA-A6-5664          TCGA-A6-5665 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-5666          TCGA-A6-6137          TCGA-A6-6138 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-6141          TCGA-A6-6142          TCGA-A6-6648 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-6651          TCGA-A6-6652          TCGA-A6-6653 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-6654          TCGA-A6-6780          TCGA-A6-6781 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-6782          TCGA-AA-3489          TCGA-AA-3492 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3502          TCGA-AA-3510          TCGA-AA-3511 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3514          TCGA-AA-3517          TCGA-AA-3518 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3519          TCGA-AA-3526          TCGA-AA-3529 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3544          TCGA-AA-3548 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3549          TCGA-AA-3553          TCGA-AA-3555 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3558          TCGA-AA-3561          TCGA-AA-3655 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3663          TCGA-AA-3664 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3666          TCGA-AA-3667          TCGA-AA-3673 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3678          TCGA-AA-3679          TCGA-AA-3680 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3681          TCGA-AA-3684          TCGA-AA-3685 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3693          TCGA-AA-3695          TCGA-AA-3696 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3710          TCGA-AA-3712          TCGA-AA-3811 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3812          TCGA-AA-3815          TCGA-AA-3818 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3819          TCGA-AA-3821          TCGA-AA-3831 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3833          TCGA-AA-3837          TCGA-AA-3842 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3861          TCGA-AA-3864 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3866          TCGA-AA-3869          TCGA-AA-3872 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3941          TCGA-AA-3947          TCGA-AA-3949 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3966 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3968          TCGA-AA-3971          TCGA-AA-3973 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3980          TCGA-AA-3982 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3989          TCGA-AA-3994 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A004          TCGA-AA-A00A          TCGA-AA-A00D 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00E          TCGA-AA-A00F          TCGA-AA-A00J 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00K          TCGA-AA-A00N          TCGA-AA-A00O 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00Q          TCGA-AA-A00R          TCGA-AA-A00U 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00W          TCGA-AA-A010          TCGA-AA-A017 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A029 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A02F          TCGA-AA-A02H          TCGA-AA-A02J 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A02K          TCGA-AA-A02O          TCGA-AA-A02W 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A02Y          TCGA-AA-A03F          TCGA-AA-A03J 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AD-5900          TCGA-AD-6889          TCGA-AD-6899 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AD-6965          TCGA-AU-3779          TCGA-AU-6004 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4323          TCGA-AZ-4616 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AZ-6605          TCGA-AZ-6606          TCGA-AZ-6607 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5913          TCGA-CK-5914 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6534 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6535          TCGA-D5-6536          TCGA-D5-6537 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6538          TCGA-D5-6540          TCGA-D5-6541 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6928          TCGA-D5-6929 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6930          TCGA-D5-6931          TCGA-D5-6932 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-7000          TCGA-DM-A0X9          TCGA-DM-A0XD 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A0XF          TCGA-DM-A1D0          TCGA-DM-A1D4 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A1D6          TCGA-DM-A1D7          TCGA-DM-A1D9 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A1DA          TCGA-DM-A1DB          TCGA-DM-A1HA 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A1HB          TCGA-DM-A282          TCGA-DM-A28C 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A28E          TCGA-DM-A28F          TCGA-DM-A28G 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-DM-A28H          TCGA-DM-A28K          TCGA-F4-6459 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6460          TCGA-F4-6569          TCGA-F4-6570 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6703          TCGA-F4-6704          TCGA-F4-6805 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6806          TCGA-F4-6807          TCGA-F4-6808 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6809          TCGA-F4-6854          TCGA-F4-6855 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6856          TCGA-G4-6293          TCGA-G4-6299 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6307 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6323 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6626 
"SFRS12IP1 WILD-TYPE" 
                     vv
clus                   T1  T2  T3  T4
  SFRS12IP1 MUTATED     1   1   1   0
  SFRS12IP1 WILD-TYPE   8  66 248  41
D1758V4, multiclass
    clus
vv   SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  T1                 1                   8
  T2                 1                  66
  T3                 1                 248
  T4                 0                  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
  SFRS12IP1 MUTATED     2   1   0
  SFRS12IP1 WILD-TYPE 218  80  66
D1758V5, multiclass
    clus
vv   SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  N0                 2                 218
  N1                 1                  80
  N2                 0                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1758V6, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     2   0
  SFRS12IP1 WILD-TYPE 283  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      2    0
  SFRS12IP1 WILD-TYPE  283   48
   clus
vv  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  0                 2                 283
  1                 0                  48
[1] 2 2
[1] FALSE
D1758V7, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     1   2
  SFRS12IP1 WILD-TYPE 169 195
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      1    2
  SFRS12IP1 WILD-TYPE  169  195
        clus
vv       SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  FEMALE                 1                 169
  MALE                   2                 195
[1] 2 2
[1] FALSE
D1758V8, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     3   0
  SFRS12IP1 WILD-TYPE 297   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      3    0
  SFRS12IP1 WILD-TYPE  297    8
     clus
vv    SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  NO                  3                 297
  YES                 0                   8
[1] 2 2
[1] FALSE
D1758V9, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     3   0
  SFRS12IP1 WILD-TYPE 311  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      3    0
  SFRS12IP1 WILD-TYPE  311   48
                               clus
vv                              SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  COLON ADENOCARCINOMA                          3                 311
  COLON MUCINOUS ADENOCARCINOMA                 0                  48
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  SFRS12IP1 MUTATED     2   0   0   0
  SFRS12IP1 WILD-TYPE 257   3  22  21
D1758V10, multiclass
[1] "Remove cluster labels:" "SFRS12IP1 MUTATED"     
clus
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  2                 303 
         TCGA-A6-2677          TCGA-AA-3496          TCGA-AA-3520 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3527          TCGA-AA-3530 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3543          TCGA-AA-3552 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3554          TCGA-AA-3556          TCGA-AA-3560 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3562          TCGA-AA-3662          TCGA-AA-3672 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3697 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3713          TCGA-AA-3715          TCGA-AA-3814 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3860          TCGA-AA-3867 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3870          TCGA-AA-3939          TCGA-AA-3950 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3972          TCGA-AA-3976 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3979          TCGA-AA-3986          TCGA-AA-A00L 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A024          TCGA-AD-6548 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6895          TCGA-AZ-4681 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-5912          TCGA-G4-6310          TCGA-G4-6321 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6586          TCGA-G4-6588          TCGA-G4-6625 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2678          TCGA-A6-2683 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-3807          TCGA-A6-3808          TCGA-A6-3809 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-3810          TCGA-A6-5657          TCGA-A6-5659 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-A6-5661          TCGA-A6-5665          TCGA-A6-6781 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3489          TCGA-AA-3492          TCGA-AA-3502 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3510          TCGA-AA-3511          TCGA-AA-3514 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3517          TCGA-AA-3518          TCGA-AA-3519 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3526          TCGA-AA-3529          TCGA-AA-3532 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3534          TCGA-AA-3538          TCGA-AA-3542 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3544          TCGA-AA-3548          TCGA-AA-3549 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3555          TCGA-AA-3558 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3655          TCGA-AA-3660 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3663          TCGA-AA-3664          TCGA-AA-3666 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3667          TCGA-AA-3673          TCGA-AA-3678 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3693 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3695          TCGA-AA-3696          TCGA-AA-3710 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3811          TCGA-AA-3812 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3845 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3846          TCGA-AA-3848          TCGA-AA-3850 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3851          TCGA-AA-3852          TCGA-AA-3854 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3855          TCGA-AA-3856          TCGA-AA-3858 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3861          TCGA-AA-3864          TCGA-AA-3866 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3872          TCGA-AA-3875 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3877          TCGA-AA-3930          TCGA-AA-3941 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3947          TCGA-AA-3949          TCGA-AA-3955 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3956          TCGA-AA-3968          TCGA-AA-3971 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3973          TCGA-AA-3975          TCGA-AA-3984 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-3989          TCGA-AA-3994          TCGA-AA-A004 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A010          TCGA-AA-A017          TCGA-AA-A01D 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01F          TCGA-AA-A01G          TCGA-AA-A01I 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01K          TCGA-AA-A01P          TCGA-AA-A01Q 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01R          TCGA-AA-A01S          TCGA-AA-A01T 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A01V          TCGA-AA-A01X          TCGA-AA-A01Z 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A022          TCGA-AA-A029          TCGA-AA-A02F 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A02H          TCGA-AA-A02J          TCGA-AA-A02K 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A02O          TCGA-AA-A02W          TCGA-AA-A02Y 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AA-A03F          TCGA-AA-A03J          TCGA-AD-5900 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AD-6889          TCGA-AD-6965          TCGA-AU-3779 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          TCGA-AZ-4682 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5913          TCGA-CK-5914 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6930 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6315 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6323          TCGA-G4-6626 
"SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" "SFRS12IP1 WILD-TYPE" 
D1758V11, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS12IP1 MUTATED                                  0     0
  SFRS12IP1 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  SFRS12IP1 MUTATED                           1     2
  SFRS12IP1 WILD-TYPE                        18   174
D1758V12, multiclass
                                  clus
vv                                 SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        1                  18
  WHITE                                            2                 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(1759) Variable = TOMM70A MUTATION ANALYSIS
D1759V1, survival
                   sevent
clus2                 0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 268  77
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               345 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
                1                77 
$`TOMM70A MUTATED`
TCGA-AA-3554 TCGA-G4-6625 TCGA-G4-6628 TCGA-AA-3815 TCGA-AA-A010 TCGA-AA-A01R 
       17.95        91.79        79.69        33.04        34.98        35.01 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-G4-6299 TCGA-G4-6304 
       58.39         6.77        74.56        53.62 

$`TOMM70A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       35.80        26.17        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
      133.18        65.85        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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            21.990 
[1] "6.8 - 91.8 (44.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "3.7"
D1759V2, continuous
                   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      62        1       26       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOMM70A MUTATED           1          0          0          1        0
  TOMM70A WILD-TYPE        17          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  TOMM70A MUTATED           0         0
  TOMM70A WILD-TYPE        12         1
D1759V3, multiclass
            clus
vv           TOMM70A MUTATED TOMM70A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  TOMM70A MUTATED     0   2   6   2
  TOMM70A WILD-TYPE   9  65 243  39
D1759V4, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               6               243
  T4               2                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
  TOMM70A MUTATED     8   0   2
  TOMM70A WILD-TYPE 212  81  64
D1759V5, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  N0               8               212
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1759V6, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   0
  TOMM70A WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    0
  TOMM70A WILD-TYPE  276   48
   clus
vv  TOMM70A MUTATED TOMM70A WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D1759V7, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     5   5
  TOMM70A WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      5    5
  TOMM70A WILD-TYPE  165  192
        clus
vv       TOMM70A MUTATED TOMM70A WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D1759V8, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 291   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    1
  TOMM70A WILD-TYPE  291    7
     clus
vv    TOMM70A MUTATED TOMM70A WILD-TYPE
  NO                9               291
  YES               1                 7
[1] 2 2
[1] FALSE
D1759V9, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    1
  TOMM70A WILD-TYPE  305   47
                               clus
vv                              TOMM70A MUTATED TOMM70A WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TOMM70A MUTATED     9   0   0   0
  TOMM70A WILD-TYPE 250   3  22  21
D1759V10, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               0                22
  RX               0                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"
D1759V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOMM70A MUTATED                                  0     0
  TOMM70A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TOMM70A MUTATED                           0     6
  TOMM70A WILD-TYPE                        19   170
D1759V12, multiclass
                                  clus
vv                                 TOMM70A MUTATED TOMM70A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = RRP9 MUTATION ANALYSIS
D1760V1, survival
                sevent
clus2              0   1
  RRP9 MUTATED    10   2
  RRP9 WILD-TYPE 267  76
  RRP9 MUTATED RRP9 WILD-TYPE 
            12            343 
  RRP9 MUTATED RRP9 WILD-TYPE 
             2             76 
$`RRP9 MUTATED`
TCGA-AA-3672 TCGA-AA-3979 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-A01R 
        0.92        24.00         6.97        15.95        53.00        35.01 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6163 TCGA-D5-6538 TCGA-D5-6927 TCGA-DM-A0XF 
       15.62        21.14        14.04        17.13         9.44        38.20 

$`RRP9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        82.95         2.01       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-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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          22.09 
[1] "0.9 - 53.0 (16.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1760V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RRP9 MUTATED         2        0        2         3         0         0
  RRP9 WILD-TYPE      62        1       24       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRP9 MUTATED           2          0          1          2        0         0
  RRP9 WILD-TYPE        16          6         43         31       35        12
                vv
clus             STAGE IVB
  RRP9 MUTATED           0
  RRP9 WILD-TYPE         1
D1760V3, multiclass
            clus
vv           RRP9 MUTATED RRP9 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             16
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  RRP9 MUTATED     2   0   9   1
  RRP9 WILD-TYPE   7  67 240  40
D1760V4, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  T1            2              7
  T2            0             67
  T3            9            240
  T4            1             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
  RRP9 MUTATED     7   1   4
  RRP9 WILD-TYPE 213  80  62
D1760V5, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  N0            7            213
  N1            1             80
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1760V6, binary
                cls
clus               0   1
  RRP9 MUTATED    12   0
  RRP9 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED     12    0
  RRP9 WILD-TYPE  273   48
   clus
vv  RRP9 MUTATED RRP9 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D1760V7, binary
                cls
clus               0   1
  RRP9 MUTATED     6   6
  RRP9 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED      6    6
  RRP9 WILD-TYPE  164  191
        clus
vv       RRP9 MUTATED RRP9 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D1760V8, binary
                cls
clus               0   1
  RRP9 MUTATED     9   1
  RRP9 WILD-TYPE 291   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED      9    1
  RRP9 WILD-TYPE  291    7
     clus
vv    RRP9 MUTATED RRP9 WILD-TYPE
  NO             9            291
  YES            1              7
[1] 2 2
[1] FALSE
D1760V9, binary
                cls
clus               0   1
  RRP9 MUTATED     9   2
  RRP9 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED      9    2
  RRP9 WILD-TYPE  305   46
                               clus
vv                              RRP9 MUTATED RRP9 WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RRP9 MUTATED     9   0   0   2
  RRP9 WILD-TYPE 250   3  22  19
D1760V10, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            2             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"
D1760V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRP9 MUTATED                                  0     0
  RRP9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RRP9 MUTATED                           0     6
  RRP9 WILD-TYPE                        19   170
D1760V12, multiclass
                                  clus
vv                                 RRP9 MUTATED RRP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = FSTL4 MUTATION ANALYSIS
D1761V1, survival
                 sevent
clus2               0   1
  FSTL4 MUTATED    13   2
  FSTL4 WILD-TYPE 264  76
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             15             340 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
              2              76 
$`FSTL4 MUTATED`
TCGA-AA-3672 TCGA-AA-3986 TCGA-AD-6964 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 
        0.92        19.07        10.88        22.06        63.98         6.97 
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 
       16.14        15.58       135.65 

$`FSTL4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        24.00        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        25.08       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        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        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FSTL4 MUTATED FSTL4 WILD-TYPE 
           0.92            0.00 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
         135.65          148.01 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
          17.85           22.39 
[1] "0.9 - 135.7 (17.9)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D1761V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FSTL4 MUTATED         3        0        2         7         0         0
  FSTL4 WILD-TYPE      61        1       24       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FSTL4 MUTATED           1          0          1          0        0         0
  FSTL4 WILD-TYPE        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  FSTL4 MUTATED           0
  FSTL4 WILD-TYPE         1
D1761V3, multiclass
            clus
vv           FSTL4 MUTATED FSTL4 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  FSTL4 MUTATED     0   3  11   1
  FSTL4 WILD-TYPE   9  64 238  40
D1761V4, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  T1             0               9
  T2             3              64
  T3            11             238
  T4             1              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
  FSTL4 MUTATED    12   2   1
  FSTL4 WILD-TYPE 208  79  65
D1761V5, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1761V6, binary
                 cls
clus                0   1
  FSTL4 MUTATED    13   0
  FSTL4 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     13    0
  FSTL4 WILD-TYPE  272   48
   clus
vv  FSTL4 MUTATED FSTL4 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D1761V7, binary
                 cls
clus                0   1
  FSTL4 MUTATED     4  11
  FSTL4 WILD-TYPE 166 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED      4   11
  FSTL4 WILD-TYPE  166  186
        clus
vv       FSTL4 MUTATED FSTL4 WILD-TYPE
  FEMALE             4             166
  MALE              11             186
[1] 2 2
[1] FALSE
D1761V8, binary
                 cls
clus                0   1
  FSTL4 MUTATED    13   0
  FSTL4 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     13    0
  FSTL4 WILD-TYPE  287    8
     clus
vv    FSTL4 MUTATED FSTL4 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D1761V9, binary
                 cls
clus                0   1
  FSTL4 MUTATED    13   1
  FSTL4 WILD-TYPE 301  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     13    1
  FSTL4 WILD-TYPE  301   47
                               clus
vv                              FSTL4 MUTATED FSTL4 WILD-TYPE
  COLON ADENOCARCINOMA                     13             301
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FSTL4 MUTATED    12   0   0   1
  FSTL4 WILD-TYPE 247   3  22  20
D1761V10, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D1761V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FSTL4 MUTATED                                  0     1
  FSTL4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FSTL4 MUTATED                           0    10
  FSTL4 WILD-TYPE                        19   166
D1761V12, multiclass
                                  clus
vv                                 FSTL4 MUTATED FSTL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       10             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(1762) Variable = HIST4H4 MUTATION ANALYSIS
D1762V1, survival
                   sevent
clus2                 0   1
  HIST4H4 MUTATED     3   0
  HIST4H4 WILD-TYPE 274  78
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               352 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                0                78 
$`HIST4H4 MUTATED`
TCGA-AA-3713 TCGA-AY-5543 TCGA-CK-4950 
       19.04        33.01        85.45 

$`HIST4H4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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            22.045 
[1] "19.0 - 85.5 (33.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1762V2, continuous
                   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      64        1       26       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST4H4 MUTATED           0          0          1          0        1
  HIST4H4 WILD-TYPE        18          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  HIST4H4 MUTATED           1         0
  HIST4H4 WILD-TYPE        11         1
D1762V3, multiclass
            clus
vv           HIST4H4 MUTATED HIST4H4 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                0               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                1                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
  HIST4H4 MUTATED     0   0   3   0
  HIST4H4 WILD-TYPE   9  67 246  41
D1762V4, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               3               246
  T4               0                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
  HIST4H4 MUTATED     1   2   0
  HIST4H4 WILD-TYPE 219  79  66
D1762V5, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  N0               1               219
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1762V6, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     1   2
  HIST4H4 WILD-TYPE 284  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      1    2
  HIST4H4 WILD-TYPE  284   46
   clus
vv  HIST4H4 MUTATED HIST4H4 WILD-TYPE
  0               1               284
  1               2                46
[1] 2 2
[1] FALSE
D1762V7, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     2   1
  HIST4H4 WILD-TYPE 168 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      2    1
  HIST4H4 WILD-TYPE  168  196
        clus
vv       HIST4H4 MUTATED HIST4H4 WILD-TYPE
  FEMALE               2               168
  MALE                 1               196
[1] 2 2
[1] FALSE
D1762V8, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     2   1
  HIST4H4 WILD-TYPE 298   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      2    1
  HIST4H4 WILD-TYPE  298    7
     clus
vv    HIST4H4 MUTATED HIST4H4 WILD-TYPE
  NO                2               298
  YES               1                 7
[1] 2 2
[1] FALSE
D1762V9, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     2   1
  HIST4H4 WILD-TYPE 312  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      2    1
  HIST4H4 WILD-TYPE  312   47
                               clus
vv                              HIST4H4 MUTATED HIST4H4 WILD-TYPE
  COLON ADENOCARCINOMA                        2               312
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HIST4H4 MUTATED     1   1   1   0
  HIST4H4 WILD-TYPE 258   2  21  21
D1762V10, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  R0               1               258
  R1               1                 2
  R2               1                21
  RX               0                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"
D1762V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST4H4 MUTATED                                  0     0
  HIST4H4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HIST4H4 MUTATED                           2     0
  HIST4H4 WILD-TYPE                        17   176
D1762V12, multiclass
[1] "Remove cluster labels:" "HIST4H4 MUTATED"       
clus
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"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-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 

Clustering(1763) Variable = C1ORF88 MUTATION ANALYSIS
D1763V1, survival
                   sevent
clus2                 0   1
  C1ORF88 MUTATED     5   1
  C1ORF88 WILD-TYPE 272  77
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                6               349 
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                1                77 
$`C1ORF88 MUTATED`
TCGA-AA-3697 TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A28G 
       85.05         6.97        18.05        34.98        12.76        60.79 

$`C1ORF88 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28H TCGA-DM-A28K 
      139.17        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  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            22.060 
[1] "7.0 - 85.0 (26.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1763V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF88 MUTATED         0        0        2         2         1         0
  C1ORF88 WILD-TYPE      64        1       24       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF88 MUTATED           0          0          1          0        0
  C1ORF88 WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF88 MUTATED           0         0
  C1ORF88 WILD-TYPE        12         1
D1763V3, multiclass
            clus
vv           C1ORF88 MUTATED C1ORF88 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C1ORF88 MUTATED     0   0   4   2
  C1ORF88 WILD-TYPE   9  67 245  39
D1763V4, multiclass
    clus
vv   C1ORF88 MUTATED C1ORF88 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               4               245
  T4               2                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
  C1ORF88 MUTATED     5   1   0
  C1ORF88 WILD-TYPE 215  80  66
D1763V5, multiclass
    clus
vv   C1ORF88 MUTATED C1ORF88 WILD-TYPE
  N0               5               215
  N1               1                80
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1763V6, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     6   0
  C1ORF88 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      6    0
  C1ORF88 WILD-TYPE  279   48
   clus
vv  C1ORF88 MUTATED C1ORF88 WILD-TYPE
  0               6               279
  1               0                48
[1] 2 2
[1] FALSE
D1763V7, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     1   5
  C1ORF88 WILD-TYPE 169 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      1    5
  C1ORF88 WILD-TYPE  169  192
        clus
vv       C1ORF88 MUTATED C1ORF88 WILD-TYPE
  FEMALE               1               169
  MALE                 5               192
[1] 2 2
[1] FALSE
D1763V8, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     5   0
  C1ORF88 WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      5    0
  C1ORF88 WILD-TYPE  295    8
     clus
vv    C1ORF88 MUTATED C1ORF88 WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1763V9, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     4   2
  C1ORF88 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      4    2
  C1ORF88 WILD-TYPE  310   46
                               clus
vv                              C1ORF88 MUTATED C1ORF88 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C1ORF88 MUTATED     4   0   0   1
  C1ORF88 WILD-TYPE 255   3  22  20
D1763V10, multiclass
    clus
vv   C1ORF88 MUTATED C1ORF88 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               1                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"
D1763V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF88 MUTATED                                  0     1
  C1ORF88 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF88 MUTATED                           0     1
  C1ORF88 WILD-TYPE                        19   175
D1763V12, multiclass
[1] "Remove cluster labels:" "C1ORF88 MUTATED"       
clus
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"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-A6-6651        TCGA-A6-6652 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-6600        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-6607        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-5913        TCGA-CK-5914        TCGA-CK-5915 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A28F        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 

Clustering(1764) Variable = SESTD1 MUTATION ANALYSIS
D1764V1, survival
                  sevent
clus2                0   1
  SESTD1 MUTATED    10   5
  SESTD1 WILD-TYPE 267  73
  SESTD1 MUTATED SESTD1 WILD-TYPE 
              15              340 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
               5               73 
$`SESTD1 MUTATED`
TCGA-AA-3554 TCGA-AA-3952 TCGA-G4-6628 TCGA-A6-2678 TCGA-A6-6653 TCGA-A6-6780 
       17.95         2.01        79.69        42.28        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3529 TCGA-AA-A00J TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-6598 
        3.02         0.00        18.05         1.02        27.09        49.41 
TCGA-CA-6717 TCGA-D5-6930 TCGA-G4-6303 
       12.76        13.35        65.85 

$`SESTD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 
       31.07        24.03        29.98        12.99        24.00        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.69        23.87        19.66        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-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SESTD1 MUTATED SESTD1 WILD-TYPE 
               0                0 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
           79.69           148.01 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
           18.05            22.09 
[1] "0.0 - 79.7 (18.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1764V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SESTD1 MUTATED         3        0        3         4         0         0
  SESTD1 WILD-TYPE      61        1       23       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SESTD1 MUTATED           0          0          2          2        1
  SESTD1 WILD-TYPE        18          6         42         31       34
                  vv
clus               STAGE IVA STAGE IVB
  SESTD1 MUTATED           0         0
  SESTD1 WILD-TYPE        12         1
D1764V3, multiclass
            clus
vv           SESTD1 MUTATED SESTD1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               4              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  SESTD1 MUTATED     0   3  11   1
  SESTD1 WILD-TYPE   9  64 238  40
D1764V4, multiclass
    clus
vv   SESTD1 MUTATED SESTD1 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             11              238
  T4              1               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
  SESTD1 MUTATED    10   3   2
  SESTD1 WILD-TYPE 210  78  64
D1764V5, multiclass
    clus
vv   SESTD1 MUTATED SESTD1 WILD-TYPE
  N0             10              210
  N1              3               78
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1764V6, binary
                  cls
clus                 0   1
  SESTD1 MUTATED    12   1
  SESTD1 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED     12    1
  SESTD1 WILD-TYPE  273   47
   clus
vv  SESTD1 MUTATED SESTD1 WILD-TYPE
  0             12              273
  1              1               47
[1] 2 2
[1] FALSE
D1764V7, binary
                  cls
clus                 0   1
  SESTD1 MUTATED     8   7
  SESTD1 WILD-TYPE 162 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED      8    7
  SESTD1 WILD-TYPE  162  190
        clus
vv       SESTD1 MUTATED SESTD1 WILD-TYPE
  FEMALE              8              162
  MALE                7              190
[1] 2 2
[1] FALSE
D1764V8, binary
                  cls
clus                 0   1
  SESTD1 MUTATED    11   0
  SESTD1 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED     11    0
  SESTD1 WILD-TYPE  289    8
     clus
vv    SESTD1 MUTATED SESTD1 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1764V9, binary
                  cls
clus                 0   1
  SESTD1 MUTATED    11   4
  SESTD1 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED     11    4
  SESTD1 WILD-TYPE  303   44
                               clus
vv                              SESTD1 MUTATED SESTD1 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SESTD1 MUTATED    11   0   0   1
  SESTD1 WILD-TYPE 248   3  22  20
D1764V10, multiclass
    clus
vv   SESTD1 MUTATED SESTD1 WILD-TYPE
  R0             11              248
  R1              0                3
  R2              0               22
  RX              1               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"
D1764V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SESTD1 MUTATED                                  0     1
  SESTD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SESTD1 MUTATED                           0     8
  SESTD1 WILD-TYPE                        19   168
D1764V12, multiclass
                                  clus
vv                                 SESTD1 MUTATED SESTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = CAPZA3 MUTATION ANALYSIS
D1765V1, survival
                  sevent
clus2                0   1
  CAPZA3 MUTATED     8   1
  CAPZA3 WILD-TYPE 269  77
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               9              346 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               1               77 
$`CAPZA3 MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3989 TCGA-AZ-4315 
       24.00        79.69         8.38        29.95         7.96        58.39 
TCGA-CM-5349 TCGA-D5-6535 TCGA-G4-6304 
       30.08        15.12        53.62 

$`CAPZA3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
            7.96             0.00 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
           79.69           148.01 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
           29.95            22.01 
[1] "8.0 - 79.7 (29.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1765V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAPZA3 MUTATED         1        0        0         5         1         0
  CAPZA3 WILD-TYPE      63        1       26       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAPZA3 MUTATED           0          0          1          0        1
  CAPZA3 WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CAPZA3 MUTATED           0         0
  CAPZA3 WILD-TYPE        12         1
D1765V3, multiclass
            clus
vv           CAPZA3 MUTATED CAPZA3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               5              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CAPZA3 MUTATED     0   1   7   1
  CAPZA3 WILD-TYPE   9  66 242  40
D1765V4, multiclass
    clus
vv   CAPZA3 MUTATED CAPZA3 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              1               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
  CAPZA3 MUTATED     7   1   1
  CAPZA3 WILD-TYPE 213  80  65
D1765V5, multiclass
    clus
vv   CAPZA3 MUTATED CAPZA3 WILD-TYPE
  N0              7              213
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1765V6, binary
                  cls
clus                 0   1
  CAPZA3 MUTATED     7   1
  CAPZA3 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPZA3 MUTATED      7    1
  CAPZA3 WILD-TYPE  278   47
   clus
vv  CAPZA3 MUTATED CAPZA3 WILD-TYPE
  0              7              278
  1              1               47
[1] 2 2
[1] FALSE
D1765V7, binary
                  cls
clus                 0   1
  CAPZA3 MUTATED     5   4
  CAPZA3 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPZA3 MUTATED      5    4
  CAPZA3 WILD-TYPE  165  193
        clus
vv       CAPZA3 MUTATED CAPZA3 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1765V8, binary
                  cls
clus                 0   1
  CAPZA3 MUTATED     9   0
  CAPZA3 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPZA3 MUTATED      9    0
  CAPZA3 WILD-TYPE  291    8
     clus
vv    CAPZA3 MUTATED CAPZA3 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1765V9, binary
                  cls
clus                 0   1
  CAPZA3 MUTATED     7   2
  CAPZA3 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPZA3 MUTATED      7    2
  CAPZA3 WILD-TYPE  307   46
                               clus
vv                              CAPZA3 MUTATED CAPZA3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CAPZA3 MUTATED     6   0   1   1
  CAPZA3 WILD-TYPE 253   3  21  20
D1765V10, multiclass
    clus
vv   CAPZA3 MUTATED CAPZA3 WILD-TYPE
  R0              6              253
  R1              0                3
  R2              1               21
  RX              1               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"
D1765V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPZA3 MUTATED                                  0     0
  CAPZA3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CAPZA3 MUTATED                           1     5
  CAPZA3 WILD-TYPE                        18   171
D1765V12, multiclass
                                  clus
vv                                 CAPZA3 MUTATED CAPZA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = LGALS9 MUTATION ANALYSIS
D1766V1, survival
                  sevent
clus2                0   1
  LGALS9 MUTATED     3   1
  LGALS9 WILD-TYPE 274  77
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               4              351 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               1               77 
$`LGALS9 MUTATED`
TCGA-AA-3672 TCGA-A6-5665 TCGA-AA-3492 TCGA-D5-6930 
        0.92        22.06         3.02        13.35 

$`LGALS9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  LGALS9 MUTATED LGALS9 WILD-TYPE 
            0.92             0.00 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
           22.06           148.01 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
           8.185           22.090 
[1] "0.9 - 22.1 (8.2)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "2.8"
D1766V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LGALS9 MUTATED         0        0        1         2         0         0
  LGALS9 WILD-TYPE      64        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LGALS9 MUTATED           1          0          0          0        0
  LGALS9 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  LGALS9 MUTATED           0         0
  LGALS9 WILD-TYPE        12         1
D1766V3, multiclass
            clus
vv           LGALS9 MUTATED LGALS9 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  LGALS9 MUTATED     0   0   4   0
  LGALS9 WILD-TYPE   9  67 245  41
D1766V4, multiclass
    clus
vv   LGALS9 MUTATED LGALS9 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              0               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
  LGALS9 MUTATED     3   1   0
  LGALS9 WILD-TYPE 217  80  66
D1766V5, multiclass
    clus
vv   LGALS9 MUTATED LGALS9 WILD-TYPE
  N0              3              217
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1766V6, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     4   0
  LGALS9 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      4    0
  LGALS9 WILD-TYPE  281   48
   clus
vv  LGALS9 MUTATED LGALS9 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1766V7, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     3   1
  LGALS9 WILD-TYPE 167 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      3    1
  LGALS9 WILD-TYPE  167  196
        clus
vv       LGALS9 MUTATED LGALS9 WILD-TYPE
  FEMALE              3              167
  MALE                1              196
[1] 2 2
[1] FALSE
D1766V8, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     4   0
  LGALS9 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      4    0
  LGALS9 WILD-TYPE  296    8
     clus
vv    LGALS9 MUTATED LGALS9 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1766V9, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     3   1
  LGALS9 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      3    1
  LGALS9 WILD-TYPE  311   47
                               clus
vv                              LGALS9 MUTATED LGALS9 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LGALS9 MUTATED     4   0   0   0
  LGALS9 WILD-TYPE 255   3  22  21
D1766V10, multiclass
    clus
vv   LGALS9 MUTATED LGALS9 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D1766V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGALS9 MUTATED                                  0     0
  LGALS9 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LGALS9 MUTATED                           0     2
  LGALS9 WILD-TYPE                        19   174
D1766V12, multiclass
[1] "Remove cluster labels:" "LGALS9 MUTATED"        
clus
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652       TCGA-A6-6653 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"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-5913       TCGA-CK-5914       TCGA-CK-5915 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 

Clustering(1767) Variable = MC3R MUTATION ANALYSIS
D1767V1, survival
                sevent
clus2              0   1
  MC3R MUTATED    10   3
  MC3R WILD-TYPE 267  75
  MC3R MUTATED MC3R WILD-TYPE 
            13            342 
  MC3R MUTATED MC3R WILD-TYPE 
             3             75 
$`MC3R MUTATED`
TCGA-G4-6586 TCGA-AA-A010 TCGA-AY-6196 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-6163 
       35.80        34.98         0.20        21.99        23.05        14.04 
TCGA-CM-6166 TCGA-CM-6679 TCGA-DM-A1D4 TCGA-DM-A1DB TCGA-F4-6808 TCGA-G4-6303 
       21.99        10.06        92.75        44.32        33.67        65.85 
TCGA-G4-6304 
       53.62 

$`MC3R WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-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-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 
        0.53        47.41        35.31       133.18        74.56        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  MC3R MUTATED MC3R WILD-TYPE 
           0.2            0.0 
  MC3R MUTATED MC3R WILD-TYPE 
         92.75         148.01 
  MC3R MUTATED MC3R WILD-TYPE 
         33.67          22.01 
[1] "0.2 - 92.8 (33.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1767V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MC3R MUTATED         3        0        0         5         2         0
  MC3R WILD-TYPE      61        1       26       103         6         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        18          6         43         32       34        12
                vv
clus             STAGE IVB
  MC3R MUTATED           0
  MC3R WILD-TYPE         1
D1767V3, multiclass
            clus
vv           MC3R MUTATED MC3R WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             0             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
  MC3R MUTATED     2   1   8   2
  MC3R WILD-TYPE   7  66 241  39
D1767V4, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  T1            2              7
  T2            1             66
  T3            8            241
  T4            2             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
  MC3R MUTATED    10   2   1
  MC3R WILD-TYPE 210  79  65
D1767V5, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  N0           10            210
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1767V6, binary
                cls
clus               0   1
  MC3R MUTATED    10   1
  MC3R WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED     10    1
  MC3R WILD-TYPE  275   47
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0           10            275
  1            1             47
[1] 2 2
[1] FALSE
D1767V7, binary
                cls
clus               0   1
  MC3R MUTATED     6   7
  MC3R WILD-TYPE 164 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      6    7
  MC3R WILD-TYPE  164  190
        clus
vv       MC3R MUTATED MC3R WILD-TYPE
  FEMALE            6            164
  MALE              7            190
[1] 2 2
[1] FALSE
D1767V8, binary
                cls
clus               0   1
  MC3R MUTATED     9   0
  MC3R WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      9    0
  MC3R WILD-TYPE  291    8
     clus
vv    MC3R MUTATED MC3R WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1767V9, binary
                cls
clus               0   1
  MC3R MUTATED    12   1
  MC3R WILD-TYPE 302  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED     12    1
  MC3R WILD-TYPE  302   47
                               clus
vv                              MC3R MUTATED MC3R WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MC3R MUTATED    10   0   0   1
  MC3R WILD-TYPE 249   3  22  20
D1767V10, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  R0           10            249
  R1            0              3
  R2            0             22
  RX            1             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"
D1767V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MC3R MUTATED                                  0     0
  MC3R WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MC3R MUTATED                           0    12
  MC3R WILD-TYPE                        19   164
D1767V12, multiclass
                                  clus
vv                                 MC3R MUTATED MC3R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      12            164
[1] 4 2
[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 = ACTL6B MUTATION ANALYSIS
D1768V1, survival
                  sevent
clus2                0   1
  ACTL6B MUTATED     8   1
  ACTL6B WILD-TYPE 269  77
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               9              346 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               1               77 
$`ACTL6B MUTATED`
TCGA-A6-4105 TCGA-G4-6321 TCGA-A6-5665 TCGA-AA-3877 TCGA-AA-A02O TCGA-CM-5860 
       14.53        22.09        22.06        31.00         0.92        32.02 
TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-6533 
       15.02        19.59        25.48 

$`ACTL6B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W 
       51.98        39.98         2.01         5.03        14.01        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        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        54.61 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ACTL6B MUTATED ACTL6B WILD-TYPE 
            0.92             0.00 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
           32.02           148.01 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
           22.06            22.06 
[1] "0.9 - 32.0 (22.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1768V2, continuous
                  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      62        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6B MUTATED           1          1          0          0        0
  ACTL6B WILD-TYPE        17          5         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ACTL6B MUTATED           0         0
  ACTL6B WILD-TYPE        12         1
D1768V3, multiclass
            clus
vv           ACTL6B MUTATED ACTL6B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              1                5
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ACTL6B MUTATED     1   2   5   1
  ACTL6B WILD-TYPE   8  65 244  40
D1768V4, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  T1              1                8
  T2              2               65
  T3              5              244
  T4              1               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
  ACTL6B MUTATED     7   2   0
  ACTL6B WILD-TYPE 213  79  66
D1768V5, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  N0              7              213
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1768V6, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     8   0
  ACTL6B WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      8    0
  ACTL6B WILD-TYPE  277   48
   clus
vv  ACTL6B MUTATED ACTL6B WILD-TYPE
  0              8              277
  1              0               48
[1] 2 2
[1] FALSE
D1768V7, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     5   4
  ACTL6B WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      5    4
  ACTL6B WILD-TYPE  165  193
        clus
vv       ACTL6B MUTATED ACTL6B WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1768V8, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     8   0
  ACTL6B WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      8    0
  ACTL6B WILD-TYPE  292    8
     clus
vv    ACTL6B MUTATED ACTL6B WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1768V9, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     7   2
  ACTL6B WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      7    2
  ACTL6B WILD-TYPE  307   46
                               clus
vv                              ACTL6B MUTATED ACTL6B WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACTL6B MUTATED     8   0   0   0
  ACTL6B WILD-TYPE 251   3  22  21
D1768V10, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  R0              8              251
  R1              0                3
  R2              0               22
  RX              0               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"
D1768V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL6B MUTATED                                  0     0
  ACTL6B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTL6B MUTATED                           0     7
  ACTL6B WILD-TYPE                        19   169
D1768V12, multiclass
                                  clus
vv                                 ACTL6B MUTATED ACTL6B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = BACH2 MUTATION ANALYSIS
D1769V1, survival
                 sevent
clus2               0   1
  BACH2 MUTATED    10   6
  BACH2 WILD-TYPE 267  72
  BACH2 MUTATED BACH2 WILD-TYPE 
             16             339 
  BACH2 MUTATED BACH2 WILD-TYPE 
              6              72 
$`BACH2 MUTATED`
TCGA-AZ-6601 TCGA-A6-2671 TCGA-A6-2676 TCGA-AA-3854 TCGA-AA-3956 TCGA-AA-3975 
      100.01        43.76        42.90        36.03        34.03        34.06 
TCGA-AA-A010 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       34.98        12.10         5.23        12.76        10.06        23.05 
TCGA-CM-5349 TCGA-D5-6539 TCGA-D5-6927 TCGA-DM-A0X9 
       30.08        12.49         9.44       119.70 

$`BACH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
        0.00        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  BACH2 MUTATED BACH2 WILD-TYPE 
           5.23            0.00 
  BACH2 MUTATED BACH2 WILD-TYPE 
         119.70          148.01 
  BACH2 MUTATED BACH2 WILD-TYPE 
         32.055          21.990 
[1] "5.2 - 119.7 (32.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1769V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BACH2 MUTATED         2        0        1         7         2         0
  BACH2 WILD-TYPE      62        1       25       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BACH2 MUTATED           0          0          1          0        2         0
  BACH2 WILD-TYPE        18          6         43         33       33        12
                 vv
clus              STAGE IVB
  BACH2 MUTATED           0
  BACH2 WILD-TYPE         1
D1769V3, multiclass
            clus
vv           BACH2 MUTATED BACH2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  BACH2 MUTATED     0   2  10   4
  BACH2 WILD-TYPE   9  65 239  37
D1769V4, multiclass
    clus
vv   BACH2 MUTATED BACH2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            10             239
  T4             4              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
  BACH2 MUTATED    13   2   1
  BACH2 WILD-TYPE 207  79  65
D1769V5, multiclass
    clus
vv   BACH2 MUTATED BACH2 WILD-TYPE
  N0            13             207
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1769V6, binary
                 cls
clus                0   1
  BACH2 MUTATED    14   2
  BACH2 WILD-TYPE 271  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACH2 MUTATED     14    2
  BACH2 WILD-TYPE  271   46
   clus
vv  BACH2 MUTATED BACH2 WILD-TYPE
  0            14             271
  1             2              46
[1] 2 2
[1] FALSE
D1769V7, binary
                 cls
clus                0   1
  BACH2 MUTATED     6  10
  BACH2 WILD-TYPE 164 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACH2 MUTATED      6   10
  BACH2 WILD-TYPE  164  187
        clus
vv       BACH2 MUTATED BACH2 WILD-TYPE
  FEMALE             6             164
  MALE              10             187
[1] 2 2
[1] FALSE
D1769V8, binary
                 cls
clus                0   1
  BACH2 MUTATED    15   0
  BACH2 WILD-TYPE 285   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACH2 MUTATED     15    0
  BACH2 WILD-TYPE  285    8
     clus
vv    BACH2 MUTATED BACH2 WILD-TYPE
  NO             15             285
  YES             0               8
[1] 2 2
[1] FALSE
D1769V9, binary
                 cls
clus                0   1
  BACH2 MUTATED    14   2
  BACH2 WILD-TYPE 300  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACH2 MUTATED     14    2
  BACH2 WILD-TYPE  300   46
                               clus
vv                              BACH2 MUTATED BACH2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BACH2 MUTATED    10   0   0   2
  BACH2 WILD-TYPE 249   3  22  19
D1769V10, multiclass
    clus
vv   BACH2 MUTATED BACH2 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D1769V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BACH2 MUTATED                                  0     2
  BACH2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BACH2 MUTATED                           1     9
  BACH2 WILD-TYPE                        18   167
D1769V12, multiclass
                                  clus
vv                                 BACH2 MUTATED BACH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        9             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(1770) Variable = PGM2 MUTATION ANALYSIS
D1770V1, survival
                sevent
clus2              0   1
  PGM2 MUTATED     3   0
  PGM2 WILD-TYPE 274  78
  PGM2 MUTATED PGM2 WILD-TYPE 
             3            352 
  PGM2 MUTATED PGM2 WILD-TYPE 
             0             78 
$`PGM2 MUTATED`
TCGA-A6-6653 TCGA-CM-5344 TCGA-CM-5860 
       24.39        22.03        32.02 

$`PGM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PGM2 MUTATED PGM2 WILD-TYPE 
         22.03           0.00 
  PGM2 MUTATED PGM2 WILD-TYPE 
         32.02         148.01 
  PGM2 MUTATED PGM2 WILD-TYPE 
        24.390         22.025 
[1] "22.0 - 32.0 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D1770V2, continuous
                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      63        1       26       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGM2 MUTATED           0          0          1          0        0         0
  PGM2 WILD-TYPE        18          6         43         33       35        12
                vv
clus             STAGE IVB
  PGM2 MUTATED           0
  PGM2 WILD-TYPE         1
D1770V3, multiclass
            clus
vv           PGM2 MUTATED PGM2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  PGM2 MUTATED     0   1   2   0
  PGM2 WILD-TYPE   9  66 247  41
D1770V4, multiclass
    clus
vv   PGM2 MUTATED PGM2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            0             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
  PGM2 MUTATED     2   1   0
  PGM2 WILD-TYPE 218  80  66
D1770V5, multiclass
    clus
vv   PGM2 MUTATED PGM2 WILD-TYPE
  N0            2            218
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1770V6, binary
                cls
clus               0   1
  PGM2 MUTATED     3   0
  PGM2 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      3    0
  PGM2 WILD-TYPE  282   48
   clus
vv  PGM2 MUTATED PGM2 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1770V7, binary
                cls
clus               0   1
  PGM2 MUTATED     1   2
  PGM2 WILD-TYPE 169 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      1    2
  PGM2 WILD-TYPE  169  195
        clus
vv       PGM2 MUTATED PGM2 WILD-TYPE
  FEMALE            1            169
  MALE              2            195
[1] 2 2
[1] FALSE
D1770V8, binary
                cls
clus               0   1
  PGM2 MUTATED     3   0
  PGM2 WILD-TYPE 297   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      3    0
  PGM2 WILD-TYPE  297    8
     clus
vv    PGM2 MUTATED PGM2 WILD-TYPE
  NO             3            297
  YES            0              8
[1] 2 2
[1] FALSE
D1770V9, binary
                cls
clus               0   1
  PGM2 MUTATED     3   0
  PGM2 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      3    0
  PGM2 WILD-TYPE  311   48
                               clus
vv                              PGM2 MUTATED PGM2 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PGM2 MUTATED     2   0   0   0
  PGM2 WILD-TYPE 257   3  22  21
D1770V10, multiclass
[1] "Remove cluster labels:" "PGM2 MUTATED"          
clus
  PGM2 MUTATED PGM2 WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     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-3527 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-A6-2676     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-3502     TCGA-AA-3510 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529     TCGA-AA-3532 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3544 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660 
"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-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3693 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     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-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3975     TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00N 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00W     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-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4682 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5348 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
D1770V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PGM2 MUTATED                                  0     0
  PGM2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PGM2 MUTATED                           0     3
  PGM2 WILD-TYPE                        19   173
D1770V12, multiclass
                                  clus
vv                                 PGM2 MUTATED PGM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       3            173
[1] 4 2
[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 = EPHB1 MUTATION ANALYSIS
D1771V1, survival
                 sevent
clus2               0   1
  EPHB1 MUTATED    24  11
  EPHB1 WILD-TYPE 253  67
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             35             320 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             11              67 
$`EPHB1 MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-G4-6628 
       14.53         6.05        85.05        19.04        24.00        79.69 
TCGA-A6-5660 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3864 
       29.19         8.38        24.39        11.01        37.05        53.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6599 
       38.07        35.01        22.42         0.20        58.39         6.77 
TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6161 
       12.10         3.19        10.06        22.98         5.03        15.02 
TCGA-CM-6162 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6920 
       12.00        54.61        19.59        25.48        16.14        12.39 
TCGA-DM-A0X9 TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6317 
      119.70        33.67        65.85        55.04        36.00 

$`EPHB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 
       63.62        22.09        35.80        26.17        91.79        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       22.52        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 
       14.01        50.04        47.01        15.02         5.98         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       49.41        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        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         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
      133.18        74.56        53.62        44.68        85.48        61.91 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  EPHB1 MUTATED EPHB1 WILD-TYPE 
            0.2             0.0 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
         119.70          148.01 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
          22.98           22.01 
[1] "0.2 - 119.7 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1771V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHB1 MUTATED         6        0        3         7         0         0
  EPHB1 WILD-TYPE      58        1       23       101         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHB1 MUTATED           2          1          4          3        7         1
  EPHB1 WILD-TYPE        16          5         40         30       28        11
                 vv
clus              STAGE IVB
  EPHB1 MUTATED           0
  EPHB1 WILD-TYPE         1
D1771V3, multiclass
            clus
vv           EPHB1 MUTATED EPHB1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              7             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             1               5
  STAGE IIIB             4              40
  STAGE IIIC             3              30
  STAGE IV               7              28
  STAGE IVA              1              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
  EPHB1 MUTATED     1   5  25   5
  EPHB1 WILD-TYPE   8  62 224  36
D1771V4, multiclass
    clus
vv   EPHB1 MUTATED EPHB1 WILD-TYPE
  T1             1               8
  T2             5              62
  T3            25             224
  T4             5              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
  EPHB1 MUTATED    19   9   8
  EPHB1 WILD-TYPE 201  72  58
D1771V5, multiclass
    clus
vv   EPHB1 MUTATED EPHB1 WILD-TYPE
  N0            19             201
  N1             9              72
  N2             8              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"
D1771V6, binary
                 cls
clus                0   1
  EPHB1 MUTATED    24   8
  EPHB1 WILD-TYPE 261  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     24    8
  EPHB1 WILD-TYPE  261   40
   clus
vv  EPHB1 MUTATED EPHB1 WILD-TYPE
  0            24             261
  1             8              40
[1] 2 2
[1] FALSE
D1771V7, binary
                 cls
clus                0   1
  EPHB1 MUTATED    15  21
  EPHB1 WILD-TYPE 155 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     15   21
  EPHB1 WILD-TYPE  155  176
        clus
vv       EPHB1 MUTATED EPHB1 WILD-TYPE
  FEMALE            15             155
  MALE              21             176
[1] 2 2
[1] FALSE
D1771V8, binary
                 cls
clus                0   1
  EPHB1 MUTATED    31   2
  EPHB1 WILD-TYPE 269   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     31    2
  EPHB1 WILD-TYPE  269    6
     clus
vv    EPHB1 MUTATED EPHB1 WILD-TYPE
  NO             31             269
  YES             2               6
[1] 2 2
[1] FALSE
D1771V9, binary
                 cls
clus                0   1
  EPHB1 MUTATED    30   6
  EPHB1 WILD-TYPE 284  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     30    6
  EPHB1 WILD-TYPE  284   42
                               clus
vv                              EPHB1 MUTATED EPHB1 WILD-TYPE
  COLON ADENOCARCINOMA                     30             284
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHB1 MUTATED    22   0   4   1
  EPHB1 WILD-TYPE 237   3  18  20
D1771V10, multiclass
    clus
vv   EPHB1 MUTATED EPHB1 WILD-TYPE
  R0            22             237
  R1             0               3
  R2             4              18
  RX             1              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"
D1771V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHB1 MUTATED                                  0     1
  EPHB1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHB1 MUTATED                           3    22
  EPHB1 WILD-TYPE                        16   154
D1771V12, multiclass
                                  clus
vv                                 EPHB1 MUTATED EPHB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       22             154
[1] 4 2
[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 = NFS1 MUTATION ANALYSIS
D1772V1, survival
                sevent
clus2              0   1
  NFS1 MUTATED     4   1
  NFS1 WILD-TYPE 273  77
  NFS1 MUTATED NFS1 WILD-TYPE 
             5            350 
  NFS1 MUTATED NFS1 WILD-TYPE 
             1             77 
$`NFS1 MUTATED`
TCGA-AA-3950 TCGA-AZ-6601 TCGA-AA-A01Q TCGA-AA-A01R TCGA-CM-6171 
       24.00       100.01         1.02        35.01        14.04 

$`NFS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       38.07         1.02        33.04         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NFS1 MUTATED NFS1 WILD-TYPE 
          1.02           0.00 
  NFS1 MUTATED NFS1 WILD-TYPE 
        100.01         148.01 
  NFS1 MUTATED NFS1 WILD-TYPE 
        24.000         22.045 
[1] "1.0 - 100.0 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1772V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFS1 MUTATED         1        0        2         1         0         0
  NFS1 WILD-TYPE      63        1       24       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NFS1 MUTATED           1          0          0          0        0         0
  NFS1 WILD-TYPE        17          6         44         33       35        12
                vv
clus             STAGE IVB
  NFS1 MUTATED           0
  NFS1 WILD-TYPE         1
D1772V3, multiclass
            clus
vv           NFS1 MUTATED NFS1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             1            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  NFS1 MUTATED     0   1   4   0
  NFS1 WILD-TYPE   9  66 245  41
D1772V4, multiclass
    clus
vv   NFS1 MUTATED NFS1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            4            245
  T4            0             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
  NFS1 MUTATED     4   0   1
  NFS1 WILD-TYPE 216  81  65
D1772V5, multiclass
    clus
vv   NFS1 MUTATED NFS1 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1772V6, binary
                cls
clus               0   1
  NFS1 MUTATED     5   0
  NFS1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFS1 MUTATED      5    0
  NFS1 WILD-TYPE  280   48
   clus
vv  NFS1 MUTATED NFS1 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1772V7, binary
                cls
clus               0   1
  NFS1 MUTATED     3   2
  NFS1 WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFS1 MUTATED      3    2
  NFS1 WILD-TYPE  167  195
        clus
vv       NFS1 MUTATED NFS1 WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D1772V8, binary
                cls
clus               0   1
  NFS1 MUTATED     3   1
  NFS1 WILD-TYPE 297   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFS1 MUTATED      3    1
  NFS1 WILD-TYPE  297    7
     clus
vv    NFS1 MUTATED NFS1 WILD-TYPE
  NO             3            297
  YES            1              7
[1] 2 2
[1] FALSE
D1772V9, binary
                cls
clus               0   1
  NFS1 MUTATED     3   2
  NFS1 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFS1 MUTATED      3    2
  NFS1 WILD-TYPE  311   46
                               clus
vv                              NFS1 MUTATED NFS1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NFS1 MUTATED     4   0   0   0
  NFS1 WILD-TYPE 255   3  22  21
D1772V10, multiclass
    clus
vv   NFS1 MUTATED NFS1 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D1772V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFS1 MUTATED                                  0     0
  NFS1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NFS1 MUTATED                           0     2
  NFS1 WILD-TYPE                        19   174
D1772V12, multiclass
[1] "Remove cluster labels:" "NFS1 MUTATED"          
clus
  NFS1 MUTATED NFS1 WILD-TYPE 
             2            204 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285     TCGA-G4-6310 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5656 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660     TCGA-A6-5661 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665     TCGA-A6-5666 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141     TCGA-A6-6142 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-6648     TCGA-A6-6651     TCGA-A6-6652     TCGA-A6-6653 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781     TCGA-A6-6782 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6899 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6172     TCGA-CM-6674 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" "NFS1 WILD-TYPE" 

Clustering(1773) Variable = CLDN17 MUTATION ANALYSIS
D1773V1, survival
                  sevent
clus2                0   1
  CLDN17 MUTATED    10   3
  CLDN17 WILD-TYPE 267  75
  CLDN17 MUTATED CLDN17 WILD-TYPE 
              13              342 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
               3               75 
$`CLDN17 MUTATED`
TCGA-AA-3543 TCGA-AD-6964 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
        0.99        10.88        18.05         4.01        34.98         1.02 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       58.39         5.13        12.76        25.48        43.27        17.85 
TCGA-D5-6538 
       17.13 

$`CLDN17 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        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        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        21.44        17.82         1.41 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 
       55.92        20.19        18.25        15.12         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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  CLDN17 MUTATED CLDN17 WILD-TYPE 
            0.99             0.00 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
           58.39           148.01 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
          17.130           22.225 
[1] "1.0 - 58.4 (17.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.5"
D1773V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLDN17 MUTATED         1        0        1         4         2         0
  CLDN17 WILD-TYPE      63        1       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN17 MUTATED           0          0          2          0        1
  CLDN17 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  CLDN17 MUTATED           0         0
  CLDN17 WILD-TYPE        12         1
D1773V3, multiclass
            clus
vv           CLDN17 MUTATED CLDN17 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  CLDN17 MUTATED     0   1   7   5
  CLDN17 WILD-TYPE   9  66 242  36
D1773V4, multiclass
    clus
vv   CLDN17 MUTATED CLDN17 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              7              242
  T4              5               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
  CLDN17 MUTATED     9   1   3
  CLDN17 WILD-TYPE 211  80  63
D1773V5, multiclass
    clus
vv   CLDN17 MUTATED CLDN17 WILD-TYPE
  N0              9              211
  N1              1               80
  N2              3               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"
D1773V6, binary
                  cls
clus                 0   1
  CLDN17 MUTATED    11   1
  CLDN17 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN17 MUTATED     11    1
  CLDN17 WILD-TYPE  274   47
   clus
vv  CLDN17 MUTATED CLDN17 WILD-TYPE
  0             11              274
  1              1               47
[1] 2 2
[1] FALSE
D1773V7, binary
                  cls
clus                 0   1
  CLDN17 MUTATED     6   7
  CLDN17 WILD-TYPE 164 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN17 MUTATED      6    7
  CLDN17 WILD-TYPE  164  190
        clus
vv       CLDN17 MUTATED CLDN17 WILD-TYPE
  FEMALE              6              164
  MALE                7              190
[1] 2 2
[1] FALSE
D1773V8, binary
                  cls
clus                 0   1
  CLDN17 MUTATED    11   0
  CLDN17 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN17 MUTATED     11    0
  CLDN17 WILD-TYPE  289    8
     clus
vv    CLDN17 MUTATED CLDN17 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1773V9, binary
                  cls
clus                 0   1
  CLDN17 MUTATED     8   5
  CLDN17 WILD-TYPE 306  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN17 MUTATED      8    5
  CLDN17 WILD-TYPE  306   43
                               clus
vv                              CLDN17 MUTATED CLDN17 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLDN17 MUTATED    10   0   0   1
  CLDN17 WILD-TYPE 249   3  22  20
D1773V10, multiclass
    clus
vv   CLDN17 MUTATED CLDN17 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              1               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"
D1773V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLDN17 MUTATED                                  0     1
  CLDN17 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLDN17 MUTATED                           0     7
  CLDN17 WILD-TYPE                        19   169
D1773V12, multiclass
                                  clus
vv                                 CLDN17 MUTATED CLDN17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         7              169
[1] 4 2
[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 = UEVLD MUTATION ANALYSIS
D1774V1, survival
                 sevent
clus2               0   1
  UEVLD MUTATED     2   1
  UEVLD WILD-TYPE 275  77
  UEVLD MUTATED UEVLD WILD-TYPE 
              3             352 
  UEVLD MUTATED UEVLD WILD-TYPE 
              1              77 
$`UEVLD MUTATED`
TCGA-AD-6964 TCGA-AZ-4315 TCGA-DM-A28K 
       10.88        58.39        98.24 

$`UEVLD WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  UEVLD MUTATED UEVLD WILD-TYPE 
          10.88            0.00 
  UEVLD MUTATED UEVLD WILD-TYPE 
          98.24          148.01 
  UEVLD MUTATED UEVLD WILD-TYPE 
         58.390          22.045 
[1] "10.9 - 98.2 (58.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1774V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UEVLD MUTATED         0        0        0         2         0         0
  UEVLD WILD-TYPE      64        1       26       106         8         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  UEVLD MUTATED           0
  UEVLD WILD-TYPE         1
D1774V3, multiclass
[1] "Remove cluster labels:" "UEVLD MUTATED"         
clus
  UEVLD MUTATED UEVLD WILD-TYPE 
              2             355 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AA-3496 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3527      TCGA-AA-3530 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552      TCGA-AA-3554 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3662 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3697 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814      TCGA-AA-3844 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870      TCGA-AA-3939 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972      TCGA-AA-3976 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L      TCGA-AA-A00Z 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6895 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A285      TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-3810      TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-5660      TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-5665      TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-6141      TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6651 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3526 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3542      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3561 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3663      TCGA-AA-3664 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3673      TCGA-AA-3678 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3811      TCGA-AA-3812 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861      TCGA-AA-3864 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872      TCGA-AA-3875 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3941      TCGA-AA-3947 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3966 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973      TCGA-AA-3975 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984      TCGA-AA-3989 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A010      TCGA-AA-A017 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      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-6889      TCGA-AD-6899      TCGA-AD-6965 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-CA-5254 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6532      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-D5-6540      TCGA-D5-6541 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-F4-6459 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6315 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
                 vv
clus               T1  T2  T3  T4
  UEVLD MUTATED     0   0   2   1
  UEVLD WILD-TYPE   9  67 247  40
D1774V4, multiclass
    clus
vv   UEVLD MUTATED UEVLD WILD-TYPE
  T1             0               9
  T2             0              67
  T3             2             247
  T4             1              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
  UEVLD MUTATED     2   0   1
  UEVLD WILD-TYPE 218  81  65
D1774V5, multiclass
    clus
vv   UEVLD MUTATED UEVLD WILD-TYPE
  N0             2             218
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1774V6, binary
                 cls
clus                0   1
  UEVLD MUTATED     2   0
  UEVLD WILD-TYPE 283  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      2    0
  UEVLD WILD-TYPE  283   48
   clus
vv  UEVLD MUTATED UEVLD WILD-TYPE
  0             2             283
  1             0              48
[1] 2 2
[1] FALSE
D1774V7, binary
                 cls
clus                0   1
  UEVLD MUTATED     0   3
  UEVLD WILD-TYPE 170 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      0    3
  UEVLD WILD-TYPE  170  194
        clus
vv       UEVLD MUTATED UEVLD WILD-TYPE
  FEMALE             0             170
  MALE               3             194
[1] 2 2
[1] FALSE
D1774V8, binary
                 cls
clus                0   1
  UEVLD MUTATED     2   0
  UEVLD WILD-TYPE 298   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      2    0
  UEVLD WILD-TYPE  298    8
     clus
vv    UEVLD MUTATED UEVLD WILD-TYPE
  NO              2             298
  YES             0               8
[1] 2 2
[1] FALSE
D1774V9, binary
                 cls
clus                0   1
  UEVLD MUTATED     2   1
  UEVLD WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      2    1
  UEVLD WILD-TYPE  312   47
                               clus
vv                              UEVLD MUTATED UEVLD WILD-TYPE
  COLON ADENOCARCINOMA                      2             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UEVLD MUTATED     1   0   0   0
  UEVLD WILD-TYPE 258   3  22  21
D1774V10, multiclass
[1] "Remove cluster labels:" "UEVLD MUTATED"         
clus
  UEVLD MUTATED UEVLD WILD-TYPE 
              1             304 
     TCGA-A6-2677      TCGA-AA-3496      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-3527 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AD-6895      TCGA-AZ-4681      TCGA-CK-5912      TCGA-G4-6310 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-2676      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-3502      TCGA-AA-3510 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3526      TCGA-AA-3529      TCGA-AA-3532 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3544 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3553      TCGA-AA-3555 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3561      TCGA-AA-3655      TCGA-AA-3660 
"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-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3815      TCGA-AA-3818 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      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-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3955 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3975      TCGA-AA-3984      TCGA-AA-3989      TCGA-AA-3994 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00N 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00W      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-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4682      TCGA-CA-5254 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
D1774V11, continuous
[1] "Remove cluster labels:" "UEVLD MUTATED"         
clus
  UEVLD MUTATED UEVLD WILD-TYPE 
              2             344 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AA-3496 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3527      TCGA-AA-3530 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552      TCGA-AA-3554 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3662 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3697 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814      TCGA-AA-3844 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870      TCGA-AA-3939 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972      TCGA-AA-3976 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L      TCGA-AA-A00Z 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6895 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-DM-A285      TCGA-G4-6310 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-2676      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-A6-5656 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3502      TCGA-AA-3510 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3526      TCGA-AA-3529      TCGA-AA-3532 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3544 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3553      TCGA-AA-3555 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3663 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3673 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693      TCGA-AA-3695 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3811 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3812      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-3845      TCGA-AA-3846      TCGA-AA-3848 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      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-3941 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3955      TCGA-AA-3956 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3973 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3975      TCGA-AA-3977      TCGA-AA-3980      TCGA-AA-3982 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      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-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6889 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AD-6890      TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-6607      TCGA-CA-6715      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-CM-4743      TCGA-CM-4744 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6806      TCGA-F4-6807 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UEVLD MUTATED                                  0     0
  UEVLD WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UEVLD MUTATED                           0     3
  UEVLD WILD-TYPE                        19   173
D1774V12, multiclass
                                  clus
vv                                 UEVLD MUTATED UEVLD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = GABRQ MUTATION ANALYSIS
D1775V1, survival
                 sevent
clus2               0   1
  GABRQ MUTATED    11   2
  GABRQ WILD-TYPE 266  76
  GABRQ MUTATED GABRQ WILD-TYPE 
             13             342 
  GABRQ MUTATED GABRQ WILD-TYPE 
              2              76 
$`GABRQ MUTATED`
TCGA-G4-6625 TCGA-AA-3555 TCGA-AA-3681 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3877 
       91.79        29.95         5.98        15.95         0.00        31.00 
TCGA-AY-5543 TCGA-AZ-5407 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-6162 TCGA-D5-6534 
       33.01        88.21        23.05        20.02        12.00        43.27 
TCGA-DM-A28F 
       35.97 

$`GABRQ WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05         2.01        24.00        33.01        26.01 
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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        49.41         6.77        12.10 
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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-4746 
       21.99        21.14        82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  GABRQ MUTATED GABRQ WILD-TYPE 
              0               0 
  GABRQ MUTATED GABRQ WILD-TYPE 
          91.79          148.01 
  GABRQ MUTATED GABRQ WILD-TYPE 
          29.95           22.01 
[1] "0.0 - 91.8 (29.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D1775V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABRQ MUTATED         3        0        0         7         1         0
  GABRQ WILD-TYPE      61        1       26       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GABRQ MUTATED           1          0          2          0        0         1
  GABRQ WILD-TYPE        17          6         42         33       35        11
                 vv
clus              STAGE IVB
  GABRQ MUTATED           0
  GABRQ WILD-TYPE         1
D1775V3, multiclass
            clus
vv           GABRQ MUTATED GABRQ WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  GABRQ MUTATED     2   1  11   1
  GABRQ WILD-TYPE   7  66 238  40
D1775V4, multiclass
    clus
vv   GABRQ MUTATED GABRQ WILD-TYPE
  T1             2               7
  T2             1              66
  T3            11             238
  T4             1              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
  GABRQ MUTATED    11   4   0
  GABRQ WILD-TYPE 209  77  66
D1775V5, multiclass
    clus
vv   GABRQ MUTATED GABRQ WILD-TYPE
  N0            11             209
  N1             4              77
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1775V6, binary
                 cls
clus                0   1
  GABRQ MUTATED    13   1
  GABRQ WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRQ MUTATED     13    1
  GABRQ WILD-TYPE  272   47
   clus
vv  GABRQ MUTATED GABRQ WILD-TYPE
  0            13             272
  1             1              47
[1] 2 2
[1] FALSE
D1775V7, binary
                 cls
clus                0   1
  GABRQ MUTATED    12   3
  GABRQ WILD-TYPE 158 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRQ MUTATED     12    3
  GABRQ WILD-TYPE  158  194
        clus
vv       GABRQ MUTATED GABRQ WILD-TYPE
  FEMALE            12             158
  MALE               3             194
[1] 2 2
[1] FALSE
D1775V8, binary
                 cls
clus                0   1
  GABRQ MUTATED    11   0
  GABRQ WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRQ MUTATED     11    0
  GABRQ WILD-TYPE  289    8
     clus
vv    GABRQ MUTATED GABRQ WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1775V9, binary
                 cls
clus                0   1
  GABRQ MUTATED    11   4
  GABRQ WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRQ MUTATED     11    4
  GABRQ WILD-TYPE  303   44
                               clus
vv                              GABRQ MUTATED GABRQ WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GABRQ MUTATED    12   0   0   1
  GABRQ WILD-TYPE 247   3  22  20
D1775V10, multiclass
    clus
vv   GABRQ MUTATED GABRQ WILD-TYPE
  R0            12             247
  R1             0               3
  R2             0              22
  RX             1              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"
D1775V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRQ MUTATED                                  0     0
  GABRQ WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GABRQ MUTATED                           1     8
  GABRQ WILD-TYPE                        18   168
D1775V12, multiclass
                                  clus
vv                                 GABRQ MUTATED GABRQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = NTSR2 MUTATION ANALYSIS
D1776V1, survival
                 sevent
clus2               0   1
  NTSR2 MUTATED     5   3
  NTSR2 WILD-TYPE 272  75
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              8             347 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              3              75 
$`NTSR2 MUTATED`
TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A01Q TCGA-CA-6717 
        3.02         0.00        53.00        33.01         1.02        12.76 
TCGA-DM-A1D6 TCGA-G4-6309 
       49.91        85.48 

$`NTSR2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  NTSR2 MUTATED NTSR2 WILD-TYPE 
              0               0 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
          85.48          148.01 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
         22.885          22.060 
[1] "0.0 - 85.5 (22.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1776V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTSR2 MUTATED         0        0        3         3         1         0
  NTSR2 WILD-TYPE      64        1       23       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTSR2 MUTATED           0          0          1          0        0         0
  NTSR2 WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  NTSR2 MUTATED           0
  NTSR2 WILD-TYPE         1
D1776V3, multiclass
            clus
vv           NTSR2 MUTATED NTSR2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  NTSR2 MUTATED     0   0   7   1
  NTSR2 WILD-TYPE   9  67 242  40
D1776V4, multiclass
    clus
vv   NTSR2 MUTATED NTSR2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             7             242
  T4             1              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
  NTSR2 MUTATED     7   1   0
  NTSR2 WILD-TYPE 213  80  66
D1776V5, multiclass
    clus
vv   NTSR2 MUTATED NTSR2 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1776V6, binary
                 cls
clus                0   1
  NTSR2 MUTATED     8   0
  NTSR2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTSR2 MUTATED      8    0
  NTSR2 WILD-TYPE  277   48
   clus
vv  NTSR2 MUTATED NTSR2 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1776V7, binary
                 cls
clus                0   1
  NTSR2 MUTATED     5   3
  NTSR2 WILD-TYPE 165 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTSR2 MUTATED      5    3
  NTSR2 WILD-TYPE  165  194
        clus
vv       NTSR2 MUTATED NTSR2 WILD-TYPE
  FEMALE             5             165
  MALE               3             194
[1] 2 2
[1] FALSE
D1776V8, binary
                 cls
clus                0   1
  NTSR2 MUTATED     5   0
  NTSR2 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTSR2 MUTATED      5    0
  NTSR2 WILD-TYPE  295    8
     clus
vv    NTSR2 MUTATED NTSR2 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1776V9, binary
                 cls
clus                0   1
  NTSR2 MUTATED     5   3
  NTSR2 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTSR2 MUTATED      5    3
  NTSR2 WILD-TYPE  309   45
                               clus
vv                              NTSR2 MUTATED NTSR2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NTSR2 MUTATED     6   0   0   1
  NTSR2 WILD-TYPE 253   3  22  20
D1776V10, multiclass
    clus
vv   NTSR2 MUTATED NTSR2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             1              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"
D1776V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTSR2 MUTATED                                  0     1
  NTSR2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTSR2 MUTATED                           1     1
  NTSR2 WILD-TYPE                        18   175
D1776V12, multiclass
                                  clus
vv                                 NTSR2 MUTATED NTSR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        1             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(1777) Variable = FRAS1 MUTATION ANALYSIS
D1777V1, survival
                 sevent
clus2               0   1
  FRAS1 MUTATED    27   8
  FRAS1 WILD-TYPE 250  70
  FRAS1 MUTATED FRAS1 WILD-TYPE 
             35             320 
  FRAS1 MUTATED FRAS1 WILD-TYPE 
              8              70 
$`FRAS1 MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-3810 
        0.92        19.04       100.01        35.80        26.17        36.53 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 
       33.53        22.06         8.38        20.12        63.98         6.97 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3980 TCGA-AA-A010 TCGA-AA-A01P 
       33.04         1.02        15.95        27.02        34.98        38.07 
TCGA-AD-6901 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-6598 
       22.42        27.09        33.01         0.20        17.82        49.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6164 TCGA-D5-6540 
        6.77        12.76        10.06        15.02        29.03        16.14 
TCGA-D5-6924 TCGA-D5-6930 TCGA-DM-A28F TCGA-F4-6856 TCGA-G4-6317 
       14.30        13.35        35.97        35.31        36.00 

$`FRAS1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        63.62        22.09        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        32.75        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 
       10.06        35.05         0.99        25.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
       27.42        26.47        14.50        16.31         0.95        21.44 
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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FRAS1 MUTATED FRAS1 WILD-TYPE 
            0.2             0.0 
  FRAS1 MUTATED FRAS1 WILD-TYPE 
         100.01          148.01 
  FRAS1 MUTATED FRAS1 WILD-TYPE 
          22.42           22.01 
[1] "0.2 - 100.0 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1777V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRAS1 MUTATED         6        0        5        15         2         0
  FRAS1 WILD-TYPE      58        1       21        93         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRAS1 MUTATED           2          0          2          2        1         1
  FRAS1 WILD-TYPE        16          6         42         31       34        11
                 vv
clus              STAGE IVB
  FRAS1 MUTATED           0
  FRAS1 WILD-TYPE         1
D1777V3, multiclass
            clus
vv           FRAS1 MUTATED FRAS1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               5              21
  STAGE IIA             15              93
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              1              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
  FRAS1 MUTATED     0   6  29   2
  FRAS1 WILD-TYPE   9  61 220  39
D1777V4, multiclass
    clus
vv   FRAS1 MUTATED FRAS1 WILD-TYPE
  T1             0               9
  T2             6              61
  T3            29             220
  T4             2              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
  FRAS1 MUTATED    29   5   3
  FRAS1 WILD-TYPE 191  76  63
D1777V5, multiclass
    clus
vv   FRAS1 MUTATED FRAS1 WILD-TYPE
  N0            29             191
  N1             5              76
  N2             3              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"
D1777V6, binary
                 cls
clus                0   1
  FRAS1 MUTATED    28   2
  FRAS1 WILD-TYPE 257  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRAS1 MUTATED     28    2
  FRAS1 WILD-TYPE  257   46
   clus
vv  FRAS1 MUTATED FRAS1 WILD-TYPE
  0            28             257
  1             2              46
[1] 2 2
[1] FALSE
D1777V7, binary
                 cls
clus                0   1
  FRAS1 MUTATED    20  17
  FRAS1 WILD-TYPE 150 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRAS1 MUTATED     20   17
  FRAS1 WILD-TYPE  150  180
        clus
vv       FRAS1 MUTATED FRAS1 WILD-TYPE
  FEMALE            20             150
  MALE              17             180
[1] 2 2
[1] FALSE
D1777V8, binary
                 cls
clus                0   1
  FRAS1 MUTATED    32   0
  FRAS1 WILD-TYPE 268   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRAS1 MUTATED     32    0
  FRAS1 WILD-TYPE  268    8
     clus
vv    FRAS1 MUTATED FRAS1 WILD-TYPE
  NO             32             268
  YES             0               8
[1] 2 2
[1] FALSE
D1777V9, binary
                 cls
clus                0   1
  FRAS1 MUTATED    30   7
  FRAS1 WILD-TYPE 284  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRAS1 MUTATED     30    7
  FRAS1 WILD-TYPE  284   41
                               clus
vv                              FRAS1 MUTATED FRAS1 WILD-TYPE
  COLON ADENOCARCINOMA                     30             284
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FRAS1 MUTATED    25   0   1   3
  FRAS1 WILD-TYPE 234   3  21  18
D1777V10, multiclass
    clus
vv   FRAS1 MUTATED FRAS1 WILD-TYPE
  R0            25             234
  R1             0               3
  R2             1              21
  RX             3              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"
D1777V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRAS1 MUTATED                                  0     2
  FRAS1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FRAS1 MUTATED                           4    20
  FRAS1 WILD-TYPE                        15   156
D1777V12, multiclass
                                  clus
vv                                 FRAS1 MUTATED FRAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    4              15
  WHITE                                       20             156
[1] 4 2
[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 = NDUFV2 MUTATION ANALYSIS
D1778V1, survival
                  sevent
clus2                0   1
  NDUFV2 MUTATED     2   0
  NDUFV2 WILD-TYPE 275  78
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2              353 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               0               78 
$`NDUFV2 MUTATED`
TCGA-A6-5665 TCGA-D5-6927 
       22.06         9.44 

$`NDUFV2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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            22.09 
[1] "9.4 - 22.1 (15.8)"  "0.0 - 148.0 (22.1)"
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
D1778V2, continuous
                  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      63        1       26       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDUFV2 MUTATED           0          0          0          0        0
  NDUFV2 WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  NDUFV2 MUTATED           0         0
  NDUFV2 WILD-TYPE        12         1
D1778V3, multiclass
            clus
vv           NDUFV2 MUTATED NDUFV2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  NDUFV2 MUTATED     0   1   2   0
  NDUFV2 WILD-TYPE   9  66 247  41
D1778V4, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              2              247
  T4              0               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
  NDUFV2 MUTATED     3   0   0
  NDUFV2 WILD-TYPE 217  81  66
D1778V5, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  N0              3              217
  N1              0               81
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1778V6, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     2   0
  NDUFV2 WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    0
  NDUFV2 WILD-TYPE  283   48
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D1778V7, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     1   2
  NDUFV2 WILD-TYPE 169 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE  169  195
        clus
vv       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  FEMALE              1              169
  MALE                2              195
[1] 2 2
[1] FALSE
D1778V8, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     2   0
  NDUFV2 WILD-TYPE 298   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    0
  NDUFV2 WILD-TYPE  298    8
     clus
vv    NDUFV2 MUTATED NDUFV2 WILD-TYPE
  NO               2              298
  YES              0                8
[1] 2 2
[1] FALSE
D1778V9, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     3   0
  NDUFV2 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      3    0
  NDUFV2 WILD-TYPE  311   48
                               clus
vv                              NDUFV2 MUTATED NDUFV2 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NDUFV2 MUTATED     2   0   0   1
  NDUFV2 WILD-TYPE 257   3  22  20
D1778V10, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  R0              2              257
  R1              0                3
  R2              0               22
  RX              1               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"
D1778V11, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2              344 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AA-3496 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527       TCGA-AA-3530 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552       TCGA-AA-3554 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3662 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3697 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814       TCGA-AA-3844 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870       TCGA-AA-3939 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972       TCGA-AA-3976 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L       TCGA-AA-A00Z 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6895 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AD-6964       TCGA-AZ-6601       TCGA-AZ-6608       TCGA-DM-A285 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652       TCGA-A6-6653 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3663 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3673 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693       TCGA-AA-3695 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3811 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3861 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       TCGA-AA-3872 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3941 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       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-3973 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3975       TCGA-AA-3977       TCGA-AA-3980       TCGA-AA-3982 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3984       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-A00N       TCGA-AA-A00O 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6889 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AZ-6600       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-CA-6715       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-A28C       TCGA-DM-A28E 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806       TCGA-F4-6807 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"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    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NDUFV2 MUTATED                           0     3
  NDUFV2 WILD-TYPE                        19   173
D1778V12, multiclass
                                  clus
vv                                 NDUFV2 MUTATED NDUFV2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = ATP2B4 MUTATION ANALYSIS
D1779V1, survival
                  sevent
clus2                0   1
  ATP2B4 MUTATED    10   6
  ATP2B4 WILD-TYPE 267  72
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              16              339 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
               6               72 
$`ATP2B4 MUTATED`
TCGA-AA-3950 TCGA-AA-A024 TCGA-AZ-6601 TCGA-G4-6588 TCGA-A6-5665 TCGA-AA-3966 
       24.00        39.06       100.01        26.17        22.06         2.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-5403 TCGA-CK-5914 TCGA-CM-5862 TCGA-CM-6161 
       34.98        83.24        62.79        21.99         5.03        15.02 
TCGA-CM-6165 TCGA-CM-6676 TCGA-DM-A28G TCGA-F4-6856 
       16.04        11.08        60.79        35.31 

$`ATP2B4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 
       21.37        15.52        25.08        10.88       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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-6162 
       32.02        15.02        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 
       14.04        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-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
            2.01             0.00 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          100.01           148.01 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          25.085           21.990 
[1] "2.0 - 100.0 (25.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1779V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP2B4 MUTATED         4        0        3         8         1         0
  ATP2B4 WILD-TYPE      60        1       23       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2B4 MUTATED           0          0          1          0        0
  ATP2B4 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP2B4 MUTATED           1         0
  ATP2B4 WILD-TYPE        11         1
D1779V3, multiclass
            clus
vv           ATP2B4 MUTATED ATP2B4 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  ATP2B4 MUTATED     0   4  13   1
  ATP2B4 WILD-TYPE   9  63 236  40
D1779V4, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             13              236
  T4              1               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
  ATP2B4 MUTATED    16   2   0
  ATP2B4 WILD-TYPE 204  79  66
D1779V5, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  N0             16              204
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1779V6, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    14   1
  ATP2B4 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     14    1
  ATP2B4 WILD-TYPE  271   47
   clus
vv  ATP2B4 MUTATED ATP2B4 WILD-TYPE
  0             14              271
  1              1               47
[1] 2 2
[1] FALSE
D1779V7, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED     7  11
  ATP2B4 WILD-TYPE 163 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED      7   11
  ATP2B4 WILD-TYPE  163  186
        clus
vv       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  FEMALE              7              163
  MALE               11              186
[1] 2 2
[1] FALSE
D1779V8, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    13   0
  ATP2B4 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     13    0
  ATP2B4 WILD-TYPE  287    8
     clus
vv    ATP2B4 MUTATED ATP2B4 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1779V9, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    14   4
  ATP2B4 WILD-TYPE 300  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     14    4
  ATP2B4 WILD-TYPE  300   44
                               clus
vv                              ATP2B4 MUTATED ATP2B4 WILD-TYPE
  COLON ADENOCARCINOMA                      14              300
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP2B4 MUTATED    12   0   0   2
  ATP2B4 WILD-TYPE 247   3  22  19
D1779V10, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  R0             12              247
  R1              0                3
  R2              0               22
  RX              2               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"
D1779V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP2B4 MUTATED                                  0     1
  ATP2B4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP2B4 MUTATED                           0    12
  ATP2B4 WILD-TYPE                        19   164
D1779V12, multiclass
                                  clus
vv                                 ATP2B4 MUTATED ATP2B4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        12              164
[1] 4 2
[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 = PLEKHA4 MUTATION ANALYSIS
D1780V1, survival
                   sevent
clus2                 0   1
  PLEKHA4 MUTATED     8   1
  PLEKHA4 WILD-TYPE 269  77
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
                9               346 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
                1                77 
$`PLEKHA4 MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-AA-3980 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6599 
       24.00        79.69        27.02        27.09        58.39         6.77 
TCGA-CM-5349 TCGA-DM-A1D9 TCGA-DM-A1HA 
       30.08       140.38       131.51 

$`PLEKHA4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       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-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
             6.77              0.00 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
           140.38            148.01 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
            30.08             21.99 
[1] "6.8 - 140.4 (30.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.7"
D1780V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHA4 MUTATED         4        0        0         4         0         0
  PLEKHA4 WILD-TYPE      60        1       26       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA4 MUTATED           1          0          0          1        0
  PLEKHA4 WILD-TYPE        17          6         44         32       35
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHA4 MUTATED           0         0
  PLEKHA4 WILD-TYPE        12         1
D1780V3, multiclass
            clus
vv           PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  PLEKHA4 MUTATED     0   4   6   0
  PLEKHA4 WILD-TYPE   9  63 243  41
D1780V4, multiclass
    clus
vv   PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  T1               0                 9
  T2               4                63
  T3               6               243
  T4               0                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
  PLEKHA4 MUTATED     8   0   2
  PLEKHA4 WILD-TYPE 212  81  64
D1780V5, multiclass
    clus
vv   PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  N0               8               212
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1780V6, binary
                   cls
clus                  0   1
  PLEKHA4 MUTATED     9   0
  PLEKHA4 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA4 MUTATED      9    0
  PLEKHA4 WILD-TYPE  276   48
   clus
vv  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D1780V7, binary
                   cls
clus                  0   1
  PLEKHA4 MUTATED     5   5
  PLEKHA4 WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA4 MUTATED      5    5
  PLEKHA4 WILD-TYPE  165  192
        clus
vv       PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D1780V8, binary
                   cls
clus                  0   1
  PLEKHA4 MUTATED     6   0
  PLEKHA4 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA4 MUTATED      6    0
  PLEKHA4 WILD-TYPE  294    8
     clus
vv    PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1780V9, binary
                   cls
clus                  0   1
  PLEKHA4 MUTATED     9   1
  PLEKHA4 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA4 MUTATED      9    1
  PLEKHA4 WILD-TYPE  305   47
                               clus
vv                              PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHA4 MUTATED     6   0   0   0
  PLEKHA4 WILD-TYPE 253   3  22  21
D1780V10, multiclass
    clus
vv   PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               0                22
  RX               0                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"
D1780V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHA4 MUTATED                                  0     0
  PLEKHA4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHA4 MUTATED                           0     7
  PLEKHA4 WILD-TYPE                        19   169
D1780V12, multiclass
                                  clus
vv                                 PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          7               169
[1] 4 2
[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 = AHNAK MUTATION ANALYSIS
D1781V1, survival
                 sevent
clus2               0   1
  AHNAK MUTATED    27  10
  AHNAK WILD-TYPE 250  68
  AHNAK MUTATED AHNAK WILD-TYPE 
             37             318 
  AHNAK MUTATED AHNAK WILD-TYPE 
             10              68 
$`AHNAK MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-A6-2672 
        1.02         0.92        85.05        19.04        19.04        46.65 
TCGA-A6-2676 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6141 TCGA-AA-3502 TCGA-AA-3510 
       42.90        29.19        27.09         8.38        35.01        63.98 
TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A00R 
       33.04        33.01         2.01        27.02         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02H TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
       34.98        35.01         2.01        83.24        27.09        58.39 
TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-4743 
       49.41         3.19        12.76        10.06       124.27        23.05 
TCGA-CM-4746 TCGA-CM-5861 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XF TCGA-F4-6570 
       37.02        15.02        11.64        13.35        38.20         6.18 
TCGA-F4-6856 
       35.31 

$`AHNAK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       36.00        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       10.88       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6651 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-3511 TCGA-AA-3514 
       19.66        20.28         7.04         3.02         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05        18.05        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        15.02        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         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       26.01        37.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       82.95         2.01        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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        13.41        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-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  AHNAK MUTATED AHNAK WILD-TYPE 
           0.92            0.00 
  AHNAK MUTATED AHNAK WILD-TYPE 
         124.27          148.01 
  AHNAK MUTATED AHNAK WILD-TYPE 
          27.09           21.99 
[1] "0.9 - 124.3 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1781V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AHNAK MUTATED         6        0        6        12         5         0
  AHNAK WILD-TYPE      58        1       20        96         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AHNAK MUTATED           2          0          3          2        3         0
  AHNAK WILD-TYPE        16          6         41         31       32        12
                 vv
clus              STAGE IVB
  AHNAK MUTATED           0
  AHNAK WILD-TYPE         1
D1781V3, multiclass
            clus
vv           AHNAK MUTATED AHNAK WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               6              20
  STAGE IIA             12              96
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               3              32
  STAGE IVA              0              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
  AHNAK MUTATED     0   6  26   7
  AHNAK WILD-TYPE   9  61 223  34
D1781V4, multiclass
    clus
vv   AHNAK MUTATED AHNAK WILD-TYPE
  T1             0               9
  T2             6              61
  T3            26             223
  T4             7              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
  AHNAK MUTATED    30   4   5
  AHNAK WILD-TYPE 190  77  61
D1781V5, multiclass
    clus
vv   AHNAK MUTATED AHNAK WILD-TYPE
  N0            30             190
  N1             4              77
  N2             5              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1781V6, binary
                 cls
clus                0   1
  AHNAK MUTATED    33   3
  AHNAK WILD-TYPE 252  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHNAK MUTATED     33    3
  AHNAK WILD-TYPE  252   45
   clus
vv  AHNAK MUTATED AHNAK WILD-TYPE
  0            33             252
  1             3              45
[1] 2 2
[1] FALSE
D1781V7, binary
                 cls
clus                0   1
  AHNAK MUTATED    18  21
  AHNAK WILD-TYPE 152 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHNAK MUTATED     18   21
  AHNAK WILD-TYPE  152  176
        clus
vv       AHNAK MUTATED AHNAK WILD-TYPE
  FEMALE            18             152
  MALE              21             176
[1] 2 2
[1] FALSE
D1781V8, binary
                 cls
clus                0   1
  AHNAK MUTATED    28   2
  AHNAK WILD-TYPE 272   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHNAK MUTATED     28    2
  AHNAK WILD-TYPE  272    6
     clus
vv    AHNAK MUTATED AHNAK WILD-TYPE
  NO             28             272
  YES             2               6
[1] 2 2
[1] FALSE
D1781V9, binary
                 cls
clus                0   1
  AHNAK MUTATED    28  10
  AHNAK WILD-TYPE 286  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHNAK MUTATED     28   10
  AHNAK WILD-TYPE  286   38
                               clus
vv                              AHNAK MUTATED AHNAK WILD-TYPE
  COLON ADENOCARCINOMA                     28             286
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AHNAK MUTATED    26   0   2   4
  AHNAK WILD-TYPE 233   3  20  17
D1781V10, multiclass
    clus
vv   AHNAK MUTATED AHNAK WILD-TYPE
  R0            26             233
  R1             0               3
  R2             2              20
  RX             4              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"
D1781V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHNAK MUTATED                                  0     3
  AHNAK WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AHNAK MUTATED                           3    16
  AHNAK WILD-TYPE                        16   160
D1781V12, multiclass
                                  clus
vv                                 AHNAK MUTATED AHNAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    3              16
  WHITE                                       16             160
[1] 4 2
[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 = TRIM25 MUTATION ANALYSIS
D1782V1, survival
                  sevent
clus2                0   1
  TRIM25 MUTATED     1   3
  TRIM25 WILD-TYPE 276  75
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               4              351 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               3               75 
$`TRIM25 MUTATED`
TCGA-AA-3715 TCGA-AA-3492 TCGA-CM-6678 TCGA-D5-6537 
       19.04         3.02        11.01         4.80 

$`TRIM25 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TRIM25 MUTATED TRIM25 WILD-TYPE 
            3.02             0.00 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
           19.04           148.01 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
           7.905           22.090 
[1] "3.0 - 19.0 (7.9)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "8.8"
D1782V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM25 MUTATED         0        0        2         0         0         0
  TRIM25 WILD-TYPE      64        1       24       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM25 MUTATED           0          0          1          0        0
  TRIM25 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM25 MUTATED           1         0
  TRIM25 WILD-TYPE        11         1
D1782V3, multiclass
            clus
vv           TRIM25 MUTATED TRIM25 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               0              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  TRIM25 MUTATED     0   0   3   1
  TRIM25 WILD-TYPE   9  67 246  40
D1782V4, multiclass
    clus
vv   TRIM25 MUTATED TRIM25 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              3              246
  T4              1               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
  TRIM25 MUTATED     2   2   0
  TRIM25 WILD-TYPE 218  79  66
D1782V5, multiclass
    clus
vv   TRIM25 MUTATED TRIM25 WILD-TYPE
  N0              2              218
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1782V6, binary
                  cls
clus                 0   1
  TRIM25 MUTATED     2   1
  TRIM25 WILD-TYPE 283  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM25 MUTATED      2    1
  TRIM25 WILD-TYPE  283   47
   clus
vv  TRIM25 MUTATED TRIM25 WILD-TYPE
  0              2              283
  1              1               47
[1] 2 2
[1] FALSE
D1782V7, binary
                  cls
clus                 0   1
  TRIM25 MUTATED     2   2
  TRIM25 WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM25 MUTATED      2    2
  TRIM25 WILD-TYPE  168  195
        clus
vv       TRIM25 MUTATED TRIM25 WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D1782V8, binary
                  cls
clus                 0   1
  TRIM25 MUTATED     4   0
  TRIM25 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM25 MUTATED      4    0
  TRIM25 WILD-TYPE  296    8
     clus
vv    TRIM25 MUTATED TRIM25 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1782V9, binary
                  cls
clus                 0   1
  TRIM25 MUTATED     4   0
  TRIM25 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM25 MUTATED      4    0
  TRIM25 WILD-TYPE  310   48
                               clus
vv                              TRIM25 MUTATED TRIM25 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM25 MUTATED     4   0   0   0
  TRIM25 WILD-TYPE 255   3  22  21
D1782V10, multiclass
    clus
vv   TRIM25 MUTATED TRIM25 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D1782V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM25 MUTATED                                  0     0
  TRIM25 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM25 MUTATED                           0     2
  TRIM25 WILD-TYPE                        19   174
D1782V12, multiclass
[1] "Remove cluster labels:" "TRIM25 MUTATED"        
clus
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6538       TCGA-D5-6539 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 

Clustering(1783) Variable = STK10 MUTATION ANALYSIS
D1783V1, survival
                 sevent
clus2               0   1
  STK10 MUTATED    11   3
  STK10 WILD-TYPE 266  75
  STK10 MUTATED STK10 WILD-TYPE 
             14             341 
  STK10 MUTATED STK10 WILD-TYPE 
              3              75 
$`STK10 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-G4-6586 TCGA-G4-6628 TCGA-AA-3663 TCGA-AA-3977 
        0.92        19.04        35.80        79.69         6.97        25.02 
TCGA-AA-A02Y TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-6599 TCGA-CK-4952 TCGA-CM-5344 
       39.98        83.24         5.79         6.77        15.62        22.03 
TCGA-D5-6539 TCGA-F4-6856 
       12.49        35.31 

$`STK10 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       91.79        43.76        46.65        43.76        42.90        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        12.16        24.53        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  STK10 MUTATED STK10 WILD-TYPE 
           0.92            0.00 
  STK10 MUTATED STK10 WILD-TYPE 
          83.24          148.01 
  STK10 MUTATED STK10 WILD-TYPE 
         20.535          22.090 
[1] "0.9 - 83.2 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1783V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK10 MUTATED         4        0        1         2         0         0
  STK10 WILD-TYPE      60        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK10 MUTATED           1          0          1          2        1         0
  STK10 WILD-TYPE        17          6         43         31       34        12
                 vv
clus              STAGE IVB
  STK10 MUTATED           0
  STK10 WILD-TYPE         1
D1783V3, multiclass
            clus
vv           STK10 MUTATED STK10 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               1              34
  STAGE IVA              0              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
  STK10 MUTATED     0   5   7   2
  STK10 WILD-TYPE   9  62 242  39
D1783V4, multiclass
    clus
vv   STK10 MUTATED STK10 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             7             242
  T4             2              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
  STK10 MUTATED    10   2   2
  STK10 WILD-TYPE 210  79  64
D1783V5, multiclass
    clus
vv   STK10 MUTATED STK10 WILD-TYPE
  N0            10             210
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1783V6, binary
                 cls
clus                0   1
  STK10 MUTATED    10   1
  STK10 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK10 MUTATED     10    1
  STK10 WILD-TYPE  275   47
   clus
vv  STK10 MUTATED STK10 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1783V7, binary
                 cls
clus                0   1
  STK10 MUTATED     5   9
  STK10 WILD-TYPE 165 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK10 MUTATED      5    9
  STK10 WILD-TYPE  165  188
        clus
vv       STK10 MUTATED STK10 WILD-TYPE
  FEMALE             5             165
  MALE               9             188
[1] 2 2
[1] FALSE
D1783V8, binary
                 cls
clus                0   1
  STK10 MUTATED    12   1
  STK10 WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK10 MUTATED     12    1
  STK10 WILD-TYPE  288    7
     clus
vv    STK10 MUTATED STK10 WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D1783V9, binary
                 cls
clus                0   1
  STK10 MUTATED    11   3
  STK10 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK10 MUTATED     11    3
  STK10 WILD-TYPE  303   45
                               clus
vv                              STK10 MUTATED STK10 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK10 MUTATED     9   0   1   1
  STK10 WILD-TYPE 250   3  21  20
D1783V10, multiclass
    clus
vv   STK10 MUTATED STK10 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             1              21
  RX             1              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"
D1783V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK10 MUTATED                                  0     1
  STK10 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK10 MUTATED                           0     8
  STK10 WILD-TYPE                        19   168
D1783V12, multiclass
                                  clus
vv                                 STK10 MUTATED STK10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = TLR9 MUTATION ANALYSIS
D1784V1, survival
                sevent
clus2              0   1
  TLR9 MUTATED    10   1
  TLR9 WILD-TYPE 267  77
  TLR9 MUTATED TLR9 WILD-TYPE 
            11            344 
  TLR9 MUTATED TLR9 WILD-TYPE 
             1             77 
$`TLR9 MUTATED`
TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3837 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A010 
       19.66         1.02        38.99         2.01        21.99        34.98 
TCGA-CK-4947 TCGA-CM-6674 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 
       17.56        12.95        11.64        13.35         6.18 

$`TLR9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TLR9 MUTATED TLR9 WILD-TYPE 
          1.02           0.00 
  TLR9 MUTATED TLR9 WILD-TYPE 
         38.99         148.01 
  TLR9 MUTATED TLR9 WILD-TYPE 
         13.35          22.39 
[1] "1.0 - 39.0 (13.3)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.5"
D1784V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TLR9 MUTATED         1        0        0         7         1         0
  TLR9 WILD-TYPE      63        1       26       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TLR9 MUTATED           0          0          1          1        0         0
  TLR9 WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  TLR9 MUTATED           0
  TLR9 WILD-TYPE         1
D1784V3, multiclass
            clus
vv           TLR9 MUTATED TLR9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TLR9 MUTATED     0   1   7   3
  TLR9 WILD-TYPE   9  66 242  38
D1784V4, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            3             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
  TLR9 MUTATED     9   2   0
  TLR9 WILD-TYPE 211  79  66
D1784V5, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  N0            9            211
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1784V6, binary
                cls
clus               0   1
  TLR9 MUTATED    10   0
  TLR9 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED     10    0
  TLR9 WILD-TYPE  275   48
   clus
vv  TLR9 MUTATED TLR9 WILD-TYPE
  0           10            275
  1            0             48
[1] 2 2
[1] FALSE
D1784V7, binary
                cls
clus               0   1
  TLR9 MUTATED     6   5
  TLR9 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      6    5
  TLR9 WILD-TYPE  164  192
        clus
vv       TLR9 MUTATED TLR9 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D1784V8, binary
                cls
clus               0   1
  TLR9 MUTATED     9   0
  TLR9 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      9    0
  TLR9 WILD-TYPE  291    8
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1784V9, binary
                cls
clus               0   1
  TLR9 MUTATED     6   5
  TLR9 WILD-TYPE 308  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      6    5
  TLR9 WILD-TYPE  308   43
                               clus
vv                              TLR9 MUTATED TLR9 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TLR9 MUTATED     9   0   0   1
  TLR9 WILD-TYPE 250   3  22  20
D1784V10, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            1             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"
D1784V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TLR9 MUTATED                                  0     0
  TLR9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TLR9 MUTATED                           0     6
  TLR9 WILD-TYPE                        19   170
D1784V12, multiclass
                                  clus
vv                                 TLR9 MUTATED TLR9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = VWA3A MUTATION ANALYSIS
D1785V1, survival
                 sevent
clus2               0   1
  VWA3A MUTATED     9   1
  VWA3A WILD-TYPE 268  77
  VWA3A MUTATED VWA3A WILD-TYPE 
             10             345 
  VWA3A MUTATED VWA3A WILD-TYPE 
              1              77 
$`VWA3A MUTATED`
TCGA-G4-6628 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3855 TCGA-AA-3966 
       79.69        19.66        63.98        15.95        32.05         2.01 
TCGA-AA-A00N TCGA-CM-5863 TCGA-CM-5868 TCGA-F4-6856 
        4.01        15.02        17.03        35.31 

$`VWA3A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 
       36.03         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  VWA3A MUTATED VWA3A WILD-TYPE 
           2.01            0.00 
  VWA3A MUTATED VWA3A WILD-TYPE 
          79.69          148.01 
  VWA3A MUTATED VWA3A WILD-TYPE 
         18.345          22.090 
[1] "2.0 - 79.7 (18.3)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1785V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VWA3A MUTATED         3        0        1         3         1         0
  VWA3A WILD-TYPE      61        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VWA3A MUTATED           0          0          1          1        0         1
  VWA3A WILD-TYPE        18          6         43         32       35        11
                 vv
clus              STAGE IVB
  VWA3A MUTATED           0
  VWA3A WILD-TYPE         1
D1785V3, multiclass
            clus
vv           VWA3A MUTATED VWA3A WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  VWA3A MUTATED     0   3   5   3
  VWA3A WILD-TYPE   9  64 244  38
D1785V4, multiclass
    clus
vv   VWA3A MUTATED VWA3A WILD-TYPE
  T1             0               9
  T2             3              64
  T3             5             244
  T4             3              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
  VWA3A MUTATED     8   3   0
  VWA3A WILD-TYPE 212  78  66
D1785V5, multiclass
    clus
vv   VWA3A MUTATED VWA3A WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1785V6, binary
                 cls
clus                0   1
  VWA3A MUTATED     9   1
  VWA3A WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      9    1
  VWA3A WILD-TYPE  276   47
   clus
vv  VWA3A MUTATED VWA3A WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1785V7, binary
                 cls
clus                0   1
  VWA3A MUTATED     5   6
  VWA3A WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      5    6
  VWA3A WILD-TYPE  165  191
        clus
vv       VWA3A MUTATED VWA3A WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1785V8, binary
                 cls
clus                0   1
  VWA3A MUTATED     8   0
  VWA3A WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      8    0
  VWA3A WILD-TYPE  292    8
     clus
vv    VWA3A MUTATED VWA3A WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1785V9, binary
                 cls
clus                0   1
  VWA3A MUTATED     6   5
  VWA3A WILD-TYPE 308  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      6    5
  VWA3A WILD-TYPE  308   43
                               clus
vv                              VWA3A MUTATED VWA3A WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VWA3A MUTATED    10   0   0   0
  VWA3A WILD-TYPE 249   3  22  21
D1785V10, multiclass
    clus
vv   VWA3A MUTATED VWA3A WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             0              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"
D1785V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VWA3A MUTATED                                  0     0
  VWA3A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VWA3A MUTATED                           0     5
  VWA3A WILD-TYPE                        19   171
D1785V12, multiclass
                                  clus
vv                                 VWA3A MUTATED VWA3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = S1PR1 MUTATION ANALYSIS
D1786V1, survival
                 sevent
clus2               0   1
  S1PR1 MUTATED     8   3
  S1PR1 WILD-TYPE 269  75
  S1PR1 MUTATED S1PR1 WILD-TYPE 
             11             344 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
              3              75 
$`S1PR1 MUTATED`
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AZ-4682 TCGA-CM-4747 
       26.99        10.06        25.02         1.02        22.36        25.02 
TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A28H TCGA-G4-6317 
       12.00        13.35        24.43       117.07        36.00 

$`S1PR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3812 
       15.02        11.01         5.98        37.05         5.03        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       33.04         0.99        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-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82        58.39         1.41         5.13        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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 
        2.01       124.27        23.05        20.02        37.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        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-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-F4-6459 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  S1PR1 MUTATED S1PR1 WILD-TYPE 
           1.02            0.00 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
         117.07          148.01 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
          24.43           22.01 
[1] "1.0 - 117.1 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1786V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  S1PR1 MUTATED         1        0        0         4         0         0
  S1PR1 WILD-TYPE      63        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  S1PR1 MUTATED           1          0          1          2        0         2
  S1PR1 WILD-TYPE        17          6         43         31       35        10
                 vv
clus              STAGE IVB
  S1PR1 MUTATED           0
  S1PR1 WILD-TYPE         1
D1786V3, multiclass
            clus
vv           S1PR1 MUTATED S1PR1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              2              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
  S1PR1 MUTATED     0   1   9   1
  S1PR1 WILD-TYPE   9  66 240  40
D1786V4, multiclass
    clus
vv   S1PR1 MUTATED S1PR1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             1              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
  S1PR1 MUTATED     6   2   3
  S1PR1 WILD-TYPE 214  79  63
D1786V5, multiclass
    clus
vv   S1PR1 MUTATED S1PR1 WILD-TYPE
  N0             6             214
  N1             2              79
  N2             3              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"
D1786V6, binary
                 cls
clus                0   1
  S1PR1 MUTATED     8   2
  S1PR1 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  S1PR1 MUTATED      8    2
  S1PR1 WILD-TYPE  277   46
   clus
vv  S1PR1 MUTATED S1PR1 WILD-TYPE
  0             8             277
  1             2              46
[1] 2 2
[1] FALSE
D1786V7, binary
                 cls
clus                0   1
  S1PR1 MUTATED     6   5
  S1PR1 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  S1PR1 MUTATED      6    5
  S1PR1 WILD-TYPE  164  192
        clus
vv       S1PR1 MUTATED S1PR1 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D1786V8, binary
                 cls
clus                0   1
  S1PR1 MUTATED     9   0
  S1PR1 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  S1PR1 MUTATED      9    0
  S1PR1 WILD-TYPE  291    8
     clus
vv    S1PR1 MUTATED S1PR1 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1786V9, binary
                 cls
clus                0   1
  S1PR1 MUTATED     8   3
  S1PR1 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  S1PR1 MUTATED      8    3
  S1PR1 WILD-TYPE  306   45
                               clus
vv                              S1PR1 MUTATED S1PR1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  S1PR1 MUTATED     9   0   0   0
  S1PR1 WILD-TYPE 250   3  22  21
D1786V10, multiclass
    clus
vv   S1PR1 MUTATED S1PR1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1786V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  S1PR1 MUTATED                                  0     0
  S1PR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  S1PR1 MUTATED                           0     7
  S1PR1 WILD-TYPE                        19   169
D1786V12, multiclass
                                  clus
vv                                 S1PR1 MUTATED S1PR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = RAPGEF2 MUTATION ANALYSIS
D1787V1, survival
                   sevent
clus2                 0   1
  RAPGEF2 MUTATED    16   4
  RAPGEF2 WILD-TYPE 261  74
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               20               335 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
                4                74 
$`RAPGEF2 MUTATED`
TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5665 TCGA-A6-6141 
       25.08       100.01        35.80        26.17        22.06         8.38 
TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3977 
       19.66        61.02         1.02        15.95        53.00        25.02 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 
       34.98        38.07        12.16        58.39        12.76        21.14 
TCGA-DM-A0XD TCGA-DM-A1HB 
       24.43       135.65 

$`RAPGEF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        22.09        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
       79.69        43.76        46.65        43.76        42.90        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
             1.02              0.00 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
           135.65            148.01 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
            25.05             21.99 
[1] "1.0 - 135.7 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1787V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAPGEF2 MUTATED         3        0        3         9         1         0
  RAPGEF2 WILD-TYPE      61        1       23        99         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAPGEF2 MUTATED           1          0          2          1        0
  RAPGEF2 WILD-TYPE        17          6         42         32       35
                   vv
clus                STAGE IVA STAGE IVB
  RAPGEF2 MUTATED           0         0
  RAPGEF2 WILD-TYPE        12         1
D1787V3, multiclass
            clus
vv           RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                9                99
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  RAPGEF2 MUTATED     1   3  15   2
  RAPGEF2 WILD-TYPE   8  64 234  39
D1787V4, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  T1               1                 8
  T2               3                64
  T3              15               234
  T4               2                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
  RAPGEF2 MUTATED    17   4   0
  RAPGEF2 WILD-TYPE 203  77  66
D1787V5, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  N0              17               203
  N1               4                77
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1787V6, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    18   0
  RAPGEF2 WILD-TYPE 267  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     18    0
  RAPGEF2 WILD-TYPE  267   48
   clus
vv  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  0              18               267
  1               0                48
[1] 2 2
[1] FALSE
D1787V7, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED     9  12
  RAPGEF2 WILD-TYPE 161 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED      9   12
  RAPGEF2 WILD-TYPE  161  185
        clus
vv       RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  FEMALE               9               161
  MALE                12               185
[1] 2 2
[1] FALSE
D1787V8, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    18   0
  RAPGEF2 WILD-TYPE 282   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     18    0
  RAPGEF2 WILD-TYPE  282    8
     clus
vv    RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  NO               18               282
  YES               0                 8
[1] 2 2
[1] FALSE
D1787V9, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    16   4
  RAPGEF2 WILD-TYPE 298  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     16    4
  RAPGEF2 WILD-TYPE  298   44
                               clus
vv                              RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  COLON ADENOCARCINOMA                       16               298
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RAPGEF2 MUTATED    14   0   0   2
  RAPGEF2 WILD-TYPE 245   3  22  19
D1787V10, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  R0              14               245
  R1               0                 3
  R2               0                22
  RX               2                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"
D1787V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAPGEF2 MUTATED                                  0     1
  RAPGEF2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RAPGEF2 MUTATED                           1    11
  RAPGEF2 WILD-TYPE                        18   165
D1787V12, multiclass
                                  clus
vv                                 RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               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(1788) Variable = SFRS2IP MUTATION ANALYSIS
D1788V1, survival
                   sevent
clus2                 0   1
  SFRS2IP MUTATED    22   3
  SFRS2IP WILD-TYPE 255  75
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               25               330 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                3                75 
$`SFRS2IP MUTATED`
TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6628 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3534 
       49.08        63.62        79.69        24.39        63.98        29.00 
TCGA-AA-3710 TCGA-AA-3949 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01P 
       26.99        26.01        38.04        34.98        32.02        38.07 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 
       12.16        22.42        21.44        58.39        12.76        51.32 
TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-5861 TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6304 
       21.99        22.98        15.02       135.65        35.31        53.62 
TCGA-G4-6309 
       85.48 

$`SFRS2IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 
      106.75       100.01         1.94         5.88        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
            12.16              0.00 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
           135.65            148.01 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
           34.980            21.075 
[1] "12.2 - 135.7 (35.0)" "0.0 - 148.0 (21.1)" 
[1] "hr=" "2.8"
D1788V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS2IP MUTATED         5        0        1         9         2         0
  SFRS2IP WILD-TYPE      59        1       25        99         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS2IP MUTATED           1          0          7          0        0
  SFRS2IP WILD-TYPE        17          6         37         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SFRS2IP MUTATED           0         0
  SFRS2IP WILD-TYPE        12         1
D1788V3, multiclass
            clus
vv           SFRS2IP MUTATED SFRS2IP WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                9                99
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               7                37
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  SFRS2IP MUTATED     0   5  19   2
  SFRS2IP WILD-TYPE   9  62 230  39
D1788V4, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  T1               0                 9
  T2               5                62
  T3              19               230
  T4               2                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
  SFRS2IP MUTATED    18   8   0
  SFRS2IP WILD-TYPE 202  73  66
D1788V5, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  N0              18               202
  N1               8                73
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1788V6, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    20   0
  SFRS2IP WILD-TYPE 265  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     20    0
  SFRS2IP WILD-TYPE  265   48
   clus
vv  SFRS2IP MUTATED SFRS2IP WILD-TYPE
  0              20               265
  1               0                48
[1] 2 2
[1] FALSE
D1788V7, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    10  16
  SFRS2IP WILD-TYPE 160 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     10   16
  SFRS2IP WILD-TYPE  160  181
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  FEMALE              10               160
  MALE                16               181
[1] 2 2
[1] FALSE
D1788V8, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    22   1
  SFRS2IP WILD-TYPE 278   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     22    1
  SFRS2IP WILD-TYPE  278    7
     clus
vv    SFRS2IP MUTATED SFRS2IP WILD-TYPE
  NO               22               278
  YES               1                 7
[1] 2 2
[1] FALSE
D1788V9, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    21   4
  SFRS2IP WILD-TYPE 293  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     21    4
  SFRS2IP WILD-TYPE  293   44
                               clus
vv                              SFRS2IP MUTATED SFRS2IP WILD-TYPE
  COLON ADENOCARCINOMA                       21               293
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SFRS2IP MUTATED    19   0   0   4
  SFRS2IP WILD-TYPE 240   3  22  17
D1788V10, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  R0              19               240
  R1               0                 3
  R2               0                22
  RX               4                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"
D1788V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS2IP MUTATED                                  0     1
  SFRS2IP WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SFRS2IP MUTATED                           1    15
  SFRS2IP WILD-TYPE                        18   161
D1788V12, multiclass
                                  clus
vv                                 SFRS2IP MUTATED SFRS2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         15               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(1789) Variable = LUZP1 MUTATION ANALYSIS
D1789V1, survival
                 sevent
clus2               0   1
  LUZP1 MUTATED    11   4
  LUZP1 WILD-TYPE 266  74
  LUZP1 MUTATED LUZP1 WILD-TYPE 
             15             340 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              4              74 
$`LUZP1 MUTATED`
TCGA-AA-3520 TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3510 
       24.03        35.80        22.06        20.12        35.01        63.98 
TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01P TCGA-AZ-4315 TCGA-AZ-6598 
       53.00        34.98        32.02        38.07        58.39        49.41 
TCGA-CA-6718 TCGA-CM-6674 TCGA-DM-A28G 
       10.06        12.95        60.79 

$`LUZP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04         3.02         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       15.02        10.98        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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LUZP1 MUTATED LUZP1 WILD-TYPE 
          10.06            0.00 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
          63.98          148.01 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
          35.01           21.99 
[1] "10.1 - 64.0 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1789V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LUZP1 MUTATED         1        0        4         7         1         0
  LUZP1 WILD-TYPE      63        1       22       101         7         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        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  LUZP1 MUTATED           0
  LUZP1 WILD-TYPE         1
D1789V3, multiclass
            clus
vv           LUZP1 MUTATED LUZP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              22
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  LUZP1 MUTATED     0   1  13   1
  LUZP1 WILD-TYPE   9  66 236  40
D1789V4, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            13             236
  T4             1              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
  LUZP1 MUTATED    13   2   0
  LUZP1 WILD-TYPE 207  79  66
D1789V5, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  N0            13             207
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1789V6, binary
                 cls
clus                0   1
  LUZP1 MUTATED    13   0
  LUZP1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED     13    0
  LUZP1 WILD-TYPE  272   48
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0            13             272
  1             0              48
[1] 2 2
[1] FALSE
D1789V7, binary
                 cls
clus                0   1
  LUZP1 MUTATED     6   9
  LUZP1 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      6    9
  LUZP1 WILD-TYPE  164  188
        clus
vv       LUZP1 MUTATED LUZP1 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D1789V8, binary
                 cls
clus                0   1
  LUZP1 MUTATED    14   0
  LUZP1 WILD-TYPE 286   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED     14    0
  LUZP1 WILD-TYPE  286    8
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO             14             286
  YES             0               8
[1] 2 2
[1] FALSE
D1789V9, binary
                 cls
clus                0   1
  LUZP1 MUTATED    14   1
  LUZP1 WILD-TYPE 300  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED     14    1
  LUZP1 WILD-TYPE  300   47
                               clus
vv                              LUZP1 MUTATED LUZP1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             300
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LUZP1 MUTATED    11   0   0   1
  LUZP1 WILD-TYPE 248   3  22  20
D1789V10, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             0              22
  RX             1              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"
D1789V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LUZP1 MUTATED                                  0     1
  LUZP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LUZP1 MUTATED                           0     7
  LUZP1 WILD-TYPE                        19   169
D1789V12, multiclass
                                  clus
vv                                 LUZP1 MUTATED LUZP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = NDUFB2 MUTATION ANALYSIS
D1790V1, survival
                  sevent
clus2                0   1
  NDUFB2 MUTATED     0   3
  NDUFB2 WILD-TYPE 277  75
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               3              352 
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               3               75 
$`NDUFB2 MUTATED`
TCGA-AA-3845 TCGA-AZ-6598 TCGA-D5-6537 
        0.00        49.41         4.80 

$`NDUFB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               0                0 
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
           49.41           148.01 
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
           4.800           22.075 
[1] "0.0 - 49.4 (4.8)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "6.7"
D1790V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NDUFB2 MUTATED         0        0        1         1         0         0
  NDUFB2 WILD-TYPE      64        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDUFB2 MUTATED           0          0          1          0        0
  NDUFB2 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  NDUFB2 MUTATED           0         0
  NDUFB2 WILD-TYPE        12         1
D1790V3, multiclass
            clus
vv           NDUFB2 MUTATED NDUFB2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  NDUFB2 MUTATED     0   0   3   0
  NDUFB2 WILD-TYPE   9  67 246  41
D1790V4, multiclass
    clus
vv   NDUFB2 MUTATED NDUFB2 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              3              246
  T4              0               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
  NDUFB2 MUTATED     2   1   0
  NDUFB2 WILD-TYPE 218  80  66
D1790V5, multiclass
    clus
vv   NDUFB2 MUTATED NDUFB2 WILD-TYPE
  N0              2              218
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1790V6, binary
                  cls
clus                 0   1
  NDUFB2 MUTATED     1   0
  NDUFB2 WILD-TYPE 284  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFB2 MUTATED      1    0
  NDUFB2 WILD-TYPE  284   48
   clus
vv  NDUFB2 MUTATED NDUFB2 WILD-TYPE
  0              1              284
  1              0               48
[1] 2 2
[1] FALSE
D1790V7, binary
                  cls
clus                 0   1
  NDUFB2 MUTATED     2   1
  NDUFB2 WILD-TYPE 168 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFB2 MUTATED      2    1
  NDUFB2 WILD-TYPE  168  196
        clus
vv       NDUFB2 MUTATED NDUFB2 WILD-TYPE
  FEMALE              2              168
  MALE                1              196
[1] 2 2
[1] FALSE
D1790V8, binary
                  cls
clus                 0   1
  NDUFB2 MUTATED     2   0
  NDUFB2 WILD-TYPE 298   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFB2 MUTATED      2    0
  NDUFB2 WILD-TYPE  298    8
     clus
vv    NDUFB2 MUTATED NDUFB2 WILD-TYPE
  NO               2              298
  YES              0                8
[1] 2 2
[1] FALSE
D1790V9, binary
                  cls
clus                 0   1
  NDUFB2 MUTATED     3   0
  NDUFB2 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFB2 MUTATED      3    0
  NDUFB2 WILD-TYPE  311   48
                               clus
vv                              NDUFB2 MUTATED NDUFB2 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NDUFB2 MUTATED     2   0   0   0
  NDUFB2 WILD-TYPE 257   3  22  21
D1790V10, multiclass
[1] "Remove cluster labels:" "NDUFB2 MUTATED"        
clus
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               2              303 
      TCGA-A6-2677       TCGA-AA-3496       TCGA-AA-3520       TCGA-AA-3521 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3527 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3543       TCGA-AA-3552 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3556       TCGA-AA-3560       TCGA-AA-3562 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3672       TCGA-AA-3688       TCGA-AA-3692 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3814 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3860       TCGA-AA-3867       TCGA-AA-3870 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3972 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3986       TCGA-AA-A00L 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A024       TCGA-AD-6548       TCGA-AD-6888 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AD-6895       TCGA-AZ-4681       TCGA-CK-5912       TCGA-G4-6310 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3502       TCGA-AA-3510 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3526       TCGA-AA-3529       TCGA-AA-3532 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3544 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3553       TCGA-AA-3555 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3561       TCGA-AA-3655       TCGA-AA-3660 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3693 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3710       TCGA-AA-3712 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3815       TCGA-AA-3818 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3846       TCGA-AA-3848 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3861 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869       TCGA-AA-3872 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3941 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3955       TCGA-AA-3956 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3973       TCGA-AA-3975 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00N       TCGA-AA-A00O 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6889 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4682       TCGA-CA-5254 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6315 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
D1790V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDUFB2 MUTATED                                  0     0
  NDUFB2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NDUFB2 MUTATED                           0     2
  NDUFB2 WILD-TYPE                        19   174
D1790V12, multiclass
[1] "Remove cluster labels:" "NDUFB2 MUTATED"        
clus
  NDUFB2 MUTATED NDUFB2 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6599       TCGA-AZ-6600 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6538       TCGA-D5-6539 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" "NDUFB2 WILD-TYPE" 

Clustering(1791) Variable = LRRFIP1 MUTATION ANALYSIS
D1791V1, survival
                   sevent
clus2                 0   1
  LRRFIP1 MUTATED     9   3
  LRRFIP1 WILD-TYPE 268  75
  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
               12               343 
  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
                3                75 
$`LRRFIP1 MUTATED`
TCGA-AA-3713 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 
       19.04        22.06        24.39         2.01         4.01        34.98 
TCGA-AY-4070 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-6164 TCGA-CM-6168 TCGA-D5-6538 
       16.31        58.39        21.14        29.03        12.99        17.13 

$`LRRFIP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
        8.38        25.08        25.18        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
             2.01              0.00 
  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
            58.39            148.01 
  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE 
            20.09             22.09 
[1] "2.0 - 58.4 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1791V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRFIP1 MUTATED         2        0        0         5         2         0
  LRRFIP1 WILD-TYPE      62        1       26       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRFIP1 MUTATED           0          0          1          1        1
  LRRFIP1 WILD-TYPE        18          6         43         32       34
                   vv
clus                STAGE IVA STAGE IVB
  LRRFIP1 MUTATED           0         0
  LRRFIP1 WILD-TYPE        12         1
D1791V3, multiclass
            clus
vv           LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  LRRFIP1 MUTATED     1   1   8   2
  LRRFIP1 WILD-TYPE   8  66 241  39
D1791V4, multiclass
    clus
vv   LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               8               241
  T4               2                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
  LRRFIP1 MUTATED    10   0   2
  LRRFIP1 WILD-TYPE 210  81  64
D1791V5, multiclass
    clus
vv   LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  N0              10               210
  N1               0                81
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1791V6, binary
                   cls
clus                  0   1
  LRRFIP1 MUTATED    11   1
  LRRFIP1 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP1 MUTATED     11    1
  LRRFIP1 WILD-TYPE  274   47
   clus
vv  LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  0              11               274
  1               1                47
[1] 2 2
[1] FALSE
D1791V7, binary
                   cls
clus                  0   1
  LRRFIP1 MUTATED     8   4
  LRRFIP1 WILD-TYPE 162 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP1 MUTATED      8    4
  LRRFIP1 WILD-TYPE  162  193
        clus
vv       LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  FEMALE               8               162
  MALE                 4               193
[1] 2 2
[1] FALSE
D1791V8, binary
                   cls
clus                  0   1
  LRRFIP1 MUTATED     9   1
  LRRFIP1 WILD-TYPE 291   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP1 MUTATED      9    1
  LRRFIP1 WILD-TYPE  291    7
     clus
vv    LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  NO                9               291
  YES               1                 7
[1] 2 2
[1] FALSE
D1791V9, binary
                   cls
clus                  0   1
  LRRFIP1 MUTATED    10   2
  LRRFIP1 WILD-TYPE 304  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP1 MUTATED     10    2
  LRRFIP1 WILD-TYPE  304   46
                               clus
vv                              LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                       10               304
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  LRRFIP1 MUTATED     7   1   1   1
  LRRFIP1 WILD-TYPE 252   2  21  20
D1791V10, multiclass
    clus
vv   LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  R0               7               252
  R1               1                 2
  R2               1                21
  RX               1                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"
D1791V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRFIP1 MUTATED                                  0     0
  LRRFIP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LRRFIP1 MUTATED                           2     6
  LRRFIP1 WILD-TYPE                        17   170
D1791V12, multiclass
                                  clus
vv                                 LRRFIP1 MUTATED LRRFIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               170
[1] 4 2
[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 = PTPRN MUTATION ANALYSIS
D1792V1, survival
                 sevent
clus2               0   1
  PTPRN MUTATED    11   2
  PTPRN WILD-TYPE 266  76
  PTPRN MUTATED PTPRN WILD-TYPE 
             13             342 
  PTPRN MUTATED PTPRN WILD-TYPE 
              2              76 
$`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 
        6.18 

$`PTPRN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  PTPRN MUTATED PTPRN WILD-TYPE 
           1.02            0.00 
  PTPRN MUTATED PTPRN WILD-TYPE 
          63.98          148.01 
  PTPRN MUTATED PTPRN WILD-TYPE 
          25.02           22.01 
[1] "1.0 - 64.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1792V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRN MUTATED         1        0        2         5         2         0
  PTPRN WILD-TYPE      63        1       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRN MUTATED           1          0          1          1        0         0
  PTPRN WILD-TYPE        17          6         43         32       35        12
                 vv
clus              STAGE IVB
  PTPRN MUTATED           0
  PTPRN WILD-TYPE         1
D1792V3, multiclass
            clus
vv           PTPRN MUTATED PTPRN WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  PTPRN MUTATED     0   2   9   3
  PTPRN WILD-TYPE   9  65 240  38
D1792V4, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             3              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
  PTPRN MUTATED    11   1   2
  PTPRN WILD-TYPE 209  80  64
D1792V5, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  N0            11             209
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1792V6, binary
                 cls
clus                0   1
  PTPRN MUTATED    10   0
  PTPRN WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED     10    0
  PTPRN WILD-TYPE  275   48
   clus
vv  PTPRN MUTATED PTPRN WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1792V7, binary
                 cls
clus                0   1
  PTPRN MUTATED     7   7
  PTPRN WILD-TYPE 163 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED      7    7
  PTPRN WILD-TYPE  163  190
        clus
vv       PTPRN MUTATED PTPRN WILD-TYPE
  FEMALE             7             163
  MALE               7             190
[1] 2 2
[1] FALSE
D1792V8, binary
                 cls
clus                0   1
  PTPRN MUTATED    12   1
  PTPRN WILD-TYPE 288   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED     12    1
  PTPRN WILD-TYPE  288    7
     clus
vv    PTPRN MUTATED PTPRN WILD-TYPE
  NO             12             288
  YES             1               7
[1] 2 2
[1] FALSE
D1792V9, binary
                 cls
clus                0   1
  PTPRN MUTATED     9   5
  PTPRN WILD-TYPE 305  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED      9    5
  PTPRN WILD-TYPE  305   43
                               clus
vv                              PTPRN MUTATED PTPRN WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRN MUTATED    10   0   0   2
  PTPRN WILD-TYPE 249   3  22  19
D1792V10, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             2              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"
D1792V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRN MUTATED                                  0     1
  PTPRN WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRN MUTATED                           0     7
  PTPRN WILD-TYPE                        19   169
D1792V12, multiclass
                                  clus
vv                                 PTPRN MUTATED PTPRN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        7             169
[1] 4 2
[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 = AVPR1A MUTATION ANALYSIS
D1793V1, survival
                  sevent
clus2                0   1
  AVPR1A MUTATED     9   1
  AVPR1A WILD-TYPE 268  77
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              10              345 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
               1               77 
$`AVPR1A MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 
       19.04        19.04        79.69        22.06        20.12         6.97 
TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6927 
       34.98        12.76        12.00         9.44 

$`AVPR1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  AVPR1A MUTATED AVPR1A WILD-TYPE 
            6.97             0.00 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
           79.69           148.01 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
           19.04            22.36 
[1] "7.0 - 79.7 (19.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.9"
D1793V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AVPR1A MUTATED         1        0        3         4         1         0
  AVPR1A WILD-TYPE      63        1       23       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AVPR1A MUTATED           0          0          1          0        1
  AVPR1A WILD-TYPE        18          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  AVPR1A MUTATED           0         0
  AVPR1A WILD-TYPE        12         1
D1793V3, multiclass
            clus
vv           AVPR1A MUTATED AVPR1A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  AVPR1A MUTATED     0   1   8   2
  AVPR1A WILD-TYPE   9  66 241  39
D1793V4, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  T1              0                9
  T2              1               66
  T3              8              241
  T4              2               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
  AVPR1A MUTATED    10   1   0
  AVPR1A WILD-TYPE 210  80  66
D1793V5, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  N0             10              210
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1793V6, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     9   1
  AVPR1A WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      9    1
  AVPR1A WILD-TYPE  276   47
   clus
vv  AVPR1A MUTATED AVPR1A WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1793V7, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     4   7
  AVPR1A WILD-TYPE 166 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      4    7
  AVPR1A WILD-TYPE  166  190
        clus
vv       AVPR1A MUTATED AVPR1A WILD-TYPE
  FEMALE              4              166
  MALE                7              190
[1] 2 2
[1] FALSE
D1793V8, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     9   1
  AVPR1A WILD-TYPE 291   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      9    1
  AVPR1A WILD-TYPE  291    7
     clus
vv    AVPR1A MUTATED AVPR1A WILD-TYPE
  NO               9              291
  YES              1                7
[1] 2 2
[1] FALSE
D1793V9, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     8   3
  AVPR1A WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      8    3
  AVPR1A WILD-TYPE  306   45
                               clus
vv                              AVPR1A MUTATED AVPR1A WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AVPR1A MUTATED     8   0   1   1
  AVPR1A WILD-TYPE 251   3  21  20
D1793V10, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  R0              8              251
  R1              0                3
  R2              1               21
  RX              1               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"
D1793V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AVPR1A MUTATED                                  0     1
  AVPR1A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AVPR1A MUTATED                           0     5
  AVPR1A WILD-TYPE                        19   171
D1793V12, multiclass
                                  clus
vv                                 AVPR1A MUTATED AVPR1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = KCNC4 MUTATION ANALYSIS
D1794V1, survival
                 sevent
clus2               0   1
  KCNC4 MUTATED     7   1
  KCNC4 WILD-TYPE 270  77
  KCNC4 MUTATED KCNC4 WILD-TYPE 
              8             347 
  KCNC4 MUTATED KCNC4 WILD-TYPE 
              1              77 
$`KCNC4 MUTATED`
TCGA-AA-3950 TCGA-A6-6142 TCGA-AA-3518 TCGA-AY-6196 TCGA-CM-6171 TCGA-DM-A1HB 
       24.00        25.08         1.02         0.20        14.04       135.65 
TCGA-F4-6460 TCGA-G4-6304 
       31.96        53.62 

$`KCNC4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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-F4-6569 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KCNC4 MUTATED KCNC4 WILD-TYPE 
            0.2             0.0 
  KCNC4 MUTATED KCNC4 WILD-TYPE 
         135.65          148.01 
  KCNC4 MUTATED KCNC4 WILD-TYPE 
          24.54           22.03 
[1] "0.2 - 135.7 (24.5)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2"  
D1794V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNC4 MUTATED         1        0        0         2         1         0
  KCNC4 WILD-TYPE      63        1       26       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNC4 MUTATED           0          0          2          1        0         1
  KCNC4 WILD-TYPE        18          6         42         32       35        11
                 vv
clus              STAGE IVB
  KCNC4 MUTATED           0
  KCNC4 WILD-TYPE         1
D1794V3, multiclass
            clus
vv           KCNC4 MUTATED KCNC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  KCNC4 MUTATED     0   1   6   1
  KCNC4 WILD-TYPE   9  66 243  40
D1794V4, multiclass
    clus
vv   KCNC4 MUTATED KCNC4 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             6             243
  T4             1              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
  KCNC4 MUTATED     4   3   1
  KCNC4 WILD-TYPE 216  78  65
D1794V5, multiclass
    clus
vv   KCNC4 MUTATED KCNC4 WILD-TYPE
  N0             4             216
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1794V6, binary
                 cls
clus                0   1
  KCNC4 MUTATED     6   1
  KCNC4 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC4 MUTATED      6    1
  KCNC4 WILD-TYPE  279   47
   clus
vv  KCNC4 MUTATED KCNC4 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1794V7, binary
                 cls
clus                0   1
  KCNC4 MUTATED     6   2
  KCNC4 WILD-TYPE 164 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC4 MUTATED      6    2
  KCNC4 WILD-TYPE  164  195
        clus
vv       KCNC4 MUTATED KCNC4 WILD-TYPE
  FEMALE             6             164
  MALE               2             195
[1] 2 2
[1] FALSE
D1794V8, binary
                 cls
clus                0   1
  KCNC4 MUTATED     5   0
  KCNC4 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC4 MUTATED      5    0
  KCNC4 WILD-TYPE  295    8
     clus
vv    KCNC4 MUTATED KCNC4 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1794V9, binary
                 cls
clus                0   1
  KCNC4 MUTATED     5   2
  KCNC4 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC4 MUTATED      5    2
  KCNC4 WILD-TYPE  309   46
                               clus
vv                              KCNC4 MUTATED KCNC4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNC4 MUTATED     6   0   0   0
  KCNC4 WILD-TYPE 253   3  22  21
D1794V10, multiclass
    clus
vv   KCNC4 MUTATED KCNC4 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1794V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNC4 MUTATED                                  0     0
  KCNC4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNC4 MUTATED                           0     6
  KCNC4 WILD-TYPE                        19   170
D1794V12, multiclass
                                  clus
vv                                 KCNC4 MUTATED KCNC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = RPAP2 MUTATION ANALYSIS
D1795V1, survival
                 sevent
clus2               0   1
  RPAP2 MUTATED     6   0
  RPAP2 WILD-TYPE 271  78
  RPAP2 MUTATED RPAP2 WILD-TYPE 
              6             349 
  RPAP2 MUTATED RPAP2 WILD-TYPE 
              0              78 
$`RPAP2 MUTATED`
TCGA-AA-3672 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CM-6171 TCGA-D5-6540 
        0.92         6.97        34.98        58.39        14.04        16.14 

$`RPAP2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RPAP2 MUTATED RPAP2 WILD-TYPE 
           0.92            0.00 
  RPAP2 MUTATED RPAP2 WILD-TYPE 
          58.39          148.01 
  RPAP2 MUTATED RPAP2 WILD-TYPE 
          15.09           22.09 
[1] "0.9 - 58.4 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1795V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPAP2 MUTATED         2        0        1         1         1         0
  RPAP2 WILD-TYPE      62        1       25       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPAP2 MUTATED           1          0          0          0        0         0
  RPAP2 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  RPAP2 MUTATED           0
  RPAP2 WILD-TYPE         1
D1795V3, multiclass
            clus
vv           RPAP2 MUTATED RPAP2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              1             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RPAP2 MUTATED     0   2   3   1
  RPAP2 WILD-TYPE   9  65 246  40
D1795V4, multiclass
    clus
vv   RPAP2 MUTATED RPAP2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             3             246
  T4             1              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
  RPAP2 MUTATED     5   1   0
  RPAP2 WILD-TYPE 215  80  66
D1795V5, multiclass
    clus
vv   RPAP2 MUTATED RPAP2 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1795V6, binary
                 cls
clus                0   1
  RPAP2 MUTATED     6   0
  RPAP2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP2 MUTATED      6    0
  RPAP2 WILD-TYPE  279   48
   clus
vv  RPAP2 MUTATED RPAP2 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1795V7, binary
                 cls
clus                0   1
  RPAP2 MUTATED     3   3
  RPAP2 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP2 MUTATED      3    3
  RPAP2 WILD-TYPE  167  194
        clus
vv       RPAP2 MUTATED RPAP2 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1795V8, binary
                 cls
clus                0   1
  RPAP2 MUTATED     6   0
  RPAP2 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP2 MUTATED      6    0
  RPAP2 WILD-TYPE  294    8
     clus
vv    RPAP2 MUTATED RPAP2 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1795V9, binary
                 cls
clus                0   1
  RPAP2 MUTATED     5   1
  RPAP2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPAP2 MUTATED      5    1
  RPAP2 WILD-TYPE  309   47
                               clus
vv                              RPAP2 MUTATED RPAP2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RPAP2 MUTATED     6   0   0   0
  RPAP2 WILD-TYPE 253   3  22  21
D1795V10, multiclass
    clus
vv   RPAP2 MUTATED RPAP2 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             0              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"
D1795V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPAP2 MUTATED                                  0     0
  RPAP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RPAP2 MUTATED                           0     3
  RPAP2 WILD-TYPE                        19   173
D1795V12, multiclass
                                  clus
vv                                 RPAP2 MUTATED RPAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = DDX24 MUTATION ANALYSIS
D1796V1, survival
                 sevent
clus2               0   1
  DDX24 MUTATED     9   4
  DDX24 WILD-TYPE 268  74
  DDX24 MUTATED DDX24 WILD-TYPE 
             13             342 
  DDX24 MUTATED DDX24 WILD-TYPE 
              4              74 
$`DDX24 MUTATED`
TCGA-G4-6628 TCGA-AA-3811 TCGA-AA-A010 TCGA-AA-A01I TCGA-AY-6197 TCGA-CA-6717 
       79.69        10.06        34.98        31.00        21.44        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6538 TCGA-F4-6570 
       10.06        21.14        23.05        14.04        17.13         6.18 
TCGA-G4-6304 
       53.62 

$`DDX24 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32        21.99        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  DDX24 MUTATED DDX24 WILD-TYPE 
           6.18            0.00 
  DDX24 MUTATED DDX24 WILD-TYPE 
          79.69          148.01 
  DDX24 MUTATED DDX24 WILD-TYPE 
          21.14           22.09 
[1] "6.2 - 79.7 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1796V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX24 MUTATED         4        0        0         5         2         0
  DDX24 WILD-TYPE      60        1       26       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX24 MUTATED           1          0          1          0        0         0
  DDX24 WILD-TYPE        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  DDX24 MUTATED           0
  DDX24 WILD-TYPE         1
D1796V3, multiclass
            clus
vv           DDX24 MUTATED DDX24 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  DDX24 MUTATED     1   3   7   2
  DDX24 WILD-TYPE   8  64 242  39
D1796V4, multiclass
    clus
vv   DDX24 MUTATED DDX24 WILD-TYPE
  T1             1               8
  T2             3              64
  T3             7             242
  T4             2              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
  DDX24 MUTATED    11   0   2
  DDX24 WILD-TYPE 209  81  64
D1796V5, multiclass
    clus
vv   DDX24 MUTATED DDX24 WILD-TYPE
  N0            11             209
  N1             0              81
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1796V6, binary
                 cls
clus                0   1
  DDX24 MUTATED    12   0
  DDX24 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX24 MUTATED     12    0
  DDX24 WILD-TYPE  273   48
   clus
vv  DDX24 MUTATED DDX24 WILD-TYPE
  0            12             273
  1             0              48
[1] 2 2
[1] FALSE
D1796V7, binary
                 cls
clus                0   1
  DDX24 MUTATED     7   6
  DDX24 WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX24 MUTATED      7    6
  DDX24 WILD-TYPE  163  191
        clus
vv       DDX24 MUTATED DDX24 WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D1796V8, binary
                 cls
clus                0   1
  DDX24 MUTATED    13   0
  DDX24 WILD-TYPE 287   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX24 MUTATED     13    0
  DDX24 WILD-TYPE  287    8
     clus
vv    DDX24 MUTATED DDX24 WILD-TYPE
  NO             13             287
  YES             0               8
[1] 2 2
[1] FALSE
D1796V9, binary
                 cls
clus                0   1
  DDX24 MUTATED    12   1
  DDX24 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX24 MUTATED     12    1
  DDX24 WILD-TYPE  302   47
                               clus
vv                              DDX24 MUTATED DDX24 WILD-TYPE
  COLON ADENOCARCINOMA                     12             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX24 MUTATED    10   0   0   3
  DDX24 WILD-TYPE 249   3  22  18
D1796V10, multiclass
    clus
vv   DDX24 MUTATED DDX24 WILD-TYPE
  R0            10             249
  R1             0               3
  R2             0              22
  RX             3              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"
D1796V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX24 MUTATED                                  0     2
  DDX24 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX24 MUTATED                           0     8
  DDX24 WILD-TYPE                        19   168
D1796V12, multiclass
                                  clus
vv                                 DDX24 MUTATED DDX24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = CUL1 MUTATION ANALYSIS
D1797V1, survival
                sevent
clus2              0   1
  CUL1 MUTATED    12   3
  CUL1 WILD-TYPE 265  75
  CUL1 MUTATED CUL1 WILD-TYPE 
            15            340 
  CUL1 MUTATED CUL1 WILD-TYPE 
             3             75 
$`CUL1 MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3713 TCGA-AZ-6601 TCGA-A6-2672 
       13.02         8.05         0.99        19.04       100.01        46.65 
TCGA-AA-3815 TCGA-AA-3949 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-4743 TCGA-DM-A1HA 
       33.04        26.01        34.98        12.76        23.05       131.51 
TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6807 
      135.65         6.18        43.04 

$`CUL1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       36.03        19.07        34.03        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       25.08        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38         7.50        44.32       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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CUL1 MUTATED CUL1 WILD-TYPE 
          0.99           0.00 
  CUL1 MUTATED CUL1 WILD-TYPE 
        135.65         148.01 
  CUL1 MUTATED CUL1 WILD-TYPE 
         26.01          22.01 
[1] "1.0 - 135.7 (26.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1797V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUL1 MUTATED         1        0        1         4         1         0
  CUL1 WILD-TYPE      63        1       25       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUL1 MUTATED           1          0          4          2        1         0
  CUL1 WILD-TYPE        17          6         40         31       34        12
                vv
clus             STAGE IVB
  CUL1 MUTATED           0
  CUL1 WILD-TYPE         1
D1797V3, multiclass
            clus
vv           CUL1 MUTATED CUL1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            4             40
  STAGE IIIC            2             31
  STAGE IV              1             34
  STAGE IVA             0             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
  CUL1 MUTATED     0   1  13   1
  CUL1 WILD-TYPE   9  66 236  40
D1797V4, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  T1            0              9
  T2            1             66
  T3           13            236
  T4            1             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
  CUL1 MUTATED     8   4   3
  CUL1 WILD-TYPE 212  77  63
D1797V5, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  N0            8            212
  N1            4             77
  N2            3             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"
D1797V6, binary
                cls
clus               0   1
  CUL1 MUTATED    14   1
  CUL1 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     14    1
  CUL1 WILD-TYPE  271   47
   clus
vv  CUL1 MUTATED CUL1 WILD-TYPE
  0           14            271
  1            1             47
[1] 2 2
[1] FALSE
D1797V7, binary
                cls
clus               0   1
  CUL1 MUTATED     7   8
  CUL1 WILD-TYPE 163 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      7    8
  CUL1 WILD-TYPE  163  189
        clus
vv       CUL1 MUTATED CUL1 WILD-TYPE
  FEMALE            7            163
  MALE              8            189
[1] 2 2
[1] FALSE
D1797V8, binary
                cls
clus               0   1
  CUL1 MUTATED    12   1
  CUL1 WILD-TYPE 288   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     12    1
  CUL1 WILD-TYPE  288    7
     clus
vv    CUL1 MUTATED CUL1 WILD-TYPE
  NO            12            288
  YES            1              7
[1] 2 2
[1] FALSE
D1797V9, binary
                cls
clus               0   1
  CUL1 MUTATED    10   4
  CUL1 WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     10    4
  CUL1 WILD-TYPE  304   44
                               clus
vv                              CUL1 MUTATED CUL1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CUL1 MUTATED     9   0   1   1
  CUL1 WILD-TYPE 250   3  21  20
D1797V10, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  R0            9            250
  R1            0              3
  R2            1             21
  RX            1             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"
D1797V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL1 MUTATED                                  0     1
  CUL1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL1 MUTATED                           0     7
  CUL1 WILD-TYPE                        19   169
D1797V12, multiclass
                                  clus
vv                                 CUL1 MUTATED CUL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = FOXF2 MUTATION ANALYSIS
D1798V1, survival
                 sevent
clus2               0   1
  FOXF2 MUTATED     0   3
  FOXF2 WILD-TYPE 277  75
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              3             352 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              3              75 
$`FOXF2 MUTATED`
TCGA-AA-3492 TCGA-AZ-6598 TCGA-CA-6718 
        3.02        49.41        10.06 

$`FOXF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        21.44        17.82        58.39         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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FOXF2 MUTATED FOXF2 WILD-TYPE 
           3.02            0.00 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
          49.41          148.01 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
         10.060          22.075 
[1] "3.0 - 49.4 (10.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "5.7"
D1798V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FOXF2 MUTATED         0        0        2         2         0         0
  FOXF2 WILD-TYPE      64        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXF2 MUTATED           0          0          0          0        0         0
  FOXF2 WILD-TYPE        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  FOXF2 MUTATED           0
  FOXF2 WILD-TYPE         1
D1798V3, multiclass
            clus
vv           FOXF2 MUTATED FOXF2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  FOXF2 MUTATED     0   0   4   0
  FOXF2 WILD-TYPE   9  67 245  41
D1798V4, multiclass
    clus
vv   FOXF2 MUTATED FOXF2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             0              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
  FOXF2 MUTATED     4   0   0
  FOXF2 WILD-TYPE 216  81  66
D1798V5, multiclass
    clus
vv   FOXF2 MUTATED FOXF2 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1798V6, binary
                 cls
clus                0   1
  FOXF2 MUTATED     3   0
  FOXF2 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXF2 MUTATED      3    0
  FOXF2 WILD-TYPE  282   48
   clus
vv  FOXF2 MUTATED FOXF2 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1798V7, binary
                 cls
clus                0   1
  FOXF2 MUTATED     3   1
  FOXF2 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXF2 MUTATED      3    1
  FOXF2 WILD-TYPE  167  196
        clus
vv       FOXF2 MUTATED FOXF2 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D1798V8, binary
                 cls
clus                0   1
  FOXF2 MUTATED     3   0
  FOXF2 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXF2 MUTATED      3    0
  FOXF2 WILD-TYPE  297    8
     clus
vv    FOXF2 MUTATED FOXF2 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1798V9, binary
                 cls
clus                0   1
  FOXF2 MUTATED     4   0
  FOXF2 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXF2 MUTATED      4    0
  FOXF2 WILD-TYPE  310   48
                               clus
vv                              FOXF2 MUTATED FOXF2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXF2 MUTATED     2   0   0   1
  FOXF2 WILD-TYPE 257   3  22  20
D1798V10, multiclass
    clus
vv   FOXF2 MUTATED FOXF2 WILD-TYPE
  R0             2             257
  R1             0               3
  R2             0              22
  RX             1              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"
D1798V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXF2 MUTATED                                  0     1
  FOXF2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXF2 MUTATED                           0     1
  FOXF2 WILD-TYPE                        19   175
D1798V12, multiclass
[1] "Remove cluster labels:" "FOXF2 MUTATED"         
clus
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6599      TCGA-AZ-6600 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6719 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 

Clustering(1799) Variable = CNKSR3 MUTATION ANALYSIS
D1799V1, survival
                  sevent
clus2                0   1
  CNKSR3 MUTATED     5   4
  CNKSR3 WILD-TYPE 272  74
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               9              346 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               4               74 
$`CNKSR3 MUTATED`
TCGA-AD-6895 TCGA-A6-6780 TCGA-AA-A029 TCGA-AD-6901 TCGA-AY-4071 TCGA-AZ-6598 
       25.08        20.12        51.98        22.42         0.95        49.41 
TCGA-CM-6680 TCGA-D5-6533 TCGA-DM-A1DA 
       12.03        25.48         7.50 

$`CNKSR3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24        24.53         5.79        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        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        54.61 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-F4-6459 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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
            0.95             0.00 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
           51.98           148.01 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
          22.420           22.045 
[1] "0.9 - 52.0 (22.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1799V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNKSR3 MUTATED         1        0        2         1         0         0
  CNKSR3 WILD-TYPE      63        1       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNKSR3 MUTATED           0          0          2          1        0
  CNKSR3 WILD-TYPE        18          6         42         32       35
                  vv
clus               STAGE IVA STAGE IVB
  CNKSR3 MUTATED           0         0
  CNKSR3 WILD-TYPE        12         1
D1799V3, multiclass
            clus
vv           CNKSR3 MUTATED CNKSR3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  CNKSR3 MUTATED     1   0   7   1
  CNKSR3 WILD-TYPE   8  67 242  40
D1799V4, multiclass
    clus
vv   CNKSR3 MUTATED CNKSR3 WILD-TYPE
  T1              1                8
  T2              0               67
  T3              7              242
  T4              1               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
  CNKSR3 MUTATED     6   1   2
  CNKSR3 WILD-TYPE 214  80  64
D1799V5, multiclass
    clus
vv   CNKSR3 MUTATED CNKSR3 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1799V6, binary
                  cls
clus                 0   1
  CNKSR3 MUTATED     5   0
  CNKSR3 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR3 MUTATED      5    0
  CNKSR3 WILD-TYPE  280   48
   clus
vv  CNKSR3 MUTATED CNKSR3 WILD-TYPE
  0              5              280
  1              0               48
[1] 2 2
[1] FALSE
D1799V7, binary
                  cls
clus                 0   1
  CNKSR3 MUTATED     5   4
  CNKSR3 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR3 MUTATED      5    4
  CNKSR3 WILD-TYPE  165  193
        clus
vv       CNKSR3 MUTATED CNKSR3 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D1799V8, binary
                  cls
clus                 0   1
  CNKSR3 MUTATED     8   0
  CNKSR3 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR3 MUTATED      8    0
  CNKSR3 WILD-TYPE  292    8
     clus
vv    CNKSR3 MUTATED CNKSR3 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1799V9, binary
                  cls
clus                 0   1
  CNKSR3 MUTATED     7   1
  CNKSR3 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR3 MUTATED      7    1
  CNKSR3 WILD-TYPE  307   47
                               clus
vv                              CNKSR3 MUTATED CNKSR3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CNKSR3 MUTATED     5   0   0   0
  CNKSR3 WILD-TYPE 254   3  22  21
D1799V10, multiclass
    clus
vv   CNKSR3 MUTATED CNKSR3 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1799V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNKSR3 MUTATED                                  0     0
  CNKSR3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CNKSR3 MUTATED                           0     8
  CNKSR3 WILD-TYPE                        19   168
D1799V12, multiclass
                                  clus
vv                                 CNKSR3 MUTATED CNKSR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = C1ORF116 MUTATION ANALYSIS
D1800V1, survival
                    sevent
clus2                  0   1
  C1ORF116 MUTATED     5   1
  C1ORF116 WILD-TYPE 272  77
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 6                349 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 1                 77 
$`C1ORF116 MUTATED`
TCGA-AA-3697 TCGA-AA-3950 TCGA-AA-A00F TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 
       85.05        24.00        34.03        83.24        58.39        12.76 

$`C1ORF116 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
             12.76               0.00 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
             85.05             148.01 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
             46.21              21.99 
[1] "12.8 - 85.0 (46.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1800V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF116 MUTATED         0        0        1         4         0         0
  C1ORF116 WILD-TYPE      64        1       25       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF116 MUTATED           0          0          0          1        0
  C1ORF116 WILD-TYPE        18          6         44         32       35
                    vv
clus                 STAGE IVA STAGE IVB
  C1ORF116 MUTATED           0         0
  C1ORF116 WILD-TYPE        12         1
D1800V3, multiclass
            clus
vv           C1ORF116 MUTATED C1ORF116 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 25
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                0                 44
  STAGE IIIC                1                 32
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  C1ORF116 MUTATED     0   0   6   0
  C1ORF116 WILD-TYPE   9  67 243  41
D1800V4, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                6                243
  T4                0                 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
  C1ORF116 MUTATED     5   0   1
  C1ORF116 WILD-TYPE 215  81  65
D1800V5, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  N0                5                215
  N1                0                 81
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1800V6, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     6   0
  C1ORF116 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      6    0
  C1ORF116 WILD-TYPE  279   48
   clus
vv  C1ORF116 MUTATED C1ORF116 WILD-TYPE
  0                6                279
  1                0                 48
[1] 2 2
[1] FALSE
D1800V7, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     1   5
  C1ORF116 WILD-TYPE 169 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      1    5
  C1ORF116 WILD-TYPE  169  192
        clus
vv       C1ORF116 MUTATED C1ORF116 WILD-TYPE
  FEMALE                1                169
  MALE                  5                192
[1] 2 2
[1] FALSE
D1800V8, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     6   0
  C1ORF116 WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      6    0
  C1ORF116 WILD-TYPE  294    8
     clus
vv    C1ORF116 MUTATED C1ORF116 WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D1800V9, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     4   2
  C1ORF116 WILD-TYPE 310  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      4    2
  C1ORF116 WILD-TYPE  310   46
                               clus
vv                              C1ORF116 MUTATED C1ORF116 WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C1ORF116 MUTATED     5   0   0   1
  C1ORF116 WILD-TYPE 254   3  22  20
D1800V10, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                1                 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"
D1800V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF116 MUTATED                                  0     2
  C1ORF116 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF116 MUTATED                           0     1
  C1ORF116 WILD-TYPE                        19   175
D1800V12, multiclass
                                  clus
vv                                 C1ORF116 MUTATED C1ORF116 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           1                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(1801) Variable = DENND2C MUTATION ANALYSIS
D1801V1, survival
                   sevent
clus2                 0   1
  DENND2C MUTATED    11   6
  DENND2C WILD-TYPE 266  72
  DENND2C MUTATED DENND2C WILD-TYPE 
               17               338 
  DENND2C MUTATED DENND2C WILD-TYPE 
                6                72 
$`DENND2C MUTATED`
TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3680 TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-A00J 
        3.02         1.02        11.01         0.00        33.01        18.05 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        35.01        21.44        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-DM-A1D8 
       10.06        23.05        20.02        37.02        12.59 

$`DENND2C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 
        7.04        35.01        63.98         6.97        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  DENND2C MUTATED DENND2C WILD-TYPE 
                0                 0 
  DENND2C MUTATED DENND2C WILD-TYPE 
            58.39            148.01 
  DENND2C MUTATED DENND2C WILD-TYPE 
            20.02             22.09 
[1] "0.0 - 58.4 (20.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1801V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DENND2C MUTATED         3        0        2         7         2         0
  DENND2C WILD-TYPE      61        1       24       101         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND2C MUTATED           1          0          1          0        1
  DENND2C WILD-TYPE        17          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  DENND2C MUTATED           0         0
  DENND2C WILD-TYPE        12         1
D1801V3, multiclass
            clus
vv           DENND2C MUTATED DENND2C WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                7               101
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  DENND2C MUTATED     0   3  11   4
  DENND2C WILD-TYPE   9  64 238  37
D1801V4, multiclass
    clus
vv   DENND2C MUTATED DENND2C WILD-TYPE
  T1               0                 9
  T2               3                64
  T3              11               238
  T4               4                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
  DENND2C MUTATED    14   2   2
  DENND2C WILD-TYPE 206  79  64
D1801V5, multiclass
    clus
vv   DENND2C MUTATED DENND2C WILD-TYPE
  N0              14               206
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1801V6, binary
                   cls
clus                  0   1
  DENND2C MUTATED    14   1
  DENND2C WILD-TYPE 271  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2C MUTATED     14    1
  DENND2C WILD-TYPE  271   47
   clus
vv  DENND2C MUTATED DENND2C WILD-TYPE
  0              14               271
  1               1                47
[1] 2 2
[1] FALSE
D1801V7, binary
                   cls
clus                  0   1
  DENND2C MUTATED     9   9
  DENND2C WILD-TYPE 161 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2C MUTATED      9    9
  DENND2C WILD-TYPE  161  188
        clus
vv       DENND2C MUTATED DENND2C WILD-TYPE
  FEMALE               9               161
  MALE                 9               188
[1] 2 2
[1] FALSE
D1801V8, binary
                   cls
clus                  0   1
  DENND2C MUTATED    14   1
  DENND2C WILD-TYPE 286   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2C MUTATED     14    1
  DENND2C WILD-TYPE  286    7
     clus
vv    DENND2C MUTATED DENND2C WILD-TYPE
  NO               14               286
  YES               1                 7
[1] 2 2
[1] FALSE
D1801V9, binary
                   cls
clus                  0   1
  DENND2C MUTATED    14   4
  DENND2C WILD-TYPE 300  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2C MUTATED     14    4
  DENND2C WILD-TYPE  300   44
                               clus
vv                              DENND2C MUTATED DENND2C WILD-TYPE
  COLON ADENOCARCINOMA                       14               300
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DENND2C MUTATED    13   0   1   2
  DENND2C WILD-TYPE 246   3  21  19
D1801V10, multiclass
    clus
vv   DENND2C MUTATED DENND2C WILD-TYPE
  R0              13               246
  R1               0                 3
  R2               1                21
  RX               2                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"
D1801V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DENND2C MUTATED                                  0     2
  DENND2C WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DENND2C MUTATED                           1     6
  DENND2C WILD-TYPE                        18   170
D1801V12, multiclass
                                  clus
vv                                 DENND2C MUTATED DENND2C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1802) Variable = ITGA9 MUTATION ANALYSIS
D1802V1, survival
                 sevent
clus2               0   1
  ITGA9 MUTATED     6   2
  ITGA9 WILD-TYPE 271  76
  ITGA9 MUTATED ITGA9 WILD-TYPE 
              8             347 
  ITGA9 MUTATED ITGA9 WILD-TYPE 
              2              76 
$`ITGA9 MUTATED`
TCGA-A6-2672 TCGA-A6-6141 TCGA-AA-3977 TCGA-AA-A02H TCGA-CK-5916 TCGA-CM-6161 
       46.65         8.38        25.02         2.01        21.14        15.02 
TCGA-CM-6165 TCGA-D5-6534 
       16.04        43.27 

$`ITGA9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       37.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ITGA9 MUTATED ITGA9 WILD-TYPE 
           2.01            0.00 
  ITGA9 MUTATED ITGA9 WILD-TYPE 
          46.65          148.01 
  ITGA9 MUTATED ITGA9 WILD-TYPE 
          18.59           22.09 
[1] "2.0 - 46.6 (18.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1802V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGA9 MUTATED         2        0        0         4         0         0
  ITGA9 WILD-TYPE      62        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGA9 MUTATED           0          0          1          0        1         0
  ITGA9 WILD-TYPE        18          6         43         33       34        12
                 vv
clus              STAGE IVB
  ITGA9 MUTATED           0
  ITGA9 WILD-TYPE         1
D1802V3, multiclass
            clus
vv           ITGA9 MUTATED ITGA9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  ITGA9 MUTATED     1   2   6   0
  ITGA9 WILD-TYPE   8  65 243  41
D1802V4, multiclass
    clus
vv   ITGA9 MUTATED ITGA9 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             6             243
  T4             0              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
  ITGA9 MUTATED     7   1   1
  ITGA9 WILD-TYPE 213  80  65
D1802V5, multiclass
    clus
vv   ITGA9 MUTATED ITGA9 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1802V6, binary
                 cls
clus                0   1
  ITGA9 MUTATED     7   1
  ITGA9 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA9 MUTATED      7    1
  ITGA9 WILD-TYPE  278   47
   clus
vv  ITGA9 MUTATED ITGA9 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D1802V7, binary
                 cls
clus                0   1
  ITGA9 MUTATED     6   3
  ITGA9 WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA9 MUTATED      6    3
  ITGA9 WILD-TYPE  164  194
        clus
vv       ITGA9 MUTATED ITGA9 WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D1802V8, binary
                 cls
clus                0   1
  ITGA9 MUTATED     7   0
  ITGA9 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA9 MUTATED      7    0
  ITGA9 WILD-TYPE  293    8
     clus
vv    ITGA9 MUTATED ITGA9 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1802V9, binary
                 cls
clus                0   1
  ITGA9 MUTATED     8   1
  ITGA9 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA9 MUTATED      8    1
  ITGA9 WILD-TYPE  306   47
                               clus
vv                              ITGA9 MUTATED ITGA9 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITGA9 MUTATED     5   0   1   1
  ITGA9 WILD-TYPE 254   3  21  20
D1802V10, multiclass
    clus
vv   ITGA9 MUTATED ITGA9 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             1              21
  RX             1              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"
D1802V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGA9 MUTATED                                  0     0
  ITGA9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGA9 MUTATED                           1     5
  ITGA9 WILD-TYPE                        18   171
D1802V12, multiclass
                                  clus
vv                                 ITGA9 MUTATED ITGA9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1803) Variable = COPB2 MUTATION ANALYSIS
D1803V1, survival
                 sevent
clus2               0   1
  COPB2 MUTATED     8   5
  COPB2 WILD-TYPE 269  73
  COPB2 MUTATED COPB2 WILD-TYPE 
             13             342 
  COPB2 MUTATED COPB2 WILD-TYPE 
              5              73 
$`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 
      135.65 

$`COPB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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-6717 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  COPB2 MUTATED COPB2 WILD-TYPE 
           3.02            0.00 
  COPB2 MUTATED COPB2 WILD-TYPE 
         135.65          148.01 
  COPB2 MUTATED COPB2 WILD-TYPE 
         21.990          22.075 
[1] "3.0 - 135.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1803V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COPB2 MUTATED         2        0        2         3         2         0
  COPB2 WILD-TYPE      62        1       24       105         6         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        18          6         42         33       35        11
                 vv
clus              STAGE IVB
  COPB2 MUTATED           0
  COPB2 WILD-TYPE         1
D1803V3, multiclass
            clus
vv           COPB2 MUTATED COPB2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  COPB2 MUTATED     0   3   7   3
  COPB2 WILD-TYPE   9  64 242  38
D1803V4, multiclass
    clus
vv   COPB2 MUTATED COPB2 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             7             242
  T4             3              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
  COPB2 MUTATED    10   3   0
  COPB2 WILD-TYPE 210  78  66
D1803V5, multiclass
    clus
vv   COPB2 MUTATED COPB2 WILD-TYPE
  N0            10             210
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1803V6, binary
                 cls
clus                0   1
  COPB2 MUTATED    10   1
  COPB2 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED     10    1
  COPB2 WILD-TYPE  275   47
   clus
vv  COPB2 MUTATED COPB2 WILD-TYPE
  0            10             275
  1             1              47
[1] 2 2
[1] FALSE
D1803V7, binary
                 cls
clus                0   1
  COPB2 MUTATED     6   7
  COPB2 WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED      6    7
  COPB2 WILD-TYPE  164  190
        clus
vv       COPB2 MUTATED COPB2 WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1803V8, binary
                 cls
clus                0   1
  COPB2 MUTATED    11   0
  COPB2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED     11    0
  COPB2 WILD-TYPE  289    8
     clus
vv    COPB2 MUTATED COPB2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1803V9, binary
                 cls
clus                0   1
  COPB2 MUTATED    11   1
  COPB2 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED     11    1
  COPB2 WILD-TYPE  303   47
                               clus
vv                              COPB2 MUTATED COPB2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  COPB2 MUTATED     9   0   0   0
  COPB2 WILD-TYPE 250   3  22  21
D1803V10, multiclass
    clus
vv   COPB2 MUTATED COPB2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             0              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"
D1803V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COPB2 MUTATED                                  0     0
  COPB2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  COPB2 MUTATED                           0     8
  COPB2 WILD-TYPE                        19   168
D1803V12, multiclass
                                  clus
vv                                 COPB2 MUTATED COPB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = GATAD2A MUTATION ANALYSIS
D1804V1, survival
                   sevent
clus2                 0   1
  GATAD2A MUTATED     8   1
  GATAD2A WILD-TYPE 269  77
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                9               346 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                1                77 
$`GATAD2A MUTATED`
TCGA-AA-3713 TCGA-AA-A01R TCGA-AA-A029 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CM-6171 
       19.04        35.01        51.98        12.16        58.39        14.04 
TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6304 
       35.74         6.18        53.62 

$`GATAD2A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        31.96        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GATAD2A MUTATED GATAD2A WILD-TYPE 
             6.18              0.00 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
            58.39            148.01 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
           35.010            22.045 
[1] "6.2 - 58.4 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1804V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GATAD2A MUTATED         3        0        1         2         1         0
  GATAD2A WILD-TYPE      61        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GATAD2A MUTATED           1          0          0          0        1
  GATAD2A WILD-TYPE        17          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  GATAD2A MUTATED           0         0
  GATAD2A WILD-TYPE        12         1
D1804V3, multiclass
            clus
vv           GATAD2A MUTATED GATAD2A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  GATAD2A MUTATED     0   3   5   1
  GATAD2A WILD-TYPE   9  64 244  40
D1804V4, multiclass
    clus
vv   GATAD2A MUTATED GATAD2A WILD-TYPE
  T1               0                 9
  T2               3                64
  T3               5               244
  T4               1                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
  GATAD2A MUTATED     8   0   1
  GATAD2A WILD-TYPE 212  81  65
D1804V5, multiclass
    clus
vv   GATAD2A MUTATED GATAD2A WILD-TYPE
  N0               8               212
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1804V6, binary
                   cls
clus                  0   1
  GATAD2A MUTATED     7   1
  GATAD2A WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GATAD2A MUTATED      7    1
  GATAD2A WILD-TYPE  278   47
   clus
vv  GATAD2A MUTATED GATAD2A WILD-TYPE
  0               7               278
  1               1                47
[1] 2 2
[1] FALSE
D1804V7, binary
                   cls
clus                  0   1
  GATAD2A MUTATED     3   6
  GATAD2A WILD-TYPE 167 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GATAD2A MUTATED      3    6
  GATAD2A WILD-TYPE  167  191
        clus
vv       GATAD2A MUTATED GATAD2A WILD-TYPE
  FEMALE               3               167
  MALE                 6               191
[1] 2 2
[1] FALSE
D1804V8, binary
                   cls
clus                  0   1
  GATAD2A MUTATED     7   2
  GATAD2A WILD-TYPE 293   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GATAD2A MUTATED      7    2
  GATAD2A WILD-TYPE  293    6
     clus
vv    GATAD2A MUTATED GATAD2A WILD-TYPE
  NO                7               293
  YES               2                 6
[1] 2 2
[1] FALSE
D1804V9, binary
                   cls
clus                  0   1
  GATAD2A MUTATED     7   2
  GATAD2A WILD-TYPE 307  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GATAD2A MUTATED      7    2
  GATAD2A WILD-TYPE  307   46
                               clus
vv                              GATAD2A MUTATED GATAD2A WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GATAD2A MUTATED     8   0   1   0
  GATAD2A WILD-TYPE 251   3  21  21
D1804V10, multiclass
    clus
vv   GATAD2A MUTATED GATAD2A WILD-TYPE
  R0               8               251
  R1               0                 3
  R2               1                21
  RX               0                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"
D1804V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GATAD2A MUTATED                                  0     0
  GATAD2A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GATAD2A MUTATED                           0     6
  GATAD2A WILD-TYPE                        19   170
D1804V12, multiclass
                                  clus
vv                                 GATAD2A MUTATED GATAD2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = TAOK1 MUTATION ANALYSIS
D1805V1, survival
                 sevent
clus2               0   1
  TAOK1 MUTATED    12   4
  TAOK1 WILD-TYPE 265  74
  TAOK1 MUTATED TAOK1 WILD-TYPE 
             16             339 
  TAOK1 MUTATED TAOK1 WILD-TYPE 
              4              74 
$`TAOK1 MUTATED`
TCGA-AA-3713 TCGA-AZ-4681 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3848 
       19.04       106.75         3.02        63.98        29.95        10.06 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-5913 
       18.05        34.98        14.50        12.10        12.76        51.32 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A0XD 
       17.13        16.14        11.64        24.43 

$`TAOK1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        10.88       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TAOK1 MUTATED TAOK1 WILD-TYPE 
           3.02            0.00 
  TAOK1 MUTATED TAOK1 WILD-TYPE 
         106.75          148.01 
  TAOK1 MUTATED TAOK1 WILD-TYPE 
          17.59           22.09 
[1] "3.0 - 106.8 (17.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1805V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAOK1 MUTATED         1        0        2         7         1         0
  TAOK1 WILD-TYPE      63        1       24       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAOK1 MUTATED           0          0          2          1        2         0
  TAOK1 WILD-TYPE        18          6         42         32       33        12
                 vv
clus              STAGE IVB
  TAOK1 MUTATED           0
  TAOK1 WILD-TYPE         1
D1805V3, multiclass
            clus
vv           TAOK1 MUTATED TAOK1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  TAOK1 MUTATED     0   1  12   3
  TAOK1 WILD-TYPE   9  66 237  38
D1805V4, multiclass
    clus
vv   TAOK1 MUTATED TAOK1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            12             237
  T4             3              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
  TAOK1 MUTATED    12   2   2
  TAOK1 WILD-TYPE 208  79  64
D1805V5, multiclass
    clus
vv   TAOK1 MUTATED TAOK1 WILD-TYPE
  N0            12             208
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1805V6, binary
                 cls
clus                0   1
  TAOK1 MUTATED    13   2
  TAOK1 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK1 MUTATED     13    2
  TAOK1 WILD-TYPE  272   46
   clus
vv  TAOK1 MUTATED TAOK1 WILD-TYPE
  0            13             272
  1             2              46
[1] 2 2
[1] FALSE
D1805V7, binary
                 cls
clus                0   1
  TAOK1 MUTATED     8   8
  TAOK1 WILD-TYPE 162 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK1 MUTATED      8    8
  TAOK1 WILD-TYPE  162  189
        clus
vv       TAOK1 MUTATED TAOK1 WILD-TYPE
  FEMALE             8             162
  MALE               8             189
[1] 2 2
[1] FALSE
D1805V8, binary
                 cls
clus                0   1
  TAOK1 MUTATED    14   1
  TAOK1 WILD-TYPE 286   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK1 MUTATED     14    1
  TAOK1 WILD-TYPE  286    7
     clus
vv    TAOK1 MUTATED TAOK1 WILD-TYPE
  NO             14             286
  YES             1               7
[1] 2 2
[1] FALSE
D1805V9, binary
                 cls
clus                0   1
  TAOK1 MUTATED    11   5
  TAOK1 WILD-TYPE 303  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK1 MUTATED     11    5
  TAOK1 WILD-TYPE  303   43
                               clus
vv                              TAOK1 MUTATED TAOK1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAOK1 MUTATED    11   0   1   2
  TAOK1 WILD-TYPE 248   3  21  19
D1805V10, multiclass
    clus
vv   TAOK1 MUTATED TAOK1 WILD-TYPE
  R0            11             248
  R1             0               3
  R2             1              21
  RX             2              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"
D1805V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAOK1 MUTATED                                  0     1
  TAOK1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAOK1 MUTATED                           1     7
  TAOK1 WILD-TYPE                        18   169
D1805V12, multiclass
                                  clus
vv                                 TAOK1 MUTATED TAOK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        7             169
[1] 4 2
[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 = KRT1 MUTATION ANALYSIS
D1806V1, survival
                sevent
clus2              0   1
  KRT1 MUTATED     8   6
  KRT1 WILD-TYPE 269  72
  KRT1 MUTATED KRT1 WILD-TYPE 
            14            341 
  KRT1 MUTATED KRT1 WILD-TYPE 
             6             72 
$`KRT1 MUTATED`
TCGA-G4-6628 TCGA-A6-3808 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 
       79.69        33.34         4.01        34.98        58.39        88.21 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6169 TCGA-D5-6533 
        6.77        29.56        12.76        10.06        13.02        25.48 
TCGA-DM-A0XD TCGA-F4-6570 
       24.43         6.18 

$`KRT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 
       43.76        42.90        42.28        16.57        34.65        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
       17.82         1.41         5.13        22.36        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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        54.61        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.35        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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KRT1 MUTATED KRT1 WILD-TYPE 
          4.01           0.00 
  KRT1 MUTATED KRT1 WILD-TYPE 
         88.21         148.01 
  KRT1 MUTATED KRT1 WILD-TYPE 
        24.955         22.030 
[1] "4.0 - 88.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1806V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT1 MUTATED         3        0        0         7         2         0
  KRT1 WILD-TYPE      61        1       26       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT1 MUTATED           0          0          0          0        0         0
  KRT1 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  KRT1 MUTATED           0
  KRT1 WILD-TYPE         1
D1806V3, multiclass
            clus
vv           KRT1 MUTATED KRT1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             7            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  KRT1 MUTATED     1   3   7   3
  KRT1 WILD-TYPE   8  64 242  38
D1806V4, multiclass
    clus
vv   KRT1 MUTATED KRT1 WILD-TYPE
  T1            1              8
  T2            3             64
  T3            7            242
  T4            3             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
  KRT1 MUTATED    13   1   0
  KRT1 WILD-TYPE 207  80  66
D1806V5, multiclass
    clus
vv   KRT1 MUTATED KRT1 WILD-TYPE
  N0           13            207
  N1            1             80
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1806V6, binary
                cls
clus               0   1
  KRT1 MUTATED    12   0
  KRT1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED     12    0
  KRT1 WILD-TYPE  273   48
   clus
vv  KRT1 MUTATED KRT1 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D1806V7, binary
                cls
clus               0   1
  KRT1 MUTATED     5   9
  KRT1 WILD-TYPE 165 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED      5    9
  KRT1 WILD-TYPE  165  188
        clus
vv       KRT1 MUTATED KRT1 WILD-TYPE
  FEMALE            5            165
  MALE              9            188
[1] 2 2
[1] FALSE
D1806V8, binary
                cls
clus               0   1
  KRT1 MUTATED    12   0
  KRT1 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED     12    0
  KRT1 WILD-TYPE  288    8
     clus
vv    KRT1 MUTATED KRT1 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1806V9, binary
                cls
clus               0   1
  KRT1 MUTATED    12   2
  KRT1 WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED     12    2
  KRT1 WILD-TYPE  302   46
                               clus
vv                              KRT1 MUTATED KRT1 WILD-TYPE
  COLON ADENOCARCINOMA                    12            302
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRT1 MUTATED     8   0   0   2
  KRT1 WILD-TYPE 251   3  22  19
D1806V10, multiclass
    clus
vv   KRT1 MUTATED KRT1 WILD-TYPE
  R0            8            251
  R1            0              3
  R2            0             22
  RX            2             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"
D1806V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT1 MUTATED                                  0     2
  KRT1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT1 MUTATED                           1     9
  KRT1 WILD-TYPE                        18   167
D1806V12, multiclass
                                  clus
vv                                 KRT1 MUTATED KRT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       9            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(1807) Variable = TACC2 MUTATION ANALYSIS
D1807V1, survival
                 sevent
clus2               0   1
  TACC2 MUTATED    21   3
  TACC2 WILD-TYPE 256  75
  TACC2 MUTATED TACC2 WILD-TYPE 
             24             331 
  TACC2 MUTATED TACC2 WILD-TYPE 
              3              75 
$`TACC2 MUTATED`
TCGA-AA-3543 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-G4-6586 TCGA-G4-6588 
        0.99        19.04        24.00        25.08        35.80        26.17 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3850 TCGA-AA-A00A 
        3.02        35.01        29.95         6.97         0.00        38.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 
       18.05        34.98         1.02        27.09        21.44        12.76 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-6162 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 
       85.45        21.99        12.00        11.64        13.35         6.18 

$`TACC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       37.05        36.03         8.05        19.07        34.03        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        10.88       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
        5.88        63.62        22.09        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        7.04        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-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-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  TACC2 MUTATED TACC2 WILD-TYPE 
              0               0 
  TACC2 MUTATED TACC2 WILD-TYPE 
          85.45          148.01 
  TACC2 MUTATED TACC2 WILD-TYPE 
          20.24           22.09 
[1] "0.0 - 85.5 (20.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1807V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TACC2 MUTATED         4        0        3        10         2         0
  TACC2 WILD-TYPE      60        1       23        98         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TACC2 MUTATED           0          0          5          0        1         0
  TACC2 WILD-TYPE        18          6         39         33       34        12
                 vv
clus              STAGE IVB
  TACC2 MUTATED           0
  TACC2 WILD-TYPE         1
D1807V3, multiclass
            clus
vv           TACC2 MUTATED TACC2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA             10              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             5              39
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  TACC2 MUTATED     0   4  18   3
  TACC2 WILD-TYPE   9  63 231  38
D1807V4, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  T1             0               9
  T2             4              63
  T3            18             231
  T4             3              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
  TACC2 MUTATED    20   5   0
  TACC2 WILD-TYPE 200  76  66
D1807V5, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  N0            20             200
  N1             5              76
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1807V6, binary
                 cls
clus                0   1
  TACC2 MUTATED    21   1
  TACC2 WILD-TYPE 264  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     21    1
  TACC2 WILD-TYPE  264   47
   clus
vv  TACC2 MUTATED TACC2 WILD-TYPE
  0            21             264
  1             1              47
[1] 2 2
[1] FALSE
D1807V7, binary
                 cls
clus                0   1
  TACC2 MUTATED    12  13
  TACC2 WILD-TYPE 158 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     12   13
  TACC2 WILD-TYPE  158  184
        clus
vv       TACC2 MUTATED TACC2 WILD-TYPE
  FEMALE            12             158
  MALE              13             184
[1] 2 2
[1] FALSE
D1807V8, binary
                 cls
clus                0   1
  TACC2 MUTATED    19   1
  TACC2 WILD-TYPE 281   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     19    1
  TACC2 WILD-TYPE  281    7
     clus
vv    TACC2 MUTATED TACC2 WILD-TYPE
  NO             19             281
  YES             1               7
[1] 2 2
[1] FALSE
D1807V9, binary
                 cls
clus                0   1
  TACC2 MUTATED    16   9
  TACC2 WILD-TYPE 298  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     16    9
  TACC2 WILD-TYPE  298   39
                               clus
vv                              TACC2 MUTATED TACC2 WILD-TYPE
  COLON ADENOCARCINOMA                     16             298
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TACC2 MUTATED    20   1   1   3
  TACC2 WILD-TYPE 239   2  21  18
D1807V10, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  R0            20             239
  R1             1               2
  R2             1              21
  RX             3              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"
D1807V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TACC2 MUTATED                                  0     1
  TACC2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TACC2 MUTATED                           1    11
  TACC2 WILD-TYPE                        18   165
D1807V12, multiclass
                                  clus
vv                                 TACC2 MUTATED TACC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       11             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(1808) Variable = GATA6 MUTATION ANALYSIS
D1808V1, survival
                 sevent
clus2               0   1
  GATA6 MUTATED     3   1
  GATA6 WILD-TYPE 274  77
  GATA6 MUTATED GATA6 WILD-TYPE 
              4             351 
  GATA6 MUTATED GATA6 WILD-TYPE 
              1              77 
$`GATA6 MUTATED`
TCGA-AA-3818 TCGA-AA-3864 TCGA-CK-6747 TCGA-G4-6293 
        0.99        53.00        82.95       133.18 

$`GATA6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  GATA6 MUTATED GATA6 WILD-TYPE 
           0.99            0.00 
  GATA6 MUTATED GATA6 WILD-TYPE 
         133.18          148.01 
  GATA6 MUTATED GATA6 WILD-TYPE 
         67.975          22.030 
[1] "1.0 - 133.2 (68.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.9"
D1808V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GATA6 MUTATED         0        0        1         2         0         0
  GATA6 WILD-TYPE      64        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA6 MUTATED           1          0          0          0        0         0
  GATA6 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  GATA6 MUTATED           0
  GATA6 WILD-TYPE         1
D1808V3, multiclass
            clus
vv           GATA6 MUTATED GATA6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  GATA6 MUTATED     0   0   4   0
  GATA6 WILD-TYPE   9  67 245  41
D1808V4, multiclass
    clus
vv   GATA6 MUTATED GATA6 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             4             245
  T4             0              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
  GATA6 MUTATED     3   1   0
  GATA6 WILD-TYPE 217  80  66
D1808V5, multiclass
    clus
vv   GATA6 MUTATED GATA6 WILD-TYPE
  N0             3             217
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1808V6, binary
                 cls
clus                0   1
  GATA6 MUTATED     3   0
  GATA6 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      3    0
  GATA6 WILD-TYPE  282   48
   clus
vv  GATA6 MUTATED GATA6 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1808V7, binary
                 cls
clus                0   1
  GATA6 MUTATED     3   1
  GATA6 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      3    1
  GATA6 WILD-TYPE  167  196
        clus
vv       GATA6 MUTATED GATA6 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D1808V8, binary
                 cls
clus                0   1
  GATA6 MUTATED     3   0
  GATA6 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      3    0
  GATA6 WILD-TYPE  297    8
     clus
vv    GATA6 MUTATED GATA6 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1808V9, binary
                 cls
clus                0   1
  GATA6 MUTATED     4   0
  GATA6 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      4    0
  GATA6 WILD-TYPE  310   48
                               clus
vv                              GATA6 MUTATED GATA6 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GATA6 MUTATED     3   0   0   1
  GATA6 WILD-TYPE 256   3  22  20
D1808V10, multiclass
    clus
vv   GATA6 MUTATED GATA6 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1808V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GATA6 MUTATED                                  0     0
  GATA6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GATA6 MUTATED                           0     2
  GATA6 WILD-TYPE                        19   174
D1808V12, multiclass
[1] "Remove cluster labels:" "GATA6 MUTATED"         
clus
  GATA6 MUTATED GATA6 WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5913      TCGA-CK-5914 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6748 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6299      TCGA-G4-6303 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 

Clustering(1809) Variable = NDC80 MUTATION ANALYSIS
D1809V1, survival
                 sevent
clus2               0   1
  NDC80 MUTATED     7   1
  NDC80 WILD-TYPE 270  77
  NDC80 MUTATED NDC80 WILD-TYPE 
              8             347 
  NDC80 MUTATED NDC80 WILD-TYPE 
              1              77 
$`NDC80 MUTATED`
TCGA-G4-6321 TCGA-G4-6588 TCGA-AA-3947 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 
       22.09        26.17        33.01        34.98        12.76        10.06 
TCGA-CM-5868 TCGA-G4-6307 
       17.03        55.04 

$`NDC80 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  NDC80 MUTATED NDC80 WILD-TYPE 
          10.06            0.00 
  NDC80 MUTATED NDC80 WILD-TYPE 
          55.04          148.01 
  NDC80 MUTATED NDC80 WILD-TYPE 
          24.13           22.03 
[1] "10.1 - 55.0 (24.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1809V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NDC80 MUTATED         0        0        0         3         2         0
  NDC80 WILD-TYPE      64        1       26       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NDC80 MUTATED           1          0          1          0        0         1
  NDC80 WILD-TYPE        17          6         43         33       35        11
                 vv
clus              STAGE IVB
  NDC80 MUTATED           0
  NDC80 WILD-TYPE         1
D1809V3, multiclass
            clus
vv           NDC80 MUTATED NDC80 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              1              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
  NDC80 MUTATED     0   1   4   3
  NDC80 WILD-TYPE   9  66 245  38
D1809V4, multiclass
    clus
vv   NDC80 MUTATED NDC80 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             4             245
  T4             3              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
  NDC80 MUTATED     5   3   0
  NDC80 WILD-TYPE 215  78  66
D1809V5, multiclass
    clus
vv   NDC80 MUTATED NDC80 WILD-TYPE
  N0             5             215
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1809V6, binary
                 cls
clus                0   1
  NDC80 MUTATED     6   1
  NDC80 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDC80 MUTATED      6    1
  NDC80 WILD-TYPE  279   47
   clus
vv  NDC80 MUTATED NDC80 WILD-TYPE
  0             6             279
  1             1              47
[1] 2 2
[1] FALSE
D1809V7, binary
                 cls
clus                0   1
  NDC80 MUTATED     6   2
  NDC80 WILD-TYPE 164 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDC80 MUTATED      6    2
  NDC80 WILD-TYPE  164  195
        clus
vv       NDC80 MUTATED NDC80 WILD-TYPE
  FEMALE             6             164
  MALE               2             195
[1] 2 2
[1] FALSE
D1809V8, binary
                 cls
clus                0   1
  NDC80 MUTATED     8   0
  NDC80 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDC80 MUTATED      8    0
  NDC80 WILD-TYPE  292    8
     clus
vv    NDC80 MUTATED NDC80 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1809V9, binary
                 cls
clus                0   1
  NDC80 MUTATED     6   2
  NDC80 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDC80 MUTATED      6    2
  NDC80 WILD-TYPE  308   46
                               clus
vv                              NDC80 MUTATED NDC80 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NDC80 MUTATED     6   0   0   2
  NDC80 WILD-TYPE 253   3  22  19
D1809V10, multiclass
    clus
vv   NDC80 MUTATED NDC80 WILD-TYPE
  R0             6             253
  R1             0               3
  R2             0              22
  RX             2              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"
D1809V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDC80 MUTATED                                  0     2
  NDC80 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NDC80 MUTATED                           0     4
  NDC80 WILD-TYPE                        19   172
D1809V12, multiclass
                                  clus
vv                                 NDC80 MUTATED NDC80 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = HLA-G MUTATION ANALYSIS
D1810V1, survival
                 sevent
clus2               0   1
  HLA-G MUTATED     9   2
  HLA-G WILD-TYPE 268  76
  HLA-G MUTATED HLA-G WILD-TYPE 
             11             344 
  HLA-G MUTATED HLA-G WILD-TYPE 
              2              76 
$`HLA-G MUTATED`
TCGA-AA-3815 TCGA-AA-3966 TCGA-AD-6963 TCGA-AY-6197 TCGA-CM-6172 TCGA-CM-6675 
       33.04         2.01        27.42        21.44        11.01        13.05 
TCGA-CM-6676 TCGA-DM-A1DB TCGA-DM-A28F TCGA-F4-6807 TCGA-F4-6856 
       11.08        44.32        35.97        43.04        35.31 

$`HLA-G WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        22.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A28C TCGA-DM-A28E 
        7.50       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-F4-6808 
        6.18        47.87         1.55        34.42        41.42        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HLA-G MUTATED HLA-G WILD-TYPE 
           2.01            0.00 
  HLA-G MUTATED HLA-G WILD-TYPE 
          44.32          148.01 
  HLA-G MUTATED HLA-G WILD-TYPE 
         27.420          22.045 
[1] "2.0 - 44.3 (27.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1810V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HLA-G MUTATED         2        0        0         4         0         0
  HLA-G WILD-TYPE      62        1       26       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-G MUTATED           0          0          2          1        0         0
  HLA-G WILD-TYPE        18          6         42         32       35        12
                 vv
clus              STAGE IVB
  HLA-G MUTATED           1
  HLA-G WILD-TYPE         0
D1810V3, multiclass
            clus
vv           HLA-G MUTATED HLA-G WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              12
  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
  HLA-G MUTATED     0   2   9   0
  HLA-G WILD-TYPE   9  65 240  41
D1810V4, multiclass
    clus
vv   HLA-G MUTATED HLA-G WILD-TYPE
  T1             0               9
  T2             2              65
  T3             9             240
  T4             0              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
  HLA-G MUTATED     7   2   2
  HLA-G WILD-TYPE 213  79  64
D1810V5, multiclass
    clus
vv   HLA-G MUTATED HLA-G WILD-TYPE
  N0             7             213
  N1             2              79
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1810V6, binary
                 cls
clus                0   1
  HLA-G MUTATED     8   1
  HLA-G WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-G MUTATED      8    1
  HLA-G WILD-TYPE  277   47
   clus
vv  HLA-G MUTATED HLA-G WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1810V7, binary
                 cls
clus                0   1
  HLA-G MUTATED     4   7
  HLA-G WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-G MUTATED      4    7
  HLA-G WILD-TYPE  166  190
        clus
vv       HLA-G MUTATED HLA-G WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D1810V8, binary
                 cls
clus                0   1
  HLA-G MUTATED     8   0
  HLA-G WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-G MUTATED      8    0
  HLA-G WILD-TYPE  292    8
     clus
vv    HLA-G MUTATED HLA-G WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1810V9, binary
                 cls
clus                0   1
  HLA-G MUTATED     9   2
  HLA-G WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-G MUTATED      9    2
  HLA-G WILD-TYPE  305   46
                               clus
vv                              HLA-G MUTATED HLA-G WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-G MUTATED     7   0   0   0
  HLA-G WILD-TYPE 252   3  22  21
D1810V10, multiclass
    clus
vv   HLA-G MUTATED HLA-G WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1810V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-G MUTATED                                  0     0
  HLA-G WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-G MUTATED                           1     8
  HLA-G WILD-TYPE                        18   168
D1810V12, multiclass
                                  clus
vv                                 HLA-G MUTATED HLA-G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        8             168
[1] 4 2
[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 = TNNT2 MUTATION ANALYSIS
D1811V1, survival
                 sevent
clus2               0   1
  TNNT2 MUTATED     7   1
  TNNT2 WILD-TYPE 270  77
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              8             347 
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              1              77 
$`TNNT2 MUTATED`
TCGA-AD-6964 TCGA-AA-3542 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00A TCGA-AY-6197 
       10.88        12.99         6.97        53.00        38.04        21.44 
TCGA-CM-6162 TCGA-G4-6304 
       12.00        53.62 

$`TNNT2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        27.02        27.02 
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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  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          22.090 
[1] "7.0 - 53.6 (17.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D1811V2, continuous
                 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      64        1       24       106         7         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        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  TNNT2 MUTATED           0
  TNNT2 WILD-TYPE         1
D1811V3, multiclass
            clus
vv           TNNT2 MUTATED TNNT2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TNNT2 MUTATED     0   0   6   2
  TNNT2 WILD-TYPE   9  67 243  39
D1811V4, multiclass
    clus
vv   TNNT2 MUTATED TNNT2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             2              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
  TNNT2 MUTATED     5   1   2
  TNNT2 WILD-TYPE 215  80  64
D1811V5, multiclass
    clus
vv   TNNT2 MUTATED TNNT2 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1811V6, binary
                 cls
clus                0   1
  TNNT2 MUTATED     6   0
  TNNT2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      6    0
  TNNT2 WILD-TYPE  279   48
   clus
vv  TNNT2 MUTATED TNNT2 WILD-TYPE
  0             6             279
  1             0              48
[1] 2 2
[1] FALSE
D1811V7, binary
                 cls
clus                0   1
  TNNT2 MUTATED     2   6
  TNNT2 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      2    6
  TNNT2 WILD-TYPE  168  191
        clus
vv       TNNT2 MUTATED TNNT2 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D1811V8, binary
                 cls
clus                0   1
  TNNT2 MUTATED     8   0
  TNNT2 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      8    0
  TNNT2 WILD-TYPE  292    8
     clus
vv    TNNT2 MUTATED TNNT2 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1811V9, binary
                 cls
clus                0   1
  TNNT2 MUTATED     7   1
  TNNT2 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      7    1
  TNNT2 WILD-TYPE  307   47
                               clus
vv                              TNNT2 MUTATED TNNT2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TNNT2 MUTATED     7   0   0   0
  TNNT2 WILD-TYPE 252   3  22  21
D1811V10, multiclass
    clus
vv   TNNT2 MUTATED TNNT2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1811V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNNT2 MUTATED                                  0     0
  TNNT2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TNNT2 MUTATED                           0     4
  TNNT2 WILD-TYPE                        19   172
D1811V12, multiclass
                                  clus
vv                                 TNNT2 MUTATED TNNT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = PPM1B MUTATION ANALYSIS
D1812V1, survival
                 sevent
clus2               0   1
  PPM1B MUTATED     4   1
  PPM1B WILD-TYPE 273  77
  PPM1B MUTATED PPM1B WILD-TYPE 
              5             350 
  PPM1B MUTATED PPM1B WILD-TYPE 
              1              77 
$`PPM1B MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-CK-4947 TCGA-D5-6540 TCGA-DM-A28E 
       42.90        22.06        17.56        16.14       119.93 

$`PPM1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30       148.01        85.45        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PPM1B MUTATED PPM1B WILD-TYPE 
          16.14            0.00 
  PPM1B MUTATED PPM1B WILD-TYPE 
         119.93          148.01 
  PPM1B MUTATED PPM1B WILD-TYPE 
          22.06           22.06 
[1] "16.1 - 119.9 (22.1)" "0.0 - 148.0 (22.1)" 
[1] "hr=" "1.6"
D1812V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPM1B MUTATED         1        0        0         2         1         0
  PPM1B WILD-TYPE      63        1       26       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPM1B MUTATED           0          0          1          0        0         0
  PPM1B WILD-TYPE        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  PPM1B MUTATED           0
  PPM1B WILD-TYPE         1
D1812V3, multiclass
            clus
vv           PPM1B MUTATED PPM1B WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  PPM1B MUTATED     0   1   2   2
  PPM1B WILD-TYPE   9  66 247  39
D1812V4, multiclass
    clus
vv   PPM1B MUTATED PPM1B WILD-TYPE
  T1             0               9
  T2             1              66
  T3             2             247
  T4             2              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
  PPM1B MUTATED     4   1   0
  PPM1B WILD-TYPE 216  80  66
D1812V5, multiclass
    clus
vv   PPM1B MUTATED PPM1B WILD-TYPE
  N0             4             216
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1812V6, binary
                 cls
clus                0   1
  PPM1B MUTATED     5   0
  PPM1B WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1B MUTATED      5    0
  PPM1B WILD-TYPE  280   48
   clus
vv  PPM1B MUTATED PPM1B WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1812V7, binary
                 cls
clus                0   1
  PPM1B MUTATED     4   1
  PPM1B WILD-TYPE 166 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1B MUTATED      4    1
  PPM1B WILD-TYPE  166  196
        clus
vv       PPM1B MUTATED PPM1B WILD-TYPE
  FEMALE             4             166
  MALE               1             196
[1] 2 2
[1] FALSE
D1812V8, binary
                 cls
clus                0   1
  PPM1B MUTATED     4   0
  PPM1B WILD-TYPE 296   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1B MUTATED      4    0
  PPM1B WILD-TYPE  296    8
     clus
vv    PPM1B MUTATED PPM1B WILD-TYPE
  NO              4             296
  YES             0               8
[1] 2 2
[1] FALSE
D1812V9, binary
                 cls
clus                0   1
  PPM1B MUTATED     4   1
  PPM1B WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1B MUTATED      4    1
  PPM1B WILD-TYPE  310   47
                               clus
vv                              PPM1B MUTATED PPM1B WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPM1B MUTATED     3   0   0   1
  PPM1B WILD-TYPE 256   3  22  20
D1812V10, multiclass
    clus
vv   PPM1B MUTATED PPM1B WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1812V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPM1B MUTATED                                  0     0
  PPM1B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PPM1B MUTATED                           0     5
  PPM1B WILD-TYPE                        19   171
D1812V12, multiclass
                                  clus
vv                                 PPM1B MUTATED PPM1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = ZNF232 MUTATION ANALYSIS
D1813V1, survival
                  sevent
clus2                0   1
  ZNF232 MUTATED     3   1
  ZNF232 WILD-TYPE 274  77
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              351 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               1               77 
$`ZNF232 MUTATED`
TCGA-G4-6586 TCGA-G4-6588 TCGA-AZ-4315 TCGA-F4-6459 
       35.80        26.17        58.39         8.61 

$`ZNF232 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       22.09        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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           22.030 
[1] "8.6 - 58.4 (31.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1813V2, continuous
                  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      64        1       26       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF232 MUTATED           0          0          1          0        0
  ZNF232 WILD-TYPE        18          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF232 MUTATED           0         0
  ZNF232 WILD-TYPE        12         1
D1813V3, multiclass
            clus
vv           ZNF232 MUTATED ZNF232 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ZNF232 MUTATED     0   0   4   0
  ZNF232 WILD-TYPE   9  67 245  41
D1813V4, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              4              245
  T4              0               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
  ZNF232 MUTATED     3   0   1
  ZNF232 WILD-TYPE 217  81  65
D1813V5, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  N0              3              217
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1813V6, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  281   48
   clus
vv  ZNF232 MUTATED ZNF232 WILD-TYPE
  0              4              281
  1              0               48
[1] 2 2
[1] FALSE
D1813V7, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     3   1
  ZNF232 WILD-TYPE 167 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      3    1
  ZNF232 WILD-TYPE  167  196
        clus
vv       ZNF232 MUTATED ZNF232 WILD-TYPE
  FEMALE              3              167
  MALE                1              196
[1] 2 2
[1] FALSE
D1813V8, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  296    8
     clus
vv    ZNF232 MUTATED ZNF232 WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1813V9, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  310   48
                               clus
vv                              ZNF232 MUTATED ZNF232 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF232 MUTATED     4   0   0   0
  ZNF232 WILD-TYPE 255   3  22  21
D1813V10, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  R0              4              255
  R1              0                3
  R2              0               22
  RX              0               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"
D1813V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF232 MUTATED                                  0     0
  ZNF232 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF232 MUTATED                           0     4
  ZNF232 WILD-TYPE                        19   172
D1813V12, multiclass
                                  clus
vv                                 ZNF232 MUTATED ZNF232 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         4              172
[1] 4 2
[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 = HRASLS5 MUTATION ANALYSIS
D1814V1, survival
                   sevent
clus2                 0   1
  HRASLS5 MUTATED     5   0
  HRASLS5 WILD-TYPE 272  78
  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
                5               350 
  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
                0                78 
$`HRASLS5 MUTATED`
TCGA-G4-6310 TCGA-A6-6654 TCGA-AA-3518 TCGA-AA-A02Y TCGA-D5-6533 
       63.62        23.87         1.02        39.98        25.48 

$`HRASLS5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
        0.92        41.00        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
             1.02              0.00 
  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
            63.62            148.01 
  HRASLS5 MUTATED HRASLS5 WILD-TYPE 
            25.48             22.01 
[1] "1.0 - 63.6 (25.5)"  "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1814V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HRASLS5 MUTATED         1        0        0         1         0         0
  HRASLS5 WILD-TYPE      63        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HRASLS5 MUTATED           0          0          2          0        0
  HRASLS5 WILD-TYPE        18          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  HRASLS5 MUTATED           0         0
  HRASLS5 WILD-TYPE        12         1
D1814V3, multiclass
            clus
vv           HRASLS5 MUTATED HRASLS5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  HRASLS5 MUTATED     0   1   3   1
  HRASLS5 WILD-TYPE   9  66 246  40
D1814V4, multiclass
    clus
vv   HRASLS5 MUTATED HRASLS5 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               1                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
  HRASLS5 MUTATED     3   2   0
  HRASLS5 WILD-TYPE 217  79  66
D1814V5, multiclass
    clus
vv   HRASLS5 MUTATED HRASLS5 WILD-TYPE
  N0               3               217
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1814V6, binary
                   cls
clus                  0   1
  HRASLS5 MUTATED     5   0
  HRASLS5 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HRASLS5 MUTATED      5    0
  HRASLS5 WILD-TYPE  280   48
   clus
vv  HRASLS5 MUTATED HRASLS5 WILD-TYPE
  0               5               280
  1               0                48
[1] 2 2
[1] FALSE
D1814V7, binary
                   cls
clus                  0   1
  HRASLS5 MUTATED     3   2
  HRASLS5 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HRASLS5 MUTATED      3    2
  HRASLS5 WILD-TYPE  167  195
        clus
vv       HRASLS5 MUTATED HRASLS5 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1814V8, binary
                   cls
clus                  0   1
  HRASLS5 MUTATED     3   1
  HRASLS5 WILD-TYPE 297   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HRASLS5 MUTATED      3    1
  HRASLS5 WILD-TYPE  297    7
     clus
vv    HRASLS5 MUTATED HRASLS5 WILD-TYPE
  NO                3               297
  YES               1                 7
[1] 2 2
[1] FALSE
D1814V9, binary
                   cls
clus                  0   1
  HRASLS5 MUTATED     5   0
  HRASLS5 WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HRASLS5 MUTATED      5    0
  HRASLS5 WILD-TYPE  309   48
                               clus
vv                              HRASLS5 MUTATED HRASLS5 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HRASLS5 MUTATED     4   0   0   0
  HRASLS5 WILD-TYPE 255   3  22  21
D1814V10, multiclass
    clus
vv   HRASLS5 MUTATED HRASLS5 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               0                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"
D1814V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRASLS5 MUTATED                                  0     0
  HRASLS5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HRASLS5 MUTATED                           0     3
  HRASLS5 WILD-TYPE                        19   173
D1814V12, multiclass
                                  clus
vv                                 HRASLS5 MUTATED HRASLS5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = PRSS35 MUTATION ANALYSIS
D1815V1, survival
                  sevent
clus2                0   1
  PRSS35 MUTATED    11   1
  PRSS35 WILD-TYPE 266  77
  PRSS35 MUTATED PRSS35 WILD-TYPE 
              12              343 
  PRSS35 MUTATED PRSS35 WILD-TYPE 
               1               77 
$`PRSS35 MUTATED`
TCGA-AA-3867 TCGA-AA-A00L TCGA-A6-6142 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00J 
       24.03        38.04        25.08         6.97        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6162 
        4.01        34.98        58.39        12.76        13.02        12.00 

$`PRSS35 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 
       50.99        26.01        24.00        19.07        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  PRSS35 MUTATED PRSS35 WILD-TYPE 
            4.01             0.00 
  PRSS35 MUTATED PRSS35 WILD-TYPE 
           58.39           148.01 
  PRSS35 MUTATED PRSS35 WILD-TYPE 
           21.04            22.06 
[1] "4.0 - 58.4 (21.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1815V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRSS35 MUTATED         0        0        1         4         2         0
  PRSS35 WILD-TYPE      64        1       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS35 MUTATED           0          0          2          0        1
  PRSS35 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  PRSS35 MUTATED           1         0
  PRSS35 WILD-TYPE        11         1
D1815V3, multiclass
            clus
vv           PRSS35 MUTATED PRSS35 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  PRSS35 MUTATED     0   1   8   3
  PRSS35 WILD-TYPE   9  66 241  38
D1815V4, multiclass
    clus
vv   PRSS35 MUTATED PRSS35 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              8              241
  T4              3               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
  PRSS35 MUTATED     8   3   1
  PRSS35 WILD-TYPE 212  78  65
D1815V5, multiclass
    clus
vv   PRSS35 MUTATED PRSS35 WILD-TYPE
  N0              8              212
  N1              3               78
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1815V6, binary
                  cls
clus                 0   1
  PRSS35 MUTATED     9   2
  PRSS35 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS35 MUTATED      9    2
  PRSS35 WILD-TYPE  276   46
   clus
vv  PRSS35 MUTATED PRSS35 WILD-TYPE
  0              9              276
  1              2               46
[1] 2 2
[1] FALSE
D1815V7, binary
                  cls
clus                 0   1
  PRSS35 MUTATED     3   9
  PRSS35 WILD-TYPE 167 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS35 MUTATED      3    9
  PRSS35 WILD-TYPE  167  188
        clus
vv       PRSS35 MUTATED PRSS35 WILD-TYPE
  FEMALE              3              167
  MALE                9              188
[1] 2 2
[1] FALSE
D1815V8, binary
                  cls
clus                 0   1
  PRSS35 MUTATED    11   0
  PRSS35 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS35 MUTATED     11    0
  PRSS35 WILD-TYPE  289    8
     clus
vv    PRSS35 MUTATED PRSS35 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1815V9, binary
                  cls
clus                 0   1
  PRSS35 MUTATED     8   4
  PRSS35 WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS35 MUTATED      8    4
  PRSS35 WILD-TYPE  306   44
                               clus
vv                              PRSS35 MUTATED PRSS35 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRSS35 MUTATED     8   0   1   1
  PRSS35 WILD-TYPE 251   3  21  20
D1815V10, multiclass
    clus
vv   PRSS35 MUTATED PRSS35 WILD-TYPE
  R0              8              251
  R1              0                3
  R2              1               21
  RX              1               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"
D1815V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRSS35 MUTATED                                  0     1
  PRSS35 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRSS35 MUTATED                           1     3
  PRSS35 WILD-TYPE                        18   173
D1815V12, multiclass
                                  clus
vv                                 PRSS35 MUTATED PRSS35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         3              173
[1] 4 2
[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 = SF3B2 MUTATION ANALYSIS
D1816V1, survival
                 sevent
clus2               0   1
  SF3B2 MUTATED     6   4
  SF3B2 WILD-TYPE 271  74
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             345 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              4              74 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        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-A6-6651 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  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          22.090 
[1] "6.2 - 88.2 (20.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D1816V2, continuous
                 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      61        1       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF3B2 MUTATED           1          0          0          1        0         0
  SF3B2 WILD-TYPE        17          6         44         32       35        12
                 vv
clus              STAGE IVB
  SF3B2 MUTATED           0
  SF3B2 WILD-TYPE         1
D1816V3, multiclass
            clus
vv           SF3B2 MUTATED SF3B2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  SF3B2 MUTATED     1   2   5   2
  SF3B2 WILD-TYPE   8  65 244  39
D1816V4, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             5             244
  T4             2              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
  SF3B2 MUTATED     8   1   1
  SF3B2 WILD-TYPE 212  80  65
D1816V5, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1816V6, binary
                 cls
clus                0   1
  SF3B2 MUTATED     7   0
  SF3B2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      7    0
  SF3B2 WILD-TYPE  278   48
   clus
vv  SF3B2 MUTATED SF3B2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1816V7, binary
                 cls
clus                0   1
  SF3B2 MUTATED     8   2
  SF3B2 WILD-TYPE 162 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      8    2
  SF3B2 WILD-TYPE  162  195
        clus
vv       SF3B2 MUTATED SF3B2 WILD-TYPE
  FEMALE             8             162
  MALE               2             195
[1] 2 2
[1] FALSE
D1816V8, binary
                 cls
clus                0   1
  SF3B2 MUTATED    10   0
  SF3B2 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     10    0
  SF3B2 WILD-TYPE  290    8
     clus
vv    SF3B2 MUTATED SF3B2 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1816V9, binary
                 cls
clus                0   1
  SF3B2 MUTATED     9   1
  SF3B2 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      9    1
  SF3B2 WILD-TYPE  305   47
                               clus
vv                              SF3B2 MUTATED SF3B2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SF3B2 MUTATED     7   0   0   0
  SF3B2 WILD-TYPE 252   3  22  21
D1816V10, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             0              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"
D1816V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SF3B2 MUTATED                                  0     0
  SF3B2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SF3B2 MUTATED                           0     8
  SF3B2 WILD-TYPE                        19   168
D1816V12, multiclass
                                  clus
vv                                 SF3B2 MUTATED SF3B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        8             168
[1] 4 2
[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 = OR5L2 MUTATION ANALYSIS
D1817V1, survival
                 sevent
clus2               0   1
  OR5L2 MUTATED    11   3
  OR5L2 WILD-TYPE 266  75
  OR5L2 MUTATED OR5L2 WILD-TYPE 
             14             341 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
              3              75 
$`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 
       92.75        36.00 

$`OR5L2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
        2.01        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        12.00        11.38        10.26        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-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        13.78        46.75 

  OR5L2 MUTATED OR5L2 WILD-TYPE 
           3.02            0.00 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
         148.01          140.38 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
          15.32           22.36 
[1] "3.0 - 148.0 (15.3)" "0.0 - 140.4 (22.4)"
[1] "hr=" "1.3"
D1817V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5L2 MUTATED         1        0        2         6         0         0
  OR5L2 WILD-TYPE      63        1       24       102         8         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        17          6         43         31       35        11
                 vv
clus              STAGE IVB
  OR5L2 MUTATED           0
  OR5L2 WILD-TYPE         1
D1817V3, multiclass
            clus
vv           OR5L2 MUTATED OR5L2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              1              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
  OR5L2 MUTATED     0   1  11   2
  OR5L2 WILD-TYPE   9  66 238  39
D1817V4, multiclass
    clus
vv   OR5L2 MUTATED OR5L2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3            11             238
  T4             2              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
  OR5L2 MUTATED     9   3   2
  OR5L2 WILD-TYPE 211  78  64
D1817V5, multiclass
    clus
vv   OR5L2 MUTATED OR5L2 WILD-TYPE
  N0             9             211
  N1             3              78
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1817V6, binary
                 cls
clus                0   1
  OR5L2 MUTATED    12   1
  OR5L2 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED     12    1
  OR5L2 WILD-TYPE  273   47
   clus
vv  OR5L2 MUTATED OR5L2 WILD-TYPE
  0            12             273
  1             1              47
[1] 2 2
[1] FALSE
D1817V7, binary
                 cls
clus                0   1
  OR5L2 MUTATED     9   5
  OR5L2 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED      9    5
  OR5L2 WILD-TYPE  161  192
        clus
vv       OR5L2 MUTATED OR5L2 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D1817V8, binary
                 cls
clus                0   1
  OR5L2 MUTATED    11   0
  OR5L2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED     11    0
  OR5L2 WILD-TYPE  289    8
     clus
vv    OR5L2 MUTATED OR5L2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1817V9, binary
                 cls
clus                0   1
  OR5L2 MUTATED    11   3
  OR5L2 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED     11    3
  OR5L2 WILD-TYPE  303   45
                               clus
vv                              OR5L2 MUTATED OR5L2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5L2 MUTATED     9   0   0   3
  OR5L2 WILD-TYPE 250   3  22  18
D1817V10, multiclass
    clus
vv   OR5L2 MUTATED OR5L2 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             3              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"
D1817V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5L2 MUTATED                                  0     2
  OR5L2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5L2 MUTATED                           0     9
  OR5L2 WILD-TYPE                        19   167
D1817V12, multiclass
                                  clus
vv                                 OR5L2 MUTATED OR5L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(1818) Variable = APAF1 MUTATION ANALYSIS
D1818V1, survival
                 sevent
clus2               0   1
  APAF1 MUTATED    14   4
  APAF1 WILD-TYPE 263  74
  APAF1 MUTATED APAF1 WILD-TYPE 
             18             337 
  APAF1 MUTATED APAF1 WILD-TYPE 
              4              74 
$`APAF1 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3502 
       19.04        19.04        24.00        22.06        32.71        35.01 
TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6718 TCGA-CK-4947 
       15.95        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        54.61        56.09        16.14        74.56 

$`APAF1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6651 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-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        12.76        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-D5-5539 TCGA-D5-5541 
       11.01        10.06        12.03        45.40        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        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6626 
       46.75 

  APAF1 MUTATED APAF1 WILD-TYPE 
           4.01            0.00 
  APAF1 MUTATED APAF1 WILD-TYPE 
          74.56          148.01 
  APAF1 MUTATED APAF1 WILD-TYPE 
          23.03           22.03 
[1] "4.0 - 74.6 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1818V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APAF1 MUTATED         3        0        1         5         2         1
  APAF1 WILD-TYPE      61        1       25       103         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APAF1 MUTATED           0          1          2          1        1         0
  APAF1 WILD-TYPE        18          5         42         32       34        12
                 vv
clus              STAGE IVB
  APAF1 MUTATED           0
  APAF1 WILD-TYPE         1
D1818V3, multiclass
            clus
vv           APAF1 MUTATED APAF1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              5             103
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  APAF1 MUTATED     0   5   9   4
  APAF1 WILD-TYPE   9  62 240  37
D1818V4, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  T1             0               9
  T2             5              62
  T3             9             240
  T4             4              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
  APAF1 MUTATED    14   3   1
  APAF1 WILD-TYPE 206  78  65
D1818V5, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  N0            14             206
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1818V6, binary
                 cls
clus                0   1
  APAF1 MUTATED    16   1
  APAF1 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     16    1
  APAF1 WILD-TYPE  269   47
   clus
vv  APAF1 MUTATED APAF1 WILD-TYPE
  0            16             269
  1             1              47
[1] 2 2
[1] FALSE
D1818V7, binary
                 cls
clus                0   1
  APAF1 MUTATED     8  10
  APAF1 WILD-TYPE 162 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED      8   10
  APAF1 WILD-TYPE  162  187
        clus
vv       APAF1 MUTATED APAF1 WILD-TYPE
  FEMALE             8             162
  MALE              10             187
[1] 2 2
[1] FALSE
D1818V8, binary
                 cls
clus                0   1
  APAF1 MUTATED    16   1
  APAF1 WILD-TYPE 284   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     16    1
  APAF1 WILD-TYPE  284    7
     clus
vv    APAF1 MUTATED APAF1 WILD-TYPE
  NO             16             284
  YES             1               7
[1] 2 2
[1] FALSE
D1818V9, binary
                 cls
clus                0   1
  APAF1 MUTATED    15   3
  APAF1 WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     15    3
  APAF1 WILD-TYPE  299   45
                               clus
vv                              APAF1 MUTATED APAF1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             299
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  APAF1 MUTATED    13   0   1   2
  APAF1 WILD-TYPE 246   3  21  19
D1818V10, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  R0            13             246
  R1             0               3
  R2             1              21
  RX             2              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"
D1818V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APAF1 MUTATED                                  0     1
  APAF1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  APAF1 MUTATED                           0     9
  APAF1 WILD-TYPE                        19   167
D1818V12, multiclass
                                  clus
vv                                 APAF1 MUTATED APAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        9             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(1819) Variable = KRT39 MUTATION ANALYSIS
D1819V1, survival
                 sevent
clus2               0   1
  KRT39 MUTATED     6   1
  KRT39 WILD-TYPE 271  77
  KRT39 MUTATED KRT39 WILD-TYPE 
              7             348 
  KRT39 MUTATED KRT39 WILD-TYPE 
              1              77 
$`KRT39 MUTATED`
TCGA-AZ-6608 TCGA-A6-5659 TCGA-AA-3861 TCGA-AA-3947 TCGA-AZ-4315 TCGA-D5-6536 
        1.94        30.44        30.05        33.01        58.39        17.85 
TCGA-DM-A1HA 
      131.51 

$`KRT39 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A28C 
      140.38         7.50        44.32       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  KRT39 MUTATED KRT39 WILD-TYPE 
           1.94            0.00 
  KRT39 MUTATED KRT39 WILD-TYPE 
         131.51          148.01 
  KRT39 MUTATED KRT39 WILD-TYPE 
          30.44           22.01 
[1] "1.9 - 131.5 (30.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1819V2, continuous
                 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      63        1       26       105         7         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        18          5         44         32       35        12
                 vv
clus              STAGE IVB
  KRT39 MUTATED           0
  KRT39 WILD-TYPE         1
D1819V3, multiclass
            clus
vv           KRT39 MUTATED KRT39 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             1               5
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  KRT39 MUTATED     0   2   4   1
  KRT39 WILD-TYPE   9  65 245  40
D1819V4, multiclass
    clus
vv   KRT39 MUTATED KRT39 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             1              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
  KRT39 MUTATED     5   1   1
  KRT39 WILD-TYPE 215  80  65
D1819V5, multiclass
    clus
vv   KRT39 MUTATED KRT39 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1819V6, binary
                 cls
clus                0   1
  KRT39 MUTATED     7   0
  KRT39 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      7    0
  KRT39 WILD-TYPE  278   48
   clus
vv  KRT39 MUTATED KRT39 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1819V7, binary
                 cls
clus                0   1
  KRT39 MUTATED     2   5
  KRT39 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      2    5
  KRT39 WILD-TYPE  168  192
        clus
vv       KRT39 MUTATED KRT39 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1819V8, binary
                 cls
clus                0   1
  KRT39 MUTATED     6   0
  KRT39 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      6    0
  KRT39 WILD-TYPE  294    8
     clus
vv    KRT39 MUTATED KRT39 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1819V9, binary
                 cls
clus                0   1
  KRT39 MUTATED     6   1
  KRT39 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      6    1
  KRT39 WILD-TYPE  308   47
                               clus
vv                              KRT39 MUTATED KRT39 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KRT39 MUTATED     5   0   0   0
  KRT39 WILD-TYPE 254   3  22  21
D1819V10, multiclass
    clus
vv   KRT39 MUTATED KRT39 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1819V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT39 MUTATED                                  0     0
  KRT39 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT39 MUTATED                           0     5
  KRT39 WILD-TYPE                        19   171
D1819V12, multiclass
                                  clus
vv                                 KRT39 MUTATED KRT39 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = IL3 MUTATION ANALYSIS
D1820V1, survival
               sevent
clus2             0   1
  IL3 MUTATED     6   0
  IL3 WILD-TYPE 271  78
  IL3 MUTATED IL3 WILD-TYPE 
            6           349 
  IL3 MUTATED IL3 WILD-TYPE 
            0            78 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  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        22.060 
[1] "0.9 - 38.0 (24.5)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1820V2, continuous
               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      63        1       26       106         8         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        17          6         44         31       35        12
               vv
clus            STAGE IVB
  IL3 MUTATED           0
  IL3 WILD-TYPE         1
D1820V3, multiclass
            clus
vv           IL3 MUTATED IL3 WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            2           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           0            44
  STAGE IIIC           2            31
  STAGE IV             0            35
  STAGE IVA            0            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
  IL3 MUTATED     0   1   5   0
  IL3 WILD-TYPE   9  66 244  41
D1820V4, multiclass
    clus
vv   IL3 MUTATED IL3 WILD-TYPE
  T1           0             9
  T2           1            66
  T3           5           244
  T4           0            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
  IL3 MUTATED     3   1   2
  IL3 WILD-TYPE 217  80  64
D1820V5, multiclass
    clus
vv   IL3 MUTATED IL3 WILD-TYPE
  N0           3           217
  N1           1            80
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1820V6, binary
               cls
clus              0   1
  IL3 MUTATED     5   0
  IL3 WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      5    0
  IL3 WILD-TYPE  280   48
   clus
vv  IL3 MUTATED IL3 WILD-TYPE
  0           5           280
  1           0            48
[1] 2 2
[1] FALSE
D1820V7, binary
               cls
clus              0   1
  IL3 MUTATED     4   2
  IL3 WILD-TYPE 166 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      4    2
  IL3 WILD-TYPE  166  195
        clus
vv       IL3 MUTATED IL3 WILD-TYPE
  FEMALE           4           166
  MALE             2           195
[1] 2 2
[1] FALSE
D1820V8, binary
               cls
clus              0   1
  IL3 MUTATED     6   0
  IL3 WILD-TYPE 294   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      6    0
  IL3 WILD-TYPE  294    8
     clus
vv    IL3 MUTATED IL3 WILD-TYPE
  NO            6           294
  YES           0             8
[1] 2 2
[1] FALSE
D1820V9, binary
               cls
clus              0   1
  IL3 MUTATED     6   0
  IL3 WILD-TYPE 308  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      6    0
  IL3 WILD-TYPE  308   48
                               clus
vv                              IL3 MUTATED IL3 WILD-TYPE
  COLON ADENOCARCINOMA                    6           308
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  IL3 MUTATED     6   0   0   0
  IL3 WILD-TYPE 253   3  22  21
D1820V10, multiclass
    clus
vv   IL3 MUTATED IL3 WILD-TYPE
  R0           6           253
  R1           0             3
  R2           0            22
  RX           0            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"
D1820V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL3 MUTATED                                  0     0
  IL3 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IL3 MUTATED                           1     2
  IL3 WILD-TYPE                        18   174
D1820V12, multiclass
                                  clus
vv                                 IL3 MUTATED IL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      2           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(1821) Variable = UST MUTATION ANALYSIS
D1821V1, survival
               sevent
clus2             0   1
  UST MUTATED     8   1
  UST WILD-TYPE 269  77
  UST MUTATED UST WILD-TYPE 
            9           346 
  UST MUTATED UST WILD-TYPE 
            1            77 
$`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        12.16        12.10        19.59 
TCGA-D5-6535 TCGA-DM-A1HB TCGA-G4-6317 
       15.12       135.65        36.00 

$`UST WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
        0.92        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6856 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  UST MUTATED UST WILD-TYPE 
         8.38          0.00 
  UST MUTATED UST WILD-TYPE 
       135.65        148.01 
  UST MUTATED UST WILD-TYPE 
        19.59         22.09 
[1] "8.4 - 135.7 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.4"
D1821V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UST MUTATED         1        0        1         1         0         0
  UST WILD-TYPE      63        1       25       107         8         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        18          5         41         32       34        12
               vv
clus            STAGE IVB
  UST MUTATED           0
  UST WILD-TYPE         1
D1821V3, multiclass
            clus
vv           UST MUTATED UST WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            25
  STAGE IIA            1           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           1             5
  STAGE IIIB           3            41
  STAGE IIIC           1            32
  STAGE IV             1            34
  STAGE IVA            0            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
  UST MUTATED     0   2   6   1
  UST WILD-TYPE   9  65 243  40
D1821V4, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  T1           0             9
  T2           2            65
  T3           6           243
  T4           1            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
  UST MUTATED     3   4   2
  UST WILD-TYPE 217  77  64
D1821V5, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  N0           3           217
  N1           4            77
  N2           2            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1821V6, binary
               cls
clus              0   1
  UST MUTATED     5   1
  UST WILD-TYPE 280  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      5    1
  UST WILD-TYPE  280   47
   clus
vv  UST MUTATED UST WILD-TYPE
  0           5           280
  1           1            47
[1] 2 2
[1] FALSE
D1821V7, binary
               cls
clus              0   1
  UST MUTATED     2   7
  UST WILD-TYPE 168 190
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      2    7
  UST WILD-TYPE  168  190
        clus
vv       UST MUTATED UST WILD-TYPE
  FEMALE           2           168
  MALE             7           190
[1] 2 2
[1] FALSE
D1821V8, binary
               cls
clus              0   1
  UST MUTATED     8   0
  UST WILD-TYPE 292   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      8    0
  UST WILD-TYPE  292    8
     clus
vv    UST MUTATED UST WILD-TYPE
  NO            8           292
  YES           0             8
[1] 2 2
[1] FALSE
D1821V9, binary
               cls
clus              0   1
  UST MUTATED     6   2
  UST WILD-TYPE 308  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      6    2
  UST WILD-TYPE  308   46
                               clus
vv                              UST MUTATED UST WILD-TYPE
  COLON ADENOCARCINOMA                    6           308
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  UST MUTATED     5   0   0   1
  UST WILD-TYPE 254   3  22  20
D1821V10, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  R0           5           254
  R1           0             3
  R2           0            22
  RX           1            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"
D1821V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UST MUTATED                                  0     0
  UST WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  UST MUTATED                           2     5
  UST WILD-TYPE                        17   171
D1821V12, multiclass
                                  clus
vv                                 UST MUTATED UST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            17
  WHITE                                      5           171
[1] 4 2
[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 = CYTSA MUTATION ANALYSIS
D1822V1, survival
                 sevent
clus2               0   1
  CYTSA MUTATED    10   1
  CYTSA WILD-TYPE 267  77
  CYTSA MUTATED CYTSA WILD-TYPE 
             11             344 
  CYTSA MUTATED CYTSA WILD-TYPE 
              1              77 
$`CYTSA MUTATED`
TCGA-AA-3979 TCGA-A6-2676 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00A 
       24.00        42.90        53.00        26.01         2.01        38.04 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6898 
        0.20        58.39        12.76        23.05         7.53 

$`CYTSA WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        33.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  CYTSA MUTATED CYTSA WILD-TYPE 
            0.2             0.0 
  CYTSA MUTATED CYTSA WILD-TYPE 
          58.39          148.01 
  CYTSA MUTATED CYTSA WILD-TYPE 
          24.00           22.01 
[1] "0.2 - 58.4 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1822V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYTSA MUTATED         1        0        1         6         1         0
  CYTSA WILD-TYPE      63        1       25       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYTSA MUTATED           0          0          1          1        0         0
  CYTSA WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  CYTSA MUTATED           0
  CYTSA WILD-TYPE         1
D1822V3, multiclass
            clus
vv           CYTSA MUTATED CYTSA WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              6             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  CYTSA MUTATED     0   1   9   1
  CYTSA WILD-TYPE   9  66 240  40
D1822V4, multiclass
    clus
vv   CYTSA MUTATED CYTSA WILD-TYPE
  T1             0               9
  T2             1              66
  T3             9             240
  T4             1              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
  CYTSA MUTATED     9   1   1
  CYTSA WILD-TYPE 211  80  65
D1822V5, multiclass
    clus
vv   CYTSA MUTATED CYTSA WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1822V6, binary
                 cls
clus                0   1
  CYTSA MUTATED    10   0
  CYTSA WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED     10    0
  CYTSA WILD-TYPE  275   48
   clus
vv  CYTSA MUTATED CYTSA WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1822V7, binary
                 cls
clus                0   1
  CYTSA MUTATED     4   7
  CYTSA WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      4    7
  CYTSA WILD-TYPE  166  190
        clus
vv       CYTSA MUTATED CYTSA WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D1822V8, binary
                 cls
clus                0   1
  CYTSA MUTATED     9   0
  CYTSA WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      9    0
  CYTSA WILD-TYPE  291    8
     clus
vv    CYTSA MUTATED CYTSA WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1822V9, binary
                 cls
clus                0   1
  CYTSA MUTATED     7   4
  CYTSA WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      7    4
  CYTSA WILD-TYPE  307   44
                               clus
vv                              CYTSA MUTATED CYTSA WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CYTSA MUTATED     9   0   0   1
  CYTSA WILD-TYPE 250   3  22  20
D1822V10, multiclass
    clus
vv   CYTSA MUTATED CYTSA WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D1822V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYTSA MUTATED                                  0     1
  CYTSA WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CYTSA MUTATED                           0     5
  CYTSA WILD-TYPE                        19   171
D1822V12, multiclass
                                  clus
vv                                 CYTSA MUTATED CYTSA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        5             171
[1] 4 2
[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 = PEAR1 MUTATION ANALYSIS
D1823V1, survival
                 sevent
clus2               0   1
  PEAR1 MUTATED     9   2
  PEAR1 WILD-TYPE 268  76
  PEAR1 MUTATED PEAR1 WILD-TYPE 
             11             344 
  PEAR1 MUTATED PEAR1 WILD-TYPE 
              2              76 
$`PEAR1 MUTATED`
TCGA-AA-3554 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 
       17.95        26.17        33.53        19.66        63.98         1.02 
TCGA-AA-3977 TCGA-AD-6965 TCGA-AZ-6598 TCGA-D5-6930 TCGA-F4-6570 
       25.02        26.47        49.41        13.35         6.18 

$`PEAR1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PEAR1 MUTATED PEAR1 WILD-TYPE 
           1.02            0.00 
  PEAR1 MUTATED PEAR1 WILD-TYPE 
          63.98          148.01 
  PEAR1 MUTATED PEAR1 WILD-TYPE 
         25.020          22.045 
[1] "1.0 - 64.0 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1823V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PEAR1 MUTATED         0        0        2         6         0         0
  PEAR1 WILD-TYPE      64        1       24       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PEAR1 MUTATED           0          0          0          2        0         0
  PEAR1 WILD-TYPE        18          6         44         31       35        12
                 vv
clus              STAGE IVB
  PEAR1 MUTATED           0
  PEAR1 WILD-TYPE         1
D1823V3, multiclass
            clus
vv           PEAR1 MUTATED PEAR1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              6             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  PEAR1 MUTATED     0   1   8   2
  PEAR1 WILD-TYPE   9  66 241  39
D1823V4, multiclass
    clus
vv   PEAR1 MUTATED PEAR1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             2              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
  PEAR1 MUTATED     9   1   1
  PEAR1 WILD-TYPE 211  80  65
D1823V5, multiclass
    clus
vv   PEAR1 MUTATED PEAR1 WILD-TYPE
  N0             9             211
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1823V6, binary
                 cls
clus                0   1
  PEAR1 MUTATED     8   0
  PEAR1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEAR1 MUTATED      8    0
  PEAR1 WILD-TYPE  277   48
   clus
vv  PEAR1 MUTATED PEAR1 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1823V7, binary
                 cls
clus                0   1
  PEAR1 MUTATED     6   5
  PEAR1 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEAR1 MUTATED      6    5
  PEAR1 WILD-TYPE  164  192
        clus
vv       PEAR1 MUTATED PEAR1 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D1823V8, binary
                 cls
clus                0   1
  PEAR1 MUTATED    10   0
  PEAR1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEAR1 MUTATED     10    0
  PEAR1 WILD-TYPE  290    8
     clus
vv    PEAR1 MUTATED PEAR1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1823V9, binary
                 cls
clus                0   1
  PEAR1 MUTATED     9   2
  PEAR1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEAR1 MUTATED      9    2
  PEAR1 WILD-TYPE  305   46
                               clus
vv                              PEAR1 MUTATED PEAR1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PEAR1 MUTATED     8   1   0   0
  PEAR1 WILD-TYPE 251   2  22  21
D1823V10, multiclass
    clus
vv   PEAR1 MUTATED PEAR1 WILD-TYPE
  R0             8             251
  R1             1               2
  R2             0              22
  RX             0              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"
D1823V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PEAR1 MUTATED                                  0     0
  PEAR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PEAR1 MUTATED                           1     6
  PEAR1 WILD-TYPE                        18   170
D1823V12, multiclass
                                  clus
vv                                 PEAR1 MUTATED PEAR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = HIST1H1B MUTATION ANALYSIS
D1824V1, survival
                    sevent
clus2                  0   1
  HIST1H1B MUTATED     7   0
  HIST1H1B WILD-TYPE 270  78
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                348 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 0                 78 
$`HIST1H1B MUTATED`
TCGA-AA-3662 TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6781 TCGA-CM-6165 TCGA-D5-6928 
        6.05        46.65        22.06        19.66        16.04        11.64 
TCGA-D5-6930 
       13.35 

$`HIST1H1B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        43.76        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-A6-6782 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
              6.05               0.00 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             46.65             148.01 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
            16.040             22.225 
[1] "6.0 - 46.6 (16.0)"  "0.0 - 148.0 (22.2)"
[1] "hr="     "9200000"
D1824V2, continuous
                    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      64        1       26       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1B MUTATED           0          0          1          1        1
  HIST1H1B WILD-TYPE        18          6         43         32       34
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1B MUTATED           0         0
  HIST1H1B WILD-TYPE        12         1
D1824V3, multiclass
            clus
vv           HIST1H1B MUTATED HIST1H1B WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 4                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                1                 32
  STAGE IV                  1                 34
  STAGE IVA                 0                 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
  HIST1H1B MUTATED     0   0   5   2
  HIST1H1B WILD-TYPE   9  67 244  39
D1824V4, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  T1                0                  9
  T2                0                 67
  T3                5                244
  T4                2                 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
  HIST1H1B MUTATED     4   2   1
  HIST1H1B WILD-TYPE 216  79  65
D1824V5, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  N0                4                216
  N1                2                 79
  N2                1                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1824V6, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     5   1
  HIST1H1B WILD-TYPE 280  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      5    1
  HIST1H1B WILD-TYPE  280   47
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0                5                280
  1                1                 47
[1] 2 2
[1] FALSE
D1824V7, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     3   4
  HIST1H1B WILD-TYPE 167 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      3    4
  HIST1H1B WILD-TYPE  167  193
        clus
vv       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  FEMALE                3                167
  MALE                  4                193
[1] 2 2
[1] FALSE
D1824V8, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     7   0
  HIST1H1B WILD-TYPE 293   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      7    0
  HIST1H1B WILD-TYPE  293    8
     clus
vv    HIST1H1B MUTATED HIST1H1B WILD-TYPE
  NO                 7                293
  YES                0                  8
[1] 2 2
[1] FALSE
D1824V9, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     4   3
  HIST1H1B WILD-TYPE 310  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      4    3
  HIST1H1B WILD-TYPE  310   45
                               clus
vv                              HIST1H1B MUTATED HIST1H1B WILD-TYPE
  COLON ADENOCARCINOMA                         4                310
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1B MUTATED     6   0   1   0
  HIST1H1B WILD-TYPE 253   3  21  21
D1824V10, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  R0                6                253
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D1824V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1B MUTATED                                  0     0
  HIST1H1B WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1B MUTATED                           0     6
  HIST1H1B WILD-TYPE                        19   170
D1824V12, multiclass
                                  clus
vv                                 HIST1H1B MUTATED HIST1H1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           6                170
[1] 4 2
[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 = SIRT4 MUTATION ANALYSIS
D1825V1, survival
                 sevent
clus2               0   1
  SIRT4 MUTATED     3   2
  SIRT4 WILD-TYPE 274  76
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              5             350 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              2              76 
$`SIRT4 MUTATED`
TCGA-AZ-6601 TCGA-AA-3864 TCGA-AA-A00N TCGA-AY-6197 TCGA-DM-A1HB 
      100.01        53.00         4.01        21.44       135.65 

$`SIRT4 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  SIRT4 MUTATED SIRT4 WILD-TYPE 
           4.01            0.00 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
         135.65          148.01 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
         53.000          22.045 
[1] "4.0 - 135.7 (53.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1825V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SIRT4 MUTATED         0        0        2         2         1         0
  SIRT4 WILD-TYPE      64        1       24       106         7         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  SIRT4 MUTATED           0
  SIRT4 WILD-TYPE         1
D1825V3, multiclass
            clus
vv           SIRT4 MUTATED SIRT4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  SIRT4 MUTATED     0   0   5   1
  SIRT4 WILD-TYPE   9  67 244  40
D1825V4, multiclass
    clus
vv   SIRT4 MUTATED SIRT4 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             5             244
  T4             1              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
  SIRT4 MUTATED     5   1   0
  SIRT4 WILD-TYPE 215  80  66
D1825V5, multiclass
    clus
vv   SIRT4 MUTATED SIRT4 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1825V6, binary
                 cls
clus                0   1
  SIRT4 MUTATED     5   0
  SIRT4 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      5    0
  SIRT4 WILD-TYPE  280   48
   clus
vv  SIRT4 MUTATED SIRT4 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1825V7, binary
                 cls
clus                0   1
  SIRT4 MUTATED     1   5
  SIRT4 WILD-TYPE 169 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      1    5
  SIRT4 WILD-TYPE  169  192
        clus
vv       SIRT4 MUTATED SIRT4 WILD-TYPE
  FEMALE             1             169
  MALE               5             192
[1] 2 2
[1] FALSE
D1825V8, binary
                 cls
clus                0   1
  SIRT4 MUTATED     3   0
  SIRT4 WILD-TYPE 297   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      3    0
  SIRT4 WILD-TYPE  297    8
     clus
vv    SIRT4 MUTATED SIRT4 WILD-TYPE
  NO              3             297
  YES             0               8
[1] 2 2
[1] FALSE
D1825V9, binary
                 cls
clus                0   1
  SIRT4 MUTATED     4   1
  SIRT4 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      4    1
  SIRT4 WILD-TYPE  310   47
                               clus
vv                              SIRT4 MUTATED SIRT4 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SIRT4 MUTATED     4   0   0   0
  SIRT4 WILD-TYPE 255   3  22  21
D1825V10, multiclass
    clus
vv   SIRT4 MUTATED SIRT4 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             0              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"
D1825V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIRT4 MUTATED                                  0     0
  SIRT4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SIRT4 MUTATED                           0     3
  SIRT4 WILD-TYPE                        19   173
D1825V12, multiclass
                                  clus
vv                                 SIRT4 MUTATED SIRT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = OLFM1 MUTATION ANALYSIS
D1826V1, survival
                 sevent
clus2               0   1
  OLFM1 MUTATED     8   2
  OLFM1 WILD-TYPE 269  76
  OLFM1 MUTATED OLFM1 WILD-TYPE 
             10             345 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
              2              76 
$`OLFM1 MUTATED`
TCGA-G4-6588 TCGA-A6-6780 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6965 
       26.17        20.12        27.02        18.05        34.98        26.47 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CM-4746 TCGA-CM-6172 
       49.41         5.23        37.02        11.01 

$`OLFM1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        19.66        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  OLFM1 MUTATED OLFM1 WILD-TYPE 
           5.23            0.00 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
          49.41          148.01 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
          26.32           22.03 
[1] "5.2 - 49.4 (26.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1826V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OLFM1 MUTATED         1        0        2         2         1         0
  OLFM1 WILD-TYPE      63        1       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OLFM1 MUTATED           0          0          4          1        0         0
  OLFM1 WILD-TYPE        18          6         40         32       35        12
                 vv
clus              STAGE IVB
  OLFM1 MUTATED           0
  OLFM1 WILD-TYPE         1
D1826V3, multiclass
            clus
vv           OLFM1 MUTATED OLFM1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             4              40
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  OLFM1 MUTATED     0   1   5   5
  OLFM1 WILD-TYPE   9  66 244  36
D1826V4, multiclass
    clus
vv   OLFM1 MUTATED OLFM1 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             5             244
  T4             5              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
  OLFM1 MUTATED     6   4   1
  OLFM1 WILD-TYPE 214  77  65
D1826V5, multiclass
    clus
vv   OLFM1 MUTATED OLFM1 WILD-TYPE
  N0             6             214
  N1             4              77
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1826V6, binary
                 cls
clus                0   1
  OLFM1 MUTATED     9   0
  OLFM1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED      9    0
  OLFM1 WILD-TYPE  276   48
   clus
vv  OLFM1 MUTATED OLFM1 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1826V7, binary
                 cls
clus                0   1
  OLFM1 MUTATED     5   6
  OLFM1 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED      5    6
  OLFM1 WILD-TYPE  165  191
        clus
vv       OLFM1 MUTATED OLFM1 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1826V8, binary
                 cls
clus                0   1
  OLFM1 MUTATED    10   0
  OLFM1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED     10    0
  OLFM1 WILD-TYPE  290    8
     clus
vv    OLFM1 MUTATED OLFM1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1826V9, binary
                 cls
clus                0   1
  OLFM1 MUTATED     8   3
  OLFM1 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED      8    3
  OLFM1 WILD-TYPE  306   45
                               clus
vv                              OLFM1 MUTATED OLFM1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OLFM1 MUTATED     7   1   0   0
  OLFM1 WILD-TYPE 252   2  22  21
D1826V10, multiclass
    clus
vv   OLFM1 MUTATED OLFM1 WILD-TYPE
  R0             7             252
  R1             1               2
  R2             0              22
  RX             0              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"
D1826V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OLFM1 MUTATED                                  0     0
  OLFM1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OLFM1 MUTATED                           1     6
  OLFM1 WILD-TYPE                        18   170
D1826V12, multiclass
                                  clus
vv                                 OLFM1 MUTATED OLFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = DDX55 MUTATION ANALYSIS
D1827V1, survival
                 sevent
clus2               0   1
  DDX55 MUTATED     9   1
  DDX55 WILD-TYPE 268  77
  DDX55 MUTATED DDX55 WILD-TYPE 
             10             345 
  DDX55 MUTATED DDX55 WILD-TYPE 
              1              77 
$`DDX55 MUTATED`
TCGA-AA-3531 TCGA-AA-3950 TCGA-AD-6895 TCGA-A6-5665 TCGA-AA-3864 TCGA-AZ-6598 
       34.03        24.00        25.08        22.06        53.00        49.41 
TCGA-CA-6717 TCGA-CM-6169 TCGA-D5-6929 TCGA-DM-A1HB 
       12.76        13.02        13.41       135.65 

$`DDX55 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        30.05        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  DDX55 MUTATED DDX55 WILD-TYPE 
          12.76            0.00 
  DDX55 MUTATED DDX55 WILD-TYPE 
         135.65          148.01 
  DDX55 MUTATED DDX55 WILD-TYPE 
          24.54           21.99 
[1] "12.8 - 135.7 (24.5)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "2.9"
D1827V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX55 MUTATED         0        0        2         5         0         0
  DDX55 WILD-TYPE      64        1       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX55 MUTATED           0          0          2          0        1         0
  DDX55 WILD-TYPE        18          6         42         33       34        12
                 vv
clus              STAGE IVB
  DDX55 MUTATED           0
  DDX55 WILD-TYPE         1
D1827V3, multiclass
            clus
vv           DDX55 MUTATED DDX55 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              5             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  DDX55 MUTATED     0   0  10   0
  DDX55 WILD-TYPE   9  67 239  41
D1827V4, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  T1             0               9
  T2             0              67
  T3            10             239
  T4             0              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
  DDX55 MUTATED     7   3   0
  DDX55 WILD-TYPE 213  78  66
D1827V5, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1827V6, binary
                 cls
clus                0   1
  DDX55 MUTATED     8   1
  DDX55 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      8    1
  DDX55 WILD-TYPE  277   47
   clus
vv  DDX55 MUTATED DDX55 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1827V7, binary
                 cls
clus                0   1
  DDX55 MUTATED     5   5
  DDX55 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      5    5
  DDX55 WILD-TYPE  165  192
        clus
vv       DDX55 MUTATED DDX55 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1827V8, binary
                 cls
clus                0   1
  DDX55 MUTATED     9   0
  DDX55 WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      9    0
  DDX55 WILD-TYPE  291    8
     clus
vv    DDX55 MUTATED DDX55 WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1827V9, binary
                 cls
clus                0   1
  DDX55 MUTATED     7   2
  DDX55 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      7    2
  DDX55 WILD-TYPE  307   46
                               clus
vv                              DDX55 MUTATED DDX55 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX55 MUTATED     7   0   0   1
  DDX55 WILD-TYPE 252   3  22  20
D1827V10, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1827V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX55 MUTATED                                  0     1
  DDX55 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX55 MUTATED                           1     5
  DDX55 WILD-TYPE                        18   171
D1827V12, multiclass
                                  clus
vv                                 DDX55 MUTATED DDX55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = CLGN MUTATION ANALYSIS
D1828V1, survival
                sevent
clus2              0   1
  CLGN MUTATED     9   1
  CLGN WILD-TYPE 268  77
  CLGN MUTATED CLGN WILD-TYPE 
            10            345 
  CLGN MUTATED CLGN WILD-TYPE 
             1             77 
$`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        12.16 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4746 
       17.82        58.39        12.76        37.02 

$`CLGN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       32.75        36.53        32.91        31.63        30.44        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  CLGN MUTATED CLGN WILD-TYPE 
         12.16           0.00 
  CLGN MUTATED CLGN WILD-TYPE 
         63.98         148.01 
  CLGN MUTATED CLGN WILD-TYPE 
         28.09          22.03 
[1] "12.2 - 64.0 (28.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.4"
D1828V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLGN MUTATED         2        0        1         5         1         0
  CLGN WILD-TYPE      62        1       25       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLGN MUTATED           0          0          1          1        0         0
  CLGN WILD-TYPE        18          6         43         32       35        12
                vv
clus             STAGE IVB
  CLGN MUTATED           0
  CLGN WILD-TYPE         1
D1828V3, multiclass
            clus
vv           CLGN MUTATED CLGN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  CLGN MUTATED     0   2   8   1
  CLGN WILD-TYPE   9  65 241  40
D1828V4, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            1             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
  CLGN MUTATED     9   1   1
  CLGN WILD-TYPE 211  80  65
D1828V5, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  N0            9            211
  N1            1             80
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1828V6, binary
                cls
clus               0   1
  CLGN MUTATED     9   0
  CLGN WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      9    0
  CLGN WILD-TYPE  276   48
   clus
vv  CLGN MUTATED CLGN WILD-TYPE
  0            9            276
  1            0             48
[1] 2 2
[1] FALSE
D1828V7, binary
                cls
clus               0   1
  CLGN MUTATED     4   7
  CLGN WILD-TYPE 166 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      4    7
  CLGN WILD-TYPE  166  190
        clus
vv       CLGN MUTATED CLGN WILD-TYPE
  FEMALE            4            166
  MALE              7            190
[1] 2 2
[1] FALSE
D1828V8, binary
                cls
clus               0   1
  CLGN MUTATED    10   0
  CLGN WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED     10    0
  CLGN WILD-TYPE  290    8
     clus
vv    CLGN MUTATED CLGN WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1828V9, binary
                cls
clus               0   1
  CLGN MUTATED     9   2
  CLGN WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      9    2
  CLGN WILD-TYPE  305   46
                               clus
vv                              CLGN MUTATED CLGN WILD-TYPE
  COLON ADENOCARCINOMA                     9            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CLGN MUTATED     7   0   0   2
  CLGN WILD-TYPE 252   3  22  19
D1828V10, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            2             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"
D1828V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLGN MUTATED                                  0     1
  CLGN WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CLGN MUTATED                           4     4
  CLGN WILD-TYPE                        15   172
D1828V12, multiclass
                                  clus
vv                                 CLGN MUTATED CLGN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                       4            172
[1] 4 2
[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 = EHBP1L1 MUTATION ANALYSIS
D1829V1, survival
                   sevent
clus2                 0   1
  EHBP1L1 MUTATED     6   1
  EHBP1L1 WILD-TYPE 271  77
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                7               348 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                1                77 
$`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 
       12.00 

$`EHBP1L1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3492 
       24.69        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
            11.74              0.00 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
            53.00            148.01 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
           19.660            22.075 
[1] "11.7 - 53.0 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1829V2, continuous
                   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      63        1       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EHBP1L1 MUTATED           0          0          1          2        1
  EHBP1L1 WILD-TYPE        18          6         43         31       34
                   vv
clus                STAGE IVA STAGE IVB
  EHBP1L1 MUTATED           0         0
  EHBP1L1 WILD-TYPE        12         1
D1829V3, multiclass
            clus
vv           EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                0               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               2                31
  STAGE IV                 1                34
  STAGE IVA                0                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
  EHBP1L1 MUTATED     0   1   3   3
  EHBP1L1 WILD-TYPE   9  66 246  38
D1829V4, multiclass
    clus
vv   EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               3               246
  T4               3                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
  EHBP1L1 MUTATED     3   2   2
  EHBP1L1 WILD-TYPE 217  79  64
D1829V5, multiclass
    clus
vv   EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  N0               3               217
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1829V6, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     5   1
  EHBP1L1 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      5    1
  EHBP1L1 WILD-TYPE  280   47
   clus
vv  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  0               5               280
  1               1                47
[1] 2 2
[1] FALSE
D1829V7, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     2   5
  EHBP1L1 WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      2    5
  EHBP1L1 WILD-TYPE  168  192
        clus
vv       EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D1829V8, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     6   0
  EHBP1L1 WILD-TYPE 294   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      6    0
  EHBP1L1 WILD-TYPE  294    8
     clus
vv    EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  NO                6               294
  YES               0                 8
[1] 2 2
[1] FALSE
D1829V9, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     4   3
  EHBP1L1 WILD-TYPE 310  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      4    3
  EHBP1L1 WILD-TYPE  310   45
                               clus
vv                              EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EHBP1L1 MUTATED     4   0   0   1
  EHBP1L1 WILD-TYPE 255   3  22  20
D1829V10, multiclass
    clus
vv   EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               0                22
  RX               1                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"
D1829V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EHBP1L1 MUTATED                                  0     0
  EHBP1L1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EHBP1L1 MUTATED                           0     5
  EHBP1L1 WILD-TYPE                        19   171
D1829V12, multiclass
                                  clus
vv                                 EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               171
[1] 4 2
[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 = ATP2A2 MUTATION ANALYSIS
D1830V1, survival
                  sevent
clus2                0   1
  ATP2A2 MUTATED    11   3
  ATP2A2 WILD-TYPE 266  75
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
              14              341 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
               3               75 
$`ATP2A2 MUTATED`
TCGA-AA-3525 TCGA-AZ-6608 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3977 
        8.05         1.94        20.12        63.98        33.04        25.02 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AD-5900 TCGA-AZ-6598 TCGA-CM-5864 TCGA-CM-6171 
        4.01         0.99        12.16        49.41        15.02        14.04 
TCGA-D5-6540 TCGA-G4-6304 
       16.14        53.62 

$`ATP2A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
      100.01        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       18.05        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
            0.99             0.00 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
           63.98           148.01 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
           15.58            22.09 
[1] "1.0 - 64.0 (15.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1830V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP2A2 MUTATED         5        0        2         2         3         0
  ATP2A2 WILD-TYPE      59        1       24       106         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2A2 MUTATED           0          1          1          0        0
  ATP2A2 WILD-TYPE        18          5         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP2A2 MUTATED           0         0
  ATP2A2 WILD-TYPE        12         1
D1830V3, multiclass
            clus
vv           ATP2A2 MUTATED ATP2A2 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               2              106
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ATP2A2 MUTATED     0   7   5   3
  ATP2A2 WILD-TYPE   9  60 244  38
D1830V4, multiclass
    clus
vv   ATP2A2 MUTATED ATP2A2 WILD-TYPE
  T1              0                9
  T2              7               60
  T3              5              244
  T4              3               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
  ATP2A2 MUTATED    13   2   0
  ATP2A2 WILD-TYPE 207  79  66
D1830V5, multiclass
    clus
vv   ATP2A2 MUTATED ATP2A2 WILD-TYPE
  N0             13              207
  N1              2               79
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1830V6, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED    10   0
  ATP2A2 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED     10    0
  ATP2A2 WILD-TYPE  275   48
   clus
vv  ATP2A2 MUTATED ATP2A2 WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D1830V7, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED     7   8
  ATP2A2 WILD-TYPE 163 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED      7    8
  ATP2A2 WILD-TYPE  163  189
        clus
vv       ATP2A2 MUTATED ATP2A2 WILD-TYPE
  FEMALE              7              163
  MALE                8              189
[1] 2 2
[1] FALSE
D1830V8, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED    12   0
  ATP2A2 WILD-TYPE 288   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED     12    0
  ATP2A2 WILD-TYPE  288    8
     clus
vv    ATP2A2 MUTATED ATP2A2 WILD-TYPE
  NO              12              288
  YES              0                8
[1] 2 2
[1] FALSE
D1830V9, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED    11   4
  ATP2A2 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED     11    4
  ATP2A2 WILD-TYPE  303   44
                               clus
vv                              ATP2A2 MUTATED ATP2A2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP2A2 MUTATED    10   0   0   1
  ATP2A2 WILD-TYPE 249   3  22  20
D1830V10, multiclass
    clus
vv   ATP2A2 MUTATED ATP2A2 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              0               22
  RX              1               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"
D1830V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP2A2 MUTATED                                  0     0
  ATP2A2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP2A2 MUTATED                           0     9
  ATP2A2 WILD-TYPE                        19   167
D1830V12, multiclass
                                  clus
vv                                 ATP2A2 MUTATED ATP2A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         9              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(1831) Variable = GRAMD1C MUTATION ANALYSIS
D1831V1, survival
                   sevent
clus2                 0   1
  GRAMD1C MUTATED     7   2
  GRAMD1C WILD-TYPE 270  76
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
                9               346 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
                2                76 
$`GRAMD1C MUTATED`
TCGA-G4-6628 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-6747 TCGA-CM-6167 TCGA-CM-6680 
       79.69        34.98        58.39        82.95        14.99        12.03 
TCGA-DM-A1D0 TCGA-F4-6460 TCGA-G4-6303 
      130.65        31.96        65.85 

$`GRAMD1C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        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-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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        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-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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
            12.03              0.00 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
           130.65            148.01 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
            58.39             21.99 
[1] "12.0 - 130.7 (58.4)" "0.0 - 148.0 (22.0)" 
[1] "hr=" "1.9"
D1831V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRAMD1C MUTATED         1        0        0         5         1         0
  GRAMD1C WILD-TYPE      63        1       26       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRAMD1C MUTATED           0          0          2          1        1
  GRAMD1C WILD-TYPE        18          6         42         32       34
                   vv
clus                STAGE IVA STAGE IVB
  GRAMD1C MUTATED           0         0
  GRAMD1C WILD-TYPE        12         1
D1831V3, multiclass
            clus
vv           GRAMD1C MUTATED GRAMD1C WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                5               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               1                32
  STAGE IV                 1                34
  STAGE IVA                0                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
  GRAMD1C MUTATED     0   1   9   1
  GRAMD1C WILD-TYPE   9  66 240  40
D1831V4, multiclass
    clus
vv   GRAMD1C MUTATED GRAMD1C WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               9               240
  T4               1                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
  GRAMD1C MUTATED     7   2   2
  GRAMD1C WILD-TYPE 213  79  64
D1831V5, multiclass
    clus
vv   GRAMD1C MUTATED GRAMD1C WILD-TYPE
  N0               7               213
  N1               2                79
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1831V6, binary
                   cls
clus                  0   1
  GRAMD1C MUTATED     9   1
  GRAMD1C WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GRAMD1C MUTATED      9    1
  GRAMD1C WILD-TYPE  276   47
   clus
vv  GRAMD1C MUTATED GRAMD1C WILD-TYPE
  0               9               276
  1               1                47
[1] 2 2
[1] FALSE
D1831V7, binary
                   cls
clus                  0   1
  GRAMD1C MUTATED     9   2
  GRAMD1C WILD-TYPE 161 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GRAMD1C MUTATED      9    2
  GRAMD1C WILD-TYPE  161  195
        clus
vv       GRAMD1C MUTATED GRAMD1C WILD-TYPE
  FEMALE               9               161
  MALE                 2               195
[1] 2 2
[1] FALSE
D1831V8, binary
                   cls
clus                  0   1
  GRAMD1C MUTATED     8   0
  GRAMD1C WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GRAMD1C MUTATED      8    0
  GRAMD1C WILD-TYPE  292    8
     clus
vv    GRAMD1C MUTATED GRAMD1C WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1831V9, binary
                   cls
clus                  0   1
  GRAMD1C MUTATED    11   0
  GRAMD1C WILD-TYPE 303  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GRAMD1C MUTATED     11    0
  GRAMD1C WILD-TYPE  303   48
                               clus
vv                              GRAMD1C MUTATED GRAMD1C WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GRAMD1C MUTATED     9   0   0   1
  GRAMD1C WILD-TYPE 250   3  22  20
D1831V10, multiclass
    clus
vv   GRAMD1C MUTATED GRAMD1C WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               0                22
  RX               1                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"
D1831V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRAMD1C MUTATED                                  0     0
  GRAMD1C WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GRAMD1C MUTATED                           1     7
  GRAMD1C WILD-TYPE                        18   169
D1831V12, multiclass
                                  clus
vv                                 GRAMD1C MUTATED GRAMD1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          7               169
[1] 4 2
[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 = TIPARP MUTATION ANALYSIS
D1832V1, survival
                  sevent
clus2                0   1
  TIPARP MUTATED     4   1
  TIPARP WILD-TYPE 273  77
  TIPARP MUTATED TIPARP WILD-TYPE 
               5              350 
  TIPARP MUTATED TIPARP WILD-TYPE 
               1               77 
$`TIPARP MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6675 
       25.02         4.01        34.98        12.76        13.05 

$`TIPARP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TIPARP MUTATED TIPARP WILD-TYPE 
            4.01             0.00 
  TIPARP MUTATED TIPARP WILD-TYPE 
           34.98           148.01 
  TIPARP MUTATED TIPARP WILD-TYPE 
          13.050           22.075 
[1] "4.0 - 35.0 (13.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1832V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TIPARP MUTATED         0        0        0         1         2         0
  TIPARP WILD-TYPE      64        1       26       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TIPARP MUTATED           0          0          0          0        0
  TIPARP WILD-TYPE        18          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  TIPARP MUTATED           0         1
  TIPARP WILD-TYPE        12         0
D1832V3, multiclass
            clus
vv           TIPARP MUTATED TIPARP WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               12
  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
  TIPARP MUTATED     0   1   2   2
  TIPARP WILD-TYPE   9  66 247  39
D1832V4, multiclass
    clus
vv   TIPARP MUTATED TIPARP WILD-TYPE
  T1              0                9
  T2              1               66
  T3              2              247
  T4              2               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
  TIPARP MUTATED     4   0   1
  TIPARP WILD-TYPE 216  81  65
D1832V5, multiclass
    clus
vv   TIPARP MUTATED TIPARP WILD-TYPE
  N0              4              216
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1832V6, binary
                  cls
clus                 0   1
  TIPARP MUTATED     3   1
  TIPARP WILD-TYPE 282  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIPARP MUTATED      3    1
  TIPARP WILD-TYPE  282   47
   clus
vv  TIPARP MUTATED TIPARP WILD-TYPE
  0              3              282
  1              1               47
[1] 2 2
[1] FALSE
D1832V7, binary
                  cls
clus                 0   1
  TIPARP MUTATED     1   4
  TIPARP WILD-TYPE 169 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIPARP MUTATED      1    4
  TIPARP WILD-TYPE  169  193
        clus
vv       TIPARP MUTATED TIPARP WILD-TYPE
  FEMALE              1              169
  MALE                4              193
[1] 2 2
[1] FALSE
D1832V8, binary
                  cls
clus                 0   1
  TIPARP MUTATED     4   0
  TIPARP WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIPARP MUTATED      4    0
  TIPARP WILD-TYPE  296    8
     clus
vv    TIPARP MUTATED TIPARP WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1832V9, binary
                  cls
clus                 0   1
  TIPARP MUTATED     3   2
  TIPARP WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIPARP MUTATED      3    2
  TIPARP WILD-TYPE  311   46
                               clus
vv                              TIPARP MUTATED TIPARP WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TIPARP MUTATED     3   0   0   1
  TIPARP WILD-TYPE 256   3  22  20
D1832V10, multiclass
    clus
vv   TIPARP MUTATED TIPARP WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              1               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"
D1832V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIPARP MUTATED                                  0     1
  TIPARP WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TIPARP MUTATED                           1     0
  TIPARP WILD-TYPE                        18   176
D1832V12, multiclass
[1] "Remove cluster labels:" "TIPARP MUTATED"        
clus
  TIPARP MUTATED TIPARP WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6889       TCGA-AD-6890 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-6607       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6718 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 

Clustering(1833) Variable = POLA1 MUTATION ANALYSIS
D1833V1, survival
                 sevent
clus2               0   1
  POLA1 MUTATED     6   1
  POLA1 WILD-TYPE 271  77
  POLA1 MUTATED POLA1 WILD-TYPE 
              7             348 
  POLA1 MUTATED POLA1 WILD-TYPE 
              1              77 
$`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 
       16.14 

$`POLA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  POLA1 MUTATED POLA1 WILD-TYPE 
          10.06            0.00 
  POLA1 MUTATED POLA1 WILD-TYPE 
          34.98          148.01 
  POLA1 MUTATED POLA1 WILD-TYPE 
         18.250          22.075 
[1] "10.1 - 35.0 (18.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D1833V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLA1 MUTATED         2        0        0         2         3         0
  POLA1 WILD-TYPE      62        1       26       106         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLA1 MUTATED           0          0          0          1        0         1
  POLA1 WILD-TYPE        18          6         44         32       35        11
                 vv
clus              STAGE IVB
  POLA1 MUTATED           0
  POLA1 WILD-TYPE         1
D1833V3, multiclass
            clus
vv           POLA1 MUTATED POLA1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              1              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
  POLA1 MUTATED     0   2   4   3
  POLA1 WILD-TYPE   9  65 245  38
D1833V4, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             4             245
  T4             3              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
  POLA1 MUTATED     7   1   1
  POLA1 WILD-TYPE 213  80  65
D1833V5, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1833V6, binary
                 cls
clus                0   1
  POLA1 MUTATED     7   1
  POLA1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      7    1
  POLA1 WILD-TYPE  278   47
   clus
vv  POLA1 MUTATED POLA1 WILD-TYPE
  0             7             278
  1             1              47
[1] 2 2
[1] FALSE
D1833V7, binary
                 cls
clus                0   1
  POLA1 MUTATED     7   2
  POLA1 WILD-TYPE 163 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      7    2
  POLA1 WILD-TYPE  163  195
        clus
vv       POLA1 MUTATED POLA1 WILD-TYPE
  FEMALE             7             163
  MALE               2             195
[1] 2 2
[1] FALSE
D1833V8, binary
                 cls
clus                0   1
  POLA1 MUTATED     7   0
  POLA1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      7    0
  POLA1 WILD-TYPE  293    8
     clus
vv    POLA1 MUTATED POLA1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1833V9, binary
                 cls
clus                0   1
  POLA1 MUTATED     7   2
  POLA1 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      7    2
  POLA1 WILD-TYPE  307   46
                               clus
vv                              POLA1 MUTATED POLA1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  POLA1 MUTATED     8   0   0   1
  POLA1 WILD-TYPE 251   3  22  20
D1833V10, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             1              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"
D1833V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLA1 MUTATED                                  0     0
  POLA1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  POLA1 MUTATED                           1     4
  POLA1 WILD-TYPE                        18   172
D1833V12, multiclass
                                  clus
vv                                 POLA1 MUTATED POLA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        4             172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1834) Variable = SAPS3 MUTATION ANALYSIS
D1834V1, survival
                 sevent
clus2               0   1
  SAPS3 MUTATED     7   3
  SAPS3 WILD-TYPE 270  75
  SAPS3 MUTATED SAPS3 WILD-TYPE 
             10             345 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
              3              75 
$`SAPS3 MUTATED`
TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A01X 
       79.69        22.06        19.66        33.01         4.01        26.01 
TCGA-AD-5900 TCGA-CA-6717 TCGA-DM-A28C TCGA-G4-6303 
       12.16        12.76        81.37        65.85 

$`SAPS3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28E TCGA-DM-A28F 
       44.32       131.51       135.65       139.17       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 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-G4-6315 
       74.56        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SAPS3 MUTATED SAPS3 WILD-TYPE 
           4.01            0.00 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
          81.37          148.01 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
         24.035          22.030 
[1] "4.0 - 81.4 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1834V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAPS3 MUTATED         2        0        0         4         2         0
  SAPS3 WILD-TYPE      62        1       26       104         6         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        17          6         44         32       34        12
                 vv
clus              STAGE IVB
  SAPS3 MUTATED           0
  SAPS3 WILD-TYPE         1
D1834V3, multiclass
            clus
vv           SAPS3 MUTATED SAPS3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  SAPS3 MUTATED     0   3   5   3
  SAPS3 WILD-TYPE   9  64 244  38
D1834V4, multiclass
    clus
vv   SAPS3 MUTATED SAPS3 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             5             244
  T4             3              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
  SAPS3 MUTATED     8   3   0
  SAPS3 WILD-TYPE 212  78  66
D1834V5, multiclass
    clus
vv   SAPS3 MUTATED SAPS3 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1834V6, binary
                 cls
clus                0   1
  SAPS3 MUTATED     8   1
  SAPS3 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED      8    1
  SAPS3 WILD-TYPE  277   47
   clus
vv  SAPS3 MUTATED SAPS3 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1834V7, binary
                 cls
clus                0   1
  SAPS3 MUTATED     5   6
  SAPS3 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED      5    6
  SAPS3 WILD-TYPE  165  191
        clus
vv       SAPS3 MUTATED SAPS3 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1834V8, binary
                 cls
clus                0   1
  SAPS3 MUTATED     8   0
  SAPS3 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED      8    0
  SAPS3 WILD-TYPE  292    8
     clus
vv    SAPS3 MUTATED SAPS3 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1834V9, binary
                 cls
clus                0   1
  SAPS3 MUTATED     6   5
  SAPS3 WILD-TYPE 308  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED      6    5
  SAPS3 WILD-TYPE  308   43
                               clus
vv                              SAPS3 MUTATED SAPS3 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SAPS3 MUTATED     8   0   0   2
  SAPS3 WILD-TYPE 251   3  22  19
D1834V10, multiclass
    clus
vv   SAPS3 MUTATED SAPS3 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             2              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"
D1834V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAPS3 MUTATED                                  0     1
  SAPS3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SAPS3 MUTATED                           0     6
  SAPS3 WILD-TYPE                        19   170
D1834V12, multiclass
                                  clus
vv                                 SAPS3 MUTATED SAPS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ZFP1 MUTATION ANALYSIS
D1835V1, survival
                sevent
clus2              0   1
  ZFP1 MUTATED     4   0
  ZFP1 WILD-TYPE 273  78
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             4            351 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             0             78 
$`ZFP1 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6890 
       63.98        25.02        34.98        24.53 

$`ZFP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         3.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       83.24         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZFP1 MUTATED ZFP1 WILD-TYPE 
         24.53           0.00 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
         63.98         148.01 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
         30.00          21.99 
[1] "24.5 - 64.0 (30.0)" "0.0 - 148.0 (22.0)"
[1] "hr="     "9100000"
D1835V2, continuous
                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      64        1       25       108         7         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ZFP1 MUTATED           0
  ZFP1 WILD-TYPE         1
D1835V3, multiclass
[1] "Remove cluster labels:" "ZFP1 MUTATED"          
clus
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             2            355 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AA-3496 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3516     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-3527     TCGA-AA-3530 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552     TCGA-AA-3554 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562     TCGA-AA-3662 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3697 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814     TCGA-AA-3844 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870     TCGA-AA-3939 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972     TCGA-AA-3976 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L     TCGA-AA-A00Z 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6895 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A285     TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-3810     TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5660     TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5665     TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6141     TCGA-A6-6142     TCGA-A6-6648     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-3502     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3526     TCGA-AA-3529 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3553 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3558     TCGA-AA-3561     TCGA-AA-3655 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3660     TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3667     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3712     TCGA-AA-3811     TCGA-AA-3812     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-3845 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3858     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3869     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-3941     TCGA-AA-3947     TCGA-AA-3949 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966     TCGA-AA-3968 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3980 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3982     TCGA-AA-3984     TCGA-AA-3989     TCGA-AA-3994 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     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-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"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-6889 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-4616     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-6605 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6606     TCGA-AZ-6607     TCGA-CA-5254     TCGA-CA-5255 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5913 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"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-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D9 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6315 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  ZFP1 MUTATED     1   1   1   1
  ZFP1 WILD-TYPE   8  66 248  40
D1835V4, multiclass
    clus
vv   ZFP1 MUTATED ZFP1 WILD-TYPE
  T1            1              8
  T2            1             66
  T3            1            248
  T4            1             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
  ZFP1 MUTATED     4   0   0
  ZFP1 WILD-TYPE 216  81  66
D1835V5, multiclass
    clus
vv   ZFP1 MUTATED ZFP1 WILD-TYPE
  N0            4            216
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1835V6, binary
                cls
clus               0   1
  ZFP1 MUTATED     2   0
  ZFP1 WILD-TYPE 283  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      2    0
  ZFP1 WILD-TYPE  283   48
   clus
vv  ZFP1 MUTATED ZFP1 WILD-TYPE
  0            2            283
  1            0             48
[1] 2 2
[1] FALSE
D1835V7, binary
                cls
clus               0   1
  ZFP1 MUTATED     1   3
  ZFP1 WILD-TYPE 169 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      1    3
  ZFP1 WILD-TYPE  169  194
        clus
vv       ZFP1 MUTATED ZFP1 WILD-TYPE
  FEMALE            1            169
  MALE              3            194
[1] 2 2
[1] FALSE
D1835V8, binary
                cls
clus               0   1
  ZFP1 MUTATED     4   0
  ZFP1 WILD-TYPE 296   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      4    0
  ZFP1 WILD-TYPE  296    8
     clus
vv    ZFP1 MUTATED ZFP1 WILD-TYPE
  NO             4            296
  YES            0              8
[1] 2 2
[1] FALSE
D1835V9, binary
                cls
clus               0   1
  ZFP1 MUTATED     4   0
  ZFP1 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      4    0
  ZFP1 WILD-TYPE  310   48
                               clus
vv                              ZFP1 MUTATED ZFP1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            310
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ZFP1 MUTATED     2   0   0   0
  ZFP1 WILD-TYPE 257   3  22  21
D1835V10, multiclass
[1] "Remove cluster labels:" "ZFP1 MUTATED"          
clus
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             2            303 
    TCGA-A6-2677     TCGA-AA-3496     TCGA-AA-3520     TCGA-AA-3521 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3527 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3543     TCGA-AA-3552 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3560     TCGA-AA-3562 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3672     TCGA-AA-3688     TCGA-AA-3692 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3814 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3860     TCGA-AA-3867     TCGA-AA-3870 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3972 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-A00L 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A024     TCGA-AD-6548     TCGA-AD-6888 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6895     TCGA-AZ-4681     TCGA-CK-5912     TCGA-G4-6310 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2676     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-3502     TCGA-AA-3511 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518     TCGA-AA-3519 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3526     TCGA-AA-3529     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-3544     TCGA-AA-3548 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3549     TCGA-AA-3553     TCGA-AA-3555     TCGA-AA-3558 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3561     TCGA-AA-3655     TCGA-AA-3660     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-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-3693     TCGA-AA-3695 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3811 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3812     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3842     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-3861 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3941 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3955     TCGA-AA-3956 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3973     TCGA-AA-3975 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3984     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-A00N     TCGA-AA-A00O 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"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-A029 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6889     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-4682     TCGA-CA-5254     TCGA-CA-5255 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5913 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     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-G4-6315 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6323     TCGA-G4-6626 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
D1835V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP1 MUTATED                                  0     0
  ZFP1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZFP1 MUTATED                           0     1
  ZFP1 WILD-TYPE                        19   175
D1835V12, multiclass
[1] "Remove cluster labels:" "ZFP1 MUTATED"          
clus
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             1            205 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6899 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965     TCGA-AU-3779 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"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-5913     TCGA-CK-5914     TCGA-CK-5915 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"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-A28C     TCGA-DM-A28E 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6309     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6626 
"ZFP1 WILD-TYPE" 

Clustering(1836) Variable = MLL MUTATION ANALYSIS
D1836V1, survival
               sevent
clus2             0   1
  MLL MUTATED    29   8
  MLL WILD-TYPE 248  70
  MLL MUTATED MLL WILD-TYPE 
           37           318 
  MLL MUTATED MLL WILD-TYPE 
            8            70 
$`MLL MUTATED`
TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3672 TCGA-G4-6310 TCGA-G4-6588 TCGA-A6-2672 
        8.05        17.95         0.92        63.62        26.17        46.65 
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6654 TCGA-AA-3510 
       33.53        32.71        27.09        25.08        23.87        63.98 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01G TCGA-AD-6889 
        5.03        10.06        53.00        34.98        12.00        83.24 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4752 
       58.39        49.41        10.06        15.62        51.32        13.02 
TCGA-CM-5349 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6529 TCGA-D5-6928 TCGA-D5-6930 
       30.08        12.00        14.04        20.19        11.64        13.35 
TCGA-DM-A1D4 TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6306 
       92.75         8.61        35.74         6.18        35.31        44.68 
TCGA-G4-6309 
       85.48 

$`MLL WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        22.09        35.80        91.79        79.69 
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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       29.19        23.61        22.09        22.06        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3710 TCGA-AA-3812 
       15.02        11.01         5.98        37.05        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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        85.45        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        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-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-F4-6460 
      119.93        35.97        60.79       117.07        98.24        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        43.04        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-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       53.62        55.04        61.91        36.00        13.78        46.75 

  MLL MUTATED MLL WILD-TYPE 
         0.92          0.00 
  MLL MUTATED MLL WILD-TYPE 
        92.75        148.01 
  MLL MUTATED MLL WILD-TYPE 
        26.17         21.99 
[1] "0.9 - 92.8 (26.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1836V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL MUTATED         3        0        3        16         1         1
  MLL WILD-TYPE      61        1       23        92         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL MUTATED           2          0          8          1        1         1
  MLL WILD-TYPE        16          6         36         32       34        11
               vv
clus            STAGE IVB
  MLL MUTATED           0
  MLL WILD-TYPE         1
D1836V3, multiclass
            clus
vv           MLL MUTATED MLL WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA           16            92
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            2            16
  STAGE IIIA           0             6
  STAGE IIIB           8            36
  STAGE IIIC           1            32
  STAGE IV             1            34
  STAGE IVA            1            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
  MLL MUTATED     0   4  31   3
  MLL WILD-TYPE   9  63 218  38
D1836V4, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  T1           0             9
  T2           4            63
  T3          31           218
  T4           3            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
  MLL MUTATED    25  10   3
  MLL WILD-TYPE 195  71  63
D1836V5, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  N0          25           195
  N1          10            71
  N2           3            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"
D1836V6, binary
               cls
clus              0   1
  MLL MUTATED    34   2
  MLL WILD-TYPE 251  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     34    2
  MLL WILD-TYPE  251   46
   clus
vv  MLL MUTATED MLL WILD-TYPE
  0          34           251
  1           2            46
[1] 2 2
[1] FALSE
D1836V7, binary
               cls
clus              0   1
  MLL MUTATED    20  18
  MLL WILD-TYPE 150 179
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     20   18
  MLL WILD-TYPE  150  179
        clus
vv       MLL MUTATED MLL WILD-TYPE
  FEMALE          20           150
  MALE            18           179
[1] 2 2
[1] FALSE
D1836V8, binary
               cls
clus              0   1
  MLL MUTATED    34   1
  MLL WILD-TYPE 266   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     34    1
  MLL WILD-TYPE  266    7
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO           34           266
  YES           1             7
[1] 2 2
[1] FALSE
D1836V9, binary
               cls
clus              0   1
  MLL MUTATED    32   6
  MLL WILD-TYPE 282  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     32    6
  MLL WILD-TYPE  282   42
                               clus
vv                              MLL MUTATED MLL WILD-TYPE
  COLON ADENOCARCINOMA                   32           282
  COLON MUCINOUS ADENOCARCINOMA           6            42
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MLL MUTATED    28   0   1   3
  MLL WILD-TYPE 231   3  21  18
D1836V10, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  R0          28           231
  R1           0             3
  R2           1            21
  RX           3            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"
D1836V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL MUTATED                                  0     2
  MLL WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MLL MUTATED                           3    23
  MLL WILD-TYPE                        16   153
D1836V12, multiclass
                                  clus
vv                                 MLL MUTATED MLL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  3            16
  WHITE                                     23           153
[1] 4 2
[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 = TSC2 MUTATION ANALYSIS
D1837V1, survival
                sevent
clus2              0   1
  TSC2 MUTATED     9   4
  TSC2 WILD-TYPE 268  74
  TSC2 MUTATED TSC2 WILD-TYPE 
            13            342 
  TSC2 MUTATED TSC2 WILD-TYPE 
             4             74 
$`TSC2 MUTATED`
TCGA-A6-6138 TCGA-AA-3492 TCGA-AA-3696 TCGA-AD-6889 TCGA-AY-6196 TCGA-AY-6197 
       22.52         3.02         5.03        83.24         0.20        21.44 
TCGA-AZ-6600 TCGA-CK-6748 TCGA-CM-5349 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6923 
       12.10         2.01        30.08        17.85        12.49        12.43 
TCGA-F4-6855 
       47.41 

$`TSC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6651 TCGA-A6-6652 
       27.09         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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        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 
       12.36        12.39        12.59        12.59        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-6751 TCGA-CM-4743 
       51.32        21.99        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-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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  TSC2 MUTATED TSC2 WILD-TYPE 
           0.2            0.0 
  TSC2 MUTATED TSC2 WILD-TYPE 
         83.24         148.01 
  TSC2 MUTATED TSC2 WILD-TYPE 
        12.490         22.225 
[1] "0.2 - 83.2 (12.5)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.8"
D1837V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSC2 MUTATED         2        0        1         5         1         0
  TSC2 WILD-TYPE      62        1       25       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSC2 MUTATED           1          0          0          1        3         0
  TSC2 WILD-TYPE        17          6         44         32       32        12
                vv
clus             STAGE IVB
  TSC2 MUTATED           0
  TSC2 WILD-TYPE         1
D1837V3, multiclass
            clus
vv           TSC2 MUTATED TSC2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              3             32
  STAGE IVA             0             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
  TSC2 MUTATED     0   2  11   2
  TSC2 WILD-TYPE   9  65 238  39
D1837V4, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  T1            0              9
  T2            2             65
  T3           11            238
  T4            2             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
  TSC2 MUTATED    10   3   2
  TSC2 WILD-TYPE 210  78  64
D1837V5, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  N0           10            210
  N1            3             78
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1837V6, binary
                cls
clus               0   1
  TSC2 MUTATED     9   3
  TSC2 WILD-TYPE 276  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      9    3
  TSC2 WILD-TYPE  276   45
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            9            276
  1            3             45
[1] 2 2
[1] FALSE
D1837V7, binary
                cls
clus               0   1
  TSC2 MUTATED     7   8
  TSC2 WILD-TYPE 163 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      7    8
  TSC2 WILD-TYPE  163  189
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  FEMALE            7            163
  MALE              8            189
[1] 2 2
[1] FALSE
D1837V8, binary
                cls
clus               0   1
  TSC2 MUTATED    12   0
  TSC2 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED     12    0
  TSC2 WILD-TYPE  288    8
     clus
vv    TSC2 MUTATED TSC2 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1837V9, binary
                cls
clus               0   1
  TSC2 MUTATED    13   2
  TSC2 WILD-TYPE 301  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED     13    2
  TSC2 WILD-TYPE  301   46
                               clus
vv                              TSC2 MUTATED TSC2 WILD-TYPE
  COLON ADENOCARCINOMA                    13            301
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TSC2 MUTATED    10   0   1   2
  TSC2 WILD-TYPE 249   3  21  19
D1837V10, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            2             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"
D1837V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC2 MUTATED                                  0     1
  TSC2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC2 MUTATED                           1    10
  TSC2 WILD-TYPE                        18   166
D1837V12, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                      10            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(1838) Variable = MAK MUTATION ANALYSIS
D1838V1, survival
               sevent
clus2             0   1
  MAK MUTATED     6   3
  MAK WILD-TYPE 271  75
  MAK MUTATED MAK WILD-TYPE 
            9           346 
  MAK MUTATED MAK WILD-TYPE 
            3            75 
$`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 
       37.02       135.65         6.18 

$`MAK WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        51.32        21.99        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  MAK MUTATED MAK WILD-TYPE 
         4.01          0.00 
  MAK MUTATED MAK WILD-TYPE 
       135.65        148.01 
  MAK MUTATED MAK WILD-TYPE 
       21.140        22.075 
[1] "4.0 - 135.7 (21.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1838V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAK MUTATED         2        0        0         3         1         0
  MAK WILD-TYPE      62        1       26       105         7         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        17          6         43         33       34        12
               vv
clus            STAGE IVB
  MAK MUTATED           0
  MAK WILD-TYPE         1
D1838V3, multiclass
            clus
vv           MAK MUTATED MAK WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             0            26
  STAGE IIA            3           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            17
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             1            34
  STAGE IVA            0            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
  MAK MUTATED     1   1   6   1
  MAK WILD-TYPE   8  66 243  40
D1838V4, multiclass
    clus
vv   MAK MUTATED MAK WILD-TYPE
  T1           1             8
  T2           1            66
  T3           6           243
  T4           1            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
  MAK MUTATED     7   1   1
  MAK WILD-TYPE 213  80  65
D1838V5, multiclass
    clus
vv   MAK MUTATED MAK WILD-TYPE
  N0           7           213
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1838V6, binary
               cls
clus              0   1
  MAK MUTATED     8   1
  MAK WILD-TYPE 277  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      8    1
  MAK WILD-TYPE  277   47
   clus
vv  MAK MUTATED MAK WILD-TYPE
  0           8           277
  1           1            47
[1] 2 2
[1] FALSE
D1838V7, binary
               cls
clus              0   1
  MAK MUTATED     3   6
  MAK WILD-TYPE 167 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      3    6
  MAK WILD-TYPE  167  191
        clus
vv       MAK MUTATED MAK WILD-TYPE
  FEMALE           3           167
  MALE             6           191
[1] 2 2
[1] FALSE
D1838V8, binary
               cls
clus              0   1
  MAK MUTATED     5   2
  MAK WILD-TYPE 295   6
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      5    2
  MAK WILD-TYPE  295    6
     clus
vv    MAK MUTATED MAK WILD-TYPE
  NO            5           295
  YES           2             6
[1] 2 2
[1] FALSE
D1838V9, binary
               cls
clus              0   1
  MAK MUTATED     4   4
  MAK WILD-TYPE 310  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      4    4
  MAK WILD-TYPE  310   44
                               clus
vv                              MAK MUTATED MAK WILD-TYPE
  COLON ADENOCARCINOMA                    4           310
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MAK MUTATED     5   0   1   2
  MAK WILD-TYPE 254   3  21  19
D1838V10, multiclass
    clus
vv   MAK MUTATED MAK WILD-TYPE
  R0           5           254
  R1           0             3
  R2           1            21
  RX           2            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"
D1838V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAK MUTATED                                  0     1
  MAK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MAK MUTATED                           1     3
  MAK WILD-TYPE                        18   173
D1838V12, multiclass
                                  clus
vv                                 MAK MUTATED MAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                      3           173
[1] 4 2
[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 = FAAH2 MUTATION ANALYSIS
D1839V1, survival
                 sevent
clus2               0   1
  FAAH2 MUTATED     9   2
  FAAH2 WILD-TYPE 268  76
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             11             344 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
              2              76 
$`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        15.02        33.01 
TCGA-AZ-6599 TCGA-CK-4947 TCGA-CM-6676 TCGA-D5-6535 TCGA-G4-6315 
        6.77        17.56        11.08        15.12        61.91 

$`FAAH2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        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-A029 
        1.02        33.04         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30       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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FAAH2 MUTATED FAAH2 WILD-TYPE 
           6.77            0.00 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
          61.91          148.01 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
          15.12           22.09 
[1] "6.8 - 61.9 (15.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1839V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAAH2 MUTATED         2        0        0         2         0         0
  FAAH2 WILD-TYPE      62        1       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAAH2 MUTATED           1          0          3          1        1         1
  FAAH2 WILD-TYPE        17          6         41         32       34        11
                 vv
clus              STAGE IVB
  FAAH2 MUTATED           0
  FAAH2 WILD-TYPE         1
D1839V3, multiclass
            clus
vv           FAAH2 MUTATED FAAH2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              1              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
  FAAH2 MUTATED     0   2   8   1
  FAAH2 WILD-TYPE   9  65 241  40
D1839V4, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             1              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
  FAAH2 MUTATED     4   5   2
  FAAH2 WILD-TYPE 216  76  64
D1839V5, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  N0             4             216
  N1             5              76
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1839V6, binary
                 cls
clus                0   1
  FAAH2 MUTATED     7   2
  FAAH2 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED      7    2
  FAAH2 WILD-TYPE  278   46
   clus
vv  FAAH2 MUTATED FAAH2 WILD-TYPE
  0             7             278
  1             2              46
[1] 2 2
[1] FALSE
D1839V7, binary
                 cls
clus                0   1
  FAAH2 MUTATED     6   5
  FAAH2 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED      6    5
  FAAH2 WILD-TYPE  164  192
        clus
vv       FAAH2 MUTATED FAAH2 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D1839V8, binary
                 cls
clus                0   1
  FAAH2 MUTATED    11   0
  FAAH2 WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED     11    0
  FAAH2 WILD-TYPE  289    8
     clus
vv    FAAH2 MUTATED FAAH2 WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1839V9, binary
                 cls
clus                0   1
  FAAH2 MUTATED    10   1
  FAAH2 WILD-TYPE 304  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED     10    1
  FAAH2 WILD-TYPE  304   47
                               clus
vv                              FAAH2 MUTATED FAAH2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FAAH2 MUTATED     7   0   0   2
  FAAH2 WILD-TYPE 252   3  22  19
D1839V10, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             2              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"
D1839V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAAH2 MUTATED                                  0     0
  FAAH2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FAAH2 MUTATED                           1     5
  FAAH2 WILD-TYPE                        18   171
D1839V12, multiclass
                                  clus
vv                                 FAAH2 MUTATED FAAH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = KIAA0355 MUTATION ANALYSIS
D1840V1, survival
                    sevent
clus2                  0   1
  KIAA0355 MUTATED     4   3
  KIAA0355 WILD-TYPE 273  75
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 7                348 
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 3                 75 
$`KIAA0355 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6888 TCGA-A6-6782 TCGA-AA-3655 TCGA-F4-6856 
       19.04        19.04        15.52        20.28        61.02        35.31 
TCGA-G4-6303 
       65.85 

$`KIAA0355 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3510 
       20.12        19.66         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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  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             22.075 
[1] "15.5 - 65.8 (20.3)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1840V2, continuous
                    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      63        1       24       108         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0355 MUTATED           0          0          1          0        2
  KIAA0355 WILD-TYPE        18          6         43         33       33
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0355 MUTATED           0         0
  KIAA0355 WILD-TYPE        12         1
D1840V3, multiclass
            clus
vv           KIAA0355 MUTATED KIAA0355 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 24
  STAGE IIA                 0                108
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  2                 33
  STAGE IVA                 0                 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
  KIAA0355 MUTATED     0   1   5   1
  KIAA0355 WILD-TYPE   9  66 244  40
D1840V4, multiclass
    clus
vv   KIAA0355 MUTATED KIAA0355 WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                5                244
  T4                1                 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
  KIAA0355 MUTATED     5   2   0
  KIAA0355 WILD-TYPE 215  79  66
D1840V5, multiclass
    clus
vv   KIAA0355 MUTATED KIAA0355 WILD-TYPE
  N0                5                215
  N1                2                 79
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1840V6, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     4   2
  KIAA0355 WILD-TYPE 281  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      4    2
  KIAA0355 WILD-TYPE  281   46
   clus
vv  KIAA0355 MUTATED KIAA0355 WILD-TYPE
  0                4                281
  1                2                 46
[1] 2 2
[1] FALSE
D1840V7, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     1   6
  KIAA0355 WILD-TYPE 169 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      1    6
  KIAA0355 WILD-TYPE  169  191
        clus
vv       KIAA0355 MUTATED KIAA0355 WILD-TYPE
  FEMALE                1                169
  MALE                  6                191
[1] 2 2
[1] FALSE
D1840V8, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     6   1
  KIAA0355 WILD-TYPE 294   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      6    1
  KIAA0355 WILD-TYPE  294    7
     clus
vv    KIAA0355 MUTATED KIAA0355 WILD-TYPE
  NO                 6                294
  YES                1                  7
[1] 2 2
[1] FALSE
D1840V9, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     6   1
  KIAA0355 WILD-TYPE 308  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      6    1
  KIAA0355 WILD-TYPE  308   47
                               clus
vv                              KIAA0355 MUTATED KIAA0355 WILD-TYPE
  COLON ADENOCARCINOMA                         6                308
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0355 MUTATED     5   0   1   0
  KIAA0355 WILD-TYPE 254   3  21  21
D1840V10, multiclass
    clus
vv   KIAA0355 MUTATED KIAA0355 WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                1                 21
  RX                0                 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"
D1840V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0355 MUTATED                                  0     0
  KIAA0355 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0355 MUTATED                           0     4
  KIAA0355 WILD-TYPE                        19   172
D1840V12, multiclass
                                  clus
vv                                 KIAA0355 MUTATED KIAA0355 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           4                172
[1] 4 2
[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 = SLC17A6 MUTATION ANALYSIS
D1841V1, survival
                   sevent
clus2                 0   1
  SLC17A6 MUTATED    10   3
  SLC17A6 WILD-TYPE 267  75
  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
               13               342 
  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
                3                75 
$`SLC17A6 MUTATED`
TCGA-G4-6586 TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3815 TCGA-AY-6197 TCGA-CA-6717 
       35.80        25.18        20.12        33.04        21.44        12.76 
TCGA-CM-4747 TCGA-CM-5861 TCGA-CM-6167 TCGA-D5-5538 TCGA-DM-A1DA TCGA-F4-6570 
       25.02        15.02        14.99        54.61         7.50         6.18 
TCGA-G4-6309 
       85.48 

$`SLC17A6 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.08        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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-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        14.04        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-D5-5539 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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        13.78        46.75 

  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
             6.18              0.00 
  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
            85.48            148.01 
  SLC17A6 MUTATED SLC17A6 WILD-TYPE 
           21.440            22.075 
[1] "6.2 - 85.5 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1841V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC17A6 MUTATED         0        0        0         7         0         0
  SLC17A6 WILD-TYPE      64        1       26       101         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC17A6 MUTATED           0          0          2          2        0
  SLC17A6 WILD-TYPE        18          6         42         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC17A6 MUTATED           2         0
  SLC17A6 WILD-TYPE        10         1
D1841V3, multiclass
            clus
vv           SLC17A6 MUTATED SLC17A6 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                7               101
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                2                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
  SLC17A6 MUTATED     0   0  12   1
  SLC17A6 WILD-TYPE   9  67 237  40
D1841V4, multiclass
    clus
vv   SLC17A6 MUTATED SLC17A6 WILD-TYPE
  T1               0                 9
  T2               0                67
  T3              12               237
  T4               1                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
  SLC17A6 MUTATED     8   3   2
  SLC17A6 WILD-TYPE 212  78  64
D1841V5, multiclass
    clus
vv   SLC17A6 MUTATED SLC17A6 WILD-TYPE
  N0               8               212
  N1               3                78
  N2               2                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1841V6, binary
                   cls
clus                  0   1
  SLC17A6 MUTATED     9   2
  SLC17A6 WILD-TYPE 276  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A6 MUTATED      9    2
  SLC17A6 WILD-TYPE  276   46
   clus
vv  SLC17A6 MUTATED SLC17A6 WILD-TYPE
  0               9               276
  1               2                46
[1] 2 2
[1] FALSE
D1841V7, binary
                   cls
clus                  0   1
  SLC17A6 MUTATED     8   5
  SLC17A6 WILD-TYPE 162 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A6 MUTATED      8    5
  SLC17A6 WILD-TYPE  162  192
        clus
vv       SLC17A6 MUTATED SLC17A6 WILD-TYPE
  FEMALE               8               162
  MALE                 5               192
[1] 2 2
[1] FALSE
D1841V8, binary
                   cls
clus                  0   1
  SLC17A6 MUTATED    12   0
  SLC17A6 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A6 MUTATED     12    0
  SLC17A6 WILD-TYPE  288    8
     clus
vv    SLC17A6 MUTATED SLC17A6 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D1841V9, binary
                   cls
clus                  0   1
  SLC17A6 MUTATED    11   2
  SLC17A6 WILD-TYPE 303  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC17A6 MUTATED     11    2
  SLC17A6 WILD-TYPE  303   46
                               clus
vv                              SLC17A6 MUTATED SLC17A6 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC17A6 MUTATED     9   0   0   1
  SLC17A6 WILD-TYPE 250   3  22  20
D1841V10, multiclass
    clus
vv   SLC17A6 MUTATED SLC17A6 WILD-TYPE
  R0               9               250
  R1               0                 3
  R2               0                22
  RX               1                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"
D1841V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC17A6 MUTATED                                  0     1
  SLC17A6 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC17A6 MUTATED                           2     9
  SLC17A6 WILD-TYPE                        17   167
D1841V12, multiclass
                                  clus
vv                                 SLC17A6 MUTATED SLC17A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          9               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(1842) Variable = HDAC2 MUTATION ANALYSIS
D1842V1, survival
                 sevent
clus2               0   1
  HDAC2 MUTATED     5   2
  HDAC2 WILD-TYPE 272  76
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              7             348 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
              2              76 
$`HDAC2 MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5348 TCGA-D5-6535 
       19.04        34.98        49.41        12.76        22.98        15.12 
TCGA-F4-6703 
       47.87 

$`HDAC2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HDAC2 MUTATED HDAC2 WILD-TYPE 
          12.76            0.00 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
          49.41          148.01 
  HDAC2 MUTATED HDAC2 WILD-TYPE 
         22.980          22.045 
[1] "12.8 - 49.4 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1842V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HDAC2 MUTATED         0        0        2         2         1         0
  HDAC2 WILD-TYPE      64        1       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HDAC2 MUTATED           0          0          2          0        0         0
  HDAC2 WILD-TYPE        18          6         42         33       35        12
                 vv
clus              STAGE IVB
  HDAC2 MUTATED           0
  HDAC2 WILD-TYPE         1
D1842V3, multiclass
            clus
vv           HDAC2 MUTATED HDAC2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  HDAC2 MUTATED     0   0   6   1
  HDAC2 WILD-TYPE   9  67 243  40
D1842V4, multiclass
    clus
vv   HDAC2 MUTATED HDAC2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  HDAC2 MUTATED     5   2   0
  HDAC2 WILD-TYPE 215  79  66
D1842V5, multiclass
    clus
vv   HDAC2 MUTATED HDAC2 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1842V6, binary
                 cls
clus                0   1
  HDAC2 MUTATED     5   0
  HDAC2 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      5    0
  HDAC2 WILD-TYPE  280   48
   clus
vv  HDAC2 MUTATED HDAC2 WILD-TYPE
  0             5             280
  1             0              48
[1] 2 2
[1] FALSE
D1842V7, binary
                 cls
clus                0   1
  HDAC2 MUTATED     3   4
  HDAC2 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      3    4
  HDAC2 WILD-TYPE  167  193
        clus
vv       HDAC2 MUTATED HDAC2 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1842V8, binary
                 cls
clus                0   1
  HDAC2 MUTATED     7   0
  HDAC2 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      7    0
  HDAC2 WILD-TYPE  293    8
     clus
vv    HDAC2 MUTATED HDAC2 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1842V9, binary
                 cls
clus                0   1
  HDAC2 MUTATED     6   1
  HDAC2 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC2 MUTATED      6    1
  HDAC2 WILD-TYPE  308   47
                               clus
vv                              HDAC2 MUTATED HDAC2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HDAC2 MUTATED     4   0   0   2
  HDAC2 WILD-TYPE 255   3  22  19
D1842V10, multiclass
    clus
vv   HDAC2 MUTATED HDAC2 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             2              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"
D1842V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC2 MUTATED                                  0     1
  HDAC2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HDAC2 MUTATED                           0     4
  HDAC2 WILD-TYPE                        19   172
D1842V12, multiclass
                                  clus
vv                                 HDAC2 MUTATED HDAC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = F9 MUTATION ANALYSIS
D1843V1, survival
              sevent
clus2            0   1
  F9 MUTATED    11   7
  F9 WILD-TYPE 266  71
  F9 MUTATED F9 WILD-TYPE 
          18          337 
  F9 MUTATED F9 WILD-TYPE 
           7           71 
$`F9 MUTATED`
TCGA-AZ-6608 TCGA-A6-2671 TCGA-A6-6141 TCGA-AA-3821 TCGA-AA-3852 TCGA-AA-3977 
        1.94        43.76         8.38         1.02         0.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-6747 TCGA-D5-6924 
        4.01        34.98        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 

$`F9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75       100.01        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       10.13        12.43         9.04        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-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-F4-6569 
       35.97        60.79       117.07        98.24         8.61        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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       53.62        44.68        55.04        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  F9 MUTATED F9 WILD-TYPE 
           0            0 
  F9 MUTATED F9 WILD-TYPE 
       85.48       148.01 
  F9 MUTATED F9 WILD-TYPE 
      12.675       22.090 
[1] "0.0 - 85.5 (12.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1843V2, continuous
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F9 MUTATED         1        0        0        10         2         0
  F9 WILD-TYPE      63        1       26        98         6         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        18          5         42         33       34        12
              vv
clus           STAGE IVB
  F9 MUTATED           0
  F9 WILD-TYPE         1
D1843V3, multiclass
            clus
vv           F9 MUTATED F9 WILD-TYPE
  STAGE I             1           63
  STAGE IA            0            1
  STAGE II            0           26
  STAGE IIA          10           98
  STAGE IIB           2            6
  STAGE IIC           0            1
  STAGE III           0           18
  STAGE IIIA          1            5
  STAGE IIIB          2           42
  STAGE IIIC          0           33
  STAGE IV            1           34
  STAGE IVA           0           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
  F9 MUTATED     0   3  14   2
  F9 WILD-TYPE   9  64 235  39
D1843V4, multiclass
    clus
vv   F9 MUTATED F9 WILD-TYPE
  T1          0            9
  T2          3           64
  T3         14          235
  T4          2           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
  F9 MUTATED    14   4   1
  F9 WILD-TYPE 206  77  65
D1843V5, multiclass
    clus
vv   F9 MUTATED F9 WILD-TYPE
  N0         14          206
  N1          4           77
  N2          1           65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1843V6, binary
              cls
clus             0   1
  F9 MUTATED    15   1
  F9 WILD-TYPE 270  47
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     15    1
  F9 WILD-TYPE  270   47
   clus
vv  F9 MUTATED F9 WILD-TYPE
  0         15          270
  1          1           47
[1] 2 2
[1] FALSE
D1843V7, binary
              cls
clus             0   1
  F9 MUTATED     9  10
  F9 WILD-TYPE 161 187
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED      9   10
  F9 WILD-TYPE  161  187
        clus
vv       F9 MUTATED F9 WILD-TYPE
  FEMALE          9          161
  MALE           10          187
[1] 2 2
[1] FALSE
D1843V8, binary
              cls
clus             0   1
  F9 MUTATED    15   0
  F9 WILD-TYPE 285   8
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     15    0
  F9 WILD-TYPE  285    8
     clus
vv    F9 MUTATED F9 WILD-TYPE
  NO          15          285
  YES          0            8
[1] 2 2
[1] FALSE
D1843V9, binary
              cls
clus             0   1
  F9 MUTATED    15   4
  F9 WILD-TYPE 299  44
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     15    4
  F9 WILD-TYPE  299   44
                               clus
vv                              F9 MUTATED F9 WILD-TYPE
  COLON ADENOCARCINOMA                  15          299
  COLON MUCINOUS ADENOCARCINOMA          4           44
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  F9 MUTATED    12   0   0   3
  F9 WILD-TYPE 247   3  22  18
D1843V10, multiclass
    clus
vv   F9 MUTATED F9 WILD-TYPE
  R0         12          247
  R1          0            3
  R2          0           22
  RX          3           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"
D1843V11, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F9 MUTATED                                  0     2                         2
  F9 WILD-TYPE                                1     8                        17
              vv
clus           WHITE
  F9 MUTATED       9
  F9 WILD-TYPE   167
D1843V12, multiclass
                                  clus
vv                                 F9 MUTATED F9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     2            8
  BLACK OR AFRICAN AMERICAN                 2           17
  WHITE                                     9          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(1844) Variable = ZNF185 MUTATION ANALYSIS
D1844V1, survival
                  sevent
clus2                0   1
  ZNF185 MUTATED     9   0
  ZNF185 WILD-TYPE 268  78
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               9              346 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               0               78 
$`ZNF185 MUTATED`
TCGA-AA-3697 TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3710 TCGA-AA-3947 TCGA-AD-5900 
       85.05        22.06        22.52        26.99        33.01        12.16 
TCGA-CM-6675 TCGA-D5-6920 TCGA-G4-6299 
       13.05        12.39        74.56 

$`ZNF185 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 
       33.53        23.61        22.09        32.71        27.09         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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         7.53        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF185 MUTATED ZNF185 WILD-TYPE 
           12.16             0.00 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           85.05           148.01 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           22.52            22.01 
[1] "12.2 - 85.0 (22.5)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D1844V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF185 MUTATED         2        0        1         4         1         0
  ZNF185 WILD-TYPE      62        1       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF185 MUTATED           0          0          0          1        0
  ZNF185 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF185 MUTATED           0         1
  ZNF185 WILD-TYPE        12         0
D1844V3, multiclass
            clus
vv           ZNF185 MUTATED ZNF185 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               4              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               12
  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
  ZNF185 MUTATED     0   2   7   1
  ZNF185 WILD-TYPE   9  65 242  40
D1844V4, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              7              242
  T4              1               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
  ZNF185 MUTATED     8   0   2
  ZNF185 WILD-TYPE 212  81  64
D1844V5, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  N0              8              212
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1844V6, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     8   1
  ZNF185 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      8    1
  ZNF185 WILD-TYPE  277   47
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0              8              277
  1              1               47
[1] 2 2
[1] FALSE
D1844V7, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     5   5
  ZNF185 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      5    5
  ZNF185 WILD-TYPE  165  192
        clus
vv       ZNF185 MUTATED ZNF185 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D1844V8, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     9   0
  ZNF185 WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      9    0
  ZNF185 WILD-TYPE  291    8
     clus
vv    ZNF185 MUTATED ZNF185 WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1844V9, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     8   2
  ZNF185 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      8    2
  ZNF185 WILD-TYPE  306   46
                               clus
vv                              ZNF185 MUTATED ZNF185 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF185 MUTATED     9   0   0   0
  ZNF185 WILD-TYPE 250   3  22  21
D1844V10, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D1844V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF185 MUTATED                                  0     0
  ZNF185 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF185 MUTATED                           1     5
  ZNF185 WILD-TYPE                        18   171
D1844V12, multiclass
                                  clus
vv                                 ZNF185 MUTATED ZNF185 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = NXT1 MUTATION ANALYSIS
D1845V1, survival
                sevent
clus2              0   1
  NXT1 MUTATED     3   2
  NXT1 WILD-TYPE 274  76
  NXT1 MUTATED NXT1 WILD-TYPE 
             5            350 
  NXT1 MUTATED NXT1 WILD-TYPE 
             2             76 
$`NXT1 MUTATED`
TCGA-G4-6310 TCGA-AA-A01D TCGA-D5-6532 TCGA-D5-6928 TCGA-DM-A1DA 
       63.62        10.98        18.25        11.64         7.50 

$`NXT1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6321 
      106.75       100.01         1.94        49.08         5.88        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  NXT1 MUTATED NXT1 WILD-TYPE 
           7.5            0.0 
  NXT1 MUTATED NXT1 WILD-TYPE 
         63.62         148.01 
  NXT1 MUTATED NXT1 WILD-TYPE 
         11.64          22.09 
[1] "7.5 - 63.6 (11.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.1"
D1845V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NXT1 MUTATED         0        0        0         2         0         0
  NXT1 WILD-TYPE      64        1       26       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NXT1 MUTATED           0          0          1          2        0         0
  NXT1 WILD-TYPE        18          6         43         31       35        12
                vv
clus             STAGE IVB
  NXT1 MUTATED           0
  NXT1 WILD-TYPE         1
D1845V3, multiclass
            clus
vv           NXT1 MUTATED NXT1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             2            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            2             31
  STAGE IV              0             35
  STAGE IVA             0             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
  NXT1 MUTATED     0   0   5   0
  NXT1 WILD-TYPE   9  67 244  41
D1845V4, multiclass
    clus
vv   NXT1 MUTATED NXT1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3            5            244
  T4            0             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
  NXT1 MUTATED     2   1   2
  NXT1 WILD-TYPE 218  80  64
D1845V5, multiclass
    clus
vv   NXT1 MUTATED NXT1 WILD-TYPE
  N0            2            218
  N1            1             80
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1845V6, binary
                cls
clus               0   1
  NXT1 MUTATED     5   0
  NXT1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXT1 MUTATED      5    0
  NXT1 WILD-TYPE  280   48
   clus
vv  NXT1 MUTATED NXT1 WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1845V7, binary
                cls
clus               0   1
  NXT1 MUTATED     2   3
  NXT1 WILD-TYPE 168 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXT1 MUTATED      2    3
  NXT1 WILD-TYPE  168  194
        clus
vv       NXT1 MUTATED NXT1 WILD-TYPE
  FEMALE            2            168
  MALE              3            194
[1] 2 2
[1] FALSE
D1845V8, binary
                cls
clus               0   1
  NXT1 MUTATED     3   1
  NXT1 WILD-TYPE 297   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXT1 MUTATED      3    1
  NXT1 WILD-TYPE  297    7
     clus
vv    NXT1 MUTATED NXT1 WILD-TYPE
  NO             3            297
  YES            1              7
[1] 2 2
[1] FALSE
D1845V9, binary
                cls
clus               0   1
  NXT1 MUTATED     3   2
  NXT1 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXT1 MUTATED      3    2
  NXT1 WILD-TYPE  311   46
                               clus
vv                              NXT1 MUTATED NXT1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NXT1 MUTATED     4   0   0   0
  NXT1 WILD-TYPE 255   3  22  21
D1845V10, multiclass
    clus
vv   NXT1 MUTATED NXT1 WILD-TYPE
  R0            4            255
  R1            0              3
  R2            0             22
  RX            0             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"
D1845V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NXT1 MUTATED                                  0     0
  NXT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NXT1 MUTATED                           0     4
  NXT1 WILD-TYPE                        19   172
D1845V12, multiclass
                                  clus
vv                                 NXT1 MUTATED NXT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = CHGB MUTATION ANALYSIS
D1846V1, survival
                sevent
clus2              0   1
  CHGB MUTATED     8   4
  CHGB WILD-TYPE 269  74
  CHGB MUTATED CHGB WILD-TYPE 
            12            343 
  CHGB MUTATED CHGB WILD-TYPE 
             4             74 
$`CHGB MUTATED`
TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
        0.92        19.04         4.01        34.98        58.39        12.76 
TCGA-CM-5862 TCGA-D5-6923 TCGA-D5-6930 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-F4-6570 
        5.03        12.43        13.35       119.70       135.65         6.18 

$`CHGB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         7.53        12.39        10.13        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        13.41        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-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-F4-6703 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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CHGB MUTATED CHGB WILD-TYPE 
          0.92           0.00 
  CHGB MUTATED CHGB WILD-TYPE 
        135.65         148.01 
  CHGB MUTATED CHGB WILD-TYPE 
        13.055         22.090 
[1] "0.9 - 135.7 (13.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D1846V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHGB MUTATED         1        0        1         5         2         0
  CHGB WILD-TYPE      63        1       25       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHGB MUTATED           1          0          1          0        0         1
  CHGB WILD-TYPE        17          6         43         33       35        11
                vv
clus             STAGE IVB
  CHGB MUTATED           0
  CHGB WILD-TYPE         1
D1846V3, multiclass
            clus
vv           CHGB MUTATED CHGB WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             1             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
  CHGB MUTATED     0   1   9   2
  CHGB WILD-TYPE   9  66 240  39
D1846V4, multiclass
    clus
vv   CHGB MUTATED CHGB WILD-TYPE
  T1            0              9
  T2            1             66
  T3            9            240
  T4            2             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
  CHGB MUTATED     9   3   0
  CHGB WILD-TYPE 211  78  66
D1846V5, multiclass
    clus
vv   CHGB MUTATED CHGB WILD-TYPE
  N0            9            211
  N1            3             78
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1846V6, binary
                cls
clus               0   1
  CHGB MUTATED    11   1
  CHGB WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED     11    1
  CHGB WILD-TYPE  274   47
   clus
vv  CHGB MUTATED CHGB WILD-TYPE
  0           11            274
  1            1             47
[1] 2 2
[1] FALSE
D1846V7, binary
                cls
clus               0   1
  CHGB MUTATED     4   8
  CHGB WILD-TYPE 166 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      4    8
  CHGB WILD-TYPE  166  189
        clus
vv       CHGB MUTATED CHGB WILD-TYPE
  FEMALE            4            166
  MALE              8            189
[1] 2 2
[1] FALSE
D1846V8, binary
                cls
clus               0   1
  CHGB MUTATED     9   0
  CHGB WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      9    0
  CHGB WILD-TYPE  291    8
     clus
vv    CHGB MUTATED CHGB WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1846V9, binary
                cls
clus               0   1
  CHGB MUTATED     8   3
  CHGB WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGB MUTATED      8    3
  CHGB WILD-TYPE  306   45
                               clus
vv                              CHGB MUTATED CHGB WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHGB MUTATED     9   0   0   1
  CHGB WILD-TYPE 250   3  22  20
D1846V10, multiclass
    clus
vv   CHGB MUTATED CHGB WILD-TYPE
  R0            9            250
  R1            0              3
  R2            0             22
  RX            1             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"
D1846V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHGB MUTATED                                  0     1
  CHGB WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHGB MUTATED                           0     7
  CHGB WILD-TYPE                        19   169
D1846V12, multiclass
                                  clus
vv                                 CHGB MUTATED CHGB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       7            169
[1] 4 2
[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 = OR14J1 MUTATION ANALYSIS
D1847V1, survival
                  sevent
clus2                0   1
  OR14J1 MUTATED     7   1
  OR14J1 WILD-TYPE 270  77
  OR14J1 MUTATED OR14J1 WILD-TYPE 
               8              347 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
               1               77 
$`OR14J1 MUTATED`
TCGA-G4-6628 TCGA-A6-6652 TCGA-AA-3815 TCGA-AA-A010 TCGA-AZ-6599 TCGA-D5-6535 
       79.69        24.69        33.04        34.98         6.77        15.12 
TCGA-D5-6538 TCGA-G4-6307 
       17.13        55.04 

$`OR14J1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 
       22.52         8.38        25.08        25.18        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OR14J1 MUTATED OR14J1 WILD-TYPE 
            6.77             0.00 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
           79.69           148.01 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
          28.865           22.030 
[1] "6.8 - 79.7 (28.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1847V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR14J1 MUTATED         2        0        0         1         1         0
  OR14J1 WILD-TYPE      62        1       26       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR14J1 MUTATED           0          0          3          0        0
  OR14J1 WILD-TYPE        18          6         41         33       35
                  vv
clus               STAGE IVA STAGE IVB
  OR14J1 MUTATED           1         0
  OR14J1 WILD-TYPE        11         1
D1847V3, multiclass
            clus
vv           OR14J1 MUTATED OR14J1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  OR14J1 MUTATED     0   2   5   1
  OR14J1 WILD-TYPE   9  65 244  40
D1847V4, multiclass
    clus
vv   OR14J1 MUTATED OR14J1 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              5              244
  T4              1               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
  OR14J1 MUTATED     5   2   1
  OR14J1 WILD-TYPE 215  79  65
D1847V5, multiclass
    clus
vv   OR14J1 MUTATED OR14J1 WILD-TYPE
  N0              5              215
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1847V6, binary
                  cls
clus                 0   1
  OR14J1 MUTATED     5   1
  OR14J1 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR14J1 MUTATED      5    1
  OR14J1 WILD-TYPE  280   47
   clus
vv  OR14J1 MUTATED OR14J1 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D1847V7, binary
                  cls
clus                 0   1
  OR14J1 MUTATED     5   3
  OR14J1 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR14J1 MUTATED      5    3
  OR14J1 WILD-TYPE  165  194
        clus
vv       OR14J1 MUTATED OR14J1 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1847V8, binary
                  cls
clus                 0   1
  OR14J1 MUTATED     8   0
  OR14J1 WILD-TYPE 292   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR14J1 MUTATED      8    0
  OR14J1 WILD-TYPE  292    8
     clus
vv    OR14J1 MUTATED OR14J1 WILD-TYPE
  NO               8              292
  YES              0                8
[1] 2 2
[1] FALSE
D1847V9, binary
                  cls
clus                 0   1
  OR14J1 MUTATED     8   0
  OR14J1 WILD-TYPE 306  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR14J1 MUTATED      8    0
  OR14J1 WILD-TYPE  306   48
                               clus
vv                              OR14J1 MUTATED OR14J1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR14J1 MUTATED     5   0   0   1
  OR14J1 WILD-TYPE 254   3  22  20
D1847V10, multiclass
    clus
vv   OR14J1 MUTATED OR14J1 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D1847V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR14J1 MUTATED                                  0     0
  OR14J1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR14J1 MUTATED                           1     5
  OR14J1 WILD-TYPE                        18   171
D1847V12, multiclass
                                  clus
vv                                 OR14J1 MUTATED OR14J1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         5              171
[1] 4 2
[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 = LYST MUTATION ANALYSIS
D1848V1, survival
                sevent
clus2              0   1
  LYST MUTATED    27   6
  LYST WILD-TYPE 250  72
  LYST MUTATED LYST WILD-TYPE 
            33            322 
  LYST MUTATED LYST WILD-TYPE 
             6             72 
$`LYST MUTATED`
TCGA-AA-3525 TCGA-AA-3715 TCGA-AA-3950 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
        8.05        19.04        24.00        15.52        25.08        10.88 
TCGA-G4-6586 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6141 
       35.80        42.90        33.53        23.61        32.71         8.38 
TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3514 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3877 
       24.69        19.66         1.02        29.95         6.97        31.00 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02W 
       33.01        25.02        38.04         4.01        34.98        41.00 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 
       27.09        21.44        58.39        49.41        12.76        15.62 
TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-6928 
       14.99        14.04        11.64 

$`LYST WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 
       36.53        32.91        31.63        30.44        29.19        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       22.06        27.09        22.52        25.08        25.18        21.76 
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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        24.00        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       27.02        18.05         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01         0.92        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        26.47        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01         0.20        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  LYST MUTATED LYST WILD-TYPE 
          1.02           0.00 
  LYST MUTATED LYST WILD-TYPE 
         58.39         148.01 
  LYST MUTATED LYST WILD-TYPE 
         24.00          22.01 
[1] "1.0 - 58.4 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1848V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LYST MUTATED         5        0        3        11         4         1
  LYST WILD-TYPE      59        1       23        97         4         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LYST MUTATED           0          0          3          3        0         2
  LYST WILD-TYPE        18          6         41         30       35        10
                vv
clus             STAGE IVB
  LYST MUTATED           0
  LYST WILD-TYPE         1
D1848V3, multiclass
            clus
vv           LYST MUTATED LYST WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             23
  STAGE IIA            11             97
  STAGE IIB             4              4
  STAGE IIC             1              0
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            3             30
  STAGE IV              0             35
  STAGE IVA             2             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
  LYST MUTATED     1   5  20   8
  LYST WILD-TYPE   8  62 229  33
D1848V4, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  T1            1              8
  T2            5             62
  T3           20            229
  T4            8             33
[1] 4 2
[1] TRUE
[1] "dimension 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    26   4   4
  LYST WILD-TYPE 194  77  62
D1848V5, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  N0           26            194
  N1            4             77
  N2            4             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1848V6, binary
                cls
clus               0   1
  LYST MUTATED    27   2
  LYST WILD-TYPE 258  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     27    2
  LYST WILD-TYPE  258   46
   clus
vv  LYST MUTATED LYST WILD-TYPE
  0           27            258
  1            2             46
[1] 2 2
[1] FALSE
D1848V7, binary
                cls
clus               0   1
  LYST MUTATED    16  18
  LYST WILD-TYPE 154 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     16   18
  LYST WILD-TYPE  154  179
        clus
vv       LYST MUTATED LYST WILD-TYPE
  FEMALE           16            154
  MALE             18            179
[1] 2 2
[1] FALSE
D1848V8, binary
                cls
clus               0   1
  LYST MUTATED    30   0
  LYST WILD-TYPE 270   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     30    0
  LYST WILD-TYPE  270    8
     clus
vv    LYST MUTATED LYST WILD-TYPE
  NO            30            270
  YES            0              8
[1] 2 2
[1] FALSE
D1848V9, binary
                cls
clus               0   1
  LYST MUTATED    25   9
  LYST WILD-TYPE 289  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     25    9
  LYST WILD-TYPE  289   39
                               clus
vv                              LYST MUTATED LYST WILD-TYPE
  COLON ADENOCARCINOMA                    25            289
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LYST MUTATED    25   0   0   2
  LYST WILD-TYPE 234   3  22  19
D1848V10, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  R0           25            234
  R1            0              3
  R2            0             22
  RX            2             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"
D1848V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LYST MUTATED                                  0     1
  LYST WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LYST MUTATED                           4    15
  LYST WILD-TYPE                        15   161
D1848V12, multiclass
                                  clus
vv                                 LYST MUTATED LYST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      15            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(1849) Variable = PPP2R2B MUTATION ANALYSIS
D1849V1, survival
                   sevent
clus2                 0   1
  PPP2R2B MUTATED     5   3
  PPP2R2B WILD-TYPE 272  75
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
                8               347 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
                3                75 
$`PPP2R2B MUTATED`
TCGA-AD-6895 TCGA-AD-6964 TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3877 TCGA-AD-6889 
       25.08        10.88        30.44        24.39        31.00        83.24 
TCGA-D5-6927 TCGA-DM-A1D6 
        9.44        49.91 

$`PPP2R2B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6601 
       21.99        39.06        21.37        15.52       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6654 TCGA-A6-6780 
       25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
             9.44              0.00 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
            83.24            148.01 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
            27.76             21.99 
[1] "9.4 - 83.2 (27.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1849V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP2R2B MUTATED         3        0        0         3         0         0
  PPP2R2B WILD-TYPE      61        1       26       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R2B MUTATED           0          0          1          0        0
  PPP2R2B WILD-TYPE        18          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R2B MUTATED           0         0
  PPP2R2B WILD-TYPE        12         1
D1849V3, multiclass
            clus
vv           PPP2R2B MUTATED PPP2R2B WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  PPP2R2B MUTATED     1   2   4   1
  PPP2R2B WILD-TYPE   8  65 245  40
D1849V4, multiclass
    clus
vv   PPP2R2B MUTATED PPP2R2B WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               4               245
  T4               1                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
  PPP2R2B MUTATED     6   1   1
  PPP2R2B WILD-TYPE 214  80  65
D1849V5, multiclass
    clus
vv   PPP2R2B MUTATED PPP2R2B WILD-TYPE
  N0               6               214
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1849V6, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     7   0
  PPP2R2B WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      7    0
  PPP2R2B WILD-TYPE  278   48
   clus
vv  PPP2R2B MUTATED PPP2R2B WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D1849V7, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     1   7
  PPP2R2B WILD-TYPE 169 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      1    7
  PPP2R2B WILD-TYPE  169  190
        clus
vv       PPP2R2B MUTATED PPP2R2B WILD-TYPE
  FEMALE               1               169
  MALE                 7               190
[1] 2 2
[1] FALSE
D1849V8, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     7   0
  PPP2R2B WILD-TYPE 293   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      7    0
  PPP2R2B WILD-TYPE  293    8
     clus
vv    PPP2R2B MUTATED PPP2R2B WILD-TYPE
  NO                7               293
  YES               0                 8
[1] 2 2
[1] FALSE
D1849V9, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     6   2
  PPP2R2B WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      6    2
  PPP2R2B WILD-TYPE  308   46
                               clus
vv                              PPP2R2B MUTATED PPP2R2B WILD-TYPE
  COLON ADENOCARCINOMA                        6               308
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PPP2R2B MUTATED     5   0   0   0
  PPP2R2B WILD-TYPE 254   3  22  21
D1849V10, multiclass
    clus
vv   PPP2R2B MUTATED PPP2R2B WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1849V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R2B MUTATED                                  0     1
  PPP2R2B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R2B MUTATED                           0     6
  PPP2R2B WILD-TYPE                        19   170
D1849V12, multiclass
                                  clus
vv                                 PPP2R2B MUTATED PPP2R2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = ACTBL2 MUTATION ANALYSIS
D1850V1, survival
                  sevent
clus2                0   1
  ACTBL2 MUTATED    14   1
  ACTBL2 WILD-TYPE 263  77
  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
              15              340 
  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
               1               77 
$`ACTBL2 MUTATED`
TCGA-A6-6653 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-3977 
       24.39        26.99        33.04         1.02        33.01        25.02 
TCGA-AA-A00E TCGA-AA-A00J TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-6169 TCGA-D5-6532 
       30.02        18.05       124.27        22.98        13.02        18.25 
TCGA-D5-6928 TCGA-F4-6570 TCGA-G4-6309 
       11.64         6.18        85.48 

$`ACTBL2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        10.06        35.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        19.00        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95         2.01        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        14.04        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        54.61        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 
       25.48        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         7.53        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       43.04        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-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
            1.02             0.00 
  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
          124.27           148.01 
  ACTBL2 MUTATED ACTBL2 WILD-TYPE 
           24.39            22.01 
[1] "1.0 - 124.3 (24.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.7"
D1850V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTBL2 MUTATED         3        0        0         8         1         0
  ACTBL2 WILD-TYPE      61        1       26       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTBL2 MUTATED           0          0          3          0        0
  ACTBL2 WILD-TYPE        18          6         41         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ACTBL2 MUTATED           0         0
  ACTBL2 WILD-TYPE        12         1
D1850V3, multiclass
            clus
vv           ACTBL2 MUTATED ACTBL2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               8              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              3               41
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  ACTBL2 MUTATED     0   4  10   2
  ACTBL2 WILD-TYPE   9  63 239  39
D1850V4, multiclass
    clus
vv   ACTBL2 MUTATED ACTBL2 WILD-TYPE
  T1              0                9
  T2              4               63
  T3             10              239
  T4              2               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
  ACTBL2 MUTATED    13   3   0
  ACTBL2 WILD-TYPE 207  78  66
D1850V5, multiclass
    clus
vv   ACTBL2 MUTATED ACTBL2 WILD-TYPE
  N0             13              207
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1850V6, binary
                  cls
clus                 0   1
  ACTBL2 MUTATED    14   0
  ACTBL2 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTBL2 MUTATED     14    0
  ACTBL2 WILD-TYPE  271   48
   clus
vv  ACTBL2 MUTATED ACTBL2 WILD-TYPE
  0             14              271
  1              0               48
[1] 2 2
[1] FALSE
D1850V7, binary
                  cls
clus                 0   1
  ACTBL2 MUTATED     8   8
  ACTBL2 WILD-TYPE 162 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTBL2 MUTATED      8    8
  ACTBL2 WILD-TYPE  162  189
        clus
vv       ACTBL2 MUTATED ACTBL2 WILD-TYPE
  FEMALE              8              162
  MALE                8              189
[1] 2 2
[1] FALSE
D1850V8, binary
                  cls
clus                 0   1
  ACTBL2 MUTATED    15   0
  ACTBL2 WILD-TYPE 285   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTBL2 MUTATED     15    0
  ACTBL2 WILD-TYPE  285    8
     clus
vv    ACTBL2 MUTATED ACTBL2 WILD-TYPE
  NO              15              285
  YES              0                8
[1] 2 2
[1] FALSE
D1850V9, binary
                  cls
clus                 0   1
  ACTBL2 MUTATED    11   5
  ACTBL2 WILD-TYPE 303  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTBL2 MUTATED     11    5
  ACTBL2 WILD-TYPE  303   43
                               clus
vv                              ACTBL2 MUTATED ACTBL2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              303
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACTBL2 MUTATED    13   0   0   1
  ACTBL2 WILD-TYPE 246   3  22  20
D1850V10, multiclass
    clus
vv   ACTBL2 MUTATED ACTBL2 WILD-TYPE
  R0             13              246
  R1              0                3
  R2              0               22
  RX              1               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"
D1850V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTBL2 MUTATED                                  0     0
  ACTBL2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTBL2 MUTATED                           2     6
  ACTBL2 WILD-TYPE                        17   170
D1850V12, multiclass
                                  clus
vv                                 ACTBL2 MUTATED ACTBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         6              170
[1] 4 2
[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 = C9ORF41 MUTATION ANALYSIS
D1851V1, survival
                   sevent
clus2                 0   1
  C9ORF41 MUTATED    10   0
  C9ORF41 WILD-TYPE 267  78
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
               10               345 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                0                78 
$`C9ORF41 MUTATED`
TCGA-AA-3672 TCGA-A6-3809 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
        0.92        32.75        25.02        34.98        58.39        12.76 
TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A1HB TCGA-DM-A282 
       15.12        11.38       135.65       139.17 

$`C9ORF41 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       44.32       131.51        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
             0.92              0.00 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
           139.17            148.01 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
           28.885            22.030 
[1] "0.9 - 139.2 (28.9)" "0.0 - 148.0 (22.0)"
[1] "hr="     "2.6e+07"
D1851V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF41 MUTATED         0        0        0         4         2         0
  C9ORF41 WILD-TYPE      64        1       26       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF41 MUTATED           1          0          2          0        0
  C9ORF41 WILD-TYPE        17          6         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF41 MUTATED           0         0
  C9ORF41 WILD-TYPE        12         1
D1851V3, multiclass
            clus
vv           C9ORF41 MUTATED C9ORF41 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                4               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  C9ORF41 MUTATED     0   1   7   2
  C9ORF41 WILD-TYPE   9  66 242  39
D1851V4, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               7               242
  T4               2                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
  C9ORF41 MUTATED     7   3   0
  C9ORF41 WILD-TYPE 213  78  66
D1851V5, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  N0               7               213
  N1               3                78
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1851V6, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     8   0
  C9ORF41 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      8    0
  C9ORF41 WILD-TYPE  277   48
   clus
vv  C9ORF41 MUTATED C9ORF41 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D1851V7, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     5   5
  C9ORF41 WILD-TYPE 165 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      5    5
  C9ORF41 WILD-TYPE  165  192
        clus
vv       C9ORF41 MUTATED C9ORF41 WILD-TYPE
  FEMALE               5               165
  MALE                 5               192
[1] 2 2
[1] FALSE
D1851V8, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     8   0
  C9ORF41 WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      8    0
  C9ORF41 WILD-TYPE  292    8
     clus
vv    C9ORF41 MUTATED C9ORF41 WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1851V9, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     7   2
  C9ORF41 WILD-TYPE 307  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      7    2
  C9ORF41 WILD-TYPE  307   46
                               clus
vv                              C9ORF41 MUTATED C9ORF41 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C9ORF41 MUTATED     5   0   0   2
  C9ORF41 WILD-TYPE 254   3  22  19
D1851V10, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               2                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"
D1851V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF41 MUTATED                                  0     1
  C9ORF41 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C9ORF41 MUTATED                           0     6
  C9ORF41 WILD-TYPE                        19   170
D1851V12, multiclass
                                  clus
vv                                 C9ORF41 MUTATED C9ORF41 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = BATF3 MUTATION ANALYSIS
D1852V1, survival
                 sevent
clus2               0   1
  BATF3 MUTATED     2   1
  BATF3 WILD-TYPE 275  77
  BATF3 MUTATED BATF3 WILD-TYPE 
              3             352 
  BATF3 MUTATED BATF3 WILD-TYPE 
              1              77 
$`BATF3 MUTATED`
TCGA-AA-3818 TCGA-AZ-4315 TCGA-CM-4743 
        0.99        58.39        23.05 

$`BATF3 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  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          22.045 
[1] "1.0 - 58.4 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1852V2, continuous
                 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      64        1       26       105         7         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        18          6         44         33       35        12
                 vv
clus              STAGE IVB
  BATF3 MUTATED           0
  BATF3 WILD-TYPE         1
D1852V3, multiclass
            clus
vv           BATF3 MUTATED BATF3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  BATF3 MUTATED     0   0   3   1
  BATF3 WILD-TYPE   9  67 246  40
D1852V4, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             3             246
  T4             1              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
  BATF3 MUTATED     4   0   0
  BATF3 WILD-TYPE 216  81  66
D1852V5, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  N0             4             216
  N1             0              81
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1852V6, binary
                 cls
clus                0   1
  BATF3 MUTATED     3   0
  BATF3 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      3    0
  BATF3 WILD-TYPE  282   48
   clus
vv  BATF3 MUTATED BATF3 WILD-TYPE
  0             3             282
  1             0              48
[1] 2 2
[1] FALSE
D1852V7, binary
                 cls
clus                0   1
  BATF3 MUTATED     2   2
  BATF3 WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      2    2
  BATF3 WILD-TYPE  168  195
        clus
vv       BATF3 MUTATED BATF3 WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D1852V8, binary
                 cls
clus                0   1
  BATF3 MUTATED     2   0
  BATF3 WILD-TYPE 298   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      2    0
  BATF3 WILD-TYPE  298    8
     clus
vv    BATF3 MUTATED BATF3 WILD-TYPE
  NO              2             298
  YES             0               8
[1] 2 2
[1] FALSE
D1852V9, binary
                 cls
clus                0   1
  BATF3 MUTATED     4   0
  BATF3 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      4    0
  BATF3 WILD-TYPE  310   48
                               clus
vv                              BATF3 MUTATED BATF3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BATF3 MUTATED     3   0   0   1
  BATF3 WILD-TYPE 256   3  22  20
D1852V10, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1852V11, continuous
[1] "Remove cluster labels:" "BATF3 MUTATED"         
clus
  BATF3 MUTATED BATF3 WILD-TYPE 
              2             344 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AA-3496 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3516      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-3527      TCGA-AA-3530 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3531      TCGA-AA-3543      TCGA-AA-3552      TCGA-AA-3554 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3662 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3697 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3814      TCGA-AA-3844 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3867      TCGA-AA-3870      TCGA-AA-3939 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3972      TCGA-AA-3976 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3986      TCGA-AA-A00L      TCGA-AA-A00Z 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6895 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6964      TCGA-AZ-6601      TCGA-AZ-6608      TCGA-DM-A285 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-2683 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810 
"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-A6-6651      TCGA-A6-6652 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3502 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3526      TCGA-AA-3529 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3553 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3655      TCGA-AA-3660 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3693 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3710      TCGA-AA-3712 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3815      TCGA-AA-3819 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3861 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3941 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      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-3973 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3975      TCGA-AA-3977      TCGA-AA-3980      TCGA-AA-3982 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3984      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-A00N      TCGA-AA-A00O 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6889 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6890      TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-6600      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-CA-6715      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-A28C      TCGA-DM-A28E 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6806      TCGA-F4-6807 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"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    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BATF3 MUTATED                           0     3
  BATF3 WILD-TYPE                        19   173
D1852V12, multiclass
                                  clus
vv                                 BATF3 MUTATED BATF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = SEC23IP MUTATION ANALYSIS
D1853V1, survival
                   sevent
clus2                 0   1
  SEC23IP MUTATED    10   6
  SEC23IP WILD-TYPE 267  72
  SEC23IP MUTATED SEC23IP WILD-TYPE 
               16               339 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
                6                72 
$`SEC23IP MUTATED`
TCGA-AA-3496 TCGA-AA-3516 TCGA-AZ-6608 TCGA-G4-6586 TCGA-A6-2676 TCGA-AA-3510 
        1.02        13.02         1.94        35.80        42.90        63.98 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       30.02         4.01        34.98        12.76        10.06       148.01 
TCGA-CM-5868 TCGA-D5-5541 TCGA-F4-6570 TCGA-G4-6309 
       17.03        55.92         6.18        85.48 

$`SEC23IP WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53        24.16        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       49.08         5.88        63.62        22.09        26.17        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        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-A6-6648 
       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-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
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        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SEC23IP MUTATED SEC23IP WILD-TYPE 
             1.02              0.00 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
           148.01            140.38 
  SEC23IP MUTATED SEC23IP WILD-TYPE 
           23.525            22.060 
[1] "1.0 - 148.0 (23.5)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.5"
D1853V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEC23IP MUTATED         0        0        2         5         3         0
  SEC23IP WILD-TYPE      64        1       24       103         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC23IP MUTATED           2          1          2          0        0
  SEC23IP WILD-TYPE        16          5         42         33       35
                   vv
clus                STAGE IVA STAGE IVB
  SEC23IP MUTATED           1         0
  SEC23IP WILD-TYPE        11         1
D1853V3, multiclass
            clus
vv           SEC23IP MUTATED SEC23IP WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                5               103
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               1                 5
  STAGE IIIB               2                42
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  SEC23IP MUTATED     0   1  11   4
  SEC23IP WILD-TYPE   9  66 238  37
D1853V4, multiclass
    clus
vv   SEC23IP MUTATED SEC23IP WILD-TYPE
  T1               0                 9
  T2               1                66
  T3              11               238
  T4               4                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
  SEC23IP MUTATED    10   5   1
  SEC23IP WILD-TYPE 210  76  65
D1853V5, multiclass
    clus
vv   SEC23IP MUTATED SEC23IP WILD-TYPE
  N0              10               210
  N1               5                76
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1853V6, binary
                   cls
clus                  0   1
  SEC23IP MUTATED    15   1
  SEC23IP WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED     15    1
  SEC23IP WILD-TYPE  270   47
   clus
vv  SEC23IP MUTATED SEC23IP WILD-TYPE
  0              15               270
  1               1                47
[1] 2 2
[1] FALSE
D1853V7, binary
                   cls
clus                  0   1
  SEC23IP MUTATED    10   6
  SEC23IP WILD-TYPE 160 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED     10    6
  SEC23IP WILD-TYPE  160  191
        clus
vv       SEC23IP MUTATED SEC23IP WILD-TYPE
  FEMALE              10               160
  MALE                 6               191
[1] 2 2
[1] FALSE
D1853V8, binary
                   cls
clus                  0   1
  SEC23IP MUTATED    14   0
  SEC23IP WILD-TYPE 286   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED     14    0
  SEC23IP WILD-TYPE  286    8
     clus
vv    SEC23IP MUTATED SEC23IP WILD-TYPE
  NO               14               286
  YES               0                 8
[1] 2 2
[1] FALSE
D1853V9, binary
                   cls
clus                  0   1
  SEC23IP MUTATED    13   3
  SEC23IP WILD-TYPE 301  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC23IP MUTATED     13    3
  SEC23IP WILD-TYPE  301   45
                               clus
vv                              SEC23IP MUTATED SEC23IP WILD-TYPE
  COLON ADENOCARCINOMA                       13               301
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SEC23IP MUTATED    12   0   0   2
  SEC23IP WILD-TYPE 247   3  22  19
D1853V10, multiclass
    clus
vv   SEC23IP MUTATED SEC23IP WILD-TYPE
  R0              12               247
  R1               0                 3
  R2               0                22
  RX               2                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"
D1853V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC23IP MUTATED                                  0     2
  SEC23IP WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SEC23IP MUTATED                           1     7
  SEC23IP WILD-TYPE                        18   169
D1853V12, multiclass
                                  clus
vv                                 SEC23IP MUTATED SEC23IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          7               169
[1] 4 2
[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 = GIMAP5 MUTATION ANALYSIS
D1854V1, survival
                  sevent
clus2                0   1
  GIMAP5 MUTATED     4   2
  GIMAP5 WILD-TYPE 273  76
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               6              349 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               2               76 
$`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 

$`GIMAP5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        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-A6-6138 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
            4.01             0.00 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
           32.02           148.01 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
           27.17            22.03 
[1] "4.0 - 32.0 (27.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1854V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GIMAP5 MUTATED         2        0        0         1         1         0
  GIMAP5 WILD-TYPE      62        1       26       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIMAP5 MUTATED           1          0          1          0        0
  GIMAP5 WILD-TYPE        17          6         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  GIMAP5 MUTATED           0         0
  GIMAP5 WILD-TYPE        12         1
D1854V3, multiclass
            clus
vv           GIMAP5 MUTATED GIMAP5 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  GIMAP5 MUTATED     0   2   3   1
  GIMAP5 WILD-TYPE   9  65 246  40
D1854V4, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  T1              0                9
  T2              2               65
  T3              3              246
  T4              1               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
  GIMAP5 MUTATED     4   1   1
  GIMAP5 WILD-TYPE 216  80  65
D1854V5, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  N0              4              216
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1854V6, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     6   0
  GIMAP5 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      6    0
  GIMAP5 WILD-TYPE  279   48
   clus
vv  GIMAP5 MUTATED GIMAP5 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1854V7, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     2   4
  GIMAP5 WILD-TYPE 168 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      2    4
  GIMAP5 WILD-TYPE  168  193
        clus
vv       GIMAP5 MUTATED GIMAP5 WILD-TYPE
  FEMALE              2              168
  MALE                4              193
[1] 2 2
[1] FALSE
D1854V8, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     5   0
  GIMAP5 WILD-TYPE 295   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      5    0
  GIMAP5 WILD-TYPE  295    8
     clus
vv    GIMAP5 MUTATED GIMAP5 WILD-TYPE
  NO               5              295
  YES              0                8
[1] 2 2
[1] FALSE
D1854V9, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     4   2
  GIMAP5 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      4    2
  GIMAP5 WILD-TYPE  310   46
                               clus
vv                              GIMAP5 MUTATED GIMAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       4              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GIMAP5 MUTATED     5   0   0   0
  GIMAP5 WILD-TYPE 254   3  22  21
D1854V10, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1854V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GIMAP5 MUTATED                                  0     0
  GIMAP5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GIMAP5 MUTATED                           0     2
  GIMAP5 WILD-TYPE                        19   174
D1854V12, multiclass
[1] "Remove cluster labels:" "GIMAP5 MUTATED"        
clus
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2678       TCGA-A6-2683 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810 
"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-A6-6651       TCGA-A6-6652       TCGA-A6-6654 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899       TCGA-AD-6901 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6603 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       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-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 

Clustering(1855) Variable = FAM91A1 MUTATION ANALYSIS
D1855V1, survival
                   sevent
clus2                 0   1
  FAM91A1 MUTATED     5   5
  FAM91A1 WILD-TYPE 272  73
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               10               345 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
                5                73 
$`FAM91A1 MUTATED`
TCGA-A6-4105 TCGA-AD-6964 TCGA-AA-3815 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 
       14.53        10.88        33.04        34.98        83.24        58.39 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-D5-6532 TCGA-DM-A1D4 
        6.77        12.76        18.25        92.75 

$`FAM91A1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        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-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
             6.77              0.00 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
            92.75            148.01 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
           25.645            22.060 
[1] "6.8 - 92.8 (25.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D1855V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM91A1 MUTATED         1        0        0         7         1         0
  FAM91A1 WILD-TYPE      63        1       26       101         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM91A1 MUTATED           0          0          0          0        0
  FAM91A1 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM91A1 MUTATED           0         0
  FAM91A1 WILD-TYPE        12         1
D1855V3, multiclass
            clus
vv           FAM91A1 MUTATED FAM91A1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                7               101
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM91A1 MUTATED     0   1   7   2
  FAM91A1 WILD-TYPE   9  66 242  39
D1855V4, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               7               242
  T4               2                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
  FAM91A1 MUTATED     9   0   1
  FAM91A1 WILD-TYPE 211  81  65
D1855V5, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  N0               9               211
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1855V6, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     8   0
  FAM91A1 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      8    0
  FAM91A1 WILD-TYPE  277   48
   clus
vv  FAM91A1 MUTATED FAM91A1 WILD-TYPE
  0               8               277
  1               0                48
[1] 2 2
[1] FALSE
D1855V7, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     2   8
  FAM91A1 WILD-TYPE 168 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      2    8
  FAM91A1 WILD-TYPE  168  189
        clus
vv       FAM91A1 MUTATED FAM91A1 WILD-TYPE
  FEMALE               2               168
  MALE                 8               189
[1] 2 2
[1] FALSE
D1855V8, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     9   0
  FAM91A1 WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      9    0
  FAM91A1 WILD-TYPE  291    8
     clus
vv    FAM91A1 MUTATED FAM91A1 WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D1855V9, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     9   1
  FAM91A1 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      9    1
  FAM91A1 WILD-TYPE  305   47
                               clus
vv                              FAM91A1 MUTATED FAM91A1 WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM91A1 MUTATED     5   0   0   1
  FAM91A1 WILD-TYPE 254   3  22  20
D1855V10, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               1                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"
D1855V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM91A1 MUTATED                                  0     2
  FAM91A1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM91A1 MUTATED                           0     6
  FAM91A1 WILD-TYPE                        19   170
D1855V12, multiclass
                                  clus
vv                                 FAM91A1 MUTATED FAM91A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               170
[1] 4 2
[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 = OSBPL5 MUTATION ANALYSIS
D1856V1, survival
                  sevent
clus2                0   1
  OSBPL5 MUTATED    10   4
  OSBPL5 WILD-TYPE 267  74
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
              14              341 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
               4               74 
$`OSBPL5 MUTATED`
TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3821 
       10.88       100.01        35.80        19.66         1.02         1.02 
TCGA-AA-3930 TCGA-AA-A01R TCGA-AZ-6599 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6898 
        2.01        35.01         6.77        25.48        17.13         7.53 
TCGA-D5-6928 TCGA-G4-6299 
       11.64        74.56 

$`OSBPL5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6782 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-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        21.44        17.82        58.39         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        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-D5-6920 TCGA-D5-6922 
        4.80        12.49        16.14        15.58        12.39        10.13 
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        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
            1.02             0.00 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
          100.01           148.01 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
          14.385           22.090 
[1] "1.0 - 100.0 (14.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1856V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL5 MUTATED         3        0        1         3         0         0
  OSBPL5 WILD-TYPE      61        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL5 MUTATED           1          0          1          2        1
  OSBPL5 WILD-TYPE        17          6         43         31       34
                  vv
clus               STAGE IVA STAGE IVB
  OSBPL5 MUTATED           0         0
  OSBPL5 WILD-TYPE        12         1
D1856V3, multiclass
            clus
vv           OSBPL5 MUTATED OSBPL5 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                1               34
  STAGE IVA               0               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
  OSBPL5 MUTATED     0   3   8   3
  OSBPL5 WILD-TYPE   9  64 241  38
D1856V4, multiclass
    clus
vv   OSBPL5 MUTATED OSBPL5 WILD-TYPE
  T1              0                9
  T2              3               64
  T3              8              241
  T4              3               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
  OSBPL5 MUTATED     8   1   5
  OSBPL5 WILD-TYPE 212  80  61
D1856V5, multiclass
    clus
vv   OSBPL5 MUTATED OSBPL5 WILD-TYPE
  N0              8              212
  N1              1               80
  N2              5               61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1856V6, binary
                  cls
clus                 0   1
  OSBPL5 MUTATED    10   1
  OSBPL5 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL5 MUTATED     10    1
  OSBPL5 WILD-TYPE  275   47
   clus
vv  OSBPL5 MUTATED OSBPL5 WILD-TYPE
  0             10              275
  1              1               47
[1] 2 2
[1] FALSE
D1856V7, binary
                  cls
clus                 0   1
  OSBPL5 MUTATED     6   8
  OSBPL5 WILD-TYPE 164 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL5 MUTATED      6    8
  OSBPL5 WILD-TYPE  164  189
        clus
vv       OSBPL5 MUTATED OSBPL5 WILD-TYPE
  FEMALE              6              164
  MALE                8              189
[1] 2 2
[1] FALSE
D1856V8, binary
                  cls
clus                 0   1
  OSBPL5 MUTATED    12   1
  OSBPL5 WILD-TYPE 288   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL5 MUTATED     12    1
  OSBPL5 WILD-TYPE  288    7
     clus
vv    OSBPL5 MUTATED OSBPL5 WILD-TYPE
  NO              12              288
  YES              1                7
[1] 2 2
[1] FALSE
D1856V9, binary
                  cls
clus                 0   1
  OSBPL5 MUTATED    10   4
  OSBPL5 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL5 MUTATED     10    4
  OSBPL5 WILD-TYPE  304   44
                               clus
vv                              OSBPL5 MUTATED OSBPL5 WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OSBPL5 MUTATED    10   0   1   0
  OSBPL5 WILD-TYPE 249   3  21  21
D1856V10, multiclass
    clus
vv   OSBPL5 MUTATED OSBPL5 WILD-TYPE
  R0             10              249
  R1              0                3
  R2              1               21
  RX              0               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"
D1856V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSBPL5 MUTATED                                  0     0
  OSBPL5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OSBPL5 MUTATED                           0    10
  OSBPL5 WILD-TYPE                        19   166
D1856V12, multiclass
                                  clus
vv                                 OSBPL5 MUTATED OSBPL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                        10              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(1857) Variable = TTLL5 MUTATION ANALYSIS
D1857V1, survival
                 sevent
clus2               0   1
  TTLL5 MUTATED     9   2
  TTLL5 WILD-TYPE 268  76
  TTLL5 MUTATED TTLL5 WILD-TYPE 
             11             344 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
              2              76 
$`TTLL5 MUTATED`
TCGA-AD-6964 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3966 TCGA-AU-6004 TCGA-AZ-4315 
       10.88         3.02        53.00         2.01        27.09        58.39 
TCGA-CA-5254 TCGA-CA-6717 TCGA-DM-A1HB TCGA-DM-A28H TCGA-G4-6306 
       12.69        12.76       135.65       117.07        44.68 

$`TTLL5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        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-6718 
       12.36        12.39        12.59        12.59        12.20        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17        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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 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-G4-6315 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TTLL5 MUTATED TTLL5 WILD-TYPE 
           2.01            0.00 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
         135.65          148.01 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
         27.090          22.045 
[1] "2.0 - 135.7 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D1857V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTLL5 MUTATED         1        0        2         4         0         0
  TTLL5 WILD-TYPE      63        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTLL5 MUTATED           0          0          1          1        0         0
  TTLL5 WILD-TYPE        18          6         43         32       35        12
                 vv
clus              STAGE IVB
  TTLL5 MUTATED           0
  TTLL5 WILD-TYPE         1
D1857V3, multiclass
            clus
vv           TTLL5 MUTATED TTLL5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  TTLL5 MUTATED     0   2   8   1
  TTLL5 WILD-TYPE   9  65 241  40
D1857V4, multiclass
    clus
vv   TTLL5 MUTATED TTLL5 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             8             241
  T4             1              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
  TTLL5 MUTATED     8   1   2
  TTLL5 WILD-TYPE 212  80  64
D1857V5, multiclass
    clus
vv   TTLL5 MUTATED TTLL5 WILD-TYPE
  N0             8             212
  N1             1              80
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1857V6, binary
                 cls
clus                0   1
  TTLL5 MUTATED    10   0
  TTLL5 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL5 MUTATED     10    0
  TTLL5 WILD-TYPE  275   48
   clus
vv  TTLL5 MUTATED TTLL5 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1857V7, binary
                 cls
clus                0   1
  TTLL5 MUTATED     4   7
  TTLL5 WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL5 MUTATED      4    7
  TTLL5 WILD-TYPE  166  190
        clus
vv       TTLL5 MUTATED TTLL5 WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D1857V8, binary
                 cls
clus                0   1
  TTLL5 MUTATED     7   0
  TTLL5 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL5 MUTATED      7    0
  TTLL5 WILD-TYPE  293    8
     clus
vv    TTLL5 MUTATED TTLL5 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1857V9, binary
                 cls
clus                0   1
  TTLL5 MUTATED     8   2
  TTLL5 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL5 MUTATED      8    2
  TTLL5 WILD-TYPE  306   46
                               clus
vv                              TTLL5 MUTATED TTLL5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TTLL5 MUTATED     5   0   0   2
  TTLL5 WILD-TYPE 254   3  22  19
D1857V10, multiclass
    clus
vv   TTLL5 MUTATED TTLL5 WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             2              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"
D1857V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTLL5 MUTATED                                  0     2
  TTLL5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTLL5 MUTATED                           0     6
  TTLL5 WILD-TYPE                        19   170
D1857V12, multiclass
                                  clus
vv                                 TTLL5 MUTATED TTLL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = TMEM171 MUTATION ANALYSIS
D1858V1, survival
                   sevent
clus2                 0   1
  TMEM171 MUTATED     5   0
  TMEM171 WILD-TYPE 272  78
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                5               350 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                0                78 
$`TMEM171 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3854 TCGA-AZ-4315 TCGA-CM-6162 
        0.92        19.04        36.03        58.39        12.00 

$`TMEM171 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07         0.00        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TMEM171 MUTATED TMEM171 WILD-TYPE 
             0.92              0.00 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
            58.39            148.01 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
           19.040            22.075 
[1] "0.9 - 58.4 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr="     "9100000"
D1858V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM171 MUTATED         1        0        0         1         0         0
  TMEM171 WILD-TYPE      63        1       26       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM171 MUTATED           1          0          1          0        1
  TMEM171 WILD-TYPE        17          6         43         33       34
                   vv
clus                STAGE IVA STAGE IVB
  TMEM171 MUTATED           0         0
  TMEM171 WILD-TYPE        12         1
D1858V3, multiclass
            clus
vv           TMEM171 MUTATED TMEM171 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                1               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  TMEM171 MUTATED     0   1   4   0
  TMEM171 WILD-TYPE   9  66 245  41
D1858V4, multiclass
    clus
vv   TMEM171 MUTATED TMEM171 WILD-TYPE
  T1               0                 9
  T2               1                66
  T3               4               245
  T4               0                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
  TMEM171 MUTATED     3   2   0
  TMEM171 WILD-TYPE 217  79  66
D1858V5, multiclass
    clus
vv   TMEM171 MUTATED TMEM171 WILD-TYPE
  N0               3               217
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1858V6, binary
                   cls
clus                  0   1
  TMEM171 MUTATED     4   1
  TMEM171 WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM171 MUTATED      4    1
  TMEM171 WILD-TYPE  281   47
   clus
vv  TMEM171 MUTATED TMEM171 WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D1858V7, binary
                   cls
clus                  0   1
  TMEM171 MUTATED     3   2
  TMEM171 WILD-TYPE 167 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM171 MUTATED      3    2
  TMEM171 WILD-TYPE  167  195
        clus
vv       TMEM171 MUTATED TMEM171 WILD-TYPE
  FEMALE               3               167
  MALE                 2               195
[1] 2 2
[1] FALSE
D1858V8, binary
                   cls
clus                  0   1
  TMEM171 MUTATED     4   1
  TMEM171 WILD-TYPE 296   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM171 MUTATED      4    1
  TMEM171 WILD-TYPE  296    7
     clus
vv    TMEM171 MUTATED TMEM171 WILD-TYPE
  NO                4               296
  YES               1                 7
[1] 2 2
[1] FALSE
D1858V9, binary
                   cls
clus                  0   1
  TMEM171 MUTATED     3   2
  TMEM171 WILD-TYPE 311  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM171 MUTATED      3    2
  TMEM171 WILD-TYPE  311   46
                               clus
vv                              TMEM171 MUTATED TMEM171 WILD-TYPE
  COLON ADENOCARCINOMA                        3               311
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM171 MUTATED     4   0   1   0
  TMEM171 WILD-TYPE 255   3  21  21
D1858V10, multiclass
    clus
vv   TMEM171 MUTATED TMEM171 WILD-TYPE
  R0               4               255
  R1               0                 3
  R2               1                21
  RX               0                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"
D1858V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM171 MUTATED                                  0     0
  TMEM171 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM171 MUTATED                           0     2
  TMEM171 WILD-TYPE                        19   174
D1858V12, multiclass
[1] "Remove cluster labels:" "TMEM171 MUTATED"       
clus
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                2               204 
       TCGA-A6-2677        TCGA-A6-4105        TCGA-A6-6649        TCGA-AD-6548 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6895        TCGA-AD-6964        TCGA-AZ-4681 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6321        TCGA-G4-6586        TCGA-G4-6588 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6628        TCGA-A6-2671        TCGA-A6-2672 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2676        TCGA-A6-2678        TCGA-A6-2683 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6651        TCGA-A6-6652 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6323        TCGA-G4-6626 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 

Clustering(1859) Variable = GPSM2 MUTATION ANALYSIS
D1859V1, survival
                 sevent
clus2               0   1
  GPSM2 MUTATED     8   3
  GPSM2 WILD-TYPE 269  75
  GPSM2 MUTATED GPSM2 WILD-TYPE 
             11             344 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3              75 
$`GPSM2 MUTATED`
TCGA-AA-3713 TCGA-AD-6895 TCGA-G4-6628 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-A010 
       19.04        25.08        79.69         3.02        63.98        34.98 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-5914 TCGA-DM-A1DA 
       58.39        12.10        12.76        21.99         7.50 

$`GPSM2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  GPSM2 MUTATED GPSM2 WILD-TYPE 
           3.02            0.00 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
          79.69          148.01 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
         21.990          22.075 
[1] "3.0 - 79.7 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1859V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPSM2 MUTATED         1        0        3         2         1         0
  GPSM2 WILD-TYPE      63        1       23       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPSM2 MUTATED           0          0          2          1        2         0
  GPSM2 WILD-TYPE        18          6         42         32       33        12
                 vv
clus              STAGE IVB
  GPSM2 MUTATED           0
  GPSM2 WILD-TYPE         1
D1859V3, multiclass
            clus
vv           GPSM2 MUTATED GPSM2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              23
  STAGE IIA              2             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             1              32
  STAGE IV               2              33
  STAGE IVA              0              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
  GPSM2 MUTATED     0   1   8   3
  GPSM2 WILD-TYPE   9  66 241  38
D1859V4, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             3              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
  GPSM2 MUTATED     8   3   1
  GPSM2 WILD-TYPE 212  78  65
D1859V5, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  N0             8             212
  N1             3              78
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1859V6, binary
                 cls
clus                0   1
  GPSM2 MUTATED     9   2
  GPSM2 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      9    2
  GPSM2 WILD-TYPE  276   46
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             9             276
  1             2              46
[1] 2 2
[1] FALSE
D1859V7, binary
                 cls
clus                0   1
  GPSM2 MUTATED     4   8
  GPSM2 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      4    8
  GPSM2 WILD-TYPE  166  189
        clus
vv       GPSM2 MUTATED GPSM2 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D1859V8, binary
                 cls
clus                0   1
  GPSM2 MUTATED     8   1
  GPSM2 WILD-TYPE 292   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      8    1
  GPSM2 WILD-TYPE  292    7
     clus
vv    GPSM2 MUTATED GPSM2 WILD-TYPE
  NO              8             292
  YES             1               7
[1] 2 2
[1] FALSE
D1859V9, binary
                 cls
clus                0   1
  GPSM2 MUTATED    11   1
  GPSM2 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED     11    1
  GPSM2 WILD-TYPE  303   47
                               clus
vv                              GPSM2 MUTATED GPSM2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             303
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPSM2 MUTATED     7   0   1   2
  GPSM2 WILD-TYPE 252   3  21  19
D1859V10, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             2              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"
D1859V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPSM2 MUTATED                                  0     1
  GPSM2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPSM2 MUTATED                           1     5
  GPSM2 WILD-TYPE                        18   171
D1859V12, multiclass
                                  clus
vv                                 GPSM2 MUTATED GPSM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        5             171
[1] 4 2
[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 = ANKRD32 MUTATION ANALYSIS
D1860V1, survival
                   sevent
clus2                 0   1
  ANKRD32 MUTATED    10   3
  ANKRD32 WILD-TYPE 267  75
  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
               13               342 
  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
                3                75 
$`ANKRD32 MUTATED`
TCGA-AA-3950 TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3877 TCGA-AU-6004 
       24.00        32.75         8.38        20.12        31.00        27.09 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6678 TCGA-D5-6927 TCGA-DM-A1D4 
       58.39        12.76        21.14        11.01         9.44        92.75 
TCGA-DM-A1D8 
       12.59 

$`ANKRD32 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
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-A6-6142 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6718 
       12.36        12.39        12.59        12.59        12.20        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-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        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 
       13.41        13.35        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-A1D9 
       24.43        38.20       130.65        49.91        13.32       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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
             8.38              0.00 
  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
            92.75            148.01 
  ANKRD32 MUTATED ANKRD32 WILD-TYPE 
           21.140            22.075 
[1] "8.4 - 92.8 (21.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1860V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD32 MUTATED         3        0        0         7         1         0
  ANKRD32 WILD-TYPE      61        1       26       101         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD32 MUTATED           0          0          0          0        0
  ANKRD32 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD32 MUTATED           1         0
  ANKRD32 WILD-TYPE        11         1
D1860V3, multiclass
            clus
vv           ANKRD32 MUTATED ANKRD32 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                7               101
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  ANKRD32 MUTATED     2   1   8   2
  ANKRD32 WILD-TYPE   7  66 241  39
D1860V4, multiclass
    clus
vv   ANKRD32 MUTATED ANKRD32 WILD-TYPE
  T1               2                 7
  T2               1                66
  T3               8               241
  T4               2                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
  ANKRD32 MUTATED    11   2   0
  ANKRD32 WILD-TYPE 209  79  66
D1860V5, multiclass
    clus
vv   ANKRD32 MUTATED ANKRD32 WILD-TYPE
  N0              11               209
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1860V6, binary
                   cls
clus                  0   1
  ANKRD32 MUTATED    10   1
  ANKRD32 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD32 MUTATED     10    1
  ANKRD32 WILD-TYPE  275   47
   clus
vv  ANKRD32 MUTATED ANKRD32 WILD-TYPE
  0              10               275
  1               1                47
[1] 2 2
[1] FALSE
D1860V7, binary
                   cls
clus                  0   1
  ANKRD32 MUTATED     7   6
  ANKRD32 WILD-TYPE 163 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD32 MUTATED      7    6
  ANKRD32 WILD-TYPE  163  191
        clus
vv       ANKRD32 MUTATED ANKRD32 WILD-TYPE
  FEMALE               7               163
  MALE                 6               191
[1] 2 2
[1] FALSE
D1860V8, binary
                   cls
clus                  0   1
  ANKRD32 MUTATED    10   0
  ANKRD32 WILD-TYPE 290   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD32 MUTATED     10    0
  ANKRD32 WILD-TYPE  290    8
     clus
vv    ANKRD32 MUTATED ANKRD32 WILD-TYPE
  NO               10               290
  YES               0                 8
[1] 2 2
[1] FALSE
D1860V9, binary
                   cls
clus                  0   1
  ANKRD32 MUTATED     8   5
  ANKRD32 WILD-TYPE 306  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD32 MUTATED      8    5
  ANKRD32 WILD-TYPE  306   43
                               clus
vv                              ANKRD32 MUTATED ANKRD32 WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD32 MUTATED     7   0   0   2
  ANKRD32 WILD-TYPE 252   3  22  19
D1860V10, multiclass
    clus
vv   ANKRD32 MUTATED ANKRD32 WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               2                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"
D1860V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD32 MUTATED                                  0     1
  ANKRD32 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD32 MUTATED                           1     9
  ANKRD32 WILD-TYPE                        18   167
D1860V12, multiclass
                                  clus
vv                                 ANKRD32 MUTATED ANKRD32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          9               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(1861) Variable = HDAC11 MUTATION ANALYSIS
D1861V1, survival
                  sevent
clus2                0   1
  HDAC11 MUTATED     4   3
  HDAC11 WILD-TYPE 273  75
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               7              348 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               3               75 
$`HDAC11 MUTATED`
TCGA-AA-3516 TCGA-AZ-6601 TCGA-G4-6628 TCGA-A6-5661 TCGA-AY-6197 TCGA-CM-5861 
       13.02       100.01        79.69        33.53        21.44        15.02 
TCGA-CM-5862 
        5.03 

$`HDAC11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  HDAC11 MUTATED HDAC11 WILD-TYPE 
            5.03             0.00 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
          100.01           148.01 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
          21.440           22.075 
[1] "5.0 - 100.0 (21.4)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D1861V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HDAC11 MUTATED         1        0        1         3         1         0
  HDAC11 WILD-TYPE      63        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HDAC11 MUTATED           1          0          0          0        0
  HDAC11 WILD-TYPE        17          6         44         33       35
                  vv
clus               STAGE IVA STAGE IVB
  HDAC11 MUTATED           1         0
  HDAC11 WILD-TYPE        11         1
D1861V3, multiclass
            clus
vv           HDAC11 MUTATED HDAC11 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               3              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  HDAC11 MUTATED     0   1   6   1
  HDAC11 WILD-TYPE   9  66 243  40
D1861V4, multiclass
    clus
vv   HDAC11 MUTATED HDAC11 WILD-TYPE
  T1              0                9
  T2              1               66
  T3              6              243
  T4              1               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
  HDAC11 MUTATED     6   1   1
  HDAC11 WILD-TYPE 214  80  65
D1861V5, multiclass
    clus
vv   HDAC11 MUTATED HDAC11 WILD-TYPE
  N0              6              214
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1861V6, binary
                  cls
clus                 0   1
  HDAC11 MUTATED     5   1
  HDAC11 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HDAC11 MUTATED      5    1
  HDAC11 WILD-TYPE  280   47
   clus
vv  HDAC11 MUTATED HDAC11 WILD-TYPE
  0              5              280
  1              1               47
[1] 2 2
[1] FALSE
D1861V7, binary
                  cls
clus                 0   1
  HDAC11 MUTATED     4   4
  HDAC11 WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HDAC11 MUTATED      4    4
  HDAC11 WILD-TYPE  166  193
        clus
vv       HDAC11 MUTATED HDAC11 WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D1861V8, binary
                  cls
clus                 0   1
  HDAC11 MUTATED     7   0
  HDAC11 WILD-TYPE 293   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HDAC11 MUTATED      7    0
  HDAC11 WILD-TYPE  293    8
     clus
vv    HDAC11 MUTATED HDAC11 WILD-TYPE
  NO               7              293
  YES              0                8
[1] 2 2
[1] FALSE
D1861V9, binary
                  cls
clus                 0   1
  HDAC11 MUTATED     7   1
  HDAC11 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HDAC11 MUTATED      7    1
  HDAC11 WILD-TYPE  307   47
                               clus
vv                              HDAC11 MUTATED HDAC11 WILD-TYPE
  COLON ADENOCARCINOMA                       7              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HDAC11 MUTATED     5   0   0   1
  HDAC11 WILD-TYPE 254   3  22  20
D1861V10, multiclass
    clus
vv   HDAC11 MUTATED HDAC11 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              1               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"
D1861V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC11 MUTATED                                  0     0
  HDAC11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HDAC11 MUTATED                           1     6
  HDAC11 WILD-TYPE                        18   170
D1861V12, multiclass
                                  clus
vv                                 HDAC11 MUTATED HDAC11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         6              170
[1] 4 2
[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 = BUB1 MUTATION ANALYSIS
D1862V1, survival
                sevent
clus2              0   1
  BUB1 MUTATED     8   4
  BUB1 WILD-TYPE 269  74
  BUB1 MUTATED BUB1 WILD-TYPE 
            12            343 
  BUB1 MUTATED BUB1 WILD-TYPE 
             4             74 
$`BUB1 MUTATED`
TCGA-AA-3697 TCGA-AA-3713 TCGA-G4-6588 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-A00N 
       85.05        19.04        26.17        20.12        78.08         4.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-4315 TCGA-D5-6930 TCGA-DM-A1DA TCGA-G4-6303 
       34.98        38.07        58.39        13.35         7.50        65.85 

$`BUB1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        19.00        36.00        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-A6-6781 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-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         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-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-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        43.04        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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  BUB1 MUTATED BUB1 WILD-TYPE 
          4.01           0.00 
  BUB1 MUTATED BUB1 WILD-TYPE 
         85.05         148.01 
  BUB1 MUTATED BUB1 WILD-TYPE 
        30.575         22.030 
[1] "4.0 - 85.0 (30.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1862V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BUB1 MUTATED         0        0        2         5         2         0
  BUB1 WILD-TYPE      64        1       24       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BUB1 MUTATED           1          0          0          1        2         0
  BUB1 WILD-TYPE        17          6         44         32       33        12
                vv
clus             STAGE IVB
  BUB1 MUTATED           0
  BUB1 WILD-TYPE         1
D1862V3, multiclass
            clus
vv           BUB1 MUTATED BUB1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              2             33
  STAGE IVA             0             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
  BUB1 MUTATED     0   0  11   2
  BUB1 WILD-TYPE   9  67 238  39
D1862V4, multiclass
    clus
vv   BUB1 MUTATED BUB1 WILD-TYPE
  T1            0              9
  T2            0             67
  T3           11            238
  T4            2             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
  BUB1 MUTATED    10   2   1
  BUB1 WILD-TYPE 210  79  65
D1862V5, multiclass
    clus
vv   BUB1 MUTATED BUB1 WILD-TYPE
  N0           10            210
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1862V6, binary
                cls
clus               0   1
  BUB1 MUTATED    10   2
  BUB1 WILD-TYPE 275  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED     10    2
  BUB1 WILD-TYPE  275   46
   clus
vv  BUB1 MUTATED BUB1 WILD-TYPE
  0           10            275
  1            2             46
[1] 2 2
[1] FALSE
D1862V7, binary
                cls
clus               0   1
  BUB1 MUTATED     7   6
  BUB1 WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED      7    6
  BUB1 WILD-TYPE  163  191
        clus
vv       BUB1 MUTATED BUB1 WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D1862V8, binary
                cls
clus               0   1
  BUB1 MUTATED     9   1
  BUB1 WILD-TYPE 291   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED      9    1
  BUB1 WILD-TYPE  291    7
     clus
vv    BUB1 MUTATED BUB1 WILD-TYPE
  NO             9            291
  YES            1              7
[1] 2 2
[1] FALSE
D1862V9, binary
                cls
clus               0   1
  BUB1 MUTATED    10   3
  BUB1 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED     10    3
  BUB1 WILD-TYPE  304   45
                               clus
vv                              BUB1 MUTATED BUB1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BUB1 MUTATED    10   0   1   0
  BUB1 WILD-TYPE 249   3  21  21
D1862V10, multiclass
    clus
vv   BUB1 MUTATED BUB1 WILD-TYPE
  R0           10            249
  R1            0              3
  R2            1             21
  RX            0             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"
D1862V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BUB1 MUTATED                                  0     0
  BUB1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BUB1 MUTATED                           0     6
  BUB1 WILD-TYPE                        19   170
D1862V12, multiclass
                                  clus
vv                                 BUB1 MUTATED BUB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = KMO MUTATION ANALYSIS
D1863V1, survival
               sevent
clus2             0   1
  KMO MUTATED     7   4
  KMO WILD-TYPE 270  74
  KMO MUTATED KMO WILD-TYPE 
           11           344 
  KMO MUTATED KMO WILD-TYPE 
            4            74 
$`KMO MUTATED`
TCGA-AD-6964 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00N 
       10.88         3.02        63.98         6.97        31.00         4.01 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5861 TCGA-CM-6677 
       12.76        10.06        21.99        15.02        11.08 

$`KMO WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  KMO MUTATED KMO WILD-TYPE 
         3.02          0.00 
  KMO MUTATED KMO WILD-TYPE 
        63.98        148.01 
  KMO MUTATED KMO WILD-TYPE 
        11.08         22.39 
[1] "3.0 - 64.0 (11.1)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2.5"
D1863V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KMO MUTATED         1        0        3         5         1         0
  KMO WILD-TYPE      63        1       23       103         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KMO MUTATED           0          0          1          0        0         0
  KMO WILD-TYPE        18          6         43         33       35        12
               vv
clus            STAGE IVB
  KMO MUTATED           0
  KMO WILD-TYPE         1
D1863V3, multiclass
            clus
vv           KMO MUTATED KMO WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             3            23
  STAGE IIA            5           103
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           1            43
  STAGE IIIC           0            33
  STAGE IV             0            35
  STAGE IVA            0            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
  KMO MUTATED     1   0   8   3
  KMO WILD-TYPE   8  67 241  38
D1863V4, multiclass
    clus
vv   KMO MUTATED KMO WILD-TYPE
  T1           1             8
  T2           0            67
  T3           8           241
  T4           3            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
  KMO MUTATED    10   1   1
  KMO WILD-TYPE 210  80  65
D1863V5, multiclass
    clus
vv   KMO MUTATED KMO WILD-TYPE
  N0          10           210
  N1           1            80
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1863V6, binary
               cls
clus              0   1
  KMO MUTATED    10   0
  KMO WILD-TYPE 275  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  KMO MUTATED     10    0
  KMO WILD-TYPE  275   48
   clus
vv  KMO MUTATED KMO WILD-TYPE
  0          10           275
  1           0            48
[1] 2 2
[1] FALSE
D1863V7, binary
               cls
clus              0   1
  KMO MUTATED     5   7
  KMO WILD-TYPE 165 190
[1] "tbl2"
               cls
clus            [,1] [,2]
  KMO MUTATED      5    7
  KMO WILD-TYPE  165  190
        clus
vv       KMO MUTATED KMO WILD-TYPE
  FEMALE           5           165
  MALE             7           190
[1] 2 2
[1] FALSE
D1863V8, binary
               cls
clus              0   1
  KMO MUTATED     9   0
  KMO WILD-TYPE 291   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  KMO MUTATED      9    0
  KMO WILD-TYPE  291    8
     clus
vv    KMO MUTATED KMO WILD-TYPE
  NO            9           291
  YES           0             8
[1] 2 2
[1] FALSE
D1863V9, binary
               cls
clus              0   1
  KMO MUTATED     9   3
  KMO WILD-TYPE 305  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  KMO MUTATED      9    3
  KMO WILD-TYPE  305   45
                               clus
vv                              KMO MUTATED KMO WILD-TYPE
  COLON ADENOCARCINOMA                    9           305
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  KMO MUTATED     8   0   0   3
  KMO WILD-TYPE 251   3  22  18
D1863V10, multiclass
    clus
vv   KMO MUTATED KMO WILD-TYPE
  R0           8           251
  R1           0             3
  R2           0            22
  RX           3            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"
D1863V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KMO MUTATED                                  0     2
  KMO WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  KMO MUTATED                           0     4
  KMO WILD-TYPE                        19   172
D1863V12, multiclass
                                  clus
vv                                 KMO MUTATED KMO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  0            19
  WHITE                                      4           172
[1] 4 2
[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 = COL6A3 MUTATION ANALYSIS
D1864V1, survival
                  sevent
clus2                0   1
  COL6A3 MUTATED    36  14
  COL6A3 WILD-TYPE 241  64
  COL6A3 MUTATED COL6A3 WILD-TYPE 
              50              305 
  COL6A3 MUTATED COL6A3 WILD-TYPE 
              14               64 
$`COL6A3 MUTATED`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-A00L 
       24.33        24.16        13.02        17.95        19.04        38.04 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6586 TCGA-A6-3807 TCGA-A6-5665 TCGA-A6-6141 
      100.01         1.94        35.80        34.65        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3519 TCGA-AA-3555 TCGA-AA-3681 
       24.39        19.66         3.02         9.07        29.95         5.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3949 TCGA-AA-3973 TCGA-AA-3977 
       15.95         0.00         0.00        26.01        13.05        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01R TCGA-AD-6889 
        4.01        34.98        10.98         1.02        35.01        83.24 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-4743 
       17.82        58.39        29.56        12.76        17.56        23.05 
TCGA-CM-5861 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 
       15.02        14.99        14.04        12.95        45.40        19.59 
TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6703 
       11.64        13.41       135.65       119.93        35.97        47.87 
TCGA-F4-6856 TCGA-G4-6309 
       35.31        85.48 

$`COL6A3 WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       14.53         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
      106.75        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.69        23.87        20.12        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        20.98        13.94        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-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         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-3846 TCGA-AA-3848 TCGA-AA-3851 
       17.98        38.99        37.02        17.03        10.06        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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        34.06        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-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-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        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-6890 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
       12.59        12.59        12.20        10.06        14.30       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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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        14.04 
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-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-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        54.61        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.04         9.44        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       131.51       139.17        81.37        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  COL6A3 MUTATED COL6A3 WILD-TYPE 
               0                0 
  COL6A3 MUTATED COL6A3 WILD-TYPE 
          135.65           148.01 
  COL6A3 MUTATED COL6A3 WILD-TYPE 
          19.625           22.090 
[1] "0.0 - 135.7 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1864V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL6A3 MUTATED         4        0        4        19         2         0
  COL6A3 WILD-TYPE      60        1       22        89         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL6A3 MUTATED           4          2          7          5        2
  COL6A3 WILD-TYPE        14          4         37         28       33
                  vv
clus               STAGE IVA STAGE IVB
  COL6A3 MUTATED           0         0
  COL6A3 WILD-TYPE        12         1
D1864V3, multiclass
            clus
vv           COL6A3 MUTATED COL6A3 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               22
  STAGE IIA              19               89
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               4               14
  STAGE IIIA              2                4
  STAGE IIIB              7               37
  STAGE IIIC              5               28
  STAGE IV                2               33
  STAGE IVA               0               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
  COL6A3 MUTATED     0   7  39   5
  COL6A3 WILD-TYPE   9  60 210  36
D1864V4, multiclass
    clus
vv   COL6A3 MUTATED COL6A3 WILD-TYPE
  T1              0                9
  T2              7               60
  T3             39              210
  T4              5               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
  COL6A3 MUTATED    29  15   7
  COL6A3 WILD-TYPE 191  66  59
D1864V5, multiclass
    clus
vv   COL6A3 MUTATED COL6A3 WILD-TYPE
  N0             29              191
  N1             15               66
  N2              7               59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1864V6, binary
                  cls
clus                 0   1
  COL6A3 MUTATED    45   2
  COL6A3 WILD-TYPE 240  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A3 MUTATED     45    2
  COL6A3 WILD-TYPE  240   46
   clus
vv  COL6A3 MUTATED COL6A3 WILD-TYPE
  0             45              240
  1              2               46
[1] 2 2
[1] FALSE
D1864V7, binary
                  cls
clus                 0   1
  COL6A3 MUTATED    26  25
  COL6A3 WILD-TYPE 144 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A3 MUTATED     26   25
  COL6A3 WILD-TYPE  144  172
        clus
vv       COL6A3 MUTATED COL6A3 WILD-TYPE
  FEMALE             26              144
  MALE               25              172
[1] 2 2
[1] FALSE
D1864V8, binary
                  cls
clus                 0   1
  COL6A3 MUTATED    42   1
  COL6A3 WILD-TYPE 258   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A3 MUTATED     42    1
  COL6A3 WILD-TYPE  258    7
     clus
vv    COL6A3 MUTATED COL6A3 WILD-TYPE
  NO              42              258
  YES              1                7
[1] 2 2
[1] FALSE
D1864V9, binary
                  cls
clus                 0   1
  COL6A3 MUTATED    39  11
  COL6A3 WILD-TYPE 275  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A3 MUTATED     39   11
  COL6A3 WILD-TYPE  275   37
                               clus
vv                              COL6A3 MUTATED COL6A3 WILD-TYPE
  COLON ADENOCARCINOMA                      39              275
  COLON MUCINOUS ADENOCARCINOMA             11               37
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  COL6A3 MUTATED    36   0   1   3
  COL6A3 WILD-TYPE 223   3  21  18
D1864V10, multiclass
    clus
vv   COL6A3 MUTATED COL6A3 WILD-TYPE
  R0             36              223
  R1              0                3
  R2              1               21
  RX              3               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"
D1864V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL6A3 MUTATED                                  0     2
  COL6A3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL6A3 MUTATED                           4    25
  COL6A3 WILD-TYPE                        15   151
D1864V12, multiclass
                                  clus
vv                                 COL6A3 MUTATED COL6A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     4               15
  WHITE                                        25              151
[1] 4 2
[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 = FKBP5 MUTATION ANALYSIS
D1865V1, survival
                 sevent
clus2               0   1
  FKBP5 MUTATED     4   2
  FKBP5 WILD-TYPE 273  76
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              6             349 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              2              76 
$`FKBP5 MUTATED`
TCGA-AA-3977 TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6171 TCGA-F4-6856 TCGA-G4-6303 
       25.02        83.24        12.76        14.04        35.31        65.85 

$`FKBP5 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-A6-6780 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        47.41       133.18        74.56        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-G4-6626 
       46.75 

  FKBP5 MUTATED FKBP5 WILD-TYPE 
          12.76            0.00 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
          83.24          148.01 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
         30.165          22.030 
[1] "12.8 - 83.2 (30.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1865V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKBP5 MUTATED         2        0        0         2         0         0
  FKBP5 WILD-TYPE      62        1       26       106         8         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  FKBP5 MUTATED           0
  FKBP5 WILD-TYPE         1
D1865V3, multiclass
            clus
vv           FKBP5 MUTATED FKBP5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  FKBP5 MUTATED     0   3   3   0
  FKBP5 WILD-TYPE   9  64 246  41
D1865V4, multiclass
    clus
vv   FKBP5 MUTATED FKBP5 WILD-TYPE
  T1             0               9
  T2             3              64
  T3             3             246
  T4             0              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
  FKBP5 MUTATED     5   1   0
  FKBP5 WILD-TYPE 215  80  66
D1865V5, multiclass
    clus
vv   FKBP5 MUTATED FKBP5 WILD-TYPE
  N0             5             215
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1865V6, binary
                 cls
clus                0   1
  FKBP5 MUTATED     4   1
  FKBP5 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      4    1
  FKBP5 WILD-TYPE  281   47
   clus
vv  FKBP5 MUTATED FKBP5 WILD-TYPE
  0             4             281
  1             1              47
[1] 2 2
[1] FALSE
D1865V7, binary
                 cls
clus                0   1
  FKBP5 MUTATED     2   4
  FKBP5 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      2    4
  FKBP5 WILD-TYPE  168  193
        clus
vv       FKBP5 MUTATED FKBP5 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D1865V8, binary
                 cls
clus                0   1
  FKBP5 MUTATED     6   0
  FKBP5 WILD-TYPE 294   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      6    0
  FKBP5 WILD-TYPE  294    8
     clus
vv    FKBP5 MUTATED FKBP5 WILD-TYPE
  NO              6             294
  YES             0               8
[1] 2 2
[1] FALSE
D1865V9, binary
                 cls
clus                0   1
  FKBP5 MUTATED     4   2
  FKBP5 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      4    2
  FKBP5 WILD-TYPE  310   46
                               clus
vv                              FKBP5 MUTATED FKBP5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FKBP5 MUTATED     4   0   0   1
  FKBP5 WILD-TYPE 255   3  22  20
D1865V10, multiclass
    clus
vv   FKBP5 MUTATED FKBP5 WILD-TYPE
  R0             4             255
  R1             0               3
  R2             0              22
  RX             1              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"
D1865V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKBP5 MUTATED                                  0     2
  FKBP5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FKBP5 MUTATED                           0     3
  FKBP5 WILD-TYPE                        19   173
D1865V12, multiclass
                                  clus
vv                                 FKBP5 MUTATED FKBP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        3             173
[1] 4 2
[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 = ASPN MUTATION ANALYSIS
D1866V1, survival
                sevent
clus2              0   1
  ASPN MUTATED     6   1
  ASPN WILD-TYPE 271  77
  ASPN MUTATED ASPN WILD-TYPE 
             7            348 
  ASPN MUTATED ASPN WILD-TYPE 
             1             77 
$`ASPN MUTATED`
TCGA-G4-6586 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3861 TCGA-AY-6196 TCGA-CM-5861 
       35.80        22.06        20.12        30.05         0.20        15.02 
TCGA-F4-6570 
        6.18 

$`ASPN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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-F4-6703 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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  ASPN MUTATED ASPN WILD-TYPE 
           0.2            0.0 
  ASPN MUTATED ASPN WILD-TYPE 
         35.80         148.01 
  ASPN MUTATED ASPN WILD-TYPE 
         20.12          22.09 
[1] "0.2 - 35.8 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1866V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASPN MUTATED         0        0        0         6         0         0
  ASPN WILD-TYPE      64        1       26       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASPN MUTATED           0          0          0          1        0         0
  ASPN WILD-TYPE        18          6         44         32       35        12
                vv
clus             STAGE IVB
  ASPN MUTATED           0
  ASPN WILD-TYPE         1
D1866V3, multiclass
            clus
vv           ASPN MUTATED ASPN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             6            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  ASPN MUTATED     0   0   7   0
  ASPN WILD-TYPE   9  67 242  41
D1866V4, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  T1            0              9
  T2            0             67
  T3            7            242
  T4            0             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
  ASPN MUTATED     6   0   1
  ASPN WILD-TYPE 214  81  65
D1866V5, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  N0            6            214
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1866V6, binary
                cls
clus               0   1
  ASPN MUTATED     5   0
  ASPN WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      5    0
  ASPN WILD-TYPE  280   48
   clus
vv  ASPN MUTATED ASPN WILD-TYPE
  0            5            280
  1            0             48
[1] 2 2
[1] FALSE
D1866V7, binary
                cls
clus               0   1
  ASPN MUTATED     4   3
  ASPN WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      4    3
  ASPN WILD-TYPE  166  194
        clus
vv       ASPN MUTATED ASPN WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D1866V8, binary
                cls
clus               0   1
  ASPN MUTATED     6   0
  ASPN WILD-TYPE 294   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      6    0
  ASPN WILD-TYPE  294    8
     clus
vv    ASPN MUTATED ASPN WILD-TYPE
  NO             6            294
  YES            0              8
[1] 2 2
[1] FALSE
D1866V9, binary
                cls
clus               0   1
  ASPN MUTATED     5   2
  ASPN WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      5    2
  ASPN WILD-TYPE  309   46
                               clus
vv                              ASPN MUTATED ASPN WILD-TYPE
  COLON ADENOCARCINOMA                     5            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ASPN MUTATED     6   0   0   0
  ASPN WILD-TYPE 253   3  22  21
D1866V10, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            0             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"
D1866V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASPN MUTATED                                  0     0
  ASPN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ASPN MUTATED                           0     6
  ASPN WILD-TYPE                        19   170
D1866V12, multiclass
                                  clus
vv                                 ASPN MUTATED ASPN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       6            170
[1] 4 2
[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 = RARS2 MUTATION ANALYSIS
D1867V1, survival
                 sevent
clus2               0   1
  RARS2 MUTATED     4   2
  RARS2 WILD-TYPE 273  76
  RARS2 MUTATED RARS2 WILD-TYPE 
              6             349 
  RARS2 MUTATED RARS2 WILD-TYPE 
              2              76 
$`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 

$`RARS2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  RARS2 MUTATED RARS2 WILD-TYPE 
           4.01            0.00 
  RARS2 MUTATED RARS2 WILD-TYPE 
         148.01          140.38 
  RARS2 MUTATED RARS2 WILD-TYPE 
         38.715          22.060 
[1] "4.0 - 148.0 (38.7)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D1867V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RARS2 MUTATED         0        0        1         3         1         0
  RARS2 WILD-TYPE      64        1       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RARS2 MUTATED           1          0          1          0        0         0
  RARS2 WILD-TYPE        17          6         43         33       35        12
                 vv
clus              STAGE IVB
  RARS2 MUTATED           0
  RARS2 WILD-TYPE         1
D1867V3, multiclass
            clus
vv           RARS2 MUTATED RARS2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  RARS2 MUTATED     0   0   6   1
  RARS2 WILD-TYPE   9  67 243  40
D1867V4, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  T1             0               9
  T2             0              67
  T3             6             243
  T4             1              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
  RARS2 MUTATED     5   2   0
  RARS2 WILD-TYPE 215  79  66
D1867V5, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  N0             5             215
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1867V6, binary
                 cls
clus                0   1
  RARS2 MUTATED     7   0
  RARS2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      7    0
  RARS2 WILD-TYPE  278   48
   clus
vv  RARS2 MUTATED RARS2 WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1867V7, binary
                 cls
clus                0   1
  RARS2 MUTATED     3   4
  RARS2 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      3    4
  RARS2 WILD-TYPE  167  193
        clus
vv       RARS2 MUTATED RARS2 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1867V8, binary
                 cls
clus                0   1
  RARS2 MUTATED     5   0
  RARS2 WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      5    0
  RARS2 WILD-TYPE  295    8
     clus
vv    RARS2 MUTATED RARS2 WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1867V9, binary
                 cls
clus                0   1
  RARS2 MUTATED     4   3
  RARS2 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      4    3
  RARS2 WILD-TYPE  310   45
                               clus
vv                              RARS2 MUTATED RARS2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RARS2 MUTATED     5   1   0   1
  RARS2 WILD-TYPE 254   2  22  20
D1867V10, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  R0             5             254
  R1             1               2
  R2             0              22
  RX             1              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"
D1867V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RARS2 MUTATED                                  0     1
  RARS2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RARS2 MUTATED                           1     2
  RARS2 WILD-TYPE                        18   174
D1867V12, multiclass
                                  clus
vv                                 RARS2 MUTATED RARS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        2             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(1868) Variable = SMPDL3B MUTATION ANALYSIS
D1868V1, survival
                   sevent
clus2                 0   1
  SMPDL3B MUTATED     6   3
  SMPDL3B WILD-TYPE 271  75
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               346 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                3                75 
$`SMPDL3B MUTATED`
TCGA-AA-3662 TCGA-G4-6321 TCGA-AA-3864 TCGA-AA-3975 TCGA-AY-5543 TCGA-AZ-6598 
        6.05        22.09        53.00        34.06        33.01        49.41 
TCGA-CK-5916 TCGA-CM-5860 TCGA-F4-6570 
       21.14        32.02         6.18 

$`SMPDL3B WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 
      100.01         1.94        49.08         5.88        63.62        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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-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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
             6.05              0.00 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
            53.00            148.01 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
            32.02             22.01 
[1] "6.0 - 53.0 (32.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1868V2, continuous
                   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      62        1       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMPDL3B MUTATED           1          0          0          0        1
  SMPDL3B WILD-TYPE        17          6         44         33       34
                   vv
clus                STAGE IVA STAGE IVB
  SMPDL3B MUTATED           1         0
  SMPDL3B WILD-TYPE        11         1
D1868V3, multiclass
            clus
vv           SMPDL3B MUTATED SMPDL3B WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                24
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                1                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
  SMPDL3B MUTATED     1   2   5   1
  SMPDL3B WILD-TYPE   8  65 244  40
D1868V4, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  T1               1                 8
  T2               2                65
  T3               5               244
  T4               1                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
  SMPDL3B MUTATED     6   2   1
  SMPDL3B WILD-TYPE 214  79  65
D1868V5, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  N0               6               214
  N1               2                79
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1868V6, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     5   2
  SMPDL3B WILD-TYPE 280  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      5    2
  SMPDL3B WILD-TYPE  280   46
   clus
vv  SMPDL3B MUTATED SMPDL3B WILD-TYPE
  0               5               280
  1               2                46
[1] 2 2
[1] FALSE
D1868V7, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     6   3
  SMPDL3B WILD-TYPE 164 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      6    3
  SMPDL3B WILD-TYPE  164  194
        clus
vv       SMPDL3B MUTATED SMPDL3B WILD-TYPE
  FEMALE               6               164
  MALE                 3               194
[1] 2 2
[1] FALSE
D1868V8, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     9   0
  SMPDL3B WILD-TYPE 291   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      9    0
  SMPDL3B WILD-TYPE  291    8
     clus
vv    SMPDL3B MUTATED SMPDL3B WILD-TYPE
  NO                9               291
  YES               0                 8
[1] 2 2
[1] FALSE
D1868V9, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     9   0
  SMPDL3B WILD-TYPE 305  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      9    0
  SMPDL3B WILD-TYPE  305   48
                               clus
vv                              SMPDL3B MUTATED SMPDL3B WILD-TYPE
  COLON ADENOCARCINOMA                        9               305
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SMPDL3B MUTATED     6   0   1   1
  SMPDL3B WILD-TYPE 253   3  21  20
D1868V10, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  R0               6               253
  R1               0                 3
  R2               1                21
  RX               1                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"
D1868V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMPDL3B MUTATED                                  0     0
  SMPDL3B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMPDL3B MUTATED                           1     5
  SMPDL3B WILD-TYPE                        18   171
D1868V12, multiclass
                                  clus
vv                                 SMPDL3B MUTATED SMPDL3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          5               171
[1] 4 2
[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 = SEMA3C MUTATION ANALYSIS
D1869V1, survival
                  sevent
clus2                0   1
  SEMA3C MUTATED     6   4
  SEMA3C WILD-TYPE 271  74
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              10              345 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
               4               74 
$`SEMA3C MUTATED`
TCGA-AA-3713 TCGA-G4-6588 TCGA-AA-A01R TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       19.04        26.17        35.01        49.41        12.76        10.06 
TCGA-CA-6719 TCGA-D5-6928 TCGA-DM-A1DA TCGA-F4-6570 
       14.30        11.64         7.50         6.18 

$`SEMA3C WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 TCGA-AZ-6605 
       62.79        88.21         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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.59        12.20        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        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-F4-6459 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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  SEMA3C MUTATED SEMA3C WILD-TYPE 
            6.18             0.00 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
           49.41           148.01 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
           13.53            22.09 
[1] "6.2 - 49.4 (13.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D1869V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEMA3C MUTATED         0        0        1         7         1         0
  SEMA3C WILD-TYPE      64        1       25       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEMA3C MUTATED           1          0          0          1        1
  SEMA3C WILD-TYPE        17          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  SEMA3C MUTATED           0         0
  SEMA3C WILD-TYPE        12         1
D1869V3, multiclass
            clus
vv           SEMA3C MUTATED SEMA3C WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               7              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               0               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
  SEMA3C MUTATED     0   0  11   1
  SEMA3C WILD-TYPE   9  67 238  40
D1869V4, multiclass
    clus
vv   SEMA3C MUTATED SEMA3C WILD-TYPE
  T1              0                9
  T2              0               67
  T3             11              238
  T4              1               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
  SEMA3C MUTATED    10   0   2
  SEMA3C WILD-TYPE 210  81  64
D1869V5, multiclass
    clus
vv   SEMA3C MUTATED SEMA3C WILD-TYPE
  N0             10              210
  N1              0               81
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1869V6, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     9   1
  SEMA3C WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      9    1
  SEMA3C WILD-TYPE  276   47
   clus
vv  SEMA3C MUTATED SEMA3C WILD-TYPE
  0              9              276
  1              1               47
[1] 2 2
[1] FALSE
D1869V7, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     6   6
  SEMA3C WILD-TYPE 164 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      6    6
  SEMA3C WILD-TYPE  164  191
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  FEMALE              6              164
  MALE                6              191
[1] 2 2
[1] FALSE
D1869V8, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     7   2
  SEMA3C WILD-TYPE 293   6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      7    2
  SEMA3C WILD-TYPE  293    6
     clus
vv    SEMA3C MUTATED SEMA3C WILD-TYPE
  NO               7              293
  YES              2                6
[1] 2 2
[1] FALSE
D1869V9, binary
                  cls
clus                 0   1
  SEMA3C MUTATED     9   3
  SEMA3C WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3C MUTATED      9    3
  SEMA3C WILD-TYPE  305   45
                               clus
vv                              SEMA3C MUTATED SEMA3C WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SEMA3C MUTATED     5   0   1   4
  SEMA3C WILD-TYPE 254   3  21  17
D1869V10, multiclass
    clus
vv   SEMA3C MUTATED SEMA3C WILD-TYPE
  R0              5              254
  R1              0                3
  R2              1               21
  RX              4               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"
D1869V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEMA3C MUTATED                                  0     3
  SEMA3C WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SEMA3C MUTATED                           0     6
  SEMA3C WILD-TYPE                        19   170
D1869V12, multiclass
                                  clus
vv                                 SEMA3C MUTATED SEMA3C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         6              170
[1] 4 2
[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 = GABRG2 MUTATION ANALYSIS
D1870V1, survival
                  sevent
clus2                0   1
  GABRG2 MUTATED     9   3
  GABRG2 WILD-TYPE 268  75
  GABRG2 MUTATED GABRG2 WILD-TYPE 
              12              343 
  GABRG2 MUTATED GABRG2 WILD-TYPE 
               3               75 
$`GABRG2 MUTATED`
TCGA-A6-6142 TCGA-AA-3561 TCGA-AA-3811 TCGA-AA-3930 TCGA-AA-3977 TCGA-CK-4947 
       25.08        13.94        10.06         2.01        25.02        17.56 
TCGA-CM-6162 TCGA-CM-6677 TCGA-D5-6532 TCGA-DM-A1D0 TCGA-F4-6809 TCGA-F4-6856 
       12.00        11.08        18.25       130.65        13.25        35.31 

$`GABRG2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       53.00        17.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61        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        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        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-A1DA TCGA-DM-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        43.04        33.67 
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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  GABRG2 MUTATED GABRG2 WILD-TYPE 
            2.01             0.00 
  GABRG2 MUTATED GABRG2 WILD-TYPE 
          130.65           148.01 
  GABRG2 MUTATED GABRG2 WILD-TYPE 
           15.75            22.09 
[1] "2.0 - 130.7 (15.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1870V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABRG2 MUTATED         1        0        1         5         0         0
  GABRG2 WILD-TYPE      63        1       25       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRG2 MUTATED           1          0          2          0        1
  GABRG2 WILD-TYPE        17          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  GABRG2 MUTATED           2         0
  GABRG2 WILD-TYPE        10         1
D1870V3, multiclass
            clus
vv           GABRG2 MUTATED GABRG2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               5              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               2               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
  GABRG2 MUTATED     0   2  10   2
  GABRG2 WILD-TYPE   9  65 239  39
D1870V4, multiclass
    clus
vv   GABRG2 MUTATED GABRG2 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             10              239
  T4              2               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
  GABRG2 MUTATED     8   4   2
  GABRG2 WILD-TYPE 212  77  64
D1870V5, multiclass
    clus
vv   GABRG2 MUTATED GABRG2 WILD-TYPE
  N0              8              212
  N1              4               77
  N2              2               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1870V6, binary
                  cls
clus                 0   1
  GABRG2 MUTATED    10   3
  GABRG2 WILD-TYPE 275  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG2 MUTATED     10    3
  GABRG2 WILD-TYPE  275   45
   clus
vv  GABRG2 MUTATED GABRG2 WILD-TYPE
  0             10              275
  1              3               45
[1] 2 2
[1] FALSE
D1870V7, binary
                  cls
clus                 0   1
  GABRG2 MUTATED     9   5
  GABRG2 WILD-TYPE 161 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG2 MUTATED      9    5
  GABRG2 WILD-TYPE  161  192
        clus
vv       GABRG2 MUTATED GABRG2 WILD-TYPE
  FEMALE              9              161
  MALE                5              192
[1] 2 2
[1] FALSE
D1870V8, binary
                  cls
clus                 0   1
  GABRG2 MUTATED    11   0
  GABRG2 WILD-TYPE 289   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG2 MUTATED     11    0
  GABRG2 WILD-TYPE  289    8
     clus
vv    GABRG2 MUTATED GABRG2 WILD-TYPE
  NO              11              289
  YES              0                8
[1] 2 2
[1] FALSE
D1870V9, binary
                  cls
clus                 0   1
  GABRG2 MUTATED    12   2
  GABRG2 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG2 MUTATED     12    2
  GABRG2 WILD-TYPE  302   46
                               clus
vv                              GABRG2 MUTATED GABRG2 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GABRG2 MUTATED     9   0   1   1
  GABRG2 WILD-TYPE 250   3  21  20
D1870V10, multiclass
    clus
vv   GABRG2 MUTATED GABRG2 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              1               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"
D1870V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRG2 MUTATED                                  0     0
  GABRG2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GABRG2 MUTATED                           0     8
  GABRG2 WILD-TYPE                        19   168
D1870V12, multiclass
                                  clus
vv                                 GABRG2 MUTATED GABRG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         8              168
[1] 4 2
[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 = MTOR MUTATION ANALYSIS
D1871V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    26   7
  MTOR WILD-TYPE 251  71
  MTOR MUTATED MTOR WILD-TYPE 
            33            322 
  MTOR MUTATED MTOR WILD-TYPE 
             7             71 
$`MTOR MUTATED`
TCGA-A6-4105 TCGA-AA-3715 TCGA-AA-3867 TCGA-AZ-6601 TCGA-G4-6586 TCGA-A6-5666 
       14.53        19.04        24.03       100.01        35.80        32.71 
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3710 
        8.38        19.66        29.95         6.97         2.01        26.99 
TCGA-AA-3821 TCGA-AA-3854 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3980 
        1.02        36.03        31.00        26.01        34.03        27.02 
TCGA-AA-A00K TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-6598 
       18.05        34.98        27.09        33.01        21.44        49.41 
TCGA-CA-6716 TCGA-CM-4752 TCGA-DM-A1D4 TCGA-DM-A282 TCGA-DM-A28K TCGA-F4-6570 
       12.20        13.02        92.75       139.17        98.24         6.18 
TCGA-F4-6806 TCGA-G4-6307 TCGA-G4-6309 
       41.42        55.04        85.48 

$`MTOR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        24.16         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       15.52        25.08        10.88       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
        5.88        63.62        22.09        26.17        91.79        79.69 
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-A6-5656 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-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.08        25.18        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        78.08        54.02        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
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-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-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        33.01        20.98         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 
       26.47        14.50        16.31         0.95         0.20        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-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-6717 
       12.69        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65        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        43.04        33.67        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  MTOR MUTATED MTOR WILD-TYPE 
          1.02           0.00 
  MTOR MUTATED MTOR WILD-TYPE 
        139.17         148.01 
  MTOR MUTATED MTOR WILD-TYPE 
         27.09          21.99 
[1] "1.0 - 139.2 (27.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1871V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTOR MUTATED         6        0        4        15         1         1
  MTOR WILD-TYPE      58        1       22        93         7         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        17          6         41         32       34        11
                vv
clus             STAGE IVB
  MTOR MUTATED           0
  MTOR WILD-TYPE         1
D1871V3, multiclass
            clus
vv           MTOR MUTATED MTOR WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              4             22
  STAGE IIA            15             93
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            3             41
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  MTOR MUTATED     1   5  25   3
  MTOR WILD-TYPE   8  62 224  38
D1871V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1            1              8
  T2            5             62
  T3           25            224
  T4            3             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
  MTOR MUTATED    27   6   1
  MTOR WILD-TYPE 193  75  65
D1871V5, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  N0           27            193
  N1            6             75
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1871V6, binary
                cls
clus               0   1
  MTOR MUTATED    29   2
  MTOR WILD-TYPE 256  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     29    2
  MTOR WILD-TYPE  256   46
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           29            256
  1            2             46
[1] 2 2
[1] FALSE
D1871V7, binary
                cls
clus               0   1
  MTOR MUTATED    18  16
  MTOR WILD-TYPE 152 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     18   16
  MTOR WILD-TYPE  152  181
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           18            152
  MALE             16            181
[1] 2 2
[1] FALSE
D1871V8, binary
                cls
clus               0   1
  MTOR MUTATED    27   0
  MTOR WILD-TYPE 273   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     27    0
  MTOR WILD-TYPE  273    8
     clus
vv    MTOR MUTATED MTOR WILD-TYPE
  NO            27            273
  YES            0              8
[1] 2 2
[1] FALSE
D1871V9, binary
                cls
clus               0   1
  MTOR MUTATED    27   7
  MTOR WILD-TYPE 287  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     27    7
  MTOR WILD-TYPE  287   41
                               clus
vv                              MTOR MUTATED MTOR WILD-TYPE
  COLON ADENOCARCINOMA                    27            287
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTOR MUTATED    23   0   1   1
  MTOR WILD-TYPE 236   3  21  20
D1871V10, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  R0           23            236
  R1            0              3
  R2            1             21
  RX            1             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"
D1871V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTOR MUTATED                                  0     1
  MTOR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED                           4    14
  MTOR WILD-TYPE                        15   162
D1871V12, multiclass
                                  clus
vv                                 MTOR MUTATED MTOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   4             15
  WHITE                                      14            162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1872) Variable = CD84 MUTATION ANALYSIS
D1872V1, survival
                sevent
clus2              0   1
  CD84 MUTATED     8   1
  CD84 WILD-TYPE 269  77
  CD84 MUTATED CD84 WILD-TYPE 
             9            346 
  CD84 MUTATED CD84 WILD-TYPE 
             1             77 
$`CD84 MUTATED`
TCGA-G4-6588 TCGA-AA-3510 TCGA-AA-3854 TCGA-AA-3977 TCGA-CA-6717 TCGA-D5-6539 
       26.17        63.98        36.03        25.02        12.76        12.49 
TCGA-D5-7000 TCGA-DM-A28C TCGA-F4-6807 
       10.26        81.37        43.04 

$`CD84 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
       33.07         0.00        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        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-A28E 
        7.50        44.32       131.51       135.65       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-F4-6703 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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  CD84 MUTATED CD84 WILD-TYPE 
         10.26           0.00 
  CD84 MUTATED CD84 WILD-TYPE 
         81.37         148.01 
  CD84 MUTATED CD84 WILD-TYPE 
         26.17          22.01 
[1] "10.3 - 81.4 (26.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D1872V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD84 MUTATED         2        0        1         3         0         0
  CD84 WILD-TYPE      62        1       25       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD84 MUTATED           0          0          0          1        0         0
  CD84 WILD-TYPE        18          6         44         32       35        12
                vv
clus             STAGE IVB
  CD84 MUTATED           0
  CD84 WILD-TYPE         1
D1872V3, multiclass
            clus
vv           CD84 MUTATED CD84 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             3            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  CD84 MUTATED     0   3   6   0
  CD84 WILD-TYPE   9  64 243  41
D1872V4, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  T1            0              9
  T2            3             64
  T3            6            243
  T4            0             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
  CD84 MUTATED     8   0   1
  CD84 WILD-TYPE 212  81  65
D1872V5, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  N0            8            212
  N1            0             81
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1872V6, binary
                cls
clus               0   1
  CD84 MUTATED     8   0
  CD84 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      8    0
  CD84 WILD-TYPE  277   48
   clus
vv  CD84 MUTATED CD84 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1872V7, binary
                cls
clus               0   1
  CD84 MUTATED     5   4
  CD84 WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      5    4
  CD84 WILD-TYPE  165  193
        clus
vv       CD84 MUTATED CD84 WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D1872V8, binary
                cls
clus               0   1
  CD84 MUTATED     8   0
  CD84 WILD-TYPE 292   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      8    0
  CD84 WILD-TYPE  292    8
     clus
vv    CD84 MUTATED CD84 WILD-TYPE
  NO             8            292
  YES            0              8
[1] 2 2
[1] FALSE
D1872V9, binary
                cls
clus               0   1
  CD84 MUTATED     6   3
  CD84 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      6    3
  CD84 WILD-TYPE  308   45
                               clus
vv                              CD84 MUTATED CD84 WILD-TYPE
  COLON ADENOCARCINOMA                     6            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD84 MUTATED     6   0   0   1
  CD84 WILD-TYPE 253   3  22  20
D1872V10, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  R0            6            253
  R1            0              3
  R2            0             22
  RX            1             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"
D1872V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD84 MUTATED                                  0     1
  CD84 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD84 MUTATED                           0     5
  CD84 WILD-TYPE                        19   171
D1872V12, multiclass
                                  clus
vv                                 CD84 MUTATED CD84 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       5            171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1873) Variable = PRKD1 MUTATION ANALYSIS
D1873V1, survival
                 sevent
clus2               0   1
  PRKD1 MUTATED    19   4
  PRKD1 WILD-TYPE 258  74
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             23             332 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
              4              74 
$`PRKD1 MUTATED`
TCGA-AA-3713 TCGA-G4-6628 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3710 TCGA-AA-3821 
       19.04        79.69        63.98        61.02        26.99         1.02 
TCGA-AA-3845 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A02J TCGA-AD-5900 
        0.00        34.06        25.02        34.98         5.03        12.16 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-5864 
       58.39         6.77         5.23        12.76        15.02        15.02 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-F4-6855 TCGA-G4-6293 
       25.48        43.27        17.13        47.41       133.18 

$`PRKD1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        78.08         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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        37.02        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3980 
       34.03         2.01        21.99        16.08        13.05        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-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-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.19        18.25 
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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
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-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  PRKD1 MUTATED PRKD1 WILD-TYPE 
              0               0 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
         133.18          148.01 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
         25.020          22.045 
[1] "0.0 - 133.2 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1873V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKD1 MUTATED         6        0        2         8         1         0
  PRKD1 WILD-TYPE      58        1       24       100         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKD1 MUTATED           1          0          2          0        2         0
  PRKD1 WILD-TYPE        17          6         42         33       33        12
                 vv
clus              STAGE IVB
  PRKD1 MUTATED           0
  PRKD1 WILD-TYPE         1
D1873V3, multiclass
            clus
vv           PRKD1 MUTATED PRKD1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              8             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             2              42
  STAGE IIIC             0              33
  STAGE IV               2              33
  STAGE IVA              0              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
  PRKD1 MUTATED     0   7  14   3
  PRKD1 WILD-TYPE   9  60 235  38
D1873V4, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  T1             0               9
  T2             7              60
  T3            14             235
  T4             3              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
  PRKD1 MUTATED    21   2   1
  PRKD1 WILD-TYPE 199  79  65
D1873V5, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  N0            21             199
  N1             2              79
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1873V6, binary
                 cls
clus                0   1
  PRKD1 MUTATED    19   2
  PRKD1 WILD-TYPE 266  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     19    2
  PRKD1 WILD-TYPE  266   46
   clus
vv  PRKD1 MUTATED PRKD1 WILD-TYPE
  0            19             266
  1             2              46
[1] 2 2
[1] FALSE
D1873V7, binary
                 cls
clus                0   1
  PRKD1 MUTATED    12  12
  PRKD1 WILD-TYPE 158 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     12   12
  PRKD1 WILD-TYPE  158  185
        clus
vv       PRKD1 MUTATED PRKD1 WILD-TYPE
  FEMALE            12             158
  MALE              12             185
[1] 2 2
[1] FALSE
D1873V8, binary
                 cls
clus                0   1
  PRKD1 MUTATED    20   1
  PRKD1 WILD-TYPE 280   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     20    1
  PRKD1 WILD-TYPE  280    7
     clus
vv    PRKD1 MUTATED PRKD1 WILD-TYPE
  NO             20             280
  YES             1               7
[1] 2 2
[1] FALSE
D1873V9, binary
                 cls
clus                0   1
  PRKD1 MUTATED    20   4
  PRKD1 WILD-TYPE 294  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     20    4
  PRKD1 WILD-TYPE  294   44
                               clus
vv                              PRKD1 MUTATED PRKD1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             294
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKD1 MUTATED    18   0   2   1
  PRKD1 WILD-TYPE 241   3  20  20
D1873V10, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  R0            18             241
  R1             0               3
  R2             2              20
  RX             1              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"
D1873V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKD1 MUTATED                                  0     1
  PRKD1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKD1 MUTATED                           0    12
  PRKD1 WILD-TYPE                        19   164
D1873V12, multiclass
                                  clus
vv                                 PRKD1 MUTATED PRKD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                       12             164
[1] 4 2
[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 = TET1 MUTATION ANALYSIS
D1874V1, survival
                sevent
clus2              0   1
  TET1 MUTATED    17   5
  TET1 WILD-TYPE 260  73
  TET1 MUTATED TET1 WILD-TYPE 
            22            333 
  TET1 MUTATED TET1 WILD-TYPE 
             5             73 
$`TET1 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A00L TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3696 
       19.04        24.00        38.04        32.75        22.06         5.03 
TCGA-AA-3837 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A01K 
       38.99        53.00         2.01        25.02        18.05        31.00 
TCGA-AA-A01Q TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-6171 
        1.02        27.09         0.20        49.41        10.06        14.04 
TCGA-CM-6678 TCGA-D5-6928 TCGA-F4-6570 TCGA-F4-6807 
       11.01        11.64         6.18        43.04 

$`TET1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        19.07        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08         5.88        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 
       42.28        16.57        34.65        33.34        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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3710 
       47.01        15.02        11.01         5.98        37.05        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-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05         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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        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-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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       35.74        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-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TET1 MUTATED TET1 WILD-TYPE 
           0.2            0.0 
  TET1 MUTATED TET1 WILD-TYPE 
         53.00         148.01 
  TET1 MUTATED TET1 WILD-TYPE 
         20.55          22.09 
[1] "0.2 - 53.0 (20.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1874V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TET1 MUTATED         2        0        5         8         1         0
  TET1 WILD-TYPE      62        1       21       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TET1 MUTATED           0          0          1          3        1         1
  TET1 WILD-TYPE        18          6         43         30       34        11
                vv
clus             STAGE IVB
  TET1 MUTATED           0
  TET1 WILD-TYPE         1
D1874V3, multiclass
            clus
vv           TET1 MUTATED TET1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              5             21
  STAGE IIA             8            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            1             43
  STAGE IIIC            3             30
  STAGE IV              1             34
  STAGE IVA             1             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
  TET1 MUTATED     0   3  16   4
  TET1 WILD-TYPE   9  64 233  37
D1874V4, multiclass
    clus
vv   TET1 MUTATED TET1 WILD-TYPE
  T1            0              9
  T2            3             64
  T3           16            233
  T4            4             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
  TET1 MUTATED    17   3   3
  TET1 WILD-TYPE 203  78  63
D1874V5, multiclass
    clus
vv   TET1 MUTATED TET1 WILD-TYPE
  N0           17            203
  N1            3             78
  N2            3             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"
D1874V6, binary
                cls
clus               0   1
  TET1 MUTATED    18   2
  TET1 WILD-TYPE 267  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET1 MUTATED     18    2
  TET1 WILD-TYPE  267   46
   clus
vv  TET1 MUTATED TET1 WILD-TYPE
  0           18            267
  1            2             46
[1] 2 2
[1] FALSE
D1874V7, binary
                cls
clus               0   1
  TET1 MUTATED    14   9
  TET1 WILD-TYPE 156 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET1 MUTATED     14    9
  TET1 WILD-TYPE  156  188
        clus
vv       TET1 MUTATED TET1 WILD-TYPE
  FEMALE           14            156
  MALE              9            188
[1] 2 2
[1] FALSE
D1874V8, binary
                cls
clus               0   1
  TET1 MUTATED    18   0
  TET1 WILD-TYPE 282   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET1 MUTATED     18    0
  TET1 WILD-TYPE  282    8
     clus
vv    TET1 MUTATED TET1 WILD-TYPE
  NO            18            282
  YES            0              8
[1] 2 2
[1] FALSE
D1874V9, binary
                cls
clus               0   1
  TET1 MUTATED    16   7
  TET1 WILD-TYPE 298  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET1 MUTATED     16    7
  TET1 WILD-TYPE  298   41
                               clus
vv                              TET1 MUTATED TET1 WILD-TYPE
  COLON ADENOCARCINOMA                    16            298
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TET1 MUTATED    18   0   1   1
  TET1 WILD-TYPE 241   3  21  20
D1874V10, multiclass
    clus
vv   TET1 MUTATED TET1 WILD-TYPE
  R0           18            241
  R1            0              3
  R2            1             21
  RX            1             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"
D1874V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TET1 MUTATED                                  0     1
  TET1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TET1 MUTATED                           0    10
  TET1 WILD-TYPE                        19   166
D1874V12, multiclass
                                  clus
vv                                 TET1 MUTATED TET1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(1875) Variable = FLG MUTATION ANALYSIS
D1875V1, survival
               sevent
clus2             0   1
  FLG MUTATED    46  16
  FLG WILD-TYPE 231  62
  FLG MUTATED FLG WILD-TYPE 
           62           293 
  FLG MUTATED FLG WILD-TYPE 
           16            62 
$`FLG MUTATED`
TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3870 TCGA-AA-3952 TCGA-AA-A024 
       24.16         1.02        13.02        29.98         2.01        39.06 
TCGA-AD-6548 TCGA-AD-6964 TCGA-A6-3808 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-6137 
       21.37        10.88        33.34        29.19        33.53        27.09 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3681 TCGA-AA-3710 
       24.39        20.12        19.66         3.02         5.98        26.99 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3854 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       15.95         0.00        36.03        31.07        30.05        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 
       31.00        33.01        25.02        27.02         4.01        34.98 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02K TCGA-AD-6890 
       35.01         1.02        37.02        51.98        14.01        24.53 
TCGA-AU-6004 TCGA-AY-4071 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       27.09         0.95        12.69        12.59        12.20        10.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6164 TCGA-D5-5540 
       22.98        32.02         5.03        17.03        29.03        56.09 
TCGA-D5-6529 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6928 TCGA-DM-A0XD TCGA-DM-A1D0 
       20.19        16.14        15.58        11.64        24.43       130.65 
TCGA-DM-A1D7 TCGA-DM-A282 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6809 
       13.32       139.17        31.96         6.18        47.87        13.25 
TCGA-G4-6309 TCGA-G4-6323 
       85.48        13.78 

$`FLG WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       24.33        14.53        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6601 
       38.04        21.99        15.52        25.08       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        32.75        36.53 
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-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       32.71        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       24.69        23.87        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.01        15.02        11.01        37.05         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-3837 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       17.98        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 
       33.07         0.00        32.05         0.99        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       18.05         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        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-A01X TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       26.01        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        83.24         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
       22.42        27.42        26.47        14.50        16.31        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74         3.19        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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-5861 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08        15.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        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-D5-6532 TCGA-D5-6533 
       45.40        54.61        19.59        55.92        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        38.20        92.75        49.91        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-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       44.68        55.04        61.91        36.00        46.75 

  FLG MUTATED FLG WILD-TYPE 
            0             0 
  FLG MUTATED FLG WILD-TYPE 
       139.17        148.01 
  FLG MUTATED FLG WILD-TYPE 
       24.275        21.990 
[1] "0.0 - 139.2 (24.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1875V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLG MUTATED         9        1        7        23         3         0
  FLG WILD-TYPE      55        0       19        85         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLG MUTATED           3          0          7          3        2         3
  FLG WILD-TYPE        15          6         37         30       33         9
               vv
clus            STAGE IVB
  FLG MUTATED           0
  FLG WILD-TYPE         1
D1875V3, multiclass
            clus
vv           FLG MUTATED FLG WILD-TYPE
  STAGE I              9            55
  STAGE IA             1             0
  STAGE II             7            19
  STAGE IIA           23            85
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            3            15
  STAGE IIIA           0             6
  STAGE IIIB           7            37
  STAGE IIIC           3            30
  STAGE IV             2            33
  STAGE IVA            3             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
  FLG MUTATED     3   8  44   8
  FLG WILD-TYPE   6  59 205  33
D1875V4, multiclass
    clus
vv   FLG MUTATED FLG WILD-TYPE
  T1           3             6
  T2           8            59
  T3          44           205
  T4           8            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  FLG MUTATED    45  12   7
  FLG WILD-TYPE 175  69  59
D1875V5, multiclass
    clus
vv   FLG MUTATED FLG WILD-TYPE
  N0          45           175
  N1          12            69
  N2           7            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1875V6, binary
               cls
clus              0   1
  FLG MUTATED    52   5
  FLG WILD-TYPE 233  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     52    5
  FLG WILD-TYPE  233   43
   clus
vv  FLG MUTATED FLG WILD-TYPE
  0          52           233
  1           5            43
[1] 2 2
[1] FALSE
D1875V7, binary
               cls
clus              0   1
  FLG MUTATED    27  37
  FLG WILD-TYPE 143 160
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     27   37
  FLG WILD-TYPE  143  160
        clus
vv       FLG MUTATED FLG WILD-TYPE
  FEMALE          27           143
  MALE            37           160
[1] 2 2
[1] FALSE
D1875V8, binary
               cls
clus              0   1
  FLG MUTATED    50   1
  FLG WILD-TYPE 250   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     50    1
  FLG WILD-TYPE  250    7
     clus
vv    FLG MUTATED FLG WILD-TYPE
  NO           50           250
  YES           1             7
[1] 2 2
[1] FALSE
D1875V9, binary
               cls
clus              0   1
  FLG MUTATED    51  11
  FLG WILD-TYPE 263  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     51   11
  FLG WILD-TYPE  263   37
                               clus
vv                              FLG MUTATED FLG WILD-TYPE
  COLON ADENOCARCINOMA                   51           263
  COLON MUCINOUS ADENOCARCINOMA          11            37
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FLG MUTATED    45   0   1   4
  FLG WILD-TYPE 214   3  21  17
D1875V10, multiclass
    clus
vv   FLG MUTATED FLG WILD-TYPE
  R0          45           214
  R1           0             3
  R2           1            21
  RX           4            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"
D1875V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLG MUTATED                                  0     4
  FLG WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FLG MUTATED                           4    29
  FLG WILD-TYPE                        15   147
D1875V12, multiclass
                                  clus
vv                                 FLG MUTATED FLG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      4             6
  BLACK OR AFRICAN AMERICAN                  4            15
  WHITE                                     29           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(1876) Variable = SCNN1G MUTATION ANALYSIS
D1876V1, survival
                  sevent
clus2                0   1
  SCNN1G MUTATED     6   3
  SCNN1G WILD-TYPE 271  75
  SCNN1G MUTATED SCNN1G WILD-TYPE 
               9              346 
  SCNN1G MUTATED SCNN1G WILD-TYPE 
               3               75 
$`SCNN1G MUTATED`
TCGA-AA-3715 TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6648 TCGA-AA-3511 
       19.04        26.17        33.53        22.06        25.18         6.97 
TCGA-AA-3811 TCGA-CK-4950 TCGA-G4-6303 
       10.06        85.45        65.85 

$`SCNN1G WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        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-A6-6651 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-3514 
       20.28         7.04         3.02        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  SCNN1G MUTATED SCNN1G WILD-TYPE 
            6.97             0.00 
  SCNN1G MUTATED SCNN1G WILD-TYPE 
           85.45           148.01 
  SCNN1G MUTATED SCNN1G WILD-TYPE 
           25.18            22.01 
[1] "7.0 - 85.5 (25.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1876V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCNN1G MUTATED         0        0        2         3         0         0
  SCNN1G WILD-TYPE      64        1       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCNN1G MUTATED           1          0          1          0        1
  SCNN1G WILD-TYPE        17          6         43         33       34
                  vv
clus               STAGE IVA STAGE IVB
  SCNN1G MUTATED           1         0
  SCNN1G WILD-TYPE        11         1
D1876V3, multiclass
            clus
vv           SCNN1G MUTATED SCNN1G WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               3              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               1               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
  SCNN1G MUTATED     0   0   8   1
  SCNN1G WILD-TYPE   9  67 241  40
D1876V4, multiclass
    clus
vv   SCNN1G MUTATED SCNN1G WILD-TYPE
  T1              0                9
  T2              0               67
  T3              8              241
  T4              1               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
  SCNN1G MUTATED     6   2   1
  SCNN1G WILD-TYPE 214  79  65
D1876V5, multiclass
    clus
vv   SCNN1G MUTATED SCNN1G WILD-TYPE
  N0              6              214
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1876V6, binary
                  cls
clus                 0   1
  SCNN1G MUTATED     7   2
  SCNN1G WILD-TYPE 278  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1G MUTATED      7    2
  SCNN1G WILD-TYPE  278   46
   clus
vv  SCNN1G MUTATED SCNN1G WILD-TYPE
  0              7              278
  1              2               46
[1] 2 2
[1] FALSE
D1876V7, binary
                  cls
clus                 0   1
  SCNN1G MUTATED     6   3
  SCNN1G WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1G MUTATED      6    3
  SCNN1G WILD-TYPE  164  194
        clus
vv       SCNN1G MUTATED SCNN1G WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D1876V8, binary
                  cls
clus                 0   1
  SCNN1G MUTATED     9   0
  SCNN1G WILD-TYPE 291   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1G MUTATED      9    0
  SCNN1G WILD-TYPE  291    8
     clus
vv    SCNN1G MUTATED SCNN1G WILD-TYPE
  NO               9              291
  YES              0                8
[1] 2 2
[1] FALSE
D1876V9, binary
                  cls
clus                 0   1
  SCNN1G MUTATED     8   1
  SCNN1G WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1G MUTATED      8    1
  SCNN1G WILD-TYPE  306   47
                               clus
vv                              SCNN1G MUTATED SCNN1G WILD-TYPE
  COLON ADENOCARCINOMA                       8              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SCNN1G MUTATED     7   1   0   0
  SCNN1G WILD-TYPE 252   2  22  21
D1876V10, multiclass
    clus
vv   SCNN1G MUTATED SCNN1G WILD-TYPE
  R0              7              252
  R1              1                2
  R2              0               22
  RX              0               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"
D1876V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCNN1G MUTATED                                  0     0
  SCNN1G WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SCNN1G MUTATED                           2     4
  SCNN1G WILD-TYPE                        17   172
D1876V12, multiclass
                                  clus
vv                                 SCNN1G MUTATED SCNN1G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               17
  WHITE                                         4              172
[1] 4 2
[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 = SLC19A2 MUTATION ANALYSIS
D1877V1, survival
                   sevent
clus2                 0   1
  SLC19A2 MUTATED     6   0
  SLC19A2 WILD-TYPE 271  78
  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
                6               349 
  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
                0                78 
$`SLC19A2 MUTATED`
TCGA-AA-3844 TCGA-AA-3663 TCGA-AA-3966 TCGA-CM-5864 TCGA-D5-6540 TCGA-DM-A1HB 
       14.93         6.97         2.01        15.02        16.14       135.65 

$`SLC19A2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
             2.01              0.00 
  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
           135.65            148.01 
  SLC19A2 MUTATED SLC19A2 WILD-TYPE 
           14.975            22.090 
[1] "2.0 - 135.7 (15.0)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D1877V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC19A2 MUTATED         2        0        1         2         0         0
  SLC19A2 WILD-TYPE      62        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC19A2 MUTATED           0          0          1          1        0
  SLC19A2 WILD-TYPE        18          6         43         32       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC19A2 MUTATED           0         0
  SLC19A2 WILD-TYPE        12         1
D1877V3, multiclass
            clus
vv           SLC19A2 MUTATED SLC19A2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               1                32
  STAGE IV                 0                35
  STAGE IVA                0                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
  SLC19A2 MUTATED     0   2   5   0
  SLC19A2 WILD-TYPE   9  65 244  41
D1877V4, multiclass
    clus
vv   SLC19A2 MUTATED SLC19A2 WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               5               244
  T4               0                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
  SLC19A2 MUTATED     5   1   1
  SLC19A2 WILD-TYPE 215  80  65
D1877V5, multiclass
    clus
vv   SLC19A2 MUTATED SLC19A2 WILD-TYPE
  N0               5               215
  N1               1                80
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1877V6, binary
                   cls
clus                  0   1
  SLC19A2 MUTATED     7   0
  SLC19A2 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC19A2 MUTATED      7    0
  SLC19A2 WILD-TYPE  278   48
   clus
vv  SLC19A2 MUTATED SLC19A2 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D1877V7, binary
                   cls
clus                  0   1
  SLC19A2 MUTATED     3   4
  SLC19A2 WILD-TYPE 167 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC19A2 MUTATED      3    4
  SLC19A2 WILD-TYPE  167  193
        clus
vv       SLC19A2 MUTATED SLC19A2 WILD-TYPE
  FEMALE               3               167
  MALE                 4               193
[1] 2 2
[1] FALSE
D1877V8, binary
                   cls
clus                  0   1
  SLC19A2 MUTATED     3   1
  SLC19A2 WILD-TYPE 297   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC19A2 MUTATED      3    1
  SLC19A2 WILD-TYPE  297    7
     clus
vv    SLC19A2 MUTATED SLC19A2 WILD-TYPE
  NO                3               297
  YES               1                 7
[1] 2 2
[1] FALSE
D1877V9, binary
                   cls
clus                  0   1
  SLC19A2 MUTATED     4   2
  SLC19A2 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC19A2 MUTATED      4    2
  SLC19A2 WILD-TYPE  310   46
                               clus
vv                              SLC19A2 MUTATED SLC19A2 WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC19A2 MUTATED     5   0   0   0
  SLC19A2 WILD-TYPE 254   3  22  21
D1877V10, multiclass
    clus
vv   SLC19A2 MUTATED SLC19A2 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               0                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"
D1877V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC19A2 MUTATED                                  0     0
  SLC19A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC19A2 MUTATED                           0     3
  SLC19A2 WILD-TYPE                        19   173
D1877V12, multiclass
                                  clus
vv                                 SLC19A2 MUTATED SLC19A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = TBC1D25 MUTATION ANALYSIS
D1878V1, survival
                   sevent
clus2                 0   1
  TBC1D25 MUTATED     9   2
  TBC1D25 WILD-TYPE 268  76
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
               11               344 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
                2                76 
$`TBC1D25 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6586 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3833 
       19.04        24.00        35.80        10.06         1.02        15.95 
TCGA-AA-3875 TCGA-AA-3977 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6928 
       18.05        25.02        12.16        14.50        11.64 

$`TBC1D25 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       37.05         5.03        26.99        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       25.02        17.98        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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
             1.02              0.00 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
            35.80            148.01 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
           15.950            22.225 
[1] "1.0 - 35.8 (15.9)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.3"
D1878V2, continuous
                   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      61        1       25       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D25 MUTATED           1          0          0          0        0
  TBC1D25 WILD-TYPE        17          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  TBC1D25 MUTATED           0         0
  TBC1D25 WILD-TYPE        12         1
D1878V3, multiclass
            clus
vv           TBC1D25 MUTATED TBC1D25 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                5               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  TBC1D25 MUTATED     1   3   7   0
  TBC1D25 WILD-TYPE   8  64 242  41
D1878V4, multiclass
    clus
vv   TBC1D25 MUTATED TBC1D25 WILD-TYPE
  T1               1                 8
  T2               3                64
  T3               7               242
  T4               0                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
  TBC1D25 MUTATED    10   0   1
  TBC1D25 WILD-TYPE 210  81  65
D1878V5, multiclass
    clus
vv   TBC1D25 MUTATED TBC1D25 WILD-TYPE
  N0              10               210
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1878V6, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED     9   0
  TBC1D25 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED      9    0
  TBC1D25 WILD-TYPE  276   48
   clus
vv  TBC1D25 MUTATED TBC1D25 WILD-TYPE
  0               9               276
  1               0                48
[1] 2 2
[1] FALSE
D1878V7, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED     7   4
  TBC1D25 WILD-TYPE 163 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED      7    4
  TBC1D25 WILD-TYPE  163  193
        clus
vv       TBC1D25 MUTATED TBC1D25 WILD-TYPE
  FEMALE               7               163
  MALE                 4               193
[1] 2 2
[1] FALSE
D1878V8, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED    11   0
  TBC1D25 WILD-TYPE 289   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED     11    0
  TBC1D25 WILD-TYPE  289    8
     clus
vv    TBC1D25 MUTATED TBC1D25 WILD-TYPE
  NO               11               289
  YES               0                 8
[1] 2 2
[1] FALSE
D1878V9, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED     7   4
  TBC1D25 WILD-TYPE 307  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED      7    4
  TBC1D25 WILD-TYPE  307   44
                               clus
vv                              TBC1D25 MUTATED TBC1D25 WILD-TYPE
  COLON ADENOCARCINOMA                        7               307
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TBC1D25 MUTATED    10   0   0   0
  TBC1D25 WILD-TYPE 249   3  22  21
D1878V10, multiclass
    clus
vv   TBC1D25 MUTATED TBC1D25 WILD-TYPE
  R0              10               249
  R1               0                 3
  R2               0                22
  RX               0                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"
D1878V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBC1D25 MUTATED                                  0     0
  TBC1D25 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TBC1D25 MUTATED                           0     4
  TBC1D25 WILD-TYPE                        19   172
D1878V12, multiclass
                                  clus
vv                                 TBC1D25 MUTATED TBC1D25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          4               172
[1] 4 2
[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 = PCDHGA9 MUTATION ANALYSIS
D1879V1, survival
                   sevent
clus2                 0   1
  PCDHGA9 MUTATED    10   2
  PCDHGA9 WILD-TYPE 267  76
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
               12               343 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                2                76 
$`PCDHGA9 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6321 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3664 
        0.92       100.01        22.09        23.61        22.06        54.02 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AY-4070 TCGA-AZ-4315 TCGA-CM-6678 TCGA-G4-6317 
       53.00        31.00        16.31        58.39        11.01        36.00 

$`PCDHGA9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
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-A6-6651 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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        30.05        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        27.09         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 
       53.62        44.68        55.04        85.48        61.91        13.78 
TCGA-G4-6626 
       46.75 

  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
             0.92              0.00 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
           100.01            148.01 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
           27.305            21.990 
[1] "0.9 - 100.0 (27.3)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1879V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGA9 MUTATED         1        0        3         2         0         0
  PCDHGA9 WILD-TYPE      63        1       23       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA9 MUTATED           2          0          0          2        0
  PCDHGA9 WILD-TYPE        16          6         44         31       35
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGA9 MUTATED           2         0
  PCDHGA9 WILD-TYPE        10         1
D1879V3, multiclass
            clus
vv           PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                23
  STAGE IIA                2               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                16
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               2                31
  STAGE IV                 0                35
  STAGE IVA                2                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
  PCDHGA9 MUTATED     1   1   9   1
  PCDHGA9 WILD-TYPE   8  66 240  40
D1879V4, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               9               240
  T4               1                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
  PCDHGA9 MUTATED     6   3   3
  PCDHGA9 WILD-TYPE 214  78  63
D1879V5, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  N0               6               214
  N1               3                78
  N2               3                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"
D1879V6, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED     8   2
  PCDHGA9 WILD-TYPE 277  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      8    2
  PCDHGA9 WILD-TYPE  277   46
   clus
vv  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  0               8               277
  1               2                46
[1] 2 2
[1] FALSE
D1879V7, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED     8   4
  PCDHGA9 WILD-TYPE 162 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      8    4
  PCDHGA9 WILD-TYPE  162  193
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  FEMALE               8               162
  MALE                 4               193
[1] 2 2
[1] FALSE
D1879V8, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED    12   0
  PCDHGA9 WILD-TYPE 288   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED     12    0
  PCDHGA9 WILD-TYPE  288    8
     clus
vv    PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  NO               12               288
  YES               0                 8
[1] 2 2
[1] FALSE
D1879V9, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED    11   1
  PCDHGA9 WILD-TYPE 303  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED     11    1
  PCDHGA9 WILD-TYPE  303   47
                               clus
vv                              PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  COLON ADENOCARCINOMA                       11               303
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PCDHGA9 MUTATED     9   1   0   0
  PCDHGA9 WILD-TYPE 250   2  22  21
D1879V10, multiclass
    clus
vv   PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  R0               9               250
  R1               1                 2
  R2               0                22
  RX               0                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"
D1879V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA9 MUTATED                                  0     0
  PCDHGA9 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA9 MUTATED                           1     7
  PCDHGA9 WILD-TYPE                        18   169
D1879V12, multiclass
                                  clus
vv                                 PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          7               169
[1] 4 2
[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 = HIF1A MUTATION ANALYSIS
D1880V1, survival
                 sevent
clus2               0   1
  HIF1A MUTATED     8   3
  HIF1A WILD-TYPE 269  75
  HIF1A MUTATED HIF1A WILD-TYPE 
             11             344 
  HIF1A MUTATED HIF1A WILD-TYPE 
              3              75 
$`HIF1A MUTATED`
TCGA-AA-3950 TCGA-G4-6628 TCGA-A6-3809 TCGA-AA-A00E TCGA-AA-A02K TCGA-AZ-4315 
       24.00        79.69        32.75        30.02        14.01        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6674 TCGA-D5-6928 
       49.41        12.76        10.06        12.95        11.64 

$`HIF1A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        91.79        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 
       42.90        42.28        16.57        34.65        33.34        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  HIF1A MUTATED HIF1A WILD-TYPE 
          10.06            0.00 
  HIF1A MUTATED HIF1A WILD-TYPE 
          79.69          148.01 
  HIF1A MUTATED HIF1A WILD-TYPE 
         24.000          22.045 
[1] "10.1 - 79.7 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1880V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIF1A MUTATED         1        0        1         7         1         0
  HIF1A WILD-TYPE      63        1       25       101         7         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        18          6         44         33       34        12
                 vv
clus              STAGE IVB
  HIF1A MUTATED           0
  HIF1A WILD-TYPE         1
D1880V3, multiclass
            clus
vv           HIF1A MUTATED HIF1A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              7             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HIF1A MUTATED     0   1   8   2
  HIF1A WILD-TYPE   9  66 241  39
D1880V4, multiclass
    clus
vv   HIF1A MUTATED HIF1A WILD-TYPE
  T1             0               9
  T2             1              66
  T3             8             241
  T4             2              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
  HIF1A MUTATED    10   0   1
  HIF1A WILD-TYPE 210  81  65
D1880V5, multiclass
    clus
vv   HIF1A MUTATED HIF1A WILD-TYPE
  N0            10             210
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1880V6, binary
                 cls
clus                0   1
  HIF1A MUTATED     9   1
  HIF1A WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED      9    1
  HIF1A WILD-TYPE  276   47
   clus
vv  HIF1A MUTATED HIF1A WILD-TYPE
  0             9             276
  1             1              47
[1] 2 2
[1] FALSE
D1880V7, binary
                 cls
clus                0   1
  HIF1A MUTATED     3   8
  HIF1A WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED      3    8
  HIF1A WILD-TYPE  167  189
        clus
vv       HIF1A MUTATED HIF1A WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1880V8, binary
                 cls
clus                0   1
  HIF1A MUTATED    11   0
  HIF1A WILD-TYPE 289   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED     11    0
  HIF1A WILD-TYPE  289    8
     clus
vv    HIF1A MUTATED HIF1A WILD-TYPE
  NO             11             289
  YES             0               8
[1] 2 2
[1] FALSE
D1880V9, binary
                 cls
clus                0   1
  HIF1A MUTATED     7   4
  HIF1A WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED      7    4
  HIF1A WILD-TYPE  307   44
                               clus
vv                              HIF1A MUTATED HIF1A WILD-TYPE
  COLON ADENOCARCINOMA                      7             307
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HIF1A MUTATED     7   0   1   2
  HIF1A WILD-TYPE 252   3  21  19
D1880V10, multiclass
    clus
vv   HIF1A MUTATED HIF1A WILD-TYPE
  R0             7             252
  R1             0               3
  R2             1              21
  RX             2              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"
D1880V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIF1A MUTATED                                  0     2
  HIF1A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIF1A MUTATED                           0     6
  HIF1A WILD-TYPE                        19   170
D1880V12, multiclass
                                  clus
vv                                 HIF1A MUTATED HIF1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        6             170
[1] 4 2
[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 = ZNF521 MUTATION ANALYSIS
D1881V1, survival
                  sevent
clus2                0   1
  ZNF521 MUTATED    20   7
  ZNF521 WILD-TYPE 257  71
  ZNF521 MUTATED ZNF521 WILD-TYPE 
              27              328 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
               7               71 
$`ZNF521 MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3950 TCGA-AA-3976 TCGA-AD-6964 TCGA-AZ-6601 
       13.02         8.05        24.00        26.01        10.88       100.01 
TCGA-G4-6588 TCGA-A6-5661 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3561 TCGA-AA-3663 
       26.17        33.53        23.87        19.66        13.94         6.97 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 
       25.02        27.02        34.98        35.01        58.39        12.76 
TCGA-CA-6718 TCGA-CM-6161 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A1D0 
       10.06        15.02        17.85         4.80        13.35       130.65 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6809 
       98.24         8.61        13.25 

$`ZNF521 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
       36.03        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 
       24.03        29.98        12.99         2.01        50.99        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
       25.08       106.75         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        20.98        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-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        30.05        53.00        17.03        27.02 
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-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-3980 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        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-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 
       43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        13.78        46.75 

  ZNF521 MUTATED ZNF521 WILD-TYPE 
             4.8              0.0 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
          130.65           148.01 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
          19.660           22.075 
[1] "4.8 - 130.7 (19.7)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D1881V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF521 MUTATED         1        0        2        12         1         0
  ZNF521 WILD-TYPE      63        1       24        96         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF521 MUTATED           2          1          5          1        0
  ZNF521 WILD-TYPE        16          5         39         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF521 MUTATED           1         0
  ZNF521 WILD-TYPE        11         1
D1881V3, multiclass
            clus
vv           ZNF521 MUTATED ZNF521 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              12               96
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              1                5
  STAGE IIIB              5               39
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF521 MUTATED     0   3  22   3
  ZNF521 WILD-TYPE   9  64 227  38
D1881V4, multiclass
    clus
vv   ZNF521 MUTATED ZNF521 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             22              227
  T4              3               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
  ZNF521 MUTATED    17   7   4
  ZNF521 WILD-TYPE 203  74  62
D1881V5, multiclass
    clus
vv   ZNF521 MUTATED ZNF521 WILD-TYPE
  N0             17              203
  N1              7               74
  N2              4               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1881V6, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    23   1
  ZNF521 WILD-TYPE 262  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     23    1
  ZNF521 WILD-TYPE  262   47
   clus
vv  ZNF521 MUTATED ZNF521 WILD-TYPE
  0             23              262
  1              1               47
[1] 2 2
[1] FALSE
D1881V7, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    11  17
  ZNF521 WILD-TYPE 159 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     11   17
  ZNF521 WILD-TYPE  159  180
        clus
vv       ZNF521 MUTATED ZNF521 WILD-TYPE
  FEMALE             11              159
  MALE               17              180
[1] 2 2
[1] FALSE
D1881V8, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    24   1
  ZNF521 WILD-TYPE 276   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     24    1
  ZNF521 WILD-TYPE  276    7
     clus
vv    ZNF521 MUTATED ZNF521 WILD-TYPE
  NO              24              276
  YES              1                7
[1] 2 2
[1] FALSE
D1881V9, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    21   7
  ZNF521 WILD-TYPE 293  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     21    7
  ZNF521 WILD-TYPE  293   41
                               clus
vv                              ZNF521 MUTATED ZNF521 WILD-TYPE
  COLON ADENOCARCINOMA                      21              293
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF521 MUTATED    18   0   0   2
  ZNF521 WILD-TYPE 241   3  22  19
D1881V10, multiclass
    clus
vv   ZNF521 MUTATED ZNF521 WILD-TYPE
  R0             18              241
  R1              0                3
  R2              0               22
  RX              2               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"
D1881V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF521 MUTATED                                  0     2
  ZNF521 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF521 MUTATED                           1    14
  ZNF521 WILD-TYPE                        18   162
D1881V12, multiclass
                                  clus
vv                                 ZNF521 MUTATED ZNF521 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        14              162
[1] 4 2
[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 = TFEC MUTATION ANALYSIS
D1882V1, survival
                sevent
clus2              0   1
  TFEC MUTATED     9   1
  TFEC WILD-TYPE 268  77
  TFEC MUTATED TFEC WILD-TYPE 
            10            345 
  TFEC MUTATED TFEC WILD-TYPE 
             1             77 
$`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        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6535 
       12.76        10.06        14.04        15.12 

$`TFEC WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        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-A6-6138 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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69        12.36        12.59        12.59        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-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        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        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  TFEC MUTATED TFEC WILD-TYPE 
         10.06           0.00 
  TFEC MUTATED TFEC WILD-TYPE 
         63.98         148.01 
  TFEC MUTATED TFEC WILD-TYPE 
         20.07          22.06 
[1] "10.1 - 64.0 (20.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.3"
D1882V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TFEC MUTATED         1        0        1         4         0         0
  TFEC WILD-TYPE      63        1       25       104         8         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        18          6         42         32       35        12
                vv
clus             STAGE IVB
  TFEC MUTATED           0
  TFEC WILD-TYPE         1
D1882V3, multiclass
            clus
vv           TFEC MUTATED TFEC WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             4            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            2             42
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  TFEC MUTATED     0   2   8   0
  TFEC WILD-TYPE   9  65 241  41
D1882V4, multiclass
    clus
vv   TFEC MUTATED TFEC WILD-TYPE
  T1            0              9
  T2            2             65
  T3            8            241
  T4            0             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
  TFEC MUTATED     7   2   1
  TFEC WILD-TYPE 213  79  65
D1882V5, multiclass
    clus
vv   TFEC MUTATED TFEC WILD-TYPE
  N0            7            213
  N1            2             79
  N2            1             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1882V6, binary
                cls
clus               0   1
  TFEC MUTATED     8   0
  TFEC WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED      8    0
  TFEC WILD-TYPE  277   48
   clus
vv  TFEC MUTATED TFEC WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1882V7, binary
                cls
clus               0   1
  TFEC MUTATED     4   6
  TFEC WILD-TYPE 166 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED      4    6
  TFEC WILD-TYPE  166  191
        clus
vv       TFEC MUTATED TFEC WILD-TYPE
  FEMALE            4            166
  MALE              6            191
[1] 2 2
[1] FALSE
D1882V8, binary
                cls
clus               0   1
  TFEC MUTATED    10   0
  TFEC WILD-TYPE 290   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED     10    0
  TFEC WILD-TYPE  290    8
     clus
vv    TFEC MUTATED TFEC WILD-TYPE
  NO            10            290
  YES            0              8
[1] 2 2
[1] FALSE
D1882V9, binary
                cls
clus               0   1
  TFEC MUTATED     8   2
  TFEC WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED      8    2
  TFEC WILD-TYPE  306   46
                               clus
vv                              TFEC MUTATED TFEC WILD-TYPE
  COLON ADENOCARCINOMA                     8            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TFEC MUTATED     5   0   0   3
  TFEC WILD-TYPE 254   3  22  18
D1882V10, multiclass
    clus
vv   TFEC MUTATED TFEC WILD-TYPE
  R0            5            254
  R1            0              3
  R2            0             22
  RX            3             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"
D1882V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TFEC MUTATED                                  0     3
  TFEC WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TFEC MUTATED                           0     4
  TFEC WILD-TYPE                        19   172
D1882V12, multiclass
                                  clus
vv                                 TFEC MUTATED TFEC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              7
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = NEFH MUTATION ANALYSIS
D1883V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    12   1
  NEFH WILD-TYPE 265  77
  NEFH MUTATED NEFH WILD-TYPE 
            13            342 
  NEFH MUTATED NEFH WILD-TYPE 
             1             77 
$`NEFH MUTATED`
TCGA-G4-6588 TCGA-A6-6142 TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6965 
       26.17        25.08        33.01        34.98        14.01        26.47 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CM-6161 TCGA-D5-6920 TCGA-DM-A28K 
       21.44        58.39       148.01        15.02        12.39        98.24 
TCGA-F4-6856 
       35.31 

$`NEFH WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        26.01        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  NEFH MUTATED NEFH WILD-TYPE 
         12.39           0.00 
  NEFH MUTATED NEFH WILD-TYPE 
        148.01         140.38 
  NEFH MUTATED NEFH WILD-TYPE 
         26.47          21.99 
[1] "12.4 - 148.0 (26.5)" "0.0 - 140.4 (22.0)" 
[1] "hr=" "4"  
D1883V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEFH MUTATED         2        0        0         5         2         0
  NEFH WILD-TYPE      62        1       26       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEFH MUTATED           1          0          0          1        1         1
  NEFH WILD-TYPE        17          6         44         32       34        11
                vv
clus             STAGE IVB
  NEFH MUTATED           0
  NEFH WILD-TYPE         1
D1883V3, multiclass
            clus
vv           NEFH MUTATED NEFH WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             26
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             17
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              1             34
  STAGE IVA             1             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
  NEFH MUTATED     0   2   7   4
  NEFH WILD-TYPE   9  65 242  37
D1883V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            0              9
  T2            2             65
  T3            7            242
  T4            4             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
  NEFH MUTATED     9   2   2
  NEFH WILD-TYPE 211  79  64
D1883V5, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  N0            9            211
  N1            2             79
  N2            2             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1883V6, binary
                cls
clus               0   1
  NEFH MUTATED    10   2
  NEFH WILD-TYPE 275  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     10    2
  NEFH WILD-TYPE  275   46
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0           10            275
  1            2             46
[1] 2 2
[1] FALSE
D1883V7, binary
                cls
clus               0   1
  NEFH MUTATED     7   6
  NEFH WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      7    6
  NEFH WILD-TYPE  163  191
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D1883V8, binary
                cls
clus               0   1
  NEFH MUTATED    12   0
  NEFH WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     12    0
  NEFH WILD-TYPE  288    8
     clus
vv    NEFH MUTATED NEFH WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1883V9, binary
                cls
clus               0   1
  NEFH MUTATED    10   3
  NEFH WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     10    3
  NEFH WILD-TYPE  304   45
                               clus
vv                              NEFH MUTATED NEFH WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEFH MUTATED     9   1   1   0
  NEFH WILD-TYPE 250   2  21  21
D1883V10, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  R0            9            250
  R1            1              2
  R2            1             21
  RX            0             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"
D1883V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           0    10
  NEFH WILD-TYPE                        19   166
D1883V12, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                      10            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(1884) Variable = AKAP13 MUTATION ANALYSIS
D1884V1, survival
                  sevent
clus2                0   1
  AKAP13 MUTATED    17   2
  AKAP13 WILD-TYPE 260  76
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              19              336 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
               2               76 
$`AKAP13 MUTATED`
TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3950 TCGA-G4-6586 TCGA-G4-6588 TCGA-A6-5661 
        6.05        19.04        24.00        35.80        26.17        33.53 
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-3982 TCGA-AA-A00R TCGA-AA-A010 
       22.06        63.98         2.01        27.02         0.99        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6924 
       58.39        12.76        10.06        55.92        18.25        14.30 
TCGA-G4-6304 
       53.62 

$`AKAP13 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6628 
       49.08         5.88        63.62        22.09        91.79        79.69 
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-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        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-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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        26.47        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        33.01         0.20        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-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-6719 
       12.36        12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        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-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  AKAP13 MUTATED AKAP13 WILD-TYPE 
            0.99             0.00 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           63.98           148.01 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           24.00            22.01 
[1] "1.0 - 64.0 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.1"
D1884V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP13 MUTATED         2        0        2        11         2         0
  AKAP13 WILD-TYPE      62        1       24        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP13 MUTATED           0          0          2          0        1
  AKAP13 WILD-TYPE        18          6         42         33       34
                  vv
clus               STAGE IVA STAGE IVB
  AKAP13 MUTATED           0         0
  AKAP13 WILD-TYPE        12         1
D1884V3, multiclass
            clus
vv           AKAP13 MUTATED AKAP13 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA              11               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                1               34
  STAGE IVA               0               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
  AKAP13 MUTATED     0   2  15   3
  AKAP13 WILD-TYPE   9  65 234  38
D1884V4, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  T1              0                9
  T2              2               65
  T3             15              234
  T4              3               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
  AKAP13 MUTATED    17   2   1
  AKAP13 WILD-TYPE 203  79  65
D1884V5, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  N0             17              203
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1884V6, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    18   1
  AKAP13 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     18    1
  AKAP13 WILD-TYPE  267   47
   clus
vv  AKAP13 MUTATED AKAP13 WILD-TYPE
  0             18              267
  1              1               47
[1] 2 2
[1] FALSE
D1884V7, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    10  10
  AKAP13 WILD-TYPE 160 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     10   10
  AKAP13 WILD-TYPE  160  187
        clus
vv       AKAP13 MUTATED AKAP13 WILD-TYPE
  FEMALE             10              160
  MALE               10              187
[1] 2 2
[1] FALSE
D1884V8, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    17   0
  AKAP13 WILD-TYPE 283   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     17    0
  AKAP13 WILD-TYPE  283    8
     clus
vv    AKAP13 MUTATED AKAP13 WILD-TYPE
  NO              17              283
  YES              0                8
[1] 2 2
[1] FALSE
D1884V9, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    17   3
  AKAP13 WILD-TYPE 297  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     17    3
  AKAP13 WILD-TYPE  297   45
                               clus
vv                              AKAP13 MUTATED AKAP13 WILD-TYPE
  COLON ADENOCARCINOMA                      17              297
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKAP13 MUTATED    14   0   1   3
  AKAP13 WILD-TYPE 245   3  21  18
D1884V10, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  R0             14              245
  R1              0                3
  R2              1               21
  RX              3               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"
D1884V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP13 MUTATED                                  0     2
  AKAP13 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AKAP13 MUTATED                           1     9
  AKAP13 WILD-TYPE                        18   167
D1884V12, multiclass
                                  clus
vv                                 AKAP13 MUTATED AKAP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         9              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(1885) Variable = FAM133A MUTATION ANALYSIS
D1885V1, survival
                   sevent
clus2                 0   1
  FAM133A MUTATED     9   0
  FAM133A WILD-TYPE 268  78
  FAM133A MUTATED FAM133A WILD-TYPE 
                9               346 
  FAM133A MUTATED FAM133A WILD-TYPE 
                0                78 
$`FAM133A MUTATED`
TCGA-AA-3672 TCGA-A6-5659 TCGA-A6-6141 TCGA-AA-3977 TCGA-AA-A010 TCGA-CA-6717 
        0.92        30.44         8.38        25.02        34.98        12.76 
TCGA-CM-6677 TCGA-D5-6930 TCGA-DM-A1HB 
       11.08        13.35       135.65 

$`FAM133A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        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-A6-6142 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  FAM133A MUTATED FAM133A WILD-TYPE 
             0.92              0.00 
  FAM133A MUTATED FAM133A WILD-TYPE 
           135.65            148.01 
  FAM133A MUTATED FAM133A WILD-TYPE 
           13.350            22.075 
[1] "0.9 - 135.7 (13.3)" "0.0 - 148.0 (22.1)"
[1] "hr="     "9300000"
D1885V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM133A MUTATED         1        0        0         6         1         0
  FAM133A WILD-TYPE      63        1       26       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133A MUTATED           1          0          1          0        0
  FAM133A WILD-TYPE        17          6         43         33       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM133A MUTATED           0         0
  FAM133A WILD-TYPE        12         1
D1885V3, multiclass
            clus
vv           FAM133A MUTATED FAM133A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                26
  STAGE IIA                6               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                17
  STAGE IIIA               0                 6
  STAGE IIIB               1                43
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  FAM133A MUTATED     0   2   8   1
  FAM133A WILD-TYPE   9  65 241  40
D1885V4, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  T1               0                 9
  T2               2                65
  T3               8               241
  T4               1                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
  FAM133A MUTATED     9   2   0
  FAM133A WILD-TYPE 211  79  66
D1885V5, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  N0               9               211
  N1               2                79
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1885V6, binary
                   cls
clus                  0   1
  FAM133A MUTATED    10   0
  FAM133A WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED     10    0
  FAM133A WILD-TYPE  275   48
   clus
vv  FAM133A MUTATED FAM133A WILD-TYPE
  0              10               275
  1               0                48
[1] 2 2
[1] FALSE
D1885V7, binary
                   cls
clus                  0   1
  FAM133A MUTATED     5   6
  FAM133A WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      5    6
  FAM133A WILD-TYPE  165  191
        clus
vv       FAM133A MUTATED FAM133A WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D1885V8, binary
                   cls
clus                  0   1
  FAM133A MUTATED     8   0
  FAM133A WILD-TYPE 292   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      8    0
  FAM133A WILD-TYPE  292    8
     clus
vv    FAM133A MUTATED FAM133A WILD-TYPE
  NO                8               292
  YES               0                 8
[1] 2 2
[1] FALSE
D1885V9, binary
                   cls
clus                  0   1
  FAM133A MUTATED     8   2
  FAM133A WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      8    2
  FAM133A WILD-TYPE  306   46
                               clus
vv                              FAM133A MUTATED FAM133A WILD-TYPE
  COLON ADENOCARCINOMA                        8               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM133A MUTATED     7   0   0   1
  FAM133A WILD-TYPE 252   3  22  20
D1885V10, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  R0               7               252
  R1               0                 3
  R2               0                22
  RX               1                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"
D1885V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM133A MUTATED                                  0     1
  FAM133A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM133A MUTATED                           1     4
  FAM133A WILD-TYPE                        18   172
D1885V12, multiclass
                                  clus
vv                                 FAM133A MUTATED FAM133A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               172
[1] 4 2
[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 = RAG1 MUTATION ANALYSIS
D1886V1, survival
                sevent
clus2              0   1
  RAG1 MUTATED    11   2
  RAG1 WILD-TYPE 266  76
  RAG1 MUTATED RAG1 WILD-TYPE 
            13            342 
  RAG1 MUTATED RAG1 WILD-TYPE 
             2             76 
$`RAG1 MUTATED`
TCGA-AA-3976 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3977 
       26.01        33.53        19.66        63.98        31.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-6161 TCGA-D5-6536 
        4.01        34.98        83.24        58.39        15.02        17.85 
TCGA-D5-6540 
       16.14 

$`RAG1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        18.05         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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        54.61        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        25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6626 
       55.04        85.48        61.91        36.00        13.78        46.75 

  RAG1 MUTATED RAG1 WILD-TYPE 
          4.01           0.00 
  RAG1 MUTATED RAG1 WILD-TYPE 
         83.24         148.01 
  RAG1 MUTATED RAG1 WILD-TYPE 
         26.01          22.01 
[1] "4.0 - 83.2 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.7"
D1886V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAG1 MUTATED         3        0        1         5         2         0
  RAG1 WILD-TYPE      61        1       25       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAG1 MUTATED           0          1          0          1        0         0
  RAG1 WILD-TYPE        18          5         44         32       35        12
                vv
clus             STAGE IVB
  RAG1 MUTATED           0
  RAG1 WILD-TYPE         1
D1886V3, multiclass
            clus
vv           RAG1 MUTATED RAG1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             25
  STAGE IIA             5            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            1              5
  STAGE IIIB            0             44
  STAGE IIIC            1             32
  STAGE IV              0             35
  STAGE IVA             0             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
  RAG1 MUTATED     1   4   6   3
  RAG1 WILD-TYPE   8  63 243  38
D1886V4, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  T1            1              8
  T2            4             63
  T3            6            243
  T4            3             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
  RAG1 MUTATED    12   2   0
  RAG1 WILD-TYPE 208  79  66
D1886V5, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  N0           12            208
  N1            2             79
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1886V6, binary
                cls
clus               0   1
  RAG1 MUTATED    12   0
  RAG1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     12    0
  RAG1 WILD-TYPE  273   48
   clus
vv  RAG1 MUTATED RAG1 WILD-TYPE
  0           12            273
  1            0             48
[1] 2 2
[1] FALSE
D1886V7, binary
                cls
clus               0   1
  RAG1 MUTATED     5   9
  RAG1 WILD-TYPE 165 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      5    9
  RAG1 WILD-TYPE  165  188
        clus
vv       RAG1 MUTATED RAG1 WILD-TYPE
  FEMALE            5            165
  MALE              9            188
[1] 2 2
[1] FALSE
D1886V8, binary
                cls
clus               0   1
  RAG1 MUTATED    12   0
  RAG1 WILD-TYPE 288   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     12    0
  RAG1 WILD-TYPE  288    8
     clus
vv    RAG1 MUTATED RAG1 WILD-TYPE
  NO            12            288
  YES            0              8
[1] 2 2
[1] FALSE
D1886V9, binary
                cls
clus               0   1
  RAG1 MUTATED    10   4
  RAG1 WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     10    4
  RAG1 WILD-TYPE  304   44
                               clus
vv                              RAG1 MUTATED RAG1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RAG1 MUTATED    13   0   0   0
  RAG1 WILD-TYPE 246   3  22  21
D1886V10, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  R0           13            246
  R1            0              3
  R2            0             22
  RX            0             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"
D1886V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAG1 MUTATED                                  0     1
  RAG1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAG1 MUTATED                           1     5
  RAG1 WILD-TYPE                        18   171
D1886V12, multiclass
                                  clus
vv                                 RAG1 MUTATED RAG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             18
  WHITE                                       5            171
[1] 4 2
[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 = ZNF615 MUTATION ANALYSIS
D1887V1, survival
                  sevent
clus2                0   1
  ZNF615 MUTATED    10   6
  ZNF615 WILD-TYPE 267  72
  ZNF615 MUTATED ZNF615 WILD-TYPE 
              16              339 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
               6               72 
$`ZNF615 MUTATED`
TCGA-AZ-6601 TCGA-G4-6586 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-5543 
      100.01        35.80        25.02         4.01        34.98        33.01 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 
       58.39        49.41         6.77        12.76        10.06        20.02 
TCGA-D5-5539 TCGA-D5-6928 TCGA-DM-A1D4 TCGA-DM-A1HB 
       19.59        11.64        92.75       135.65 

$`ZNF615 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      106.75         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        62.79        88.21        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ZNF615 MUTATED ZNF615 WILD-TYPE 
            4.01             0.00 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
          135.65           148.01 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
          29.015           22.030 
[1] "4.0 - 135.7 (29.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D1887V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF615 MUTATED         2        0        2         7         2         0
  ZNF615 WILD-TYPE      62        1       24       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF615 MUTATED           0          1          1          0        0
  ZNF615 WILD-TYPE        18          5         43         33       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF615 MUTATED           1         0
  ZNF615 WILD-TYPE        11         1
D1887V3, multiclass
            clus
vv           ZNF615 MUTATED ZNF615 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               24
  STAGE IIA               7              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              1                5
  STAGE IIIB              1               43
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF615 MUTATED     0   3  12   2
  ZNF615 WILD-TYPE   9  64 237  39
D1887V4, multiclass
    clus
vv   ZNF615 MUTATED ZNF615 WILD-TYPE
  T1              0                9
  T2              3               64
  T3             12              237
  T4              2               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
  ZNF615 MUTATED    14   3   0
  ZNF615 WILD-TYPE 206  78  66
D1887V5, multiclass
    clus
vv   ZNF615 MUTATED ZNF615 WILD-TYPE
  N0             14              206
  N1              3               78
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1887V6, binary
                  cls
clus                 0   1
  ZNF615 MUTATED    13   1
  ZNF615 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF615 MUTATED     13    1
  ZNF615 WILD-TYPE  272   47
   clus
vv  ZNF615 MUTATED ZNF615 WILD-TYPE
  0             13              272
  1              1               47
[1] 2 2
[1] FALSE
D1887V7, binary
                  cls
clus                 0   1
  ZNF615 MUTATED     5  12
  ZNF615 WILD-TYPE 165 185
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF615 MUTATED      5   12
  ZNF615 WILD-TYPE  165  185
        clus
vv       ZNF615 MUTATED ZNF615 WILD-TYPE
  FEMALE              5              165
  MALE               12              185
[1] 2 2
[1] FALSE
D1887V8, binary
                  cls
clus                 0   1
  ZNF615 MUTATED    13   0
  ZNF615 WILD-TYPE 287   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF615 MUTATED     13    0
  ZNF615 WILD-TYPE  287    8
     clus
vv    ZNF615 MUTATED ZNF615 WILD-TYPE
  NO              13              287
  YES              0                8
[1] 2 2
[1] FALSE
D1887V9, binary
                  cls
clus                 0   1
  ZNF615 MUTATED    12   4
  ZNF615 WILD-TYPE 302  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF615 MUTATED     12    4
  ZNF615 WILD-TYPE  302   44
                               clus
vv                              ZNF615 MUTATED ZNF615 WILD-TYPE
  COLON ADENOCARCINOMA                      12              302
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF615 MUTATED     9   0   0   2
  ZNF615 WILD-TYPE 250   3  22  19
D1887V10, multiclass
    clus
vv   ZNF615 MUTATED ZNF615 WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              2               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"
D1887V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF615 MUTATED                                  0     2
  ZNF615 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF615 MUTATED                           1    10
  ZNF615 WILD-TYPE                        18   166
D1887V12, multiclass
                                  clus
vv                                 ZNF615 MUTATED ZNF615 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                        10              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(1888) Variable = ENGASE MUTATION ANALYSIS
D1888V1, survival
                  sevent
clus2                0   1
  ENGASE MUTATED     3   1
  ENGASE WILD-TYPE 274  77
  ENGASE MUTATED ENGASE WILD-TYPE 
               4              351 
  ENGASE MUTATED ENGASE WILD-TYPE 
               1               77 
$`ENGASE MUTATED`
TCGA-AD-6964 TCGA-A6-6781 TCGA-AA-3815 TCGA-CM-6171 
       10.88        19.66        33.04        14.04 

$`ENGASE WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       21.99        39.06        21.37        15.52        25.08       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  ENGASE MUTATED ENGASE WILD-TYPE 
           10.88             0.00 
  ENGASE MUTATED ENGASE WILD-TYPE 
           33.04           148.01 
  ENGASE MUTATED ENGASE WILD-TYPE 
           16.85            22.09 
[1] "10.9 - 33.0 (16.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D1888V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENGASE MUTATED         1        0        0         1         0         0
  ENGASE WILD-TYPE      63        1       26       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENGASE MUTATED           0          0          0          1        0
  ENGASE WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  ENGASE MUTATED           0         0
  ENGASE WILD-TYPE        12         1
D1888V3, multiclass
            clus
vv           ENGASE MUTATED ENGASE WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               1              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  ENGASE MUTATED     0   1   1   2
  ENGASE WILD-TYPE   9  66 248  39
D1888V4, multiclass
    clus
vv   ENGASE MUTATED ENGASE WILD-TYPE
  T1              0                9
  T2              1               66
  T3              1              248
  T4              2               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
  ENGASE MUTATED     2   1   1
  ENGASE WILD-TYPE 218  80  65
D1888V5, multiclass
    clus
vv   ENGASE MUTATED ENGASE WILD-TYPE
  N0              2              218
  N1              1               80
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1888V6, binary
                  cls
clus                 0   1
  ENGASE MUTATED     2   0
  ENGASE WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      2    0
  ENGASE WILD-TYPE  283   48
   clus
vv  ENGASE MUTATED ENGASE WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D1888V7, binary
                  cls
clus                 0   1
  ENGASE MUTATED     2   2
  ENGASE WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      2    2
  ENGASE WILD-TYPE  168  195
        clus
vv       ENGASE MUTATED ENGASE WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D1888V8, binary
                  cls
clus                 0   1
  ENGASE MUTATED     4   0
  ENGASE WILD-TYPE 296   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      4    0
  ENGASE WILD-TYPE  296    8
     clus
vv    ENGASE MUTATED ENGASE WILD-TYPE
  NO               4              296
  YES              0                8
[1] 2 2
[1] FALSE
D1888V9, binary
                  cls
clus                 0   1
  ENGASE MUTATED     3   1
  ENGASE WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      3    1
  ENGASE WILD-TYPE  311   47
                               clus
vv                              ENGASE MUTATED ENGASE WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ENGASE MUTATED     3   0   0   0
  ENGASE WILD-TYPE 256   3  22  21
D1888V10, multiclass
    clus
vv   ENGASE MUTATED ENGASE WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1888V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENGASE MUTATED                                  0     0
  ENGASE WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ENGASE MUTATED                           0     3
  ENGASE WILD-TYPE                        19   173
D1888V12, multiclass
                                  clus
vv                                 ENGASE MUTATED ENGASE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1889) Variable = CCDC144A MUTATION ANALYSIS
D1889V1, survival
                    sevent
clus2                  0   1
  CCDC144A MUTATED     5   4
  CCDC144A WILD-TYPE 272  74
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                 9                346 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                 4                 74 
$`CCDC144A MUTATED`
TCGA-A6-5661 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6605 
       33.53         2.01        25.02         4.01        58.39         5.23 
TCGA-CM-4743 TCGA-DM-A28G TCGA-F4-6570 
       23.05        60.79         6.18 

$`CCDC144A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        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-A6-6648 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       34.03        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10        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        12.36        12.39        12.59        12.59        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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CCDC144A MUTATED CCDC144A WILD-TYPE 
              2.01               0.00 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
             60.79             148.01 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
            23.050             22.045 
[1] "2.0 - 60.8 (23.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.3"
D1889V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC144A MUTATED         0        0        0         6         1         0
  CCDC144A WILD-TYPE      64        1       26       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC144A MUTATED           0          0          1          0        0
  CCDC144A WILD-TYPE        18          6         43         33       35
                    vv
clus                 STAGE IVA STAGE IVB
  CCDC144A MUTATED           0         0
  CCDC144A WILD-TYPE        12         1
D1889V3, multiclass
            clus
vv           CCDC144A MUTATED CCDC144A WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 26
  STAGE IIA                 6                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 18
  STAGE IIIA                0                  6
  STAGE IIIB                1                 43
  STAGE IIIC                0                 33
  STAGE IV                  0                 35
  STAGE IVA                 0                 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
  CCDC144A MUTATED     0   1   6   2
  CCDC144A WILD-TYPE   9  66 243  39
D1889V4, multiclass
    clus
vv   CCDC144A MUTATED CCDC144A WILD-TYPE
  T1                0                  9
  T2                1                 66
  T3                6                243
  T4                2                 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
  CCDC144A MUTATED     8   1   0
  CCDC144A WILD-TYPE 212  80  66
D1889V5, multiclass
    clus
vv   CCDC144A MUTATED CCDC144A WILD-TYPE
  N0                8                212
  N1                1                 80
  N2                0                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1889V6, binary
                    cls
clus                   0   1
  CCDC144A MUTATED     8   0
  CCDC144A WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED      8    0
  CCDC144A WILD-TYPE  277   48
   clus
vv  CCDC144A MUTATED CCDC144A WILD-TYPE
  0                8                277
  1                0                 48
[1] 2 2
[1] FALSE
D1889V7, binary
                    cls
clus                   0   1
  CCDC144A MUTATED     3   6
  CCDC144A WILD-TYPE 167 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED      3    6
  CCDC144A WILD-TYPE  167  191
        clus
vv       CCDC144A MUTATED CCDC144A WILD-TYPE
  FEMALE                3                167
  MALE                  6                191
[1] 2 2
[1] FALSE
D1889V8, binary
                    cls
clus                   0   1
  CCDC144A MUTATED     6   0
  CCDC144A WILD-TYPE 294   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED      6    0
  CCDC144A WILD-TYPE  294    8
     clus
vv    CCDC144A MUTATED CCDC144A WILD-TYPE
  NO                 6                294
  YES                0                  8
[1] 2 2
[1] FALSE
D1889V9, binary
                    cls
clus                   0   1
  CCDC144A MUTATED     7   2
  CCDC144A WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED      7    2
  CCDC144A WILD-TYPE  307   46
                               clus
vv                              CCDC144A MUTATED CCDC144A WILD-TYPE
  COLON ADENOCARCINOMA                         7                307
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CCDC144A MUTATED     5   0   0   0
  CCDC144A WILD-TYPE 254   3  22  21
D1889V10, multiclass
    clus
vv   CCDC144A MUTATED CCDC144A WILD-TYPE
  R0                5                254
  R1                0                  3
  R2                0                 22
  RX                0                 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"
D1889V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC144A MUTATED                                  0     0
  CCDC144A WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CCDC144A MUTATED                           1     5
  CCDC144A WILD-TYPE                        18   171
D1889V12, multiclass
                                  clus
vv                                 CCDC144A MUTATED CCDC144A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           5                171
[1] 4 2
[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 = CCDC112 MUTATION ANALYSIS
D1890V1, survival
                   sevent
clus2                 0   1
  CCDC112 MUTATED     2   4
  CCDC112 WILD-TYPE 275  74
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                6               349 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                4                74 
$`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 

$`CCDC112 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-A00O 
       19.00        30.02        34.03        18.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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-6747 
      148.01        85.45        15.62        51.32        21.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CCDC112 MUTATED CCDC112 WILD-TYPE 
                0                 0 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
            21.14            148.01 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
            13.40             22.36 
[1] "0.0 - 21.1 (13.4)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "6.6"
D1890V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC112 MUTATED         2        0        1         3         1         0
  CCDC112 WILD-TYPE      62        1       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC112 MUTATED           0          0          0          0        0
  CCDC112 WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  CCDC112 MUTATED           0         0
  CCDC112 WILD-TYPE        12         1
D1890V3, multiclass
            clus
vv           CCDC112 MUTATED CCDC112 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                0                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
  CCDC112 MUTATED     1   1   4   1
  CCDC112 WILD-TYPE   8  66 245  40
D1890V4, multiclass
    clus
vv   CCDC112 MUTATED CCDC112 WILD-TYPE
  T1               1                 8
  T2               1                66
  T3               4               245
  T4               1                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
  CCDC112 MUTATED     7   0   0
  CCDC112 WILD-TYPE 213  81  66
D1890V5, multiclass
    clus
vv   CCDC112 MUTATED CCDC112 WILD-TYPE
  N0               7               213
  N1               0                81
  N2               0                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1890V6, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     7   0
  CCDC112 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      7    0
  CCDC112 WILD-TYPE  278   48
   clus
vv  CCDC112 MUTATED CCDC112 WILD-TYPE
  0               7               278
  1               0                48
[1] 2 2
[1] FALSE
D1890V7, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     4   3
  CCDC112 WILD-TYPE 166 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      4    3
  CCDC112 WILD-TYPE  166  194
        clus
vv       CCDC112 MUTATED CCDC112 WILD-TYPE
  FEMALE               4               166
  MALE                 3               194
[1] 2 2
[1] FALSE
D1890V8, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     4   0
  CCDC112 WILD-TYPE 296   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      4    0
  CCDC112 WILD-TYPE  296    8
     clus
vv    CCDC112 MUTATED CCDC112 WILD-TYPE
  NO                4               296
  YES               0                 8
[1] 2 2
[1] FALSE
D1890V9, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     5   2
  CCDC112 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      5    2
  CCDC112 WILD-TYPE  309   46
                               clus
vv                              CCDC112 MUTATED CCDC112 WILD-TYPE
  COLON ADENOCARCINOMA                        5               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC112 MUTATED     5   0   0   2
  CCDC112 WILD-TYPE 254   3  22  19
D1890V10, multiclass
    clus
vv   CCDC112 MUTATED CCDC112 WILD-TYPE
  R0               5               254
  R1               0                 3
  R2               0                22
  RX               2                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"
D1890V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC112 MUTATED                                  0     1
  CCDC112 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC112 MUTATED                           0     2
  CCDC112 WILD-TYPE                        19   174
D1890V12, multiclass
                                  clus
vv                                 CCDC112 MUTATED CCDC112 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          2               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(1891) Variable = ZNF286B MUTATION ANALYSIS
D1891V1, survival
                   sevent
clus2                 0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 273  77
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               350 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                1                77 
$`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-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        22.09        22.06        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-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-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        3.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41         5.13        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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  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            22.045 
[1] "6.2 - 64.0 (23.6)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1891V2, continuous
                   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      64        1       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF286B MUTATED           0          0          0          0        0
  ZNF286B WILD-TYPE        18          6         44         33       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF286B MUTATED           1         0
  ZNF286B WILD-TYPE        11         1
D1891V3, multiclass
            clus
vv           ZNF286B MUTATED ZNF286B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                25
  STAGE IIA                3               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               0                44
  STAGE IIIC               0                33
  STAGE IV                 0                35
  STAGE IVA                1                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
  ZNF286B MUTATED     0   0   5   0
  ZNF286B WILD-TYPE   9  67 244  41
D1891V4, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  T1               0                 9
  T2               0                67
  T3               5               244
  T4               0                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
  ZNF286B MUTATED     4   0   1
  ZNF286B WILD-TYPE 216  81  65
D1891V5, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  N0               4               216
  N1               0                81
  N2               1                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1891V6, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      4    1
  ZNF286B WILD-TYPE  281   47
   clus
vv  ZNF286B MUTATED ZNF286B WILD-TYPE
  0               4               281
  1               1                47
[1] 2 2
[1] FALSE
D1891V7, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     1   4
  ZNF286B WILD-TYPE 169 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      1    4
  ZNF286B WILD-TYPE  169  193
        clus
vv       ZNF286B MUTATED ZNF286B WILD-TYPE
  FEMALE               1               169
  MALE                 4               193
[1] 2 2
[1] FALSE
D1891V8, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     5   0
  ZNF286B WILD-TYPE 295   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      5    0
  ZNF286B WILD-TYPE  295    8
     clus
vv    ZNF286B MUTATED ZNF286B WILD-TYPE
  NO                5               295
  YES               0                 8
[1] 2 2
[1] FALSE
D1891V9, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      4    1
  ZNF286B WILD-TYPE  310   47
                               clus
vv                              ZNF286B MUTATED ZNF286B WILD-TYPE
  COLON ADENOCARCINOMA                        4               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF286B MUTATED     3   0   0   1
  ZNF286B WILD-TYPE 256   3  22  20
D1891V10, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  R0               3               256
  R1               0                 3
  R2               0                22
  RX               1                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"
D1891V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF286B MUTATED                                  0     1
  ZNF286B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF286B MUTATED                           0     3
  ZNF286B WILD-TYPE                        19   173
D1891V12, multiclass
                                  clus
vv                                 ZNF286B MUTATED ZNF286B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               173
[1] 4 2
[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 = SFTPB MUTATION ANALYSIS
D1892V1, survival
                 sevent
clus2               0   1
  SFTPB MUTATED     8   1
  SFTPB WILD-TYPE 269  77
  SFTPB MUTATED SFTPB WILD-TYPE 
              9             346 
  SFTPB MUTATED SFTPB WILD-TYPE 
              1              77 
$`SFTPB MUTATED`
TCGA-G4-6628 TCGA-A6-5661 TCGA-AA-3681 TCGA-AA-3833 TCGA-AZ-6605 TCGA-CM-5344 
       79.69        33.53         5.98        15.95         5.23        22.03 
TCGA-D5-6535 TCGA-G4-6299 TCGA-G4-6317 
       15.12        74.56        36.00 

$`SFTPB WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        13.78        46.75 

  SFTPB MUTATED SFTPB WILD-TYPE 
           5.23            0.00 
  SFTPB MUTATED SFTPB WILD-TYPE 
          79.69          148.01 
  SFTPB MUTATED SFTPB WILD-TYPE 
         22.030          22.075 
[1] "5.2 - 79.7 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.2"
D1892V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFTPB MUTATED         1        0        0         2         0         0
  SFTPB WILD-TYPE      63        1       26       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SFTPB MUTATED           1          0          3          2        0         0
  SFTPB WILD-TYPE        17          6         41         31       35        12
                 vv
clus              STAGE IVB
  SFTPB MUTATED           0
  SFTPB WILD-TYPE         1
D1892V3, multiclass
            clus
vv           SFTPB MUTATED SFTPB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              2             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             3              41
  STAGE IIIC             2              31
  STAGE IV               0              35
  STAGE IVA              0              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
  SFTPB MUTATED     0   1   7   1
  SFTPB WILD-TYPE   9  66 242  40
D1892V4, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  T1             0               9
  T2             1              66
  T3             7             242
  T4             1              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
  SFTPB MUTATED     3   4   2
  SFTPB WILD-TYPE 217  77  64
D1892V5, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  N0             3             217
  N1             4              77
  N2             2              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1892V6, binary
                 cls
clus                0   1
  SFTPB MUTATED     7   0
  SFTPB WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      7    0
  SFTPB WILD-TYPE  278   48
   clus
vv  SFTPB MUTATED SFTPB WILD-TYPE
  0             7             278
  1             0              48
[1] 2 2
[1] FALSE
D1892V7, binary
                 cls
clus                0   1
  SFTPB MUTATED     6   3
  SFTPB WILD-TYPE 164 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      6    3
  SFTPB WILD-TYPE  164  194
        clus
vv       SFTPB MUTATED SFTPB WILD-TYPE
  FEMALE             6             164
  MALE               3             194
[1] 2 2
[1] FALSE
D1892V8, binary
                 cls
clus                0   1
  SFTPB MUTATED     9   0
  SFTPB WILD-TYPE 291   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      9    0
  SFTPB WILD-TYPE  291    8
     clus
vv    SFTPB MUTATED SFTPB WILD-TYPE
  NO              9             291
  YES             0               8
[1] 2 2
[1] FALSE
D1892V9, binary
                 cls
clus                0   1
  SFTPB MUTATED     9   0
  SFTPB WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      9    0
  SFTPB WILD-TYPE  305   48
                               clus
vv                              SFTPB MUTATED SFTPB WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SFTPB MUTATED     7   0   0   1
  SFTPB WILD-TYPE 252   3  22  20
D1892V10, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1892V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFTPB MUTATED                                  0     0
  SFTPB WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SFTPB MUTATED                           1     6
  SFTPB WILD-TYPE                        18   170
D1892V12, multiclass
                                  clus
vv                                 SFTPB MUTATED SFTPB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = WNT8A MUTATION ANALYSIS
D1893V1, survival
                 sevent
clus2               0   1
  WNT8A MUTATED     5   0
  WNT8A WILD-TYPE 272  78
  WNT8A MUTATED WNT8A WILD-TYPE 
              5             350 
  WNT8A MUTATED WNT8A WILD-TYPE 
              0              78 
$`WNT8A MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-A010 TCGA-CK-6751 TCGA-G4-6315 
       32.71        19.66        34.98       124.27        61.91 

$`WNT8A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A017 
       27.02        42.02         0.99        17.03        14.99        15.02 
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         1.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         2.01        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        85.48        36.00 
TCGA-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  WNT8A MUTATED WNT8A WILD-TYPE 
          19.66            0.00 
  WNT8A MUTATED WNT8A WILD-TYPE 
         124.27          148.01 
  WNT8A MUTATED WNT8A WILD-TYPE 
          34.98           22.01 
[1] "19.7 - 124.3 (35.0)" "0.0 - 148.0 (22.0)" 
[1] "hr="     "9300000"
D1893V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNT8A MUTATED         1        0        0         0         1         1
  WNT8A WILD-TYPE      63        1       26       108         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNT8A MUTATED           0          0          0          1        1         0
  WNT8A WILD-TYPE        18          6         44         32       34        12
                 vv
clus              STAGE IVB
  WNT8A MUTATED           0
  WNT8A WILD-TYPE         1
D1893V3, multiclass
            clus
vv           WNT8A MUTATED WNT8A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              0             108
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  WNT8A MUTATED     0   1   1   3
  WNT8A WILD-TYPE   9  66 248  38
D1893V4, multiclass
    clus
vv   WNT8A MUTATED WNT8A WILD-TYPE
  T1             0               9
  T2             1              66
  T3             1             248
  T4             3              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
  WNT8A MUTATED     3   2   0
  WNT8A WILD-TYPE 217  79  66
D1893V5, multiclass
    clus
vv   WNT8A MUTATED WNT8A WILD-TYPE
  N0             3             217
  N1             2              79
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1893V6, binary
                 cls
clus                0   1
  WNT8A MUTATED     2   1
  WNT8A WILD-TYPE 283  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT8A MUTATED      2    1
  WNT8A WILD-TYPE  283   47
   clus
vv  WNT8A MUTATED WNT8A WILD-TYPE
  0             2             283
  1             1              47
[1] 2 2
[1] FALSE
D1893V7, binary
                 cls
clus                0   1
  WNT8A MUTATED     2   3
  WNT8A WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT8A MUTATED      2    3
  WNT8A WILD-TYPE  168  194
        clus
vv       WNT8A MUTATED WNT8A WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D1893V8, binary
                 cls
clus                0   1
  WNT8A MUTATED     5   0
  WNT8A WILD-TYPE 295   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT8A MUTATED      5    0
  WNT8A WILD-TYPE  295    8
     clus
vv    WNT8A MUTATED WNT8A WILD-TYPE
  NO              5             295
  YES             0               8
[1] 2 2
[1] FALSE
D1893V9, binary
                 cls
clus                0   1
  WNT8A MUTATED     3   2
  WNT8A WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT8A MUTATED      3    2
  WNT8A WILD-TYPE  311   46
                               clus
vv                              WNT8A MUTATED WNT8A WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WNT8A MUTATED     3   0   0   1
  WNT8A WILD-TYPE 256   3  22  20
D1893V10, multiclass
    clus
vv   WNT8A MUTATED WNT8A WILD-TYPE
  R0             3             256
  R1             0               3
  R2             0              22
  RX             1              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"
D1893V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNT8A MUTATED                                  0     0
  WNT8A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WNT8A MUTATED                           0     4
  WNT8A WILD-TYPE                        19   172
D1893V12, multiclass
                                  clus
vv                                 WNT8A MUTATED WNT8A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = GPR61 MUTATION ANALYSIS
D1894V1, survival
                 sevent
clus2               0   1
  GPR61 MUTATED     6   2
  GPR61 WILD-TYPE 271  76
  GPR61 MUTATED GPR61 WILD-TYPE 
              8             347 
  GPR61 MUTATED GPR61 WILD-TYPE 
              2              76 
$`GPR61 MUTATED`
TCGA-AA-3715 TCGA-AA-3492 TCGA-AA-3667 TCGA-AA-3980 TCGA-AZ-4315 TCGA-CM-5860 
       19.04         3.02        14.01        27.02        58.39        32.02 
TCGA-D5-6536 TCGA-G4-6299 
       17.85        74.56 

$`GPR61 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       54.61        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 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        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-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  GPR61 MUTATED GPR61 WILD-TYPE 
           3.02            0.00 
  GPR61 MUTATED GPR61 WILD-TYPE 
          74.56          148.01 
  GPR61 MUTATED GPR61 WILD-TYPE 
          23.03           22.06 
[1] "3.0 - 74.6 (23.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1894V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR61 MUTATED         2        0        2         4         0         0
  GPR61 WILD-TYPE      62        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR61 MUTATED           0          0          0          1        0         0
  GPR61 WILD-TYPE        18          6         44         32       35        12
                 vv
clus              STAGE IVB
  GPR61 MUTATED           0
  GPR61 WILD-TYPE         1
D1894V3, multiclass
            clus
vv           GPR61 MUTATED GPR61 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             1              32
  STAGE IV               0              35
  STAGE IVA              0              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
  GPR61 MUTATED     0   2   7   0
  GPR61 WILD-TYPE   9  65 242  41
D1894V4, multiclass
    clus
vv   GPR61 MUTATED GPR61 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             0              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
  GPR61 MUTATED     8   0   1
  GPR61 WILD-TYPE 212  81  65
D1894V5, multiclass
    clus
vv   GPR61 MUTATED GPR61 WILD-TYPE
  N0             8             212
  N1             0              81
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1894V6, binary
                 cls
clus                0   1
  GPR61 MUTATED     9   0
  GPR61 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED      9    0
  GPR61 WILD-TYPE  276   48
   clus
vv  GPR61 MUTATED GPR61 WILD-TYPE
  0             9             276
  1             0              48
[1] 2 2
[1] FALSE
D1894V7, binary
                 cls
clus                0   1
  GPR61 MUTATED     4   5
  GPR61 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED      4    5
  GPR61 WILD-TYPE  166  192
        clus
vv       GPR61 MUTATED GPR61 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1894V8, binary
                 cls
clus                0   1
  GPR61 MUTATED     8   0
  GPR61 WILD-TYPE 292   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED      8    0
  GPR61 WILD-TYPE  292    8
     clus
vv    GPR61 MUTATED GPR61 WILD-TYPE
  NO              8             292
  YES             0               8
[1] 2 2
[1] FALSE
D1894V9, binary
                 cls
clus                0   1
  GPR61 MUTATED     9   0
  GPR61 WILD-TYPE 305  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED      9    0
  GPR61 WILD-TYPE  305   48
                               clus
vv                              GPR61 MUTATED GPR61 WILD-TYPE
  COLON ADENOCARCINOMA                      9             305
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR61 MUTATED     8   0   0   0
  GPR61 WILD-TYPE 251   3  22  21
D1894V10, multiclass
    clus
vv   GPR61 MUTATED GPR61 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1894V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR61 MUTATED                                  0     0
  GPR61 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR61 MUTATED                           0     4
  GPR61 WILD-TYPE                        19   172
D1894V12, multiclass
                                  clus
vv                                 GPR61 MUTATED GPR61 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = CACNA1H MUTATION ANALYSIS
D1895V1, survival
                   sevent
clus2                 0   1
  CACNA1H MUTATED    20   6
  CACNA1H WILD-TYPE 257  72
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               26               329 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
                6                72 
$`CACNA1H MUTATED`
TCGA-A6-6649 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-G4-6586 TCGA-G4-6588 
       24.16        25.08        10.88       100.01        35.80        26.17 
TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 
       91.79        43.76        33.53        63.98        78.08         6.97 
TCGA-AA-3815 TCGA-AA-3864 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-5407 TCGA-AZ-6598 
       33.04        53.00        83.24        21.44        88.21        49.41 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       12.76        51.32        15.02        14.04        12.95        11.08 
TCGA-D5-5537 TCGA-G4-6309 
       45.40        85.48 

$`CACNA1H WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53         1.02        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       39.06        21.37        15.52       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6628 TCGA-A6-2672 TCGA-A6-2674 
        5.88        63.62        22.09        79.69        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        30.05        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-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        12.36        12.39        12.59        12.59        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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       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        14.04        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       13.05        11.08        11.01        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        36.00        13.78        46.75 

  CACNA1H MUTATED CACNA1H WILD-TYPE 
             6.97              0.00 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
           100.01            148.01 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
           34.665            21.990 
[1] "7.0 - 100.0 (34.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D1895V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CACNA1H MUTATED         3        0        7        12         0         0
  CACNA1H WILD-TYPE      61        1       19        96         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNA1H MUTATED           0          0          3          0        1
  CACNA1H WILD-TYPE        18          6         41         33       34
                   vv
clus                STAGE IVA STAGE IVB
  CACNA1H MUTATED           0         0
  CACNA1H WILD-TYPE        12         1
D1895V3, multiclass
            clus
vv           CACNA1H MUTATED CACNA1H WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 7                19
  STAGE IIA               12                96
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                18
  STAGE IIIA               0                 6
  STAGE IIIB               3                41
  STAGE IIIC               0                33
  STAGE IV                 1                34
  STAGE IVA                0                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
  CACNA1H MUTATED     1   2  22   2
  CACNA1H WILD-TYPE   8  65 227  39
D1895V4, multiclass
    clus
vv   CACNA1H MUTATED CACNA1H WILD-TYPE
  T1               1                 8
  T2               2                65
  T3              22               227
  T4               2                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
  CACNA1H MUTATED    21   3   3
  CACNA1H WILD-TYPE 199  78  63
D1895V5, multiclass
    clus
vv   CACNA1H MUTATED CACNA1H WILD-TYPE
  N0              21               199
  N1               3                78
  N2               3                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"
D1895V6, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    21   1
  CACNA1H WILD-TYPE 264  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     21    1
  CACNA1H WILD-TYPE  264   47
   clus
vv  CACNA1H MUTATED CACNA1H WILD-TYPE
  0              21               264
  1               1                47
[1] 2 2
[1] FALSE
D1895V7, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    13  14
  CACNA1H WILD-TYPE 157 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     13   14
  CACNA1H WILD-TYPE  157  183
        clus
vv       CACNA1H MUTATED CACNA1H WILD-TYPE
  FEMALE              13               157
  MALE                14               183
[1] 2 2
[1] FALSE
D1895V8, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    26   0
  CACNA1H WILD-TYPE 274   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     26    0
  CACNA1H WILD-TYPE  274    8
     clus
vv    CACNA1H MUTATED CACNA1H WILD-TYPE
  NO               26               274
  YES               0                 8
[1] 2 2
[1] FALSE
D1895V9, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    26   1
  CACNA1H WILD-TYPE 288  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     26    1
  CACNA1H WILD-TYPE  288   47
                               clus
vv                              CACNA1H MUTATED CACNA1H WILD-TYPE
  COLON ADENOCARCINOMA                       26               288
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CACNA1H MUTATED    19   0   0   3
  CACNA1H WILD-TYPE 240   3  22  18
D1895V10, multiclass
    clus
vv   CACNA1H MUTATED CACNA1H WILD-TYPE
  R0              19               240
  R1               0                 3
  R2               0                22
  RX               3                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"
D1895V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1H MUTATED                                  0     2
  CACNA1H WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1H MUTATED                           2    17
  CACNA1H WILD-TYPE                        17   159
D1895V12, multiclass
                                  clus
vv                                 CACNA1H MUTATED CACNA1H WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         17               159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1896) Variable = G3BP1 MUTATION ANALYSIS
D1896V1, survival
                 sevent
clus2               0   1
  G3BP1 MUTATED     9   2
  G3BP1 WILD-TYPE 268  76
  G3BP1 MUTATED G3BP1 WILD-TYPE 
             11             344 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              2              76 
$`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 
       83.24        58.39        12.76        16.14        11.64 

$`G3BP1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       29.95        20.98        13.94        61.02        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       30.05        17.03        27.02        18.05        31.00         2.01 
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-3973 TCGA-AA-3975 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        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         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.20        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  G3BP1 MUTATED G3BP1 WILD-TYPE 
           4.01            0.00 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
          83.24          148.01 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
         25.020          22.045 
[1] "4.0 - 83.2 (25.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D1896V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  G3BP1 MUTATED         1        0        2         4         2         0
  G3BP1 WILD-TYPE      63        1       24       104         6         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        18          6         43         33       35        12
                 vv
clus              STAGE IVB
  G3BP1 MUTATED           0
  G3BP1 WILD-TYPE         1
D1896V3, multiclass
            clus
vv           G3BP1 MUTATED G3BP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA              4             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              18
  STAGE IIIA             0               6
  STAGE IIIB             1              43
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  G3BP1 MUTATED     0   2   7   2
  G3BP1 WILD-TYPE   9  65 242  39
D1896V4, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             7             242
  T4             2              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
  G3BP1 MUTATED    10   1   0
  G3BP1 WILD-TYPE 210  80  66
D1896V5, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  N0            10             210
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1896V6, binary
                 cls
clus                0   1
  G3BP1 MUTATED    10   0
  G3BP1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED     10    0
  G3BP1 WILD-TYPE  275   48
   clus
vv  G3BP1 MUTATED G3BP1 WILD-TYPE
  0            10             275
  1             0              48
[1] 2 2
[1] FALSE
D1896V7, binary
                 cls
clus                0   1
  G3BP1 MUTATED     2   9
  G3BP1 WILD-TYPE 168 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      2    9
  G3BP1 WILD-TYPE  168  188
        clus
vv       G3BP1 MUTATED G3BP1 WILD-TYPE
  FEMALE             2             168
  MALE               9             188
[1] 2 2
[1] FALSE
D1896V8, binary
                 cls
clus                0   1
  G3BP1 MUTATED    10   0
  G3BP1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED     10    0
  G3BP1 WILD-TYPE  290    8
     clus
vv    G3BP1 MUTATED G3BP1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1896V9, binary
                 cls
clus                0   1
  G3BP1 MUTATED     6   5
  G3BP1 WILD-TYPE 308  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      6    5
  G3BP1 WILD-TYPE  308   43
                               clus
vv                              G3BP1 MUTATED G3BP1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             308
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  G3BP1 MUTATED     9   0   0   1
  G3BP1 WILD-TYPE 250   3  22  20
D1896V10, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  R0             9             250
  R1             0               3
  R2             0              22
  RX             1              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"
D1896V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G3BP1 MUTATED                                  0     2
  G3BP1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  G3BP1 MUTATED                           0     4
  G3BP1 WILD-TYPE                        19   172
D1896V12, multiclass
                                  clus
vv                                 G3BP1 MUTATED G3BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              19
  WHITE                                        4             172
[1] 4 2
[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 = SULF2 MUTATION ANALYSIS
D1897V1, survival
                 sevent
clus2               0   1
  SULF2 MUTATED    19   2
  SULF2 WILD-TYPE 258  76
  SULF2 MUTATED SULF2 WILD-TYPE 
             21             334 
  SULF2 MUTATED SULF2 WILD-TYPE 
              2              76 
$`SULF2 MUTATED`
TCGA-AA-3525 TCGA-AD-6895 TCGA-G4-6321 TCGA-AA-3518 TCGA-AA-3861 TCGA-AA-3864 
        8.05        25.08        22.09         1.02        30.05        53.00 
TCGA-AA-A00E TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-5541 
       30.02        10.06        32.02        15.02        19.59        55.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6928 TCGA-D5-6929 
       17.85         4.80        16.14        15.58        11.64        13.41 
TCGA-DM-A1D9 TCGA-G4-6309 TCGA-G4-6317 
      140.38        85.48        36.00 

$`SULF2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
        1.94        49.08         5.88        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       91.79        79.69        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 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-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-3519 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
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-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        27.02        27.02         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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       33.01         0.20        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-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 
       12.36        12.39        12.59        12.59        12.20        12.76 
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 
       21.99        21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-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-D5-6529 TCGA-D5-6532 
       12.03        45.40        54.61        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       25.48        43.27        15.12        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67        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-G4-6323 TCGA-G4-6626 
       55.04        61.91        13.78        46.75 

  SULF2 MUTATED SULF2 WILD-TYPE 
           1.02            0.00 
  SULF2 MUTATED SULF2 WILD-TYPE 
         140.38          148.01 
  SULF2 MUTATED SULF2 WILD-TYPE 
         19.590          22.075 
[1] "1.0 - 140.4 (19.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "2.5"
D1897V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SULF2 MUTATED         1        0        2        10         0         0
  SULF2 WILD-TYPE      63        1       24        98         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SULF2 MUTATED           1          1          5          1        1         0
  SULF2 WILD-TYPE        17          5         39         32       34        12
                 vv
clus              STAGE IVB
  SULF2 MUTATED           0
  SULF2 WILD-TYPE         1
D1897V3, multiclass
            clus
vv           SULF2 MUTATED SULF2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              24
  STAGE IIA             10              98
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             1               5
  STAGE IIIB             5              39
  STAGE IIIC             1              32
  STAGE IV               1              34
  STAGE IVA              0              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
  SULF2 MUTATED     0   2  20   0
  SULF2 WILD-TYPE   9  65 229  41
D1897V4, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  T1             0               9
  T2             2              65
  T3            20             229
  T4             0              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
  SULF2 MUTATED    13   8   1
  SULF2 WILD-TYPE 207  73  65
D1897V5, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  N0            13             207
  N1             8              73
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1897V6, binary
                 cls
clus                0   1
  SULF2 MUTATED    18   1
  SULF2 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     18    1
  SULF2 WILD-TYPE  267   47
   clus
vv  SULF2 MUTATED SULF2 WILD-TYPE
  0            18             267
  1             1              47
[1] 2 2
[1] FALSE
D1897V7, binary
                 cls
clus                0   1
  SULF2 MUTATED     7  15
  SULF2 WILD-TYPE 163 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED      7   15
  SULF2 WILD-TYPE  163  182
        clus
vv       SULF2 MUTATED SULF2 WILD-TYPE
  FEMALE             7             163
  MALE              15             182
[1] 2 2
[1] FALSE
D1897V8, binary
                 cls
clus                0   1
  SULF2 MUTATED    19   0
  SULF2 WILD-TYPE 281   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     19    0
  SULF2 WILD-TYPE  281    8
     clus
vv    SULF2 MUTATED SULF2 WILD-TYPE
  NO             19             281
  YES             0               8
[1] 2 2
[1] FALSE
D1897V9, binary
                 cls
clus                0   1
  SULF2 MUTATED    19   3
  SULF2 WILD-TYPE 295  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     19    3
  SULF2 WILD-TYPE  295   45
                               clus
vv                              SULF2 MUTATED SULF2 WILD-TYPE
  COLON ADENOCARCINOMA                     19             295
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SULF2 MUTATED    20   0   0   1
  SULF2 WILD-TYPE 239   3  22  20
D1897V10, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  R0            20             239
  R1             0               3
  R2             0              22
  RX             1              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"
D1897V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULF2 MUTATED                                  0     1
  SULF2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SULF2 MUTATED                           1    14
  SULF2 WILD-TYPE                        18   162
D1897V12, multiclass
                                  clus
vv                                 SULF2 MUTATED SULF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       14             162
[1] 4 2
[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 = KDR MUTATION ANALYSIS
D1898V1, survival
               sevent
clus2             0   1
  KDR MUTATED    20   5
  KDR WILD-TYPE 257  73
  KDR MUTATED KDR WILD-TYPE 
           25           330 
  KDR MUTATED KDR WILD-TYPE 
            5            73 
$`KDR MUTATED`
TCGA-AA-3697 TCGA-AD-6895 TCGA-G4-6628 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3489 
       85.05        25.08        79.69        22.06        20.12         7.04 
TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 
       29.95        26.01        25.02         4.01        34.98        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6161 TCGA-CM-6168 
       58.39        49.41        12.76        10.06        15.02        12.99 
TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A28F 
       12.49        13.41        12.00        11.38       140.38        35.97 
TCGA-G4-6315 
       61.91 

$`KDR WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       39.06        21.37        15.52        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       26.17        91.79        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       42.28        16.57        34.65        33.34        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6781 
       25.18        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
        2.01        21.99        16.08        13.05        34.06        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-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        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        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        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         1.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01         0.20        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-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        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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        14.04        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 
       54.61        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       14.30         9.04         9.44        11.64        13.35        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 
       44.68        55.04        85.48        36.00        13.78        46.75 

  KDR MUTATED KDR WILD-TYPE 
         4.01          0.00 
  KDR MUTATED KDR WILD-TYPE 
       140.38        148.01 
  KDR MUTATED KDR WILD-TYPE 
        22.06         22.06 
[1] "4.0 - 140.4 (22.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D1898V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDR MUTATED         3        0        4        11         2         0
  KDR WILD-TYPE      61        1       22        97         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDR MUTATED           0          0          3          1        2         0
  KDR WILD-TYPE        18          6         41         32       33        12
               vv
clus            STAGE IVB
  KDR MUTATED           0
  KDR WILD-TYPE         1
D1898V3, multiclass
            clus
vv           KDR MUTATED KDR WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             4            22
  STAGE IIA           11            97
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            18
  STAGE IIIA           0             6
  STAGE IIIB           3            41
  STAGE IIIC           1            32
  STAGE IV             2            33
  STAGE IVA            0            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
  KDR MUTATED     0   4  20   4
  KDR WILD-TYPE   9  63 229  37
D1898V4, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  T1           0             9
  T2           4            63
  T3          20           229
  T4           4            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
  KDR MUTATED    22   5   1
  KDR WILD-TYPE 198  76  65
D1898V5, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  N0          22           198
  N1           5            76
  N2           1            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1898V6, binary
               cls
clus              0   1
  KDR MUTATED    21   2
  KDR WILD-TYPE 264  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     21    2
  KDR WILD-TYPE  264   46
   clus
vv  KDR MUTATED KDR WILD-TYPE
  0          21           264
  1           2            46
[1] 2 2
[1] FALSE
D1898V7, binary
               cls
clus              0   1
  KDR MUTATED    12  16
  KDR WILD-TYPE 158 181
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     12   16
  KDR WILD-TYPE  158  181
        clus
vv       KDR MUTATED KDR WILD-TYPE
  FEMALE          12           158
  MALE            16           181
[1] 2 2
[1] FALSE
D1898V8, binary
               cls
clus              0   1
  KDR MUTATED    22   0
  KDR WILD-TYPE 278   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     22    0
  KDR WILD-TYPE  278    8
     clus
vv    KDR MUTATED KDR WILD-TYPE
  NO           22           278
  YES           0             8
[1] 2 2
[1] FALSE
D1898V9, binary
               cls
clus              0   1
  KDR MUTATED    23   5
  KDR WILD-TYPE 291  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     23    5
  KDR WILD-TYPE  291   43
                               clus
vv                              KDR MUTATED KDR WILD-TYPE
  COLON ADENOCARCINOMA                   23           291
  COLON MUCINOUS ADENOCARCINOMA           5            43
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  KDR MUTATED    20   0   0   3
  KDR WILD-TYPE 239   3  22  18
D1898V10, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  R0          20           239
  R1           0             3
  R2           0            22
  RX           3            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"
D1898V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDR MUTATED                                  0     2
  KDR WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  KDR MUTATED                           1    16
  KDR WILD-TYPE                        18   160
D1898V12, multiclass
                                  clus
vv                                 KDR MUTATED KDR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  1            18
  WHITE                                     16           160
[1] 4 2
[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 = CPB2 MUTATION ANALYSIS
D1899V1, survival
                sevent
clus2              0   1
  CPB2 MUTATED     6   3
  CPB2 WILD-TYPE 271  75
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            346 
  CPB2 MUTATED CPB2 WILD-TYPE 
             3             75 
$`CPB2 MUTATED`
TCGA-AA-3950 TCGA-G4-6625 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 
       24.00        91.79        63.98        34.98        83.24        49.41 
TCGA-CA-6717 TCGA-CM-5864 TCGA-F4-6570 
       12.76        15.02         6.18 

$`CPB2 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       35.80        26.17        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-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         1.02        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-6890 
       41.00        39.98        18.05        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        26.47        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59        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        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  CPB2 MUTATED CPB2 WILD-TYPE 
          6.18           0.00 
  CPB2 MUTATED CPB2 WILD-TYPE 
         91.79         148.01 
  CPB2 MUTATED CPB2 WILD-TYPE 
         34.98          22.01 
[1] "6.2 - 91.8 (35.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1899V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPB2 MUTATED         1        0        2         5         1         0
  CPB2 WILD-TYPE      63        1       24       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPB2 MUTATED           0          0          0          0        0         0
  CPB2 WILD-TYPE        18          6         44         33       35        12
                vv
clus             STAGE IVB
  CPB2 MUTATED           0
  CPB2 WILD-TYPE         1
D1899V3, multiclass
            clus
vv           CPB2 MUTATED CPB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             5            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  CPB2 MUTATED     0   1   7   1
  CPB2 WILD-TYPE   9  66 242  40
D1899V4, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            7            242
  T4            1             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
  CPB2 MUTATED     9   0   0
  CPB2 WILD-TYPE 211  81  66
D1899V5, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  N0            9            211
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1899V6, binary
                cls
clus               0   1
  CPB2 MUTATED     8   0
  CPB2 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      8    0
  CPB2 WILD-TYPE  277   48
   clus
vv  CPB2 MUTATED CPB2 WILD-TYPE
  0            8            277
  1            0             48
[1] 2 2
[1] FALSE
D1899V7, binary
                cls
clus               0   1
  CPB2 MUTATED     5   4
  CPB2 WILD-TYPE 165 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      5    4
  CPB2 WILD-TYPE  165  193
        clus
vv       CPB2 MUTATED CPB2 WILD-TYPE
  FEMALE            5            165
  MALE              4            193
[1] 2 2
[1] FALSE
D1899V8, binary
                cls
clus               0   1
  CPB2 MUTATED     9   0
  CPB2 WILD-TYPE 291   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      9    0
  CPB2 WILD-TYPE  291    8
     clus
vv    CPB2 MUTATED CPB2 WILD-TYPE
  NO             9            291
  YES            0              8
[1] 2 2
[1] FALSE
D1899V9, binary
                cls
clus               0   1
  CPB2 MUTATED     7   2
  CPB2 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      7    2
  CPB2 WILD-TYPE  307   46
                               clus
vv                              CPB2 MUTATED CPB2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CPB2 MUTATED     7   0   0   1
  CPB2 WILD-TYPE 252   3  22  20
D1899V10, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  R0            7            252
  R1            0              3
  R2            0             22
  RX            1             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"
D1899V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPB2 MUTATED                                  0     2
  CPB2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CPB2 MUTATED                           0     4
  CPB2 WILD-TYPE                        19   172
D1899V12, multiclass
                                  clus
vv                                 CPB2 MUTATED CPB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   0             19
  WHITE                                       4            172
[1] 4 2
[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 = TMEM20 MUTATION ANALYSIS
D1900V1, survival
                  sevent
clus2                0   1
  TMEM20 MUTATED     1   1
  TMEM20 WILD-TYPE 276  77
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               2              353 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               1               77 
$`TMEM20 MUTATED`
TCGA-A6-2676 TCGA-A6-6781 
       42.90        19.66 

$`TMEM20 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       46.65        43.76        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  TMEM20 MUTATED TMEM20 WILD-TYPE 
           19.66             0.00 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
           42.90           148.01 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
           31.28            22.06 
[1] "19.7 - 42.9 (31.3)" "0.0 - 148.0 (22.1)"
[1] "Remove cluster labels:" "TMEM20 MUTATED"        
D1900V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM20 MUTATED         0        0        1         0         1         0
  TMEM20 WILD-TYPE      64        1       25       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM20 MUTATED           0          0          0          1        0
  TMEM20 WILD-TYPE        18          6         44         32       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM20 MUTATED           0         0
  TMEM20 WILD-TYPE        12         1
D1900V3, multiclass
            clus
vv           TMEM20 MUTATED TMEM20 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               25
  STAGE IIA               0              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                0               35
  STAGE IVA               0               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
  TMEM20 MUTATED     0   0   0   3
  TMEM20 WILD-TYPE   9  67 249  38
D1900V4, multiclass
    clus
vv   TMEM20 MUTATED TMEM20 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              0              249
  T4              3               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
  TMEM20 MUTATED     2   1   0
  TMEM20 WILD-TYPE 218  80  66
D1900V5, multiclass
    clus
vv   TMEM20 MUTATED TMEM20 WILD-TYPE
  N0              2              218
  N1              1               80
  N2              0               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1900V6, binary
                  cls
clus                 0   1
  TMEM20 MUTATED     2   0
  TMEM20 WILD-TYPE 283  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM20 MUTATED      2    0
  TMEM20 WILD-TYPE  283   48
   clus
vv  TMEM20 MUTATED TMEM20 WILD-TYPE
  0              2              283
  1              0               48
[1] 2 2
[1] FALSE
D1900V7, binary
                  cls
clus                 0   1
  TMEM20 MUTATED     2   1
  TMEM20 WILD-TYPE 168 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM20 MUTATED      2    1
  TMEM20 WILD-TYPE  168  196
        clus
vv       TMEM20 MUTATED TMEM20 WILD-TYPE
  FEMALE              2              168
  MALE                1              196
[1] 2 2
[1] FALSE
D1900V8, binary
                  cls
clus                 0   1
  TMEM20 MUTATED     2   0
  TMEM20 WILD-TYPE 298   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM20 MUTATED      2    0
  TMEM20 WILD-TYPE  298    8
     clus
vv    TMEM20 MUTATED TMEM20 WILD-TYPE
  NO               2              298
  YES              0                8
[1] 2 2
[1] FALSE
D1900V9, binary
                  cls
clus                 0   1
  TMEM20 MUTATED     2   1
  TMEM20 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM20 MUTATED      2    1
  TMEM20 WILD-TYPE  312   47
                               clus
vv                              TMEM20 MUTATED TMEM20 WILD-TYPE
  COLON ADENOCARCINOMA                       2              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM20 MUTATED     3   0   0   0
  TMEM20 WILD-TYPE 256   3  22  21
D1900V10, multiclass
    clus
vv   TMEM20 MUTATED TMEM20 WILD-TYPE
  R0              3              256
  R1              0                3
  R2              0               22
  RX              0               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"
D1900V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM20 MUTATED                                  0     0
  TMEM20 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM20 MUTATED                           0     2
  TMEM20 WILD-TYPE                        19   174
D1900V12, multiclass
[1] "Remove cluster labels:" "TMEM20 MUTATED"        
clus
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               2              204 
      TCGA-A6-2677       TCGA-A6-4105       TCGA-A6-6649       TCGA-AD-6548 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6895       TCGA-AD-6964       TCGA-AZ-4681 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6608       TCGA-CK-5912       TCGA-DM-A285 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6321       TCGA-G4-6586       TCGA-G4-6588 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6628       TCGA-A6-2671       TCGA-A6-2672 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-2674       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5656 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660       TCGA-A6-5661 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665       TCGA-A6-5666 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6651       TCGA-A6-6652       TCGA-A6-6653 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6782       TCGA-AD-5900 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899       TCGA-AD-6901 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AD-6963       TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6603 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-CA-5254 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A282       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6323       TCGA-G4-6626 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 

Clustering(1901) Variable = KCNQ1 MUTATION ANALYSIS
D1901V1, survival
                 sevent
clus2               0   1
  KCNQ1 MUTATED     7   1
  KCNQ1 WILD-TYPE 270  77
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              8             347 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              1              77 
$`KCNQ1 MUTATED`
TCGA-G4-6628 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CK-4948 
       79.69        33.53        22.06         1.02        58.39       148.01 
TCGA-CK-5916 TCGA-CM-6171 
       21.14        14.04 

$`KCNQ1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2672 
       22.09        35.80        26.17        91.79        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        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-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-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       37.05         5.03        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         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-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59        12.59 
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-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.99        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-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        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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 
       43.04        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-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        13.78        46.75 

  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
           1.02            0.00 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
         148.01          140.38 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
         27.795          22.030 
[1] "1.0 - 148.0 (27.8)" "0.0 - 140.4 (22.0)"
[1] "hr=" "2.6"
D1901V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNQ1 MUTATED         3        0        1         3         0         0
  KCNQ1 WILD-TYPE      61        1       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNQ1 MUTATED           1          0          0          0        0         0
  KCNQ1 WILD-TYPE        17          6         44         33       35        12
                 vv
clus              STAGE IVB
  KCNQ1 MUTATED           0
  KCNQ1 WILD-TYPE         1
D1901V3, multiclass
            clus
vv           KCNQ1 MUTATED KCNQ1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              3             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               0              35
  STAGE IVA              0              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
  KCNQ1 MUTATED     1   2   5   0
  KCNQ1 WILD-TYPE   8  65 244  41
D1901V4, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  T1             1               8
  T2             2              65
  T3             5             244
  T4             0              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
  KCNQ1 MUTATED     7   1   0
  KCNQ1 WILD-TYPE 213  80  66
D1901V5, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  N0             7             213
  N1             1              80
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1901V6, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     8   0
  KCNQ1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      8    0
  KCNQ1 WILD-TYPE  277   48
   clus
vv  KCNQ1 MUTATED KCNQ1 WILD-TYPE
  0             8             277
  1             0              48
[1] 2 2
[1] FALSE
D1901V7, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     6   2
  KCNQ1 WILD-TYPE 164 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      6    2
  KCNQ1 WILD-TYPE  164  195
        clus
vv       KCNQ1 MUTATED KCNQ1 WILD-TYPE
  FEMALE             6             164
  MALE               2             195
[1] 2 2
[1] FALSE
D1901V8, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     7   0
  KCNQ1 WILD-TYPE 293   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      7    0
  KCNQ1 WILD-TYPE  293    8
     clus
vv    KCNQ1 MUTATED KCNQ1 WILD-TYPE
  NO              7             293
  YES             0               8
[1] 2 2
[1] FALSE
D1901V9, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     8   0
  KCNQ1 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      8    0
  KCNQ1 WILD-TYPE  306   48
                               clus
vv                              KCNQ1 MUTATED KCNQ1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             306
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNQ1 MUTATED     7   0   0   1
  KCNQ1 WILD-TYPE 252   3  22  20
D1901V10, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  R0             7             252
  R1             0               3
  R2             0              22
  RX             1              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"
D1901V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNQ1 MUTATED                                  0     0
  KCNQ1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNQ1 MUTATED                           1     6
  KCNQ1 WILD-TYPE                        18   170
D1901V12, multiclass
                                  clus
vv                                 KCNQ1 MUTATED KCNQ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                        6             170
[1] 4 2
[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 = CAMK2G MUTATION ANALYSIS
D1902V1, survival
                  sevent
clus2                0   1
  CAMK2G MUTATED     9   3
  CAMK2G WILD-TYPE 268  75
  CAMK2G MUTATED CAMK2G WILD-TYPE 
              12              343 
  CAMK2G MUTATED CAMK2G WILD-TYPE 
               3               75 
$`CAMK2G MUTATED`
TCGA-AA-3713 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A01Q 
       19.04        22.06         6.97        33.04        33.01         1.02 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-CA-6717 TCGA-CK-5913 TCGA-DM-A0XF 
       83.24        58.39        22.36        12.76        51.32        38.20 

$`CAMK2G WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02        78.08        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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        25.02        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        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-A029 TCGA-AA-A02F 
       33.04         1.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        21.44        17.82         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  CAMK2G MUTATED CAMK2G WILD-TYPE 
            1.02             0.00 
  CAMK2G MUTATED CAMK2G WILD-TYPE 
           83.24           148.01 
  CAMK2G MUTATED CAMK2G WILD-TYPE 
          27.685           21.990 
[1] "1.0 - 83.2 (27.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D1902V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAMK2G MUTATED         0        0        3         6         1         0
  CAMK2G WILD-TYPE      64        1       23       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAMK2G MUTATED           0          0          0          1        1
  CAMK2G WILD-TYPE        18          6         44         32       34
                  vv
clus               STAGE IVA STAGE IVB
  CAMK2G MUTATED           1         0
  CAMK2G WILD-TYPE        11         1
D1902V3, multiclass
            clus
vv           CAMK2G MUTATED CAMK2G WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               6              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               18
  STAGE IIIA              0                6
  STAGE IIIB              0               44
  STAGE IIIC              1               32
  STAGE IV                1               34
  STAGE IVA               1               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
  CAMK2G MUTATED     0   0  11   2
  CAMK2G WILD-TYPE   9  67 238  39
D1902V4, multiclass
    clus
vv   CAMK2G MUTATED CAMK2G WILD-TYPE
  T1              0                9
  T2              0               67
  T3             11              238
  T4              2               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
  CAMK2G MUTATED    12   0   1
  CAMK2G WILD-TYPE 208  81  65
D1902V5, multiclass
    clus
vv   CAMK2G MUTATED CAMK2G WILD-TYPE
  N0             12              208
  N1              0               81
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1902V6, binary
                  cls
clus                 0   1
  CAMK2G MUTATED    10   2
  CAMK2G WILD-TYPE 275  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMK2G MUTATED     10    2
  CAMK2G WILD-TYPE  275   46
   clus
vv  CAMK2G MUTATED CAMK2G WILD-TYPE
  0             10              275
  1              2               46
[1] 2 2
[1] FALSE
D1902V7, binary
                  cls
clus                 0   1
  CAMK2G MUTATED     7   6
  CAMK2G WILD-TYPE 163 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMK2G MUTATED      7    6
  CAMK2G WILD-TYPE  163  191
        clus
vv       CAMK2G MUTATED CAMK2G WILD-TYPE
  FEMALE              7              163
  MALE                6              191
[1] 2 2
[1] FALSE
D1902V8, binary
                  cls
clus                 0   1
  CAMK2G MUTATED     9   1
  CAMK2G WILD-TYPE 291   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMK2G MUTATED      9    1
  CAMK2G WILD-TYPE  291    7
     clus
vv    CAMK2G MUTATED CAMK2G WILD-TYPE
  NO               9              291
  YES              1                7
[1] 2 2
[1] FALSE
D1902V9, binary
                  cls
clus                 0   1
  CAMK2G MUTATED    10   2
  CAMK2G WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMK2G MUTATED     10    2
  CAMK2G WILD-TYPE  304   46
                               clus
vv                              CAMK2G MUTATED CAMK2G WILD-TYPE
  COLON ADENOCARCINOMA                      10              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CAMK2G MUTATED     9   0   1   2
  CAMK2G WILD-TYPE 250   3  21  19
D1902V10, multiclass
    clus
vv   CAMK2G MUTATED CAMK2G WILD-TYPE
  R0              9              250
  R1              0                3
  R2              1               21
  RX              2               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"
D1902V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAMK2G MUTATED                                  0     2
  CAMK2G WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CAMK2G MUTATED                           0     5
  CAMK2G WILD-TYPE                        19   171
D1902V12, multiclass
                                  clus
vv                                 CAMK2G MUTATED CAMK2G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         5              171
[1] 4 2
[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 = SAMD11 MUTATION ANALYSIS
D1903V1, survival
                  sevent
clus2                0   1
  SAMD11 MUTATED     4   2
  SAMD11 WILD-TYPE 273  76
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               6              349 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               2               76 
$`SAMD11 MUTATED`
TCGA-AA-3516 TCGA-AA-3947 TCGA-AD-6889 TCGA-CM-5348 TCGA-D5-5541 TCGA-D5-6928 
       13.02        33.01        83.24        22.98        55.92        11.64 

$`SAMD11 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        42.90        42.28        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        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-A6-6138 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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        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-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        24.00        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        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        54.61        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        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        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        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       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-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6626 
       46.75 

  SAMD11 MUTATED SAMD11 WILD-TYPE 
           11.64             0.00 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
           83.24           148.01 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
          27.995           22.030 
[1] "11.6 - 83.2 (28.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D1903V2, continuous
                  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      64        1       26       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD11 MUTATED           1          0          2          0        0
  SAMD11 WILD-TYPE        17          6         42         33       35
                  vv
clus               STAGE IVA STAGE IVB
  SAMD11 MUTATED           0         0
  SAMD11 WILD-TYPE        12         1
D1903V3, multiclass
            clus
vv           SAMD11 MUTATED SAMD11 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               26
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               17
  STAGE IIIA              0                6
  STAGE IIIB              2               42
  STAGE IIIC              0               33
  STAGE IV                0               35
  STAGE IVA               0               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
  SAMD11 MUTATED     0   0   5   1
  SAMD11 WILD-TYPE   9  67 244  40
D1903V4, multiclass
    clus
vv   SAMD11 MUTATED SAMD11 WILD-TYPE
  T1              0                9
  T2              0               67
  T3              5              244
  T4              1               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
  SAMD11 MUTATED     3   2   1
  SAMD11 WILD-TYPE 217  79  65
D1903V5, multiclass
    clus
vv   SAMD11 MUTATED SAMD11 WILD-TYPE
  N0              3              217
  N1              2               79
  N2              1               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1903V6, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     6   0
  SAMD11 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      6    0
  SAMD11 WILD-TYPE  279   48
   clus
vv  SAMD11 MUTATED SAMD11 WILD-TYPE
  0              6              279
  1              0               48
[1] 2 2
[1] FALSE
D1903V7, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     2   4
  SAMD11 WILD-TYPE 168 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      2    4
  SAMD11 WILD-TYPE  168  193
        clus
vv       SAMD11 MUTATED SAMD11 WILD-TYPE
  FEMALE              2              168
  MALE                4              193
[1] 2 2
[1] FALSE
D1903V8, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     6   0
  SAMD11 WILD-TYPE 294   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      6    0
  SAMD11 WILD-TYPE  294    8
     clus
vv    SAMD11 MUTATED SAMD11 WILD-TYPE
  NO               6              294
  YES              0                8
[1] 2 2
[1] FALSE
D1903V9, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     3   3
  SAMD11 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      3    3
  SAMD11 WILD-TYPE  311   45
                               clus
vv                              SAMD11 MUTATED SAMD11 WILD-TYPE
  COLON ADENOCARCINOMA                       3              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SAMD11 MUTATED     5   0   0   0
  SAMD11 WILD-TYPE 254   3  22  21
D1903V10, multiclass
    clus
vv   SAMD11 MUTATED SAMD11 WILD-TYPE
  R0              5              254
  R1              0                3
  R2              0               22
  RX              0               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"
D1903V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD11 MUTATED                                  0     1
  SAMD11 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SAMD11 MUTATED                           0     3
  SAMD11 WILD-TYPE                        19   173
D1903V12, multiclass
                                  clus
vv                                 SAMD11 MUTATED SAMD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     0               19
  WHITE                                         3              173
[1] 4 2
[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 = FAM83D MUTATION ANALYSIS
D1904V1, survival
                  sevent
clus2                0   1
  FAM83D MUTATED    10   1
  FAM83D WILD-TYPE 267  77
  FAM83D MUTATED FAM83D WILD-TYPE 
              11              344 
  FAM83D MUTATED FAM83D WILD-TYPE 
               1               77 
$`FAM83D MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3864 
       29.19        22.06         3.02         6.97        26.99        53.00 
TCGA-AA-A010 TCGA-AA-A01R TCGA-DM-A1HB TCGA-G4-6293 TCGA-G4-6317 
       34.98        35.01       135.65       133.18        36.00 

$`FAM83D WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 
      106.75       100.01         1.94        49.08         5.88        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 
       22.09        35.80        26.17        91.79        79.69        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        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-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        5.03        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-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-3866 TCGA-AA-3869 
       32.05         0.99        31.07        30.05        17.03        27.02 
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-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-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        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        15.02        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         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.20        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-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        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 
       21.99        21.14        82.95         2.01       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        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25        25.48        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         7.53        12.39        10.13        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        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       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        43.04 
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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  FAM83D MUTATED FAM83D WILD-TYPE 
            3.02             0.00 
  FAM83D MUTATED FAM83D WILD-TYPE 
          135.65           148.01 
  FAM83D MUTATED FAM83D WILD-TYPE 
           34.98            21.99 
[1] "3.0 - 135.7 (35.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "3.5"
D1904V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM83D MUTATED         0        0        3         2         1         0
  FAM83D WILD-TYPE      64        1       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM83D MUTATED           2          0          1          2        0
  FAM83D WILD-TYPE        16          6         43         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM83D MUTATED           0         0
  FAM83D WILD-TYPE        12         1
D1904V3, multiclass
            clus
vv           FAM83D MUTATED FAM83D WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               23
  STAGE IIA               2              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               16
  STAGE IIIA              0                6
  STAGE IIIB              1               43
  STAGE IIIC              2               31
  STAGE IV                0               35
  STAGE IVA               0               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
  FAM83D MUTATED     0   0  10   1
  FAM83D WILD-TYPE   9  67 239  40
D1904V4, multiclass
    clus
vv   FAM83D MUTATED FAM83D WILD-TYPE
  T1              0                9
  T2              0               67
  T3             10              239
  T4              1               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
  FAM83D MUTATED     6   2   3
  FAM83D WILD-TYPE 214  79  63
D1904V5, multiclass
    clus
vv   FAM83D MUTATED FAM83D WILD-TYPE
  N0              6              214
  N1              2               79
  N2              3               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"
D1904V6, binary
                  cls
clus                 0   1
  FAM83D MUTATED    10   0
  FAM83D WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED     10    0
  FAM83D WILD-TYPE  275   48
   clus
vv  FAM83D MUTATED FAM83D WILD-TYPE
  0             10              275
  1              0               48
[1] 2 2
[1] FALSE
D1904V7, binary
                  cls
clus                 0   1
  FAM83D MUTATED     6   5
  FAM83D WILD-TYPE 164 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED      6    5
  FAM83D WILD-TYPE  164  192
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  FEMALE              6              164
  MALE                5              192
[1] 2 2
[1] FALSE
D1904V8, binary
                  cls
clus                 0   1
  FAM83D MUTATED     9   1
  FAM83D WILD-TYPE 291   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED      9    1
  FAM83D WILD-TYPE  291    7
     clus
vv    FAM83D MUTATED FAM83D WILD-TYPE
  NO               9              291
  YES              1                7
[1] 2 2
[1] FALSE
D1904V9, binary
                  cls
clus                 0   1
  FAM83D MUTATED     9   1
  FAM83D WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED      9    1
  FAM83D WILD-TYPE  305   47
                               clus
vv                              FAM83D MUTATED FAM83D WILD-TYPE
  COLON ADENOCARCINOMA                       9              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM83D MUTATED     9   0   0   0
  FAM83D WILD-TYPE 250   3  22  21
D1904V10, multiclass
    clus
vv   FAM83D MUTATED FAM83D WILD-TYPE
  R0              9              250
  R1              0                3
  R2              0               22
  RX              0               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"
D1904V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM83D MUTATED                                  0     0
  FAM83D WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM83D MUTATED                           1     4
  FAM83D WILD-TYPE                        18   172
D1904V12, multiclass
                                  clus
vv                                 FAM83D MUTATED FAM83D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               18
  WHITE                                         4              172
[1] 4 2
[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 = ALG9 MUTATION ANALYSIS
D1905V1, survival
                sevent
clus2              0   1
  ALG9 MUTATED     2   1
  ALG9 WILD-TYPE 275  77
  ALG9 MUTATED ALG9 WILD-TYPE 
             3            352 
  ALG9 MUTATED ALG9 WILD-TYPE 
             1             77 
$`ALG9 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AU-6004 
        1.02        19.04        27.09 

$`ALG9 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        85.05        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08         5.88        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       26.17        91.79        79.69        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       42.90        42.28        16.57        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
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-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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       26.47        14.50        16.31         0.95        33.01         0.20 
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-6603 
       62.79        88.21        49.41         6.77        12.10        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25        25.48        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 
        7.53        12.39        10.13        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        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 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-G4-6626 
       61.91        36.00        13.78        46.75 

  ALG9 MUTATED ALG9 WILD-TYPE 
          1.02           0.00 
  ALG9 MUTATED ALG9 WILD-TYPE 
         27.09         148.01 
  ALG9 MUTATED ALG9 WILD-TYPE 
        19.040         22.075 
[1] "1.0 - 27.1 (19.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D1905V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALG9 MUTATED         1        0        2         0         0         0
  ALG9 WILD-TYPE      63        1       24       108         8         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        18          6         44         33       35        12
                vv
clus             STAGE IVB
  ALG9 MUTATED           0
  ALG9 WILD-TYPE         1
D1905V3, multiclass
            clus
vv           ALG9 MUTATED ALG9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             24
  STAGE IIA             0            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             18
  STAGE IIIA            0              6
  STAGE IIIB            0             44
  STAGE IIIC            0             33
  STAGE IV              0             35
  STAGE IVA             0             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
  ALG9 MUTATED     0   1   2   0
  ALG9 WILD-TYPE   9  66 247  41
D1905V4, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  T1            0              9
  T2            1             66
  T3            2            247
  T4            0             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
  ALG9 MUTATED     3   0   0
  ALG9 WILD-TYPE 217  81  66
D1905V5, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  N0            3            217
  N1            0             81
  N2            0             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1905V6, binary
                cls
clus               0   1
  ALG9 MUTATED     3   0
  ALG9 WILD-TYPE 282  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      3    0
  ALG9 WILD-TYPE  282   48
   clus
vv  ALG9 MUTATED ALG9 WILD-TYPE
  0            3            282
  1            0             48
[1] 2 2
[1] FALSE
D1905V7, binary
                cls
clus               0   1
  ALG9 MUTATED     2   1
  ALG9 WILD-TYPE 168 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      2    1
  ALG9 WILD-TYPE  168  196
        clus
vv       ALG9 MUTATED ALG9 WILD-TYPE
  FEMALE            2            168
  MALE              1            196
[1] 2 2
[1] FALSE
D1905V8, binary
                cls
clus               0   1
  ALG9 MUTATED     1   0
  ALG9 WILD-TYPE 299   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      1    0
  ALG9 WILD-TYPE  299    8
     clus
vv    ALG9 MUTATED ALG9 WILD-TYPE
  NO             1            299
  YES            0              8
[1] 2 2
[1] FALSE
D1905V9, binary
                cls
clus               0   1
  ALG9 MUTATED     3   0
  ALG9 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      3    0
  ALG9 WILD-TYPE  311   48
                               clus
vv                              ALG9 MUTATED ALG9 WILD-TYPE
  COLON ADENOCARCINOMA                     3            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ALG9 MUTATED     3   0   0   0
  ALG9 WILD-TYPE 256   3  22  21
D1905V10, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  R0            3            256
  R1            0              3
  R2            0             22
  RX            0             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"
D1905V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG9 MUTATED                                  0     0
  ALG9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALG9 MUTATED                           0     1
  ALG9 WILD-TYPE                        19   175
D1905V12, multiclass
[1] "Remove cluster labels:" "ALG9 MUTATED"          
clus
  ALG9 MUTATED ALG9 WILD-TYPE 
             1            205 
    TCGA-A6-2677     TCGA-A6-4105     TCGA-A6-6649     TCGA-AD-6548 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6895     TCGA-AD-6964     TCGA-AZ-4681 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6608     TCGA-CK-5912     TCGA-DM-A285 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6321     TCGA-G4-6586     TCGA-G4-6588 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6625     TCGA-G4-6628     TCGA-A6-2671     TCGA-A6-2672 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2678     TCGA-A6-2683 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810 
"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-A6-6651     TCGA-A6-6652 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6889     TCGA-AD-6890 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6965 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"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-5913     TCGA-CK-5914     TCGA-CK-5915 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A28C     TCGA-DM-A28E 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6309     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6323 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6626 
"ALG9 WILD-TYPE" 

Clustering(1906) Variable = BCL7A MUTATION ANALYSIS
D1906V1, survival
                 sevent
clus2               0   1
  BCL7A MUTATED     3   2
  BCL7A WILD-TYPE 274  76
  BCL7A MUTATED BCL7A WILD-TYPE 
              5             350 
  BCL7A MUTATED BCL7A WILD-TYPE 
              2              76 
$`BCL7A MUTATED`
TCGA-AA-3554 TCGA-A6-2683 TCGA-AA-3877 TCGA-AA-A01R TCGA-CM-5862 
       17.95        16.57        31.00        35.01         5.03 

$`BCL7A WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6321 
      100.01         1.94        49.08         5.88        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 
       35.80        26.17        91.79        79.69        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        42.90        42.28        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-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 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-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         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-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        53.00        17.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 
       21.99        16.08        13.05        34.06        25.02        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-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
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         1.02        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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       24.53         5.79        22.42        27.42        26.47        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        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-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        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        14.04        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        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        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-G4-6323 TCGA-G4-6626 
       13.78        46.75 

  BCL7A MUTATED BCL7A WILD-TYPE 
           5.03            0.00 
  BCL7A MUTATED BCL7A WILD-TYPE 
          35.01          148.01 
  BCL7A MUTATED BCL7A WILD-TYPE 
         17.950          22.075 
[1] "5.0 - 35.0 (17.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D1906V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCL7A MUTATED         1        0        0         1         0         0
  BCL7A WILD-TYPE      63        1       26       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL7A MUTATED           1          0          0          0        1         1
  BCL7A WILD-TYPE        17          6         44         33       34        11
                 vv
clus              STAGE IVB
  BCL7A MUTATED           0
  BCL7A WILD-TYPE         1
D1906V3, multiclass
            clus
vv           BCL7A MUTATED BCL7A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              26
  STAGE IIA              1             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              17
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              1              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
  BCL7A MUTATED     1   0   3   1
  BCL7A WILD-TYPE   8  67 246  40
D1906V4, multiclass
    clus
vv   BCL7A MUTATED BCL7A WILD-TYPE
  T1             1               8
  T2             0              67
  T3             3             246
  T4             1              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
  BCL7A MUTATED     3   1   1
  BCL7A WILD-TYPE 217  80  65
D1906V5, multiclass
    clus
vv   BCL7A MUTATED BCL7A WILD-TYPE
  N0             3             217
  N1             1              80
  N2             1              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1906V6, binary
                 cls
clus                0   1
  BCL7A MUTATED     3   2
  BCL7A WILD-TYPE 282  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL7A MUTATED      3    2
  BCL7A WILD-TYPE  282   46
   clus
vv  BCL7A MUTATED BCL7A WILD-TYPE
  0             3             282
  1             2              46
[1] 2 2
[1] FALSE
D1906V7, binary
                 cls
clus                0   1
  BCL7A MUTATED     3   2
  BCL7A WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL7A MUTATED      3    2
  BCL7A WILD-TYPE  167  195
        clus
vv       BCL7A MUTATED BCL7A WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1906V8, binary
                 cls
clus                0   1
  BCL7A MUTATED     4   1
  BCL7A WILD-TYPE 296   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL7A MUTATED      4    1
  BCL7A WILD-TYPE  296    7
     clus
vv    BCL7A MUTATED BCL7A WILD-TYPE
  NO              4             296
  YES             1               7
[1] 2 2
[1] FALSE
D1906V9, binary
                 cls
clus                0   1
  BCL7A MUTATED     3   2
  BCL7A WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL7A MUTATED      3    2
  BCL7A WILD-TYPE  311   46
                               clus
vv                              BCL7A MUTATED BCL7A WILD-TYPE
  COLON ADENOCARCINOMA                      3             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BCL7A MUTATED     5   0   0   0
  BCL7A WILD-TYPE 254   3  22  21
D1906V10, multiclass
    clus
vv   BCL7A MUTATED BCL7A WILD-TYPE
  R0             5             254
  R1             0               3
  R2             0              22
  RX             0              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"
D1906V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL7A MUTATED                                  0     0
  BCL7A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BCL7A MUTATED                           0     2
  BCL7A WILD-TYPE                        19   174
D1906V12, multiclass
[1] "Remove cluster labels:" "BCL7A MUTATED"         
clus
  BCL7A MUTATED BCL7A WILD-TYPE 
              2             204 
     TCGA-A6-2677      TCGA-A6-4105      TCGA-A6-6649      TCGA-AD-6548 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6895      TCGA-AD-6964      TCGA-AZ-4681 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6608      TCGA-CK-5912      TCGA-DM-A285 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6321      TCGA-G4-6586      TCGA-G4-6588 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6628      TCGA-A6-2671      TCGA-A6-2672 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2678      TCGA-A6-3807 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5656 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6651      TCGA-A6-6652      TCGA-A6-6653 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781      TCGA-A6-6782 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6899 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6965      TCGA-AU-3779 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-DM-A282      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6626 
"BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" "BCL7A WILD-TYPE" 

Clustering(1907) Variable = HOXA1 MUTATION ANALYSIS
D1907V1, survival
                 sevent
clus2               0   1
  HOXA1 MUTATED     7   3
  HOXA1 WILD-TYPE 270  75
  HOXA1 MUTATED HOXA1 WILD-TYPE 
             10             345 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              3              75 
$`HOXA1 MUTATED`
TCGA-AA-3672 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6588 TCGA-A6-2676 TCGA-A6-5661 
        0.92       100.01        22.09        26.17        42.90        33.53 
TCGA-AA-3710 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CM-6171 
       26.99        58.39        12.10        14.04 

$`HOXA1 WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 
       39.06        21.37        15.52        25.08        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 
        1.94        49.08         5.88        63.62        35.80        91.79 
TCGA-G4-6628 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 
       79.69        43.76        46.65        43.76        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-A6-5662 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-A6-6651 
       27.09        22.52         8.38        25.08        25.18        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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        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-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        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-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-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-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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 
        1.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01         0.20        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-6603 
       22.36        62.79        88.21        49.41         6.77        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        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        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        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       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        14.04        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        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25        25.48        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        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        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        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-G4-6323 TCGA-G4-6626 
       36.00        13.78        46.75 

  HOXA1 MUTATED HOXA1 WILD-TYPE 
           0.92            0.00 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
         100.01          148.01 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
          26.58           21.99 
[1] "0.9 - 100.0 (26.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1907V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HOXA1 MUTATED         1        0        1         4         1         0
  HOXA1 WILD-TYPE      63        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HOXA1 MUTATED           2          0          0          0        1         0
  HOXA1 WILD-TYPE        16          6         44         33       34        12
                 vv
clus              STAGE IVB
  HOXA1 MUTATED           0
  HOXA1 WILD-TYPE         1
D1907V3, multiclass
            clus
vv           HOXA1 MUTATED HOXA1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              25
  STAGE IIA              4             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              16
  STAGE IIIA             0               6
  STAGE IIIB             0              44
  STAGE IIIC             0              33
  STAGE IV               1              34
  STAGE IVA              0              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
  HOXA1 MUTATED     0   2   6   2
  HOXA1 WILD-TYPE   9  65 243  39
D1907V4, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  T1             0               9
  T2             2              65
  T3             6             243
  T4             2              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
  HOXA1 MUTATED     7   3   0
  HOXA1 WILD-TYPE 213  78  66
D1907V5, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  N0             7             213
  N1             3              78
  N2             0              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1907V6, binary
                 cls
clus                0   1
  HOXA1 MUTATED     8   1
  HOXA1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      8    1
  HOXA1 WILD-TYPE  277   47
   clus
vv  HOXA1 MUTATED HOXA1 WILD-TYPE
  0             8             277
  1             1              47
[1] 2 2
[1] FALSE
D1907V7, binary
                 cls
clus                0   1
  HOXA1 MUTATED     7   3
  HOXA1 WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      7    3
  HOXA1 WILD-TYPE  163  194
        clus
vv       HOXA1 MUTATED HOXA1 WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D1907V8, binary
                 cls
clus                0   1
  HOXA1 MUTATED    10   0
  HOXA1 WILD-TYPE 290   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED     10    0
  HOXA1 WILD-TYPE  290    8
     clus
vv    HOXA1 MUTATED HOXA1 WILD-TYPE
  NO             10             290
  YES             0               8
[1] 2 2
[1] FALSE
D1907V9, binary
                 cls
clus                0   1
  HOXA1 MUTATED    10   0
  HOXA1 WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED     10    0
  HOXA1 WILD-TYPE  304   48
                               clus
vv                              HOXA1 MUTATED HOXA1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             304
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HOXA1 MUTATED     8   0   0   0
  HOXA1 WILD-TYPE 251   3  22  21
D1907V10, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  R0             8             251
  R1             0               3
  R2             0              22
  RX             0              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"
D1907V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HOXA1 MUTATED                                  0     0
  HOXA1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HOXA1 MUTATED                           2     6
  HOXA1 WILD-TYPE                        17   170
D1907V12, multiclass
                                  clus
vv                                 HOXA1 MUTATED HOXA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              17
  WHITE                                        6             170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
